Patent Publication Number: US-2019194682-A1

Title: Yield improvement in plants

Description:
FIELD OF THE INVENTION 
     The present invention relates to plant genomics and plant improvement. 
     BACKGROUND OF THE INVENTION 
     A plant&#39;s phenotypic characteristics that enhance photosynthetic resource use efficiency may be controlled through a number of cellular processes. One important way to manipulate that control is by manipulating the characteristics or expression of regulatory proteins, proteins that influence the expression of a particular gene or sets of genes. For example, transformed or transgenic plants that comprise cells with altered levels of at least one selected regulatory polypeptide may possess advantageous or desirable traits, and strategies for manipulating traits by altering a plant cell&#39;s regulatory polypeptide content or expression level can result in plants and crops with commercially valuable properties. Examples of such trait manipulation include: 
     Increasing Canopy Photosynthesis to Increase Crop Yield. 
     Recent studies by crop physiologists have provided evidence that crop-canopy photosynthesis is correlated with crop yield, and that increasing canopy photosynthesis can increase crop yield (Long et al., 2006 . Plant Cell Environ.  29:315-33; Murchie et al., 2009  New Phytol.  181:532-552; Zhu et al., 2010 . Ann. Rev. Plant Biol.  61:235-261). Two overlapping strategies for increasing canopy photosynthesis have been proposed. The first recognizes great potential to increase canopy photosynthesis by improving multiple discrete reactions that currently limit photosynthetic capacity (reviewed in Zhu et al., 2010. supra). The second focuses upon improving plant physiological status during environmental conditions that limit the realization of photosynthetic capacity. It is important to distinguish this second goal from recent industry and academic screening for genes to improve stress tolerance. Arguably, these efforts may have identified genes that improve plant physiological status during severe stresses not typically experienced on productive acres (Jones, 2007 . J. Exp. Bot.  58:119-130; Passioura, 2007 . J. Exp. Bot.  58:113-117). In contrast, improving the efficiency with which photosynthesis operates relative to the availability of key resources of water, nitrogen and light, is thought to be more appropriate for improving yield on productive acres (Long et al., 1994 . Ann. Rev. Plant Physiol. Plant Molec. Biol.  45:633-662; Morison et al., 2008 . Philosophical Transactions of the Royal Society B: Biological Sciences  363:639-658; Passioura, 2007, supra). 
     Increasing Nitrogen Use Efficiency (NUE) to Increase Crop Yield. 
     There has been a large increase in food productivity over the past 50 years causing a decrease in world hunger despite a significant increase in population (Godfray et al., 2010 . Science  327:812-818). A significant contribution to this increased yield was a 20-fold increase in the application of nitrogen fertilizers (Glass, 2003 . Crit. Rev. Plant Sci.  22:453-470). About 85 million to 90 million metric tons of nitrogen are applied annually to soil, and this application rate is expected to increase to 240 million metric tons by 2050 (Good et al., 2004 . Trends Plant Sci.  9:597-605). However, plants use only 30 to 40% of the applied nitrogen and the rest is lost through a combination of leaching, surface run-off, denitrification, volatilization, and microbial consumption (Frink et al., 1999 . Proc. Natl. Acad. Sci. USA  96:1175-1180; Glass, 2003, supra; Good et al., 2004, supra; Raun and Johnson, 1999 . Agron. J.  91:357-363). The loss of more than 60% of applied nitrogen can have serious environmental effects, such as groundwater contamination, anoxic coastal zones, and conversion to greenhouse gases. In addition, while most fertilizer components are mined (such as phosphates), inorganic nitrogen is derived from the energy intensive conversion of gaseous nitrogen to ammonia. Thus, the addition of nitrogen fertilizer is typically the highest single input cost for many crops, and since its production is energy intensive, the cost is dependent on the price of energy (Rothstein, 2007 . Plant Cell  19:2695-2699). With an increasing demand for food from an increasing human population, agriculture yields must be increased at the same time as dependence on applied fertilizers is decreased. Therefore, to minimize nitrogen loss, reduce environmental pollution, and decrease input cost, it is crucial to develop crop varieties with higher nitrogen use efficiency (Garnett et al., 2009 . Plant Cell Environ.  32:1272-1283; Hirel et al., 2007 . J. Exp. Bot.  58:2369-2387; Lea and Azevedo, 2007 . Ann. Appl. Biol.  151:269-275; Masclaux-Daubresse et al., 2010 . Ann. Bot.  105:1141-1157; Moll et al., 1982 . Agron. J.  74:562-564; Sylvester-Bradley and Kindred, 2009 . J. Exp. Bot.  60:1939-1951). 
     Improving Water Use Efficiency (WUE) to Improve Yield. 
     Freshwater is a limited and dwindling global resource; therefore, improving the efficiency with which food and biofuel crops use water is a prerequisite for maintaining and improving yield (Karaba et al., 2007 . Proc. Natl. Acad. Sci. USA.  104:15270-15275). WUE can be used to describe the relationship between water use and crop productivity over a range of time integrals. The basic physiological definition of WUE equates the ratio of photosynthesis (A) to transpiration (T) at a given moment in time, also referred to as transpiration efficiency. However, the WUE concept can be scaled significantly, for example, over the complete lifecycle of a crop, where biomass or yield can be expressed per cumulative total of water transpired from the canopy. Thus far, the engineering of major field crops for improved WUE with single genes has not yet been achieved (Karaba et al., 2007. supra). Regardless, increased yields of wheat cultivars bred for increased transpiration efficiency (the ratio of photosynthesis to transpiration) have provided important support for the proposition that crop yield can be increased over broad acres through improvement in crop water-use efficiency (Condon et al., 2004 . J. Exp. Bot.  55:2447-2460). 
     Estimates of water-use efficiency integrated over the life of plant tissues can be derived from analysis of the ratio of the  13 C carbon isotope to the  12 C carbon isotope in those tissues. The theory that underlies this means to estimating WUE is that during photosynthesis, incorporation of  13 C into the products of photosynthesis is slower than the lighter isotope  12 C. Effectively,  13 C is discriminated against relative to  12 C during photosynthesis, an effect that is integrated over the life of the plant resulting in biomass with a distinct  13 C/ 12 C signature. Of the many steps in the photosynthetic process during which this discrimination occurs, discrimination at the active site of Rubisco is of most significance, a consequence of kinetic constraints associated with the  13 CO 2  molecule being larger. Significantly, the discrimination by Rubisco is not constant, but varies depending on the CO 2  concentration within the leaf. At high CO 2  concentration discrimination by Rubisco is highest, however as CO 2  concentration decreases discrimination decreases. Because the CO 2  concentration within the leaf is overwhelmingly dependent on the balance between CO 2  influx through the stomatal pore and the rate of photosynthesis, and because the stomatal pore controls the rate of transpiration from the leaf, the  13 C/ 12 C isotopic signature of plant material provides an integrated record of the balance between transpiration and photosynthesis during the life of the plant and as such a surrogate measure of water-use efficiency (Farquhar et al. 1989 . Annu. Rev. Plant Physiol. Plant Mol. Biol.  40:503-537). 
     With these needs in mind, new technologies for yield enhancement are required. In this disclosure, a phenotypic screening platform that directly measures photosynthetic capacity, water use efficiency, and nitrogen use efficiency of mature plants was used to discover advantageous properties conferred by ectopic expression of the described regulatory proteins in plants. 
     SUMMARY 
     The instant description is directed to a transgenic plant or plants that have increased photosynthetic resource use efficiency with respect to a control plant, or a plant part derived from such a plant, e.g., shoot vegetative organs/structures (e.g., leaves, stems and tubers), roots, flowers and floral organs/structures (e.g., bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (e.g., vascular tissue, ground tissue, and the like), pulped, pureed, ground-up, macerated or broken-up tissue, and cells (e.g., guard cells, egg cells, etc.)). In this regard, the transgenic plant or plants comprise a recombinant polynucleotide comprising a promoter of interest. The choice of promoter may include a constitutive promoter or a promoter with enhanced activity in a tissue capable of photosynthesis (also referred to herein as a “photosynthetic promoter” or a “photosynthetic tissue-enhanced promoter”) such as a leaf tissue or other green tissue. Examples of photosynthetic promoters include for example, an RBCS3 promoter, an RBCS4 promoter or others such as the At4g01060 (also referred to as “G682”) promoter, the latter regulating expression in a guard cell. The promoter regulates a polypeptide that is encoded by the recombinant polynucleotide or by a second (or target) recombinant polynucleotide (in which case expression of the polypeptide may be regulated by a trans-regulatory element). The promoter may also regulate expression of a polypeptide to an effective level of expression in a photosynthetic tissue, that is, to a level that, as a result of expression of the polypeptide to that level, improves photosynthetic resource use efficiency in a transgenic plant relative to a control plant. The recombinant polynucleotide may comprise the promoter and also encode the polypeptide or alternatively, the polynucleotide may comprise the promoter and drive expression of the polypeptide that is encoded by the second recombinant polynucleotide. In an exemplary embodiment, the polypeptide comprises a sequence listed in the sequence listing, or a sequence that is homologous, paralogous or orthologous to said polypeptide, being structurally-related to said polypeptide and having a function similar to said polypeptide as described herein. Expression of the polypeptide under the regulatory control of the constitutive or leaf-enhanced or photosynthetic tissue-enhanced promoter in the transgenic plant confers greater photosynthetic resource use efficiency to the transgenic plants, and may ultimately increase yield that may be obtained from the plants. 
     The instant description also pertains to methods for increasing photosynthetic resource use efficiency in, or increasing yield from, a plant or plants including the method conducted by growing a transgenic plant comprising and/or transformed with an expression cassette comprising the recombinant polynucleotide that comprises a constitutive promoter or a promoter expressed in photosynthetic tissue, which may be a leaf-enhanced or green tissue-enhanced promoter, such as for example, the RBCS3, RBCS4, At4g01060, or another photosynthetic tissue-enhanced promoter. Examples of photosynthetic tissue-enhanced promoters are found in the Sequence Listing or in Table 22. The promoter regulates expression of a polypeptide that comprises a polypeptide listed in the Sequence Listing. Recombinant polynucleotides encoding these clade polypeptides are described in the following paragraphs (a)-(c), and exemplary polypeptides within the clade are described in the following paragraphs (d)-(f) and are shown in the instant sequence alignments and Figures. 
     The recombinant polynucleotide that is introduced into a transgenic plant may encode a listed polypeptide sequence or encodes a polypeptide that is phylogenetically-related to a listed polypeptide sequence, including sequences that include: 
     (a) nucleic acid sequences that are at least 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to any of the listed polypeptides; and/or 
     (b) nucleic acid sequences that encode polypeptide sequences that are at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical in their amino acid sequences to the entire length to any of the listed polypeptides; and/or 
     (c) nucleic acid sequences that hybridize under stringent conditions (e.g., hybridization followed by one, by two, or by more than two wash steps of 6× saline-sodium citrate buffer (SSC) and 65° C. for ten to thirty minutes per step) to any of the listed polynucleotides. 
     The listed polypeptides and polypeptides member of their protein clade may include: 
     (d) polypeptide sequences encoded by the nucleic acid sequences of (a), (b) and/or (c); and/or 
     (e) polypeptide sequences that have at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65f %, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to any of the listed polypeptides, including SEQ ID NO: 2n, where n=1 to 241 (i.e., even integers 2, 4, 6, 8, . . . 482); 
     and/or at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65f %, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100 amino acid identity to a conserved domain of any of the listed polypeptides, including SEQ ID NO: 483 to 841; and/or 
     (f) polypeptide sequences that comprise a subsequence that are at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to any of the consensus sequences provided in the Sequence Listing, including SEQ ID NO: 842 to 861. 
     Expression of these polypeptides in the transgenic plant may confer increased photosynthetic resource use efficiency relative to a control plant. The transgenic plant may be selected for increased photosynthetic resource use efficiency or greater yield relative to the control plant. The transgenic plant may also be crossed with itself, a second plant from the same line as the transgenic plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed. 
     The instant description also pertains to methods for producing and selecting a crop plant with a greater yield than a control plant, the method comprising producing a transgenic plant by introducing into a target plant a recombinant polynucleotide that comprises a promoter, such as a leaf- or photosynthetic tissue-enhanced promoter that regulates a polypeptide encoded by the recombinant polynucleotide or a second recombinant polynucleotide, wherein the polypeptide comprises a polypeptide listed in the Sequence Listing, or a member of a clades of polypeptides phylogenetically related to a polypeptide listed in the Sequence Listing. A plurality of the transgenic plants is then grown, and a transgenic plant is selected that produces greater yield or has greater photosynthetic resource use efficiency than a control plant. The expression of the polypeptide in the selected transgenic plant confers the greater photosynthetic resource use efficiency and/or greater yield relative to the control plant. Optionally, the selected transgenic plant may be crossed with itself, a second plant from the same line as the transgenic plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed. A plurality of the selected transgenic plants will generally have greater cumulative canopy photosynthesis than the canopy photosynthesis of an identical number of the control plants. 
     The transgenic plant(s) described herein and produced by the instantly described methods may also possess one or more altered traits that result in greater photosynthetic resource use efficiency. The altered trait may include: increased photosynthetic capacity, increased photosynthetic rate, a decrease in leaf chlorophyll content, a decrease in percentage of nitrogen in leaf dry weight, increased leaf transpiration efficiency, an increase in resistance to water vapor diffusion from the leaf exerted by stomata, an increased rate of relaxation of photoprotective reactions operating in the light harvesting antennae, a decrease in the ratio of the carbon isotope  12 C to  13 C in above-ground biomass, and/or an increase in the total dry weight of above-ground plant material. 
     At least one advantage of greater photosynthetic resource use efficiency is that the transgenic plant, or a plurality of the transgenic plants, will have greater cumulative canopy photosynthesis than the canopy photosynthesis of an identical number of the control plants, or produce greater yield than an identical number of the control plants. A wide variety of transgenic plants are envisioned, including corn, wheat, rice,  Setaria, Miscanthus , switchgrass, ryegrass, sugarcane, miscane, barley, sorghum, turfgrass, soy, cotton, canola, rapeseed,  Crambe, Camelina , sugar beet, alfalfa, tomato,  Eucalyptus , poplar, willow, pine, birch and other woody plants. 
     The instant description also pertains to expression vectors that comprise a recombinant polynucleotide that comprises a promoter expressed in photosynthetic tissue, for example, a constitutive promoter, or a leaf- or green tissue-enhanced promoter including the RBCS3, RBCS4, or At4g01060 promoters, or another photosynthetic tissue-enhanced promoter, for example, such a promoter found in the Sequence Listing or in Table 22, and a subsequence that encodes a polypeptide comprising a polypeptide sequence provided in the Sequence Listing or a member of the polypeptide clades of the polypeptide sequences listed in the Sequence Listing, or, alternatively, two expression constructs, one of which encodes a promoter such as a constitutive promoter, or a leaf-enhanced promoter or other photosynthetic tissue-enhanced promoter, and the second encodes a polypeptide sequence provided in the Sequence Listing or a member of the polypeptide clades of the polypeptide sequences listed in the Sequence Listing. In either instance, whether the polypeptide is encoded by the first or second expression constructs, the promoter regulates expression of the polypeptide by being responsible for production of cis- or trans-regulatory elements, respectively. In some embodiments, the expression vectors or cassettes comprise a promoter of the present application, and a gene of interest, wherein the promoter and the gene of interest do not link to each other under natural conditions, e.g., the linkage between the promoter and the gene of interest does not exist in nature. 
     The instant description is also directed to a method for producing a monocot plant with increased grain yield by providing a monocot plant cell or plant tissue with stably integrated, exogenous, recombinant polynucleotide comprising a promoter (for example, a constitutive, a non-constitutive, an inducible, a tissue-enhanced, or a photosynthetic tissue-enhanced promoter) that is functional in plant cells and that is operably linked to an exogenous or an endogenous nucleic acid sequence that encodes a listed polypeptide, that is expressed in a photosynthetic tissue of the transgenic plant to a level effective in conferring greater photosynthetic resource use efficiency relative to a control plant that does not contain the recombinant polynucleotide. A plant is generated from the plant cell or the plant tissue that comprises the recombinant polynucleotide, the plant is then grown and an increase in photosynthetic resource use efficiency or grain yield is measured relative to the control plant. 
     In the above paragraphs, the control plant may be exemplified by a plant of the same species as the plant comprising the recombinant polynucleotide, but the control plant does not comprise the recombinant polynucleotide that encodes a listed polypeptide of interest. 
    
    
     
       BRIEF DESCRIPTION OF THE SEQUENCE LISTING AND DRAWINGS 
       The Sequence Listing provides exemplary polynucleotide and polypeptide sequences of the instant description. The traits associated with the use of the sequences are included in the Examples. 
       Incorporation of the Sequence Listing. 
       The Sequence Listing provides exemplary polynucleotide and polypeptide sequences. The copy of the Sequence Listing being submitted electronically with this patent application under 37 CFR § 1.821-1.825, is a read-only memory computer-readable file in ASCII text format. The Sequence Listing is named “MPS-0216P_ST25.txt”, the electronic file of the Sequence Listing was created on Oct. 2, 2013, and is (1,651,577 bytes in size (157 megabytes in size as measured in MS-WINDOWS). The Sequence Listing is herein incorporated by reference in its entirety. 
       In  FIG. 1 , a phylogenetic tree of ATMYB27 or AT3G53200 (also referred to as G1311) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. ATMYB27 (AT3G53200.1) appears in the rounded rectangle. An ancestral sequence of ATMYB27 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 1 . ATMYB27 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by AT3G53200.1 and GSVIVT01033670001_VITVI. 
         FIGS. 2A-2D  show an alignment of ATMYB27 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second Myb domains appear in boxes in  FIGS. 2A-2B  and  FIG. 2B , respectively (for which the consensus sequences are SEQ ID NOs 842 and 843). 
         FIG. 3 : Plot showing increased light saturated photosynthesis (A sat ) over a range of leaf sub-stomatal CO 2  concentration (C i ) in three ATMYB27 overexpression lines, compared to a control line. Data was collected over a range of C i  over which the activity of Rubisco is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line. 
       Legend for  FIG. 3 : 
          Control 
       □ Line 1 
       Δ Line 2 
       X Line 4 
       ⋄ Line 5 
       ◯ Line 6 
         FIG. 4 : Plot showing increased light saturated photosynthesis (A sat ) over a range of leaf sub-stomatal CO 2  concentration (C i ) in four ATMYB27 overexpression lines, compared to a control line. Data was collected over a range of C i  over which the capacity to regenerate RuBP is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line. 
       Legend for  FIG. 4 : 
          Control 
       □ Line 1 
       Δ Line 2 
       X Line 4 
       ⋄ Line 5 
       ◯ Line 6 
       In  FIGS. 5A and 5B , a phylogenetic tree of RPB45A or AT5G54900 (also referred to as G1940) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. RPB45A (AT5G54900.1) appears in the rounded rectangle in  FIG. 5B . An ancestral sequence of RPB45A and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 5B . RPB45A clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi5g22410.1_BRADI and Solyc03g031720.2.1_SOLLY. 
         FIGS. 6A-6AF  show an alignment of RPB45A and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first, second, and third RNA Recognition Motif (RRM) domains appear in boxes in  FIGS. 6I-6N ,  FIGS. 6M-6R, and 6S-6X , respectively (for which the consensus sequences are SEQ ID NOs 844, 845 and 846, respectively). 
       In  FIG. 7 , a phylogenetic tree of TCP6 or AT5G41030 (also referred to as G1936) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. TCP6 (AT5G41030.1) appears in the rounded rectangle. An ancestral sequence of TCP6 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 7 . TCP6 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi2g59240.1_BRADI and Solyc02g094290.1.1_SOLLY. 
         FIGS. 8A-8L  show an alignment of TCP6 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved TCP domain appears in boxes in  FIGS. 8C-8E  (for which the consensus sequence is SEQ ID NO 847). 
       In  FIG. 9 , a phylogenetic tree of PIL1 or AT2G46970 (also referred to as G1649) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. The PIL1 clade members appear in the large box with the solid line boundary. PIL1 (AT2G46970.1) appears in the rounded rectangle. An ancestral sequence of PIL1 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 9 . PIL1 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by AT2G46970.1_ARATH and POPTR_0014 s10700.1_POPTR. 
         FIGS. 10A-10F  show an alignment of PIL1 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved bHLH domain appears in boxes in  FIGS. 10D-10E  (for which the consensus sequence is SEQ ID NO 848). 
       In  FIG. 11 , a phylogenetic tree of PCL1 or AT3G46640 (also referred to as G2741) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. PCL1 (AT3G46640.3) appears in the rounded rectangle. An ancestral sequence of PCL1 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 11 . PCL1 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi2g62067.1_BRADI and GSVIVT01024916001_VITVI. 
         FIGS. 12A-12N  show an alignment of PCL1 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved SANT (aka Myb-related or GARP) domain appears in boxes in  FIGS. 12H-12I  (for which the consensus sequence is SEQ ID NO 849). 
         FIG. 13 : Plot showing increased light saturated photosynthesis (A sat ) over a range of leaf sub-stomatal CO 2  concentration (C i ) in four PCL1 overexpression lines, compared to a control line. Data was collected over a range of C i  where the activity of Rubisco is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least seven replicate plants for each line. 
       Legend for  FIG. 13 : 
          Control 
       □ Line 1 
       Δ Line 2 
       X Line 3 
       ⋄ Line 4 
       ◯ Line 5 
       In  FIG. 14 , a phylogenetic tree of GTL1 or AT1G33240 (also referred to as G634) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. GTL1 (AT1G33240.1) appears in the rounded rectangle. An ancestral sequence of GTL1 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 14 . GTL1 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi5g17150.1_BRADI and POPTR_0005 s21420.1_POPTR. 
         FIGS. 15A-15X  show an alignment of GTL1 and representative clade-related proteins. The sequence denoted G634_P 77591  was the splice variant of GTL1 that was expressed in plants. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second trihelix (aka GT or Myb/SANT-related) domains appear in boxes in  FIGS. 15C-15E  and  FIGS. 15O-15Q , respectively (for which the consensus sequences are SEQ ID NOs 850 and 851). 
       In  FIG. 16 , a phylogenetic tree of DREB2H or AT2G40350 (also referred to as G1755) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. DREB2H (AT2G40350.1) appears in the rounded rectangle. An ancestral sequence of DREB2H and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 16 . DREB2H clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi2g04000.1_BRADI and Solyc06g050520.1.1_SOLLY. 
         FIGS. 17A-17N  show an alignment of DREB2H and representative clade-related proteins. The sequence denoted G1755_P4407 was the sequence of the DREB2H clone expressed in plants. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved AP2 domain appears in boxes in  FIGS. 17E-17F  (for which the consensus sequence is SEQ ID NO 852). 
       In  FIG. 18 , a phylogenetic tree of ERF087 or AT1G28160 (also referred to as G2292) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. ERF087 (AT1G28160.1) appears in the rounded rectangle. An ancestral sequence of ERF087 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 18 . ERF087 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi3g44470.1_BRADI and Glyma16g05070.1_GLYMA. 
         FIGS. 19A-19J  show an alignment of ERF087 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved AP2 domain appears in boxes in  FIGS. 19C-19D , respectively (for which the consensus sequence is SEQ ID NO 853). 
         FIG. 20 : Non-photochemical quenching (NPQ) dynamics at 22° C. Plot showing decreased NPQ in multiple ERF087 overexpression lines, during short term acclimation to high light. NPQ was calculated from an initial measurement of maximal, dark adapted fluorescence (F m ) and subsequent measurements of fluorescence made under varying incident light (F m ), as NPQ=(F m /F′ m )−1. During the nine minute assay F′ m  was measured at 30 second intervals: initially after exposure to 700 μmol PAR m −2  s −1  beginning immediately after F m  was measured; then, after a decrease to 0 μmol PAR m −2  s −1  after 3 minutes; then, after an increase to 2000 μmol PAR m −2  s −1  after 4 minutes. All symbols are the mean±1 standard error of measurements made on at least five replicate leaves for a given line (TAR′ refers to photosynthetically active radiation). 
       Legend for  FIG. 20 : 
          Control 
       □ Line 1 
       ⋄ Line 2 
       X Line 3 
       ◯ Line 4 
       Δ Line 5 
       + Line 6 
         FIG. 21 : Non-photochemical quenching (NPQ) dynamics at 35° C. Plot showing decreased NPQ in multiple ERF087 overexpression lines, during short term acclimation to high light. NPQ was calculated from an initial measurement of maximal, dark adapted fluorescence (F m ) and subsequent measurements of fluorescence made under varying incident light (F′ m ), as NPQ=(F m /F′ m )−1. During the nine minute assay F′ m  was measured at 30 second intervals: initially after exposure to 700 μmol PAR m −2  s −1  beginning immediately after F m  was measured; then, after a decrease to 0 μmol PAR m −2  s −1  after 3 minutes; then, after an increase to 2000 μmol PAR m −2  s −1  after 4 minutes. All symbols are the mean±1 standard error of measurements made on at least five replicate leaves for a given line. 
       Legend for  FIG. 21 : 
          Control 
       □ Line 1 
       ⋄ Line 2 
       X Line 3 
       ◯ Line 4 
       Δ Line 5 
       + Line 6 
       In  FIG. 22 , a phylogenetic tree of BBX18 or AT2G21320 (also referred to as G1881) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. BBX18 (AT2G21320.1) appears in the rounded rectangle. An ancestral sequence of BBX18 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 22 . BBX18 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi4g35950.1_BRADI and Solyc02g084420.2.1_SOLLY. 
         FIGS. 23A-23G  show an alignment of BBX18 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second B-box domains appear in boxes in  FIGS. 23A-23B  and  FIGS. 23B-23C , respectively (for which the consensus sequences are SEQ ID NOs 854 and 855). 
         FIG. 24 : Plot showing increased light saturated photosynthesis (A sat ) over a range of leaf sub-stomatal CO 2  concentration (C i ) in three BBX18 overexpression lines, compared to a control line. Data was collected over a range of C i , from low, where the activity of Rubisco is known to limit A sat , to high, where the capacity to regenerate RuBP limits A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least seven replicate plants for each line. 
       Legend for  FIG. 24 : 
          Control 
       Δ Line 4 
       ⋄ Line 5 
       □ Line 6 
       In  FIG. 25 , a phylogenetic tree of bHLH60 or AT3G57800 (also referred to as G2144) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. bHLH60 (AT3G57800.1) appears in the rounded rectangle. An ancestral sequence of bHLH60 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 25 . bHLH60 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi1g35990.1_BRADI and Solyc10g079070.1.1_SOLLY. 
         FIGS. 26A-26N  show an alignment of bHLH60 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved bHLH domain appears in boxes  FIGS. 26H-26I  (for which the consensus sequence is SEQ ID NO 856). 
       In  FIG. 27 , a phylogenetic tree of NF-YC6 or AT5G50480 (also referred to as G1820) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. NF-YC6 (AT5G50480.1) appears in the rounded rectangle. An ancestral sequence of NF-YC6 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 27 . NF-YC6 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi3g17790.1_BRADI and Solyc03g111450.1.1_SOLLY. 
         FIGS. 28A-28T  show an alignment of NF-YC6 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved NF-Y/histone-like domain appears in boxes in  FIGS. 28J-28L  (for which the consensus sequence is SEQ ID NO 857). 
       In  FIG. 29 , a phylogenetic tree of bHLH121 or AT3G19860 (also referred to as G782) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. bHLH121 (AT3G19860.2) appears in the rounded rectangle. An ancestral sequence of bHLH121 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 29 . bHLH121 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi3g11520.1_BRADI and Solyc01g111130.2.1_SOLLY. 
         FIGS. 30A-30K  show an alignment of bHLH121 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved bHLH domains appear in boxes in  FIGS. 30B-30D , respectively (SEQ ID NO 858). A distinct putative leucine zipper motif and its consensus sequence that is found with these clade members comprising is found in  FIG. 30D  (SEQ ID NO: 859), enclosed in a dotted line box. 
         FIG. 31 : Plot showing increased light saturated photosynthesis (A sat ) over a range of leaf sub-stomatal CO 2  concentration (C i ) in four out of five bHLH121 overexpression lines, compared to a control line. Data was collected over a range of C i  over which the capacity to regenerate RuBP is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least five replicate plants for each line. 
       Legend for  FIG. 31 : 
          Control 
       + Line 1 
       Δ Line 2 
       □ Line 3 
       ◯ Line 4 
       X Line 5 
       In  FIG. 32 , a phylogenetic tree of BBX26 or AT1G60250 (also referred to as G1486) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. BBX26 (AT1G60250) appears in the rounded rectangle. An ancestral sequence of BBX26 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 32 . BBX26 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by AT3G53200 ARATH and Solyc04007470.2 SOLLY. 
         FIGS. 33A-33E  show an alignment of BBX26 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved B-box domain appears in boxes in  FIG. 33A  (for which the consensus sequence is SEQ ID NO 860). 
         FIG. 34 : Plot showing increased light saturated photosynthesis (A sat ) over a range of leaf sub-stomatal CO 2  concentration (C i ) in four BBX26 overexpression lines, compared to a control line. Data was collected over a range of C i  over which the capacity to regenerate RuBP is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line. 
       Legend for  FIG. 34 : 
          Control 
          Line 1 
       + Line 2 
       ◯ Line 3 
       Δ Line 4 
       □ Line 5 
       In  FIGS. 35A and 35B , a phylogenetic tree of PMT24 or AT1G29470 (also referred to as G837) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res.  36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. PMT24 (AT1G29470.1) appears in the rounded rectangle in  FIG. 35B . An ancestral sequence of PMT24 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in  FIG. 35B . PMT24 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi2g57087.1_BRADI and GSVIVT01026451001_VITVI. 
         FIGS. 36A-36X  show an alignment of PMT24 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved putative methyltransferase domain appears in boxes in  FIGS. 36M-36S  (for which the consensus sequence is SEQ ID NO 861). 
         FIG. 37 : Plot showing increased light saturated photosynthesis (A sat ) over a range of leaf sub-stomatal CO 2  concentration (C i ) in four out of five PMT24 overexpression lines, compared to a control line. Data was collected over a range of C i  over which the capacity to regenerate RuBP is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least five replicate plants for each line. 
       Legend for  FIG. 37 : 
          Control 
       □ Line 3 
       ◯ Line 4 
       X Line 5 
       Δ Line 6 
          Line 7 
     
    
    
     DETAILED DESCRIPTION 
     The present description relates to polynucleotides and polypeptides for modifying phenotypes of plants, particularly those associated with increased photosynthetic resource use efficiency and increased yield with respect to a control plant. Throughout this disclosure, various information sources are referred to and/or are specifically incorporated. The information sources include scientific journal articles, patent documents, textbooks, and internet entries. While the reference to these information sources clearly indicates that they can be used by one of skill in the art, each and every one of the information sources cited herein are specifically incorporated in their entirety, whether or not a specific mention of “incorporation by reference” is noted. The contents and teachings of each and every one of the information sources can be relied on and used to make and use embodiments of the instant description. 
     As used herein and in the appended claims, the singular forms “a”, “an”, and “the” include the plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a host cell” includes a plurality of such host cells, and a reference to “a plant” is a reference to one or more plants, and so forth. 
     A “recombinant polynucleotide” is a polynucleotide that is not in its native state, e.g., the polynucleotide comprises a nucleotide sequence not found in nature, or the polynucleotide is in a context other than that in which it is naturally found, e.g., separated from nucleotide sequences with which it typically is in proximity in nature, or adjacent (or contiguous with) nucleotide sequences with which it typically is not in proximity. For example, the sequence at issue can be cloned into a vector, or otherwise recombined with one or more additional nucleic acid. 
     A “polypeptide” is an amino acid sequence comprising a plurality of consecutive polymerized amino acid residues e.g., at least about 15 consecutive polymerized amino acid residues. In many instances, a polypeptide comprises a polymerized amino acid residue sequence that is a regulatory polypeptide or a domain or portion or fragment thereof. Additionally, the polypeptide may comprise: (i) a localization domain; (ii) an activation domain; (iii) a repression domain; (iv) an oligomerization domain; (v) a protein-protein interaction domain; (vi) a DNA-binding domain; or the like. The polypeptide optionally comprises modified amino acid residues, naturally occurring amino acid residues not encoded by a codon, or non-naturally occurring amino acid residues. 
     “Protein” refers to an amino acid sequence, oligopeptide, peptide, polypeptide or portions thereof whether naturally occurring or synthetic. 
     In the instant description, “exogenous” refers to a heterologous nucleic acid or polypeptide that may not be naturally expressed in a plant of interest. Exogenous nucleic acids may be introduced into a plant in a stable or transient manner via, for example, transformation or breeding, and may thus serve to produce in planta a homologous RNA molecule and an encoded and functional polypeptide. Exogenous nucleic acids and polypeptides introduced thusly may comprise sequences that are wholly or partially identical or homologous to sequences that naturally occur in (i.e., are endogenous with respect to) the plant. 
     A “recombinant polypeptide” is a polypeptide produced by translation of a recombinant polynucleotide. A “synthetic polypeptide” is a polypeptide created by consecutive polymerization of isolated amino acid residues using methods well known in the art. An “isolated polypeptide,” whether a naturally occurring or a recombinant polypeptide, is more enriched in (or out of) a cell than the polypeptide in its natural state in a wild-type cell, e.g., more than about 5% enriched, more than about 10% enriched, or more than about 20%, or more than about 50%, or more, enriched, i.e., alternatively denoted: 105%, 110%, 120%, 150% or more, enriched relative to wild type standardized at 100%. Such an enrichment is not the result of a natural response of a wild-type plant. Alternatively, or additionally, the isolated polypeptide is separated from other cellular components with which it is typically associated, e.g., by any of the various protein purification methods herein. 
     “Identity” or “similarity” refers to sequence similarity between two polynucleotide sequences or between two polypeptide sequences, with identity being a more strict comparison. The phrases “percent identity” and “% identity” refer to the percentage of sequence similarity found in a comparison of two or more polynucleotide sequences or two or more polypeptide sequences. “Sequence similarity” refers to the percent similarity in base pair sequence (as determined by any suitable method) between two or more polynucleotide sequences. Two or more sequences can be anywhere from 0-100% similar or identical, or any integer value between 0-100%. Identity or similarity can be determined by comparing a position in each sequence that may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same nucleotide base or amino acid, then the molecules are identical at that position. A degree of similarity or identity between polyBLAST nucleotide sequences is a function of the number of identical, matching or corresponding nucleotides at positions shared by the polynucleotide sequences. A degree of identity of polypeptide sequences is a function of the number of identical amino acids at corresponding positions shared by the polypeptide sequences. A degree of homology or similarity of polypeptide sequences is a function of the number of amino acids at corresponding positions shared by the polypeptide sequences. The fraction or percentage of components in common is related to the homology or identity between the sequences. Alignments such as those of  FIG. 2A-2E  may be used to identify conserved domains and relatedness within these domains. An alignment may suitably be determined by means of computer programs known in the art, such as MACVECTOR software, (1999; Accelrys, Inc., San Diego, Calif.). 
     “Homologous sequences” refers to polynucleotide or polypeptide sequences that are similar due to common ancestry and sequence conservation. The terms “ortholog” and “paralog” are defined below in the section entitled “Orthologs and Paralogs”. In brief, orthologs and paralogs are evolutionarily related genes that have similar sequences and functions. Orthologs are structurally related genes in different species that are derived by a speciation event. Paralogs are structurally related genes within a single species that are derived by a duplication event. 
     “Functional homologs” are polynucleotide or polypeptide sequences, including orthologs and paralogs, that are similar due to common ancestry and sequence conservation and have identical or similar function at the catalytic, cellular, or organismal levels. The presently disclosed polypeptides, clade members and phylogenetically related sequences are “functionally-related and/or closely-related” by having descended from common ancestral sequences, and/or by being sufficiently similar to the sequences and domains listed in the instant Tables and Sequence Listing that they confer the same function to plants of increased photosynthetic resource use efficiency, increased yield, increased grain yield, increased light use efficiency, increased photosynthetic capacity, increased photosynthetic rate, greater vigor, and/or greater biomass as compared to a control plant. 
     Functionally-related and/or closely-related polypeptides may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed closely-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants. 
     “Conserved domains” are recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis. A “conserved domain” or “conserved region” as used herein refers to a region in heterologous polynucleotide or polypeptide sequences where there is a relatively high degree of sequence identity between the distinct sequences. Conserved domains contain conserved sequence patterns or motifs that allow for their detection in, and identification and characterization of, polypeptide sequences. A Myb domain is an example of a conserved domain. 
     A transgenic plant is expected to have improved or increased photosynthetic resource use efficiency relative to a control plant when the transgenic plant is transformed with a recombinant polynucleotide encoding any of the listed polypeptide sequences or polypeptide found in polypeptide clade of any of the listed polypeptide sequences, or when the transgenic plant contains or expresses a listed polypeptide or a member of any of the same polypeptide clades sequence in which the listed polypeptides may be found. 
     The terms “highly stringent” or “highly stringent condition” refer to conditions that permit hybridization of DNA strands whose sequences are highly complementary, wherein these same conditions exclude hybridization of significantly mismatched DNAs. Polynucleotide sequences capable of hybridizing under stringent conditions with the polynucleotides of the present description may be, for example, variants of the disclosed polynucleotide sequences, including allelic or splice variants, or sequences that encode orthologs or paralogs of presently disclosed polypeptides. Nucleic acid hybridization methods are disclosed in detail by Kashima et al., 1985 . Nature  313: 402-404; Sambrook et al., 1989 . Molecular Cloning: A Laboratory Manual,  2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., and by Haymes et al., 1985 . Nucleic Acid Hybridization: A Practical Approach , IRL Press, Washington, D.C., which references are incorporated herein by reference. 
     In general, stringency is determined by the temperature, ionic strength, and concentration of denaturing agents (e.g., formamide) used in a hybridization and washing procedure (for a more detailed description of establishing and determining stringency, see the section “Identifying Polynucleotides or Nucleic Acids by Hybridization”, below). The degree to which two nucleic acids hybridize under various conditions of stringency is correlated with the extent of their similarity. Thus, similar nucleic acid sequences from a variety of sources, such as within a plant&#39;s genome (as in the case of paralogs) or from another plant (as in the case of orthologs) that may perform similar functions can be isolated on the basis of their ability to hybridize with known related polynucleotide sequences. Numerous variations are possible in the conditions and means by which nucleic acid hybridization can be performed to isolate related polynucleotide sequences having similarity to sequences known in the art and are not limited to those explicitly disclosed herein. Such an approach may be used to isolate polynucleotide sequences having various degrees of similarity with disclosed polynucleotide sequences, such as, for example, encoded regulatory polypeptides listed in the Sequence Listing, or polypeptides that are phylogenetically related to the polypeptides listed in the Sequence Listing. 
     “Fragment”, with respect to a polynucleotide, refers to a clone or any part of a polynucleotide molecule that retains a usable, functional characteristic. Useful fragments include oligonucleotides and polynucleotides that may be used in hybridization or amplification technologies or in the regulation of replication, transcription or translation. A “polynucleotide fragment” refers to any subsequence of a polynucleotide, typically, of at least about nine consecutive nucleotides, preferably at least about 30 nucleotides, more preferably at least about 50 nucleotides, of any of the sequences provided herein. Exemplary polynucleotide fragments are the first sixty consecutive nucleotides of the polynucleotides listed in the Sequence Listing. Exemplary fragments also include fragments that comprise a region that encodes an conserved domain of a polypeptide. Exemplary fragments also include fragments that comprise a conserved domain of a polypeptide. Exemplary fragments include fragments that comprise an conserved domain of a polypeptide, for example, any of the domains listed in in the instant Tables or in the Sequence Listing. 
     Fragments may also include subsequences of polypeptides and protein molecules, or a subsequence of the polypeptide. Fragments may have uses in that they may have antigenic potential. In some cases, the fragment or domain is a subsequence of the polypeptide which performs at least one biological function of the intact polypeptide in substantially the same manner, or to a similar extent, as does the intact polypeptide. For example, a polypeptide fragment can comprise a recognizable structural motif or functional domain such as a DNA-binding site or domain that binds to a DNA promoter region, an activation domain, or a domain for protein-protein interactions, and may initiate transcription. Fragments can vary in size from as few as three amino acid residues to the full length of the intact polypeptide, but are preferably at least about 30 amino acid residues in length and more preferably at least about 60 amino acid residues in length. 
     Fragments may also refer to a functional fragment of a promoter region. For example, a recombinant polynucleotide capable of modulating transcription in a plant may comprise a nucleic acid sequence with similarity to, or a percentage identity to, a promoter region exemplified by a promoter sequence provided in the Sequence Listing (also see promoters listed in Example II), a fragment thereof, or a complement thereof, wherein the nucleic acid sequence, or the fragment thereof, or the complement thereof, regulates expression of a polypeptide in a plant cell. 
     The term “plant” includes whole plants, shoot vegetative organs/structures (for example, leaves, stems and tubers), roots, flowers and floral organs/structures (for example, bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (for example, vascular tissue, ground tissue, and the like), pulped, pureed, ground-up, macerated or broken-up tissue, and cells (for example, guard cells, egg cells, and the like), and progeny of same. The class of the plants that can be transformed using the methods provided of the instant description is generally as broad as the class of higher and lower plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), gymnosperms, ferns, horsetails, psilophytes, lycophytes, and bryophytes. These plant parts, organs, structures, cells, tissue, or progeny may contain a recombinant polynucleotide of interest, such as one that comprises a described or listed polynucleotide or one that encodes a described or listed polypeptide or a polypeptide that is phylogenetically-related to a listed polypeptide, and is thus a member of the same polypeptide clade. 
     A “control plant” as used in the present description refers to a plant cell, seed, plant component, plant tissue, plant organ or whole plant used to compare against transgenic or genetically modified plant for the purpose of identifying an enhanced phenotype in the transgenic or genetically modified plant. A control plant may in some cases be a transgenic plant line that comprises an empty vector or marker gene, but does not contain the recombinant polynucleotide of the present description that is expressed in the transgenic or genetically modified plant being evaluated. In general, a control plant is a plant of the same line or variety as the transgenic or genetically modified plant being tested. A suitable control plant would include a genetically unaltered or non-transgenic plant of the parental line used to generate a transgenic plant herein. 
     A “transgenic plant” refers to a plant that contains genetic material not found in a wild-type plant of the same species, variety or cultivar. The genetic material may include a transgene, an insertional mutagenesis event (such as by transposon or T-DNA insertional mutagenesis), an activation tagging sequence, a mutated sequence, a homologous recombination event or a sequence modified by chimeraplasty. Typically, the foreign genetic material has been introduced into the plant by human manipulation, but any method can be used as one of skill in the art recognizes. 
     A transgenic line or transgenic plant line refers to the progeny plant or plants deriving from the stable integration of heterologous genetic material into a specific location or locations within the genome of the original transformed cell. 
     A transgenic plant may contain an expression vector or cassette. The expression vector or cassette typically comprises a polypeptide-encoding sequence operably linked (i.e., under regulatory control of) to appropriate inducible, tissue-enhanced, tissue-specific, or constitutive regulatory sequences that allow for the controlled expression of the polypeptide. The expression vector or cassette can be introduced into a plant by transformation or by breeding after transformation of a parent plant. A plant refers to a whole plant as well as to a plant part, such as seed, fruit, leaf, or root, plant tissue, plant cells or any other plant material, e.g., a plant explant, as well as to progeny thereof, and to in vitro systems that mimic biochemical or cellular components or processes in a cell. In some other embodiments, the expression vectors or cassettes do not occur naturally. In some embodiments, the expression vectors or cassettes comprise a promoter of the present application, and a gene of interest, wherein the promoter and the gene of interest do not link to each other under natural conditions, e.g., the linkage between the promoter and the gene of interest does not exist in nature. For example, in some embodiments, the promoter and the gene of interest are derived from a same plant species, but are not linked to each other under natural conditions. In some embodiments, the promoter and the gene of interest are derived from two different species, e.g., the promoter and the gene of interest are heterologous to each other. In some embodiments, the gene of interest is derived from a different plant species, a bacteria species, a fungal species, a viral species, an algae species, or an animal species. In some embodiments, the expression vectors or cassettes comprise synthetic sequences. 
     “Germplasm” refers to a genetic material or a collection of genetic resources for an organism from an individual plant, a group of related individual plants (for example, a plant line, a plant variety or a plant family), or a clone derived from a plant line, plant variety, plant species, or plant culture. 
     A constitutive promoter is active under most environmental conditions, and in most plant parts. Regulation of protein expression in a constitutive manner refers to the control of expression of a gene and/or its encoded protein in all tissues regardless of the surrounding environment or development stage of the plant. 
     Alternatively, expression of the disclosed or listed polypeptides may be under the regulatory control of a promoter that is not a constitutive promoter. For example, tissue-enhanced (also referred to as tissue-preferred), tissue-specific, cell type-specific, and inducible promoters constitute non-constitutive promoters; that is, these promoters do not regulate protein expression in a constitutive manner. Tissue-enhanced or tissue-preferred promoters facilitate expression of a gene and/or its encoded protein in specific tissue(s) and generally, although perhaps not completely, do not express the gene and/or protein in all other tissues of the plant, or do so to a much lesser extent. Promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as xylem, leaves, roots, or seeds. Such promoters are examples of tissue-enhanced or tissue-preferred promoters (see U.S. Pat. No. 7,365,186). Tissue-specific promoters generally confine transgene expression to a single plant part, tissue or cell-type, although many such promoters are not perfectly restricted in their expression and their regulatory control is more properly described as being “tissue-enhanced” or “tissue-preferred”. Tissue-enhanced promoters primarily regulate transgene expression in a limited number of plant parts, tissues or cell-types and cause the expression of proteins to be overwhelming restricted to a few particular tissues, plant parts, or cell types. An example of a tissue-enhanced promoter is a “photosynthetic tissue-enhanced promoter”, for which the promoter preferentially regulates gene or protein expression in photosynthetic tissues (e.g., leaves, cotyledons, stems, etc.). Tissue-enhanced promoters can be found upstream and operatively linked to DNA sequences normally transcribed in higher levels in certain plant tissues or specifically in certain plant tissues, respectively. “Cell-enhanced”, “tissue-enhanced”, or “tissue-specific” regulation thus refer to the control of gene or protein expression, for example, by a promoter that drives expression that is not necessarily totally restricted to a single type of cell or tissue, but where expression is elevated in particular cells or tissues to a greater extent than in other cells or tissues within the organism, and in the case of tissue-specific regulation, in a manner that is primarily elevated in a specific tissue. Tissue-enhanced or preferred promoters have been described in, for example, U.S. Pat. No. 7,365,186, or 7,619,133. 
     Another example of a promoter that is not a constitutive promoter is a “condition-enhanced” promoter, the latter term referring to a promoter that activates a gene in response to a particular environmental stimulus. This may include, for example, an abiotic stress, infection caused by a pathogen, light treatment, etc., and a condition-enhanced promoter drives expression in a unique pattern which may include expression in specific cell and/or tissue types within the organism (as opposed to a constitutive expression pattern in all cell types of an organism at all times). 
     “Wild type” or “wild-type”, as used herein, refers to a plant cell, seed, plant component, plant tissue, plant organ or whole plant that has not been genetically modified or treated in an experimental sense. Wild-type cells, seed, components, tissue, organs or whole plants may be used as controls to compare levels of expression and the extent and nature of trait modification with cells, tissue or plants of the same species in which a polypeptide&#39;s expression is altered, e.g., in that it has been knocked out, overexpressed, or ectopically expressed. 
     When two or more plants have “similar morphologies”, “substantially similar morphologies”, “a morphology that is substantially similar”, or are “morphologically similar”, the plants have comparable forms or appearances, including analogous features such as overall dimensions, height, width, mass, root mass, shape, glossiness, color, stem diameter, leaf size, leaf dimension, leaf density, internode distance, branching, root branching, number and form of inflorescences, and other macroscopic characteristics at a particular stage of growth. It may be difficult to distinguish two plants that are genotypically distinct but morphologically similar based on morphological characteristics alone. If the plants are morphologically similar at all stages of growth, they are also “developmentally similar”. 
     With regard to gene knockouts as used herein, the term “knockout” (KO) refers to a plant or plant cell having a disruption in at least one gene in the plant or cell, where the disruption results in a reduced expression or activity of the polypeptide encoded by that gene compared to a control cell. The knockout can be the result of, for example, genomic disruptions, including transposons, tilling, and homologous recombination, antisense constructs, sense constructs, RNA silencing constructs, or RNA interference. A T-DNA insertion within a gene is an example of a genotypic alteration that may abolish expression of that gene. 
     “Ectopic expression” or “altered expression” in reference to a polynucleotide indicates that the pattern of expression in, e.g., a transgenic plant or plant tissue, is different from the expression pattern in a wild-type plant or a reference plant of the same species. The pattern of expression may also be compared with a reference expression pattern in a wild-type plant of the same species. For example, the polynucleotide or polypeptide is expressed in a cell or tissue type other than a cell or tissue type in which the sequence is expressed in the wild-type plant, or by expression at a time other than at the time the sequence is expressed in the wild-type plant, or by a response to different inducible agents, such as hormones or environmental signals, or at different expression levels (either higher or lower) compared with those found in a wild-type plant. The term also refers to altered expression patterns that are produced by lowering the levels of expression to below the detection level or completely abolishing expression. The resulting expression pattern can be transient or stable, constitutive or inducible. In reference to a polypeptide, the term “ectopic expression or altered expression” further may relate to altered activity levels resulting from the interactions of the polypeptides with exogenous or endogenous modulators or from interactions with factors or as a result of the chemical modification of the polypeptides. 
     The term “overexpression” as used herein refers to a greater expression level of a gene in a plant, plant cell or plant tissue, compared to expression of that gene in a wild-type plant, cell or tissue, at any developmental or temporal stage. Overexpression can occur when, for example, the genes encoding one or more polypeptides are under the control of a strong promoter (e.g., the cauliflower mosaic virus 35S transcription initiation region). Overexpression may also be achieved by placing a gene of interest under the control of an inducible or tissue specific promoter, or may be achieved through integration of transposons or engineered T-DNA molecules into regulatory regions of a target gene. Other means for inducing overexpression may include making targeted changes in a gene&#39;s native promoter, e.g. through elimination of negative regulatory sequences or engineering positive regulatory sequences, though the use of targeted nuclease activity (such as zinc finger nucleases or TAL effector nucleases) for genome editing. Elimination of micro-RNA binding sites in a gene&#39;s transcript may also result in overexpression of that gene. Additionally, a gene may be overexpressed by creating an artificial transcriptional activator targeted to bind specifically to its promoter sequences, comprising an engineered sequence-specific DNA binding domain such as a zinc finger protein or TAL effector protein fused to a transcriptional activation domain. Thus, overexpression may occur throughout a plant, in specific tissues of the plant, or in the presence or absence of particular environmental signals, depending on the promoter or overexpression approach used. 
     Overexpression may take place in plant cells normally lacking expression of polypeptides functionally equivalent or identical to the present polypeptides. Overexpression may also occur in plant cells where endogenous expression of the present polypeptides or functionally equivalent molecules normally occurs, but such normal expression is at a lower level. Overexpression thus results in a greater than normal production, or “overproduction” of the polypeptide in the plant, cell or tissue. 
     “Photosynthetic resource-use efficiency” is defined as the rate of photosynthesis achieved per unit use of a given resource. Consequently, increases in photosynthesis relative to the use of a given resource will improve photosynthetic resource-use efficiency. Photosynthesis is constrained by the availability of various resources, including light, water and nitrogen. Improving the efficiency with which photosynthesis makes use of light, water and nitrogen is a means for increasing plant productivity, crop growth, and yield. For the purposes of comparing a plant of interest to a reference or control plant, the ratio of photosynthesis to use of a given resource is often determined for a fixed unit of leaf area. Examples of increased photosynthetic resource-use efficiency would be an increase in the ratio of the rate of photosynthesis for a given leaf relative to, for example, the rate of transpiration from the same leaf area, nitrogen or chlorophyll invested in that leaf area, or light absorbed by that same leaf area. Increased photosynthetic resource use efficiency may result from increased photosynthetic rate, photosynthetic capacity, a decrease in leaf chlorophyll content, a decrease in percentage of nitrogen in leaf dry weight, increased transpiration efficiency, an increase in resistance to water vapor diffusion exerted by leaf stomata, an increased rate of relaxation of photoprotective reactions operating in the light harvesting antennae, a decrease in the ratio of the carbon isotope  12 C to  13 C in above-ground biomass, and/or an increase in the total dry weight of above-ground plant material. 
     “Photosynthetic rate” refers to the rate of photosynthesis achieved by a leaf, and is typically expressed relative to a unit of leaf area. The photosynthetic rate at any given time results from the photosynthetic capacity of the leaf (see below) and the biotic or abiotic environmental constraints prevailing at that time. 
     “Photosynthetic capacity” refers to the capacity for photosynthesis per unit leaf area and is set by the leafs investment in the components of the photosynthetic apparatus. Key components, among many, would be the pigments and proteins required to regulate light absorption and transduction of light energy to the photosynthetic reaction centers, and the enzymes required to operate the C3 and C4 dark reactions of photosynthesis. Increasing photosynthetic capacity is seen as an important means of increasing leaf and crop-canopy photosynthesis, and crop yield. 
     “Rubisco (ribulose-1,5-bisphosphate carboxylase oxygenase) activity” refers to the activation state of Rubisco, the most abundant protein in the chloroplast and a key limitation to C3 photosynthesis. Increasing Rubisco activity by: increasing the amount of Rubisco in the chloroplast; impacting any combination of specific reactions that regulate Rubisco activity; or increasing the concentration of CO 2  in the chloroplast, is seen as an important means to improving C3 leaf and crop-canopy photosynthesis and crop yield. 
     The “capacity for RuBP (ribulose-1,5-bisphosphate) regeneration” refers to the rate at which RuBP, a key photosynthetic substrate is regenerated in the Calvin cycle. Increasing the capacity for RuBP regeneration by increasing the activity of enzymes in the regenerative phase of the Calvin cycle is seen as an important means to improving C3 leaf and crop-canopy photosynthesis and crop yield that will become progressively more important as atmospheric CO 2  concentrations continue to rise. 
     “Leaf chlorophyll content” refers to the chlorophyll content of the leaf expressed either per unit leaf area or unit weight. Sun leaves in the upper part of crop canopies are thought to have higher leaf chlorophyll content than is required for photosynthesis. The consequence is that these leaves: invest more nitrogen in chlorophyll than is required for photosynthesis; are prone to photodamage associated with absorbing more light energy than can be dissipated via photosynthesis; and impair the transmission of light into the leaf and lower canopy where photosynthesis is light limited. Consequently, decreasing leaf chlorophyll content of upper canopy leaves is considered an effective means to improving photosynthetic resource-use efficiency. 
     “Non-photochemical quenching” is a term that covers photoprotective processes that dissipate absorbed light energy as heat from the light-harvesting antenna of photosystem II. Non-photochemical quenching is a key regulator of the efficiency with which electron transport is initiated by PSII and the efficiency of photosynthesis at low light. Decreasing the level of non-photochemical quenching, or increasing the speed with which it relaxes is expected to confer cumulative gains in photosynthesis every time the light intensity to which the canopy is exposed transitions from high to low, and is considered a means to improving canopy photosynthesis when integrated over a growing season. 
     “Nitrogen limitation” or “nitrogen-limiting” refers to nitrogen levels that act as net limitations on primary production in terrestrial or aquatic biomes. Much of terrestrial growth, including much of crop growth, is limited by the availability of nitrogen, which can be alleviated by nitrogen input through deposition or fertilization. 
     “Water use efficiency”, or WUE, measured as the biomass produced per unit transpiration, describes the relationship between water use and crop production. The basic physiological definition of WUE equates to the ratio of photosynthesis (A) to transpiration (T), also referred to as transpiration efficiency (Karaba et al. 2007, supra; Morison et al., 2008, supra). 
     “Stomatal conductance” refers to a measurement of the limitation that the stomatal pore imposes on CO 2  diffusion into, and H 2 O diffusion out of, the leaf. Decreasing stomatal conductance will decrease water loss from the leaf and crop canopy via transpiration. This will conserve soil water, delay the onset and reduce the severity of drought effects on canopy photosynthesis and other physiology. Decreasing stomatal conductance will also decrease photosynthesis. However, the magnitude of the decrease in photosynthesis will typically be less than the decrease in transpiration, and transpiration efficiency will increase as a result. Conversely, increasing stomatal conductance can increase the diffusion of CO 2  into the leaf and increase photosynthesis in a C3 leaf. Typically, transpiration will increase to a greater extent than photosynthesis, and transpiration efficiency will therefore decrease. 
     “Yield” or “plant yield” refers to increased plant growth, increased crop growth, increased biomass, and/or increased plant product production (including grain), and is dependent to some extent on temperature, plant size, organ size, planting density, light, water and nutrient availability, and how the plant copes with various stresses, such as through temperature acclimation and water or nutrient use efficiency. For grain crops, yield generally refers to an amount of grain produced or harvested per unit of land area, such as bushels or tons per acre or tonnes per hectare. Increased or improved yield may be measured as increased seed yield, increased plant product yield (plant products include, for example, plant tissue, including ground or otherwise broken-up plant tissue, and products derived from one or more types of plant tissue), or increased vegetative yield. 
     DESCRIPTION OF THE SPECIFIC EMBODIMENTS 
     Regulatory Polypeptides Modify Expression of Endogenous Genes. 
     A regulatory polypeptide may include, but is not limited to, any polypeptide that can activate or repress transcription of a single gene or a number of genes. As one of ordinary skill in the art recognizes, regulatory polypeptides can be identified by the presence of a region or domain of structural similarity or identity to a specific consensus sequence or the presence of a specific consensus DNA-binding motif (see, for example, Riechmann et al., 2000a. supra). 
     Generally, regulatory polypeptides control the manner in which information encoded by genes is used to produce gene products and control various pathways, and may be involved in diverse processes including, but not limited to, cell differentiation, proliferation, morphogenesis, and the regulation of growth or environmental responses. Accordingly, one skilled in the art would recognize that by expressing the present sequences in a plant, one may change the expression of autologous genes or induce the expression of introduced genes. By affecting the expression of similar autologous sequences in a plant that have the biological activity of the present sequences, or by introducing the present sequences into a plant, one may alter a plant&#39;s phenotype to one with improved traits related to photosynthetic resource use efficiency. The sequences of the instant description may also be used to transform a plant and introduce desirable traits not found in the wild-type cultivar or strain. Plants may then be selected for those that produce the most desirable degree of over- or under-expression of target genes of interest and coincident trait improvement. 
     The sequences of the present description may be from any species, particularly plant species, in a naturally occurring form or from any source whether natural, synthetic, semi-synthetic or recombinant. The sequences of the instant description may also include fragments of the present amino acid sequences. Where “amino acid sequence” is recited to refer to an amino acid sequence of a naturally occurring protein molecule, “amino acid sequence” and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule. 
     In addition to methods for modifying a plant phenotype by employing one or more polynucleotides and polypeptides of the instant description described herein, the polynucleotides and polypeptides of the instant description have a variety of additional uses. These uses include their use in the recombinant production (i.e., expression) of proteins; as regulators of plant gene expression, as diagnostic probes for the presence of complementary or partially complementary nucleic acids (including for detection of natural coding nucleic acids); as substrates for further reactions, e.g., mutation reactions, PCR reactions, or the like; as substrates for cloning e.g., including digestion or ligation reactions; and for identifying exogenous or endogenous modulators of the regulatory polypeptides. The polynucleotide can be, e.g., genomic DNA or RNA, a transcript (such as an mRNA), a cDNA, a PCR product, a cloned DNA, a synthetic DNA or RNA, or the like. The polynucleotide can comprise a sequence in either sense or antisense orientations. 
     Expression of genes that encode polypeptides that modify expression of endogenous genes, polynucleotides, and proteins are well known in the art. In addition, transgenic plants comprising polynucleotides encoding regulatory polypeptides may also modify expression of endogenous genes, polynucleotides, and proteins. Examples include Peng et al., 1997 . Genes Development  11: 3194-3205, and Peng et al., 1999 . Nature  400: 256-261. In addition, many others have demonstrated that an  Arabidopsis  regulatory polypeptide expressed in an exogenous plant species elicits the same or very similar phenotypic response. See, for example, Fu et al., 2001 . Plant Cell  13: 1791-1802; Nandi et al., 2000 . Curr. Biol.  10: 215-218; Coupland, 1995 . Nature  377: 482-483; and Weigel and Nilsson, 1995 . Nature  377: 482-500. 
     In another example, Mandel et al., 1992b.  Cell  71-133-143, and Suzuki et al., 2001 . Plant J.  28: 409-418, teach that a transcription factor expressed in another plant species elicits the same or very similar phenotypic response of the endogenous sequence, as often predicted in earlier studies of  Arabidopsis  transcription factors in  Arabidopsis  (see Mandel et al., 1992a.  Nature  360: 273-277; Suzuki et al., 2001. supra). Other examples include Müller et al., 2001 . Plant J.  28: 169-179; Kim et al., 2001 . Plant J.  25: 247-259; Kyozuka and Shimamoto, 2002 . Plant Cell Physiol.  43: 130-135; Boss and Thomas, 2002 . Nature,  416: 847-850; He et al., 2000 . Transgenic Res.  9: 223-227; and Robson et al., 2001 . Plant J.  28: 619-631. 
     In yet another example, Gilmour et al., 1998 . Plant J.  16: 433-442 teach an  Arabidopsis  AP2 transcription factor, CBF1, which, when overexpressed in transgenic plants, increases plant freezing tolerance. Jaglo et al., 2001 . Plant Physiol.  127: 910-917, further identified sequences in  Brassica napus  which encode CBF-like genes and that transcripts for these genes accumulated rapidly in response to low temperature. Transcripts encoding CBF proteins were also found to accumulate rapidly in response to low temperature in wheat, as well as in tomato. An alignment of the CBF proteins from  Arabidopsis, B. napus , wheat, rye, and tomato revealed the presence of conserved consecutive amino acid residues which bracket the AP2/EREBP DNA binding domains of the proteins and distinguish them from other members of the AP2/EREBP protein family (Jaglo et al., 2001. supra). 
     Regulatory polypeptides mediate cellular responses and control traits through altered expression of genes containing cis-acting nucleotide sequences that are targets of the introduced regulatory polypeptide. It is well appreciated in the art that the effect of a regulatory polypeptide on cellular responses or a cellular trait is determined by the particular genes whose expression is either directly or indirectly (e.g., by a cascade of regulatory polypeptide binding events and transcriptional changes) altered by regulatory polypeptide binding. In a global analysis of transcription comparing a standard condition with one in which a regulatory polypeptide is overexpressed, the resulting transcript profile associated with regulatory polypeptide overexpression is related to the trait or cellular process controlled by that regulatory polypeptide. For example, the PAP2 gene and other genes in the Myb family have been shown to control anthocyanin biosynthesis through regulation of the expression of genes known to be involved in the anthocyanin biosynthetic pathway (Bruce et al., 2000 . Plant Cell  12: 65-79; and Borevitz et al., 2000 . Plant Cell  12: 2383-2393). Further, global transcript profiles have been used successfully as diagnostic tools for specific cellular states (e.g., cancerous vs. non-cancerous; Bhattacharjee et al., 2001 . Proc. Natl. Acad. Sci. USA  98: 13790-13795; and Xu et al., 2001 . Proc. Natl. Acad. Sci. USA  98: 15089-15094). Consequently, it is evident to one skilled in the art that similarity of transcript profile upon overexpression of different regulatory polypeptides would indicate similarity of regulatory polypeptide function. 
     Polypeptides and Polynucleotides of the Present Description. 
     The present description includes putative regulatory polypeptides, and isolated or recombinant polynucleotides encoding the polypeptides, or novel sequence variant polypeptides or polynucleotides encoding novel variants of polypeptides derived from the specific sequences provided in the Sequence Listing; the recombinant polynucleotides of the instant description may be incorporated in expression vectors for the purpose of producing transformed plants. 
     Because of their relatedness at the nucleotide level, the claimed sequences will typically share at least about 30% nucleotide sequence identity, or at least 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% sequence identity to one or more of the listed full-length sequences, or to a listed sequence but excluding or outside of the region(s) encoding a known consensus sequence or consensus DNA-binding site, or outside of the region(s) encoding one or all conserved domains. The degeneracy of the genetic code enables major variations in the nucleotide sequence of a polynucleotide while maintaining the amino acid sequence of the encoded protein. 
     Because of their relatedness at the protein level, the claimed nucleotide sequences will typically encode a polypeptide that is at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical in its amino acid sequence to the entire length of any of the polypeptides listed in the Sequence Listing or the instant Tables, or closely- or phylogenetically-related sequences. 
     Also provided are methods for modifying yield from a plant by modifying the mass, size or number of plant organs or seed of a plant by controlling a number of cellular processes, and for increasing a plant&#39;s photosynthetic resource use efficiency. These methods are based on the ability to alter the expression of critical regulatory molecules that may be conserved between diverse plant species. Related conserved regulatory molecules may be originally discovered in a model system such as  Arabidopsis  and homologous, functional molecules then discovered in other plant species. The latter may then be used to confer increased yield or photosynthetic resource use efficiency in diverse plant species. 
     Sequences in the Sequence Listing, derived from diverse plant species, may be ectopically expressed in overexpressor plants. The changes in the characteristic(s) or trait(s) of the plants may then be observed and found to confer increased yield and/or increased photosynthetic resource use efficiency. Therefore, the polynucleotides and polypeptides can be used to improve desirable characteristics of plants. 
     The polynucleotides of the instant description are also ectopically expressed in overexpressor plant cells and the changes in the expression levels of a number of genes, polynucleotides, and/or proteins of the plant cells observed. Therefore, the polynucleotides and polypeptides can be used to change expression levels of genes, polynucleotides, and/or proteins of plants or plant cells. 
     The data presented herein represent the results obtained in experiments with polynucleotides and polypeptides that may be expressed in plants for the purpose of increasing yield that arises from improved photosynthetic resource use efficiency. 
     Variants of the Disclosed Sequences. 
     Also within the scope of the instant description is a variant of a nucleic acid listed in the Sequence Listing, that is, one having a sequence that differs from the one of the polynucleotide sequences in the Sequence Listing, or a complementary sequence, that encodes a functionally equivalent polypeptide (i.e., a polypeptide having some degree of equivalent or similar biological activity) but differs in sequence from the sequence in the Sequence Listing, due to degeneracy in the genetic code. Included within this definition are polymorphisms that may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding polypeptide, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding polypeptide. 
     Differences between presently disclosed polypeptides and polypeptide variants are limited so that the sequences of the former and the latter are closely similar overall and, in many regions, identical. Presently disclosed polypeptide sequences and similar polypeptide variants may differ in amino acid sequence by one or more substitutions, additions, deletions, fusions and truncations, which may be present in any combination. These differences may produce silent changes and result in a functionally equivalent polypeptides. Thus, it will be readily appreciated by those of skill in the art, that any of a variety of polynucleotide sequences is capable of encoding the polypeptides and homolog polypeptides of the instant description. A polypeptide sequence variant may have “conservative” changes, wherein a substituted amino acid has similar structural or chemical properties. 
     Conservative substitutions include substitutions in which at least one residue in the amino acid sequence has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the Table 1 when it is desired to maintain the activity of the protein. Table 1 shows amino acids which can be substituted for an amino acid in a protein and which are typically regarded as conservative substitutions. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Possible conservative amino acid substitutions 
               
            
           
           
               
               
               
            
               
                   
                 Amino Acid 
                 Conservative 
               
               
                   
                 Residue 
                 substitutions 
               
               
                   
                   
               
               
                   
                 Ala 
                 Ser 
               
               
                   
                 Arg 
                 Lys 
               
               
                   
                 Asn 
                 Gln; His 
               
               
                   
                 Asp 
                 Glu 
               
               
                   
                 Gln 
                 Asn 
               
               
                   
                 Cys 
                 Ser 
               
               
                   
                 Glu 
                 Asp 
               
               
                   
                 Gly 
                 Pro 
               
               
                   
                 His 
                 Asn; Gln 
               
               
                   
                 Ile 
                 Leu, Val 
               
               
                   
                 Leu 
                 Ile; Val 
               
               
                   
                 Lys 
                 Arg; Gln 
               
               
                   
                 Met 
                 Leu; Ile 
               
               
                   
                 Phe 
                 Met; Leu; Tyr 
               
               
                   
                 Pro 
                 Gly 
               
               
                   
                 Ser 
                 Thr; Gly 
               
               
                   
                 Thr 
                 Ser; Val 
               
               
                   
                 Trp 
                 Tyr 
               
               
                   
                 Tyr 
                 Trp; Phe 
               
               
                   
                 Val 
                 Ile; Leu 
               
               
                   
                   
               
            
           
         
       
     
     The polypeptides provided in the Sequence Listing have a novel activity, such as, for example, regulatory activity. Although all conservative amino acid substitutions (for example, one basic amino acid substituted for another basic amino acid) in a polypeptide will not necessarily result in the polypeptide retaining its activity, it is expected that many of these conservative mutations would result in the polypeptide retaining its activity. Most mutations, conservative or non-conservative, made to a protein but outside of a conserved domain required for function and protein activity will not affect the activity of the protein to any great extent. 
     Deliberate amino acid substitutions may thus be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as a significant amount of the functional or biological activity of the polypeptide is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, positively charged amino acids may include lysine and arginine, and amino acids with uncharged polar head groups having similar hydrophilicity values may include leucine, isoleucine, and valine; glycine and alanine; asparagine and glutamine; serine and threonine; and phenylalanine and tyrosine. More rarely, a variant may have “non-conservative” changes, e.g., replacement of a glycine with a tryptophan Similar minor variations may also include amino acid deletions or insertions, or both. Related polypeptides may comprise, for example, additions and/or deletions of one or more N-linked or O-linked glycosylation sites, or an addition and/or a deletion of one or more cysteine residues. Guidance in determining which and how many amino acid residues may be substituted, inserted or deleted without abolishing functional or biological activity may be found using computer programs well known in the art, for example, DNASTAR software (see U.S. Pat. No. 5,840,544). 
     Conserved Domains. 
     Conserved domains are recurring functional and/or structural units of a protein sequence within a protein family (for example, a family of regulatory proteins), and distinct conserved domains have been used as building blocks in molecular evolution and recombined in various arrangements to make proteins of different protein families with different functions. Conserved domains often correspond to the 3-dimensional domains of proteins and contain conserved sequence patterns or motifs, which allow for their detection in polypeptide sequences with, for example, the use of a Conserved Domain Database (for example, at www.ncbi.nlm.nih.gov/cdd). The National Center for Biotechnology Information Conserved Domain Database defines conserved domains as recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis. Conserved domains contain conserved sequence patterns or motifs, which allow for their detection in polypeptide sequences (Conserved Domain Database; www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml). 
     Conserved domains may also be identified as regions or domains of identity to a specific consensus sequence (see, for example, Riechmann et al., 2000a.  Science  290, 2105-2110; Riechmann et al., 2000b.  Curr Opin Plant Biol  3: 423-434). Thus, by using alignment methods well known in the art, the conserved domains of the plant polypeptides, for example, for the Myb domain polypeptides may be determined. The polypeptides of the instant Tables have conserved domains associated with the disclosed functions of the proteins in which they are found and specifically indicated by amino acid coordinate start and stop sites. A comparison of the regions of these polypeptides allows one of skill in the art (see, for example, Reeves and Nissen, 1990 . J. Biol. Chem.  265, 8573-8582; Reeves and Nissen, 1995 . Prog. Cell Cycle Res.  1: 339-349) to identify domains or conserved domains for any of the polypeptides listed or referred to in this disclosure. 
     Conserved domain models are generally identified with multiple sequence alignments of related proteins spanning a variety of organisms (for example, conserved domains of the disclosed sequences can be found in the instant Figures, Tables, and the Sequence Listing). These alignments reveal sequence regions containing the same, or similar, patterns of amino acids. Multiple sequence alignments, three-dimensional structure and three-dimensional structure superposition of conserved domains can be used to infer sequence, structure, and functional relationships (Conserved Domain Database, supra). Since the presence of a particular conserved domain within a polypeptide (prophetically including any of the instantly listed polypeptides) is highly correlated with an evolutionarily conserved function, a conserved domain database may be used to identify the amino acids in a protein sequence that are putatively involved in functions such as binding or catalysis, as mapped from conserved domain annotations to the query sequence. For example, the presence in a protein of Myb domain that is structurally and phylogenetically similar to one or more domains shown in the instant Tables would be a strong indicator of a related function in plants (e.g., the function of regulating and/or improving yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant; i.e., a polypeptide with such a domain is expected to confer altered yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant when its expression level is altered). Sequences herein referred to as functionally-related and/or closely-related to the sequences or domains listed in the instant Tables, including polypeptides that are closely related to the polypeptides of the instant description, may have conserved domains that share at least at least nine base pairs (bp) in length and at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to the sequences provided in the Sequence Listing or in the instant Tables, and have similar functions in that the polypeptides of the instant description. Said polypeptides may, when their expression level is altered by suppressing their expression, knocking out their expression, or increasing their expression, confer at least one regulatory activity selected from the group consisting of increased yield, increased light use efficiency, increased photosynthetic capacity, increased photosynthetic rate, increased photosynthetic resource use efficiency, greater vigor, and/or greater biomass as compared to a control plant. 
     Methods using manual alignment of sequences similar or homologous to one or more polynucleotide sequences or one or more polypeptides encoded by the polynucleotide sequences may be used to identify regions of similarity and conserved domains or other motifs. Such manual methods are well-known of those of skill in the art and can include, for example, comparisons of tertiary structure between a polypeptide sequence encoded by a polynucleotide that comprises a known function and a polypeptide sequence encoded by a polynucleotide sequence that has a function not yet determined. Such examples of tertiary structure may comprise predicted alpha helices, beta-sheets, amphipathic helices, leucine zipper motifs, zinc finger motifs, proline-rich regions, cysteine repeat motifs, and the like. 
     With respect to polynucleotides encoding presently disclosed polypeptides, a conserved domain refers to a subsequence within a polypeptide family (for example, in any of the instantly listed polypeptides or members of the listed polypeptide families) the presence of which is correlated with at least one function exhibited by members of the polypeptide family, and which exhibits a high degree of sequence homology, such as at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identity to a conserved domain of a polypeptide of the Sequence Listing or listed in the instant Tables that show the instant polypeptides and closely-related or phylogenetically-related sequences. Sequences that possess or encode for conserved domains that meet these criteria of percentage identity, and that have comparable biological and regulatory activity to the present polypeptide sequences, thus being members of the clade polypeptides or sequences listed in the sequence Listing or in Example I, are described. Sequences having lesser degrees of identity but comparable biological activity are considered to be equivalents. 
     Orthologs and Paralogs. 
     Homologous sequences as described above can comprise orthologous or paralogous sequences. Several different methods are known by those of skill in the art for identifying and defining these functionally homologous sequences. General methods for identifying orthologs and paralogs, including phylogenetic methods, sequence similarity and hybridization methods, are described herein; an ortholog or paralog, including equivalogs, may be identified by one or more of the methods described below. 
     As described by Eisen, 1998 . Genome Res.  8: 163-167, evolutionary information may be used to predict gene function. It is common for groups of genes that are homologous in sequence to have diverse, although usually related, functions. However, in many cases, the identification of homologs is not sufficient to make specific predictions because not all homologs have the same function. Thus, an initial analysis of functional relatedness based on sequence similarity alone may not provide one with a means to determine where similarity ends and functional relatedness begins. Fortunately, it is well known in the art that protein function can be classified using phylogenetic analysis of gene trees combined with the corresponding species. Functional predictions can be greatly improved by focusing on how the genes became similar in sequence (i.e., by evolutionary processes) rather than on the sequence similarity itself (Eisen, supra). In fact, many specific examples exist in which gene function has been shown to correlate well with gene phylogeny (Eisen, supra). Thus, “[t]he first step in making functional predictions is the generation of a phylogenetic tree representing the evolutionary history of the gene of interest and its homologs. Such trees are distinct from clusters and other means of characterizing sequence similarity because they are inferred by techniques that help convert patterns of similarity into evolutionary relationships . . . . After the gene tree is inferred, biologically determined functions of the various homologs are overlaid onto the tree. Finally, the structure of the tree and the relative phylogenetic positions of genes of different functions are used to trace the history of functional changes, which is then used to predict functions of [as yet] uncharacterized genes” (Eisen, supra). 
     Within a single plant species, gene duplication may cause two copies of a particular gene, giving rise to two or more genes with similar sequence and often similar function known as paralogs. A paralog is therefore a similar gene formed by duplication within the same species. Paralogs typically cluster together or in the same clade (a group of similar genes) when a gene family phylogeny is analyzed using programs such as CLUSTAL (Thompson et al., 1994 . Nucleic Acids Res.  22: 4673-4680; Higgins et al., 1996 . Methods Enzymol.  266: 383-402). Groups of similar genes can also be identified with pair-wise BLAST analysis (Feng and Doolittle, 1987 . J. Mol. Evol.  25: 351-360). For example, a clade of very similar MADS domain transcription factors from  Arabidopsis  all share a common function in flowering time (Ratcliffe et al., 2001 . Plant Physiol.  126: 122-132), and a group of very similar AP2 domain transcription factors from  Arabidopsis  are involved in tolerance of plants to freezing (Gilmour et al., 1998. supra). Analysis of groups of similar genes with similar function that fall within one clade can yield sub-sequences that are particular to the clade. These sub-sequences, known as consensus sequences, can not only be used to define the sequences within each clade, but define the functions of these genes; genes within a clade may contain paralogous sequences, or orthologous sequences that share the same function (see also, for example, Mount, 2001, in  Bioinformatics: Sequence and Genome Analysis , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., p. 543). 
     Regulatory polypeptide gene sequences are conserved across diverse eukaryotic species lines (Goodrich et al., 1993 . Cell  75:519-530; Lin et al., 1991 . Nature  353:569-571; Sadowski et al., 1988 . Nature  335: 563-564). Plants are no exception to this observation; diverse plant species possess regulatory polypeptides that have similar sequences and functions. Speciation, the production of new species from a parental species, gives rise to two or more genes with similar sequence and similar function. These genes, termed orthologs, often have an identical function within their host plants and are often interchangeable between species without losing function. Because plants have common ancestors, many genes in any plant species will have a corresponding orthologous gene in another plant species. Once a phylogenic tree for a gene family of one species has been constructed using a program such as CLUSTAL (Thompson et al., 1994. supra; Higgins et al., 1996. supra) potential orthologous sequences can be placed into the phylogenetic tree and their relationship to genes from the species of interest can be determined. Orthologous sequences can also be identified by a reciprocal BLAST strategy. Once an orthologous sequence has been identified, the function of the ortholog can be deduced from the identified function of the reference sequence. 
     By using a phylogenetic analysis, one skilled in the art would recognize that the ability to deduce similar functions conferred by closely-related polypeptides is predictable. This predictability has been confirmed by our own many studies in which we have found that a wide variety of polypeptides have orthologous or closely-related homologous sequences that function as does the first, closely-related reference sequence. For example, distinct regulatory polypeptides, including: 
     (i) AP2 family  Arabidopsis  G47 (found in U.S. Pat. No. 7,135,616), a phylogenetically-related sequence from soybean, and two phylogenetically-related homologs from rice all can confer greater tolerance to drought, hyperosmotic stress, or delayed flowering as compared to control plants; 
     (ii) CAAT family  Arabidopsis  G481 (found in PCT patent publication no. WO2004076638), and numerous phylogenetically-related sequences from eudicots and monocots can confer greater tolerance to drought-related stress as compared to control plants; 
     (iii) Myb-related  Arabidopsis  G682 (found in U.S. Pat. Nos. 7,223,904 and 7,193,129) and numerous phylogenetically-related sequences from eudicots and monocots can confer greater tolerance to heat, drought-related stress, cold, and salt as compared to control plants; 
     (iv) WRKY family  Arabidopsis  G1274 (found in U.S. Pat. No. 7,196,245) and numerous closely-related sequences from eudicots and monocots have been shown to confer increased water deprivation tolerance, and 
     (v) AT-hook family soy sequence G3456 (found in U.S. patent publication no. 20040128712A1) and numerous phylogenetically-related sequences from eudicots and monocots, increased biomass compared to control plants when these sequences are overexpressed in plants. 
     Examples of Methods for Identifying Identity, Similarity, Homology and Relatedness. 
     Percent identity can be determined electronically, e.g., by using the MEGALIGN program (DNASTAR, Inc. Madison, Wis.). The MEGALIGN program can create alignments between two or more sequences according to different methods, for example, the clustal method (see, for example, Higgins and Sharp, 1988 . Gene  73: 237-244). The clustal algorithm groups sequences into clusters by examining the distances between all pairs. The clusters are aligned pairwise and then in groups. Other alignment algorithms or programs may be used for preparing alignments and/or determining percentage identities, including Accelrys Gene, FASTA, BLAST, or ENTREZ, FASTA and BLAST, some of which may also be used to calculate percent similarity. Accelrys Gene is available from Accelrys, Inc., San Diego, Calif. Other programs are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with or without default settings. ENTREZ is available through the National Center for Biotechnology Information. In one embodiment, the percent identity of two sequences can be determined by the GCG program with a gap weight of 1, e.g., each amino acid gap is weighted as if it were a single amino acid or nucleotide mismatch between the two sequences (see U.S. Pat. No. 6,262,333). 
     Software for performing BLAST analyses is publicly available, e.g., through the National Center for Biotechnology Information (see internet website at www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul, 1990 . J. Mol. Biol.  215: 403-410; Altschul, 1993 . J. Mol. Evol.  36: 290-300). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always &gt;0) and N (penalty score for mismatching residues; always &lt;0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff, 1989. supra; Henikoff and Henikoff, 1991. supra). Unless otherwise indicated for comparisons of predicted polynucleotides, “sequence identity” refers to the % sequence identity generated from a tBLASTx using the NCBI version of the algorithm at the default settings using gapped alignments with the filter “off” (see, for example, internet website at www.ncbi.nlm.nih.gov). 
     Other techniques for alignment are described by Doolittle, ed., 1996 . Methods in Enzymology , vol. 266: “Computer Methods for Macromolecular Sequence Analysis” Academic Press, Inc., San Diego, Calif., USA. Preferably, an alignment program that permits gaps in the sequence is utilized to align the sequences. The Smith-Waterman is one type of algorithm that permits gaps in sequence alignments (see Shpaer, 1997 . Methods Mol. Biol.  70: 173-187). Also, the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. An alternative search strategy uses MPSRCH software, which runs on a MASPAR computer. MPSRCH uses a Smith-Waterman algorithm to score sequences on a massively parallel computer. This approach improves ability to pick up distantly related matches, and is especially tolerant of small gaps and nucleotide sequence errors. Nucleic acid-encoded amino acid sequences can be used to search both protein and DNA databases. 
     The percentage similarity between two polypeptide sequences, e.g., sequence A and sequence B, is calculated by dividing the length of sequence A, minus the number of gap residues in sequence A, minus the number of gap residues in sequence B, into the sum of the residue matches between sequence A and sequence B, times one hundred. Gaps of low or of no similarity between the two amino acid sequences are not included in determining percentage similarity. Percent identity between polynucleotide sequences can also be counted or calculated by other methods known in the art, e.g., the Jotun Hein method (see, for example, Hein, 1990 . Methods Enzymol.  183: 626-645). Identity between sequences can also be determined by other methods known in the art, e.g., by varying hybridization conditions (see U.S. patent publication no. 20010010913). 
     The percent identity between two polypeptide sequences can also be determined using Accelrys Gene v2.5, 2006 with default parameters: Pairwise Matrix: GONNET; Align Speed: Slow; Open Gap Penalty: 10.000; Extended Gap Penalty: 0.100; Multiple Matrix: GONNET; Multiple Open Gap Penalty: 10.000; Multiple Extended Gap Penalty: 0.05; Delay Divergent: 30; Gap Separation Distance: 8; End Gap Separation: false; Residue Specific Penalties: false; Hydrophilic Penalties: false; Hydrophilic Residues: GPSNDQEKR. The default parameters for determining percent identity between two polynucleotide sequences using Accelrys Gene are: Align Speed: Slow; Open Gap Penalty: 10.000; Extended Gap Penalty: 5.000; Multiple Open Gap Penalty: 10.000; Multiple Extended Gap Penalty: 5.000; Delay Divergent: 40; Transition: Weighted. 
     In addition, one or more polynucleotide sequences or one or more polypeptides encoded by the polynucleotide sequences may be used to search against a BLOCKS (Bairoch et al., 1997 . Nucleic Acids Res.  25: 217-221), PFAM, and other databases which contain previously identified and annotated motifs, sequences and gene functions. Methods that search for primary sequence patterns with secondary structure gap penalties (Smith et al., 1992 . Protein Engineering  5: 35-51) as well as algorithms such as Basic Local Alignment Search Tool (BLAST; Altschul, 1990, supra; Altschul et al., 1993, supra), BLOCKS (Henikoff and Henikoff, 1991, supra), Hidden Markov Models (HMM; Eddy, 1996 . Curr. Opin. Str. Biol.  6: 361-365; Sonnhammer et al., 1997 . Proteins  28: 405-420), and the like, can be used to manipulate and analyze polynucleotide and polypeptide sequences encoded by polynucleotides. These databases, algorithms and other methods are well known in the art and are described in Ausubel et al., 1997 . Short Protocols in Molecular Biology , John Wiley &amp; Sons, New York, N.Y., unit 7.7, and in Meyers, 1995 . Molecular Biology and Biotechnology , Wiley VCH, New York, N.Y., p 856-853. 
     Thus, the instant description provides methods for identifying a sequence similar or paralogous or orthologous or homologous to one or more polynucleotides as noted herein, or one or more target polypeptides encoded by the polynucleotides, or otherwise noted herein and may include linking or associating a given plant phenotype or gene function with a sequence. In the methods, a sequence database is provided (locally or across an internet or intranet) and a query is made against the sequence database using the relevant sequences herein and associated plant phenotypes or gene functions. 
     A further method for identifying or confirming that specific homologous sequences control the same function is by comparison of the transcript profile(s) obtained upon overexpression or knockout of two or more related polypeptides. Since transcript profiles are diagnostic for specific cellular states, one skilled in the art will appreciate that genes that have a highly similar transcript profile (e.g., with greater than 50% regulated transcripts in common, or with greater than 70% regulated transcripts in common, or with greater than 90% regulated transcripts in common) will have highly similar functions. Fowler and Thomashow, 2002 . Plant Cell  14, 1675-1690, have shown that three paralogous AP2 family genes (CBF1, CBF2 and CBF3) are induced upon cold treatment, each of which can condition improved freezing tolerance, and all have highly similar transcript profiles. Once a polypeptide has been shown to provide a specific function, its transcript profile becomes a diagnostic tool to determine whether paralogs or orthologs have the same function. 
     Identifying Polynucleotides or Nucleic Acids by Hybridization. 
     Polynucleotides homologous to the sequences illustrated in the Sequence Listing and tables can be identified, e.g., by hybridization to each other under stringent or under highly stringent conditions. Stringency is influenced by a variety of factors, including temperature, salt concentration and composition, organic and non-organic additives, solvents, etc. present in both the hybridization and wash solutions and incubations, and the number of washes, as described in more detail in the references cited below (e.g., Sambrook et al., 1989. supra; Berger and Kimmel, eds., 1987 . Methods Enzymol.  152: 507-511; Anderson and Young, 1985. “Quantitative Filter Hybridisation”, In: Hames and Higgins, ed.,  Nucleic Acid Hybridisation, A Practical Approach . Oxford, IRL Press, 73-111), each of which are incorporated herein by reference. Conditions that are highly stringent, and means for achieving them, are also well known in the art and described in, for example, Sambrook et al., 1989. supra; Berger and Kimmel, eds., 1987 . Meth. Enzymol.  152:467-469; and Anderson and Young, 1985. supra. 
     Also provided in the instant description are polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, including any of the polynucleotides within the Sequence Listing, and fragments thereof under various conditions of stringency (see, for example, Wahl and Berger, 1987 . Methods Enzymol.  152: 399-407; Berger and Kimmel, ed., 1987 . Methods Enzymol.  152:507-511). In addition to the nucleotide sequences listed in the Sequence Listing, full length cDNA, orthologs, and paralogs of the present nucleotide sequences may be identified and isolated using well-known methods. The cDNA libraries, orthologs, and paralogs of the present nucleotide sequences may be screened using hybridization methods to determine their utility as hybridization target or amplification probes. 
     Stability of DNA duplexes is affected by such factors as base composition, length, and degree of base pair mismatch. Hybridization conditions may be adjusted to allow DNAs of different sequence relatedness to hybridize. The melting temperature (T m ) is defined as the temperature when 50% of the duplex molecules have dissociated into their constituent single strands. The melting temperature of a perfectly matched duplex, where the hybridization buffer contains formamide as a denaturing agent, may be estimated by the following equations: 
         T   m (° C.)=81.5+16.6(log [Na+])+0.41(% G+C)−0.62(% formamide)−500/L  (I) DNA-DNA:
 
         T   m (° C.)=79.8+18.5(log [Na+])+0.58(% G+C)+0.12(% G+C) 2 −0.5(% formamide)−820/L  (II) DNA-RNA:
 
         T   m (° C.)=79.8+18.5(log [Na+])+0.58(% G+C)+0.12(% G+C) 2 −0.35(% formamide)−820/L  (III) RNA-RNA:
 
     where L is the length of the duplex formed, [Na+] is the molar concentration of the sodium ion in the hybridization or washing solution, and % G+C is the percentage of (guanine+cytosine) bases in the hybrid. For imperfectly matched hybrids, approximately 1° C. is required to reduce the melting temperature for each 1% mismatch. 
     Hybridization experiments are generally conducted in a buffer of pH between 6.8 to 7.4, although the rate of hybridization is nearly independent of pH at ionic strengths likely to be used in the hybridization buffer (Anderson and Young, 1985. supra). In addition, one or more of the following may be used to reduce non-specific hybridization: sonicated salmon sperm DNA or another non-complementary DNA, bovine serum albumin, sodium pyrophosphate, sodium dodecylsulfate (SDS), polyvinyl-pyrrolidone, ficoll and Denhardt&#39;s solution. Dextran sulfate and polyethylene glycol 6000 act to exclude DNA from solution, thus raising the effective probe DNA concentration and the hybridization signal within a given unit of time. In some instances, conditions of even greater stringency may be desirable or required to reduce non-specific and/or background hybridization. These conditions may be created with the use of higher temperature, lower ionic strength and higher concentration of a denaturing agent such as formamide. 
     Stringency conditions can be adjusted to screen for moderately similar fragments such as homologous sequences from distantly related organisms, or to highly similar fragments such as genes that duplicate functional enzymes from closely related organisms. The stringency can be adjusted either during the hybridization step or in the post-hybridization washes. Salt concentration, formamide concentration, hybridization temperature and probe lengths are variables that can be used to alter stringency (as described by the formula above). As a general guideline, high stringency is typically performed at T m −5° C. to T m −20° C., moderate stringency at T m −20° C. to T m −35° C. and low stringency at T m −35° C. to T m −50° C. for duplex &gt;150 base pairs. Hybridization may be performed at low to moderate stringency (25-50° C. below T m ), followed by post-hybridization washes at increasing stringencies. Maximum rates of hybridization in solution are determined empirically to occur at T m −25° C. for DNA-DNA duplex and T m −15° C. for RNA-DNA duplex. Optionally, the degree of dissociation may be assessed after each wash step to determine the need for subsequent, higher stringency wash steps. 
     High stringency conditions may be used to select for nucleic acid sequences with high degrees of identity to the disclosed sequences. An example of stringent hybridization conditions obtained in a filter-based method such as a Southern or Northern blot for hybridization of complementary nucleic acids that have more than 100 complementary residues is about 5° C. to 20° C. lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH. Conditions used for hybridization may include about 0.02 M to about 0.15 M sodium chloride, about 0.5% to about 5% casein, about 0.02% SDS or about 0.1% N-laurylsarcosine, about 0.001 M to about 0.03 M sodium citrate, at hybridization temperatures between about 50° C. and about 70° C. More preferably, high stringency conditions are about 0.02 M sodium chloride, about 0.5% casein, about 0.02% SDS, about 0.001 M sodium citrate, at a temperature of about 50° C. Nucleic acid molecules that hybridize under stringent conditions will typically hybridize to a probe based on either the entire DNA molecule or selected portions, e.g., to a unique subsequence, of the DNA. 
     Stringent salt concentration will ordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate. Increasingly stringent conditions may be obtained with less than about 500 mM NaCl and 50 mM trisodium citrate, to even greater stringency with less than about 250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, whereas high stringency hybridization may be obtained in the presence of at least about 35% formamide, and more preferably at least about 50% formamide. Stringent temperature conditions will ordinarily include temperatures of at least about 30° C., more preferably of at least about 37° C., and most preferably of at least about 42° C. with formamide present. Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS) and ionic strength, are well known to those skilled in the art. Various levels of stringency are accomplished by combining these various conditions as needed. 
     The washing steps that follow hybridization may also vary in stringency; the post-hybridization wash steps primarily determine hybridization specificity, with the most critical factors being temperature and the ionic strength of the final wash solution. Wash stringency can be increased by decreasing salt concentration or by increasing temperature. Stringent salt concentration for the wash steps will preferably be less than about 30 mM NaCl and 3 mM trisodium citrate, and most preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate. 
     Thus, high stringency hybridization and wash conditions that may be used to bind and remove polynucleotides with less than the desired homology to the nucleic acid sequences or their complements that encode the present polypeptides include, for example: 
     6×SSC at 65° C.; 
     50% formamide, 4×SSC at 42° C.; or 
     0.5×SSC, 0.1% SDS at 65° C.; 
     with, for example, two wash steps of 10-30 minutes each. Useful variations on these conditions will be readily apparent to those skilled in the art. 
     A person of skill in the art would not expect substantial variation among polynucleotide species provided with the present description because the highly stringent conditions set forth in the above formulae yield structurally similar polynucleotides. 
     If desired, one may employ wash steps of even greater stringency, including about 0.2×SSC, 0.1% SDS at 65° C. and washing twice, each wash step being about 30 minutes, or about 0.1×SSC, 0.1% SDS at 65° C. and washing twice for 30 minutes. The temperature for the wash solutions will ordinarily be at least about 25° C., and for greater stringency at least about 42° C. Hybridization stringency may be increased further by using the same conditions as in the hybridization steps, with the wash temperature raised about 3° C. to about 5° C., and stringency may be increased even further by using the same conditions except the wash temperature is raised about 6° C. to about 9° C. For identification of less closely related homologs, wash steps may be performed at a lower temperature, e.g., 50° C. 
     An example of a low stringency wash step employs a solution and conditions of at least 25° C. in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS over 30 minutes. Greater stringency may be obtained at 42° C. in 15 mM NaCl, with 1.5 mM trisodium citrate, and 0.1% SDS over 30 minutes. Even higher stringency wash conditions are obtained at 65° C.-68° C. in a solution of 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Wash procedures will generally employ at least two final wash steps. Additional variations on these conditions will be readily apparent to those skilled in the art (see, for example, U.S. patent publication no. 20010010913). 
     Stringency conditions can be selected such that an oligonucleotide that is perfectly complementary to the coding oligonucleotide hybridizes to the coding oligonucleotide with at least about a 5-10× higher signal to noise ratio than the ratio for hybridization of the perfectly complementary oligonucleotide to a nucleic acid encoding a polypeptide known as of the filing date of the application. It may be desirable to select conditions for a particular assay such that a higher signal to noise ratio, that is, about 15× or more, is obtained. Accordingly, a subject nucleic acid will hybridize to a unique coding oligonucleotide with at least a 2× or greater signal to noise ratio as compared to hybridization of the coding oligonucleotide to a nucleic acid encoding known polypeptide. The particular signal will depend on the label used in the relevant assay, e.g., a fluorescent label, a colorimetric label, a radioactive label, or the like. Labeled hybridization or PCR probes for detecting related polynucleotide sequences may be produced by oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide. 
     The present description also provides polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, including any of the polynucleotides within the Sequence Listing, and fragments thereof under various conditions of stringency (see, for example, Wahl and Berger, 1987, supra, pages 399-407; and Kimmel, 1987 . Meth. Enzymol.  152, 507-511). In addition to the nucleotide sequences in the Sequence Listing, full length cDNA, orthologs, and paralogs of the present nucleotide sequences may be identified and isolated using well-known methods. The cDNA libraries, orthologs, and paralogs of the present nucleotide sequences may be screened using hybridization methods to determine their utility as hybridization target or amplification probes. 
     Examples 
     It is to be understood that this description is not limited to the particular devices, machines, materials and methods described. Although particular embodiments are described, equivalent embodiments may be used to practice the claims. 
     The specification, now being generally described, will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present description and are not intended to limit the claims or description. It will be recognized by one of skill in the art that a polypeptide that is associated with a particular first trait may also be associated with at least one other, unrelated and inherent second trait which was not predicted by the first trait. 
     Example I. The Instant Polynucleotides and their Encoded or Predicted Polypeptides 
     The instant polypeptides sequences belong to distinct clades of polypeptides that include members from diverse species. In each case, clade member sequences derived from both eudicots and monocots may be shown to confer increased yield or tolerance to one or more abiotic stresses when the sequences were overexpressed. These studies can demonstrate that evolutionarily conserved genes from diverse species are likely to function similarly (i.e., by regulating similar target sequences and controlling the same traits), and that polynucleotides from one species may be transformed into closely-related or distantly-related plant species to confer or improve traits. 
     The listed polypeptide sequences may be found within the polypeptide clades of Myb Domain Protein 27 (“AtMYB27”; AT3G53200; G1311), ACBF-like family member RNA-binding protein 45A (“RBP45A”; AT5G54900; G1940), PCF family member TEOSINTE BRANCHED1 //CYCLOIDEA//PCF 6 transcription factor 6 (“TCP6”; AT5G41030; G1936), Basic helix-loop-helix protein (bHLH) family member Phytochrome Interacting Factor 3-like 1 (“PIL1”: AT2G46970; G1649), GARP family member PHYTOCLOCK 1 (“PCL1”; AT3G46640.3; G2741), TH family member GT-2-Like1 (“GTL1”; AT1G33240; G634), AP2 family members Dehydration-Responsive Element-Binding Protein 2H (“DREB2H”; AT2G40350; G1755), and ethylene-responsive transcription factor ERF087 (“ERF087”; AT1G28160; G2292), CCAAT family member Nuclear Transcription Factor Y subunit C-6 (“NF-YC6”; AT5G50480; G1820), Z—CO-like family member CONSTANS-like B-box zinc finger protein (“BBX18”, “F3K23.8”; AT2G21320; G1881), HLH/MYC family member Basic Helix-Loop-Helix 60 (“bHLH60”; AT3G57800.2; G2144), Z—CO-like family member CONSTANS-like B-box zinc finger protein (“BBX26”, AT1G60250, G1486), bHLH family member bHLH121 (At3g19860, G782), and Putative MethylTransferase 24 (“PMT24” NP_174240, G837). 
     Orthologs and paralogs of presently disclosed polypeptides may be cloned using compositions provided by the present description according to methods well known in the art. cDNAs can be cloned using mRNA from a plant cell or tissue that expresses one of the present sequences. Appropriate mRNA sources may be identified by interrogating Northern blots with probes designed from the present sequences, after which a library is prepared from the mRNA obtained from a positive cell or tissue. Polypeptide-encoding cDNA is then isolated using, for example, PCR, using primers designed from a presently disclosed gene sequence, or by probing with a partial or complete cDNA or with one or more sets of degenerate probes based on the disclosed sequences. The cDNA library may be used to transform plant cells. Expression of the cDNAs of interest is detected using, for example, microarrays, Northern blots, quantitative PCR, or any other technique for monitoring changes in expression. Genomic clones may be isolated using similar techniques to those. 
     Examples of orthologs of the  Arabidopsis  polypeptide sequences and their functionally similar orthologs are listed in the instant Tables and the Sequence Listing. In addition to the sequences in the instant Tables and the Sequence Listing, the claimed nucleotide sequences are phylogenetically and structurally similar to sequences listed in the Sequence Listing and can function in a plant by increasing yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant when ectopically expressed, or overexpressed, in a plant. Since a significant number of these sequences are phylogenetically and sequentially related to each other and may be shown to increase yield from a plant and/or photosynthetic resource use efficiency, one skilled in the art would predict that other similar, phylogenetically related sequences falling within the present clades of polypeptides, including AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide sequences, would also perform similar functions when ectopically expressed. 
     Background Information for AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24, and their Clade Member Sequences 
     A number of phylogenetically-related sequences have been found in other plant species. The instant Tables list a number of AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade sequences from diverse species. The tables include the SEQ ID NO: (Column 1), the species from which the sequence was derived and the Gene Identifier (“GID”; Column 2), the percent identity of the polypeptide in Column 1 to the first listed full length polypeptide (SEQ ID NO: 2, 42, 86, 108, 126, 156, 192, 246, 278, 318, 356, 388, 410, or 444), as determined by a BLASTp analysis, for example, with a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (Henikoff and Henikoff, 1989 . Proc. Natl. Acad. Sci. USA  89:10915; Henikoff and Henikoff, 1991 . Nucleic Acids Res.  19: 6565-6572) (Column 3), the amino acid residue coordinates for the conserved domains in amino acid coordinates beginning at the N-terminus, of each of the sequences (Column 4), the conserved domain sequences of the respective polypeptides (Column 5); the SEQ ID NO: of each of the domains (Column 6), and the percentage identity of the conserved domain in Column 5 to the conserved domain of the first listed sequence (as determined by a BLASTp analysis, wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix, and with the proportion of identical amino acids in parentheses; Column 7). 
     Species abbreviations that appear in Columns 2 of the following Tables include: At— Arabidopsis thaliana ; Bd—Brachypodium distachyon; Cc—Citrus clementina; Eg— Eucalyptus grandis ; Gm— Glycine max ; Os— Oryza sativa ; Pt— Populus trichocarpa ; Si— Setaria italica ; Sl— Solanum lycopersicum ; Vv—Vitus  vinifera ; Zm— Zea mays.    
     AtMYB27 Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Conserved ‘Myb domain 1’ of AtMYB27 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity 
               
               
                   
                   
                 Col. 3 
                 Col. 4 
                   
                   
                 of the 
               
               
                   
                   
                 Percent 
                 Myb 
                   
                 Col. 6 
                 Myb domain 
               
               
                 Col. 1 
                   
                 identity of 
                 domain 1 
                   
                 SEQ ID 
                 in Col. 5  
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 in amino 
                 Col. 5 
                 NO: of 
                 to the Myb 
               
               
                 ID 
                 Species/ 
                 in Col. 1  
                 acid co- 
                 Conserved Myb 
                 Myb do- 
                 domain 1  
               
               
                 NO: 
                 Identifier 
                 to AtMyb27 
                 ordinates 
                 domain 1 
                 main 1 
                 of AtMyb27 
               
               
                   
               
               
                  2 
                 At/AtMyb27 or 
                 100% 
                 11-58 
                 RGPWLEEEDERLVKVI 
                 483 
                 100%  
               
               
                   
                 AT3G53200.1 
                 (238/238) 
                   
                 SLLGERRWDSLAIVSG 
                   
                 (48/48) 
               
               
                   
                   
                   
                   
                 LKRSGKSCRLRWMNY 
                   
                   
               
               
                   
                   
                   
                   
                 L 
                   
                   
               
               
                   
               
               
                 14 
                 Vv/GSVIVT010 
                  72% 
                  8-55 
                 KGSWLEEEDERLTAF 
                 489 
                  77%  
               
               
                   
                 33670001 
                  (83/115) 
                   
                 VGLLGERRWDSIARA 
                   
                 (37/48) 
               
               
                   
                   
                   
                   
                 SGLKRSGKSCRLRWL 
                   
                   
               
               
                   
                   
                   
                   
                 NYL 
                   
                   
               
               
                   
               
               
                  4 
                 Gm/Glyma10g0 
                  44% 
                  8-55 
                 KGTWLQEEDEQLTSF 
                 484 
                  75%  
               
               
                   
                 6680.1 
                 (106/236) 
                   
                 VTRLGERRWDSLAKV 
                   
                 (36/48) 
               
               
                   
                   
                   
                   
                 AGLKRSGKSCRLRWM 
                   
                   
               
               
                   
                   
                   
                   
                 NYL 
                   
                   
               
               
                   
               
               
                  6 
                 Gm/Glyma13g2 
                  70% 
                  8-55 
                 KGTWLQEEDEQLTSF 
                 485 
                  75%  
               
               
                   
                 0880.1 
                  (77/110) 
                   
                 VARLGERRWDSLAKV 
                   
                 (36/48) 
               
               
                   
                   
                   
                   
                 AGLKRSGKSCRLRWM 
                   
                   
               
               
                   
                   
                   
                   
                 NYL 
                   
                   
               
               
                   
               
               
                  8 
                 Cc/clementine0. 
                  49% 
                 38-85 
                 KGPWHEEEDELLVTF 
                 486 
                  72%  
               
               
                   
                 9_029544m 
                  (90/182) 
                   
                 VTLFGERRWDYIAKA 
                   
                 (35/48) 
               
               
                   
                   
                   
                   
                 SGLKRSGKSCRLRWL 
                   
                   
               
               
                   
                   
                   
                   
                 NYL 
                   
                   
               
               
                   
               
               
                 10 
                 Eg/Eucgr.A016 
                  43% 
                 15-62 
                 KGPWIEQEDEILTAFV 
                 487 
                  68%  
               
               
                   
                 48.1 
                 (102/234) 
                   
                 TVLGERRWDYIAKTS 
                   
                 (33/48) 
               
               
                   
                   
                   
                   
                 GLKRSGKSCRLRWKN 
                   
                   
               
               
                   
                   
                   
                   
                 YL 
                   
                   
               
               
                   
               
               
                 12 
                 Pt/POPTR_000 
                  48% 
                 10-57 
                 KGSWQEEEDERLTAS 
                 488 
                  68%  
               
               
                   
                 6s12400.1 
                  (98/203) 
                   
                 ATLLGERKWDSIARLS 
                   
                 (33/48) 
               
               
                   
                   
                   
                   
                 GLMRSGKSCRMRWL 
                   
                   
               
               
                   
                   
                   
                   
                 NYL 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Conserved ‘Myb domain 2’ of AtMYB27 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity 
               
               
                   
                   
                 Col. 3 
                 Col. 4 
                   
                   
                 of second 
               
               
                   
                   
                 Percent 
                 Myb 
                   
                 Col. 6 
                 Myb domain 
               
               
                 Col. 1 
                   
                 identity of 
                 domain 2 
                   
                 SEQ ID 
                 in Col. 5 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 in amino 
                 Col. 5 
                 NO: of 
                 to Myb do- 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 acid co- 
                 Conserved Myb 
                 Myb do- 
                 main 2 of 
               
               
                 NO: 
                 Identifier 
                 to AtMyb27 
                 ordinates 
                 domain 2 
                 main 2 
                 AtMyb27 
               
               
                   
               
               
                  2 
                 At/AtMyb27 or 
                 100% 
                 64-109 
                 RGPMSQEEERIIFQLH 
                 490 
                 100%  
               
               
                   
                 AT3G53200.1 
                 (238/238) 
                   
                 ALWGNKWSKIARRL 
                   
                 (46/46) 
               
               
                   
                   
                   
                   
                 PGRTDNEIKNYWRTH 
                   
                   
               
               
                   
                   
                   
                   
                 Y 
                   
                   
               
               
                   
               
               
                 12 
                 Pt/POPTR_000 
                  48% 
                 63-108 
                 RGHISAEEEQIIIQFHG 
                 495 
                  77%  
               
               
                   
                 6s12400.1 
                  (98/203) 
                   
                 QWGNKWARIARRLP 
                   
                 (35/45) 
               
               
                   
                   
                   
                   
                 GRTDNEIKNYWRTH 
                   
                   
               
               
                   
                   
                   
                   
                 M 
                   
                   
               
               
                   
               
               
                 14 
                 Vv/GSVIVT01 
                  72% 
                 61-106 
                 RCQISAEEEQIILQLH 
                 496 
                  76%  
               
               
                   
                 033670001 
                  (83/115) 
                   
                 KRWGNKWSWIARSL 
                   
                 (35/46) 
               
               
                   
                   
                   
                   
                 PGRTDNEIKNYWRTH 
                   
                   
               
               
                   
                   
                   
                   
                 L 
                   
                   
               
               
                   
               
               
                 10 
                 Eg/Eucgr.A016 
                  43% 
                 68-113 
                 HGPISPEEERIIIKFHE 
                 494 
                  72%  
               
               
                   
                 48.Eg/1 
                 (102/234) 
                   
                 QWGNKWSRIAEKLP 
                   
                 (32/44) 
               
               
                   
                   
                   
                   
                 GRTDNEIKNFWKTHL 
                   
                   
               
               
                   
               
               
                  4 
                 Gm/Glyma10g0 
                  44% 
                 61-106 
                 HGHFSVEEEQLIVQL 
                 491 
                  70%  
               
               
                   
                 6680.1 
                 (106/236) 
                   
                 QQQLGNKWAKIARK 
                   
                 (31/44) 
               
               
                   
                   
                   
                   
                 LPGRTDNEIKNFWRT 
                   
                   
               
               
                   
                   
                   
                   
                 HL 
                   
                   
               
               
                   
               
               
                  6 
                 Gm/Glyma13g2 
                  70% 
                 61-106 
                 HGHFSVEEEQLIVQL 
                 492 
                  68%  
               
               
                   
                 0880.1 
                  (77/110) 
                   
                 QQELGNKWAKIARK 
                   
                 (31/45) 
               
               
                   
                   
                   
                   
                 LPGRTDNEIKNYWKT 
                   
                   
               
               
                   
                   
                   
                   
                 HL 
                   
                   
               
               
                   
               
               
                  8 
                 Cc/clementine0. 
                  49% 
                 91-139 
                 HGYISTEEEQIIIQLHK 
                 493 
                  63%  
               
               
                   
                 9_029544m 
                  (90/182) 
                   
                 NIKIYLHGWSRIARSL 
                   
                 (29/46) 
               
               
                   
                   
                   
                   
                 PGRTDNEIKNCWRTR 
                   
                   
               
               
                   
                   
                   
                   
                 I 
               
               
                   
               
            
           
         
       
     
     Sequences that are functionally-related and/or closely-related to the polypeptides in the above Tables may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed closely-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants. 
     These functionally-related and/or closely-related AtMYB27 clade polypeptides may be identified by a consensus first Myb domain (Myb domain 1) consensus sequence, SEQ ID NO: 842: 
     
       
         
           
               
               
            
               
                   
                 X 1 GX 3 WX 5 X 6 X 7 EDEX 11 LX 13 X 14 X 15 X 16 X 17 X 18 X 19 GERX 23   
               
               
                   
                   
               
               
                   
                 WDX 26 X 27 AX 29 X 30 X 31 GLX 34 RSGKSCRX 42 RWX 45 NYL 
               
            
           
         
       
     
     where X 1 =K or R; X 3 =any amino acid; X 5 =any amino acid; X 6 =Q or E; X 7 =Q or E; X 11 =any amino acid; X 13 =T or V; X 14 =any amino acid; X 15 =any amino acid; X 16 =any amino acid; X 17 =S, A, T or G; X 18 =any amino acid; X 19 =F, I, L, V or M; X 23 =R or K; X 26 =any amino acid; X 27 =I, L, V or M; X 29 =any amino acid; X 30 =any amino acid; X 31 =S or A; X 34 =any amino acid; X 42 =I, L, V or M; and X 45 =any amino acid. 
     These functionally-related and/or closely-related AtMYB27 clade polypeptides also may be identified by a consensus second Myb domain (Myb domain 2) consensus sequence, SEQ ID NO: 843: 
                            X 1 X 2 X 3 X 4 SX 6 EEEX 10 X 11 IX 13 X 14 X 15 X 16 X 17 X 18 X 19 X 20 X 21                         X 22 X 23 X 24 X 25 WX 27 X 28 IAX 31 X 32 LPGRTDNEIKNX 44 WX 46 TX 48                         X 49              
where X 1 =any amino acid; X 2 =any amino acid; X 3 =any amino acid; X 4 =F, I, L, V or M; X 6 =any amino acid; X 10 =any amino acid; X 11 =I, L, V or M; X 13 =F, I, L, V or M; X 14 =Q or K; X 15 =F, I, L, V or M; X 16 =H or Q; X 17 =any amino acid; X 18 =any amino acid; X 19 =any amino acid; X 20 =any amino acid; X 21 =any amino acid; X 22 =any amino acid; X 23 =L or absent; X 24 =H or absent; X 25 =G or absent; X 27 =S or A; X 28 =any amino acid; X 31 =any amino acid; X 32 =any amino acid; X 44 =any amino acid; X 46 =K or R; X 48 =any amino acid; and X 49 =any amino acid.
 
     RBP45A Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Conserved ‘RRM1 domain’ of RBP45A and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity  
               
               
                   
                   
                   
                   
                   
                   
                 of RRM1 
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 domain 
               
               
                 Col. 
                   
                 Percent 
                 Col. 4 
                   
                 Col. 6 
                 in Col.  
               
               
                 1 
                   
                 identity of 
                 RRM1 
                 Col. 5 
                 SEQ ID 
                 5 to  
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Conserved 
                 NO: of 
                 RRM1 do- 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 RRM1 
                 RRM1 
                 main of 
               
               
                 NO: 
                 Identifier 
                 to RBP45A 
                 coordinates 
                 domain 
                 domain 
                 RBP45A 
               
               
                   
               
               
                 42 
                 At/RBP45A or 
                 100% 
                  61-141 
                 SLWIGDLQQWMDE 
                 510 
                 100% 
               
               
                   
                 AT5G54900.1 
                 (387/387) 
                   
                 NYIMSVFAQSGEAT 
                   
                 (81/81) 
               
               
                   
                   
                   
                   
                 SAKVIRNKLTGQSE 
                   
                   
               
               
                   
                   
                   
                   
                 GYGFIEFVSHSVAER 
                   
                   
               
               
                   
                   
                   
                   
                 VLQTYNGAPMPSTE 
                   
                   
               
               
                   
                   
                   
                   
                 QTFRLNWAQAG 
                   
                   
               
               
                   
               
               
                 40 
                 At/AT4G27000 
                  71% 
                  81-161 
                 SLWIGDLQPWMDEN 
                 509 
                  79% 
               
               
                   
                 .1 
                 (282/394) 
                   
                 YLMNVFGLTGEATA 
                   
                 (64/81) 
               
               
                   
                   
                   
                   
                 AKVIRNKQNGYSEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFIEFVNHATAER 
                   
                   
               
               
                   
                   
                   
                   
                 NLQTYNGAPMPSSE 
                   
                   
               
               
                   
                   
                   
                   
                 QAFRLNWAQLG 
                   
                   
               
               
                   
               
               
                 44 
                 Pt/POPTR_000 
                  70% 
                  68-148 
                 SLWIGDLQQWMDE 
                 511 
                  76% 
               
               
                   
                 1s45000.1 
                 (228/323) 
                   
                 NYILSIFSTTGEVVQ 
                   
                 (62/81) 
               
               
                   
                   
                   
                   
                 AKVIRNKQTGYPEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFIEFVSHAAAERI 
                   
                   
               
               
                   
                   
                   
                   
                 LQTYNGTPMPNSEQ 
                   
                   
               
               
                   
                   
                   
                   
                 TFRLNWATLG 
                   
                   
               
               
                   
               
               
                 46 
                 Pt/POPTR_001 
                  69% 
                  71-151 
                 SLWIGDLQQWMDE 
                 512 
                  72% 
               
               
                   
                 1s14150.1 
                 (231/331) 
                   
                 NYLLSIFSATGEIVQ 
                   
                 (59/81) 
               
               
                   
                   
                   
                   
                 AKVIRNKQTGYPEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFIEFVSRAAAERI 
                   
                   
               
               
                   
                   
                   
                   
                 LQTYNGTPMPNSEQ 
                   
                   
               
               
                   
                   
                   
                   
                 AFRLNWATLG 
                   
                   
               
               
                   
               
               
                 66 
                 S1/Solyc02g080 
                  66% 
                  80-160 
                 SLWIGDLQFWMDEQ 
                 522 
                  72% 
               
               
                   
                 420.2.1 
                 (216/325) 
                   
                 YLLNCFAQTGEVTS 
                   
                 (59/81) 
               
               
                   
                   
                   
                   
                 AKVIRNKQSGQSEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFIEFISHAAAERN 
                   
                   
               
               
                   
                   
                   
                   
                 LQAYNGTLMPNIEQ 
                   
                   
               
               
                   
                   
                   
                   
                 NFRLNWASLG 
                   
                   
               
               
                   
               
               
                 68 
                 Sl/Solyc10g005 
                  65% 
                  77-157 
                 TLWIGDLQFWMDE 
                 523 
                  71% 
               
               
                   
                 260.2.1 
                 (218/333) 
                   
                 QYLYSCFAQTGEVV 
                   
                 (58/81) 
               
               
                   
                   
                   
                   
                 SAKVIRNKQTQQSE 
                   
                   
               
               
                   
                   
                   
                   
                 GYGFIEFNSHAAAER 
                   
                   
               
               
                   
                   
                   
                   
                 NLQAYNGTLMPNIE 
                   
                   
               
               
                   
                   
                   
                   
                 QNFRLNWASLG 
                   
                   
               
               
                   
               
               
                 70 
                 Sl/Solyc03g031 
                  64% 
                  73-153 
                 SLWIGDLQFWMDEQ 
                 524 
                  70% 
               
               
                   
                 720.2.1 
                 (215/335) 
                   
                 YIQNCFAHTGEVAS 
                   
                 (57/81) 
               
               
                   
                   
                   
                   
                 VKVIRNKQSGQSEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFVEFISHAAAERN 
                   
                   
               
               
                   
                   
                   
                   
                 LQTYNGSMMPNSEQ 
                   
                   
               
               
                   
                   
                   
                   
                 PFRLNWASLG 
                   
                   
               
               
                   
               
               
                 48 
                 Sl/Solyc07g064 
                  67% 
                  82-162 
                 SLWIGDLQYWMDES 
                 513 
                  69% 
               
               
                   
                 510.2.1 
                 (218/324) 
                   
                 YLSTCFYHTGELVS 
                   
                 (56/81) 
               
               
                   
                   
                   
                   
                 AKVIRNKQSGQSEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFLEFRSHAAAET 
                   
                   
               
               
                   
                   
                   
                   
                 VLQTYNGALMPNVE 
                   
                   
               
               
                   
                   
                   
                   
                 QNFRMNWASLG 
                   
                   
               
               
                   
               
               
                 62 
                 Gm/Glymal3g2 
                  64% 
                  67-147 
                 TLWIGDLQYWMDE 
                 520 
                  69% 
               
               
                   
                 7570.1 
                 (214/331) 
                   
                 NYLYTCFAHTGEVT 
                   
                 (56/81) 
               
               
                   
                   
                   
                   
                 SVKVIRNKQTSQSEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFIEFNSRAGAERI 
                   
                   
               
               
                   
                   
                   
                   
                 LQTYNGAIMPNGGQ 
                   
                   
               
               
                   
                   
                   
                   
                 SFRLNWATFS 
                   
                   
               
               
                   
               
               
                 24 
                 Os/LOC_Os08g 
                  63% 
                  96-174 
                 TLWIGDLQYWMDE 
                 501 
                  69% 
               
               
                   
                 09100.1 
                 (206/325) 
                   
                 NYISACFAPTGELQS 
                   
                 (56/81) 
               
               
                   
                   
                   
                   
                 VKLIRDKQTGQLQG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFIEFTSHAGAERV 
                   
                   
               
               
                   
                   
                   
                   
                 LQTYNGAMMPNVE 
                   
                   
               
               
                   
                   
                   
                   
                 QTYRLNWAS 
                   
                   
               
               
                   
               
               
                 54 
                 Pt/POPTR_000 
                  61% 
                  78-158 
                 TLWIGDLQYWMDE 
                 516 
                  69% 
               
               
                   
                 4s01690.1 
                 (213/349) 
                   
                 NYIASCFAHTGEVAS 
                   
                 (56/81) 
               
               
                   
                   
                   
                   
                 VKIIRNKQTSQIEGY 
                   
                   
               
               
                   
                   
                   
                   
                 GFIEMTSHGAAERIL 
                   
                   
               
               
                   
                   
                   
                   
                 QTYNGTPMPNGEQN 
                   
                   
               
               
                   
                   
                   
                   
                 FRLNWASFS 
                   
                   
               
               
                   
               
               
                 52 
                 At/AT1G11650 
                  63% 
                  63-144 
                 TLWIGDLQYWMDE 
                 515 
                  68% 
               
               
                   
                 .2 
                 (206/325) 
                   
                 NFLYGCFAHTGEMV 
                   
                 (56/82) 
               
               
                   
                   
                   
                   
                 SAKVIRNKQTGQVE 
                   
                   
               
               
                   
                   
                   
                   
                 GYGFIEFASHAAAER 
                   
                   
               
               
                   
                   
                   
                   
                 VLQTFNNAPIPSFPD 
                   
                   
               
               
                   
                   
                   
                   
                 QLFRLNWASLS 
                   
                   
               
               
                   
               
               
                 60 
                 Gm/Glyma17g0 
                  66% 
                  66-146 
                 TLWIGDLQYWMDE 
                 519 
                  67% 
               
               
                   
                 1800.1 
                 (218/327) 
                   
                 NYLYTCFAHTGELA 
                   
                 (55/81) 
               
               
                   
                   
                   
                   
                 SVKVIRNKQTSQSEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFIEFTSRAGAERV 
                   
                   
               
               
                   
                   
                   
                   
                 LQTYNGTIMPNGGQ 
                   
                   
               
               
                   
                   
                   
                   
                 NFRLNWATFS 
                   
                   
               
               
                   
               
               
                 64 
                 Gm/Glyma15g1 
                  64% 
                  68-148 
                 TLWIGDLQYWMDE 
                 521 
                  67% 
               
               
                   
                 1380.1 
                 (215/333) 
                   
                 NYLYTCFAHTGEVS 
                   
                 (55/81) 
               
               
                   
                   
                   
                   
                 SVKVIRNKQTSQSEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFIEFNSRAGAERI 
                   
                   
               
               
                   
                   
                   
                   
                 LQTYNGAIMPNGGQ 
                   
                   
               
               
                   
                   
                   
                   
                 SFRLNWATFS 
                   
                   
               
               
                   
               
               
                 38 
                 Zm/GRMZM2 
                  68% 
                  71-151 
                 TLWIGDLQYWMDE 
                 508 
                  66% 
               
               
                   
                 G002874_T01 
                 (219/322) 
                   
                 NYLYSCFSQAGEVIS 
                   
                 (54/81) 
               
               
                   
                   
                   
                   
                 VKIIRNKQTGQPEGY 
                   
                   
               
               
                   
                   
                   
                   
                 GFIEFSNHAVAEQVL 
                   
                   
               
               
                   
                   
                   
                   
                 QNYNGQMMPNVNQ 
                   
                   
               
               
                   
                   
                   
                   
                 PFKLNWATSG 
                   
                   
               
               
                   
               
               
                 58 
                 Gm/Glyma07g3 
                  66% 
                  62-142 
                 TLWIGDLQYWMDE 
                 518 
                  66% 
               
               
                   
                 8940.1 
                 (217/326) 
                   
                 NYLYTCLAHTGEVA 
                   
                 (54/81) 
               
               
                   
                   
                   
                   
                 SVKVIRNKQTSQSEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFIEFTSRAGAERV 
                   
                   
               
               
                   
                   
                   
                   
                 LQTYNGTIMPNGGQ 
                   
                   
               
               
                   
                   
                   
                   
                 NFRLNWATLS 
                   
                   
               
               
                   
               
               
                 50 
                 Eg/Eucgr.F034 
                  69% 
                  65-145 
                 SLWIGDLQPHMDET 
                 514 
                  65% 
               
               
                   
                 62.1 
                 (226/323) 
                   
                 YLLNCFAHSGEVLS 
                   
                 (53/81) 
               
               
                   
                   
                   
                   
                 AKVIRNKQTALPEG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFIEFMTRAAAERI 
                   
                   
               
               
                   
                   
                   
                   
                 LQTYNGTLMPNSDQ 
                   
                   
               
               
                   
                   
                   
                   
                 NFRLNWATLG 
                   
                   
               
               
                   
               
               
                 36 
                 Os/LOC_Os03g 
                  67% 
                  68-148 
                 TLWIGDLQFWMEEN 
                 507 
                  65% 
               
               
                   
                 37270.1 
                 (218/323) 
                   
                 YLYNCFSQAGELISA 
                   
                 (53/81) 
               
               
                   
                   
                   
                   
                 KIIRNKQTGQPEGYG 
                   
                   
               
               
                   
                   
                   
                   
                 FIEFGSHAIAEQVLQ 
                   
                   
               
               
                   
                   
                   
                   
                 GYNGQMMPNGNQV 
                   
                   
               
               
                   
                   
                   
                   
                 FKLNWATSG 
                   
                   
               
               
                   
               
               
                 56 
                 Eg/Eucgr.D013 
                  63% 
                  93-171 
                 TLWIGDLQYWMDE 
                 517 
                  64% 
               
               
                   
                 10.1 
                 (193/303) 
                   
                 AYLGTCFAATGEVA 
                   
                 (52/81) 
               
               
                   
                   
                   
                   
                 NVKVIRNKQTMQPE 
                   
                   
               
               
                   
                   
                   
                   
                 GYGFIEFYTRAAAER 
                   
                   
               
               
                   
                   
                   
                   
                 VLQTYNGAIMPNGG 
                   
                   
               
               
                   
                   
                   
                   
                 QSFRLNWAS 
                   
                   
               
               
                   
               
               
                 26 
                 Zm/GRMZM2 
                  62% 
                 122-200 
                 TLWIGDLQYWMDD 
                 502 
                  62% 
               
               
                   
                 G426591_T01 
                 (204/324) 
                   
                 NYIYGCFASTGEVQ 
                   
                 (51/81) 
               
               
                   
                   
                   
                   
                 NVKLIRDKHTGQLQ 
                   
                   
               
               
                   
                   
                   
                   
                 GYGFIEFISRAAAER 
                   
                   
               
               
                   
                   
                   
                   
                 VLQTYNGTMMPNV 
                   
                   
               
               
                   
                   
                   
                   
                 ELPFRLNWAS 
                   
                   
               
               
                   
               
               
                 22 
                 Bd/Bradi3g151 
                  56% 
                  99-177 
                 TLWIGDLQYWMDE 
                 500 
                  61% 
               
               
                   
                 80.1 
                 (213/376) 
                   
                 NYVYGCFAHTGEVQ 
                   
                 (50/81) 
               
               
                   
                   
                   
                   
                 SVKLIRDKQTGQLQ 
                   
                   
               
               
                   
                   
                   
                   
                 GYGFVEFTTRAGAE 
                   
                   
               
               
                   
                   
                   
                   
                 RVLQTYNGATMPN 
                   
                   
               
               
                   
                   
                   
                   
                 VEMPYRLNWAS 
                   
                   
               
               
                   
               
               
                 16 
                 Bd/Bradi5g224 
                  61% 
                  89-167 
                 TLWIGDLQYWMDE 
                 497 
                  60% 
               
               
                   
                 10.1 
                 (201/327) 
                   
                 TYIHGCFASTGELQS 
                   
                 (49/81) 
               
               
                   
                   
                   
                   
                 VKLIRDKQTGQLQG 
                   
                   
               
               
                   
                   
                   
                   
                 YGFVEFTSHAAAER 
                   
                   
               
               
                   
                   
                   
                   
                 VLQGYNGHAMPNV 
                   
                   
               
               
                   
                   
                   
                   
                 DLAYRLNWAS 
                   
                   
               
               
                   
               
               
                 30 
                 Os/LOC_Os07g 
                  58% 
                 129-210 
                 SLWIGDLQYWMDES 
                 504 
                  59% 
               
               
                   
                 33330.1 
                 (205/348) 
                   
                 YLSNAFAPMGQQVT 
                   
                 (49/82) 
               
               
                   
                   
                   
                   
                 SVKVIRNKQSGHSE 
                   
                   
               
               
                   
                   
                   
                   
                 GYGFIEFQSHAAAE 
                   
                   
               
               
                   
                   
                   
                   
                 YALANFNGRMMLN 
                   
                   
               
               
                   
                   
                   
                   
                 VDQLFKLNWASSG 
                   
                   
               
               
                   
               
               
                 18 
                 Zm/GRMZM2 
                  58% 
                  93-171 
                 TLWIGDLQYWMDE 
                 498 
                  59% 
               
               
                   
                 G012628_T01 
                 (191/329) 
                   
                 NYVFGCFSNTGEVQ 
                   
                 (48/81) 
               
               
                   
                   
                   
                   
                 NVKLIRDKNSGQLQ 
                   
                   
               
               
                   
                   
                   
                   
                 GYGFVEFTSRAAAE 
                   
                   
               
               
                   
                   
                   
                   
                 RVLQTYNGQMMPN 
                   
                   
               
               
                   
                   
                   
                   
                 VDLTFRLNWAS 
                   
                   
               
               
                   
               
               
                 20 
                 Zm/GRMZM2 
                  58% 
                  87-165 
                 TLWIGDLQYWMDD 
                 499 
                  58% 
               
               
                   
                 G058098_T02 
                 (192/331) 
                   
                 NYVFGCFSNTGEVQ 
                   
                 (47/81) 
               
               
                   
                   
                   
                   
                 NVKLIRDKNSGQLQ 
                   
                   
               
               
                   
                   
                   
                   
                 GYGFVEFTSRAAAE 
                   
                   
               
               
                   
                   
                   
                   
                 RVLQTYNGQMMPN 
                   
                   
               
               
                   
                   
                   
                   
                 VDLTFRLNWAS 
                   
                   
               
               
                   
               
               
                 32 
                 Zm/GRMZM2 
                  53% 
                 115-197 
                 TLWIGDLQHWMDE 
                 505 
                  57% 
               
               
                   
                 G127510_T01 
                 (191/354) 
                   
                 NYLHYNAFAAVAQ 
                   
                 (48/83) 
               
               
                   
                   
                   
                   
                 QIASVKIIRNKQTGH 
                   
                   
               
               
                   
                   
                   
                   
                 SEGYGFIEFYSRAAA 
                   
                   
               
               
                   
                   
                   
                   
                 EHTLMNFNGQMMP 
                   
                   
               
               
                   
                   
                   
                   
                 NVEMTFKLNWASAS 
                   
                   
               
               
                   
               
               
                 34 
                 Zm/GRMZM2 
                  55% 
                 147-229 
                 TLWIGDLQYWMDE 
                 506 
                  56% 
               
               
                   
                 G169615_T01 
                 (188/338) 
                   
                 NYLHYNAFAPVAQQ 
                   
                 (47/83) 
               
               
                   
                   
                   
                   
                 IASVKIIRNKQTGHS 
                   
                   
               
               
                   
                   
                   
                   
                 EGYGFIEFYSQAAAE 
                   
                   
               
               
                   
                   
                   
                   
                 HTLMNFNGQMMPNI 
                   
                   
               
               
                   
                   
                   
                   
                 EMAFKLNWASAS 
                   
                   
               
               
                   
               
               
                 28 
                 Bd/Bradi1g262 
                  55% 
                 115-197 
                 SLWIGDLQYWMDE 
                 503 
                  56% 
               
               
                   
                 10.1 
                 (181/324) 
                   
                 AYLHNAFAPMGPQQ 
                   
                 (47/83) 
               
               
                   
                   
                   
                   
                 VASVKIIRNKQTGQP 
                   
                   
               
               
                   
                   
                   
                   
                 EGYGFIEFHSRAAAE 
                   
                   
               
               
                   
                   
                   
                   
                 YALASFNGHAMPNV 
                   
                   
               
               
                   
                   
                   
                   
                 DLPFKLNWASAS 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Conserved ‘RRM2 domain’ of RBP45A and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity  
               
               
                   
                   
                   
                   
                   
                   
                 of RRM2 
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 domain 
               
               
                 Col. 
                   
                 Percent 
                 Col. 4 
                   
                 Col. 6 
                 in Col.  
               
               
                 1 
                   
                 identity of 
                 RRM2 
                 Col. 5 
                 SEQ ID 
                 5 to  
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Conserved 
                 NO: of 
                 RRM2 do- 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 RRM2 
                 RRM2 
                 main of 
               
               
                 NO: 
                 Identifier 
                 to RBP45A 
                 coordinates 
                 domain 
                 domain 
                 RBP45A 
               
               
                   
               
               
                 42 
                 At/RBP45A or 
                 100% 
                 153-232 
                 DHTIFVGDLAPEVTD 
                 538 
                 100% 
               
               
                   
                 AT5G54900.1 
                 (387/387) 
                   
                 YMLSWITKNVYGSV 
                   
                 (80/80) 
               
               
                   
                   
                   
                   
                 KGAKVVLDRTTGRS 
                   
                   
               
               
                   
                   
                   
                   
                 KGYGFVRFADENEQ 
                   
                   
               
               
                   
                   
                   
                   
                 MRAMTEMNGQYCS 
                   
                   
               
               
                   
                   
                   
                   
                 TRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 40 
                 At/AT4G27000 
                  71% 
                 172-251 
                 EHTVFVGDLAPDVT 
                 537 
                  83% 
               
               
                   
                 .1 
                 (282/394) 
                   
                 DHMLTETFKAVYSS 
                   
                 (67/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVNDRTTG 
                   
                   
               
               
                   
                   
                   
                   
                 RSKGYGFVRFADES 
                   
                   
               
               
                   
                   
                   
                   
                 EQIRAMTEMNGQYC 
                   
                   
               
               
                   
                   
                   
                   
                 SSRPMRTGPAA 
                   
                   
               
               
                   
               
               
                 44 
                 Pt/POPTR_000 
                  70% 
                 159-238 
                 DYTVFIGDLAADVN 
                 539 
                  82% 
               
               
                   
                 1s45000.1 
                 (228/323) 
                   
                 DYLLQETFRNVYSS 
                   
                 (66/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVTDRVTG 
                   
                   
               
               
                   
                   
                   
                   
                 RSKGYGFVRFADEN 
                   
                   
               
               
                   
                   
                   
                   
                 EQMRAMVEMNGQY 
                   
                   
               
               
                   
                   
                   
                   
                 CSTRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 46 
                 Pt/POPTR_001 
                  69% 
                 162-241 
                 DFTVFVGDLAADVN 
                 540 
                  81% 
               
               
                   
                 1s14150.1 
                 (231/331) 
                   
                 DYLLQETFRNVYPS 
                   
                 (65/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVTDRVTG 
                   
                   
               
               
                   
                   
                   
                   
                 RSKGYGFIRFADENE 
                   
                   
               
               
                   
                   
                   
                   
                 QRRAMVEMNGQYC 
                   
                   
               
               
                   
                   
                   
                   
                 STRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 50 
                 Eg/Eucgr.F034 
                  69% 
                 156-235 
                 DYTIFVGDLAADVT 
                 542 
                  78% 
               
               
                   
                 62.1 
                 (226/323) 
                   
                 DHMLQETFRAHYPS 
                   
                 (63/80) 
               
               
                   
                   
                   
                   
                 VKGAKIVIDRTTGRS 
                   
                   
               
               
                   
                   
                   
                   
                 KGYGFVRFGDETEQ 
                   
                   
               
               
                   
                   
                   
                   
                 LRAMTEMNGMYCS 
                   
                   
               
               
                   
                   
                   
                   
                 SRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 38 
                 Zm/GRMZM2 
                  68% 
                 162-241 
                 DYTIFVGDLASDVT 
                 536 
                  77% 
               
               
                   
                 G002874_T01 
                 (219/322) 
                   
                 DFILQDTFKSRYPSV 
                   
                 (62/80) 
               
               
                   
                   
                   
                   
                 KGAKVVFDRTTGRS 
                   
                   
               
               
                   
                   
                   
                   
                 KGYGFVKFADSDEQ 
                   
                   
               
               
                   
                   
                   
                   
                 TRAMTEMNGQYCSS 
                   
                   
               
               
                   
                   
                   
                   
                 RAMRLGPAS 
                   
                   
               
               
                   
               
               
                 36 
                 Os/LOC_Os03g 
                  67% 
                 159-238 
                 DYTIFVGDLASDVT 
                 535 
                  77% 
               
               
                   
                 37270.1 
                 (218/323) 
                   
                 DLILQDTFKAHYQS 
                   
                   
               
               
                   
                   
                   
                   
                 VKGAKVVFDRSTGR 
                   
                 (62/80) 
               
               
                   
                   
                   
                   
                 SKGYGFVKFGDLDE 
                   
                   
               
               
                   
                   
                   
                   
                 QTRAMTEMNGQYC 
                   
                   
               
               
                   
                   
                   
                   
                 SSRPMRIGPAS 
                   
                   
               
               
                   
               
               
                 52 
                 At/AT1G11650 
                  63% 
                 154-233 
                 DYTIFVGDLAADVT 
                 543 
                  77% 
               
               
                   
                 .2 
                 (206/325) 
                   
                 DYILLETFRASYPSV 
                   
                 (62/80) 
               
               
                   
                   
                   
                   
                 KGAKVVIDRVTGRT 
                   
                   
               
               
                   
                   
                   
                   
                 KGYGFVRFSDESEQI 
                   
                   
               
               
                   
                   
                   
                   
                 RAMTEMNGVPCSTR 
                   
                   
               
               
                   
                   
                   
                   
                 PMRIGPAA 
                   
                   
               
               
                   
               
               
                 48 
                 Sl/Solyc07g064 
                  67% 
                 172-251 
                 EYTIFVGDLAADVT 
                 541 
                  76% 
               
               
                   
                 510.2.1 
                 (218/324) 
                   
                 DYVLQETFKPVYSS 
                   
                 (61/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVTDRITGR 
                   
                   
               
               
                   
                   
                   
                   
                 TKGYGFVKFSDESE 
                   
                   
               
               
                   
                   
                   
                   
                 QLRAMTEMNGVLC 
                   
                   
               
               
                   
                   
                   
                   
                 SSRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 70 
                 Sl/Solyc03g031 
                  64% 
                 164-243 
                 EYTIFVGDLAADVT 
                 552 
                  76% 
               
               
                   
                 720.2.1 
                 (215/335) 
                   
                 DYMLQETFRANYPS 
                   
                 (61/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVTDRVTG 
                   
                   
               
               
                   
                   
                   
                   
                 RTKGYGFVKFADES 
                   
                   
               
               
                   
                   
                   
                   
                 EQLHAMTEMNGKF 
                   
                   
               
               
                   
                   
                   
                   
                 CSTRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 66 
                 Sl/Solyc02g080 
                  66% 
                 171-250 
                 EYTIFVGDLAADVS 
                 550 
                  75% 
               
               
                   
                 420.2.1 
                 (216/325) 
                   
                 DYMLQETFRANYPS 
                   
                 (60/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVTDKATG 
                   
                   
               
               
                   
                   
                   
                   
                 RTKGYGFVKFGDES 
                   
                   
               
               
                   
                   
                   
                   
                 EQLRAMTEMNGQF 
                   
                   
               
               
                   
                   
                   
                   
                 CSTRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 58 
                 Gm/Glyma07g3 
                  66% 
                 153-232 
                 DHTIFVGDLAADVT 
                 546 
                  75% 
               
               
                   
                 8940.1 
                 (217/326) 
                   
                 DYLLQETFRARYPSI 
                   
                 (60/80) 
               
               
                   
                   
                   
                   
                 KGAKVVIDRLTGRT 
                   
                   
               
               
                   
                   
                   
                   
                 KGYGFVRFGDESEQ 
                   
                   
               
               
                   
                   
                   
                   
                 VRAMTEMQGVLCS 
                   
                   
               
               
                   
                   
                   
                   
                 TRPMRIGPAS 
                   
                   
               
               
                   
               
               
                 68 
                 Sl/Solyc10g005 
                  65% 
                 168-247 
                 EYTIFVGDLAADVT 
                 551 
                  75% 
               
               
                   
                 260.2.1 
                 (218/333) 
                   
                 DYMLQETFRPNYPSI 
                   
                 (60/80) 
               
               
                   
                   
                   
                   
                 KGAKVVTDRATGH 
                   
                   
               
               
                   
                   
                   
                   
                 TKGYGFVRFGDESE 
                   
                   
               
               
                   
                   
                   
                   
                 QLRAMTEMNGKFCS 
                   
                   
               
               
                   
                   
                   
                   
                 TRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 62 
                 Gm/Glyma13g2 
                  64% 
                 159-238 
                 DYTIFVGDLAADVT 
                 548 
                  75% 
               
               
                   
                 7570.1 
                 (214/331) 
                   
                 DYLLQETFRARYNS 
                   
                 (60/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVIDRLTGR 
                   
                   
               
               
                   
                   
                   
                   
                 TKGYGFVRFSDESE 
                   
                   
               
               
                   
                   
                   
                   
                 QVRAMTEMQGVLC 
                   
                   
               
               
                   
                   
                   
                   
                 STRPMRIGPAS 
                   
                   
               
               
                   
               
               
                 64 
                 Gm/Glyma15g1 
                  64% 
                 160-239 
                 DYTIFVGDLAADVT 
                 549 
                  75% 
               
               
                   
                 1380.1 
                 (215/333) 
                   
                 DYLLQETFRARYNS 
                   
                 (60/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVIDRLTGR 
                   
                   
               
               
                   
                   
                   
                   
                 TKGYGFVRFSEESEQ 
                   
                   
               
               
                   
                   
                   
                   
                 MRAMTEMQGVLCS 
                   
                   
               
               
                   
                   
                   
                   
                 TRPMRIGPAS 
                   
                   
               
               
                   
               
               
                 60 
                 Gm/Glyma17g0 
                  66% 
                 157-236 
                 DHTIFVGDLAADVT 
                 547 
                  73% 
               
               
                   
                 1800.1 
                 (218/327) 
                   
                 DYLLQETFRARYPS 
                   
                 (59/80) 
               
               
                   
                   
                   
                   
                 AKGAKVVIDRLTGR 
                   
                   
               
               
                   
                   
                   
                   
                 TKGYGFVRFGDESE 
                   
                   
               
               
                   
                   
                   
                   
                 QVRAMSEMQGVLC 
                   
                   
               
               
                   
                   
                   
                   
                 STRPMRIGPAS 
                   
                   
               
               
                   
               
               
                 30 
                 Os/LOC_Os07g 
                  58% 
                 222-301 
                 EHTIFVGDLASDVTD 
                 532 
                  73% 
               
               
                   
                 33330.1 
                 (205/348) 
                   
                 SMLEEAFKTSYPSVR 
                   
                 (59/80) 
               
               
                   
                   
                   
                   
                 GAKVVFDKVTGRSK 
                   
                   
               
               
                   
                   
                   
                   
                 GYGFVRFGDENEQT 
                   
                   
               
               
                   
                   
                   
                   
                 RAMTEMNGATLSTR 
                   
                   
               
               
                   
                   
                   
                   
                 QMRLGPAA 
                   
                   
               
               
                   
               
               
                 24 
                 Os/LOC_Os08g 
                  63% 
                 184-263 
                 DYTIFVGDLAADVT 
                 529 
                  72% 
               
               
                   
                 09100.1 
                 (206/325) 
                   
                 DYILQETFRVHYPSV 
                   
                 (58/80) 
               
               
                   
                   
                   
                   
                 KGAKVVTDKMTMR 
                   
                   
               
               
                   
                   
                   
                   
                 SKGYGFVKFGDPSE 
                   
                   
               
               
                   
                   
                   
                   
                 QARAMTEMNGMVC 
                   
                   
               
               
                   
                   
                   
                   
                 SSRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 26 
                 Zm/GRMZM2 
                  62% 
                 210-289 
                 DYTIFVGDLAADVT 
                 530 
                  72% 
               
               
                   
                 G426591_T01 
                 (204/324) 
                   
                 DYVLQETFRAHYPS 
                   
                 (58/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVTDKLTM 
                   
                   
               
               
                   
                   
                   
                   
                 RTKGYGFVKFGDPN 
                   
                   
               
               
                   
                   
                   
                   
                 EQARAMTEMNGML 
                   
                   
               
               
                   
                   
                   
                   
                 CSSRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 16 
                 Bd/Bradi5g224 
                  61% 
                 177-256 
                 DYTIFVGDLAADVT 
                 525 
                  72% 
               
               
                   
                 10.1 
                 (201/327) 
                   
                 DYILQETFRVHYPSV 
                   
                 (58/80) 
               
               
                   
                   
                   
                   
                 KGAKVVTDKMTMR 
                   
                   
               
               
                   
                   
                   
                   
                 SKGYGFVKFGDPTE 
                   
                   
               
               
                   
                   
                   
                   
                 QARAMTEMNGMPC 
                   
                   
               
               
                   
                   
                   
                   
                 SSRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 54 
                 Pt/POPTR_000 
                  61% 
                 168-247 
                 DFTIFVGDLAADVT 
                 544 
                  72% 
               
               
                   
                 4s01690.1 
                 (213/349) 
                   
                 DFMLQETFRAHFPS 
                   
                 (58/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVIDRLTGR 
                   
                   
               
               
                   
                   
                   
                   
                 TKGYGFVRFGDESE 
                   
                   
               
               
                   
                   
                   
                   
                 QLRAMTEMNGAFCS 
                   
                   
               
               
                   
                   
                   
                   
                 TRPMRVGLAS 
                   
                   
               
               
                   
               
               
                 22 
                 Bd/Bradi3g151 
                  56% 
                 187-266 
                 DYTIFVGDLAADVT 
                 528 
                  72% 
               
               
                   
                 80.1 
                 (213/376) 
                   
                 DYILQETFRVHYPSV 
                   
                 (58/80) 
               
               
                   
                   
                   
                   
                 KGAKVVTDKLTMR 
                   
                   
               
               
                   
                   
                   
                   
                 SKGYGFVKFSDPTE 
                   
                   
               
               
                   
                   
                   
                   
                 QTRAMTEMNGMVC 
                   
                   
               
               
                   
                   
                   
                   
                 SSRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 34 
                 Zm/GRMZM2 
                  55% 
                 240-319 
                 DHAIFVGDLAPDVT 
                 534 
                  72% 
               
               
                   
                 G169615_T01 
                 (188/338) 
                   
                 DSMLEDVFRANYPS 
                   
                 (58/80) 
               
               
                   
                   
                   
                   
                 VRGAKVVVDRITGR 
                   
                   
               
               
                   
                   
                   
                   
                 PKGYGFVHFGDLNE 
                   
                   
               
               
                   
                   
                   
                   
                 QARAMTEMNGMML 
                   
                   
               
               
                   
                   
                   
                   
                 STRKMRIGAAA 
                   
                   
               
               
                   
               
               
                 28 
                 Bd/Bradi1g262 
                  55% 
                 208-287 
                 DHTIFVGDLASDVT 
                 531 
                  72% 
               
               
                   
                 10.1 
                 (181/324) 
                   
                 DSMLQEIFKASYPSV 
                   
                 (58/80) 
               
               
                   
                   
                   
                   
                 RGANVVTDRATGRS 
                   
                   
               
               
                   
                   
                   
                   
                 KGYGFVRFGDVNEQ 
                   
                   
               
               
                   
                   
                   
                   
                 TRAMTEMNGVTLSS 
                   
                   
               
               
                   
                   
                   
                   
                 RQLRIGPAA 
                   
                   
               
               
                   
               
               
                 20 
                 Zm/GRMZM2 
                  58% 
                 175-254 
                 DYTIFVGDLAADVT 
                 527 
                  71% 
               
               
                   
                 G058098_T02 
                 (192/331) 
                   
                 DYLLQETFRVHYPS 
                   
                 (57/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVTDKLTM 
                   
                   
               
               
                   
                   
                   
                   
                 RTKGYGFVKFGDPT 
                   
                   
               
               
                   
                   
                   
                   
                 EQARAMTEMNGMP 
                   
                   
               
               
                   
                   
                   
                   
                 CSSRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 18 
                 Zm/GRMZM2 
                  58% 
                 181-260 
                 EYTIFVGDLAADVT 
                 526 
                  70% 
               
               
                   
                 G012628_T01 
                 (191/329) 
                   
                 DYLLQETFRVHYPS 
                   
                 (56/80) 
               
               
                   
                   
                   
                   
                 VKGAKVVTDKLTM 
                   
                   
               
               
                   
                   
                   
                   
                 RTKGYGFVKFGDPT 
                   
                   
               
               
                   
                   
                   
                   
                 EQARAMTEMNGMP 
                   
                   
               
               
                   
                   
                   
                   
                 CSSRPMRIGPAA 
                   
                   
               
               
                   
               
               
                 32 
                 Zm/GRMZM2 
                  53% 
                 208-287 
                 DRTIFVGDLAHDVT 
                 533 
                  68% 
               
               
                   
                 G127510_T01 
                 (191/354) 
                   
                 DSMLEDVFRAKYPS 
                   
                 (55/80) 
               
               
                   
                   
                   
                   
                 VRGANVVVDRMTG 
                   
                   
               
               
                   
                   
                   
                   
                 WPKGFGFVRFGDLN 
                   
                   
               
               
                   
                   
                   
                   
                 EQARAMTEMNGML 
                   
                   
               
               
                   
                   
                   
                   
                 LSTRQMRIGAAA 
                   
                   
               
               
                   
               
               
                 56 
                 Eg/Eucgr.D013 
                  63% 
                 182-261 
                 DYTIFVGDLASDVT 
                 545 
                  67% 
               
               
                   
                 10.1 
                 (193/303) 
                   
                 DYMLQEMFRGRYPS 
                   
                 (54/80) 
               
               
                   
                   
                   
                   
                 VRSAKVVMDRLTSR 
                   
                   
               
               
                   
                   
                   
                   
                 TKGYGFVKFGDESE 
                   
                   
               
               
                   
                   
                   
                   
                 QIRAMSEMNGVFLS 
                   
                   
               
               
                   
                   
                   
                   
                 TRPMRIGLAT 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Conserved ‘RRM3 domain’ of RBP45A and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity 
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 of RRM3 
               
               
                 Col. 
                   
                 Percent 
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                 1 
                   
                 identity of 
                 RRM3 
                 Col. 5 
                 SEQ ID 
                 Col. 5 to 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Conserved 
                 NO: of 
                 RRM3 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 RRM3 
                 RRM3 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to RBP45A 
                 coordinates 
                 domain 
                 domain 
                 RBP45A 
               
               
                   
               
               
                 42 
                 At/RBP45A or 
                 100% 
                 260-332 
                 TTIFVGGLDANVTD 
                 566 
                 100% 
               
               
                   
                 AT5G54900.1 
                 (387/387) 
                   
                 DELKSIFGQFGELLH 
                   
                 (73/73) 
               
               
                   
                   
                   
                   
                 VKIPPGKRCGFVQY 
                   
                   
               
               
                   
                   
                   
                   
                 ANKASAEHALSVLN 
                   
                   
               
               
                   
                   
                   
                   
                 GTQLGGQSIRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 40 
                 At/AT4G27000 
                  71% 
                 278-350 
                 TTIFVGAVDQSVTED 
                 565 
                  83% 
               
               
                   
                 .1 
                 (282/394) 
                   
                 DLKSVFGQFGELVH 
                   
                 (61/73) 
               
               
                   
                   
                   
                   
                 VKIPAGKRCGFVQY 
                   
                   
               
               
                   
                   
                   
                   
                 ANRACAEQALSVLN 
                   
                   
               
               
                   
                   
                   
                   
                 GTQLGGQSIRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 50 
                 Eg/Eucgr.F034 
                  69% 
                 265-337 
                 TTIFVGGLDPSVSDD 
                 570 
                  75% 
               
               
                   
                 62.1 
                 (226/323) 
                   
                 LLRQVFSQYGELHH 
                   
                 (55/73) 
               
               
                   
                   
                   
                   
                 VKIPPGKRCGFVQFT 
                   
                   
               
               
                   
                   
                   
                   
                 SRACAEQALLMLNG 
                   
                   
               
               
                   
                   
                   
                   
                 TQLGGQSIRLSWGR 
                   
                   
               
               
                   
                   
                   
                   
                 S 
                   
                   
               
               
                   
               
               
                 38 
                 Zm/GRMZM2 
                  68% 
                 271-343 
                 TTVFVGGLDPSVTD 
                 564 
                  75% 
               
               
                   
                 G002874_T01 
                 (219/322) 
                   
                 ELLKQTFSPYGELLY 
                   
                 (55/73) 
               
               
                   
                   
                   
                   
                 VKIPVGKRCGFVQY 
                   
                   
               
               
                   
                   
                   
                   
                 SNRASAEEAIRVLNG 
                   
                   
               
               
                   
                   
                   
                   
                 SQLGGQSIRLSWGRS 
                   
                   
               
               
                   
               
               
                 66 
                 Sl/Solyc02g080 
                  66% 
                 278-350 
                 TTIFVGNLDSNITDE 
                 578 
                  73% 
               
               
                   
                 420.2.1 
                 (216/325) 
                   
                 HLRQIFGHYGQLLH 
                   
                 (54/73) 
               
               
                   
                   
                   
                   
                 VKIPVGKRCGFIQFA 
                   
                   
               
               
                   
                   
                   
                   
                 DRSCAEEALRVLNG 
                   
                   
               
               
                   
                   
                   
                   
                 TQLGGQSIRLSWGR 
                   
                   
               
               
                   
                   
                   
                   
                 S 
                   
                   
               
               
                   
               
               
                 60 
                 Gm/Glyma17g0 
                  66% 
                 265-337 
                 TTIFVGNLDPNVTDD 
                 575 
                  73% 
               
               
                   
                 1800.1 
                 (218/327) 
                   
                 HLRQVFGQYGELVH 
                   
                 (54/73) 
               
               
                   
                   
                   
                   
                 VKIPAGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 ADRSCAEEALRVLN 
                   
                   
               
               
                   
                   
                   
                   
                 GTLLGGQNVRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 70 
                 Sl/Solyc03g031 
                  64% 
                 271-343 
                 TTIFVGNLDANVTD 
                 580 
                  73% 
               
               
                   
                 720.2.1 
                 (215/335) 
                   
                 DHLRQVFGNYGQLL 
                   
                 (54/73) 
               
               
                   
                   
                   
                   
                 HVKIPVGKRCGFVQ 
                   
                   
               
               
                   
                   
                   
                   
                 FADRSCAEEALRAL 
                   
                   
               
               
                   
                   
                   
                   
                 SGTQLGGQTIRLSW 
                   
                   
               
               
                   
                   
                   
                   
                 GRS 
                   
                   
               
               
                   
               
               
                 46 
                 Pt/POPTR_001 
                  69% 
                 270-342 
                 TTIFVGALDPSVTDD 
                 568 
                  72% 
               
               
                   
                 1s14150.1 
                 (231/331) 
                   
                 TLRAVFSKYGELVH 
                   
                 (53/73) 
               
               
                   
                   
                   
                   
                 VKIPAGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 ANRTSAEQALSMLN 
                   
                   
               
               
                   
                   
                   
                   
                 GTQIAGQNIRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 36 
                 Os/LOC_Os03g 
                  67% 
                 268-340 
                 TTVFVGGLDPSVTD 
                 563 
                  72% 
               
               
                   
                 37270.1 
                 (218/323) 
                   
                 EVLKQAFSPYGELV 
                   
                 (53/73) 
               
               
                   
                   
                   
                   
                 YVKIPVGKRCGFVQ 
                   
                   
               
               
                   
                   
                   
                   
                 YSNRASAEEAIRML 
                   
                   
               
               
                   
                   
                   
                   
                 NGSQLGGQSIRLSW 
                   
                   
               
               
                   
                   
                   
                   
                 GRS 
                   
                   
               
               
                   
               
               
                 58 
                 Gm/Glyma07g3 
                  66% 
                 261-333 
                 TTIFVGNLDPNVTDD 
                 574 
                  72% 
               
               
                   
                 8940.1 
                 (217/326) 
                   
                 HLRQVFGHYGELVH 
                   
                 (53/73) 
               
               
                   
                   
                   
                   
                 VKIPAGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 ADRSCAEEALRVLN 
                   
                   
               
               
                   
                   
                   
                   
                 GTLLGGQNVRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 62 
                 Gm/Glyma13g2 
                  64% 
                 269-341 
                 TTIFVGNLDPNVTDD 
                 576 
                  72% 
               
               
                   
                 7570.1 
                 (214/331) 
                   
                 HLRQVFSQYGELVH 
                   
                 (53/73) 
               
               
                   
                   
                   
                   
                 VKIPAGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 ADRSCAEEALRVLN 
                   
                   
               
               
                   
                   
                   
                   
                 GTLLGGQNVRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 64 
                 Gm/Glyma15g1 
                  64% 
                 270-342 
                 TTIFVGNLDPNVTDD 
                 577 
                  72% 
               
               
                   
                 1380.1 
                 (215/333) 
                   
                 HLRQVFSQYGELVH 
                   
                 (53/73) 
               
               
                   
                   
                   
                   
                 VKIPAGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 ADRSCAEEALRVLN 
                   
                   
               
               
                   
                   
                   
                   
                 GTLLGGQNVRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 56 
                 Eg/Eucgr.D013 
                  63% 
                 291-363 
                 KTVFVGGLDPNVTD 
                 573 
                  72% 
               
               
                   
                 10.1 
                 (193/303) 
                   
                 DHLRQVFGQYGEIV 
                   
                 (53/73) 
               
               
                   
                   
                   
                   
                 QVKIPPGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 ADRSCAEEALRMLN 
                   
                   
               
               
                   
                   
                   
                   
                 GTQLGGQNIRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 54 
                 Pt/POPTR_000 
                  61% 
                 276-348 
                 TTIFVGNLDSNVMD 
                 572 
                  72% 
               
               
                   
                 4s01690.1 
                 (213/349) 
                   
                 DHLKELFGQYGQLL 
                   
                 (53/73) 
               
               
                   
                   
                   
                   
                 HVKIPAGKRCGFVQ 
                   
                   
               
               
                   
                   
                   
                   
                 FADRSSAEEALKML 
                   
                   
               
               
                   
                   
                   
                   
                 NGAQLSGQNIRLSW 
                   
                   
               
               
                   
                   
                   
                   
                 GRN 
                   
                   
               
               
                   
               
               
                 44 
                 Pt/POPTR_000 
                  70% 
                 267-339 
                 TTIFVGALDPSVTDD 
                 567 
                  71% 
               
               
                   
                 1s45000.1 
                 (228/323) 
                   
                 TLRAVFSKYGELVH 
                   
                 (52/73) 
               
               
                   
                   
                   
                   
                 VKIPAGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 ANRTCAEQALSMLN 
                   
                   
               
               
                   
                   
                   
                   
                 GTQIAGQNIRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 48 
                 Sl/Solyc07g064 
                  67% 
                 279-351 
                 TTIFVGGLDPSVAEE 
                 569 
                  71% 
               
               
                   
                 510.2.1 
                 (218/324) 
                   
                 HLRQVFSPYGELVH 
                   
                 (52/73) 
               
               
                   
                   
                   
                   
                 VKIVAGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 GSRASAEQALSSLN 
                   
                   
               
               
                   
                   
                   
                   
                 GTQLGGQSIRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 68 
                 Sl/Solyc10g005 
                  65% 
                 274-346 
                 TTIFVGNLDASVTDD 
                 579 
                  71% 
               
               
                   
                 260.2.1 
                 (218/333) 
                   
                 HLRQVFGNYGQLLH 
                   
                 (52/73) 
               
               
                   
                   
                   
                   
                 VKIPLGKRCGFVQFT 
                   
                   
               
               
                   
                   
                   
                   
                 DRSCAEEALNALSG 
                   
                   
               
               
                   
                   
                   
                   
                 TQLGGQTIRLSWGR 
                   
                   
               
               
                   
                   
                   
                   
                 S 
                   
                   
               
               
                   
               
               
                 52 
                 At/AT1G11650 
                  63% 
                 261-333 
                 TTVFVGGLDASVTD 
                 571 
                  69% 
               
               
                   
                 .2 
                 (206/325) 
                   
                 DHLKNVFSQYGEIV 
                   
                 (51/73) 
               
               
                   
                   
                   
                   
                 HVKIPAGKRCGFVQ 
                   
                   
               
               
                   
                   
                   
                   
                 FSEKSCAEEALRML 
                   
                   
               
               
                   
                   
                   
                   
                 NGVQLGGTTVRLSW 
                   
                   
               
               
                   
                   
                   
                   
                 GRS 
                   
                   
               
               
                   
               
               
                 26 
                 Zm/GRMZM2 
                  62% 
                 315-387 
                 TTIFVGGLDPNVTED 
                 558 
                  69% 
               
               
                   
                 G426591_T01 
                 (204/324) 
                   
                 MLKQVFTPYGDVV 
                   
                 (51/73) 
               
               
                   
                   
                   
                   
                 HVKIPVGKRCGFVQ 
                   
                   
               
               
                   
                   
                   
                   
                 YANRSSAEEALVILQ 
                   
                   
               
               
                   
                   
                   
                   
                 GTLVGGQNVRLSW 
                   
                   
               
               
                   
                   
                   
                   
                 GRS 
                   
                   
               
               
                   
               
               
                 24 
                 Os/LOC_Os08g 
                  63% 
                 289-361 
                 TTIFVGGLDPSVTDD 
                 557 
                  68% 
               
               
                   
                 09100.1 
                 (206/325) 
                   
                 MLKQVFTPYGDVV 
                   
                 (50/73) 
               
               
                   
                   
                   
                   
                 HVKIPVGKRCGFVQ 
                   
                   
               
               
                   
                   
                   
                   
                 FANRASADEALVLL 
                   
                   
               
               
                   
                   
                   
                   
                 QGTLIGGQNVRLSW 
                   
                   
               
               
                   
                   
                   
                   
                 GRS 
                   
                   
               
               
                   
               
               
                 16 
                 Bd/Bradi5g224 
                  61% 
                 284-356 
                 TTIFVGGLDPNVTED 
                 553 
                  68% 
               
               
                   
                 10.1 
                 (201/327) 
                   
                 ALKQVFAPYGEVIH 
                   
                 (50/73) 
               
               
                   
                   
                   
                   
                 VKIPVGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 VNRPSAEQALQMLQ 
                   
                   
               
               
                   
                   
                   
                   
                 GTPIGGQNVRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 22 
                 Bd/Bradi3g151 
                  56% 
                 293-365 
                 TTIFVGGLDPNVTED 
                 556 
                  68% 
               
               
                   
                 80.1 
                 (213/376) 
                   
                 MLKQVFAPYGEVV 
                   
                 (50/73) 
               
               
                   
                   
                   
                   
                 HVKIPVGKRCGFVQ 
                   
                   
               
               
                   
                   
                   
                   
                 YASRSSSEEALLML 
                   
                   
               
               
                   
                   
                   
                   
                 QGTVIGGQNVRLSW 
                   
                   
               
               
                   
                   
                   
                   
                 GRS 
                   
                   
               
               
                   
               
               
                 30 
                 Os/LOC_Os07g 
                  58% 
                 332-404 
                 TTIFVGGLDSNVNED 
                 560 
                  64% 
               
               
                   
                 33330.1 
                 (205/348) 
                   
                 HLKQVFTPYGEIGY 
                   
                 (47/73) 
               
               
                   
                   
                   
                   
                 VKIPLGKRCGFVQFT 
                   
                   
               
               
                   
                   
                   
                   
                 SRSSAEEAIRVLNGS 
                   
                   
               
               
                   
                   
                   
                   
                 QIGGQQVRLSWGRT 
                   
                   
               
               
                   
               
               
                 18 
                 Zm/GRMZM2 
                  58% 
                 288-360 
                 TTIFVGGLDPNVTED 
                 554 
                  64% 
               
               
                   
                 G012628_T01 
                 (191/329) 
                   
                 TLKQVFSPYGEVVH 
                   
                 (47/73) 
               
               
                   
                   
                   
                   
                 VKIPVGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 VTRPSAEQALLMLQ 
                   
                   
               
               
                   
                   
                   
                   
                 GALIGAQNVRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 20 
                 Zm/GRMZM2 
                  58% 
                 282-354 
                 TTIFVGGLDPNVTED 
                 555 
                  64% 
               
               
                   
                 G058098_T02 
                 (192/331) 
                   
                 VLKQAFSPYGEVIH 
                   
                 (47/73) 
               
               
                   
                   
                   
                   
                 VKIPVGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 VTRPSAEQALLMLQ 
                   
                   
               
               
                   
                   
                   
                   
                 GALIGAQNVRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 34 
                 Zm/GRMZM2 
                  55% 
                 351-423 
                 TTVFVGGLDSNVDE 
                 562 
                  58% 
               
               
                   
                 G169615_T01 
                 (188/338) 
                   
                 EYLRQIFTPYGEISY 
                   
                 (43/73) 
               
               
                   
                   
                   
                   
                 VKIPVGKHCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 TSRSCAEEAIQMLN 
                   
                   
               
               
                   
                   
                   
                   
                 GSQIGGQKARLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 32 
                 Zm/GRMZM2 
                  53% 
                 319-391 
                 TTVFVGGLDSNVNE 
                 561 
                  58% 
               
               
                   
                 G127510_T01 
                 (191/354) 
                   
                 EYLRQIFTPYGEISY 
                   
                 (43/73) 
               
               
                   
                   
                   
                   
                 VKIPVGKHCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 TSRSCAEEAIRMLNG 
                   
                   
               
               
                   
                   
                   
                   
                 SQVGGQKVRLSWG 
                   
                   
               
               
                   
                   
                   
                   
                 RS 
                   
                   
               
               
                   
               
               
                 28 
                 Bd/Bradi1g262 
                  55% 
                 320-392 
                 TTIFVGGLDSNIDEN 
                 559 
                  57% 
               
               
                   
                 10.1 
                 (181/324) 
                   
                 YLRQVFTPYGEVGY 
                   
                 (42/73) 
               
               
                   
                   
                   
                   
                 VKIPVGKRCGFVQF 
                   
                   
               
               
                   
                   
                   
                   
                 TSRSCAEEAINALNG 
                   
                   
               
               
                   
                   
                   
                   
                 TPIGGNNVRLSWGR 
                   
                   
               
               
                   
                   
                   
                   
                 S 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related RBP45A clade polypeptides may be identified by a consensus first RRM domain (RRM1 domain) sequence, SEQ ID NO: 844: 
                            X 1 LWIGDLQX 9 X 10 MX 12 X 13 X 14 X 15 X 16 X 17 X 18 X 19 X 20 X 21 X 22                         X 23 X 24 X 25 X 26 X 27 X 28 X 29 X 30 X 31 X 32 KX 34 IRX 37 KX 39 X 40                         X 41 X 42 X 43 X 44 GYGFX 49 EX 51 X 52 X 53 X 54 X 55 X 56 AEX 59 X 60                         LX 62 X 63 X 64 NX 66 X 67 X 68 X 69 X 70 X 71 X 72 X 73 X 74 X 75 X 76 X 77                         X 78 X 79 NWAX 83 X 84 X 85              
where X 1 =S or T; X 9 =any amino acid; X 10 =H or W; X 12 =D or E; X 13 =D or E; X 14 =any amino acid; X 15 =F or Y; X 16 =I, L, V or M; X 17 =H or absent; X 18 =any amino acid; X 19 =any amino acid; X 20 =any amino acid; X 21 =F, I, L, V or M; X 22 =any amino acid; X 23 =any amino acid; X 24 =any amino acid; X 25 =A or G; X 26 =P or absent; X 27 =Q or absent; X 28 =E or Q; X 29 =any amino acid; X 30 =any amino acid; X 31 =any amino acid; X 32 =any amino acid; X 34 =I, L, V or M; X 37 =N or D; X 39 =any amino acid; X 40 =any amino acid; X 41 =any amino acid; X 42 =any amino acid; X 43 =any amino acid; X 44 =E or Q; X 49 =I, L, V or M; X 51 =F, I, L, V or M; X 52 =any amino acid; X 53 =any amino acid; X 54 =H, Q or R; X 55 =A, S or G; X 56 =any amino acid; X 59 =any amino acid; X 60 =any amino acid; X 62 =any amino acid; X 63 =any amino acid; X 64 =F or Y; X 66 =any amino acid; X 67 =any amino acid; X 68 =any amino acid; X 69 =I, L, V or M; X 70 =any amino acid; X 71 =any amino acid; X 72 =any amino acid; X 73 =P or absent; X 74 =any amino acid; X 75 =any amino acid; X 76 =any amino acid; X 77 =F or Y; X 78 =K or R; X 79 =I, L, V or M; X 83 =any amino acid or absent; X 84 =any amino acid or absent; and X 85 =S or G.
 
     These functionally-related and/or closely-related RBP45A clade polypeptides also may be identified by a consensus second RRM domain (RRM2 domain) sequence, SEQ ID NO: 845: 
                            X 1 X 2 X 3 X 4 FX 6 GDLAX 11 X 12 VX 14 DX 16 X 17 LX 19 X 20 X 21 FX 23 X 24                         X 25 X 26 X 27 SX 29 X 30 X 31 AX 33 X 34 VX 36 DX 38 X 39 TX 41 X 42 X 43                         KGX 46 GFX 49 X 50 FX 52 X 53 X 54 X 55 EQX 58 X 59 AMX 62 EMX 65 GX 67                         X 68 X 69 SX 71 RX 73 X 74 RX 76 GX 78 AX 80              
where X 1 =E or D; X 2 =any amino acid; X 3 =A or T; X 4 =I, L, V or M; X 6 =I, L, V or M; X 11 =any amino acid; X 12 =E or D; X 14 =any amino acid; X 16 =any amino acid; X 17 =I, L, V or M; X 19 =any amino acid; X 20 =E or D; X 21 =any amino acid; X 23 =K or R; X 24 =any amino acid; X 25 =any amino acid; X 26 =F or Y; X 27 =any amino acid; X 29 =any amino acid; X 30 =K or R; X 31 =S or G; X 33 =Nor K; X 34 =I, L, V or M; X 36 =any amino acid; X 38 =K or R; X 39 =any amino acid; X 41 =any amino acid; X 42 =any amino acid; X 43 =any amino acid; X 46 =F or Y; X 49 =I, L, V or M; X 50 =any amino acid; X 52 =A, S or G; X 53 =E or D; X 54 =any amino acid; X 55 =any amino acid; X 58 =any amino acid; X 59 =any amino acid; X 62 =any amino acid; X 65 =N or Q; X 67 =any amino acid; X 68 =any amino acid; X 69 =any amino acid; X 71 =S or T; X 73 =any amino acid; X 74 =I, L, V or M; X 76 =any amino acid; X 78 =any amino acid; and X 80 =A, S or T.
 
     These functionally-related and/or closely-related RBP45A clade polypeptides also may be identified by a consensus third RRM domain (RRM3 domain) sequence, SEQ ID NO: 846: 
                            X 1 TX 3 FVGX 7 X 8 DX 10 X 11 X 12 X 13 X 14 X 15 X 16 LX 18 X 19 X 20 FX 22                         X 23 X 24 GX 26 X 27 X 28 X 29 VKIX 33 X 34 GKX 37 CGFX 41 QX 43 X 44                         X 45 X 46 X 47 X 48 X 49 X 50 X 51 AX 53 X 54 X 55 LX 57 GX 59 X 60 X 61 X 62                         X 63 X 64 X 65 X 66 RLSWGRX 73              
where X 1 =any amino acid; X 3 =I, L, V or M; X 7 =any amino acid; X 8 =I, L, V or M; X 10 =any amino acid; X 11 =any amino acid; X 12 =I, L, V or M; X 13 =any amino acid; X 14 =E or D; X 15 =N, E or D; X 16 =any amino acid; X 18 =K or R; X 19 =any amino acid; X 20 =any amino acid; X 22 =any amino acid; X 23 =any amino acid; X 24 =F or Y; X 26 =E, Q or D; X 27 =I, L, V or M; X 28 =any amino acid; X 29 =any amino acid; X 33 =any amino acid; X 34 =any amino acid; X 37 =any amino acid; X 41 =I, L, V or M; X 43 =F or Y; X 44 =any amino acid; X 45 =any amino acid; X 46 =K or R; X 47 =any amino acid; X 48 =S or C; X 49 =A or S; X 50 =E or D; X 51 =any amino acid; X 53 =I, L, V or M; X 54 =any amino acid; X 55 =any amino acid; X 57 =any amino acid; X 59 =any amino acid; X 60 =any amino acid; X 61 =I, L, V or M; X 62 =S, A or G; X 63 =A or G; X 64 =any amino acid; X 65 =any amino acid; X 66 =any amino acid; and X 73 =any amino acid.
 
     TCP6 Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Conserved ‘TCP domain’ of TCP6 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity  
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 of TCP 
               
               
                 Col. 
                   
                 Percent 
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                 1 
                   
                 identity of 
                 TCP 
                 Col. 5 
                 SEQ ID 
                 Col. 5 to 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Conserved 
                 NO: of 
                 TCP 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 TCP 
                 TCP 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to TCP6 
                 coordinates 
                 domain 
                 domain 
                 TCP6 
               
               
                   
               
               
                  86 
                 At/TCP6 or 
                 100% 
                  64-125 
                 KKKPNKDRHLKVEG 
                 588 
                 100% 
               
               
                   
                 AT5G41030.1 
                 (243/243) 
                   
                 RGRRVRLPPLCAARI 
                   
                 (62/62) 
               
               
                   
                   
                   
                   
                 YQLTKELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TLEWLLQHAEPSILS 
                   
                   
               
               
                   
                   
                   
                   
                 ATVN 
                   
                   
               
               
                   
               
               
                 106 
                 SL/soLyc02g094 
                  76% 
                 33-94 
                 KRKSNKDRHTKVEG 
                 598 
                  75% 
               
               
                   
                 290.1.1 
                 (48/63) 
                   
                 RGRRIRMPALCAARI 
                   
                 (47/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQKAEPSIIA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGH 
                   
                   
               
               
                   
               
               
                  96 
                 Gm/Glyma16g0 
                  48% 
                  68-129 
                 KRSSNKDRHTKVEG 
                 593 
                  74% 
               
               
                   
                 5840.1 
                  (67/138) 
                   
                 RGRRIRMPALCAARI 
                   
                 (46/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQQAEPSIIA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGT 
                   
                   
               
               
                   
               
               
                  84 
                 At/AT3G27010 
                  41% 
                  74-135 
                 KRSSNKDRHTKVEG 
                 587 
                  74% 
               
               
                   
                 .1 
                 (128/311) 
                   
                 RGRRIRMPALCAARI 
                   
                 (46/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQQAEPSIIA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGS 
                   
                   
               
               
                   
               
               
                  94 
                 Pt/POPTR_001 
                  37% 
                  83-144 
                 KRSSNKDRHTKVEG 
                 592 
                  74% 
               
               
                   
                 7s09820.1 
                 (113/300) 
                   
                 RGRRIRMPALCAARI 
                   
                 (46/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQQAEPSIIA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGT 
                   
                   
               
               
                   
               
               
                  88 
                 Cc/clementine0. 
                  36% 
                  66-127 
                 KRSSNKDRHTKVEG 
                 589 
                  74% 
               
               
                   
                 9_016144m 
                 (114/312) 
                   
                 RGRRIRMPALCAARI 
                   
                 (46/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQQAEPSIIA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGT 
                   
                   
               
               
                   
               
               
                  90 
                 Cc/clementine0. 
                  36% 
                  66-127 
                 KRSSNKDRHTKVEG 
                 590 
                  74% 
               
               
                   
                 9_016174m 
                 (114/312) 
                   
                 RGRRIRMPALCAARI 
                   
                 (46/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQQAEPSIIA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGT 
                   
                   
               
               
                   
               
               
                  92 
                 Pt/POPTR_000 
                  34% 
                  78-139 
                 KRSSNKDRHTKVEG 
                 591 
                  74% 
               
               
                   
                 1s33470.1 
                 (115/332) 
                   
                 RGRRIRMPALCAARI 
                   
                 (46/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQQAEPSIIA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGT 
                   
                   
               
               
                   
               
               
                  98 
                 Gm/Glyma19g2 
                  34% 
                  68-129 
                 KRSSNKDRHTKVEG 
                 594 
                  74% 
               
               
                   
                 6560.1 
                 (100/290) 
                   
                 RGRRIRMPALCAARI 
                   
                 (46/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQQAEPSIIA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGT 
                   
                   
               
               
                   
               
               
                 100 
                 Cc/clementine0. 
                  38% 
                 30-91 
                 KRSSNKDRHKKVDG 
                 595 
                  73% 
               
               
                   
                 9_018374m 
                  (95/245) 
                   
                 RGRRIRMPALCAARI 
                   
                 (45/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQQAEPSIIA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGT 
                   
                   
               
               
                   
               
               
                 104 
                 Pt/POPTR_000 
                  35% 
                  60-121 
                 KRSSNKDRHKKVEG 
                 597 
                  72% 
               
               
                   
                 3s16630.1 
                  (99/280) 
                   
                 RGRRIRIPALCAARIF 
                   
                 (45/62) 
               
               
                   
                   
                   
                   
                 QLTRELEHKSDGETI 
                   
                   
               
               
                   
                   
                   
                   
                 QWLLQQAEPSIIAAT 
                   
                   
               
               
                   
                   
                   
                   
                 GT 
                   
                   
               
               
                   
               
               
                  72 
                 Bd/Bradi2g592 
                  39% 
                  84-145 
                 KRSSNKDRHTKVDG 
                 581 
                  70% 
               
               
                   
                 40.1 
                  (86/220) 
                   
                 RGRRIRMPALCAARI 
                   
                 (44/62)) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TVQWLLQQAEPAIV 
                   
                   
               
               
                   
                   
                   
                   
                 AATGS 
                   
                   
               
               
                   
               
               
                  74 
                 Os/LOC_Os01g 
                  39% 
                  83-144 
                 KRSSNKDRHTKVDG 
                 582 
                  70% 
               
               
                   
                 69980.1 
                  (76/194) 
                   
                 RGRRIRMPALCAARI 
                   
                 (44/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TVQWLLQQAEPAIV 
                   
                   
               
               
                   
                   
                   
                   
                 AATGT 
                   
                   
               
               
                   
               
               
                  78 
                 Zm/GRMZM2 
                  38% 
                  98-159 
                 KRSSNKDRHTKVDG 
                 584 
                  70% 
               
               
                   
                 G092214_T01 
                  (85/218) 
                   
                 RGRRIRMPALCAARI 
                   
                 (44/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TVQWLLQQAEPAIV 
                   
                   
               
               
                   
                   
                   
                   
                 AATGT 
                   
                   
               
               
                   
               
               
                  80 
                 Zm/GRMZM2 
                  38% 
                  98-159 
                 KRSSNKDRHTKVDG 
                 585 
                  70% 
               
               
                   
                 G092214_T02 
                  (85/218) 
                   
                 RGRRIRMPALCAARI 
                   
                 (44/62)) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TVQWLLQQAEPAIV 
                   
                   
               
               
                   
                   
                   
                   
                 AATGT 
                   
                   
               
               
                   
               
               
                  76 
                 Zm/GRMZM2 
                  37% 
                  88-149 
                 KRSSNKDRHTKVDG 
                 583 
                  70% 
               
               
                   
                 G034638_T01 
                  (82/216) 
                   
                 RGRRIRMPALCAARI 
                   
                 (44/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TVQWLLQQAEPAIV 
                   
                   
               
               
                   
                   
                   
                   
                 AATGT 
                   
                   
               
               
                   
               
               
                 102 
                 Pt/POPTR_000 
                  36% 
                  60-121 
                 KRSSNKDRHKKVDG 
                 596 
                  70% 
               
               
                   
                 1s13500.1 
                  (85/236) 
                   
                 RGRRIRMPALCAARI 
                   
                 (44/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGNKSDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQQAEPSIIA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGT 
                   
                   
               
               
                   
               
               
                  82 
                 Eg/Eucgr.B035 
                  36% 
                  40-101 
                 KRSSNKDRHKKVDG 
                 586 
                  70% 
               
               
                   
                 29.1 
                 (105/286) 
                   
                 RGRRIRMPALCAARI 
                   
                 (44/62) 
               
               
                   
                   
                   
                   
                 FQLTRELGHKTDGE 
                   
                   
               
               
                   
                   
                   
                   
                 TIQWLLQQAEPSIVA 
                   
                   
               
               
                   
                   
                   
                   
                 ATGT 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related TCP6 clade polypeptides may be identified by a consensus TCP domain sequence, SEQ ID NO: 847: 
                            KX 2 X 3 X 4 NKDRHX 10 KVX 13 GRGRRX 19 RX 21 PX 23 LCAARIX 30 QLTX 34             ELX 37 X 38 KX 40 DGETX 45 X 46 WLLQX 51 AEPX 55 IX 57 X 58 ATX 61 X 62              
where X 2 =K or R; X 3 =any amino acid; X 4 =S or P; X 10 =any amino acid; X 13 =D or E; X 19 =I, L, V or M; X 21 =I, L, V or M; X 23 =A or P; X 30 =F or Y; X 34 =K or R; X 37 =any amino acid; X 38 =H or N; X 40 =S or T; X 45 =I, L, V or M; X 46 =Q or E; X 51 =H, Q or K; X 55 =S or A; X 57 =I, L, V or M; X 58 =S or A; X 61 =any amino acid; and X 62 =any amino acid.
 
     PIL1 Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 8 
               
             
            
               
                   
               
               
                 Conserved ′bHLH domain′ of PIL1 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 bHLH 
               
               
                   
                   
                 Percent 
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                 Col. 1 
                   
                 identity of 
                 bHLH 
                   
                 SEQ ID 
                 Col. 5 to 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Col. 5 
                 NO: of 
                 bHLH 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 Conserved bHLH 
                 bHLH 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to PIL1 
                 coordinates 
                 domain 
                 domain 
                 PIL1 
               
               
                   
               
               
                 108 
                 At/PIL1 pr 
                 100% 
                 227-283 
                 RKRSTEVHKLYER 
                 599 
                 100% 
               
               
                   
                 AT2G46970.1 
                 (416/416) 
                   
                 KRRDEFNKKMRAL 
                   
                 (57/57) 
               
               
                   
                   
                   
                   
                 QDLLPNCYKDDKA 
                   
                   
               
               
                   
                   
                   
                   
                 SLLDEAIKYMRTLQ 
                   
                   
               
               
                   
                   
                   
                   
                 LQVQ 
                   
                   
               
               
                   
               
               
                 112 
                 Cc/clementine 
                  41% 
                 309-365 
                 KKRTPEVHKRYER 
                 601 
                  70% 
               
               
                   
                 0.9_007946m 
                 (96/231) 
                   
                 KRRDKINKKMRAL 
                   
                 (40/57) 
               
               
                   
                   
                   
                   
                 QELIPNCNKVDKAS 
                   
                   
               
               
                   
                   
                   
                   
                 VLEEAIDYLKTLQF 
                   
                   
               
               
                   
                   
                   
                   
                 QVM 
                   
                   
               
               
                   
               
               
                 116 
                 Pt/POPTR_00 
                  40% 
                 379-435 
                 RRRAIEIHNLSERK 
                 603 
                  70% 
               
               
                   
                 14s10700.1 
                 (104/254) 
                   
                 RRDRINKKMRALQ 
                   
                 (40/57) 
               
               
                   
                   
                   
                   
                 DLIPNSNKVDKAS 
                   
                   
               
               
                   
                   
                   
                   
                 MLGEAIDYLKSLQL 
                   
                   
               
               
                   
                   
                   
                   
                 QVQ 
                   
                   
               
               
                   
               
               
                 114 
                 Gm/Glyma10g 
                  39% 
                 187-243 
                 RSRNAEVHNLCER 
                 602 
                  63% 
               
               
                   
                 27910.1 
                 (104/262) 
                   
                 KRRDKINKRMRILK 
                   
                 (36/57) 
               
               
                   
                   
                   
                   
                 ELIPNCNKTDKASM 
                   
                   
               
               
                   
                   
                   
                   
                 LDDAIEYLKTLKLQ 
                   
                   
               
               
                   
                   
                   
                   
                 LQ 
                   
                   
               
               
                   
               
               
                 110 
                 At/AT3G6209 
                  43% 
                 186-242 
                 RKRNAEAYNSPER 
                 600 
                  61% 
               
               
                   
                 0.2 
                 (173/399) 
                   
                 NQRNDINKKMRTL 
                   
                 (35/57) 
               
               
                   
                   
                   
                   
                 QNLLPNSHKDDNE 
                   
                   
               
               
                   
                   
                   
                   
                 SMLDEAINYMTNL 
                   
                   
               
               
                   
                   
                   
                   
                 QLQVQ 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related PIL1 clade polypeptides may be identified by a consensus bHLH domain sequence, SEQ ID NO: 848: 
                            X 1 X 2 RX 4 X 5 EX 7 X 8 X 9 X 10 X 11 ERX 14 X 15 RX 17 X 18 X 19 NRX 22 MRX 25 LX 27             X 28 LX 30 PNX 33 X 34 RX 36 DX 38 X 39 SX 41 LX 43 X 44 AIX 47 YX 49 X 50 X 51             LX 53 X 54 QX 56 X 57              
where X 1 =R or K; X 2 =any amino acid; X 4 =any amino acid; X 5 =any amino acid; X 7 =any amino acid; X 8 =H or Y; X 9 =N or K; X 10 =any amino acid; X 11 =any amino acid; X 14 =N or K; X 15 =any amino acid; X 17 =D or N; X 18 =any amino acid; X 19 =F, I, L, V or M; X 22 =R or K; X 25 =any amino acid; X 27 =Q or K; X 28 =N, D or E; X 30 =I, L, V or M; X 33 =S or C; X 34 =any amino acid; X 36 =any amino acid; X 38 =N or K; X 39 =any amino acid; X 41 =I, L, V or M; X 43 =any amino acid; X 44 =D or E; X 47 =any amino acid; X 49 =I, L, V or M; X 50 =any amino acid; X 51 =any amino acid; X 53 =Q or K; X 54 =F, I, L, V or M; X 56 =I, L, V or M; and X 57 =any amino acid.
 
     PCL1 Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 9 
               
             
            
               
                   
               
               
                 Conserved ′SANT domain′ of PCL1 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 bHLH 
               
               
                   
                   
                 Percent 
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                 Col. 1 
                   
                 identity of 
                 SANT 
                   
                 SEQ ID 
                 Col. 5 to 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Col. 5 
                 NO: of 
                 SANT 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 Conserved SANT 
                 SANT 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to PCL1 
                 coordinates 
                 domain 
                 domain 
                 PCL1 
               
               
                   
               
               
                 126 
                 At/PCL1 or 
                 100% 
                 146-196 
                 RLVWTPQLHKRFVD 
                 608 
                 100% 
               
               
                   
                 AT3G46640.3 
                 (324/324) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 128 
                 At/ 
                  63% 
                 143-193 
                 RLVWTPQLHKRFVD 
                 609 
                 100% 
               
               
                   
                 AT5G59570.1 
                 (181/286) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 148 
                 Gm/Glyma11g1 
                  62% 
                 146-196 
                 RLVWTPQLHKRFVD 
                 619 
                 100% 
               
               
                   
                 4490.1 
                 (156/249) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 150 
                 Gm/Glyma11g1 
                  62% 
                 146-196 
                 RLVWTPQLHKRFVD 
                 620 
                 100% 
               
               
                   
                 4490.2 
                 (156/249) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 152 
                 Gm/Glyma12g0 
                  60% 
                 145-195 
                 RLVWTPQLHKRFVD 
                 621 
                 100% 
               
               
                   
                 6410.1 
                 (148/245) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 144 
                 S1/Solyc06g005 
                  59% 
                 148-198 
                 RLVWTPQLHKRFVD 
                 617 
                 100% 
               
               
                   
                 680.2.1 
                 (145/242) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 130 
                 Cc/clementine0. 
                  58% 
                 158-208 
                 RLVWTPQLHKRFVD 
                 610 
                 100% 
               
               
                   
                 9_013078m 
                 (146/251) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 132 
                 Cc/clementine0. 
                  58% 
                 158-208 
                 RLVWTPQLHKRFVD 
                 611 
                 100% 
               
               
                   
                 9_013095m 
                 (146/251) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 134 
                 Cc/clementine0. 
                  58% 
                 158-208 
                 RLVWTPQLHKRFVD 
                 612 
                 100% 
               
               
                   
                 9_013088m 
                 (146/251) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 136 
                 Eg/Eucgr.B023 
                  53% 
                 170-220 
                 RLVWTPQLHKRFVD 
                 613 
                 100% 
               
               
                   
                 13.1 
                 (150/281) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 124 
                 Si/Si002653m 
                  47% 
                 129-179 
                 RLVWTPQLHKRFVD 
                 607 
                 100% 
               
               
                   
                   
                 (137/291) 
                   
                 VVAHLGIKNAVPKTI 
                   
                 (51/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 142 
                 Pt/POPTR_000 
                  56% 
                 133-183 
                 RLVWTPQLHKRFVD 
                 616 
                  98% 
               
               
                   
                 9s03990.2 
                 (167/297) 
                   
                 VVSHLGIKNAVPKTI 
                   
                 (50/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 154 
                 Vv/GSVIVT01 
                  54% 
                 233-283 
                 RLVWTPQLHKRFVD 
                 622 
                  98% 
               
               
                   
                 024916001 
                 (160/291) 
                   
                 VVGHLGIKNAVPKTI 
                   
                 (50/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 140 
                 Pt/POPTR_000 
                  53% 
                 161-211 
                 RLVWTPQLHKRFVD 
                 615 
                  98% 
               
               
                   
                 9s03990.1 
                 (170/315) 
                   
                 VVSHLGIKNAVPKTI 
                   
                 (50/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 120 
                 Os/LOC_Os01g 
                  55% 
                 120-170 
                 RLVWTPQLHKRFVE 
                 605 
                  96% 
               
               
                   
                 74020.1 
                 (129/233) 
                   
                 VVAHLGMKNAVPK 
                   
                 (49/51) 
               
               
                   
                   
                   
                   
                 TIMQLMNVEGLTRE 
                   
                   
               
               
                   
                   
                   
                   
                 NVASHLQKYR 
                   
                   
               
               
                   
               
               
                 122 
                 Zm/GRMZM2 
                  51% 
                 118-168 
                 RLVWTPQLHKRFVD 
                 606 
                  96% 
               
               
                   
                 G067702_T01 
                 (118/229) 
                   
                 VVAHLGIKKAVPKTI 
                   
                 (49/51) 
               
               
                   
                   
                   
                   
                 MELMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 146 
                 Sl/Solyc06g076 
                  53% 
                 152-202 
                 RLVWTPQLHKRFIE 
                 618 
                  94% 
               
               
                   
                 350.2.1 
                 (129/241) 
                   
                 VVAHLGIKGAVPKTI 
                   
                 (48/51) 
               
               
                   
                   
                   
                   
                 MQLMNVEGLTREN 
                   
                   
               
               
                   
                   
                   
                   
                 VASHLQKYR 
                   
                   
               
               
                   
               
               
                 138 
                 Pt/POPTR_000 
                  50% 
                 118-168 
                 RLVWTPQLHKRFVD 
                 614 
                  94% 
               
               
                   
                 1s25040.1 
                 (155/310) 
                   
                 VVGHLGMKNAVPK 
                   
                 (48/51) 
               
               
                   
                   
                   
                   
                 TIMQWMNVEGLTRE 
                   
                   
               
               
                   
                   
                   
                   
                 NVASHLQKYR 
                   
                   
               
               
                   
               
               
                 118 
                 Bd/Bradi2g620 
                  47% 
                 116-166 
                 RMVWNPQLHKRFV 
                 604 
                  94% 
               
               
                   
                 67.1 
                 (142/301) 
                   
                 DVVAHLGIKSAVPK 
                   
                 (48/51) 
               
               
                   
                   
                   
                   
                 TIMQLMNVEGLTRE 
                   
                   
               
               
                   
                   
                   
                   
                 NVASHLQKYR 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related PCL1 clade polypeptides may be identified by a consensus SANT domain sequence, SEQ ID NO: 849: 
                    RX 2 VWX 5 PQLHKRFX 13 X 14 VVX 17 HLGX 21 KX 23 AVPKTIMX 31 X 32 MNVEGLTRE       NVASHLQKYR            
where X 2 =I, L, V, or M; X 5 =any amino acid; X 13 =I, L, V, or M; X 14 =D or E; X 17 =A, S or G; X 21 =I, L, V, or M; X 23 =any amino acid; X 31 =Q or E; and X 32 =any amino acid.
 
     GTL1 Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 10 
               
             
            
               
                   
               
               
                 Conserved ′Tribelix domain l′ of GTL1 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                   
                   
                   
                   
                 trihelix 
               
               
                   
                   
                 Col. 3 
                 Col. 4 
                   
                   
                 domain 1 
               
               
                   
                   
                 Percent 
                 Trihelix 
                   
                 Col. 6 
                 in Col. 5 
               
               
                 Col. 1 
                   
                 identity of 
                 domain 1 
                 Col. 5 
                 SEQ ID 
                 to first 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 in amino 
                 Conserved 
                 NO: of 
                 trihelix 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 acid 
                 trihelix 
                 trihelix 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to GTL1 
                 coordinates 
                 domain 1 
                 domain 1 
                 GTL1 
               
               
                   
               
               
                 168 
                 At/GTL1 or 
                 100% 
                  60-143 
                 GNRWPREETLALLRI 
                 629 
                 100% 
               
               
                   
                 AT1G33240.1 
                 (669/669) 
                   
                 RSDMDSTFRDATLK 
                   
                 (84/84) 
               
               
                   
                   
                   
                   
                 APLWEHVSRKLLEL 
                   
                   
               
               
                   
                   
                   
                   
                 GYKRSSKKCKEKFE 
                   
                   
               
               
                   
                   
                   
                   
                 NVQKYYKRTKETRG 
                   
                   
               
               
                   
                   
                   
                   
                 GRHDGKAYKFFSQ 
                   
                   
               
               
                   
               
               
                 156 
                 At/GTL1 or 
                 100% 
                  60-143 
                 GNRWPREETLALLRI 
                 623 
                 100% 
               
               
                   
                 G634 
                 (152/152) 
                   
                 RSDMDSTFRDATLK 
                   
                 (84/84) 
               
               
                   
                   
                   
                   
                 APLWEHVSRKLLEL 
                   
                   
               
               
                   
                   
                   
                   
                 GYKRSSKKCKEKFE 
                   
                   
               
               
                   
                   
                   
                   
                 NVQKYYKRTKETRG 
                   
                   
               
               
                   
                   
                   
                   
                 GRHDGKAYKFFSQ 
                   
                   
               
               
                   
               
               
                 158 
                 Bd/Bradi5g171 
                  72% 
                  85-168 
                 GNRWPREETLALIRI 
                 624 
                  82% 
               
               
                   
                 50.1 
                 (66/91) 
                   
                 RSEMDATFRDATLK 
                   
                 (69/84) 
               
               
                   
                   
                   
                   
                 GPLWEEVSRKLAEL 
                   
                   
               
               
                   
                   
                   
                   
                 GYKRNAKKCKEKFE 
                   
                   
               
               
                   
                   
                   
                   
                 NVHKYYKRTKEGRT 
                   
                   
               
               
                   
                   
                   
                   
                 GRQDGKSYRFFSE 
                   
                   
               
               
                   
               
               
                 166 
                 Pt/POPTR_000 
                  75% 
                 104-187 
                 GNRWPRQETLALLQ 
                 628 
                  80% 
               
               
                   
                 1s45870.1 
                 (70/93) 
                   
                 IRSEMDAAFRDATL 
                   
                 (68/84) 
               
               
                   
                   
                   
                   
                 KGPLWEDVSRKLAE 
                   
                   
               
               
                   
                   
                   
                   
                 MGYKRSAKKCKEK 
                   
                   
               
               
                   
                   
                   
                   
                 FENVHKYYKRTKEG 
                   
                   
               
               
                   
                   
                   
                   
                 RAGRQDGKSYRFFS 
                   
                   
               
               
                   
                   
                   
                   
                 Q 
                   
                   
               
               
                   
               
               
                 172 
                 Gm/Glyma20g3 
                  68% 
                  63-146 
                 GNRWPRQETLALLR 
                 631 
                  77% 
               
               
                   
                 0640.1 
                 (73/107) 
                   
                 IRSDMDVAFRDASV 
                   
                 (65/84) 
               
               
                   
                   
                   
                   
                 KGPLWEEVSRKMAE 
                   
                   
               
               
                   
                   
                   
                   
                 LGYHRSSKKCKEKF 
                   
                   
               
               
                   
                   
                   
                   
                 ENVYKYHKRTKEGR 
                   
                   
               
               
                   
                   
                   
                   
                 SGKQDGKTYRFFDQ 
                   
                   
               
               
                   
               
               
                 186 
                 Gm/Glyma20g3 
                  75% 
                  66-149 
                 GNRWPRQETLALLK 
                 638 
                  76% 
               
               
                   
                 0650.1 
                 (66/87) 
                   
                 IRSDMDAVFRDSSL 
                   
                 (64/84) 
               
               
                   
                   
                   
                   
                 KGPLWEEVARKLSE 
                   
                   
               
               
                   
                   
                   
                   
                 LGYHRSAKKCKEKF 
                   
                   
               
               
                   
                   
                   
                   
                 ENVYKYHKRTKESR 
                   
                   
               
               
                   
                   
                   
                   
                 SGKHEGKTYKFFDQ 
                   
                   
               
               
                   
               
               
                 162 
                 Bd/Bradi3g304 
                  52% 
                  86-169 
                 GNRWPRQETLVLLK 
                 626 
                  76% 
               
               
                   
                 57.1 
                 (143/275) 
                   
                 IRSDMDAAFRDATL 
                   
                 (64/84) 
               
               
                   
                   
                   
                   
                 KGPLWEEVSRKLAE 
                   
                   
               
               
                   
                   
                   
                   
                 EGYRRNAKKCKEKF 
                   
                   
               
               
                   
                   
                   
                   
                 ENVHKYYKRTKDSR 
                   
                   
               
               
                   
                   
                   
                   
                 AGRNDGKTYRFFQQ 
                   
                   
               
               
                   
               
               
                 164 
                 Si/Si034382m 
                  63% 
                  74-157 
                 GNRWPRQETLALLK 
                 627 
                  75% 
               
               
                   
                   
                 (74/116) 
                   
                 IRSEMDAAFREAAL 
                   
                 (63/84) 
               
               
                   
                   
                   
                   
                 KGPLWEQVSRKLEA 
                   
                   
               
               
                   
                   
                   
                   
                 MGYKRSAKKCREKF 
                   
                   
               
               
                   
                   
                   
                   
                 ENVDKYYKRTKDG 
                   
                   
               
               
                   
                   
                   
                   
                 RAGRGDGKAYRFFS 
                   
                   
               
               
                   
                   
                   
                   
                 E 
                   
                   
               
               
                   
               
               
                 160 
                 Zm/GRMZM2 
                  58% 
                  98-181 
                 GNRWPREETLALIRI 
                 625 
                  75% 
               
               
                   
                 G169580_T01 
                 (80/136) 
                   
                 RTEMDADFRNAPLK 
                   
                 (63/84) 
               
               
                   
                   
                   
                   
                 APLWEDVARKLAGL 
                   
                   
               
               
                   
                   
                   
                   
                 GYHRSAKKCKEKFE 
                   
                   
               
               
                   
                   
                   
                   
                 NVHKYYKRTKDAH 
                   
                   
               
               
                   
                   
                   
                   
                 AGRQDGKSYRFFSQ 
                   
                   
               
               
                   
               
               
                 188 
                 Pt/POPTR_000 
                  71% 
                  58-141 
                 ANRWPRQETLALLK 
                 639 
                  73% 
               
               
                   
                 2s06900.1 
                 (68/95) 
                   
                 IRSDMDAVFRDSGL 
                   
                 (62/84) 
               
               
                   
                   
                   
                   
                 KGPLWEEVSRKLAE 
                   
                   
               
               
                   
                   
                   
                   
                 LGYHRSAKKCKEKF 
                   
                   
               
               
                   
                   
                   
                   
                 ENVYKYHKRTKEGR 
                   
                   
               
               
                   
                   
                   
                   
                 TGKSEGKSYKFFDE 
                   
                   
               
               
                   
               
               
                 184 
                 Gm/Glyma16g2 
                  41% 
                  53-136 
                 GNRWPRQETLALLK 
                 763 
                  73% 
               
               
                   
                 8240.1 
                 (108/260) 
                   
                 IRSDMDTVFRDSSLK 
                   
                 (62/84) 
               
               
                   
                   
                   
                   
                 GPLWEEVSRKLAEL 
                   
                   
               
               
                   
                   
                   
                   
                 GYQRSAKKCKEKFE 
                   
                   
               
               
                   
                   
                   
                   
                 NVYKYNKRTKDNK 
                   
                   
               
               
                   
                   
                   
                   
                 SGKSHGKTYKFFDQ 
                   
                   
               
               
                   
               
               
                 190 
                 Pt/POPTR_000 
                  72% 
                  61-144 
                 ANRWPRQETLALLK 
                 640 
                  71% 
               
               
                   
                 5s21420.1 
                 (63/87) 
                   
                 IRSAMDAVFRDSSL 
                   
                 (60/84) 
               
               
                   
                   
                   
                   
                 KGPLWEEVSRKLAE 
                   
                   
               
               
                   
                   
                   
                   
                 LGYHRSAKKCKEKF 
                   
                   
               
               
                   
                   
                   
                   
                 ENLYKYHKRTKEGR 
                   
                   
               
               
                   
                   
                   
                   
                 TGKSEGKTYKFFDE 
                   
                   
               
               
                   
               
               
                 178 
                 Pt/POPTR_000 
                  70% 
                  40-123 
                 GNRWPKQETLALLK 
                 634 
                  71% 
               
               
                   
                 1s31660.1 
                 (64/91) 
                   
                 IRSDMDVAFKDSGL 
                   
                 (60/84) 
               
               
                   
                   
                   
                   
                 KAPLWEEVSKKLNE 
                   
                   
               
               
                   
                   
                   
                   
                 LGYNRSAKKCKEKF 
                   
                   
               
               
                   
                   
                   
                   
                 ENIYKYHRRTKEGR 
                   
                   
               
               
                   
                   
                   
                   
                 SGRPNGKTYRFEEQ 
                   
                   
               
               
                   
               
               
                 170 
                 Pt/POPTR_000 
                 44% 
                  64-147 
                 GSRWPRQETLALLKI 
                 630 
                  71% 
               
               
                   
                 5s21410.1 
                 (117/262) 
                   
                 RSGMDVAFRDASVK 
                   
                 (60/84) 
               
               
                   
                   
                   
                   
                 GPLWEEVSRKLAEL 
                   
                   
               
               
                   
                   
                   
                   
                 GYNRSGKKCKEKFE 
                   
                   
               
               
                   
                   
                   
                   
                 NVYKYHKRTKDGR 
                   
                   
               
               
                   
                   
                   
                   
                 TGKQEGKTYRFFDQ 
                   
                   
               
               
                   
               
               
                 176 
                 Sl/Solyc12g056 
                  40% 
                  70-153 
                 GNRWPRQETLALLK 
                 633 
                  70% 
               
               
                   
                 510.1.1 
                 (212/519) 
                   
                 IRSEMDVVFKDSSLK 
                   
                 (59/84) 
               
               
                   
                   
                   
                   
                 GPLWEEVSRKLAEL 
                   
                   
               
               
                   
                   
                   
                   
                 GYHRSAKKCKEKFE 
                   
                   
               
               
                   
                   
                   
                   
                 NVYKYHRRTKDGR 
                   
                   
               
               
                   
                   
                   
                   
                 ASKADGKTYRFFDQ 
                   
                   
               
               
                   
               
               
                 180 
                 Pt/POPTR_001 
                  69% 
                  40-123 
                 ANRWPKQETLALLE 
                 635 
                  69% 
               
               
                   
                 9s02650.1 
                 (64/92) 
                   
                 IRSDMDVAFRDSVV 
                   
                 (58/84) 
               
               
                   
                   
                   
                   
                 KAPLWEEVSRKLNE 
                   
                   
               
               
                   
                   
                   
                   
                 LGYNRSAKKCKEKF 
                   
                   
               
               
                   
                   
                   
                   
                 ENIYKYHRRTKGSQ 
                   
                   
               
               
                   
                   
                   
                   
                 SGRPNGKTYRFIAEQ 
                   
                   
               
               
                   
               
               
                 174 
                 Sl/Solyc04g071 
                  42% 
                  58-141 
                 GNRWPRQETIALLKI 
                 632 
                  69% 
               
               
                   
                 360.2.1 
                 (74/175) 
                   
                 RSEMDVIFRDSSLKG 
                   
                 (58/84) 
               
               
                   
                   
                   
                   
                 PLWEEVSRKMADLG 
                   
                   
               
               
                   
                   
                   
                   
                 FHRSSKKCKEKEEN 
                   
                   
               
               
                   
                   
                   
                   
                 VYKYHKRTKDGRA 
                   
                   
               
               
                   
                   
                   
                   
                 SKADGKNYRFFEQ 
                   
                   
               
               
                   
               
               
                 182 
                 Sl/Solyc11g005 
                  69% 
                  52-135 
                 GNRWPHEETLALLK 
                 636 
                  66% 
               
               
                   
                 380.1.1 
                 (64/92) 
                   
                 IRSEMDVAFRDSNL 
                   
                 (56/84) 
               
               
                   
                   
                   
                   
                 KSPLWDEISRKMAE 
                   
                   
               
               
                   
                   
                   
                   
                 LGYNRNAKKCREKF 
                   
                   
               
               
                   
                   
                   
                   
                 ENIYKYHKRTKDGR 
                   
                   
               
               
                   
                   
                   
                   
                 SGRQTGKNYRFFEQ 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 11 
               
             
            
               
                   
               
               
                 Conserved ′Tribelix domain 2′ of GTL1 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                   
                   
                   
                   
                 trihelix 
               
               
                   
                   
                 Col. 3 
                 Col. 4 
                   
                   
                 domain 2 
               
               
                   
                   
                 Percent 
                 Trihelix 
                   
                 Col. 6 
                 in Col. 5 
               
               
                 Col. 1 
                   
                 identity of 
                 domain 2 
                 Col. 5 
                 SEQ ID 
                 to second 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 in amino 
                 Conserved 
                 NO: of 
                 trihelix 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 acid 
                 trihelix 
                 trihelix 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to GTL1 
                 coordinates 
                 domain 2 
                 domain 2 
                 GTL1 
               
               
                   
               
               
                 168 
                 At/GTL1 or 
                 100% 
                 433-517 
                 SSRWPKAEILALINL 
                 647 
                 100% 
               
               
                   
                 AT1G33240.1 
                 (669/669) 
                   
                 RSGMEPRYQDNVPK 
                   
                 (85/85) 
               
               
                   
                   
                   
                   
                 GLLWEEISTSMKRM 
                   
                   
               
               
                   
                   
                   
                   
                 GYNRNAKRCKEKW 
                   
                   
               
               
                   
                   
                   
                   
                 ENINKYYKKVKESN 
                   
                   
               
               
                   
                   
                   
                   
                 KKRPQDAKTCPYFH 
                   
                   
               
               
                   
                   
                   
                   
                 R 
                   
                   
               
               
                   
               
               
                 156 
                 At/GTL1 or 
                 100% 
                 187-259 
                 SSRWPKAEILALINL 
                 641 
                  82% 
               
               
                   
                 G634 
                 (152/152) 
                   
                 RSGMEPRYQDNVPK 
                   
                 (70/85) 
               
               
                   
                   
                   
                   
                 GLLWEEISTSMKRM 
                   
                   
               
               
                   
                   
                   
                   
                 GYNRNAKRCKEKW 
                   
                   
               
               
                   
                   
                   
                   
                 ENINKYYKKVKESN 
                   
                   
               
               
                   
                   
                   
                   
                 NSN 
                   
                   
               
               
                   
               
               
                 166 
                 Pt/POPTR_000 
                  75% 
                 520-604 
                 SSRWPKPEVLALIKL 
                 646 
                  76% 
               
               
                   
                 1s45870.1 
                 (70/93) 
                   
                 RSGLETRYQEAGPK 
                   
                 (65/85) 
               
               
                   
                   
                   
                   
                 GPLWEEISAGMLRL 
                   
                   
               
               
                   
                   
                   
                   
                 GYKRSSKRCKEKWE 
                   
                   
               
               
                   
                   
                   
                   
                 NINKYFKKVKESNK 
                   
                   
               
               
                   
                   
                   
                   
                 KRFEDAKTCPYFHE 
                   
                   
               
               
                   
               
               
                 172 
                 Gm/Glyma20g3 
                  68% 
                 457-541 
                 SSRWPKVEVQALIK 
                 649 
                  76% 
               
               
                   
                 0640.1 
                 (73/107) 
                   
                 LRTSMDEKYQENGP 
                   
                 (65/85) 
               
               
                   
                   
                   
                   
                 KGPLWEEISASMKK 
                   
                   
               
               
                   
                   
                   
                   
                 LGYNRNAKRCKEK 
                   
                   
               
               
                   
                   
                   
                   
                 WENINKYFKKVKES 
                   
                   
               
               
                   
                   
                   
                   
                 NKRRPEDSKTCPYF 
                   
                   
               
               
                   
                   
                   
                   
                 HQ 
                   
                   
               
               
                   
               
               
                 174 
                 Sl/Solyc04g071 
                  42% 
                 459-543 
                 SSRWPKAEVEALIKL 
                 650 
                  76% 
               
               
                   
                 360.2.1 
                 (74/175) 
                   
                 RTNLDVKYQENGPK 
                   
                 (65/85) 
               
               
                   
                   
                   
                   
                 GPLWEEISSGMKKIG 
                   
                   
               
               
                   
                   
                   
                   
                 YNRNAKRCKEKWE 
                   
                   
               
               
                   
                   
                   
                   
                 NINKYFKKVKESNK 
                   
                   
               
               
                   
                   
                   
                   
                 KRPEDSKTCPYFHQ 
                   
                   
               
               
                   
               
               
                 158 
                 Bd/Bradi5g171 
                  72% 
                 496-580 
                 SSRWPKTEVHALIQL 
                 642 
                  75% 
               
               
                   
                 50.1 
                 (66/91) 
                   
                 RMDMDNRYQENGP 
                   
                 (64/85) 
               
               
                   
                   
                   
                   
                 KGPLWEEISSGMRR 
                   
                   
               
               
                   
                   
                   
                   
                 LGYNRNPKRCKEK 
                   
                   
               
               
                   
                   
                   
                   
                 WENINKYFKKVKES 
                   
                   
               
               
                   
                   
                   
                   
                 NKRRPEDSKTCPYF 
                   
                   
               
               
                   
                   
                   
                   
                 HQ 
                   
                   
               
               
                   
               
               
                 162 
                 Bd/Bradi3g304 
                  52% 
                 453-537 
                 SSRWPKAEVHALIQ 
                 644 
                  75% 
               
               
                   
                 57.1 
                 (143/275) 
                   
                 LRSNLDTRYQEAGP 
                   
                 (64/85) 
               
               
                   
                   
                   
                   
                 KGPLWEEISAGMRR 
                   
                   
               
               
                   
                   
                   
                   
                 MGYSRSSKRCKEK 
                   
                   
               
               
                   
                   
                   
                   
                 WENINKYFKKVKES 
                   
                   
               
               
                   
                   
                   
                   
                 NKKRPEDSKTCPYF 
                   
                   
               
               
                   
                   
                   
                   
                 HQ 
                   
                   
               
               
                   
               
               
                 176 
                 Sl/Solyc12g056 
                  40% 
                 455-539 
                 SSRWPKEEIEALISLR 
                 651 
                  75% 
               
               
                   
                 510.1.1 
                 (212/519) 
                   
                 TCLDLKYQENGPKG 
                   
                 (64/85) 
               
               
                   
                   
                   
                   
                 PLWEEISSGMRKIGY 
                   
                   
               
               
                   
                   
                   
                   
                 NRNAKRCKEKWENI 
                   
                   
               
               
                   
                   
                   
                   
                 NKYFKKVKESNKKR 
                   
                   
               
               
                   
                   
                   
                   
                 PEDSKTCPYFHQ 
                   
                   
               
               
                   
               
               
                 164 
                 Si/Si034382m 
                  63% 
                 458-542 
                 PSRWPKAEVHALIQ 
                 645 
                  74% 
               
               
                   
                   
                 (74/116) 
                   
                 LRTELEARYQDSGP 
                   
                 (63/85) 
               
               
                   
                   
                   
                   
                 KGPLWEDISAGMRR 
                   
                   
               
               
                   
                   
                   
                   
                 LGYNRSAKRCKEK 
                   
                   
               
               
                   
                   
                   
                   
                 WENINKYFKKVKES 
                   
                   
               
               
                   
                   
                   
                   
                 NKKRPEDSKTCPYY 
                   
                   
               
               
                   
                   
                   
                   
                 HQ 
                   
                   
               
               
                   
               
               
                 188 
                 Pt/POPTR_000 
                  71% 
                 405-489 
                 SSRWPKVEVQALIN 
                 657 
                  70% 
               
               
                   
                 2s06900.1 
                 (68/95) 
                   
                 LRANLDVKYQENG 
                   
                 (60/85) 
               
               
                   
                   
                   
                   
                 AKGPLWEDISAGMQ 
                   
                   
               
               
                   
                   
                   
                   
                 KLGYNRSAKRCKEK 
                   
                   
               
               
                   
                   
                   
                   
                 WENINKYFKKVKES 
                   
                   
               
               
                   
                   
                   
                   
                 NKKRPEDSKTCPYF 
                   
                   
               
               
                   
                   
                   
                   
                 DQ 
                   
                   
               
               
                   
               
               
                 182 
                 Sl/Solyc11g005 
                  69% 
                 363-448 
                 SSRWPKAEVEALIKL 
                 654 
                  70% 
               
               
                   
                 380.1.1 
                 (64/92) 
                   
                 RTNVDLQYQDNGSS 
                   
                 (61/86) 
               
               
                   
                   
                   
                   
                 KGPLWEDISCGMKK 
                   
                   
               
               
                   
                   
                   
                   
                 LGYDRNAKRCKEK 
                   
                   
               
               
                   
                   
                   
                   
                 WENINKYYRRVKES 
                   
                   
               
               
                   
                   
                   
                   
                 QKKRPEDSKTCPYF 
                   
                   
               
               
                   
                   
                   
                   
                 HQ 
                   
                   
               
               
                   
               
               
                 180 
                 Pt/POPTR_001 
                  69% 
                 331-415 
                 SSRWPKEEIESLIKIR 
                 653 
                  70% 
               
               
                   
                 9s02650.1 
                 (64/92) 
                   
                 TYLEFQYQENGPKG 
                   
                 (60/85) 
               
               
                   
                   
                   
                   
                 PLWEEISTSMKNLG 
                   
                   
               
               
                   
                   
                   
                   
                 YDRSAKRCKEKWE 
                   
                   
               
               
                   
                   
                   
                   
                 NMNKYFKRVKDSN 
                   
                   
               
               
                   
                   
                   
                   
                 KKRPGDSKTCPYFQ 
                   
                   
               
               
                   
                   
                   
                   
                 Q 
                   
                   
               
               
                   
               
               
                 170 
                 Pt/POPTR_000 
                  44% 
                 404-488 
                 PSRWPKVEVEALIRI 
                 648 
                  70% 
               
               
                   
                 5s21410.1 
                 (117/262) 
                   
                 RTNLDCKYQDNGPK 
                   
                 (60/85) 
               
               
                   
                   
                   
                   
                 GPLWEEISARMRKL 
                   
                   
               
               
                   
                   
                   
                   
                 GYNRNAKRCKEKW 
                   
                   
               
               
                   
                   
                   
                   
                 ENINKYFKKVKESK 
                   
                   
               
               
                   
                   
                   
                   
                 KKRPEDSKTCPYFQ 
                   
                   
               
               
                   
                   
                   
                   
                 Q 
                   
                   
               
               
                   
               
               
                 186 
                 Gm/Glyma20g3 
                  75% 
                 442-526 
                 SSRWPKTEVHALIRL 
                 656 
                  69% 
               
               
                   
                 0650.1 
                 (66/87) 
                   
                 RTSLEAKYQENGPK 
                   
                 (59/85) 
               
               
                   
                   
                   
                   
                 APFWEDISAGMLRL 
                   
                   
               
               
                   
                   
                   
                   
                 GYNRSAKRCKEKW 
                   
                   
               
               
                   
                   
                   
                   
                 ENINKYFKKVKESN 
                   
                   
               
               
                   
                   
                   
                   
                 KQRREDSKTCPYFH 
                   
                   
               
               
                   
                   
                   
                   
                 E 
                   
                   
               
               
                   
               
               
                 178 
                 Pt/POPTR_000 
                  70% 
                 337-421 
                 PSRWPKEEIEALIGL 
                 652 
                  69% 
               
               
                   
                 1s31660.1 
                 (64/91) 
                   
                 RTKLEFQYEENGPK 
                   
                 (59/85) 
               
               
                   
                   
                   
                   
                 GPLWEEISASMKKL 
                   
                   
               
               
                   
                   
                   
                   
                 GYDRSAKRCKEKW 
                   
                   
               
               
                   
                   
                   
                   
                 ENMNKYFKRVKESN 
                   
                   
               
               
                   
                   
                   
                   
                 KRRPGDSKTCPYFQ 
                   
                   
               
               
                   
                   
                   
                   
                 Q 
                   
                   
               
               
                   
               
               
                 160 
                 Zm/GRMZM2 
                  58% 
                 411-495 
                 SSRWPKEEVEALIQV 
                 643 
                  68% 
               
               
                   
                 G169580_T01 
                 (80/136) 
                   
                 RNEKDEQYHDAGG 
                   
                 (58/85) 
               
               
                   
                   
                   
                   
                 KGPLWEDIAAGMRR 
                   
                   
               
               
                   
                   
                   
                   
                 IGYNRSAKRCKEKW 
                   
                   
               
               
                   
                   
                   
                   
                 ENINKYYKKVKESN 
                   
                   
               
               
                   
                   
                   
                   
                 KRRPEDSKTCPYFH 
                   
                   
               
               
                   
                   
                   
                   
                 Q 
                   
                   
               
               
                   
               
               
                 190 
                 Pt/POPTR_000 
                  72% 
                 406-490 
                 SSRWPKVEVQALISL 
                 658 
                  67% 
               
               
                   
                 5s21420.1 
                 (63/87) 
                   
                 RADLDIKYQEHGAK 
                   
                 (57/85) 
               
               
                   
                   
                   
                   
                 GPLWEDISAGMQKL 
                   
                   
               
               
                   
                   
                   
                   
                 GYNRSAKRCKEKW 
                   
                   
               
               
                   
                   
                   
                   
                 ENINKYFKKVKESN 
                   
                   
               
               
                   
                   
                   
                   
                 RKRPGDSKTCPYFD 
                   
                   
               
               
                   
                   
                   
                   
                 Q 
                   
                   
               
               
                   
               
               
                 184 
                 Gm/Glyma16g2 
                  41% 
                 412-496 
                 SSRWPKAEVHALIRI 
                 655 
                  67% 
               
               
                   
                 8240.1 
                 (108/260) 
                   
                 RTSLETKYQENGPK 
                   
                 (57/85) 
               
               
                   
                   
                   
                   
                 APLWEDISIAMQRL 
                   
                   
               
               
                   
                   
                   
                   
                 GYNRSAKRCKEKW 
                   
                   
               
               
                   
                   
                   
                   
                 ENINKYFKRVRESSK 
                   
                   
               
               
                   
                   
                   
                   
                 ERREDSKTCPYFHE 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related GTL1 clade polypeptides may be identified by a consensus first Trihelix domain sequence (Trihelix 1), SEQ ID NO: 850: 
                    X 1 X 2 RWPX 6 X 7 ETX 10 X 11 LX 13 X 14 IRX 17 X 18 MDX 21 X 22 PX 24 X 25 X 26 X 27 X 28         RX 30 PLWX 34 X 35 X 36 X 37 X 38 RX 40 X 41 X 42 X 43 GX 45 X 46 RX 48 X 49 RRCX 53 EK       FENX 59 X 60 KYX 63 X 64 RTKX 68 X 69 X 70 X 71 X 72 X 73 X 74 X 75 GKX 78 YX 80 FFX 83 X 84              
where X 1 =A or G; X 2 =any amino acid; X 6 =any amino acid; X 7 =Q or E; X 10 =I, L, V or M; X 11 =any amino acid; X 13 =I, L, V or M; X 14 =any amino acid; X 17 =S or T; X 18 =any amino acid; X 21 =any amino acid; X 22 =any amino acid; X 24 =R or K; X 25 =N, D or E; X 26 =A or S; X 27 =any amino acid; X 28 =I, L, V or M; X 30 =A, S or G; X 34 =D or E; X 35 =any amino acid; X 36 =I, L, V or M; X 37 =A or S; X 38 =R or K; X 40 =I, L, V or M; X 41 =any amino acid; X 42 =any amino acid; X 43 =any amino acid; X 45 =F or Y; X 46 =H, Q, N, R or K; X 48 =any amino acid; X 49 =A, S or G; X 53 =K or R; X 59 =I, L, V or M; X 60 =any amino acid; X 63 =any amino acid; X 64 =K or R; X 68 =any amino acid; X 69 =any amino acid; X 70 =H, Q, K or, R; X 71 =any amino acid; X 72 =S or G; X 73 =R or K; X 74 =any amino acid; X 75 =any amino acid; X 78 =any amino acid; X 80 =R or K; X 83 =any amino acid; and X 84 =Q or E.
 
     These functionally-related and/or closely-related GTL1 clade polypeptides may also be identified by a consensus first Trihelix domain sequence (Trihelix 2), SEQ ID NO: 851: 
                    X 1 SRWPKX 7 EX 9 X 10 X 11 LIX 14 X 15 RX 17 X 18 X 19 X 20 X 21 X 22 YX 24 X 25 X 26 X 27 X 28                 X 29 KX 31 X 32 X 33 WEX 36 IX 38 X 39 X 40 MX 42 X 43 X 44 GYX 47 RX 49 X 50 KRCKEKWEN               X 60 NKYX 64 X 65 X 66 VX 68 X 69 SX 71 X 72 X 73 X 74 X 75 X 76 X 77 X 78 X 79 X 80 X 81 X 82 X 83                 X 84 X 85 X 86              
where X 1 =S or P; X 7 =any amino acid; X 9 =I, L, V or M; X 10 =any amino acid; X 11 =A or S; X 14 =any amino acid; X 15 =I, L, V or M; X 17 =any amino acid; X 18 =any amino acid; X 19 =any amino acid; X 20 =E or D; X 21 =any amino acid; X 22 =K, Q or R; X 24 =any amino acid; X 25 =E or D; X 26 =any amino acid; X 27 =any amino acid; X 28 =S or absent; X 29 =any amino acid; X 31 =A or G; X 32 =any amino acid; X 33 =F or L; X 36 =E or D; X 38 =A or S; X 39 =any amino acid; X 40 =any amino acid; X 42 =any amino acid; X 43 =N, K or R; X 44 =I, L, V or M; X 47 =any amino acid; X 49 =any amino acid; X 50 =A, S or P; X 60 =I, L, V or M; X 64 =F or Y; X 65 =K or R; X 66 =K or R; X 68 =K or R; X 69 =E or D; X 71 =any amino acid; X 72 =N, K or R; X 73 =any amino acid; X 74 =N or R; X 75 =any amino acid or absent; X 76 =any amino acid or absent; X 77 =D or absent; X 78 =S, A or absent; X 79 =K or absent; X 80 =T or absent; X 81 =C or absent; X 82 =P or absent; X 83 =Y or absent; X 84 =F, Y or absent; X 85 =H, Q, D or absent; X 86 =any amino acid or absent.
 
     DREB2H Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 12 
               
             
            
               
                   
               
               
                 Conserved ′AP2 domain′ of DREB2H and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 AP2 
               
               
                   
                   
                 Percent 
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                 Col. 1 
                   
                 identity of 
                 AP2 
                 Col. 5 
                 SEQ ID 
                 Col. 5 to 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Conserved 
                 NO: of 
                 AP2 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 AP2 
                 AP2 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to DREB2H 
                 coordinates 
                 domain 
                 domain 
                 DREB2H 
               
               
                   
               
               
                 218 
                 At/DREB2H or 
                 100% 
                  65-122 
                 CDYTGVRQRTWGK 
                 672 
                 100% 
               
               
                   
                 AT2G40350.1 
                 (157/157) 
                   
                 WVAEIREPGRGAKL 
                   
                 (58/58) 
               
               
                   
                   
                   
                   
                 WLGTFSSSYEAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEASKAIYGQSAR 
                   
                   
               
               
                   
                   
                   
                   
                 LNL 
                   
                   
               
               
                   
               
               
                 192 
                 At/G1755 
                 100% 
                  72-129 
                 CDYTGVRQRTWGK 
                 659 
                 100% 
               
               
                   
                   
                 (155/155) 
                   
                 WVAEIREPGRGAKL 
                   
                 (58/58) 
               
               
                   
                   
                   
                   
                 WLGTFSSSYEAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEASKAIYGQSAR 
                   
                   
               
               
                   
                   
                   
                   
                 LNL 
                   
                   
               
               
                   
               
               
                 216 
                 At/AT2G40340.1 
                  86% 
                  70-127 
                 CDYRGVRQRRWGK 
                 671 
                  89% 
               
               
                   
                   
                 (108/125) 
                   
                 WVAEIREPDGGARL 
                   
                 (52/58) 
               
               
                   
                   
                   
                   
                 WLGTFSSSYEAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAAKAIYGQSAR 
                   
                   
               
               
                   
                   
                   
                   
                 LNL 
                   
                   
               
               
                   
               
               
                 232 
                 Sl/Solyc05g052 
                  65% 
                  72-129 
                 CKYRGVRQRTWGK 
                 679 
                  75% 
               
               
                   
                 410.1.1 
                 (82/125) 
                   
                 WVAEIREPHRGRRL 
                   
                 (44/58) 
               
               
                   
                   
                   
                   
                 WLGTFDTAIEAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAARAMYGPCA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNL 
                   
                   
               
               
                   
               
               
                 230 
                 Pt/POPTR_001 
                  65% 
                  78-135 
                 CNYRGVRQRTWGK 
                 678 
                  75% 
               
               
                   
                 0s19100.1 
                 (79/121) 
                   
                 WVAEIREPNRGPRL 
                   
                 (44/58) 
               
               
                   
                   
                   
                   
                 WLGTFPTAYEAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAARAMYGPYA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNV 
                   
                   
               
               
                   
               
               
                 226 
                 Gm/Glyma14g0 
                  64% 
                  78-135 
                 CNYRGVRQRTWGK 
                 676 
                  75% 
               
               
                   
                 6080.1 
                 (80/125) 
                   
                 WVGEIREPNRGSRL 
                   
                 (44/58) 
               
               
                   
                   
                   
                   
                 WLGTFSSAQEAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAARAMYGPCA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNF 
                   
                   
               
               
                   
               
               
                 224 
                 Gm/Glyma02g4 
                  62% 
                  78-135 
                 CNYRGVRQRTWGK 
                 675 
                  75% 
               
               
                   
                 2960.1 
                 (79/127) 
                   
                 WVGEIREPNRGSRL 
                   
                 (44/58) 
               
               
                   
                   
                   
                   
                 WLGTFSSAQEAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAARAMYGPCA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNF 
                   
                   
               
               
                   
               
               
                 228 
                 Pt/POPTR_000 
                  65% 
                  78-135 
                 CNYRGVRQRTWGK 
                 677 
                  74% 
               
               
                   
                 8s07360.1 
                 (79/121) 
                   
                 WVAEIREPNRGPRL 
                   
                 (43/58) 
               
               
                   
                   
                   
                   
                 WLGTFPTAYEAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDNAARAMYGSCA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNI 
                   
                   
               
               
                   
               
               
                 234 
                 Sl/Solyc06g050 
                   63% 
                  80-137 
                 CKYRGVRQRIWGK 
                 680 
                  72% 
               
               
                   
                 520.1.1 
                 (79/125) 
                   
                 WVAEIREPKRGSRL 
                   
                 (42/58) 
               
               
                   
                   
                   
                   
                 WLGTFGTAIEAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDDAARAMYGPCA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNL 
                   
                   
               
               
                   
               
               
                 214 
                 Gm/Glyma13g3 
                 61% 
                  63-120 
                 CNYRGVRQRTWGK 
                 670 
                  72% 
               
               
                   
                 8030.1 
                 (76/123) 
                   
                 WVAEIREPNRGNRL 
                   
                 (42/58) 
               
               
                   
                   
                   
                   
                 WLGTFPTAIGAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAARAMYGSCA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNF 
                   
                   
               
               
                   
               
               
                 208 
                 Gm/Glyma06g4 
                  61% 
                  65-122 
                 CNYRGVRQRTWGK 
                 667 
                  72% 
               
               
                   
                 5680.1 
                 (72/118) 
                   
                 WVAEIREPNRGSRL 
                   
                 (42/58) 
               
               
                   
                   
                   
                   
                 WLGTFPTAISAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAARAMYGSCA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNF 
                   
                   
               
               
                   
               
               
                 212 
                 Gm/Glyma12g3 
                  60% 
                  63-120 
                 CNYRGVRQRTWGK 
                 669 
                  72% 
               
               
                   
                 2400.1 
                 (75/123) 
                   
                 WVAEIREPNRGNRL 
                   
                 (42/58) 
               
               
                   
                   
                   
                   
                 WLGTFPTAIGAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAARAMYGSCA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNF 
                   
                   
               
               
                   
               
               
                 210 
                 Gm/Glyma12g1 
                  60% 
                  65-122 
                 CNYRGVRQRTWGK 
                 668 
                  72% 
               
               
                   
                 1150.1 
                 (72/119) 
                   
                 WVAEIREPNRGSRL 
                   
                 (42/58) 
               
               
                   
                   
                   
                   
                 WLGTFPTAISAALA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAAMAMYGFCA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNF 
                   
                   
               
               
                   
               
               
                 206 
                 Eg/Eucgr.G030 
                  61% 
                  69-126 
                 FNYRGVRQRTWGK 
                 666 
                  70% 
               
               
                   
                 94.1 
                 (74/121) 
                   
                 WVAEIREPNRGSRL 
                   
                 (41/58) 
               
               
                   
                   
                   
                   
                 WLGTFPTAIEAAKA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAATAMYGPCA 
                   
                   
               
               
                   
                   
                   
                   
                 RLNF 
                   
                   
               
               
                   
               
               
                 198 
                 Si/Si002067m 
                  60% 
                 167-224 
                 CPYRGVRQRTWGK 
                 662 
                  70% 
               
               
                   
                   
                 (72/120) 
                   
                 WVAEIREPNRGKRL 
                   
                 (41/58) 
               
               
                   
                   
                   
                   
                 WLGSFPTAVEAAHA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAAKAMYGPKA 
                   
                   
               
               
                   
                   
                   
                   
                 RVNF 
                   
                   
               
               
                   
               
               
                 194 
                 Bd/Bradi2g040 
                  56% 
                  76-133 
                 CAYRGVRQRTWGK 
                 660 
                  68% 
               
               
                   
                 00.1 
                 (67/119) 
                   
                 WVAEIREPNRGKRL 
                   
                 (40/58) 
               
               
                   
                   
                   
                   
                 WLGSFPTAVEAAHA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAARAMYGAKA 
                   
                   
               
               
                   
                   
                   
                   
                 RVNF 
                   
                   
               
               
                   
               
               
                 196 
                 Os/LOC_Os01g 
                  55% 
                  81-138 
                 CAYRGVRQRTWGK 
                 661 
                  68% 
               
               
                   
                 07120.1 
                 (66/119) 
                   
                 WVAEIREPNRGRRL 
                   
                 (40/58) 
               
               
                   
                   
                   
                   
                 WLGSFPTALEAAHA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAARAMYGPTA 
                   
                   
               
               
                   
                   
                   
                   
                 RVNF 
                   
                   
               
               
                   
               
               
                 202 
                 Si/Si022619m 
                  58% 
                  83-140 
                 CGYRGVRQRTWGK 
                 664 
                  65% 
               
               
                   
                   
                 (73/125) 
                   
                 WVAEIREPNRANRL 
                   
                 (38/58) 
               
               
                   
                   
                   
                   
                 WLGTFPTAEDAARA 
                   
                   
               
               
                   
                   
                   
                   
                 YDQAARAMYGEVA 
                   
                   
               
               
                   
                   
                   
                   
                 RTNF 
                   
                   
               
               
                   
               
               
                 204 
                 Si/Si022621m 
                  58% 
                  82-139 
                 CGYRGVRQRTWGK 
                 665 
                  65% 
               
               
                   
                   
                 (73/125) 
                   
                 WVAEIREPNRANRL 
                   
                 (38/58) 
               
               
                   
                   
                   
                   
                 WLGTFPTAEDAARA 
                   
                   
               
               
                   
                   
                   
                   
                 YDQAARAMYGEVA 
                   
                   
               
               
                   
                   
                   
                   
                 RTNF 
                   
                   
               
               
                   
               
               
                 200 
                 Bd/Bradi2g299 
                  56% 
                 130-187 
                 CKFRGVRQRTWGK 
                 663 
                  65% 
               
               
                   
                 60.1 
                 (70/123) 
                   
                 WVAEIREPNRVSRL 
                   
                 (38/58) 
               
               
                   
                   
                   
                   
                 WLGTFPTAETAACA 
                   
                   
               
               
                   
                   
                   
                   
                 YDEAARAMYGPLA 
                   
                   
               
               
                   
                   
                   
                   
                 RTNF 
                   
                   
               
               
                   
               
               
                 220 
                 Gm/Glyma07g1 
                  57% 
                  65-129 
                 CKFRGVRQRIWGK 
                 673 
                  63% 
               
               
                   
                 9220.1 
                 (73/128) 
                   
                 WVAEIREPINGKLV 
                   
                 (41/65) 
               
               
                   
                   
                   
                   
                 GEKANRLWLGTFST 
                   
                   
               
               
                   
                   
                   
                   
                 ALEAALAYDEAAKA 
                   
                   
               
               
                   
                   
                   
                   
                 MYGPCARLNF 
                   
                   
               
               
                   
               
               
                 222 
                 Gm/Glyma18g4 
                  57% 
                  65-129 
                 CKFRGVRQRIWGK 
                 674 
                  63% 
               
               
                   
                 3750.1 
                 (73/127) 
                   
                 WVAEIREPINGKLV 
                   
                 (41/65) 
               
               
                   
                   
                   
                   
                 GEKANRLWLGTFST 
                   
                   
               
               
                   
                   
                   
                   
                 ALEAALAYDEAAKA 
                   
                   
               
               
                   
                   
                   
                   
                 LYGPCARLNF 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related DREB2H clade polypeptides may be identified by a consensus AP2 domain sequence, SEQ ID NO: 852: 
                    X 1 X 2 X 3 GVRQRX 9 WGKWVX 15 EIREPX 21 X 22 X 23 X 24 X 25 X 26 X 27 X 28 X 29 X 30 X 31         X 32 LWWX 37 FX 39 X 40 X 41 X 42 X 43 AAX 46 AYDX 50 AX 52 X 53 AX 55 YGX 58 X 59 AR       X 62 NX 64              
where X 1 =any amino acid; X 2 =F or Y; X 3 =any amino acid; X 9 =any amino acid; X 15 =A or G; X 21 =I or absent; X 22 =Nor absent; X 23 =G or absent; X 24 =K or absent; X 25 =L or absent; X 26 =V or absent; X 27 =G or absent; X 28 =any amino acid; X 29 =any amino acid; X 30 =any amino acid; X 31 =any amino acid; X 32 =R or K; X 37 =S or T; X 39 =any amino acid; X 40 =S or T; X 41 =A or S; X 42 =any amino acid; X 43 =any amino acid; X 46 =any amino acid; X 50 =Q, D, N or E; X 52 =A or S; X 53 =any amino acid; X 55 =I, L, V or M; X 58 =any amino acid; X 59 =any amino acid; X 62 =any amino acid; and X 64 =F, I, L, V or M
 
     ERF087 Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 13 
               
             
            
               
                   
               
               
                 Conserved ′AP2 domain′ of ERF087and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 AP2 
               
               
                   
                   
                 Percent 
                 Col. 4 
                   
                   
                 domain in 
               
               
                 Col. 1 
                   
                 identity of 
                 AP2 
                 Col. 5 
                 Col. 6 
                 Col. 5 to 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Conserved 
                 SEQ ID 
                 AP2 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 AP2 NO: of 
                 AP2 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to ERF087 
                 coordinates 
                 domain 
                 domain 
                 ERF087 
               
               
                   
               
               
                 246 
                 At/ERF087 or 
                 100% 
                 38-101 
                 KYVGVRRRPWGRY 
                 686 
                 100% 
               
               
                   
                 AT1G28160.1 
                 (245/245) 
                   
                 AAEIRNPTTKERYW 
                   
                 (64/64) 
               
               
                   
                   
                   
                   
                 LGTFDTAEEAALAY 
                   
                   
               
               
                   
                   
                   
                   
                 DRAARSIRGLTART 
                   
                   
               
               
                   
                   
                   
                   
                 NFVYSDMPR 
                   
                   
               
               
                   
               
               
                 254 
                 At/AT5G13910.1 
                  83% 
                 19-82 
                 RFLGVRRRPWGRYA 
                 690 
                  85% 
               
               
                   
                   
                 (64/77) 
                   
                 AEIRDPTTKERHWL 
                   
                 (55/64) 
               
               
                   
                   
                   
                   
                 GTFDTAEEAALAYD 
                   
                   
               
               
                   
                   
                   
                   
                 RAARSMRGTRARTN 
                   
                   
               
               
                   
                   
                   
                   
                 FVYSDMPP 
                   
                   
               
               
                   
               
               
                 248 
                 Eg/Eucgr.B035 
                  47% 
                 46-109 
                 RFLGVRRRPWGRYA 
                 687 
                  85% 
               
               
                   
                 65.1 
                 (104/221) 
                   
                 AEIRDPTTKERHWL 
                   
                 (55/64) 
               
               
                   
                   
                   
                   
                 GTFDTAEEAALAYD 
                   
                   
               
               
                   
                   
                   
                   
                 RAARSMRGAKART 
                   
                   
               
               
                   
                   
                   
                   
                 NFVYSDMPP 
                   
                   
               
               
                   
               
               
                 266 
                 Vv/GSVIVT01 
                  84% 
                 21-84 
                 RFLGVRRRPWGRYA 
                 696 
                  84% 
               
               
                   
                 032961001 
                 (65/77) 
                   
                 AEIRDPSTKERHWL 
                   
                 (54/64) 
               
               
                   
                   
                   
                   
                 GTFDTAEEAALAYD 
                   
                   
               
               
                   
                   
                   
                   
                 RAARSMRGSRARTN 
                   
                   
               
               
                   
                   
                   
                   
                 FVYSDMPP 
                   
                   
               
               
                   
               
               
                 256 
                 Pt/POPTR_000 
                  81% 
                 25-88 
                 RFLGVRRRPWGRYA 
                 691 
                  84% 
               
               
                   
                 is 15710.1 
                 (64/79) 
                   
                 AEIRDPSTKERHWL 
                   
                 (54/64) 
               
               
                   
                   
                   
                   
                 GTFDTAEEAALAYD 
                   
                   
               
               
                   
                   
                   
                   
                 RAARSMRGSRARTN 
                   
                   
               
               
                   
                   
                   
                   
                 FVYSDMPA 
                   
                   
               
               
                   
               
               
                 258 
                 Pt/POPTR_000 
                  81% 
                 25-88 
                 RFLGVRRRPWGRYA 
                 692 
                  84% 
               
               
                   
                 3s07540.1 
                 (64/79) 
                   
                 AEIRDPSTKERHWL 
                   
                 (54/64) 
               
               
                   
                   
                   
                   
                 GTFDTAEEAALAYD 
                   
                   
               
               
                   
                   
                   
                   
                 RAARSMRGPRARTN 
                   
                   
               
               
                   
                   
                   
                   
                 FVYSDMPA 
                   
                   
               
               
                   
               
               
                 252 
                 Pt/POPTR_000 
                  70% 
                 39-102 
                 RFLGVRRRPWGRYA 
                 689 
                  84% 
               
               
                   
                 3s15940.1 
                 (84/120) 
                   
                 AEIRDPSTKERHWL 
                   
                 (54/64) 
               
               
                   
                   
                   
                   
                 GTFDTAEEAALAYD 
                   
                   
               
               
                   
                   
                   
                   
                 RAARSMRGSKARTN 
                   
                   
               
               
                   
                   
                   
                   
                 FVYSDMPP 
                   
                   
               
               
                   
               
               
                 250 
                 Pt/POPTR_000 
                  45% 
                 37-100 
                 RFLGVRRRPWGRYA 
                 688 
                  84% 
               
               
                   
                 1s12820.1 
                 (109/240) 
                   
                 AEIRDPSTKERHWL 
                   
                 (54/64) 
               
               
                   
                   
                   
                   
                 GTFDTAEEAALAYD 
                   
                   
               
               
                   
                   
                   
                   
                 RAARSMRGSKARTN 
                   
                   
               
               
                   
                   
                   
                   
                 FVYSDMPP 
                   
                   
               
               
                   
               
               
                 262 
                 Gm/Glyma02g0 
                  72% 
                 31-94 
                 RYLGVRRRPWGRY 
                 694 
                  82% 
               
               
                   
                 7460.1 
                 (69/95) 
                   
                 AAEIRDPSTKERHW 
                   
                 (53/64) 
               
               
                   
                   
                   
                   
                 LGTFDTAEEAALAY 
                   
                   
               
               
                   
                   
                   
                   
                 DRAARSMRGSRART 
                   
                   
               
               
                   
                   
                   
                   
                 NFVYPDTPP 
                   
                   
               
               
                   
               
               
                 260 
                 Eg/Eucgr.I0157 
                  51% 
                 27-90 
                 RFLGVRRRPWGRYA 
                 693 
                  82% 
               
               
                   
                 6.1 
                 (81/157) 
                   
                 AEIRDPSTKERHWL 
                   
                 (53/64) 
               
               
                   
                   
                   
                   
                 GTFDTAEEAALAYD 
                   
                   
               
               
                   
                   
                   
                   
                 RAARSMRGSRARTN 
                   
                   
               
               
                   
                   
                   
                   
                 FVYSDLPA 
                   
                   
               
               
                   
               
               
                 238 
                 Os/LOC_Os02g 
                  75% 
                 39-102 
                 RYLGVRRRPWGRY 
                 682 
                  79% 
               
               
                   
                 32040.1 
                 (60/79) 
                   
                 AAEIRDPATKERHW 
                   
                 (51/64) 
               
               
                   
                   
                   
                   
                 LGTFDTAEEAAVAY 
                   
                   
               
               
                   
                   
                   
                   
                 DRAARTIRGAAART 
                   
                   
               
               
                   
                   
                   
                   
                 NFAYPDLPP 
                   
                   
               
               
                   
               
               
                 264 
                 Gm/Glyma16g2 
                  70% 
                 31-94 
                 RYLGVRRRPWGRY 
                 695 
                  79% 
               
               
                   
                 6460.1 
                 (67/95) 
                   
                 AAEIRDPSTKERHW 
                   
                 (51/64) 
               
               
                   
                   
                   
                   
                 LGTFDTAEEAALAY 
                   
                   
               
               
                   
                   
                   
                   
                 DKAARSMRGSRART 
                   
                   
               
               
                   
                   
                   
                   
                 NFIYPDTPP 
                   
                   
               
               
                   
               
               
                 240 
                 Os/LOC_Os04g 
                  69% 
                 51-114 
                 RYLGVRRRPWGRY 
                 683 
                  79% 
               
               
                   
                 32790.1 
                 (62/89) 
                   
                 AAEIRDPATKERHW 
                   
                 (51/64) 
               
               
                   
                   
                   
                   
                 LGTFDTAEEAAVAY 
                   
                   
               
               
                   
                   
                   
                   
                 DRAARSLRGARART 
                   
                   
               
               
                   
                   
                   
                   
                 NFAYPDLPP 
                   
                   
               
               
                   
               
               
                 242 
                 Zm/GRMZM2 
                  69% 
                 41-104 
                 RYLGVRRRPWGRY 
                 684 
                  79% 
               
               
                   
                 G023708_T01 
                 (62/89) 
                   
                 AAEIRDPATKERHW 
                   
                 (51/64) 
               
               
                   
                   
                   
                   
                 LGTFDTAEEAAVAY 
                   
                   
               
               
                   
                   
                   
                   
                 DRAARSLRGARART 
                   
                   
               
               
                   
                   
                   
                   
                 NFAYPDLPP 
                   
                   
               
               
                   
               
               
                 236 
                 Zm/GRMZM2 
                  64% 
                 73-136 
                 RYLGVRRRPWGRY 
                 681 
                  79% 
               
               
                   
                 G047999_T01 
                 (73/114) 
                   
                 AAEIRDPATKERHW 
                   
                 (51/64) 
               
               
                   
                   
                   
                   
                 LGTFDTAEEAAIAY 
                   
                   
               
               
                   
                   
                   
                   
                 DRAARNIRGANART 
                   
                   
               
               
                   
                   
                   
                   
                 NFAYPDLPP 
                   
                   
               
               
                   
               
               
                 244 
                 Zm/GRMZM2 
                  63% 
                 37-100 
                 RYLGVRRRPWGRY 
                 685 
                  79% 
               
               
                   
                 G079825_T01 
                 (73/115) 
                   
                 AAEIRDPATKERHW 
                   
                 (51/64) 
               
               
                   
                   
                   
                   
                 LGTFDTAEEAAVAY 
                   
                   
               
               
                   
                   
                   
                   
                 DRAARSLRGARART 
                   
                   
               
               
                   
                   
                   
                   
                 NFAYPDLPP 
                   
                   
               
               
                   
               
               
                 268 
                 Gm/Glyma16g0 
                  49% 
                 14-77 
                 RYLGVRRRPWGRY 
                 697 
                  78% 
               
               
                   
                 5070.1 
                 (74/150) 
                   
                 AAEIRDPSTKERHW 
                   
                 (50/64) 
               
               
                   
                   
                   
                   
                 LGTFDTADEAALAY 
                   
                   
               
               
                   
                   
                   
                   
                 DRAARAMRGSRAR 
                   
                   
               
               
                   
                   
                   
                   
                 TNFVYADTTP 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related ERF087 clade polypeptides may be identified by a consensus AP2 domain sequence, SEQ ID NO: 853: 
                    X 1 X 2 X 3 GVRRRPWGRYAAEIRX 19 PX 21 TKERX 26 WLGTFDTAX 35 EAAX 39 AY       DX 43 AARX 47 X 48 RGX 51 X 52 ARTNFX 58 YX 60 DX 62 X 63 X 64              
where X 1 =K or R; X 2 =F or Y; X 3 =I, L, V or M; X 19 =N or D; X 21 =A, S or T; X 26 =H or Y; X 35 =D or E; X 39 =I, L, V or M; X 43 =R or K; X 47 =any amino acid; X 48 =I, L, V or M; X 51 =any amino acid; X 52 =any amino acid; X 58 =any amino acid; X 60 =S, A or P; X 62 =any amino acid; X 63 =T or P; and X 64 =any amino acid.
 
     BBX18 Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 14 
               
             
            
               
                   
               
               
                 Conserved first ′BBX domain′ of BBX18 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                 Col. 3 
                 Col. 4 
                   
                   
                 first BBX 
               
               
                   
                   
                 Percent 
                 BBX 
                   
                 Col. 6 
                 domain in 
               
               
                 Col. 1 
                   
                 identity of 
                 domain 1 
                 Col. 5 
                 SEQ ID 
                 Col. 5 to 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 in amino 
                 Conserved 
                 NO: of 
                 first BBX 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 acid 
                 BBX 
                 BBX 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to BBX18 
                 coordinates 
                 domain 1 
                 domain 1 
                 BBX18 
               
               
                   
               
               
                 278 
                 At/BBX18 or 
                 100% 
                 5-42 
                 CDACESAAAIVFCA 
                 702 
                 100% 
               
               
                   
                 AT2G21320.1 
                 (172/172) 
                   
                 ADEAALCCSCDEKV 
                   
                 (38/38) 
               
               
                   
                   
                   
                   
                 HKCNKLASRH 
                   
                   
               
               
                   
               
               
                 290 
                 Pt/POPTR_000 
                  61% 
                 5-42 
                 CDACESAAAIVFCA 
                 708 
                  92% 
               
               
                   
                 7s13830.1 
                 (114/184) 
                   
                 ADEAALCLACDEKV 
                   
                 (35/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 284 
                 Gm/Glyma01g3 
                  60% 
                 5-42 
                 CDACESAAAIVFCA 
                 705 
                  92% 
               
               
                   
                 7370.1 
                 (111/183) 
                   
                 ADEAALCRACDEKV 
                   
                 (35/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 286 
                 Gm/Glyma11g0 
                  59% 
                 5-42 
                 CDACESAAAIVFCA 
                 706 
                  92% 
               
               
                   
                 7930.1 
                 (112/189) 
                   
                 ADEAALCRACDEKV 
                   
                 (35/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 296 
                 Pt/POPTR_000 
                  60% 
                 5-42 
                 CDVCESAAAILFCA 
                 711 
                  89% 
               
               
                   
                 4s16950.1 
                 (111/184) 
                   
                 ADEAALCRSCDEKV 
                   
                 (34/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 298 
                 Pt/POPTR_000 
                  60% 
                 5-42 
                 CDVCESAAAILFCA 
                 712 
                  89% 
               
               
                   
                 9s12730.1 
                 (111/184) 
                   
                 ADEAALCRSCDEKV 
                   
                 (34/38) 
               
               
                   
                   
                   
                   
                 HLCNKLASRH 
                   
                   
               
               
                   
               
               
                 300 
                 Vv/GSVIVT01 
                  59% 
                 5-42 
                 CDACESAAAILFCA 
                 713 
                  89% 
               
               
                   
                 024173001 
                 (117/198) 
                   
                 ADEAALCRACDEKV 
                   
                 (34/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 302 
                 Sl/Solyc01g110 
                  58% 
                 5-42 
                 CDVCESAAAILFCA 
                 714 
                  89% 
               
               
                   
                 370.2.1 
                 (114/196) 
                   
                 ADEAALCRSCDEKV 
                   
                 (34/38) 
               
               
                   
                   
                   
                   
                 HLCNKLASRH 
                   
                   
               
               
                   
               
               
                 280 
                 At/AT4G38960.1 
                  76% 
                 5-42 
                 CDACENAAAIIFCAA 
                 703 
                  86% 
               
               
                   
                   
                 (131/171) 
                   
                 DEAALCRPCDEKVH 
                   
                 (33/38) 
               
               
                   
                   
                   
                   
                 MCNKLASRH 
                   
                   
               
               
                   
               
               
                 288 
                 Pt/POPTR_000 
                  61% 
                 5-42 
                 CDACESAFAIVFCAA 
                 707 
                  86% 
               
               
                   
                 5s11900.1 
                 (114/184) 
                   
                 DEAALCLACDKKVH 
                   
                 (33/38) 
               
               
                   
                   
                   
                   
                 MCNKLASRH 
                   
                   
               
               
                   
               
               
                 292 
                 Vv/GSVIVT01 
                  60% 
                 5-42 
                 CDVCESAAAILFCA 
                 709 
                  86% 
               
               
                   
                 018818001 
                 (110/183) 
                   
                 ADEAALCRVCDEKV 
                   
                 (33/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 282 
                 Eg/Eucgr.I0236 
                  57% 
                 5-42 
                 CDACESAAAVVFCA 
                 704 
                  86% 
               
               
                   
                 8.1 
                 (107/185) 
                   
                 ADEAALCSACDDKV 
                   
                 (33/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 306 
                 Gm/Glyma12g0 
                  63% 
                 5-42 
                 CDVCESAAAIVFCA 
                 716 
                  84% 
               
               
                   
                 4130.1 
                 (110/172) 
                   
                 ADEAALCSACDHKI 
                   
                 (32/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 294 
                 Eg/Eucgr.I0132 
                  57% 
                 5-42 
                 CDVCENAAAIFFCA 
                 710 
                  84% 
               
               
                   
                 8.1 
                 (111/193) 
                   
                 ADEAALCRACDEKV 
                   
                 (32/38) 
               
               
                   
                   
                   
                   
                 HLCNKLASRH 
                   
                   
               
               
                   
               
               
                 270 
                 Bd/Bradi4g359 
                  55% 
                 5-42 
                 CDVCESAVAVLFCA 
                 698 
                  84% 
               
               
                   
                 50.1 
                 (108/196) 
                   
                 ADEAALCRSCDEKV 
                   
                 (32/38) 
               
               
                   
                   
                   
                   
                 HLCNKLASRH 
                   
                   
               
               
                   
               
               
                 274 
                 Zm/GRMZM2 
                  57% 
                 5-42 
                 CDVCESAPAVLFCA 
                 700 
                  81% 
               
               
                   
                 G143718_T01 
                 (109/191) 
                   
                 ADEAALCRPCDEKV 
                   
                 (31/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 276 
                 Zm/GRMZM2 
                  57% 
                 5-42 
                 CDVCESAPAVLFCA 
                 701 
                  81% 
               
               
                   
                 G422644_T01 
                 (109/190) 
                   
                 ADEAALCRPCDEKV 
                   
                 (31/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 304 
                 Gm/Glyma11g1 
                  57% 
                 5-42 
                 CDVCESAAAILFCA 
                 715 
                  81% 
               
               
                   
                 1850.1 
                 (112/196) 
                   
                 ADEAALCSACDHKI 
                   
                 (31/38) 
               
               
                   
                   
                   
                   
                 HMCNKLASRH 
                   
                   
               
               
                   
               
               
                 272 
                 Os/LOC_Os09g 
                  57% 
                 5-42 
                 CDVCESAPAVLFCV 
                 699 
                  78% 
               
               
                   
                 35880.1 
                 (113/197) 
                   
                 ADEAALCRSCDEKV 
                   
                 (30/38) 
               
               
                   
                   
                   
                   
                 HMCNKLARRH 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 15 
               
             
            
               
                   
               
               
                 Conserved second ′BBX domain of BBX18 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                   
                   
                   
                   
                 second 
               
               
                   
                   
                   
                   
                   
                   
                 BBX 
               
               
                   
                   
                 Col. 3 
                 Col. 4 
                   
                   
                 domain in 
               
               
                   
                   
                 Percent 
                 BBX 
                   
                 Col. 6 
                 Col. 5 to 
               
               
                 Col. 1 
                   
                 identity of 
                 domain 2 
                   
                 SEQ ID 
                 second 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 in amino 
                 Col. 5 
                 NO: of 
                 BBX 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 acid 
                 Conserved BBX 
                 BBX 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to BBX18 
                 coordinates 
                 domain 2 
                 domain 2 
                 BBX18 
               
               
                   
               
               
                 278 
                 At/BBX18 or 
                 100% 
                 56-91 
                 CDICENAPAFFYCEI 
                 721 
                 100% 
               
               
                   
                 AT2G21320.1 
                 (172/172) 
                   
                 DGSSLCLQCDMVVH 
                   
                 (36/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 280 
                 At/AT4G38960.1 
                  76% 
                 56-91 
                 CDICENAPAFFYCEI 
                 722 
                 100% 
               
               
                   
                   
                 (131/171) 
                   
                 DGSSLCLQCDMVVH 
                   
                 (36/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 306 
                 Gm/Glyma12g0 
                  63% 
                 56-91 
                 CDICENAPAFFYCEI 
                 735 
                  97% 
               
               
                   
                 4130.1 
                 (110/172) 
                   
                 DGSSLCLQCDMIVH 
                   
                 (35/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 298 
                 Pt/POPTR_000 
                  60% 
                 56-91 
                 CDICENAPAFFYCEI 
                 731 
                  97% 
               
               
                   
                 9s12730.1 
                 (111/184) 
                   
                 DGSSLCLQCDMIVH 
                   
                 (35/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 302 
                 Sl/Solyc01g110 
                  58% 
                 56-91 
                 CDICENAPAFFYCEI 
                 733 
                  97% 
               
               
                   
                 370.2.1 
                 (114/196) 
                   
                 DGSSLCLQCDMIVH 
                   
                 (35/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 294 
                 Eg/Eucgr.I0132 
                  57% 
                 56-91 
                 CDICENAPAFFYCEI 
                 729 
                  97% 
               
               
                   
                 8.1 
                 (111/193) 
                   
                 DGSSLCLQCDMLVH 
                   
                 (35/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 304 
                 Gm/Glyma11g1 
                  57% 
                 56-91 
                 CDICENAPAFFYCEI 
                 734 
                  97% 
               
               
                   
                 1850.1 
                 (112/196) 
                   
                 DGSSLCLQCDMIVH 
                   
                 (35/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 288 
                 Pt/POPTR_000 
                  61% 
                 56-91 
                 CDICENAPAFFYCET 
                 726 
                  94% 
               
               
                   
                 5s11900.1 
                 (114/184) 
                   
                 DGSSLCLQCDMTVH 
                   
                 (34/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 290 
                 Pt/POPTR_000 
                  61% 
                 56-91 
                 CDICENAPAFFYCET 
                 727 
                  94% 
               
               
                   
                 7s13830.1 
                 (114/184) 
                   
                 DGSSLCLQCDMTVH 
                   
                 (34/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 296 
                 Pt/POPTR_000 
                  60% 
                 56-91 
                 CDICEKAPAFFYCEI 
                 730 
                  94% 
               
               
                   
                 4s16950.1 
                 (111/184) 
                   
                 DGSSLCLQCDMIVH 
                   
                 (34/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 284 
                 Gm/Glyma01g3 
                  60% 
                 56-91 
                 CDICENAPAFFYCET 
                 724 
                  94% 
               
               
                   
                 7370.1 
                 (111/183) 
                   
                 DGSSLCLQCDMIVH 
                   
                 (34/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 292 
                 Vv/GSVIVT01 
                  60% 
                 56-91 
                 CDICENAPAFFYCEI 
                 728 
                  94% 
               
               
                   
                 018818001 
                 (110/183) 
                   
                 DGTSLCLQCDMIVH 
                   
                 (34/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 286 
                 Gm/Glyma11g0 
                  59% 
                 56-91 
                 CDICENAPAFFYCET 
                 725 
                  94% 
               
               
                   
                 7930.1 
                 (112/189) 
                   
                 DGSSLCLQCDMIVH 
                   
                 (34/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 300 
                 Vv/GSVIVT01 
                  59% 
                 56-91 
                 CDICENAPAFFYCEV 
                 732 
                  91% 
               
               
                   
                 024173001 
                 (117/198) 
                   
                 DGTSLCLQCDMIVH 
                   
                 (33/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 272 
                 Os/LOC_Os09g 
                  57% 
                 56-91 
                 CDICENAPAFFYCEI 
                 718 
                  91% 
               
               
                   
                 35880.1 
                 (113/197) 
                   
                 DGTSLCLSCDMTVH 
                   
                 (33/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 282 
                 Eg/Eucgr.I0236 
                  57% 
                 56-91 
                 CDICENAPAFFYCEV 
                 723 
                  91% 
               
               
                   
                 8.1 
                 (107/185) 
                   
                 DGTSLCLQCDMIVH 
                   
                 (33/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 274 
                 Zm/GRMZM2 
                  57% 
                 56-91 
                 CDICENSPAFFYCEI 
                 719 
                  88% 
               
               
                   
                 G143718_T01 
                 (109/191) 
                   
                 DGTSLCLSCDMTVH 
                   
                 (32/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 276 
                 Zm/GRMZM2 
                  57% 
                 56-91 
                 CDICENSPAFFYCEI 
                 720 
                  88% 
               
               
                   
                 G422644_T01 
                 (109/190) 
                   
                 DGTSLCLSCDMTVH 
                   
                 (32/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
                   
                   
               
               
                   
               
               
                 270 
                 Bd/Bradi4g359 
                  55% 
                 56-91 
                 CDICENSPAFFYCDI 
                 717 
                  86% 
               
               
                   
                 50.1 
                 (108/196) 
                   
                 DGTSLCLSCDMAVH 
                   
                 (31/36) 
               
               
                   
                   
                   
                   
                 VGGKRTH 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related BBX18 clade polypeptides may be identified by a first consensus BBX domain sequence (BBX1), SEQ ID NO: 854: 
                    CDX 3 CEX 6 AX 8 AX 10 X 11 FCX 14 ADEAALCX 22 X 23 CDX 26 KX 28 HX 30 CNKLAX 36 RH            
where X 3 =any amino acid; X 6 =any amino acid; X 8 =any amino acid; X 10 =I, L, V or M; X 11 =F, I, L, V or M; X 14 =any amino acid; X 22 =any amino acid; X 23 =any amino acid; X 26 =any amino acid; X 28 =I, L, V or M; X 30 =any amino acid; and X 36 =any amino acid.
 
     These functionally-related and/or closely-related BBX18 clade polypeptides may also be identified by a second consensus BBX domain sequence (BBX2), SEQ ID NO: 855: 
                            CDICEX 6 X 7 PAFFYCX 14 X 15 DGX 18 SLCLX 23 CDMX 27 VHVGGKRTH            
X 6 =N or K; X 7 =S or A; X 14 =D or E; X 15 =T, I, L, V or M; X 18 =S or T; X 23 =I, L, V or M; and X 27 =I, L, V or M.
 
bHLH60 Clade Polypeptides
 
     
       
         
           
               
             
               
                 TABLE 16 
               
             
            
               
                   
               
               
                 Conserved ′bHLH domain′ of bHLH60 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 bHLH 
               
               
                   
                   
                 Percent 
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                 Col. 1 
                   
                 identity of 
                 bHLH 
                 Col. 5 
                 SEQ ID 
                 Col. 5 to 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Conserved 
                 NO: of 
                 bHLH 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 bHLH 
                 bHLH 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to bHLH60 
                 coordinates 
                 domain 
                 domain 
                 bHLH60 
               
               
                   
               
               
                 318 
                 At/bHLH60 or 
                 100% 
                 208-265 
                 RGQATDSHSLAER 
                 741 
                 100% 
               
               
                   
                 AT3G57800.2 
                 (379/379) 
                   
                 ARREKINARMKLL 
                   
                 (58/58) 
               
               
                   
                   
                   
                   
                 QELVPGCDKIQGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 316 
                 At/AT2G4230 
                  68% 
                 189-246 
                 RGQATDNHSLAER 
                 740 
                  96% 
               
               
                   
                 0.1 
                 (261/380) 
                   
                 ARREKINARMKLL 
                   
                 (56/58) 
               
               
                   
                   
                   
                   
                 QELVPGCDKIQGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDEIINHVQTLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 330 
                 Cc/clementine 
                  55% 
                 242-299 
                 RGQATDSHSLAER 
                 747 
                  96% 
               
               
                   
                 0.9_015567m 
                 (178/321) 
                   
                 ARREKINARMKLL 
                   
                 (56/58) 
               
               
                   
                   
                   
                   
                 QELVPGCNKISGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 322 
                 Gm/Glyma03g 
                  53% 
                 210-267 
                 RGQATDSHSLAER 
                 743 
                  96% 
               
               
                   
                 29710.1 
                 (190/352) 
                   
                 ARREKINARMKLL 
                   
                 (56/58) 
               
               
                   
                   
                   
                   
                 QELVPGCDKISGTA 
                   
                   
               
               
                   
                   
                   
                   
                 MVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 324 
                 Gm/Glyma19g 
                  52% 
                 204-261 
                 RGQATDSHSLAER 
                 744 
                  96% 
               
               
                   
                 32570.1 
                 (203/388) 
                   
                 ARREKINARMKLL 
                   
                 (56/58) 
               
               
                   
                   
                   
                   
                 QELVPGCDKISGTA 
                   
                   
               
               
                   
                   
                   
                   
                 MVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 328 
                 Cc/clementine 
                  51% 
                 242-299 
                 RGQATDSHSLAER 
                 746 
                  96% 
               
               
                   
                 0.9_011877m 
                 (214/418) 
                   
                 ARREKINARMKLL 
                   
                 (56/58) 
               
               
                   
                   
                   
                   
                 QELVPGCNKISGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 334 
                 Vv/GSVIVTO 
                  55% 
                 201-258 
                 RGQATDSHSLAER 
                 749 
                  94% 
               
               
                   
                 1033350001 
                 (218/396) 
                   
                 ARREKINARMKLL 
                   
                 (55/58) 
               
               
                   
                   
                   
                   
                 QELVPGCNKISGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDEIISHVQSLQR 
                   
                   
               
               
                   
                   
                   
                   
                 QVE 
                   
                   
               
               
                   
               
               
                 320 
                 Eg/Eucgr.A02 
                  52% 
                 185-242 
                 RGQATDSHSLAER 
                 742 
                  94% 
               
               
                   
                 413.1 
                 (179/338) 
                   
                 ARREKINARMKLL 
                   
                 (55/58) 
               
               
                   
                   
                   
                   
                 QELVPGCSKISGTA 
                   
                   
               
               
                   
                   
                   
                   
                 SVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 336 
                 Sl/Solyc10g07 
                  47% 
                 198-255 
                 RGQATDSHSLAER 
                 750 
                  94% 
               
               
                   
                 9070.1.1 
                 (163/342) 
                   
                 ARREKINARMKLL 
                   
                 (55/58) 
               
               
                   
                   
                   
                   
                 QELVPGCNKISGTA 
                   
                   
               
               
                   
                   
                   
                   
                 MVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 332 
                 Pt/POPTR_00 
                  53% 
                 181-238 
                 RGQATDSHSLAER 
                 748 
                  93% 
               
               
                   
                 06s05600.1 
                 (188/354) 
                   
                 ARREKINQRMKLL 
                   
                 (54/58) 
               
               
                   
                   
                   
                   
                 QELVPGCNKISGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 CQVE 
                   
                   
               
               
                   
               
               
                 326 
                 Gm/Glyma10g 
                  46% 
                 196-253 
                 RGQATDSHSLAER 
                 745 
                  91% 
               
               
                   
                 12210.1 
                 (179/386) 
                   
                 ARREKINARMKLL 
                   
                 (53/58) 
               
               
                   
                   
                   
                   
                 QELVPGCNKISGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDKIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 NEVE 
                   
                   
               
               
                   
               
               
                 310 
                 Zm/GRMZM2 
                  43% 
                 161-218 
                 RGQATDSHSLAER 
                 737 
                  91% 
               
               
                   
                 G074438_T01 
                 (134/309) 
                   
                 ARREKINARMELL 
                   
                 (53/58) 
               
               
                   
                   
                   
                   
                 KELVPGCSKVSGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 314 
                 Si/Si006781m 
                  43% 
                 177-234 
                 RGQATDSHSLAER 
                 739 
                  91% 
               
               
                   
                   
                 (132/307) 
                   
                 ARREKINARMELL 
                   
                 (53/58) 
               
               
                   
                   
                   
                   
                 KELVPGCSKVSGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 312 
                 Zm/GRMZM2 
                  43% 
                 184-241 
                 RGQATDSHSLAER 
                 738 
                  91% 
               
               
                   
                 G378653_T01 
                 (135/309) 
                   
                 ARREKINARMELL 
                   
                 (53/58) 
               
               
                   
                   
                   
                   
                 KELVPGCSKVSGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
                   
                   
               
               
                   
               
               
                 308 
                 Bd/Bradi1g35 
                  42% 
                 145-202 
                 RGQATDSHSLAER 
                 736 
                  91% 
               
               
                   
                 990.1 
                 (147/348) 
                   
                 ARREKINARMELL 
                   
                 (53/58) 
               
               
                   
                   
                   
                   
                 KELVPGCSKVSGTA 
                   
                   
               
               
                   
                   
                   
                   
                 LVLDEIINHVQSLQ 
                   
                   
               
               
                   
                   
                   
                   
                 RQVE 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related bHLH60 clade polypeptides may be identified by a consensus bHLH domain sequence, SEQ ID NO: 856: 
                    RGQATDX 7 HSLAERARREKINX 21 RMX 24 LLX 27 ELVPGCX 34 KX 36 X 37 GTAX 41         VLDX 45 IIX 48 HVQX 52 LQX 55 X 56 VE            
where X 7 =any amino acid; X 21 =any amino acid; X 24 =K or E; X 27 =Q or K; X 34 =any amino acid; X 36 =I, L, V or M; X 37 =any amino acid; X 41 =any amino acid; X 45 =K or E; X 48 =any amino acid; X 52 =S or T; X 55 =any amino acid; and X 56 =Q or E.
 
     NF-YC6 Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 17 
               
             
            
               
                   
               
               
                 Conserved ′NF-Y/histone-like domain′ of NF-YC6 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                   
                   
                   
                   
                 NF- 
               
               
                   
                   
                   
                   
                   
                   
                 Y/histone- 
               
               
                   
                   
                   
                   
                   
                   
                 like 
               
               
                   
                   
                   
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                   
                   
                 Col. 3 
                 NF- 
                   
                 SEQ ID 
                 Col. 5 to 
               
               
                   
                   
                 Percent 
                 Y/histone- 
                   
                 NO: of 
                 NF- 
               
               
                 Col. 1 
                   
                 identity of 
                 like domain 
                 Col. 5 
                 NF- 
                 Y/histone- 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 in amino 
                 Conserved NF- 
                 Y/histone- 
                 like 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 acid 
                 Y/histone-like 
                 like 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to NF-YC6 
                 coordinates 
                 domain 
                 domain 
                 NF-YC6 
               
               
                   
               
               
                 356 
                 At/NF-YC6 or 
                 100% 
                  53-117 
                 RQLPLARIKKIMKA 
                 760 
                 100% 
               
               
                   
                 AT5G50480.1 
                 (202/202) 
                   
                 DPDVHMVSAEAPII 
                   
                 (65/65) 
               
               
                   
                   
                   
                   
                 FAKACEMFIVDLT 
                   
                   
               
               
                   
                   
                   
                   
                 MRSWLKAEENKRH 
                   
                   
               
               
                   
                   
                   
                   
                 TLQKSDISNAV 
                   
                   
               
               
                   
               
               
                 348 
                 Si/Si015775m 
                  55% 
                  55-119 
                 HSLPLARIKKIMKA 
                 756 
                  67% 
               
               
                   
                   
                 (57/103) 
                   
                 DEDVKMIAAEAPV 
                   
                 (44/65) 
               
               
                   
                   
                   
                   
                 VFAKACEMFILELT 
                   
                   
               
               
                   
                   
                   
                   
                 LRSWLHTEGTKRR 
                   
                   
               
               
                   
                   
                   
                   
                 TMQRSDVSAAI 
                   
                   
               
               
                   
               
               
                 350 
                 At/AT5G2791 
                  54% 
                  35-99 
                 HDLPITRIKKIMKY 
                 757 
                  67% 
               
               
                   
                 0.1 
                 (92/168) 
                   
                 DPDVTMIASEAPIL 
                   
                 (44/65) 
               
               
                   
                   
                   
                   
                 LSKACEMFIMDLT 
                   
                   
               
               
                   
                   
                   
                   
                 MRSWLHAQESKRV 
                   
                   
               
               
                   
                   
                   
                   
                 TLQKSNVDAAV 
                   
                   
               
               
                   
               
               
                 338 
                 Bd/Bradi3g17 
                  52% 
                  77-141 
                 HSLPLARIKKIMKA 
                 751 
                  67% 
               
               
                   
                 790.1 
                 (55/105) 
                   
                 DEDVQMIAGEAPA 
                   
                 (44/65) 
               
               
                   
                   
                   
                   
                 VFAKACEMFILELT 
                   
                   
               
               
                   
                   
                   
                   
                 LRSWLQTRENNRN 
                   
                   
               
               
                   
                   
                   
                   
                 TLQKNDIATVV 
                   
                   
               
               
                   
               
               
                 346 
                 Os/LOC_Os08 
                  47% 
                 380-444 
                 PNLPLARIKKIMKA 
                 755 
                  63% 
               
               
                   
                 g10560.1 
                 (59/125) 
                   
                 DEDVKMIAGEAPA 
                   
                 (41/65) 
               
               
                   
                   
                   
                   
                 LFAKACEMFILDMT 
                   
                   
               
               
                   
                   
                   
                   
                 LRSWQHFLEGRRR 
                   
                   
               
               
                   
                   
                   
                   
                 TLQRSDVEAVI 
                   
                   
               
               
                   
               
               
                 340 
                 Bd/Bradi3g17 
                  48% 
                 240-305 
                 HSLPLARIKKIMKA 
                 752 
                  60% 
               
               
                   
                 800.1 
                 (56/116) 
                   
                 SGENVQMIAGEAH 
                   
                 (40/66) 
               
               
                   
                   
                   
                   
                 GLLAKACEIFIQELT 
                   
                   
               
               
                   
                   
                   
                   
                 LRSWLQTRENNRR 
                   
                   
               
               
                   
                   
                   
                   
                 TLQKNDIAAAV 
                   
                   
               
               
                   
               
               
                 344 
                 Bd/Bradi3g17 
                  51% 
                  99-164 
                 HSLPLARIKKIMKA 
                 754 
                  59% 
               
               
                   
                 810.1 
                 (51/100) 
                   
                 SGEDIRMIASEAPG 
                   
                 (39/66) 
               
               
                   
                   
                   
                   
                 LLAKASEIFIQELTL 
                   
                   
               
               
                   
                   
                   
                   
                 RSWLETRDNNRRT 
                   
                   
               
               
                   
                   
                   
                   
                 LQKNDIGAAV 
                   
                   
               
               
                   
               
               
                 352 
                 At/AT5G5049 
                  45% 
                  35-99 
                 HEFPISRIKRIMKED 
                 758 
                  58% 
               
               
                   
                 0.1 
                 (78/172) 
                   
                 PDVSMIAAEAPNLL 
                   
                 (38/65) 
               
               
                   
                   
                   
                   
                 SKACEMFVMDLTM 
                   
                   
               
               
                   
                   
                   
                   
                 RSWLHAQESNRLTI 
                   
                   
               
               
                   
                   
                   
                   
                 RKSDVDAVV 
                   
                   
               
               
                   
               
               
                 368 
                 Sl/Solyc03g11 
                  43% 
                  64-128 
                 HSLPISRIKKIMKSD 
                 766 
                  58% 
               
               
                   
                 1460.1.1 
                 (69/158) 
                   
                 KEVRMISAESPILLA 
                   
                 (38/65) 
               
               
                   
                   
                   
                   
                 KACELFIQELTHRS 
                   
                   
               
               
                   
                   
                   
                   
                 WLKAQECQRQTLK 
                   
                   
               
               
                   
                   
                   
                   
                 KIDLFTVL 
                   
                   
               
               
                   
               
               
                 342 
                 Bd/Bradi3g17 
                  52% 
                   7-72 
                 HSLPLERIKKIMKA 
                 753 
                  56% 
               
               
                   
                 820.1 
                 (45/85) 
                   
                 SGENVQVIAGEAPG 
                   
                 (37/66) 
               
               
                   
                   
                   
                   
                 VLTKACEIFIQELTL 
                   
                   
               
               
                   
                   
                   
                   
                 RSWLQTREKNRRT 
                   
                   
               
               
                   
                   
                   
                   
                 LQKNDIAAAV 
                   
                   
               
               
                   
               
               
                 370 
                 Sl/Solyc03g11 
                  48% 
                  74-138 
                 HSLPIFRIKKIMKSD 
                 767 
                  56% 
               
               
                   
                 1470.1.1 
                 (45/92) 
                   
                 KEVRMISAESPILLD 
                   
                 (37/65) 
               
               
                   
                   
                   
                   
                 KACELFIQELTHRS 
                   
                   
               
               
                   
                   
                   
                   
                 WLKAQECQRRTLK 
                   
                   
               
               
                   
                   
                   
                   
                 KIDFFTTE 
                   
                   
               
               
                   
               
               
                 354 
                 At/AT5G5047 
                  48% 
                  62-132 
                 HAFPLTRIKKIMKS 
                 759 
                  56% 
               
               
                   
                 0.1 
                 (92/189) 
                   
                 NPEVNMVTAEAPV 
                   
                 (40/71) 
               
               
                   
                   
                   
                   
                 LISKACEMLILDLT 
                   
                   
               
               
                   
                   
                   
                   
                 MRSWLHTVEGGRQ 
                   
                   
               
               
                   
                   
                   
                   
                 TLKRSDTLTRSDIS 
                   
                   
               
               
                   
                   
                   
                   
                 AAT 
                   
                   
               
               
                   
               
               
                 362 
                 Sl/Solyc03g11 
                  49% 
                  52-117 
                 RLLLPPTRIKKIMK 
                 763 
                  53% 
               
               
                   
                 0840.1.1 
                 (51/104) 
                   
                 KNEDVRMVAGESP 
                   
                 (35/66) 
               
               
                   
                   
                   
                   
                 VLLAKACELFIQDL 
                   
                   
               
               
                   
                   
                   
                   
                 TLRSSIHAQENHRRI 
                   
                   
               
               
                   
                   
                   
                   
                 LKKDDLTDVI 
                   
                   
               
               
                   
               
               
                 364 
                 Sl/Solyc03g11 
                  46% 
                  53-118 
                 NLLPRIHRIKKIMKT 
                 764 
                  53% 
               
               
                   
                 0850.1.1 
                 (54/116) 
                   
                 DKDVRMIATESPVL 
                   
                 (35/66) 
               
               
                   
                   
                   
                   
                 LAKACELFIQELTL 
                   
                   
               
               
                   
                   
                   
                   
                 RSWFKAEENHRRIL 
                   
                   
               
               
                   
                   
                   
                   
                 KKDDVTDVI 
                   
                   
               
               
                   
               
               
                 366 
                 Sl/Solyc11g01 
                  45% 
                  53-118 
                 NLLPSINRIKKIMKT 
                 765 
                  50% 
               
               
                   
                 6920.1.1 
                 (53/116) 
                   
                 DKDVRMIATESPVL 
                   
                 (33/66) 
               
               
                   
                   
                   
                   
                 LAKACELFIQELTL 
                   
                   
               
               
                   
                   
                   
                   
                 RSWFKTEKNHRRIL 
                   
                   
               
               
                   
                   
                   
                   
                 KKDDVTDVI 
                   
                   
               
               
                   
               
               
                 360 
                 Sl/Solyc02g02 
                  40% 
                  54-119 
                 NHLLPPNLIKKLMK 
                 762 
                  46% 
               
               
                   
                 1330.1.1 
                 (55/137) 
                   
                 TDEDDQMIAAESPV 
                   
                 (31/66) 
               
               
                   
                   
                   
                   
                 LLAKTCELFIQELTL 
                   
                   
               
               
                   
                   
                   
                   
                 RSWLNAQEKHQHI 
                   
                   
               
               
                   
                   
                   
                   
                 LKKDDVTDVI 
                   
                   
               
               
                   
               
               
                 358 
                 Sl/Solyc00g10 
                  42% 
                  55-120 
                 NLLVSPNRIKNIMK 
                 761 
                  45% 
               
               
                   
                 7050.1.1 
                 (40/94) 
                   
                 TNKDVRRITSESPV 
                   
                 (30/66) 
               
               
                   
                   
                   
                   
                 LLAKACDFFIQELT 
                   
                   
               
               
                   
                   
                   
                   
                 LRSWLNAQENHRR 
                   
                   
               
               
                   
                   
                   
                   
                 ILKKKDVTDVI 
                   
                   
               
               
                   
               
               
                 372 
                 Sl/Solyc03g11 
                  40% 
                 102-166 
                 HHFPISRIKRIIKSEN 
                 768 
                  44% 
               
               
                   
                 1450.1.1 
                 (69/171) 
                   
                 NAIKLSAETPILFSK 
                   
                 (29/65) 
               
               
                   
                   
                   
                   
                 ACELFVLELTLRSW 
                   
                   
               
               
                   
                   
                   
                   
                 FHAQQNNRGSLKK 
                   
                   
               
               
                   
                   
                   
                   
                 TDFAAAI 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related NF-YC6 clade polypeptides may be identified by a consensus NF-Y/histone-like domain sequence, SEQ ID NO: 857: 
                    X 1 X 2 X 3 X 4 X 5 X 6 X 7 X 8 IKX 11 X 12 X 13 KX 15 X 16 X 17 X 18 X 19 X 20 X 21 X 22 X 23 X 24 X 25                 EX 27 X 28 X 29 X 30 X 31 X 32 KX 34 X 35 X 36 X 37 X 38 X 39 X 40 X 41 X 42 TX 44 RSX 47 X 48 X 49                 X 50 X 51 X 52 X 53 X 54 X 55 X 56 X 57 X 58 X 59 X 60 X 61 X 62 X 63 X 64 X 65 X 66 X 67 X 68 X 69 X 70                 X 71 X 72 X 73              
where X 1 =any amino acid; X 2 =any amino acid; X 3 =F, I, L, V or M; X 4 =any amino acid or absent; X 5 =any amino acid; X 6 =any amino acid; X 7 =any amino acid; X 8 =any amino acid; X 11 =N, K or R; X 12 =I, L, V or M; X 13 =I, L, V or M; X 15 =any amino acid; X 16 =any amino acid; X 17 =G or absent; X 18 =any amino acid; X 19 =N, E or D; X 20 =any amino acid; X 21 =any amino acid; X 22 =any amino acid; X 23 =I, L, V or M; X 24 =S, A or T; X 25 =A, S, T or G; X 27 =A, S or T; X 28 =any amino acid; X 29 =any amino acid; X 30 =I, L, V or M; X 31 =F, I, L, V or M; X 32 =any amino acid; X 34 =any amino acid; X 35 =S or C; X 36 =E or D; X 37 =F, I, L, V or M; X 38 =I, L, V or M; X 39 =I, L, V or M; X 40 =any amino acid; X 41 =E or D; X 42 =I, L, V or M; X 44 =any amino acid; X 47 =any amino acid; X 48 =any amino acid; X 49 =any amino acid; X 50 =A or T; X 51 =any amino acid; X 52 =any amino acid; X 53 =any amino acid; X 54 =any amino acid; X 55 =Q, R; X 56 =any amino acid; X 57 =any amino acid; X 58 =I, L, V or M; X 59 =K, Q, R; X 60 =R or absent; X 61 =S or absent; X 62 =D or absent; X 63 =T or absent; X 64 =L or absent; X 65 =T or absent; X 66 =K, R; X 67 =any amino acid; X 68 =N, D; X 69 =F, I, L, V or M; X 70 =any amino acid; X 71 =any amino acid; X 72 =A, T, V; and X 73 =any amino acid.
 
bHLH121 Clade Polypeptides
 
     
       
         
           
               
             
               
                 TABLE 18 
               
             
            
               
                   
               
               
                 Conserved ′bHLH domain′ of bHLH121 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 bHLH 
               
               
                   
                   
                 Percent 
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                 Col. 1 
                   
                 identity of 
                 bHLH 
                 Col. 5 
                 SEQ ID 
                 Col. 5 to 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Conserved 
                 NO: of 
                 bHLH 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 bHLH 
                 bHLH 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to bHLH121 
                 coordinates 
                 domain 
                 domain 
                 bHLH121 
               
               
                   
               
               
                 388 
                 At/bHLH121 
                 100% 
                  6-60 
                 RKSQKAGREKLRR 
                 813 
                 100% 
               
               
                   
                 or 
                 (284/284) 
                   
                 EKLNEHFVELGNV 
                   
                 (55/55) 
               
               
                   
                 AT3G19860.1 
                   
                   
                 LDPERPKNDKATIL 
                   
                   
               
               
                   
                   
                   
                   
                 TDTVQLLKELTSEV 
                   
                   
               
               
                   
                   
                   
                   
                 N 
                   
                   
               
               
                   
               
               
                 390 
                 Cc/clementine 
                  64% 
                 60-114 
                 RKMQKADREKLRR 
                 814 
                  80% 
               
               
                   
                 0.9_014901m 
                 (185/288) 
                   
                 DRLNEHFFELGNAL 
                   
                 (44/55) 
               
               
                   
                   
                   
                   
                 DPDRPKNDKATILA 
                   
                   
               
               
                   
                   
                   
                   
                 DTVQLLKDLTSQV 
                   
                   
               
               
                   
                   
                   
                   
                 E 
                   
                   
               
               
                   
               
               
                 392 
                 Cc/clementine 
                  64% 
                 60-114 
                 RKMQKADREKLRR 
                 815 
                  80% 
               
               
                   
                 0.9_014926m 
                 (185/288) 
                   
                 DRLNEHFFELGNAL 
                   
                 (44/55) 
               
               
                   
                   
                   
                   
                 DPDRPKNDKATILA 
                   
                   
               
               
                   
                   
                   
                   
                 DTVQLLKDLTSQV 
                   
                   
               
               
                   
                   
                   
                   
                 E 
                   
                   
               
               
                   
               
               
                 400 
                 Pt/POPTR_00 
                  62% 
                 42-96 
                 RKIQKADREKLRR 
                 819 
                  80% 
               
               
                   
                 04s17540.1 
                 (156/249) 
                   
                 DRLNEHFVELGNTL 
                   
                 (44/55) 
               
               
                   
                   
                   
                   
                 DPDRPKNDKATILA 
                   
                   
               
               
                   
                   
                   
                   
                 DTIQLLKDLTSQVD 
                   
                   
               
               
                   
               
               
                 402 
                 Pt/POPTR_00 
                  61% 
                 38-92 
                 RKIQKADREKLRR 
                 820 
                  80% 
               
               
                   
                 09s13220.1 
                 (176/288) 
                   
                 DRLNEHFVELGNTL 
                   
                 (44/55) 
               
               
                   
                   
                   
                   
                 DPDRPKNDKATILA 
                   
                   
               
               
                   
                   
                   
                   
                 DTVQLLKDLNSKV 
                   
                   
               
               
                   
                   
                   
                   
                 D 
                   
                   
               
               
                   
               
               
                 386 
                 Vv/GSVIVTO 
                  56% 
                 50-104 
                 RKVQKADREKLRR 
                 812 
                  78% 
               
               
                   
                 1018777001 
                 (141/248) 
                   
                 DRLNEHFLELGNTL 
                   
                 (43/55) 
               
               
                   
                   
                   
                   
                 DPDRPKNDKATILA 
                   
                   
               
               
                   
                   
                   
                   
                 DTIQMLKDLTAEV 
                   
                   
               
               
                   
                   
                   
                   
                 N 
                   
                   
               
               
                   
               
               
                 382 
                 Gm/Glyma07g 
                  53% 
                 56-110 
                 RKVLKADREKLRR 
                 810 
                  78% 
               
               
                   
                 26910.1 
                 (123/232) 
                   
                 DRLNEHFQELGNA 
                   
                 (43/55) 
               
               
                   
                   
                   
                   
                 LDPDRPKNDKATIL 
                   
                   
               
               
                   
                   
                   
                   
                 TETVQMLKDLTAE 
                   
                   
               
               
                   
                   
                   
                   
                 VN 
                   
                   
               
               
                   
               
               
                 394 
                 Gm/Glyma08g 
                  65% 
                  7-61 
                 RKTQKADREKLRR 
                 816 
                 76% 
               
               
                   
                 15740.1 
                 (157/238) 
                   
                 DRLNEQFVELGNIL 
                   
                 (42/55) 
               
               
                   
                   
                   
                   
                 DPDRPKNDKATIIG 
                   
                   
               
               
                   
                   
                   
                   
                 DTIQLLKDLTSQVS 
                   
                   
               
               
                   
               
               
                 398 
                 Gm/Glyma12g 
                  57% 
                  7-61 
                 RKTQKADREKLRR 
                 818 
                   76% 
               
               
                   
                 02740.1 
                 (137/239) 
                   
                 DRFNVQFVELGNIL 
                   
                 (42/55) 
               
               
                   
                   
                   
                   
                 DPDRPKNDKATILG 
                   
                   
               
               
                   
                   
                   
                   
                 DTIQLLKDLTSEVS 
                   
                   
               
               
                   
               
               
                 396 
                 Gm/Glyma15g 
                  63% 
                 21-75 
                 RKTQKADREKLRR 
                 817 
                  74% 
               
               
                   
                 29630.1 
                 (151/238) 
                   
                 DRINEQFVELGNIL 
                   
                 (41/55) 
               
               
                   
                   
                   
                   
                 DPDRPKNDKATILC 
                   
                   
               
               
                   
                   
                   
                   
                 DTIQLLKDLISQVS 
                   
                   
               
               
                   
               
               
                 404 
                 Vv/GSVIVTO 
                  57% 
                 46-100 
                 RKVQKADREKLRR 
                 821 
                  74% 
               
               
                   
                 1024084001 
                 (166/288) 
                   
                 DRLNEQFIELGNAL 
                   
                 (41/55) 
               
               
                   
                   
                   
                   
                 DPDRPKNDKATILS 
                   
                   
               
               
                   
                   
                   
                   
                 DTIQLLKDLTAQVE 
                   
                   
               
               
                   
               
               
                 384 
                 Pt/POPTR_00 
                  51% 
                 61-115 
                 KKVQKADREKLRR 
                 811 
                  74% 
               
               
                   
                 05s11550.1 
                 (116/227) 
                   
                 DNLNEQFLELGTTL 
                   
                 (41/55) 
               
               
                   
                   
                   
                   
                 DPDRPKNDKATILT 
                   
                   
               
               
                   
                   
                   
                   
                 DTIQVLKDLTAEVN 
                   
                   
               
               
                   
               
               
                 378 
                 Si/Si017804m 
                  48% 
                 36-90 
                 RKVQKADREKMRR 
                 808 
                  74% 
               
               
                   
                   
                 (130/268) 
                   
                 DKLNEQFQELGNT 
                   
                 (41/55) 
               
               
                   
                   
                   
                   
                 LDPDRPRNDKATIL 
                   
                   
               
               
                   
                   
                   
                   
                 GDTIQMLKDLTSH 
                   
                   
               
               
                   
                   
                   
                   
                 VN 
                   
                   
               
               
                   
               
               
                 406 
                 Sl/Solyc01g11 
                  61% 
                 57-111 
                 RKVQKADREKLRR 
                 822 
                  70% 
               
               
                   
                 1130.2.1 
                 (151/247) 
                   
                 DRLNEQFMELGKT 
                   
                 (39/55) 
               
               
                   
                   
                   
                   
                 LDPDRPKNDKASIL 
                   
                   
               
               
                   
                   
                   
                   
                 SDTVQILKDLTAQV 
                   
                   
               
               
                   
                   
                   
                   
                 S 
                   
                   
               
               
                   
               
               
                 408 
                 Zm/GRMZM2 
                  50% 
                 30-84 
                 RKVQKADREKMRR 
                 823 
                  70% 
               
               
                   
                 G114444_T02 
                 (119/236) 
                   
                 DKLNEQFQDLGNA 
                   
                 (39/55) 
               
               
                   
                   
                   
                   
                 LDPDRPRNDKATIL 
                   
                   
               
               
                   
                   
                   
                   
                 GDTIQMLKDLTTQ 
                   
                   
               
               
                   
                   
                   
                   
                 VN 
                   
                   
               
               
                   
               
               
                 374 
                 Bd/Bradi3g11 
                  49% 
                 40-94 
                 RKVQKADRERMRR 
                 806 
                  69% 
               
               
                   
                 520.1 
                 (127/256) 
                   
                 DKLNEQFQELGTTL 
                   
                 (38/55) 
               
               
                   
                   
                   
                   
                 DPDRPRNDKATILG 
                   
                   
               
               
                   
                   
                   
                   
                 DTIQMLKDLSSQVN 
                   
                   
               
               
                   
               
               
                 376 
                 Os/LOC_Os02 
                  48% 
                 40-94 
                 RKVQKADREKMRR 
                 807 
                  69% 
               
               
                   
                 g23823.1 
                 (116/241) 
                   
                 DRLNEQFQELGSTL 
                   
                 (38/55) 
               
               
                   
                   
                   
                   
                 DPDRPRNDKATILS 
                   
                   
               
               
                   
                   
                   
                   
                 DAIQMLKDLTSQV 
                   
                   
               
               
                   
                   
                   
                   
                 N 
                   
                   
               
               
                   
               
               
                 380 
                 At/AT4G3606 
                  65% 
                 41-99 
                 KKEAVCSQKAERE 
                 809 
                  61% 
               
               
                   
                 0.1 
                 (68/104) 
                   
                 KLRRDKLKEQFLEL 
                   
                 (36/59) 
               
               
                   
                   
                   
                   
                 GNALDPNRPKSDK 
                   
                   
               
               
                   
                   
                   
                   
                 ASVLTDTIQMLKD 
                   
                   
               
               
                   
                   
                   
                   
                 VMNQVD 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 19 
               
             
            
               
                   
               
               
                 Conserved ′putative leucine zipper domain′ of bHLH121 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                   
                   
                   
                   
                 putative 
               
               
                   
                   
                   
                   
                   
                   
                 leucine 
               
               
                   
                   
                   
                   
                   
                   
                 zipper 
               
               
                   
                   
                   
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                   
                   
                 Col. 3 
                 Putative 
                   
                 SEQ ID 
                 Col. 5 to 
               
               
                   
                   
                 Percent 
                 leucine 
                 Col. 5 
                 NO: of 
                 putative 
               
               
                 Col. 1 
                   
                 identity of 
                 zipper 
                 Conserved 
                 putative 
                 leucine 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 putative 
                 leucine 
                 zipper 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 leucine zipper 
                 zipper 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to bHLH121 
                 coordinates 
                 domain 
                 domain 
                 bHLH121 
               
               
                   
               
               
                 388 
                 At1bHLH121 
                 100% 
                  61-97 
                 KLKSEYTALTDESR 
                 831 
                 100% 
               
               
                   
                 or 
                 (284/284) 
                   
                 ELTQEKNDLREEKT 
                   
                 (37/37) 
               
               
                   
                 AT3G19860.1 
                   
                   
                 SLKSDIENL 
                   
                   
               
               
                   
               
               
                 406 
                 Sl/Solyc01g11 
                  61% 
                 112-148 
                 RLKSEYAALTDESR 
                 840 
                  89% 
               
               
                   
                 1130.2.1 
                 (151/247) 
                   
                 ELTQEKNDLREEK 
                   
                 (33/37) 
               
               
                   
                   
                   
                   
                 ASLKSDIESL 
                   
                   
               
               
                   
               
               
                 394 
                 Gm/Glyma08g 
                  65% 
                  62-98 
                 KLKDEYATLNEESR 
                 834 
                  81% 
               
               
                   
                 15740.1 
                 (157/238) 
                   
                 ELTQEKNDLREEK 
                   
                 (30/37) 
               
               
                   
                   
                   
                   
                 ASLKSDIGNL 
                   
                   
               
               
                   
               
               
                 390 
                 Cc/clementine 
                  64% 
                 115-151 
                 KLKTEHAALTEESR 
                 832 
                  81% 
               
               
                   
                 0.9_014901m 
                 (185/288) 
                   
                 ELTQEKNDLREEKL 
                   
                 (30/37) 
               
               
                   
                   
                   
                   
                 SLRSEIENL 
                   
                   
               
               
                   
               
               
                 392 
                 Cc/clementine 
                  64% 
                 115-151 
                 KLKTEHAALTEESR 
                 833 
                  81% 
               
               
                   
                 0.9_014926m 
                 (185/288) 
                   
                 ELTQEKNDLREEKL 
                   
                 (30/37) 
               
               
                   
                   
                   
                   
                 SLRSEIENL 
                   
                   
               
               
                   
               
               
                 400 
                 Pt/POPTR_00 
                  62% 
                  97-133 
                 KLKAEYATLSEESL 
                 837 
                  81% 
               
               
                   
                 04s17540.1 
                 (156/249) 
                   
                 ELTQEKNDLREEK 
                   
                 (30/37) 
               
               
                   
                   
                   
                   
                 ASLKSDIENL 
                   
                   
               
               
                   
               
               
                 402 
                 Pt/POPTR_00 
                  61% 
                  93-129 
                 KLKAEHAALSEESR 
                 838 
                  78% 
               
               
                   
                 09s13220.1 
                 (176/288) 
                   
                 ELTLEKNDLREEKA 
                   
                 (29/37) 
               
               
                   
                   
                   
                   
                 SLKSDVENL 
                   
                   
               
               
                   
               
               
                 396 
                 Gm/Glyma15g 
                  63% 
                  6-112 
                 KLKDEYAMLNEES 
                 835 
                  75% 
               
               
                   
                 29630.1 
                 (151/238) 
                   
                 RELTLEKTDLREEK 
                   
                 (28/37) 
               
               
                   
                   
                   
                   
                 ASLKSDIDNL 
                   
                   
               
               
                   
               
               
                 404 
                 Vv/GSVIVTO 
                  57% 
                 101-137 
                 KLKAENASLNEESR 
                 839 
                  75% 
               
               
                   
                 1024084001 
                 (166/288) 
                   
                 ELTQEKNDLREEK 
                   
                 (28/37) 
               
               
                   
                   
                   
                   
                 ASLKSATENL 
                   
                   
               
               
                   
               
               
                 382 
                 Gm/Glyma07g 
                  53% 
                 111-147 
                 RLKTEHKTLSEESR 
                 828 
                  75% 
               
               
                   
                 26910.1 
                 (123/232) 
                   
                 ELMQEKNELREEK 
                   
                 (28/37) 
               
               
                   
                   
                   
                   
                 TSLKSDIENL 
                   
                   
               
               
                   
               
               
                 374 
                 Bd/Bradi3g11 
                  49% 
                  95-131 
                 KLKAEYSSLSEEER 
                 824 
                  72% 
               
               
                   
                 520.1 
                 (127/256) 
                   
                 ELTQEKNELRDEK 
                   
                 (27/37) 
               
               
                   
                   
                   
                   
                 ASLKSDIDNL 
                   
                   
               
               
                   
               
               
                 398 
                 Gm/Glyma12g 
                  57% 
                  62-98 
                 KLKDEYATLNEESC 
                 836 
                  70% 
               
               
                   
                 02740.1 
                 (137/239) 
                   
                 ELAQEKNELREEK 
                   
                 (26/37) 
               
               
                   
                   
                   
                   
                 ASLKSDILKL 
                   
                   
               
               
                   
               
               
                 386 
                 Vv/GSVIVTO 
                  56% 
                 105-141 
                 RLKVECAALSEESR 
                 830 
                  70% 
               
               
                   
                 1018777001 
                 (141/248) 
                   
                 ELVQEKNELREEK 
                   
                 (26/37) 
               
               
                   
                   
                   
                   
                 VALKSDIDNL 
                   
                   
               
               
                   
               
               
                 378 
                 Si/Si017804m 
                  48% 
                  91-127 
                 KLKAEYTSLSEEAR 
                 826 
                  70% 
               
               
                   
                   
                 (130/268) 
                   
                 ELTQEKNELRDEK 
                   
                 (26/37) 
               
               
                   
                   
                   
                   
                 ASLKSEVDNL 
                   
                   
               
               
                   
               
               
                 380 
                 At/AT4G3606 
                  65% 
                 100-136 
                 RLKAEYETLSQESR 
                 827 
                  67% 
               
               
                   
                 0.1 
                 (68/104) 
                   
                 ELIQEKSELREEKA 
                   
                 (25/37) 
               
               
                   
                   
                   
                   
                 TLKSDIEIL 
                   
                   
               
               
                   
               
               
                 408 
                 Zm/GRMZM2 
                  50% 
                  85-121 
                 KLKAEYTSLSEEAC 
                 841 
                  67% 
               
               
                   
                 G114444_T02 
                 (119/236) 
                   
                 ELTQEKNELRDEK 
                   
                 (25/37) 
               
               
                   
                   
                   
                   
                 ASLKSEVDNL 
                   
                   
               
               
                   
               
               
                 376 
                 Os/LOC_Os02 
                  48% 
                  95-131 
                 KLKAEYTSLSEEAR 
                 825 
                  67% 
               
               
                   
                 g23823.1 
                 (116/241) 
                   
                 ELTQEKNELRDEK 
                   
                 (25/37) 
               
               
                   
                   
                   
                   
                 VSLKFEVDNL 
                   
                   
               
               
                   
               
               
                 384 
                 Pt/POPTR_00 
                  51% 
                 116-152 
                 RLKAECATLSEETH 
                 829 
                  62% 
               
               
                   
                 05s11550.1 
                 (116/227) 
                   
                 ELMQEKNELREEK 
                   
                 (23/37) 
               
               
                   
                   
                   
                   
                 ASLKADTENL 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related bHLH121 clade polypeptides may be identified by a consensus bHLH domain sequence, SEQ ID NO: 858: 
                    X 1 KX 3 X 4 X 5 X 6 X 7 X 8 KAX 11 REX 14 X 15 RRX 18 X 19 X 20 X 21 X 22 X 23 FX 25 X 26 LGX 29         X 30 LDPX 34 RPX 37 X 38 DKAX 42 X 43 X 44 X 45 X 46 X 47 X 48 QX 50 LKX 53 X 54 X 55 X 56 X 57         VX 59              
where X 1 =K or R; X 3 =E or absent; X 4 =A or absent; X 5 =V or absent; X 6 =C or absent; X 7 =any amino acid; X 8 =any amino acid; X 11 =any amino acid; X 14 =K or R; X 15 =I, L, V or M; X 18 =D or E; X 19 =N, K or R; X 20 =F, I, L, V or M; X 21 =N or K; X 22 =any amino acid; X 23 =H or Q; X 25 =any amino acid; X 26 =D or E; X 29 =any amino acid; X 30 =any amino acid; X 34 =N, D or E; X 37 =K or R; X 38 =any amino acid; X 42 =S or T; X 43 =I, L, V or M; X 44 =I, L, V or M; X 45 =any amino acid; X 46 =D, E; X 47 =A or T; X 48 =I, L, V or M; X 50 =I, L, V or M; X 53 =D or E; X 54 =I, L, V or M; X 55 =any amino acid; X 56 =any amino acid; X 57 =any amino acid; and X 59 =any amino acid.
 
     These functionally-related and/or closely-related bHLH121 clade polypeptides may also be identified by a consensus putative leucine zipper domain sequence, SEQ ID NO: 859: 
                    X 1 LKX 3 X 4 EX 6 X 7 X 8 LX 10 X 11 EX 13 X 14 ELX 17 X 18 EKX 21 X 22 LRX 25 EKX 28 X 29         LX 31 X 32 X 33 X 34 X 35 X 36 L            
where X 1 =R or K; X 4 =any amino acid; X 6 =any amino acid; X 7 =any amino acid; X 8 =any amino acid; X 10 =any amino acid; X 11 =Q, D or E; X 13 =any amino acid; X 14 =any amino acid; X 17 =A, I, L, V or M; X 18 =any amino acid; X 21 =any amino acid; X 22 =D or E; X 25 =D or E; X 28 =any amino acid; X 29 =S, A or T; X 31 =K or R; X 32 =any amino acid; X 33 =any amino acid; X 34 =T, I, L, V or M; X 35 =any amino acid; and X 36 =any amino acid.
 
     BBX26 Clade Polypeptides 
       
     
       
         
           
               
             
               
                 TABLE 20 
               
             
            
               
                   
               
               
                 Conserved ′BBX domain′ of BBX26 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                 Col. 3 
                   
                   
                   
                 BBX 
               
               
                   
                   
                 Percent 
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                 Col. 1 
                   
                 identity of 
                 BBX 
                 Col. 5 
                 SEQ ID 
                 Col. 5 to 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 domain in 
                 Conserved 
                 NO: of 
                 BBX 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 BBX 
                 BBX 
                 domain of 
               
               
                 NO: 
                 Identifier 
                 to BBX26 
                 coordinates 
                 domain 
                 domain 
                 BBX26 
               
               
                   
               
               
                 410 
                 At/BBX26 or 
                 100% 
                  5-41 
                 CHTCRHVTAVIHC 
                 769 
                 100% 
               
               
                   
                 AT1G60250.1 
                 (251/251) 
                   
                 VTEALNFCLTCDNL 
                   
                 (37/37) 
               
               
                   
                   
                   
                   
                 RHHNNIHAEH 
                   
                   
               
               
                   
               
               
                 412 
                 At/AT1G6819 
                  33% 
                 14-51 
                 CEFCKAYRAVVYCI 
                 770 
                  36% 
               
               
                   
                 0.1 
                 (28/84) 
                   
                 ADTANLCLTCDAK 
                   
                 (14/38) 
               
               
                   
                   
                   
                   
                 VHSANSLSGRH 
                   
                   
               
               
                   
               
               
                 414 
                 Pt/POPTR_00 
                  33% 
                  5-42 
                 CEFCMALRPVVYC 
                 771 
                  31% 
               
               
                   
                 08s12410.1 
                 (24/71) 
                   
                 NADAAYLCLSCDA 
                   
                 (12/38) 
               
               
                   
                   
                   
                   
                 KVHSANALFNRH 
                   
                   
               
               
                   
               
               
                 420 
                 Sl/Solyc04g00 
                  26% 
                  7-44 
                 CEFCMLLKPVVYC 
                 774 
                  31% 
               
               
                   
                 7470.2 
                 (25/94) 
                   
                 EADAAHLCLSCDA 
                   
                 (12/38) 
               
               
                   
                   
                   
                   
                 KVHSANALSNRH 
                   
                   
               
               
                   
               
               
                 416 
                 Gm/Glyma10g 
                  27% 
                  5-42 
                 CEFCTALRPLVYCK 
                 772 
                  28% 
               
               
                   
                 41540.1 
                 (22/79) 
                   
                 ADAAYLCLSCDAK 
                   
                 (11/38) 
               
               
                   
                   
                   
                   
                 VHLANAVSGRH 
                   
                   
               
               
                   
               
               
                 418 
                 Gm/Glyma20g 
                  27% 
                  5-42 
                 CEFCTALRPLVYCK 
                 773 
                  28% 
               
               
                   
                 25700.1 
                 (22/79) 
                   
                 ADAAYLCLSCDSK 
                   
                 (11/38) 
               
               
                   
                   
                   
                   
                 VHLANAVSGRH 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related BBX26 clade polypeptides may be identified by a consensus BBX domain sequence, SEQ ID NO: 860: 
                    CX 2 X 3 CX 5 X 6 X 7 X 8 X 9 X 10 X 11 X 12 CX 14 X 15 X 16 X 17 X 18 X 19 X 20 CLX 23 CDX 26 X 27         X 28 HX 30 X 31 NX 33 X 34 X 35 X 36 X 37 H            
where X 2 =any amino acid; X 3 =any amino acid; X 5 =any amino acid; X 6 =any amino acid; X 7 =Y, I, L, V, or M; X 8 =any amino acid; X 9 =A or P; X 10 =I, L, V, or M; X 11 =I, L, V, or M; X 12 =any amino acid; X 14 =any amino acid; X 15 =A or T; X 16 =D or E; X 17 =A or T; X 18 =any amino acid; X 19 =any amino acid; X 20 =F, I, L, V, or M; X 23 =S or T; X 26 =any amino acid; X 27 =any amino acid; X 28 =any amino acid; X 30 =any amino acid; X 31 =A or absent; X 33 =any amino acid; X 34 =I, L, V, or M; X 35 =any amino acid; X 36 =any amino acid; and X 37 =any amino acid.
 
bHLH121 Clade Polypeptides
 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Conserved ′Methyltransferase domain′ of PMT24 and closely related sequences 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                 Col. 7 
               
               
                   
                   
                   
                   
                   
                   
                 Percent 
               
               
                   
                   
                   
                   
                   
                   
                 identity of 
               
               
                   
                   
                   
                   
                   
                   
                 methyl- 
               
               
                   
                   
                   
                   
                   
                   
                 transferase 
               
               
                   
                   
                 Col. 3 
                 Col. 4 
                   
                 Col. 6 
                 domain in 
               
               
                   
                   
                 Percent 
                 Methyl 
                 Col. 5 
                 SEQ ID 
                 Col. 5 to 
               
               
                 Col. 1 
                   
                 identity of 
                 trans- 
                 Conserved 
                 NO: of 
                 methyl- 
               
               
                 SEQ 
                 Col. 2 
                 polypeptide 
                 ferase 
                 methyl- 
                 methyl- 
                 transferase 
               
               
                 ID 
                 Species/ 
                 in Col. 1 
                 amino acid 
                 transferase 
                 transferase 
                 domain 
               
               
                 NO: 
                 Identifier 
                 to PMT24 
                 coordinates 
                 domain 
                 domain 
                 of PMT24 
               
               
                   
               
               
                 444 
                 At1bHLH121 
                 100% 
                 367-584 
                 VILDVGCGVASFGG 
                 786 
                 100% 
               
               
                   
                 or 
                 (770/770) 
                   
                 YLFDRDVLALSFAP 
                   
                 (218/218) 
               
               
                   
                 AT1G29470.1 
                   
                   
                 KDEHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAMSNVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPGSVFDLIHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRALRPGGF 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYRKTE 
                   
                   
               
               
                   
                   
                   
                   
                 EDVGIWKAMSKLT 
                   
                   
               
               
                   
                   
                   
                   
                 KAMCWELMTIKKD 
                   
                   
               
               
                   
                   
                   
                   
                 ELNEVGAAIYQKP 
                   
                   
               
               
                   
                   
                   
                   
                 MSNKCYNERSQNE 
                   
                   
               
               
                   
                   
                   
                   
                 PPLCKDSDDQNAA 
                   
                   
               
               
                   
                   
                   
                   
                 WNVPLEACIHKVT 
                   
                   
               
               
                   
                   
                   
                   
                 EDSSKRGAVWPES 
                   
                   
               
               
                   
                   
                   
                   
                 WPERVETVPQWLD 
                   
                   
               
               
                   
                   
                   
                   
                 SQEGVY 
                   
                   
               
               
                   
               
               
                 446 
                 At/AT2G3430 
                  81% 
                 367-584 
                 VILDVGCGVASFGG 
                 787 
                  92% 
               
               
                   
                 0.1 
                 (638/783) 
                   
                 YLFERDVLALSFAP 
                   
                 (202/218) 
               
               
                   
                   
                   
                   
                 KDEHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAMLNVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPGSVFDLIHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRALRPGGF 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYRKNE 
                   
                   
               
               
                   
                   
                   
                   
                 EDSGIWKAMSELT 
                   
                   
               
               
                   
                   
                   
                   
                 KAMCWKLVTIKKD 
                   
                   
               
               
                   
                   
                   
                   
                 KLNEVGAAIYQKPT 
                   
                   
               
               
                   
                   
                   
                   
                 SNKCYNKRPQNEPP 
                   
                   
               
               
                   
                   
                   
                   
                 LCKDSDDQNAAW 
                   
                   
               
               
                   
                   
                   
                   
                 NVPLEACMHKVTE 
                   
                   
               
               
                   
                   
                   
                   
                 DSSKRGAVWPNM 
                   
                   
               
               
                   
                   
                   
                   
                 WPERVETAPEWLD 
                   
                   
               
               
                   
                   
                   
                   
                 SQEGVY 
                   
                   
               
               
                   
               
               
                 450 
                 Pt/POPTR_00 
                  66% 
                 423-640 
                 VILDVGCGVASFGG 
                 789 
                  81% 
               
               
                   
                 05s20670.1 
                 (548/826) 
                   
                 YLFERDVLAMSFAP 
                   
                 (177/218) 
               
               
                   
                   
                   
                   
                 KDEHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAMLAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPSSVFDVVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHVEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGY 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVGIWKAMSKLT 
                   
                   
               
               
                   
                   
                   
                   
                 KSMCWDLVVIKKD 
                   
                   
               
               
                   
                   
                   
                   
                 KLNGVGAAIFRKPT 
                   
                   
               
               
                   
                   
                   
                   
                 SNDCYNNRPQNEPP 
                   
                   
               
               
                   
                   
                   
                   
                 LCKESDDPNAAWN 
                   
                   
               
               
                   
                   
                   
                   
                 VPLEACMHKVPED 
                   
                   
               
               
                   
                   
                   
                   
                 ASVRGSRWPEQWP 
                   
                   
               
               
                   
                   
                   
                   
                 QRLEKPPYWLNSQ 
                   
                   
               
               
                   
                   
                   
                   
                 VGVY 
                   
                   
               
               
                   
               
               
                 448 
                 Pt/POPTR_00 
                  64% 
                 412-629 
                 VILDVGCGVASFGG 
                 788 
                  80% 
               
               
                   
                 02s07640.1 
                 (526/815) 
                   
                 YLLEKDVLAMSFA 
                   
                 (176/218) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAMLAVMGT 
                   
                   
               
               
                   
                   
                   
                   
                 KRLPFPNSVFDLVH 
                   
                   
               
               
                   
                   
                   
                   
                 CARCRVPWHIEGG 
                   
                   
               
               
                   
                   
                   
                   
                 KLLLELNRVLRPGG 
                   
                   
               
               
                   
                   
                   
                   
                 YFVWSATPVYRKR 
                   
                   
               
               
                   
                   
                   
                   
                 PEDVGIWKAMSKL 
                   
                   
               
               
                   
                   
                   
                   
                 TKSMCWDLVVIKT 
                   
                   
               
               
                   
                   
                   
                   
                 DTLNGVGAAIYRK 
                   
                   
               
               
                   
                   
                   
                   
                 PTSNDCYNNRPQN 
                   
                   
               
               
                   
                   
                   
                   
                 EPPLCKESDDPNAA 
                   
                   
               
               
                   
                   
                   
                   
                 WNVLLEACMHKVP 
                   
                   
               
               
                   
                   
                   
                   
                 VDASVRGSHWPEQ 
                   
                   
               
               
                   
                   
                   
                   
                 WPKRLEKPPYVVLN 
                   
                   
               
               
                   
                   
                   
                   
                 SQVGVY 
                   
                   
               
               
                   
               
               
                 478 
                 Pt/POPTR_00 
                  62% 
                 392-610 
                 VILDVGCGVASFGG 
                 803 
                  75% 
               
               
                   
                 05s06640.1 
                 (499/803) 
                   
                 YLFDRDVLAMSFA 
                   
                 (166/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQIQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAISAVMGTKR 
                   
                   
               
               
                   
                   
                   
                   
                 LPYPGRVFDAVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGF 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLA 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWQAMTELT 
                   
                   
               
               
                   
                   
                   
                   
                 KAMCWELVSINKD 
                   
                   
               
               
                   
                   
                   
                   
                 TLNGVGVATYRKP 
                   
                   
               
               
                   
                   
                   
                   
                 TSNDCYEKRSKQEP 
                   
                   
               
               
                   
                   
                   
                   
                 PLCEASDDPNAAW 
                   
                   
               
               
                   
                   
                   
                   
                 NVPLQACMHKVPV 
                   
                   
               
               
                   
                   
                   
                   
                 GSLERGSQWPEQW 
                   
                   
               
               
                   
                   
                   
                   
                 PARLDKTPYWMLS 
                   
                   
               
               
                   
                   
                   
                   
                 SQVGVY 
                   
                   
               
               
                   
               
               
                 468 
                 Gm/Glyma04g 
                  62% 
                 390-608 
                 VILDVGCGVASFGG 
                 798 
                  75% 
               
               
                   
                 38870.1 
                 (494/794) 
                   
                 FLFDRDVLAMSLAP 
                   
                 (165/219) 
               
               
                   
                   
                   
                   
                 KDEHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAISAVMGTKR 
                   
                   
               
               
                   
                   
                   
                   
                 LPFPGKVFDVVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGF 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPIYQKLPE 
                   
                   
               
               
                   
                   
                   
                   
                 DVEIWKAMKTLTK 
                   
                   
               
               
                   
                   
                   
                   
                 AMCWEVVSISKDQ 
                   
                   
               
               
                   
                   
                   
                   
                 VNGVGVAVYKKPT 
                   
                   
               
               
                   
                   
                   
                   
                 SNECYEQRSKNEPP 
                   
                   
               
               
                   
                   
                   
                   
                 LCPDSDDPNAAWN 
                   
                   
               
               
                   
                   
                   
                   
                 IKLQACMHKVPASS 
                   
                   
               
               
                   
                   
                   
                   
                 KERGSKLPELWPA 
                   
                   
               
               
                   
                   
                   
                   
                 RLTKVPYWLLSSQ 
                   
                   
               
               
                   
                   
                   
                   
                 VGVY 
                   
                   
               
               
                   
               
               
                 480 
                 Pt/POPTR_00 
                  61% 
                 420-638 
                 VILDVGCGVASFGG 
                 804 
                  75% 
               
               
                   
                 07s04340.1 
                 (506/829) 
                   
                 YLFDRDVLTMSFAP 
                   
                 (165/219) 
               
               
                   
                   
                   
                   
                 KDEHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAISAVMGTKR 
                   
                   
               
               
                   
                   
                   
                   
                 LPYPGRVFDAVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGL 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLA 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWQAMTELT 
                   
                   
               
               
                   
                   
                   
                   
                 KAMCWELVSINKD 
                   
                   
               
               
                   
                   
                   
                   
                 TINGVGVATYRKPT 
                   
                   
               
               
                   
                   
                   
                   
                 SNDCYEKRSKQEPP 
                   
                   
               
               
                   
                   
                   
                   
                 LCEASDDPNAAWN 
                   
                   
               
               
                   
                   
                   
                   
                 VPLQACMHKVPVD 
                   
                   
               
               
                   
                   
                   
                   
                 SLERGSQWPEQWP 
                   
                   
               
               
                   
                   
                   
                   
                 ARLGKTPYWMLSS 
                   
                   
               
               
                   
                   
                   
                   
                 QVGVY 
                   
                   
               
               
                   
               
               
                 428 
                 Si/Si000354m 
                  60% 
                 397-615 
                 VILDVGCGVASFGG 
                 778 
                  75% 
               
               
                   
                   
                 (486/810) 
                   
                 YMFDRDVLTMSFA 
                   
                 (166/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAISAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPYPSRVFDVIHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGM 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRLLRPGGY 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWNAMSALT 
                   
                   
               
               
                   
                   
                   
                   
                 KSMCWKMVNKTK 
                   
                   
               
               
                   
                   
                   
                   
                 DKLNQVGMAIYQK 
                   
                   
               
               
                   
                   
                   
                   
                 PMDNNCYEKRSEN 
                   
                   
               
               
                   
                   
                   
                   
                 NPPLCKDSDDADA 
                   
                   
               
               
                   
                   
                   
                   
                 AWNVPLEACMHKL 
                   
                   
               
               
                   
                   
                   
                   
                 PAGPTVRGAKWPE 
                   
                   
               
               
                   
                   
                   
                   
                 SWPQRLEKTPFVVL 
                   
                   
               
               
                   
                   
                   
                   
                 NGSQVGVY 
                   
                   
               
               
                   
               
               
                 466 
                 Eg/Eucgr.I001 
                  59% 
                 410-628 
                 VILDVGCGVASFGG 
                 797 
                  75% 
               
               
                   
                 86.1 
                 (487/819) 
                   
                 YLFDRDVLAMSLA 
                   
                 (165/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAISAVMGTT 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPSRVFDIVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRLLRPGGF 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKIPD 
                   
                   
               
               
                   
                   
                   
                   
                 DVAIWKAMSALLK 
                   
                   
               
               
                   
                   
                   
                   
                 SMCWELISINKDTL 
                   
                   
               
               
                   
                   
                   
                   
                 NGVGVATYRKPMS 
                   
                   
               
               
                   
                   
                   
                   
                 NECYEKRSQNDPP 
                   
                   
               
               
                   
                   
                   
                   
                 MCADSDDSNAAW 
                   
                   
               
               
                   
                   
                   
                   
                 YVPLQTCMHKIPID 
                   
                   
               
               
                   
                   
                   
                   
                 SAERGSQWPEEWP 
                   
                   
               
               
                   
                   
                   
                   
                 ARLVKTPYWLLSS 
                   
                   
               
               
                   
                   
                   
                   
                 QVGVY 
                   
                   
               
               
                   
               
               
                 470 
                 Gm/Glyma06g 
                  62% 
                 402-620 
                 VILDVGCGVASFGG 
                 799 
                  74% 
               
               
                   
                 16050.1 
                 (503/810) 
                   
                 FLFDRDVLAMSLAP 
                   
                 (164/219) 
               
               
                   
                   
                   
                   
                 KDEHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAISAVMGTKR 
                   
                   
               
               
                   
                   
                   
                   
                 LPFPGKVFDVVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGF 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPIYQKLPE 
                   
                   
               
               
                   
                   
                   
                   
                 DVEIWKAMKALTK 
                   
                   
               
               
                   
                   
                   
                   
                 AMCWEVVSISKDP 
                   
                   
               
               
                   
                   
                   
                   
                 VNGVGVAVYRKPT 
                   
                   
               
               
                   
                   
                   
                   
                 SNECYEQRSKNEPP 
                   
                   
               
               
                   
                   
                   
                   
                 LCPDSDDPNAAWN 
                   
                   
               
               
                   
                   
                   
                   
                 IQLQACLHKAPVSS 
                   
                   
               
               
                   
                   
                   
                   
                 KERGSKLPELWPA 
                   
                   
               
               
                   
                   
                   
                   
                 RLIKVPYWLSSSQV 
                   
                   
               
               
                   
                   
                   
                   
                 GVY 
                   
                   
               
               
                   
               
               
                 482 
                 Vv/GSVIVTO 
                  61% 
                 357-575 
                 VVLDVGCGVASFG 
                 805 
                  74% 
               
               
                   
                 1026451001 
                 (480/775) 
                   
                 GYLFDKDVLTMSF 
                   
                 (164/219) 
               
               
                   
                   
                   
                   
                 APKDEHEAQVQFA 
                   
                   
               
               
                   
                   
                   
                   
                 LERGIPGISAVMGT 
                   
                   
               
               
                   
                   
                   
                   
                 KRLPFPAMVFDVV 
                   
                   
               
               
                   
                   
                   
                   
                 HCARCRVPWHIEG 
                   
                   
               
               
                   
                   
                   
                   
                 GKLLLELNRVLRPG 
                   
                   
               
               
                   
                   
                   
                   
                 GFFVWSATPVYQK 
                   
                   
               
               
                   
                   
                   
                   
                 LADDVAIWNAMTE 
                   
                   
               
               
                   
                   
                   
                   
                 LMKSMCWELVVIK 
                   
                   
               
               
                   
                   
                   
                   
                 RDVVNRVAAAIYK 
                   
                   
               
               
                   
                   
                   
                   
                 KPTSNDCYEKRSQ 
                   
                   
               
               
                   
                   
                   
                   
                 NEPPICADSEDANA 
                   
                   
               
               
                   
                   
                   
                   
                 AWNVPLQACMHK 
                   
                   
               
               
                   
                   
                   
                   
                 VPVDASKRGSQWP 
                   
                   
               
               
                   
                   
                   
                   
                 ELWPARLDKSPYW 
                   
                   
               
               
                   
                   
                   
                   
                 LTSSQVGVY 
                   
                   
               
               
                   
               
               
                 452 
                 Eg/Eucgr.F042 
                  55% 
                 423-639 
                 VILDVGCGVASFGG 
                 790 
                  74% 
               
               
                   
                 85.1 
                 (465/832) 
                   
                 YLFERDVLTMSFAP 
                   
                 (162/218) 
               
               
                   
                   
                   
                   
                 KDVHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAILGVMGTKR 
                   
                   
               
               
                   
                   
                   
                   
                 LPFPGGVFDVIHCA 
                   
                   
               
               
                   
                   
                   
                   
                 RCRVPWHIEGGKL 
                   
                   
               
               
                   
                   
                   
                   
                 LLELNRVLRPGGYF 
                   
                   
               
               
                   
                   
                   
                   
                 LWSATPIYRRDQED 
                   
                   
               
               
                   
                   
                   
                   
                 IGIWKEMSKLTMA 
                   
                   
               
               
                   
                   
                   
                   
                 MCWDLVMIKKDK 
                   
                   
               
               
                   
                   
                   
                   
                 LNKVAIAMYRKPT 
                   
                   
               
               
                   
                   
                   
                   
                 SNECYEKRPQNEPP 
                   
                   
               
               
                   
                   
                   
                   
                 LCDNFDDPNSAWN 
                   
                   
               
               
                   
                   
                   
                   
                 VTLQACMHKVPVD 
                   
                   
               
               
                   
                   
                   
                   
                 MSKRGSNWPEKWP 
                   
                   
               
               
                   
                   
                   
                   
                 VRLEKPPYWLNEL 
                   
                   
               
               
                   
                   
                   
                   
                 GVY 
                   
                   
               
               
                   
               
               
                 460 
                 Vv/GSVIVTO 
                  73% 
                 150-368 
                 VILDVGCGVASFGG 
                 794 
                  73% 
               
               
                   
                 1008776001 
                 (409/554) 
                   
                 YIFERDVLAMSFAP 
                   
                 (162/219) 
               
               
                   
                   
                   
                   
                 KDEHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAISAVMGTTR 
                   
                   
               
               
                   
                   
                   
                   
                 LPFPSRVFDVVHCA 
                   
                   
               
               
                   
                   
                   
                   
                 RCRVPWHIEGGKL 
                   
                   
               
               
                   
                   
                   
                   
                 LLELNRVLRPGGYF 
                   
                   
               
               
                   
                   
                   
                   
                 VWSATPVYRKVPE 
                   
                   
               
               
                   
                   
                   
                   
                 DVGIWNAMSEITK 
                   
                   
               
               
                   
                   
                   
                   
                 KICWDLVAMSKDS 
                   
                   
               
               
                   
                   
                   
                   
                 LNGIGAAIYRKPTS 
                   
                   
               
               
                   
                   
                   
                   
                 NECYEKRPRNEPPL 
                   
                   
               
               
                   
                   
                   
                   
                 CEESDNADAAWNI 
                   
                   
               
               
                   
                   
                   
                   
                 PLQACMHKVPVLT 
                   
                   
               
               
                   
                   
                   
                   
                 SERGSQWPEQWPL 
                   
                   
               
               
                   
                   
                   
                   
                 RVEKAPNWLKSSQ 
                   
                   
               
               
                   
                   
                   
                   
                 VGVY 
                   
                   
               
               
                   
               
               
                 462 
                 Sl/Solyc04g06 
                  59% 
                 364-582 
                 VILDVGCGVASFGG 
                 795 
                  73% 
               
               
                   
                 3230.2.1 
                 (470/784) 
                   
                 YLFERDVLAMSLA 
                   
                 (162/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAISAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPGKVFDAVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGH 
                   
                   
               
               
                   
                   
                   
                   
                 FIWSATPVYRKDEE 
                   
                   
               
               
                   
                   
                   
                   
                 NVGIWEAMSELTK 
                   
                   
               
               
                   
                   
                   
                   
                 SMCWELLEINEDKL 
                   
                   
               
               
                   
                   
                   
                   
                 NEVGVAIFRKPTTN 
                   
                   
               
               
                   
                   
                   
                   
                 DCYQSRTQNDPPM 
                   
                   
               
               
                   
                   
                   
                   
                 CEEADDPDAAWNI 
                   
                   
               
               
                   
                   
                   
                   
                 TLQACLHKAPADA 
                   
                   
               
               
                   
                   
                   
                   
                 SARGAKWPAKWPL 
                   
                   
               
               
                   
                   
                   
                   
                 RSEKLPYWLKSSQ 
                   
                   
               
               
                   
                   
                   
                   
                 VGVY 
                   
                   
               
               
                   
               
               
                 426 
                 Zm/GRMZM2 
                  59% 
                 392-610 
                 VILDVGCGVASFGG 
                 777 
                  73% 
               
               
                   
                 G049269_T01 
                 (479/801) 
                   
                 YMFDRDALTMSFA 
                   
                 (160/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAISAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPYPSRVFDVIHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGM 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRLLRPGGY 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWNAMSTLT 
                   
                   
               
               
                   
                   
                   
                   
                 KSMCWKMVNKTK 
                   
                   
               
               
                   
                   
                   
                   
                 DKLNQVGMVIYQK 
                   
                   
               
               
                   
                   
                   
                   
                 PMDNICYEKRSENS 
                   
                   
               
               
                   
                   
                   
                   
                 PPLCKESDDADAA 
                   
                   
               
               
                   
                   
                   
                   
                 WNVPLEACMHKLP 
                   
                   
               
               
                   
                   
                   
                   
                 GGSKVRGSKWPEL 
                   
                   
               
               
                   
                   
                   
                   
                 WPQRLEKTPFWID 
                   
                   
               
               
                   
                   
                   
                   
                 GSKVGVY 
                   
                   
               
               
                   
               
               
                 476 
                 Sl/Solyc05g05 
                  59% 
                 409-627 
                 VILDVGCGVASFGG 
                 802 
                  73% 
               
               
                   
                 6580.2.1 
                 (486/818) 
                   
                 YLFERDVLAMSLA 
                   
                 (160/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAISAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPSRVFDVVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGL 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWEAMQKLT 
                   
                   
               
               
                   
                   
                   
                   
                 KAMCWDLVSKTK 
                   
                   
               
               
                   
                   
                   
                   
                 DRVNGVGVAVYR 
                   
                   
               
               
                   
                   
                   
                   
                 KPTSNECYEQRSKD 
                   
                   
               
               
                   
                   
                   
                   
                 APPICQGSDDPNAA 
                   
                   
               
               
                   
                   
                   
                   
                 WNVPLQACMHKA 
                   
                   
               
               
                   
                   
                   
                   
                 PVATSERGSQWPEP 
                   
                   
               
               
                   
                   
                   
                   
                 WPARLSKSPYWLL 
                   
                   
               
               
                   
                   
                   
                   
                 SSQVGVY 
                   
                   
               
               
                   
               
               
                 474 
                 Gm/Glyma08g 
                  58% 
                 438-656 
                 VILDVGCGVASFGG 
                 801 
                  73% 
               
               
                   
                 00320.1 
                 (493/847) 
                   
                 FLEERDVLTMSLAP 
                   
                 (162/219) 
               
               
                   
                   
                   
                   
                 KDEHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAISAVMGTKR 
                   
                   
               
               
                   
                   
                   
                   
                 LPYPGRVFDVVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGF 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPIYQKLPE 
                   
                   
               
               
                   
                   
                   
                   
                 DVEIWNEMKALTK 
                   
                   
               
               
                   
                   
                   
                   
                 AMCWEVVSISKDK 
                   
                   
               
               
                   
                   
                   
                   
                 LNGVGIAVYKKPTS 
                   
                   
               
               
                   
                   
                   
                   
                 NECYEKRSQNQPPI 
                   
                   
               
               
                   
                   
                   
                   
                 CPDSDDPNAAWNV 
                   
                   
               
               
                   
                   
                   
                   
                 PLQACMHKVPVSS 
                   
                   
               
               
                   
                   
                   
                   
                 TERGSQWPEKWPA 
                   
                   
               
               
                   
                   
                   
                   
                 RLTNIPYWLTNSQV 
                   
                   
               
               
                   
                   
                   
                   
                 GVY 
                   
                   
               
               
                   
               
               
                 472 
                 Gm/Glyma05g 
                  58% 
                 427-645 
                 VILDVGCGVASFGG 
                 800 
                  73% 
               
               
                   
                 32670.1 
                 (492/837) 
                   
                 FLEERDVLTMSLAP 
                   
                 (161/219) 
               
               
                   
                   
                   
                   
                 KDEHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAISAVMGTKR 
                   
                   
               
               
                   
                   
                   
                   
                 LPYPGRVFDVVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGF 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPIYQKLPE 
                   
                   
               
               
                   
                   
                   
                   
                 DVEIWNEMKALTK 
                   
                   
               
               
                   
                   
                   
                   
                 AMCWEVVSISKDK 
                   
                   
               
               
                   
                   
                   
                   
                 LNGVGIAVYKKPTS 
                   
                   
               
               
                   
                   
                   
                   
                 NECYEKRSQNQPPI 
                   
                   
               
               
                   
                   
                   
                   
                 CPDSDDPNAAWNIP 
                   
                   
               
               
                   
                   
                   
                   
                 LQACMHKVPVSST 
                   
                   
               
               
                   
                   
                   
                   
                 ERGSQWPEKWPAR 
                   
                   
               
               
                   
                   
                   
                   
                 LTNTPYWLTNSQV 
                   
                   
               
               
                   
                   
                   
                   
                 GVY 
                   
                   
               
               
                   
               
               
                 456 
                 Gm/Glyma04g 
                  56% 
                 429-646 
                 VILDVGCGVASFGG 
                 792 
                  73% 
               
               
                   
                 42270.1 
                 (473/835) 
                   
                 YLFEKDVLTMSFAP 
                   
                 (160/218) 
               
               
                   
                   
                   
                   
                 KDVHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPATLGVMGTV 
                   
                   
               
               
                   
                   
                   
                   
                 RLPYPGSVFDLVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGH 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKDP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWKAMGEIT 
                   
                   
               
               
                   
                   
                   
                   
                 KSMCWDLVVIAKD 
                   
                   
               
               
                   
                   
                   
                   
                 KLNGVAAAIYRKP 
                   
                   
               
               
                   
                   
                   
                   
                 TDNECYNNRIKHEP 
                   
                   
               
               
                   
                   
                   
                   
                 PMCSESDDPNTAW 
                   
                   
               
               
                   
                   
                   
                   
                 NVSLQACMHKVPV 
                   
                   
               
               
                   
                   
                   
                   
                 DASERGSIWPEQWP 
                   
                   
               
               
                   
                   
                   
                   
                 LRLEKPPYWIDSQA 
                   
                   
               
               
                   
                   
                   
                   
                 GVY 
                   
                   
               
               
                   
               
               
                 422 
                 Bd/Bradi2g57 
                  59% 
                 394-612 
                 VILDVGCGVASFGG 
                 775 
                  72% 
               
               
                   
                 087.1 
                 (485/810) 
                   
                 YMFDRDVLTMSFA 
                   
                 (158/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAISAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPYPSRVFDVIHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRLLRPGGY 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWNAMSSLT 
                   
                   
               
               
                   
                   
                   
                   
                 KSMCWKMVKKTK 
                   
                   
               
               
                   
                   
                   
                   
                 DTLNQVGMAIYQK 
                   
                   
               
               
                   
                   
                   
                   
                 PMDNNCYEKRSED 
                   
                   
               
               
                   
                   
                   
                   
                 SPPLCKETDDADAS 
                   
                   
               
               
                   
                   
                   
                   
                 WNITLQACIHKLPV 
                   
                   
               
               
                   
                   
                   
                   
                 GPSVRGSKWPEFW 
                   
                   
               
               
                   
                   
                   
                   
                 PQRLEKTPFVVIDGS 
                   
                   
               
               
                   
                   
                   
                   
                 HVGVY 
                   
                   
               
               
                   
               
               
                 424 
                 Os/LOC_Os01 
                  58% 
                 406-624 
                 VILDVGCGVASFGG 
                 776 
                  72% 
               
               
                   
                 g66110.1 
                 (479/812) 
                   
                 YMFERDVLTMSFA 
                   
                 (159/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAISAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPYPSRVFDVIHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGM 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRLLRPGGY 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWNAMSSLT 
                   
                   
               
               
                   
                   
                   
                   
                 KAMCWKMVNKTK 
                   
                   
               
               
                   
                   
                   
                   
                 DKLNQVGMAIYQK 
                   
                   
               
               
                   
                   
                   
                   
                 PMDNSCYEKRPEN 
                   
                   
               
               
                   
                   
                   
                   
                 SPPLCKETDDADAA 
                   
                   
               
               
                   
                   
                   
                   
                 WNVPLQACMHKLP 
                   
                   
               
               
                   
                   
                   
                   
                 AGQSVRGSKWPET 
                   
                   
               
               
                   
                   
                   
                   
                 WPQRLEKTPYWID 
                   
                   
               
               
                   
                   
                   
                   
                 DSHVGIY 
                   
                   
               
               
                   
               
               
                 464 
                 At/AT5G6403 
                  58% 
                 425-643 
                 VVLDVGCGVASFG 
                 796 
                  72% 
               
               
                   
                 0.1 
                 (490/834) 
                   
                 GFLFDRDVITMSLA 
                   
                 (159/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAISAVMGTT 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPGRVFDIVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGF 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKKT 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWKAMSELIK 
                   
                   
               
               
                   
                   
                   
                   
                 KMCWELVSINKDTI 
                   
                   
               
               
                   
                   
                   
                   
                 NGVGVATYRKPTS 
                   
                   
               
               
                   
                   
                   
                   
                 NECYKNRSEPVPPI 
                   
                   
               
               
                   
                   
                   
                   
                 CADSDDPNASWKV 
                   
                   
               
               
                   
                   
                   
                   
                 PLQACMHTAPEDK 
                   
                   
               
               
                   
                   
                   
                   
                 TQRGSQWPEQWPA 
                   
                   
               
               
                   
                   
                   
                   
                 RLEKAPFVVLSSSQT 
                   
                   
               
               
                   
                   
                   
                   
                 GVY 
                   
                   
               
               
                   
               
               
                 458 
                 Gm/Glyma06g 
                  57% 
                 406-623 
                 VILDVGCGVASFGG 
                 793 
                  72% 
               
               
                   
                 12540.1 
                 (464/811) 
                   
                 YLFEKDVLTMSFAP 
                   
                 (159/218) 
               
               
                   
                   
                   
                   
                 KDVHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPATLGVMGTV 
                   
                   
               
               
                   
                   
                   
                   
                 RLPYPGSVFDLLHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHVEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRVLRPGGY 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKDP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWKAMGEIT 
                   
                   
               
               
                   
                   
                   
                   
                 KSMCWDLVVIAKD 
                   
                   
               
               
                   
                   
                   
                   
                 KLNGVAAAIYRKP 
                   
                   
               
               
                   
                   
                   
                   
                 TDNECYNNRIKNEP 
                   
                   
               
               
                   
                   
                   
                   
                 SMCSESDDPNTAW 
                   
                   
               
               
                   
                   
                   
                   
                 NVSLQACMHKVPV 
                   
                   
               
               
                   
                   
                   
                   
                 DASERGSIWPEQWP 
                   
                   
               
               
                   
                   
                   
                   
                 LRLEKPPYWIDSQA 
                   
                   
               
               
                   
                   
                   
                   
                 GVY 
                   
                   
               
               
                   
               
               
                 438 
                 Bd/Bradi4g23 
                   50% 
                 469-688 
                 VVLDVGCGVASFG 
                 783 
                 70% 
               
               
                   
                 610.1 
                 (440/868) 
                   
                 GFLFDRGALTMSFA 
                   
                 (155/220) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPALSAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPAGVFDVVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIDGGM 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRLLRPGGF 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWDDMVKLT 
                   
                   
               
               
                   
                   
                   
                   
                 KAMCWEMVKKIL 
                   
                   
               
               
                   
                   
                   
                   
                 DTLDQVGLVIFRKP 
                   
                   
               
               
                   
                   
                   
                   
                 KSNRCYETRRQKEP 
                   
                   
               
               
                   
                   
                   
                   
                 PLCDGSDDPNAAW 
                   
                   
               
               
                   
                   
                   
                   
                 NIKLRACMHRAPA 
                   
                   
               
               
                   
                   
                   
                   
                 DYPSVRGSRWPAP 
                   
                   
               
               
                   
                   
                   
                   
                 WPERAEAVPYWLN 
                   
                   
               
               
                   
                   
                   
                   
                 NSQVGVY 
                   
                   
               
               
                   
               
               
                 434 
                 Zm/GRMZM2 
                  69% 
                 271-489 
                 VVLDVGCGVASFG 
                 781 
                  69% 
               
               
                   
                 G002642_T02 
                 (387/557) 
                   
                 GYLFDRDVITMSFA 
                   
                 (152/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAISAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPSRVFDVVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELDRLLRPGGY 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWQAMSALT 
                   
                   
               
               
                   
                   
                   
                   
                 SSMCWKMVNKVK 
                   
                   
               
               
                   
                   
                   
                   
                 DRVNRVGIAIYRKP 
                   
                   
               
               
                   
                   
                   
                   
                 TDNSCYEARSETNP 
                   
                   
               
               
                   
                   
                   
                   
                 PLCGEYDDPDAAW 
                   
                   
               
               
                   
                   
                   
                   
                 NISLGACMHKLPV 
                   
                   
               
               
                   
                   
                   
                   
                 DPTVRGSQWPELW 
                   
                   
               
               
                   
                   
                   
                   
                 PLRLEKPPYWLRGS 
                   
                   
               
               
                   
                   
                   
                   
                 EAGVY 
                   
                   
               
               
                   
               
               
                 440 
                 Os/LOC_Os11 
                  57% 
                 468-686 
                 VALDVGCGVASFG 
                 784 
                  69% 
               
               
                   
                 g08314.1 
                 (418/726) 
                   
                 GYLFDHDVLTMSL 
                   
                 (153/219) 
               
               
                   
                   
                   
                   
                 APKDEHEAQVQFA 
                   
                   
               
               
                   
                   
                   
                   
                 LERGIPAISAVMGT 
                   
                   
               
               
                   
                   
                   
                   
                 RRLPFPSNVFDAVH 
                   
                   
               
               
                   
                   
                   
                   
                 CARCRVPWHIEGG 
                   
                   
               
               
                   
                   
                   
                   
                 MLLLELNRLLRPGG 
                   
                   
               
               
                   
                   
                   
                   
                 FFVWSATPVYQELP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWGEMVKLT 
                   
                   
               
               
                   
                   
                   
                   
                 KAMCWEMVSKTS 
                   
                   
               
               
                   
                   
                   
                   
                 DTVDQVGLVTFRK 
                   
                   
               
               
                   
                   
                   
                   
                 PADNACYMKRRQK 
                   
                   
               
               
                   
                   
                   
                   
                 EPPLCEPSDDPNAA 
                   
                   
               
               
                   
                   
                   
                   
                 WNITLRACMHWVP 
                   
                   
               
               
                   
                   
                   
                   
                 TDPSVRGSWVVPER 
                   
                   
               
               
                   
                   
                   
                   
                 WPERMEKTPYWLN 
                   
                   
               
               
                   
                   
                   
                   
                 SSQVGVY 
                   
                   
               
               
                   
               
               
                 430 
                 Bd/Bradi5g27 
                  55% 
                 319-537 
                 VVLDVGCGVASFG 
                 779 
                  69% 
               
               
                   
                 590.1 
                 (429/773) 
                   
                 GYLFDRDVLTMSF 
                   
                 (153/219) 
               
               
                   
                   
                   
                   
                 APKDEHEAQVQFA 
                   
                   
               
               
                   
                   
                   
                   
                 LERGIPAISAVMGT 
                   
                   
               
               
                   
                   
                   
                   
                 KRLPFPGRVFDAVH 
                   
                   
               
               
                   
                   
                   
                   
                 CARCRVPWHIEGG 
                   
                   
               
               
                   
                   
                   
                   
                 KLLLELDRLLRPGG 
                   
                   
               
               
                   
                   
                   
                   
                 YFVWSATPAYQKL 
                   
                   
               
               
                   
                   
                   
                   
                 PEDVEIWQAMSAL 
                   
                   
               
               
                   
                   
                   
                   
                 TRSMCWKMVNKV 
                   
                   
               
               
                   
                   
                   
                   
                 KDRLNRVGVAIFQ 
                   
                   
               
               
                   
                   
                   
                   
                 KPIDNRCYDGRSAA 
                   
                   
               
               
                   
                   
                   
                   
                 NLPLCGEYDNVDA 
                   
                   
               
               
                   
                   
                   
                   
                 AWNVSLESCIHKLP 
                   
                   
               
               
                   
                   
                   
                   
                 VDPAIRSSRWPEEW 
                   
                   
               
               
                   
                   
                   
                   
                 PLRLERAPYWLKSS 
                   
                   
               
               
                   
                   
                   
                   
                 EPGVY 
                   
                   
               
               
                   
               
               
                 454 
                 Eg/Eucgr.F042 
                  54% 
                 407-624 
                 VILDVGCGVGSFGG 
                 791 
                  69% 
               
               
                   
                 86.1 
                 (441/813) 
                   
                 YLFERDVLTMSFAP 
                   
                 (152/219) 
               
               
                   
                   
                   
                   
                 KDEHEAQVQFALE 
                   
                   
               
               
                   
                   
                   
                   
                 RGIPAMLAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPSGVFDAIHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELNRLLRPGGY 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPIYRKGPE 
                   
                   
               
               
                   
                   
                   
                   
                 DLGIWKEMSKLTT 
                   
                   
               
               
                   
                   
                   
                   
                 AMCWNFTLIKRKD 
                   
                   
               
               
                   
                   
                   
                   
                 KMNKVSIALYRKP 
                   
                   
               
               
                   
                   
                   
                   
                 TSNECIESRTKNEPP 
                   
                   
               
               
                   
                   
                   
                   
                 LCNGLDDANSTWN 
                   
                   
               
               
                   
                   
                   
                   
                 VTLQACMHKVPTD 
                   
                   
               
               
                   
                   
                   
                   
                 MSERGSQWPENWL 
                   
                   
               
               
                   
                   
                   
                   
                 HRLGKPPYWLNKV 
                   
                   
               
               
                   
                   
                   
                   
                 AVN 
                   
                   
               
               
                   
               
               
                 442 
                 Si/Si028042m 
                  51% 
                 434-654 
                 VVLDVGCGVASFG 
                 785 
                  69% 
               
               
                   
                   
                 (436/840) 
                   
                 GYLFDRDVLTMSL 
                   
                 (154/221) 
               
               
                   
                   
                   
                   
                 APKDEHEAQVQFA 
                   
                   
               
               
                   
                   
                   
                   
                 LERGIPAISAVMGT 
                   
                   
               
               
                   
                   
                   
                   
                 RRLPFPGGVFDVVH 
                   
                   
               
               
                   
                   
                   
                   
                 CARCRVPWHIDGG 
                   
                   
               
               
                   
                   
                   
                   
                 MLLLELNRLLRPGG 
                   
                   
               
               
                   
                   
                   
                   
                 VFVWSATPVYQKL 
                   
                   
               
               
                   
                   
                   
                   
                 PDDVEIWDEMAKL 
                   
                   
               
               
                   
                   
                   
                   
                 TKAMCWEMVAKT 
                   
                   
               
               
                   
                   
                   
                   
                 KHTVVDDQVGVAI 
                   
                   
               
               
                   
                   
                   
                   
                 FRKPERNGCYEKRP 
                   
                   
               
               
                   
                   
                   
                   
                 EKAPPLCEPSDDPN 
                   
                   
               
               
                   
                   
                   
                   
                 AAWNIKLRACMHR 
                   
                   
               
               
                   
                   
                   
                   
                 VPEDPSERGARWPE 
                   
                   
               
               
                   
                   
                   
                   
                 PWPERLGKAPYWL 
                   
                   
               
               
                   
                   
                   
                   
                 DGSQTGVY 
                   
                   
               
               
                   
               
               
                 432 
                 Os/LOC_Os04 
                  65% 
                 275-493 
                 VVLDVGCGVASFG 
                 780 
                  68% 
               
               
                   
                 g59590.1 
                 (393/599) 
                   
                 GYLFDRDVLTMSF 
                   
                 (151/219) 
               
               
                   
                   
                   
                   
                 APKDEHEAQVQFA 
                   
                   
               
               
                   
                   
                   
                   
                 LERGIPAMSAVMG 
                   
                   
               
               
                   
                   
                   
                   
                 TKRLPFPGRVFDVV 
                   
                   
               
               
                   
                   
                   
                   
                 HCARCRVPWHIEG 
                   
                   
               
               
                   
                   
                   
                   
                 GKLLLELDRLLRPG 
                   
                   
               
               
                   
                   
                   
                   
                 GYFVWSATPVYQK 
                   
                   
               
               
                   
                   
                   
                   
                 LPEDVEIWEAMSTL 
                   
                   
               
               
                   
                   
                   
                   
                 TRSMCWEMVNKV 
                   
                   
               
               
                   
                   
                   
                   
                 KDRVNRVGIAIFRK 
                   
                   
               
               
                   
                   
                   
                   
                 PTDNSCYEARSAA 
                   
                   
               
               
                   
                   
                   
                   
                 NPPICGEYDDPDAA 
                   
                   
               
               
                   
                   
                   
                   
                 WNISLQSCVHRLPT 
                   
                   
               
               
                   
                   
                   
                   
                 DPAIRGSQWPVEW 
                   
                   
               
               
                   
                   
                   
                   
                 PLRLEKPPYWLKNS 
                   
                   
               
               
                   
                   
                   
                   
                 EAGVY 
                   
                   
               
               
                   
               
               
                 436 
                 Si/Si021320m 
                  55% 
                 337-555 
                 VVLDVGCGVASFG 
                 782 
                  68% 
               
               
                   
                   
                 (432/776) 
                   
                 GYLFDRDVITMSFA 
                   
                 (150/219) 
               
               
                   
                   
                   
                   
                 PKDEHEAQVQFAL 
                   
                   
               
               
                   
                   
                   
                   
                 ERGIPAISAVMGTK 
                   
                   
               
               
                   
                   
                   
                   
                 RLPFPSRVFDVVHC 
                   
                   
               
               
                   
                   
                   
                   
                 ARCRVPWHIEGGK 
                   
                   
               
               
                   
                   
                   
                   
                 LLLELDRLLRPGGY 
                   
                   
               
               
                   
                   
                   
                   
                 FVWSATPVYQKLP 
                   
                   
               
               
                   
                   
                   
                   
                 EDVEIWEAMSALT 
                   
                   
               
               
                   
                   
                   
                   
                 RSMCWKMVNKVK 
                   
                   
               
               
                   
                   
                   
                   
                 DRVNRVGIAIFRKP 
                   
                   
               
               
                   
                   
                   
                   
                 TDNSCYEERSEANS 
                   
                   
               
               
                   
                   
                   
                   
                 PICGEYDDPDAAW 
                   
                   
               
               
                   
                   
                   
                   
                 NVSLRTCMHKLPV 
                   
                   
               
               
                   
                   
                   
                   
                 DLTIRGSKWPELWP 
                   
                   
               
               
                   
                   
                   
                   
                 LRLEKPPYWLKSSE 
                   
                   
               
               
                   
                   
                   
                   
                 AGVY 
               
               
                   
               
            
           
         
       
     
     These functionally-related and/or closely-related PMT24 clade polypeptides may be identified by a consensus methyltransferase domain sequence, SEQ ID NO: 861: 
                    VX 2 LDVGCGVASFGGX 15 X 16 FX 18 X 19 X 20 X 21 X 22 X 23 X 24 SX 26 AFKDX 31 HEA               QVQFALERGIPAX 47 X 48 X 49 VMGTX 54 RLPX 58 PX 60 X 61 VFDX 65 X 66 HCARC               RVPWHX 77 X 78 GGX 81 LLLELX 87 RX 89 LRPGGX 95 FX 97 WSATPX 103 YX 105 X 106                 X 107 X 108 X 109 X 110 X 111 X 112 IWX 115 X 116 MX 118 X 119 X 120 X 121 X 122 X 123 MCWX 127                 X 128 X 129 X 130 X 131 X 132 X 133 X 134 X 135 X 136 X 137 X 138 X 139 X 140 VX 142 X 143 X 144                 X 145 X 146 X 147 KPX 150 X 151 NX 153 CYX 156 X 157 RX 159 X 160 X 161 X 162 X 163 X 164 X 165                 CX 167 X 168 X 169 DX 171 X 172 X 173 X 174 X 175 WX 177 X 178 X 179 LX 181 X 182 CX 184 HX 186                 X 187 X 188 X 189 X 190 X 191 X 192 X 193 X 19 RX 196 X 197 X 198 X 199 PX 201 X 202 WPX 205 R               X 207 X 208 X 209 X 210 FX 212 WX 214 X 215 X 216 SX 218 X 219 GX 221 Y            
where X 2 =any amino acid; X 15 =F or Y; X 16 =I, L, V or M; X 18 =D or E; X 19 =H, K or R; X 20 =D or G; X 21 =any amino acid; X 22 =I, L, V or M; X 23 =A or T; X 24 =I, L, V or M; X 26 =F, I, L, V or M; X 31 =any amino acid; X 47 =T, I, L, V or M; X 48 =any amino acid; X 49 =any amino acid; X 54 =I, L, V or M; X 58 =F or Y; X 60 =A, S or G; X 61 =any amino acid; X 65 =I, L, V or M; X 66 =I, L, V or M; X 77 =I, L, V or M; X 78 =D or E; X 81 =any amino acid; X 87 =N or D; X 89 =A, I, L, V or M; X 95 =any amino acid; X 97 =I, L, V or M; X 103 =A, I, L, V, or M; X 105 =Q or R; X 106 =any amino acid; X 107 =any amino acid; X 108 =any amino acid; X 109 =D or E; X 110 =D or N; X 111 =any amino acid; X 112 =any amino acid; X 115 =any amino acid; X 116 =any amino acid; X 118 =any amino acid; X 119 =any amino acid; X 120 =I, L, V or M; X 121 =T, I, L, V or M; X 122 =any amino acid; X 123 =any amino acid; X 127 =any amino acid; X 128 =I, L, V or M; X 129 =I, L, V or M; X 130 =any amino acid; X 131 =any amino acid; X 132 =any amino acid; X 133 =any amino acid; X 134 =H, D; X 135 =any amino acid; X 136 =I, L, V or M; X 137 =V or absent; X 138 =D or absent; X 139 =I, L, V or M; X 140 =any amino acid; X 142 =A or G; X 143 =any amino acid; X 144 =any amino acid; X 145 =T, I, L, V or M; X 146 =F or Y; X 147 =Q, R or K; X 150 =any amino acid; X 151 =any amino acid; X 153 =any amino acid; X 156 =any amino acid; X 157 =any amino acid; X 159 =any amino acid; X 160 =any amino acid; X 161 =any amino acid; X 162 =any amino acid; X 163 =any amino acid; X 164 =S or P; X 165 =I, L, V or M; X 167 =any amino acid; X 168 =any amino acid; X 169 =any amino acid; X 171 =N or D; X 172 =any amino acid; X 173 =N or D; X 174 =A or T; X 175 =A or S; X 177 =any amino acid; X 178 =I, L, V or M; X 179 =any amino acid; X 181 =any amino acid; X 182 =A, S or T; X 184 =I, L, V or M; X 186 =any amino acid; X 187 =A, I, L, V or M; X 188 =any amino acid; X 189 =any amino acid; X 190 =any amino acid; X 191 =Y or absent; X 192 =any amino acid; X 193 =any amino acid; X 194 =any amino acid; X 196 =S or G; X 197 =S or A; X 198 =any amino acid; X 199 =any amino acid; X 201 =any amino acid; X 202 =any amino acid; X 205 =any amino acid; X 207 =any amino acid; X 208 =any amino acid; X 209 =any amino acid; X 210 =any amino acid; X 212 =any amino acid; X 214 =I, L, V or M; X 215 =any amino acid; X 216 =any amino acid or absent; X 218 =K, E, H or Q; X 219 =any amino acid; and X 221 =I, L, V or M.
 
     Alternative consensus sequences comprising the above with conservative substitutions found in the instant Tables are also envisaged and may be expected to provide equivalent function(s). 
     The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. An AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in the instant Tables may also have, to any of the listed sequences found in the Sequence Listing or to the entire length of a listed sequence, at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to any of SEQ ID NOs: 2, 42, 86, 108, 126, 156, 192, 246, 278, 318, 356, 388, 410, 444 or SEQ ID NOs: 2n where n=1 to 241, and/or at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to a domain of any of SEQ ID NOs: 483, 490, 510, 538, 566, 588, 599, 608, 623, 629, 659, 686, 702, 721, 741, 760, 769, 786, 813, and/or at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identity to any of consensus sequences SEQ ID NOs: 842-861. The presence of the listed domains in a listed polypeptide sequence is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptides, or which fall within the AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade exemplified in the phylogenetic trees presented in the Figures. 
     Example II. Plant Genotypes and Vector and Cloning Information 
     A variety of constructs may be used to modulate the activity of regulatory polypeptides (RPs), and to test the activity of orthologs and paralogs in transgenic plant material. This platform provides the material for all subsequent analysis. 
     An individual plant “genotype” refers to a set of plant lines containing a particular construct or knockout (for example, this might be 35S lines for a given gene sequence (GID, Gene Identifier) being tested, 35S lines for a paralog or ortholog of that gene sequence, lines for an RNAi construct, lines for a GAL4 fusion construct, or lines in which expression of the gene sequence is driven from a particular promoter that enhances expression in particular cell, tissue or condition). For a given genotype arising from a particular transformed construct, multiple independent transgenic lines may be examined for morphological and physiological phenotypes. Each individual “line” (also sometimes known as an “event”) refers to the progeny plant or plants deriving from the stable integration of the transgene(s), carried within the T-DNA borders contained within a transformation construct, into a specific location or locations within the genome of the original transformed cell. It is well known in the art that different lines deriving from transformation with a given transgene may exhibit different levels of expression of that transgene due to so called “position effects” of the surrounding chromatin at the locus of integration in the genome, and therefore it is necessary to examine multiple lines containing each construct of interest. 
     (1) Overexpression/Tissue-Enhanced/Conditional Expression. 
     Expression of a given regulatory protein from a particular promoter, for example a photosynthetic tissue-enhanced promoter (e.g., a green tissue- or leaf-enhanced promoter), is achieved either by a direct-promoter fusion construct in which that regulatory protein is cloned directly behind the promoter of interest or by a two component system. 
     The Two-Component Expression System. 
     For the two-component system, two separate constructs are used: Promoter::LexA-GAL4TA and opLexA::RP. The first of these (Promoter::LexA-GAL4TA) comprises a desired promoter cloned in front of a LexA DNA binding domain fused to a GAL4 activation domain. The construct vector backbone (pMEN48, also known as P5375) also carries a kanamycin resistance marker, along with an opLexA::GFP (green fluorescent protein) reporter. Transgenic lines are obtained containing this first component, and a line is selected that shows reproducible expression of the reporter gene in the desired pattern through a number of generations. A homozygous population is established for that line, and the population is supertransformed with the second construct (opLexA::RP) carrying the regulatory protein of interest cloned behind a LexA operator site. This second construct vector backbone (pMEN53, also known as P5381) also contains a sulfonamide resistance marker. 
     Conditional Expression. 
     Various promoters can be used to overexpress disclosed polypeptides in plants to confer improved photosynthetic resource use efficiency. However, in some cases, there may be limitations in the use of various proteins that confer increased photosynthetic resource use efficiency when the proteins are overexpressed. Negative side effects associated with constitutive overexpression such as small size, delayed growth, increased disease sensitivity, and development and alteration in flowering time are not uncommon. A number of stress-inducible promoters can be used promote protein expression during the periods of stress, and therefore may be used to induce overexpression of polypeptides that can confer improved stress tolerance when they are needed without the adverse developmental or morphological effects that may be associated with their constitutive overexpression. 
     Promoters that drive protein expression in response to stress can be used to regulate the expression of the disclosed polypeptides to confer photosynthetic resource use efficiency to plants. The promoter may regulate expression of a disclosed polypeptide to an effective level in a photosynthetic tissue. Effective level in this regard refers to an expression level that confers greater photosynthetic resource use efficiency in the transgenic plant relative to the control plant that, for example, does not comprise a recombinant polynucleotide that encodes the disclosed polypeptide. Optionally, the promoter does not regulate protein expression in a constitutive manner. 
     Such promoters include, but are not limited to, the sequences located in the promoter regions of At5g52310 (RD29A), At5g52300, AT1G16850, At3g46230, AT1G52690, At2g37870, AT5G43840, At5g66780, At3g17520, and At4g09600. 
     In addition, promoters with expression specific to or enhanced in particular cells or tissue types may be used to express a given regulatory protein only in these cells or tissues. Examples of such promoter types include but are not limited to promoters expressed in green tissue, guard cell, epidermis, whole root, root hairs, vasculature, apical meristems, and developing leaves. 
     Table 22 lists a number of photosynthetic tissue-enhanced promoters, specifically, mesophyll tissue-enhanced promoters from rice, that may be used to regulate expression of polynucleotides and polypeptides found in the Sequence Listing and structurally and functionally-related sequences. Promoters that may be used to drive expression of polynucleotides and polypeptides found in the Sequence Listing and structurally and functionally-related sequences included, but are not limited to, promoter sequences SEQ ID NO: 862-864 and the following promoters listed in Table 22, as well as promoters that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to SEQ ID NO: 862-888, or comprise a functional fragment of promoters that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to SEQ ID NO: 862-888. 
     
       
         
           
               
             
               
                 TABLE 22 
               
             
            
               
                   
               
               
                 Rice Genes with Photosynthetic Tissue-Enhanced Promoters 
               
            
           
           
               
               
               
            
               
                   
                   
                 Rice Gene Identifier of Photosynthetic 
               
               
                   
                 SEQ ID NO: 
                 Tissue-Enhanced Promoter 
               
               
                   
                   
               
               
                   
                 865 
                 Os02g09720 
               
               
                   
                 866 
                 Os05g34510 
               
               
                   
                 867 
                 Os11g08230 
               
               
                   
                 868 
                 Os01g64390 
               
               
                   
                 869 
                 Os06g15760 
               
               
                   
                 870 
                 Os12g37560 
               
               
                   
                 871 
                 Os03g17420 
               
               
                   
                 872 
                 Os04g51000 
               
               
                   
                 873 
                 Os01g01960 
               
               
                   
                 874 
                 Os05g04990 
               
               
                   
                 875 
                 Os02g44970 
               
               
                   
                 876 
                 Os01g25530 
               
               
                   
                 877 
                 Os03g30650 
               
               
                   
                 878 
                 Os01g64910 
               
               
                   
                 879 
                 Os07g26810 
               
               
                   
                 880 
                 Os07g26820 
               
               
                   
                 881 
                 Os09g11220 
               
               
                   
                 882 
                 Os04g21800 
               
               
                   
                 883 
                 Os10g23840 
               
               
                   
                 884 
                 Os08g13850 
               
               
                   
                 885 
                 Os12g42980 
               
               
                   
                 886 
                 Os03g29280 
               
               
                   
                 887 
                 Os03g20650 
               
               
                   
                 888 
                 Os06g43920 
               
               
                   
                   
               
            
           
         
       
     
     Tissue-enhanced promoters that may be used to drive expression of polynucleotides and polypeptides found in the Sequence Listing and structurally and functionally-related sequences have also been described in U.S. patent publication no. 20110179520A1, incorporated herein by reference. Such promoters include, but are not limited to,  Arabidopsis  sequences located in the promoter regions of AT1G08465, AT1G10155, AT1G14190, AT1G24130, AT1G24735, AT1G29270, AT1G30950, AT1G31310, AT1G37140, AT1G49320, AT1G49475, AT1G52100, AT1G60540, AT1G60630, AT1G64625, AT1G65150, AT1G68480, AT1G68780, AT1G69180, AT1G77145, AT1G80580, AT2G03500, AT2G17950, AT2G19910, AT2G27250, AT2G33880, AT2G39850, AT3G02500, AT3G12750, AT3G15170, AT3G16340, AT3G27920, AT3G30340, AT3G42670, AT3G44970, AT3G49950, AT3G50870, AT3G54990, AT3G59270, AT4G00180, AT4G00480, AT4G12450, AT4G14819, AT4G31610, AT4G31615, AT4G31620, AT4G31805, AT4G31877, AT4G36060, AT4G36470, AT4G36850, AT4G37970, AT5G03840, AT5G12330, AT5G14070, AT5G16410, AT5G20740, AT5G27690, AT5G35770, AT5G39330, AT5G42655, AT5G53210, AT5G56530, AT5G58780, AT5G61070, and AT5G6491. 
     In addition to the sequences provided in the Sequence Listing or in this Example, a promoter region may include a fragment of the promoter sequences provided in the Sequence Listing or in this Example, or a complement thereof, wherein the promoter sequence, or the fragment thereof, or the complement thereof, regulates expression of a polypeptide in a plant cell, for example, in response to a biotic or abiotic stress, or in a manner that is enhanced or preferred in certain plant tissues. 
     (2) Knock-Out/Knock-Down 
     In some cases, lines mutated in a given regulatory protein may be analyzed. Where available, T-DNA insertion lines in a given gene are isolated and characterized. In cases where a T-DNA insertion line is unavailable, an RNA interference (RNAi) strategy is sometimes used. 
     Example III. Transformation Methods 
     Crop species that overexpress polypeptides of the instant description may produce plants with increased photosynthetic resource use efficiency and/or yield. Thus, polynucleotide sequences listed in the Sequence Listing recombined into, for example, one of the expression vectors of the instant description, or another suitable expression vector, may be transformed into a plant for the purpose of modifying plant traits for the purpose of improving yield, quality, and/or photosynthetic resource use efficiency. The expression vector may contain a constitutive, tissue-enhanced or inducible promoter operably linked to the polynucleotide. The cloning vector may be introduced into a variety of plants by means well known in the art such as, for example, direct DNA transfer or  Agrobacterium tumefaciens -mediated transformation. 
     Transformation of Monocots. 
     Cereal plants including corn, wheat, rice, sorghum, barley, or other monocots may be transformed with the present polynucleotide sequences, including monocot or eudicot-derived sequences such as those presented in the present Tables, cloned into a vector such as pGA643 and containing a kanamycin-resistance marker, and expressed constitutively under, for example, the CaMV35S or COR15 promoters, or with tissue-enhanced or inducible promoters. The expression vectors may be one found in the Sequence Listing, or any other suitable expression vector may be similarly used. For example, pMEN020 may be modified to replace the NptII coding region with the BAR gene of  Streptomyces hygroscopicus  that confers resistance to phosphinothricin. The KpnI and BglII sites of the Bar gene are removed by site-directed mutagenesis with silent codon changes. 
     The cloning vector may be introduced into a variety of cereal plants by means well known in the art including direct DNA transfer or  Agrobacterium tumefaciens -mediated transformation. The latter approach may be accomplished by a variety of means, including, for example, that of U.S. Pat. No. 5,591,616, in which monocotyledon callus is transformed by contacting dedifferentiating tissue with the  Agrobacterium  containing the cloning vector. 
     The sample tissues are immersed in a suspension of 3×10 −9  cells of  Agrobacterium  containing the cloning vector for 3-10 minutes. The callus material is cultured on solid medium at 25° C. in the dark for several days. The calli grown on this medium are transferred to a Regeneration Medium. Transfers are continued every two to three weeks (two or three times) until shoots develop. Shoots are then transferred to Shoot-Elongation Medium every 2-3 weeks. Healthy looking shoots are transferred to Rooting Medium and after roots have developed, the plants are placed into moist potting soil. 
     The transformed plants are then analyzed for the presence of the NPTII gene/kanamycin resistance by ELISA, using the ELISA NPTII kit from 5Prime-3Prime Inc. (Boulder, Colo.). 
     It is also routine to use other methods to produce transgenic plants of most cereal crops (Vasil, 1994 . Plant Mol. Biol.  25: 925-937) such as corn, wheat, rice, sorghum (Cassas et al., 1993 . Proc. Natl. Acad. Sci. USA  90: 11212-11216), and barley (Wan and Lemeaux, 1994 . Plant Physiol.  104: 37-48). DNA transfer methods such as the microprojectile method can be used for corn (Fromm et al., 1990 . Bio/Technol.  8: 833-839; Gordon-Kamm et al., 1990 . Plant Cell  2: 603-618; Ishida, 1990 . Nature Biotechnol.  14:745-750), wheat (Vasil et al., 1992 . Bio/Technol.  10:667-674; Vasil et al., 1993 . Bio/Technol.  11:1553-1558; Weeks et al., 1993 . Plant Physiol.  102:1077-1084), and rice (Christou, 1991 . Bio/Technol.  9:957-962; Hiei et al., 1994 . Plant J.  6:271-282; Aldemita and Hodges, 1996 . Planta  199: 612-617; and Hiei et al., 1997 . Plant Mol. Biol.  35:205-218). For most cereal plants, embryogenic cells derived from immature scutellum tissues are the preferred cellular targets for transformation (Hiei et al., 1997. supra; Vasil, 1994. supra). For transforming corn embryogenic cells derived from immature scutellar tissue using microprojectile bombardment, the A188XB73 genotype is the preferred genotype (Fromm et al., 1990 . Bio/Technol.  8: 833-839; Gordon-Kamm et al., 1990. supra). After microprojectile bombardment the tissues are selected on phosphinothricin to identify the transgenic embryogenic cells (Gordon-Kamm et al., 1990. supra). Transgenic plants from transformed host plant cells may be regenerated by standard corn regeneration techniques (Fromm et al., 1990 . Bio/Technol.  8: 833-839; Gordon-Kamm et al., 1990. supra). 
     Transformation of Dicots. 
     It is now routine to produce transgenic plants using most eudicot plants (see U.S. Pat. No. 8,273,954 (Rogers et al.) issued Sep. 25, 2012; Weissbach and Weissbach, 1989 . Methods for Plant Molecular Biology , Academic Press; Gelvin et al., 1990 . Plant Molecular Biology Manual , Kluwer Academic Publishers; Herrera-Estrella et al., 1983 . Nature  303: 209; Bevan, 1984 . Nucleic Acids Res.  12: 8711-8721; and Klee, 1985 . Bio/Technology  3: 637-642). Methods for analysis of traits are routine in the art and examples are disclosed above. 
     Numerous protocols for the transformation of tomato and soy plants have been previously described, and are well known in the art. Gruber et al., in Glick and Thompson, 1993 . Methods in Plant Molecular Biology and Biotechnology . eds., CRC Press, Inc., Boca Raton, describe several expression vectors and culture methods that may be used for cell or tissue transformation and subsequent regeneration. For soybean transformation, methods are described by Miki et al., 1993. in  Methods in Plant Molecular Biology and Biotechnology , p. 67-88, Glick and Thompson, eds., CRC Press, Inc., Boca Raton; and U.S. Pat. No. 5,563,055, (Townsend and Thomas), issued Oct. 8, 1996. 
     There are a substantial number of alternatives to  Agrobacterium -mediated transformation protocols, other methods for the purpose of transferring exogenous genes into soybeans or tomatoes. One such method is microprojectile-mediated transformation, in which DNA on the surface of microprojectile particles is driven into plant tissues with a biolistic device (see, for example, Sanford et al., 1987 . Part. Sci. Technol.  5:27-37; Sanford, 1993 . Methods Enzymol.  217: 483-509; Christou et al., 1992 . Plant. J.  2: 275-281; Klein et al., 1987 . Nature  327: 70-73; U.S. Pat. No. 5,015,580 (Christou et al), issued May 14, 1991; and U.S. Pat. No. 5,322,783 (Tomes et al.), issued Jun. 21, 1994). 
     Alternatively, sonication methods (see, for example, Zhang et al., 1991 . Bio/Technology  9: 996-997); direct uptake of DNA into protoplasts using CaCl 2  precipitation, polyvinyl alcohol or poly-L-ornithine (see, for example, Hain et al., 1985 . Mol. Gen. Genet.  199: 161-168; Draper et al., 1982 . Plant Cell Physiol.  23: 451-458); liposome or spheroplast fusion (see, for example, Deshayes et al., 1985 . EMBO J.,  4: 2731-2737; Christou et al., 1987 . Proc. Natl. Acad. Sci. USA  84: 3962-3966); and electroporation of protoplasts and whole cells and tissues (see, for example, Donn et al. 1990. in  Abstracts of VIIth International Congress on Plant Cell and Tissue Culture IAPTC , A2-38: 53; D&#39;Halluin et al., 1992 . Plant Cell  4: 1495-1505; and Spencer et al., 1994 . Plant Mol. Biol.  24: 51-61) have been used to introduce foreign DNA and expression vectors into plants. 
     After a plant or plant cell is transformed (and the transformed host plant cell then regenerated into a plant), the transformed plant may propagated vegetatively or it may be crossed with itself or a plant from the same line, a non-transformed or wild-type plant, or another transformed plant from a different transgenic line of plants. Crossing provides the advantages of producing new and often stable transgenic varieties. Genes and the traits they confer that have been introduced into a tomato or soybean line may be moved into distinct line of plants using traditional backcrossing techniques well known in the art. Transformation of tomato plants may be conducted using the protocols of Koornneef et al, 1986. In  Tomato Biotechnology : Alan R. Liss, Inc., 169-178, and in U.S. Pat. No. 6,613,962, the latter method described in brief here. Eight day old cotyledon explants are precultured for 24 hours in Petri dishes containing a feeder layer of  Petunia hybrida  suspension cells plated on MS medium with 2% (w/v) sucrose and 0.8% agar supplemented with 10 μM α-naphthalene acetic acid and 4.4 μM 6-benzylaminopurine. The explants are then infected with a diluted overnight culture of  Agrobacterium tumefaciens  containing an expression vector comprising a polynucleotide of the instant description for 5-10 minutes, blotted dry on sterile filter paper and cocultured for 48 hours on the original feeder layer plates. Culture conditions are as described above. Overnight cultures of  Agrobacterium tumefaciens  are diluted in liquid MS medium with 2% (w/v/) sucrose, pH 5.7, to an OD 600  of 0.8. 
     Following cocultivation, the cotyledon explants are transferred to Petri dishes with selective medium comprising MS medium with 4.56 μM zeatin, 67.3 μM vancomycin, 418.9 μM cefotaxime and 171.6 μM kanamycin sulfate, and cultured under the culture conditions described above. The explants are subcultured every three weeks onto fresh medium. Emerging shoots are dissected from the underlying callus and transferred to glass jars with selective medium without zeatin to form roots. The formation of roots in a kanamycin sulfate-containing medium is a positive indication of a successful transformation. 
     Transformation of soybean plants may be conducted using the methods found in, for example, U.S. Pat. No. 5,563,055 (Townsend et al., issued Oct. 8, 1996), described in brief here. In this method soybean seed is surface sterilized by exposure to chlorine gas evolved in a glass bell jar. Seeds are germinated by plating on 1/10 strength agar solidified medium without plant growth regulators and culturing at 28° C. with a 16 hour day length. After three or four days, seed may be prepared for cocultivation. The seedcoat is removed and the elongating radicle removed 3-4 mm below the cotyledons. 
       Eucalyptus  is now considered an important crop that is grown for example to provide feedstocks for the pulp and paper and biofuel markets. This species is also amenable to transformation as described in PCT patent publication WO/2005/032241. 
       Crambe  has been recognized as a high potential oilseed crop that may be grown for the production of high value oils. An efficient method for transformation of this species has been described in PCT patent publication WO 2009/067398 A1. 
     Overnight cultures of  Agrobacterium tumefaciens  harboring the expression vector comprising a polynucleotide of the instant description are grown to log phase, pooled, and concentrated by centrifugation. Inoculations are conducted in batches such that each plate of seed was treated with a newly resuspended pellet of  Agrobacterium . The pellets are resuspended in 20 ml inoculation medium. The inoculum is poured into a Petri dish containing prepared seed and the cotyledonary nodes are macerated with a surgical blade. After 30 minutes the explants are transferred to plates of the same medium that has been solidified. Explants are embedded with the adaxial side up and level with the surface of the medium and cultured at 22° C. for three days under white fluorescent light. These plants may then be regenerated according to methods well established in the art, such as by moving the explants after three days to a liquid counter-selection medium (see U.S. Pat. No. 5,563,055). 
     The explants may then be picked, embedded and cultured in solidified selection medium. After one month on selective media transformed tissue becomes visible as green sectors of regenerating tissue against a background of bleached, less healthy tissue. Explants with green sectors are transferred to an elongation medium. Culture is continued on this medium with transfers to fresh plates every two weeks. When shoots are 0.5 cm in length they may be excised at the base and placed in a rooting medium. 
     Experimental Methods; Transformation of  Arabidopsis.    
     Transformation of  Arabidopsis  is performed by an  Agrobacterium -mediated protocol based on the method of Bechtold and Pelletier, 1998. Unless otherwise specified, all experimental work is performed using the Columbia ecotype. 
     Plant Preparation. 
       Arabidopsis  seeds are gas sterilized and sown on plates with media containing 80% MS with vitamins, 0.3% sucrose and 1% Bacto™ agar. The plates are placed at 4° in the dark for the days then transferred to 24 hour light at 22° for 7 days. After 7 days the seedlings are transplanted to soil, placing individual seedlings in each pot. The primary bolts are cut off a week before transformation to break apical dominance and encourage auxiliary shoots to form. Transformation is typically performed at 4-5 weeks after sowing. 
     Bacterial Culture Preparation. 
       Agrobacterium  stocks are inoculated from single colony plates or from glycerol stocks and grown with the appropriate antibiotics until saturation. On the morning of transformation, the saturated cultures are centrifuged and bacterial pellets are re-suspended in Infiltration Media (0.5×MS, 1× Gamborg&#39;s Vitamins, 5% sucrose, 200 μl/L Silwet® L77) until an A 600  reading of 0.8 is reached. 
     Transformation and Harvest of Transgenic Seeds. 
     The  Agrobacterium  solution is poured into dipping containers. All flower buds and rosette leaves of the plants are immersed in this solution for 30 seconds. The plants are laid on their side and wrapped to keep the humidity high. The plants are kept this way overnight at 22° C. and then the pots are turned upright, unwrapped, and moved to the growth racks. In most cases, the transformation process is repeated one week later to increase transformation efficiency. 
     The plants are maintained on the growth rack under 24-hour light until seeds are ready to be harvested. Seeds are harvested when 80% of the siliques of the transformed plants are ripe (approximately five weeks after the initial transformation). This seed is deemed T 0  seed, since it is obtained from the T 0  generation, and is later plated on selection plates (either kanamycin or sulfonamide). Resistant plants that are identified on such selection plates comprise the T1 generation, from which transgenic seed comprising an expression vector of interest may be derived. 
     Example IV. Primary Screening Materials and Methods 
     Plant Growth Conditions. 
     Seeds from  Arabidopsis  lines are chlorine gas sterilized using a standard protocol and spread onto plates containing a sucrose-based media augmented with vitamins (80% MS+Vit, 1% sucrose, 0.65% PhytoBlend™ Agar; Caisson Laboratories, Inc., North Logan, Utah) and appropriate kanamycin or sulfonamide concentrations where selection is required. Seeds are stratified in the dark on plates, at 4° C. for 3 days then moved to a walk-in growth chamber (Conviron MTW120, Conviron Controlled Environments Ltd, Winnipeg, Manitoba, Canada) running at a 10 hour photoperiod at a photosynthetic photon flux of approximately 200 μmol m −2  s −1  at plant height and a photoperiod/night temperature regime of 22° C./19° C. After seven days of light exposure seedlings are transplanted into 164 ml volume pots containing autoclaved ProMix® soil. All pots are returned to the same growth-chamber where they are stood in water and covered with a lid for the first seven days. This protocol keeps the soil moist during this period. Seven days after transplanting lids are removed and a watering and nutrition regime begun. All plants receive water three times a week, and a weekly a fertilizer treatment (80% Peter&#39;s NPK fertilizer). 
     Primary Screening. 
     Between 35 and 38 days after being transferred to lighted conditions on plates, and after between 28 and 31 days growth in soil, a suite of leaf-physiological parameters are measured using an infrared gas analyzer (LI-6400XT, LI-COR® Biosciences, Lincoln, Neb., USA) integrated with a fluorimeter that measures fluorescence from Chlorophyll A (LI-6400-40, LI-COR Biosciences). This technique involves clamping a leaf between two gaskets, effectively sealing it inside a chamber, then measuring the exchange of carbon dioxide and water vapor between the leaf and the air flowing through the chamber. This gas exchange is monitored simultaneously with the fluorescence levels from the chlorophyll a molecules in the leaf. The growth conditions used, and plant age and leaf selection criteria for measurement are designed to maximize the chance that the leaves sampled fill the 2 cm 2  leaf chamber of the gas-exchange system and that plants show no visible signs of having transitioned to reproductive growth. 
     Screening High-Light Leaf Physiology at Two Air Temperatures. 
     Leaf physiology is screened after plants have been acclimated to high light (700 μmol photons m −2  s −1 ) under LED light banks emitting visible light (400-700 nm, Photon Systems Instruments, Brno, Czech Republic), for 40 minutes. Other than the change in light level, the atmospheric environment is the same as that in which the plants have been grown, and the LI-6400 leaf chamber is set to reflect this, being set to deliver a photosynthetic photon flux of 700 μmol photons m −2  s −1  and operate at an air temperature of 22° C. Forty minutes acclimation to a photosynthetic photon flux of 700 μmol photons m −2  s −1  has repeatedly been shown to be sufficient to achieve a steady-state rate of light-saturated photosynthesis and stomatal conductance in control plants. Gas exchange and fluorescence data are logged simultaneously two minutes after the leaf has been closed in the chamber. Two minutes is found to be long enough for the leaf chamber CO 2  and H 2 O concentrations to stabilize after closing a new leaf inside, and thereby minimizing leaf physiological adjustment to small differences between the growth environment and the LI-6400 chamber. Screening at the growth air temperature of 22° C. is begun one hour into the photoperiod and is typically completed in two hours. After being screened at 22° C., plants are returned to growth-light levels prior to being screened again at 35° C. later in the photoperiod. The higher-temperature screening begins six hours into the photoperiod and measurements are made after the rosettes have been acclimated to the same high light dose as described above, but this time in a controlled environment with an air temperature set to 35° C. Measurements are again made in a leaf chamber set to match the warmer air temperature and logged using the protocol described above for the 22° C. measurements. Data generated at both 22° C. and 35° C. are used to calculate: rates of CO 2  assimilation by photosynthesis (A, μmol CO 2  m −2  s −1 ); rates of H 2 O loss through transpiration (Tr, mmol H 2 O m −2  s −1 ); the conductance to CO 2  and H 2 O movement between the leaf and air through the stomatal pore (g mol. H 2 O m −2  s −1 ); the sub-stomatal CO 2  concentration (C i , μmol CO 2  mol −1 ); transpiration efficiency, the instantaneous ratio of photosynthesis to transpiration, (TE=A/Tr (μmol CO 2  mmol H 2 O m −2  s −1 )); the rate of electron flow through photosystem two (ETR μmol e-m −2  s −1 ). Derivation of the parameters described above followed established published protocols (Long &amp; Bernacchi, 2003 . J. Exp. Botany;  54:2393-24) 
     Leaves from up to 10 replicate plants are screened for a given line of interest. Data generated from these lines are compared with that from an empty vector control line planted at the same time, grown within the same flats, and screened at the same time. 
     For control lines, data are collected not only at an atmospheric CO 2  concentration of 400 μmol CO 2  mol −1 , but also after stepwise changes in CO 2  concentration to 350, 300, 450 and 500 μmol CO 2  mol −1 . These measurements underlay screening for more complex physiological traits of: (1) photosynthetic capacity; (2) Non-photochemical quenching; and (3) non-photosynthetic metabolism. 
     Screening Photosynthetic Capacity. 
     Under most conditions, the rate of light-saturated photosynthesis in a C3 leaf is a product of the biochemical capacity of the Calvin cycle and the transfer conductance of CO 2  concentration to the sites of carboxylation (Farquhar et al., 1980 . Planta:  149, 78-90). Plotting the rate of photosynthesis against an estimate of the sub-stomatal CO 2  concentration (C i ) provides a means to identify changes in photosynthetic capacity of the Calvin cycle independent of changes in stomatal conductance, a key component of the total transfer conductance to CO 2  of the leaf. Consequently, for lines being screened, rates of photosynthesis are plotted against a regression plot of A vs. C i  generated for the control lines over a range of atmospheric CO 2  concentration, as described above. This technique enables visual confirmation of changes in photosynthetic capacity in lines of interest. 
     Screening Non-Photochemical Quenching. 
     During acclimation to high light, the efficiency with which photosystem PSII operates will reach a steady state regulated largely by the feedback between non-photochemical quenching (NPQ) in the antenna and the metabolic demand for energy produced in the chloroplast (Genty et al., 1989 . Biochim. Biophys. Acta  990:87-92; Baker et al., 2007 . Plant Cell Environ.  30:1107-1125). This understanding is used in this screen to identify lines in which the limitation that non-photochemical quenching exerts on the efficiency with which photosystem II operates is decreased or increased. A decrease in non-photochemical quenching may be the consequence of a decrease in the capacity for NPQ. This would result in lower levels of non-photochemical quenching and a higher efficiency of photosynthesis over a range of light levels, but importantly, higher rates of photosynthesis at low light where light-use efficiency is important. However, changes in rate at which NPQ responds to light could also underlie any increases or decreases in NPQ. Of these, an increase in the rate at which NPQ relaxes has the potential to increase rates of photosynthesis as leaves in crop canopies transition from high to low light, and is therefore relevant to increasing crop-canopy photosynthesis (Zhu et al., 2010 . Plant Biol.  61:235-261). In keeping with the A/Ci analysis described above, a regression of the operating efficiency of PSII against non-photochemical quenching is generated for the control line from data collected over a range of atmospheric CO 2  concentration. This technique enables visual confirmation of changes in the regulation of PSII operation that are driven by changes in non-photochemical quenching in lines of interest. 
     Screening for Non-Photosynthetic Metabolism. 
     Measurement of the ratio of the rate of electron flow through PSII (ETR) to the rate of photosynthesis (A) is used to screen for changes in non-photosynthetic metabolism. This screen is based upon the understanding that the transport of four μmol of electrons from PSII to photosystem one PSI will supply the NADPH and ATP required to fix one μmol of CO 2  in the Calvin cycle. For a C3 leaf operating in an atmosphere with 21% oxygen, the ratio of electron flow to photosynthesis should be higher than four, reflecting photorespiratory and other metabolism. However, because the rate of photorespiration in a C3 leaf is dependent upon the concentration of CO 2  at the active site of Rubisco, a regression of the ratio of electron flow to photosynthesis, generated over the range of CO 2  concentrations described above, provides the reference regression against which lines being screened can be compared to controls. Changes in the ratio of ETR to A, when observed at the same C i  as the control line, could indicate changes in the specificity of the Rubisco active site for O 2  relative to CO 2  and or other metabolic sinks which would be expected to have important implications for crop productivity and/or stress tolerance. 
     Surrogate Screening for Growth-Light Physiology. 
     Rosette biomass: the dry weight of whole  Arabidopsis  rosettes (i.e., above-ground biomass) is measured after being dried down at 80° C. for 24 hours, a time found to be sufficient to reach constant weight. Samples are taken after 35-38 days growth, and used as an assay of above-ground productivity at growth light. Typically, five replicate rosettes are sampled per  Arabidopsis  line being screened. 
     Rosette chemical and isotopic C and N analysis: after weighing, the five rosettes sampled for each line screened are pooled together and ground to a fine powder. The pooled sample generated is sub-sampled and approximately 4 μg samples are prepared for analysis. 
     Chlorophyll content index (CCI): measurements of light transmission through the leaf are made for plants being screened using a chlorophyll content meter (CCM-200, Apogee Instruments, Logan, Utah, USA). The first is made within the first hour of the photoperiod prior to any acclimation to high light on leaves of plants samples for rosette analysis. The second is made later in the photoperiod on leaves of plants that had undergone the high-temperature screening. 
     Light absorption: measurements of CCI are used as a surrogate for leaf light absorption, based upon a known relationship between the two. The estimates of light absorption by the leaf, required to construct this relationship, were made by placing the leaf on top of a quantum sensor (LI-190, LI-COR Biosciences) with both the leaf and quantum sensor then pressed firmly up to the foam gasket underneath the LI-6400 light source. This procedure provides an estimate of the transmission of a known light flux through the leaf and is used to estimate the fraction of light absorbed by the leaf. 
     Example V. Experimental Results 
     This Example provides experimental observations for transgenic plants overexpressing AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 related polypeptides assayed for improved photosynthetic resource use efficiency. 
     The ability of a crop canopy to photosynthesize, and the rate at which it can do this relative to the availability of resources, is an important determinant of crop yield. Consequently, increasing the rate of photosynthesis relative to resources that can limit productivity and yield is considered a pathway to improving crop yield across broad acres. 
     The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air to sugars, in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthetic capacity is considered a pathway to improving crop yield across broad acres. 
     Tables 23-35 and the instant Figures provide evidence for improved photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 in experiments conducted to date. All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding an AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24-related polypeptide or overexpress an AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses. 
     Table 23 describes an increased capacity for photosynthesis and increased photosynthetic rate in five independent lines overexpressing AtMYB27. Table 23 describes increased photosynthesis in five out of six independent lines overexpressing MYB27. When averaged for these five MYB27 overexpression lines, photosynthetic rate was increased by 23%. Table 5 also details how for four of these MYB27 overexpression lines this increase in photosynthetic rate is clearly linked to an increase in capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the activity of Rubisco and the capacity to regenerate RuBP in the Calvin cycle are key constraints.  FIGS. 3 and 4  display evidence of increases in both Rubisco activity and the capacity to regenerate RuBP in multiple MYB27 overexpression lines (Long &amp; Bernacchi 2003 already cited above, describe the basis for assaying Rubisco activity and RuBP regeneration capacity). For lines 1, 2 and 6, both the activity of Rubisco and the capacity to regenerate RuBP were increased by MYB27 overexpression. For line 5, only an increase in the capacity for RuBP regeneration was observed. Photosynthetic resource use efficiency was also increased in five of the six lines assayed. When averaged for these five lines, the 23% increase in photosynthetic rate was observed in tandem with a smaller, 13% increase in the nitrogen content of the rosette tissue. 
     
       
         
           
               
             
               
                 TABLE 23 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in AtMYB27 overexpression 
               
               
                 lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis) and 
               
               
                 rosette nitrogen concentration (rosette [N]). Effects on photosynthetic capacity are also described and 
               
               
                 where known the biochemical basis for the effect is described as either due to effects on Rubisco activity 
               
               
                 (Rubisco) or the capacity to regenerate RuBP (RuBP). 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Poly- 
                   
                   
                   
                   
                   
                   
               
               
                 peptide 
                 SEQ 
                   
                   
                   
                   
                   
               
               
                 Sequence/ 
                 ID 
                   
                   
                   
                 Photosynthetic 
                   
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Photosynthesis 
                 Capacity 
                 Rosette [N] 
               
               
                   
               
               
                 AtMYB 
                 2 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 27/ 
                   
                 GAL4_opLexA::GFP 
                 G1311 
                 (43%) 
                 Rubisco and 
                 (25%) 
               
               
                 Line 1 
                   
                   
                   
                   
                 RuBP 
                   
               
               
                 AtMYB 
                 2 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 27/ 
                   
                 GAL4_opLexA::GFP 
                 G1311 
                 (30%) 
                 Rubisco and 
                 (30%) 
               
               
                 Line 2 
                   
                   
                   
                   
                 RuBP 
                   
               
               
                 AtMYB 
                 2 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 No effect 
                 No effect 
                 No effect 
               
               
                 27/ 
                   
                 GAL4_opLexA::GFP 
                 G1311 
                   
                   
                   
               
               
                 Line 3 
                   
                   
                   
                   
                   
                   
               
               
                 AtMYB 
                 2 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 No effect 
                 Increased 
               
               
                 27/ 
                   
                 GAL4_opLexA::GFP 
                 G1311 
                 (14%) 
                   
                 (8%) 
               
               
                 Line 4 
                   
                   
                   
                   
                   
                   
               
               
                 AtMYB 
                 2 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 No effect 
               
               
                 27/ 
                   
                 GAL4_opLexA::GFP 
                 G1311 
                 (8%) 
                 RuBP 
                   
               
               
                 Line 5 
                   
                   
                   
                   
                   
                   
               
               
                 AtMYB 
                 2 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 27/ 
                   
                 GAL4_opLexA::GFP 
                 G1311 
                 (20%) 
                 Rubisco and 
                 (3%) 
               
               
                 Line 6 
                   
                   
                   
                   
                 RuBP 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 23 were determined after screening six independent transgenic events. Lines 1 and 2 were screened twice and the effect size reported for a given parameter is the mean of the two screening runs. For both lines the direction of the effect was the same in both runs. Lines 3, 4, 5 and 6 were screened once. 
     Table 24 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing RBP45A in experiments conducted to date. Table 24 describes increased photosynthesis in five out of six independent lines overexpressing RBP45A. When averaged for these six lines, photosynthetic rate was increased by 11% in the RBP45A overexpression lines. Leaf chlorophyll absorbs light energy utilized for photosynthesis, and was increased by 5% when average across all six lines. Rosette nitrogen content was reduced by 3% in the five lines for which it was measured. That photosynthesis is increased in RBP45A overexpression lines to a greater extent than the investment in chlorophyll, while rosette nitrogen content is decreased, provides evidence that RBP45A overexpression improves the efficiency with which photosynthesis operates relative to availability of the key resources of light and nitrogen. 
     
       
         
           
               
             
               
                 TABLE 24 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in RBP45A overexpression 
               
               
                 lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), leaf 
               
               
                 chlorophyll content and rosette nitrogen concentration (rosette [N]). 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Poly- 
                   
                   
                   
                   
                   
                   
               
               
                 peptide 
                 SEQ 
                   
                   
                   
                   
                   
               
               
                 Sequence/ 
                 ID 
                   
                   
                   
                 Leaf 
                   
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Photosynthesis 
                 Chlorophyll 
                 Rosette [N] 
               
               
                   
               
               
                 RBP45A/ 
                 42 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 No effect 
               
               
                 Line 1 
                   
                 GAL4_opLexA::GFP 
                 G1940 
                 (15%) 
                 (8%) 
                 (&lt;1%) 
               
               
                 RBP45A/ 
                 42 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Decreased 
                 — 
               
               
                 Line 2 
                   
                 GAL4_opLexA::GFP 
                 G1940 
                 (12%) 
                 (10%) 
                   
               
               
                 RBP45A/ 
                 42 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 3 
                   
                 GAL4_opLexA::GFP 
                 G1940 
                 (11%) 
                 (4%) 
                 (3%) 
               
               
                 RBP45A/ 
                 42 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 4 
                   
                 GAL4_opLexA::GFP 
                 G1940 
                 (14%) 
                 (16%) 
                 (4%) 
               
               
                 RBP45A/ 
                 42 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Decreased 
                 Decreased 
               
               
                 Line 5 
                   
                 GAL4_opLexA::GFP 
                 G1940 
                 (15%) 
                 (1%) 
                 (5%) 
               
               
                 RBP45A/ 
                 42 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Decreased 
                 Increased 
                 Increased 
               
               
                 Line 6 
                   
                 GAL4_opLexA::GFP 
                 G1940 
                 (3%) 
                 (11%) 
                 (1%) 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 24 were determined after screening six independent transgenic events. Photosynthetic rate and leaf chlorophyll were screened in two independent experiments for lines 1, and 3, and the effect size reported for is the mean of the two screening runs. The direction of the effect was the same in each screening run. Lines 2, 4, 5, and 6 were screened once. Rosette nitrogen data was collected in one experiment. 
     Table 25 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing TCP6 in experiments conducted to date. Table 25 describes increased photosynthesis in eight independent lines overexpressing TCP6. When averaged for these eight lines, photosynthetic rate was increased by 14% in the TCP6 overexpression lines. Leaf chlorophyll absorbs light energy utilized for photosynthesis, and was increased by 17% across the eight lines studied. Leaf chlorophyll and photosynthetic enzymes are a major sink for plant nitrogen. However, rosette nitrogen content increased by only 3% when averaged across the six lines for which data is available in Table 7. That photosynthesis and leaf chlorophyll content can be increased with negligible effects on rosette nitrogen content is evidence that TCP6 overexpression improves the efficiency with which photosynthesis operates relative to nitrogen availability. 
     All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a TCP6 related polypeptide or overexpress a TCP6 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses. 
     
       
         
           
               
             
               
                 TABLE 25 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in TCP6 overexpression lines. 
               
               
                 Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), leaf 
               
               
                 chlorophyll content and rosette nitrogen concentration (rosette [N]). 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Poly- 
                   
                   
                   
                   
                   
                   
               
               
                 peptide 
                 SEQ 
                   
                   
                   
                   
                   
               
               
                 Sequence 
                 ID 
                   
                   
                   
                 Leaf 
                   
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Photosynthesis 
                 Chlorophyll 
                 Rosette [N] 
               
               
                   
               
               
                 TCP6/ 
                 86 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 1 
                   
                 GAL4_opLexA::GFP 
                 G1936 
                 (9%) 
                 (10%) 
                 (2%) 
               
               
                 TCP6/ 
                 86 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 2 
                   
                 GAL4_opLexA::GFP 
                 G1936 
                 (14%) 
                 (15%) 
                 (4%) 
               
               
                 TCP6/ 
                 86 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 3 
                   
                 GAL4_opLexA::GFP 
                 G1936 
                 (10%) 
                 (17%) 
                 (18%) 
               
               
                 TCP6/ 
                 86 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 4 
                   
                 GAL4_opLexA::GFP 
                 G1936 
                 (19%) 
                 (14%) 
                 (4%) 
               
               
                 TCP6/ 
                 86 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 No effect 
               
               
                 Line 5 
                   
                 GAL4_opLexA::GFP 
                 G1936 
                 (20%) 
                 (10%) 
                   
               
               
                 TCP6/ 
                 86 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 6 
                   
                 GAL4_opLexA::GFP 
                 G1936 
                 (17%) 
                 (24%) 
                 (4%) 
               
               
                 TCP6/ 
                 86 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 — 
               
               
                 Line 7 
                   
                 GAL4_opLexA::GFP 
                 G1936 
                 (21%) 
                 (42%) 
                   
               
               
                 TCP6/ 
                 86 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 — 
               
               
                 Line 8 
                   
                 GAL4_opLexA::GFP 
                 G1936 
                 (3%) 
                 (6%) 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 25 were determined after screening eight independent transgenic events. Lines 1, 2 and 3 were screened in three independent experiments and the effect size reported for a given parameter is the mean of the three screening runs. Lines 4, 5, 6, 7 and 8 were screened once. 
     Table 26 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing PIL1 in experiments conducted to date. Table 26 describes increased photosynthesis in six independent lines overexpressing PIL1. When averaged for these six lines, photosynthetic rate was increased by 15% in the PIL1 overexpression lines. Leaf chlorophyll absorbs light energy utilized for photosynthesis, and was decreased by 2% across three lines for which data was collected. Rosette nitrogen content was increased by 1% in the same three lines. That photosynthesis could be increased in PIL1 overexpression lines while decreasing investment in chlorophyll and for a much smaller relative increase in nitrogen is evidence that PIL1 overexpression improves the efficiency with which photosynthesis operates relative to availability of the key resources of light and nitrogen. 
     All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a PIL1-related polypeptide or overexpress a PIL1 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses. 
     
       
         
           
               
             
               
                 TABLE 26 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in PIL1 overexpression lines. 
               
               
                 Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), leaf 
               
               
                 chlorophyll content and rosette nitrogen concentration (rosette [N]). 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Poly- 
                   
                   
                   
                   
                   
                   
               
               
                 peptide 
                 SEQ 
                   
                   
                   
                   
                   
               
               
                 Sequence/ 
                 ID 
                   
                   
                   
                 Leaf 
                   
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Photosynthesis 
                 Chlorophyll 
                 Rosette [N] 
               
               
                   
               
               
                 PIL1/ 
                 108 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Decreased 
                 Decreased 
               
               
                 Line 1 
                   
                 GAL4_opLexA::GFP 
                 G1649 
                 (17%) 
                 (2%) 
                 (3%) 
               
               
                 PIL1/ 
                 108 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Decreased 
                 Decreased 
               
               
                 Line 2 
                   
                 GAL4_opLexA::GFP 
                 G1649 
                 (9%) 
                 (6%) 
                 (2%) 
               
               
                 PIL1/ 
                 108 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Decreased 
                 Increased 
               
               
                 Line 3 
                   
                 GAL4_opLexA::GFP 
                 G1649 
                 (16%) 
                 (4%) 
                 (3%) 
               
               
                 PIL1/ 
                 108 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 — 
                 — 
               
               
                 Line 4 
                   
                 GAL4_opLexA::GFP 
                 G1649 
                 (23%) 
                   
                   
               
               
                 PIL1/ 
                 108 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 — 
                 — 
               
               
                 Line 5 
                   
                 GAL4_opLexA::GFP 
                 G1649 
                 (19%) 
                   
                   
               
               
                 PIL1/ 
                 108 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 — 
                 — 
               
               
                 Line 6 
                   
                 GAL4_opLexA::GFP 
                 G1649 
                 (18%) 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 26 were determined after screening six independent transgenic events. Photosynthetic rate was screened in two independent experiments for lines 1, and 2, and the effect size reported for is the mean of the two screening runs. The direction of the effect was the same in each screening run. Lines 3, 4, 5, and 6 were screened once. 
     Table 27 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing PCL1 in experiments conducted to date. 
     The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air, to sugars in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthesis and photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Table 27 describes increased photosynthesis in four out of five independent lines overexpressing PCL1. When averaged for these five lines photosynthetic rate was increased by 14% in the PCL1 overexpression lines. Table 27 also details how for four of these PCL1 overexpression lines this increase in photosynthetic rate is observed in lines that also displayed an increase in the capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the activity of Rubisco is a key constraint.  FIG. 13  displays evidence of increased in both Rubisco activity in four out of five PCL1 overexpression lines (Long &amp; Bernacchi 2003 already cited above, describe the basis for assaying Rubisco activity and RuBP regeneration capacity). 
     
       
         
           
               
             
               
                 TABLE 27 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in PCL1 overexpression lines. 
               
               
                 The effects and relative effect size is displayed for leaf photosynthetic rate (photosynthesis) Effects on 
               
               
                 photosynthetic capacity are also described and where known the biochemical basis for the effect is 
               
               
                 described as either due to effects on Rubisco activity (Rubisco) or the capacity to regenerate RuBP 
               
               
                 (RuBP). 
               
            
           
           
               
               
               
               
               
               
            
               
                 Poly- 
                   
                   
                   
                   
                   
               
               
                 peptide 
                 SEQ 
                   
                   
                   
                   
               
               
                 Sequence/ 
                 ID 
                   
                   
                   
                 Photosynthetic 
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Photosynthesis 
                 Capacity 
               
               
                   
               
               
                 PCL1/ 
                 126 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
               
               
                 Line 1 
                   
                 GAL4_opLexA::GFP 
                 G2741 
                 (16%) 
                 Rubisco 
               
               
                 PCL1/ 
                 126 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
               
               
                 Line 2 
                   
                 GAL4_opLexA::GFP 
                 G2741 
                 (30%) 
                 Rubisco 
               
               
                 PCL1/ 
                 126 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
               
               
                 Line 3 
                   
                 GAL4_opLexA::GFP 
                 G2741 
                 (9%) 
                 Rubisco 
               
               
                 PCL1/ 
                 126 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Decreased (3%) 
                 No effect 
               
               
                 Line 4 
                   
                 GAL4_opLexA::GFP 
                 G2741 
                   
                   
               
               
                 PCL1/ 
                 126 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
               
               
                 Line 5 
                   
                 GAL4_opLexA::GFP 
                 G2741 
                 (17%) 
                 Rubisco 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 27 were determined after screening five independent transgenic events. Lines 1 and 2 were screened three times, lines 3, 4 and 5 were screened twice. For all lines the effect size shown is the mean of the individual effects recorded in each independent screening run. 
     Table 28 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing GTL1 in experiments conducted to date. 
     The ability of a crop canopy to photosynthesize, and the rate at which it can do this relative to the availability of resources, is an important determinant of crop yield. Consequently, increasing the rate of photosynthesis relative to resources that can limit productivity and yield is considered a pathway to improving crop yield across broad acres. Table 28 describes an increase in leaf photosynthetic rate in GTL1 overexpression lines for plants that had decreased leaf chlorophyll content and rosette nitrogen concentration. When averaged for the four lines studied, photosynthetic rate was increased by 12% and leaf chlorophyll content decreased by 20%. Rosette nitrogen content was decreased by 6%, when averaged over the three out of the four lines for which it was measured. Increasing photosynthesis while decreasing both chlorophyll and nitrogen in the rosette provides evidence that GTL1 overexpression improves the efficiency with which photosynthesis operates relative to availability of the key resources of light and nitrogen. This combination of phenotypes would be expected to increase light-limited photosynthesis in the crop canopy while providing protection against photodamage to the photosynthetic apparatus, associated with excess light absorption, in upper canopy leaves. 
     
       
         
           
               
             
               
                 TABLE 28 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in GTL1 overexpression lines. 
               
               
                 Effects and relative effect size are displayed for leaf chlorophyll content, photosynthetic rate 
               
               
                 (photosynthesis) and rosette nitrogen concentration (rosette [N]). 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Poly- 
                   
                   
                   
                   
                   
                   
               
               
                 peptide 
                 SEQ 
                   
                   
                   
                   
                   
               
               
                 Sequence/ 
                 ID 
                   
                   
                 Leaf 
                   
                 Rosette 
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Chlorophyll 
                 Photosynthesis 
                 [N] 
               
               
                   
               
               
                 GTL1/ 
                 156 
                 prRBCS4::LexA:GAL4_ 
                 opLexA:: 
                 Decreased 
                 Increased 
                 Decreased 
               
               
                 Line 1 
                   
                 opLexA::GFP, 
                 G634 
                 (18%) 
                 (10%) 
                 (7%) 
               
               
                   
                   
                 Col_Wt 
                   
                   
                   
                   
               
               
                 GTL1/ 
                 156 
                 prRBCS4::LexA:GAL4_ 
                 opLexA:: 
                 Decreased 
                 Decreased 
                 Decreased 
               
               
                 Line 2 
                   
                 opLexA::GFP, 
                 G634 
                 (12%) 
                 (3%) 
                 (6%) 
               
               
                   
                   
                 Col_Wt 
                   
                   
                   
                   
               
               
                 GTL1/ 
                 156 
                 prRBCS4::LexA:GAL4_ 
                 opLexA:: 
                 Decreased 
                 Increased 
                 Decreased 
               
               
                 Line 3 
                   
                 opLexA::GFP, 
                 G634 
                 (22%) 
                 (14%) 
                 (5%) 
               
               
                   
                   
                 Col_Wt 
                   
                   
                   
                   
               
               
                 GTL1/ 
                 156 
                 prRBCS4::LexA:GAL4_ 
                 opLexA:: 
                 Decreased 
                 Increased 
                 — 
               
               
                 Line 4 
                   
                 opLexA::GFP, 
                 G634 
                 (26%) 
                 (22%) 
                   
               
               
                   
                   
                 Col_Wt 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 28 were determined after screening four independent transgenic events. Lines 1 and 3 were screened twice, and the effect shown is the mean of the effect observed in both experiments. Lines 2 and 4 were screened once. 
     Table 29 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing DREB2H in experiments conducted to date. Table 29 describes a decrease in leaf chlorophyll in G1755 overexpression lines that has no effect on photosynthetic rate. When averaged for the six lines studied, leaf chlorophyll content was decreased by 19%, while photosynthetic rate was increased by 2%. 
     Increasing photosynthesis while decreasing chlorophyll provides evidence that DREB2H overexpression improves the efficiency with which photosynthesis operates relative to light availability. This combination of phenotypes would be expected to increase light-limited photosynthesis in the crop canopy while providing protection against photodamage to the photosynthetic apparatus, associated with excess light absorption, in upper canopy leaves. 
     All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a DREB2H-related polypeptide or overexpress a DREB2H clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses. 
     
       
         
           
               
             
               
                 TABLE 29 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in DREB2H overexpression 
               
               
                 lines. Effects and relative effect size are displayed for leaf chlorophyll content and photosynthetic rate 
               
               
                 (photosynthesis). 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 SEQ 
                   
                   
                   
                   
               
               
                 Polypeptide 
                 ID 
                   
                   
                 Leaf 
                   
               
               
                 Sequence/Line 
                 NO: 
                 Driver 
                 Target 
                 Chlorophyll 
                 Photosynthesis 
               
               
                   
               
               
                 DREB2H/ 
                 192 
                 35S::m35S::oEnh:LexA:GAL4_ 
                 opLexA::G1755 
                 Decreased 
                 Increased 
               
               
                 Line 1 
                   
                 opLexA::GFP, Col_Wt 
                   
                 (18%) 
                 (6%) 
               
               
                 DREB2H/ 
                 192 
                 35S::m35S::oEnh:LexA:GAL4_ 
                 opLexA::G1755 
                 Decreased 
                 No effect 
               
               
                 Line 2 
                   
                 opLexA::GFP, Col_Wt 
                   
                 (19%) 
                 (&lt;1%) 
               
               
                 DREB2H/ 
                 192 
                 35S::m35S::oEnh:LexA:GAL4_ 
                 opLexA::G1755 
                 Decreased 
                 Decreased 
               
               
                 Line 3 
                   
                 opLexA::GFP, Col_Wt 
                   
                 (17%) 
                 (9%) 
               
               
                 DREB2H/ 
                 192 
                 35S::m35S::oEnh:LexA:GAL4_ 
                 opLexA::G1755 
                 Decreased 
                 Decreased 
               
               
                 Line 4 
                   
                 opLexA::GFP, Col_Wt 
                   
                 (21%) 
                 (9%) 
               
               
                 DREB2H/ 
                 192 
                 35S::m35S::oEnh:LexA:GAL4_ 
                 opLexA::G1755 
                 Decreased 
                 Increased 
               
               
                 Line 5 
                   
                 opLexA::GFP, Col_Wt 
                   
                 (14%) 
                 (32%) 
               
               
                 DREB2H/ 
                 192 
                 35S::m35S::oEnh:LexA:GAL4_ 
                 opLexA::G1755 
                 Decreased 
                 Increased 
               
               
                 Line 6 
                   
                 opLexA::GFP, Col_Wt 
                   
                 (24%) 
                 (4%) 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 29 were determined after screening six independent transgenic events. Lines 2 and 3 were screened twice, and the effect shown is the mean of the effect observed in both experiments. Lines 1, 4, 5 and 6 were screened once. 
       FIGS. 20 and 21  detail indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing ERF087 in experiments conducted to date. 
     The ability of a crop canopy to photosynthesize, and the rate at which it can do this relative to the availability of resources, is an important determinant of crop yield. Consequently, increasing the rate of photosynthesis relative to resources that can limit productivity and yield is considered a pathway to improving crop yield across broad acres.  FIGS. 20 and 21  show lower levels of non-photochemical quenching in five out of six ERF087 overexpression lines, as plants acclimated to a sudden increase in light incident on the leaves. The decrease in the ERF087 overexpression lines was most pronounced for plants acclimated to an air temperature of 35° C. ( FIG. 21 ), but was also seen for measurements made at a growth temperature of 22° C. ( FIG. 20 ). Non-photochemical quenching is a term that covers a range of processes that collectively dissipate absorbed light energy as heat from the light harvesting antenna, and thereby regulating the supply of light energy to photosystem two. Decreasing non-photochemical quenching would be expected to increase the efficiency of light energy transfer to the photosynthetic reaction centers and increase the light-use efficiency of photosynthesis. 
     Table 30 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing BBX18 in experiments conducted to date. 
     The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air, to sugars in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthesis and photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Table 30 describes increased photosynthesis in six out of six independent lines overexpressing BBX18. When averaged for these six lines photosynthetic rate was increased by 28% in the BBX18 overexpression lines. Table 30 also details how for all six of these BBX18 overexpression lines this increase in photosynthetic rate is observed in with an increase in the capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the activity of Rubisco and the capacity to regenerate RuBP, in the Calvin cycle are key constraints.  FIG. 24  displays evidence of an increase in both Rubisco activity and the capacity to regenerate RuBP in the three of the six BBX18 overexpression lines that were assayed for insights into the biochemical basis for increased photosynthetic capacity (Long &amp; Bernacchi 2003 already cited above, describe the basis for assaying Rubisco activity and RuBP regeneration capacity). When averaged over the six lines assayed, the increase in photosynthetic capacity and photosynthetic rate observed in the BBX18 overexpression lines was achieved with no increase in leaf chlorophyll content, providing evidence of optimization of resources within the photosynthetic apparatus. 
     
       
         
           
               
             
               
                 TABLE 30 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in BBX18 overexpression 
               
               
                 lines. The effects and relative effect size is displayed for leaf photosynthetic rate (photosynthesis) Effects 
               
               
                 on photosynthetic capacity are also described and, where known the biochemical basis for the effect is 
               
               
                 described as either due to effects on Rubisco activity (Rubisco) or the capacity to regenerate RuBP 
               
               
                 (RuBP). 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Poly- 
                   
                   
                   
                   
                   
                   
               
               
                 peptide 
                 SEQ 
                   
                   
                   
                   
                 Chlorophyll 
               
               
                 Sequence/ 
                 ID 
                   
                   
                   
                 Photosynthetic 
                 Content 
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Photosynthesis 
                 Capacity 
                 Index 
               
               
                   
               
               
                 BBX18/ 
                 278 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 1 
                   
                 GAL4_opLexA::GFP 
                 G1881 
                 (3%) 
                   
                 (7%) 
               
               
                 BBX18/ 
                 278 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 2 
                   
                 GAL4_opLexA::GFP 
                 G1881 
                 (16%) 
                   
                 (10%) 
               
               
                 BBX18/ 
                 278 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 3 
                   
                 GAL4_opLexA::GFP 
                 G1881 
                 (16%) 
                   
                 (6%) 
               
               
                 BBX18/ 
                 278 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 4 
                   
                 GAL4_opLexA::GFP 
                 G1881 
                 (30%) 
                 Rubisco/RuBP 
                 (8%) 
               
               
                 BBX18/ 
                 278 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 5 
                   
                 GAL4_opLexA::GFP 
                 G1881 
                 (72%) 
                 Rubisco/RuBP 
                 (5%) 
               
               
                 BBX18/ 
                 278 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 6 
                   
                 GAL4_opLexA::GFP 
                 G1881 
                 (30%) 
                 Rubisco/RuBP 
                 (10%) 
               
               
                   
               
            
           
         
       
     
     Table 31 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing bHLH60 in experiments conducted to date. Table 31 describes a decrease in leaf chlorophyll in bHLH60 overexpression lines that has no effect on photosynthetic rate. When averaged for the six lines studied, leaf chlorophyll content was decreased by 15%, while photosynthetic rate was decreased by 7%. 
     Decreasing chlorophyll provides evidence that bHLH60 overexpression improves the efficiency with which photosynthesis operates relative to light availability. This combination of phenotypes would be expected to increase light-limited photosynthesis in the crop canopy while providing protection against photodamage to the photosynthetic apparatus, associated with excess light absorption, in upper canopy leaves. 
     
       
         
           
               
             
               
                 TABLE 31 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in bHLH60 overexpression 
               
               
                 lines. Effects and relative effect size are displayed for leaf chlorophyll  
               
               
                 content and photosynthetic rate (photosynthesis). 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 SEQ 
                   
                   
                   
                   
               
               
                 Polypeptide 
                 ID 
                   
                   
                 Leaf 
                   
               
               
                 Sequence/Line 
                 NO: 
                 Driver 
                 Target 
                 Chlorophyll 
                 Photosynthesis 
               
               
                   
               
               
                 bHLH60/ 
                 318 
                 35S::m35S::oEnh:LexA:GA 
                 opLexA::G2144 
                 Decreased 
                 Decreased 
               
               
                 Line 1 
                   
                 L4_opLexA::GFP, Col_Wt 
                   
                 (16%) 
                 (8%) 
               
               
                 bHLH60/ 
                 318 
                 35S::m35S::oEnh:LexA:GA 
                 opLexA::G2144 
                 Decreased 
                 Increased 
               
               
                 Line 2 
                   
                 L4_opLexA::GFP, Col_Wt 
                   
                 (14%) 
                 (2%) 
               
               
                 bHLH60/ 
                 318 
                 35S::m35S::oEnh:LexA:GA 
                 opLexA::G2144 
                 Decreased 
                 Decreased 
               
               
                 Line 3 
                   
                 L4_opLexA::GFP, Col_Wt 
                   
                 (17%) 
                 (4%) 
               
               
                 bHLH60/ 
                 318 
                 35S::m35S::oEnh:LexA:GA 
                 opLexA::G2144 
                 Decreased 
                 Decreased 
               
               
                 Line 4 
                   
                 L4_opLexA::GFP, Col_Wt 
                   
                 (11%) 
                 (17%) 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 31 were determined after screening four independent transgenic events. Line 1 and 2 were screened twice and the data presented is the mean of the results of those two experiments. Lines 3 and 4 were screened once. 
     Table 32 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing NF-YC6 in experiments conducted to date. Table 32 describes a decrease in leaf chlorophyll in NF-YC6 overexpression lines that has no effect on photosynthetic rate. When averaged for the five lines studied, leaf chlorophyll content was decreased by 13%, while photosynthetic rate was unaffected (&lt;1% change). Rosette nitrogen content was measured for three of the five lines studied. Averaged for these three lines, rosette nitrogen content was decreased by 7% from 7.3 to 6.7% of rosette dry weight. Increasing photosynthesis while decreasing both chlorophyll and nitrogen in the rosette provides evidence that NF-YC6 overexpression improves the efficiency with which photosynthesis operates relative to the availability of the key resources of light and nitrogen. This combination of phenotypes would be expected to increase light-limited photosynthesis in the crop canopy while providing protection against photodamage to the photosynthetic apparatus, associated with excess light absorption, in upper canopy leaves. 
     
       
         
           
               
             
               
                 TABLE 32 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in NF-YC6 overexpression 
               
               
                 lines. Effects and relative effect size are displayed for leaf chlorophyll content, photosynthetic rate 
               
               
                 (photosynthesis) and rosette nitrogen concentration (rosette [N]). 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Poly- 
                   
                   
                   
                   
                   
                   
               
               
                 peptide 
                 SEQ 
                   
                   
                   
                   
                   
               
               
                 Sequence/ 
                 ID 
                   
                   
                 Leaf 
                   
                 Rosette 
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Chlorophyll 
                 Photosynthesis 
                 [N] 
               
               
                   
               
               
                 NF-YC6/ 
                 356 
                 35S::m35S::oEnh:LexA:GA 
                 opLexA:: 
                 Decreased 
                 Decreased 
                 Decreased 
               
               
                 Line 1 
                   
                 L4_opLexA::GFP, Col_Wt 
                 G1820 
                 (12%) 
                 (2%) 
                 (2%) 
               
               
                 NF-YC6/ 
                 356 
                 35S::m35S::oEnh:LexA:GA 
                 opLexA:: 
                 Decreased 
                 Increased 
                 Decreased 
               
               
                 Line 2 
                   
                 L4_opLexA::GFP, Col_Wt 
                 G1820 
                 (17%) 
                 (8%) 
                 (9%) 
               
               
                 NF-YC6/ 
                 356 
                 35S::m35S::oEnh:LexA:GA 
                 opLexA:: 
                 Decreased 
                 Decreased 
                 Decreased 
               
               
                 Line 3 
                   
                 L4_opLexA::GFP, Col_Wt 
                 G1820 
                 (11%) 
                 (3%) 
                 (11%) 
               
               
                 NF-YC6/ 
                 356 
                 35S::m35S::oEnh:LexA:GA 
                 opLexA:: 
                 Decreased 
                 No effect 
                   
               
               
                 Line 4 
                   
                 L4_opLexA::GFP, Col_Wt 
                 G1820 
                 (20%) 
                 (&lt;1%) 
                   
               
               
                 NF-YC6/ 
                 356 
                 35S::m35S::oEnh:LexA:GA 
                 opLexA:: 
                 Decreased 
                 No effect 
                   
               
               
                 Line 5 
                   
                 L4_opLexA::GFP, Col_Wt 
                 G1820 
                 (4%) 
                 (&lt;1%) 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 32 were determined after screening five independent transgenic events. Lines 1, 2 and 3 were screened twice and the effect size reported for a given parameter is the mean of the two screening runs. Lines 4 and 5 were screened once. 
     Table 33 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing bHLH121 in experiments conducted to date. 
     The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air, to sugars in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthesis and photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Table 33 describes increased photosynthesis in five out of five independent lines overexpressing bHLH121. When averaged for these five bHLH121 overexpression lines, photosynthetic rate was increased by 11%. Table 33 also details how for four of the five lines, the increase in photosynthetic rate is linked to an increase in capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the capacity to regenerate RuBP in the Calvin cycle is a key constraint.  FIG. 31  displays evidence of an increase in the capacity to regenerate RuBP in four of the five bHLH121 overexpression lines (Long &amp; Bernacchi 2003 already cited above, describe the basis for RuBP regeneration capacity). All the bHLH121 lines screened were grown in the same environment as the control lines, consequently the increase in photosynthetic capacity and photosynthetic rate observed has been achieved through an increase in photosynthetic resource-use efficiency in these lines. 
     
       
         
           
               
             
               
                 TABLE 33 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in bHLH121 overexpression 
               
               
                 lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), 
               
               
                 photosynthetic capacity and leaf chlorophyll content. Where known, the biochemical basis for increase in 
               
               
                 photosynthetic capacity is described as either due to effects on Rubisco activity (Rubisco) or the capacity 
               
               
                 to regenerate RuBP (RuBP). 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Polypeptide 
                 SEQ 
                   
                   
                   
                   
                 Leaf 
               
               
                 Sequence/ 
                 ID 
                   
                   
                   
                 Photosynthetic 
                 Chlorophyll 
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Photosynthesis 
                 capacity 
                 content 
               
               
                   
               
               
                 bHLH121/ 
                 388 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 1 
                   
                 GAL4_opLexA::GFP 
                 G782 
                 (18%) 
                 RuBP 
                 (21%) 
               
               
                 bHLH121/ 
                 388 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 No effect 
                 Increased 
               
               
                 Line 2 
                   
                 GAL4_opLexA::GFP 
                 G782 
                 (12%) 
                   
                 (18%) 
               
               
                 bHLH121/ 
                 388 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 3 
                   
                 GAL4_opLexA::GFP 
                 G782 
                 (8%) 
                 RuBP 
                 (8%) 
               
               
                 bHLH121/ 
                 388 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 4 
                   
                 GAL4_opLexA::GFP 
                 G782 
                 (2%) 
                 RuBP 
                 (9%) 
               
               
                 bHLH121/ 
                 388 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 5 
                   
                 GAL4_opLexA::GFP 
                 G782 
                 (14%) 
                 RuBP 
                 (21%) 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 33 were determined after screening six independent transgenic events. Lines 1 and 2 were screened twice and the effect size reported for a given parameter is the mean of the two screening runs. For both lines the direction of the effect was the same in both runs. Lines 3, 4 and 5 were screened once. 
     Table 34 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing BBX26 in experiments conducted to date. Table 34 describes increased photosynthesis in five out of five independent lines overexpressing BBX26 When averaged for these five BBX26 overexpression lines, photosynthetic rate was increased by 14%. Table 34 also details how for all five lines, the increase in photosynthetic rate is linked to an increase in capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the capacity to regenerate RuBP in the Calvin cycle is a key constraint.  FIG. 34  displays evidence of an increase in the capacity to regenerate RuBP in four of the five BBX26 overexpression lines (Long &amp; Bernacchi 2003 already cited above, describe the basis for RuBP regeneration capacity). Photosynthetic resource use efficiency was also increased in lines overexpressing BBX26. When averaged for these five lines, the 14% increase in photosynthetic rate was observed in tandem with a 13% increase in leaf chlorophyll content, but also with an 8% decrease in rosette nitrogen content from 7.0% to 6.4%, evidence that leaf nitrogen was being preferentially apportioned to the photosynthetic apparatus. 
     
       
         
           
               
             
               
                 TABLE 34 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in BBX26 
               
               
                 overexpression lines. Effects and relative effect size are displayed for leaf photosynthetic rate 
               
               
                 (photosynthesis), leaf chlorophyll content and rosette nitrogen concentration (rosette [N]). Effects on 
               
               
                 photosynthetic capacity (P. Cap) are also described and where known, the biochemical basis for the effect 
               
               
                 is described as either due to effects on Rubisco activity (Rubisco) or the capacity to regenerate RuBP 
               
               
                 (RuBP). 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Poly- 
                   
                   
                   
                   
                   
                   
                   
               
               
                 peptide 
                 SEQ 
                   
                   
                   
                   
                 Leaf 
                   
               
               
                 Sequence/ 
                 ID 
                   
                   
                   
                   
                 Chlorophyll 
                 Rosette 
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Photosynthesis 
                 P. Cap 
                 content 
                 [N] 
               
               
                   
               
               
                 BBX26/ 
                 410 
                 35S::m35S::oEnh:Le 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 1 
                   
                 xA:GAL4_opLexA:: 
                 G1486 
                 (15%) 
                 RuBP 
                 (9%) 
                 (6%) 
               
               
                   
                   
                 GFP 
                   
                   
                   
                   
                   
               
               
                 BBX26/ 
                 410 
                 35S::m35S::oEnh:Le 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 2 
                   
                 xA:GAL4_opLexA:: 
                 G1486 
                 (13%) 
                   
                 (24%) 
                 (5%) 
               
               
                   
                   
                 GFP 
                   
                   
                   
                   
                   
               
               
                 BBX26/ 
                 410 
                 35S::m35S::oEnh:Le 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 3 
                   
                 xA:GAL4_opLexA:: 
                 G1486 
                 (17%) 
                 RuBP 
                 (20%) 
                 (4%) 
               
               
                   
                   
                 GFP 
                   
                   
                   
                   
                   
               
               
                 BBX26/ 
                 410 
                 35S::m35S::oEnh:Le 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 4 
                   
                 xA:GAL4_opLexA:: 
                 G1486 
                 (15%) 
                 RuBP 
                 (23%) 
                 (2%) 
               
               
                   
                   
                 GFP 
                   
                   
                   
                   
                   
               
               
                 BBX26/ 
                 410 
                 35S::m35S::oEnh:Le 
                 opLexA:: 
                 Increased 
                 Increased 
                 Decreased 
                 Decreased 
               
               
                 Line 5 
                   
                 xA:GAL4_opLexA:: 
                 G1486 
                 (10%) 
                 RuBP 
                 (10%) 
                 (2%) 
               
               
                   
                   
                 GFP 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 34 were determined after screening six independent transgenic events. Lines 1 and 2 were screened twice and the effect size reported for a given parameter is the mean of the two screening runs. For both lines the direction of the effect was the same in both runs. Lines 3, 4, 5 and 6 were screened once. 
     Table 35 details indicators of photosynthetic resource use efficiency observed in  Arabidopsis  plants overexpressing PMT24 in experiments conducted to date. 
     The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air, to sugars in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthesis and photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Table 35 describes increased photosynthesis in five out of seven independent lines overexpressing PMT24. When averaged for these seven PMT24 overexpression lines, photosynthetic rate was increased by 18%. Table 35 also details how for five out of seven lines, the increase in photosynthetic rate is linked to an increase in capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the capacity to regenerate RuBP in the Calvin cycle is a key constraint.  FIG. 34  displays evidence of an increase in the capacity to regenerate RuBP in four of the five PMT24 overexpression lines run through a focused secondary screen (Long &amp; Bernacchi 2003 already cited above, describe the basis for RuBP regeneration capacity). This increase in photosynthetic capacity was achieved without any increase in leaf chlorophyll content, which was increased by less than 1% when averaged across all seven lines. These findings suggest that PMT24 overexpression changes resource investment in different components of the photosynthetic apparatus and, because all the PMT24 lines screened were grown in the same environment as the control lines, that the increase in photosynthetic capacity and photosynthetic rate observed has been achieved through an increase in photosynthetic resource-use efficiency in these lines. 
     
       
         
           
               
             
               
                 TABLE 35 
               
             
            
               
                   
               
               
                 Components of increased photosynthetic resource use efficiency in PMT24 overexpression 
               
               
                 lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), 
               
               
                 photosynthetic capacity and leaf chlorophyll content. Where know the biochemical basis for increase in 
               
               
                 photosynthetic capacity is described as either due to effects on Rubisco activity (Rubisco) or the capacity 
               
               
                 to regenerate RuBP (RuBP). 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Poly- 
                   
                   
                   
                   
                   
                   
               
               
                 peptide 
                 SEQ 
                   
                   
                   
                   
                 Leaf 
               
               
                 Sequence/ 
                 ID 
                   
                   
                   
                 Photosynthetic 
                 chlorophyll 
               
               
                 Line 
                 NO: 
                 Driver 
                 Target 
                 Photosynthesis 
                 capacity 
                 content 
               
               
                   
               
               
                 PMT24/ 
                 444 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 1 
                   
                 GAL4_opLexA::GFP 
                 G837 
                 (46%) 
                   
                 (3%) 
               
               
                 PMT24/ 
                 444 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 No effect 
                 Increased 
               
               
                 Line 2 
                   
                 GAL4_opLexA::GFP 
                 G837 
                 (26%) 
                   
                 (2%) 
               
               
                 PMT24/ 
                 444 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Increased 
               
               
                 Line 3 
                   
                 GAL4_opLexA::GFP 
                 G837 
                 (34%) 
                 RuBP 
                 (2%) 
               
               
                 PMT24/ 
                 444 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 No effect 
                 Increased 
                 Increased 
               
               
                 Line 4 
                   
                 GAL4_opLexA::GFP 
                 G837 
                 (&lt;1%) 
                 RuBP 
                 (4%) 
               
               
                 PMT24/ 
                 444 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Decreased 
                 Increased 
                 No effect 
               
               
                 Line 5 
                   
                 GAL4_opLexA::GFP 
                 G837 
                 (6%) 
                 RuBP 
                 (&lt;1%) 
               
               
                 PMT24/ 
                 444 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 Increased 
                 Decreased 
               
               
                 Line 6 
                   
                 GAL4_opLexA::GFP 
                 G837 
                 (14%) 
                 RuBP 
                 (4%) 
               
               
                 PMT24/ 
                 444 
                 35S::m35S::oEnh:LexA: 
                 opLexA:: 
                 Increased 
                 No effect 
                 Increased 
               
               
                 Line 7 
                   
                 GAL4_opLexA::GFP 
                 G837 
                 (11%) 
                   
                 (3%) 
               
               
                   
               
            
           
         
       
     
     The results presented in Table 35 were determined after screening seven independent transgenic events. Line 3 was screened twice and the effect size reported for a given parameter is the mean of the two screening runs. All other lines were screened once. 
     The present disclosure thus describes how the transformation of plants, which may include monocots and/or dicots, with an AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide can confer to the transformed plants greater photosynthetic resource use efficiency than the level of photosynthetic resource use efficiency exhibited by control plants. In one embodiment, expression of AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 is driven by a constitutive promoter. In another embodiment, expression of AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 is driven by a promoter with enhanced activity in a tissue capable of photosynthesis (also referred to herein as a “photosynthetic promoter” or a “photosynthetic tissue-enhanced promoter”) such as a leaf tissue or other green tissue. Examples of photosynthetic tissue-enhanced promoters include for example, an RBCS3 promoter (SEQ ID NO: 862), an RBCS4 promoter (SEQ ID NO: 863) or others such as the At4g01060 (also referred to as “G682”) promoter (SEQ ID NO: 864), the latter regulating expression in guard cells, or promoters listed in Table 4. Other photosynthetic tissue-enhanced promoters have been taught by Bassett et al., 2007 . BMC Biotechnol.  7: 47, specifically incorporated herein by reference in its entirety. Other photosynthetic tissue-enhanced promoters of interest include those from the maize aldolase gene FDA (U.S. patent publication no. 20040216189, specifically incorporated herein by reference in its entirety), and the aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al., 2000 . Plant Cell Physiol.  41:42-48, specifically incorporated herein by reference in its entirety). Other tissue enhanced promoters or inducible promoters are also envisioned that may be used to regulate expression of the disclosed clade member polypeptides and improve photosynthetic resource use efficiency in a variety of plants. 
     Example VI. Utilities of AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 Clade Sequences for Improving Photosynthetic Resource Use Efficiency, Yield or Biomass 
     By expressing the present polynucleotide sequences in a commercially valuable plant, the plant&#39;s phenotype may be altered to one with improved traits related to photosynthetic resource use efficiency or yield. The sequences may be introduced into the commercially valuable plant, by, for example, introducing the polynucleotide in an expression vector or cassette to produce a transgenic plant, or by crossing a target plant with a second plant that comprises said polynucleotide. The transgenic or target plant may be any valuable species of interest, including but not limited to a crop or model plant such as a wheat,  Setaria , corn (maize), rice, barley, rye, millet, sorghum, turfgrass, sugarcane, miscane, turfgrass,  Miscanthus , switchgrass, soybean, cotton, rape, oilseed rape including canola,  Eucalyptus , or poplar plant. The present polynucleotide sequences encode an AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide sequence and the ectopic expression or overexpression in the transgenic or target plant of any of said polypeptides, for example, a polypeptide comprising any of SEQ ID NOs: 2, 42, 86, 108, 126, 156, 192, 246, 278, 318, 356, 388, 410, 444, or SEQ ID NOs: 2n where n=1 to 241, or at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to any of SEQ ID NOs: 2, 42, 86, 108, 126, 156, 192, 246, 278, 318, 356, 388, 410, or 444, and/or SEQ ID NOs: 2n, where n=1 to 241, and/or at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to a domain of any of SEQ ID NOs: 483, 490, 510, 538, 566, 588, 599, 608, 623, 629, 659, 686, 702, 721, 741, 760, 769, 786, 813, and/or at least 90%, 91%, 92%, 93%, 94%, 95% m 96% m 97%, 98%, 99%, or about 100% identity to any of consensus sequences SEQ ID NOs: 842-861, can confer improved photosynthetic resource use efficiency or yield in the plant. For plants for which biomass is the product of interest, increasing the expression level of AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade of polypeptide sequences may increase yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant of the plants. Thus, it is thus expected that these sequences will improve yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant in non- Arabidopsis  plants relative to control plants. This yield improvement may result in yield increases of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30% or greater yield relative to the yield that may be obtained with control plants. 
     It is expected that the same methods may be applied to identify other useful and valuable sequences that are functionally-related and/or closely-related to the listed sequences or domains provided in the instant Tables, and the sequences may be derived from diverse species. Because of morphological, physiological and photosynthetic resource use efficiency similarities that may occur among closely-related sequences, the disclosed clade sequences are expected to increase yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant to a variety of crop plants, ornamental plants, and woody plants used in the food, ornamental, paper, pulp, lumber or other industries. 
     Example VII: Expression and Analysis of Increased Yield or Photosynthetic Resource Use Efficiency in Non- Arabidopsis  or Crop Species 
     Northern blot analysis, RT-PCR or microarray analysis of the regenerated, transformed plants may be used to show expression of a polypeptide or the instant description and related genes that are capable of inducing improved photosynthetic resource use efficiency, and/or larger size. 
     After a eudicot plant, monocot plant or plant cell has been transformed (and the latter plant host cell regenerated into a plant) and shown to have or produce increased yield, increased light use efficiency, increased photosynthetic capacity, increased photosynthetic rate, photosynthetic resource use efficiency, greater vigor, and/or greater biomass as compared to a control plant relative to a control plant, the transformed monocot plant may be crossed with itself or a plant from the same line, a non-transformed or wild-type monocot plant, or another transformed monocot plant from a different transgenic line of plants. 
     The function of one or more specific polypeptides of the instant description has been analyzed and may be further characterized and incorporated into crop plants. The ectopic overexpression of one or more of the disclosed clade polypeptide sequences may be regulated using constitutive, inducible, or tissue-enhanced regulatory elements. Genes that have been examined have been shown to modify plant traits including increasing yield and/or photosynthetic resource use efficiency. It is expected that newly discovered polynucleotide and polypeptide sequences closely related, as determined by the disclosed hybridization or identity analyses, to polynucleotide and polypeptide sequences found in the Sequence Listing can also confer alteration of traits in a similar manner to the sequences found in the Sequence Listing, when transformed into any of a considerable variety of plants of different species, and including dicots and monocots. The polynucleotide and polypeptide sequences derived from monocots (e.g., the rice sequences) may be used to transform both monocot and dicot plants, and those derived from dicots (e.g., the  Arabidopsis  and soy genes) may be used to transform either group, although it is expected that some of these sequences will function best if the gene is transformed into a plant from the same group as that from which the sequence is derived. 
     As an example of a first step to determine photosynthetic resource use efficiency, seeds of these transgenic plants may be grown as described above or methods known in the art. 
     Closely-related homologs of AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 derived from various diverse plant species may be overexpressed in plants and have the same functions of conferring increased photosynthetic resource use efficiency. It is thus expected that structurally similar orthologs of the disclosed polypeptide clades, including SEQ ID NOs: 2n where n=1 to 241, orthologs that comprise any of consensus sequences SEQ ID NOs: 842-861, can confer increased yield, increased light use efficiency, increased photosynthetic capacity, increased photosynthetic rate, increased photosynthetic resource use efficiency, greater vigor, greater biomass, and/or size, relative to control plants. As at least one sequence of the instant description has increased photosynthetic resource use efficiency in  Arabidopsis , it is expected that the sequences provided in the Sequence Listing, or polypeptide sequences comprising one of or any of the conserved domains provided in the instant Tables, will increase the photosynthetic resource use efficiency and/or yield of transgenic plants including transgenic non- Arabidopsis  (plant species other than  Arabidopsis  species) crop or other commercially important plant species, including, but not limited to, non- Arabidopsis  plants and plant species such as monocots and dicots, wheat,  Setaria , corn (maize), teosinte ( Zea  species which is related to maize), rice, barley, rye, millet, sorghum, turfgrass, sugarcane, miscane, turfgrass,  Miscanthus , switchgrass, soybean, cotton, rape, oilseed rape including canola, tobacco, tomato, tomatillo, potato, sunflower, alfalfa, clover, banana, blackberry, blueberry, strawberry, raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion,  papaya , peas, peppers, pineapple, pumpkin, spinach, squash, sweet corn, watermelon, rosaceous fruits including apple, peach, pear, cherry and plum, and brassicas including broccoli, cabbage, cauliflower, Brussels sprouts, and kohlrabi, currant, avocado, citrus fruits including oranges, lemons, grapefruit and tangerines, artichoke, cherries, endive, leek, roots such as arrowroot, beet, cassava, turnip, radish, yam, and sweet potato, beans, woody species including pine, poplar,  Eucalyptus , mint or other labiates, nuts such as walnut and peanut. Within each of these species the closely-related homologs of AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 may be overexpressed or ectopically expressed in different varieties, cultivars, or germplasm. 
     The instantly disclosed transgenic plants comprising the disclosed recombinant polynucleotides can be enhanced with other polynucleotides, resulting in a plant or plants with “stacked” or jointly introduced traits, for example, the traits of increased photosynthetic resource use efficiency and improved yield combined with an enhanced trait resulting from expression of a polynucleotide that confers herbicide, insect or and/or pest resistance in a single plant or in two or more parental lines. The disclosed polynucleotides may thus be stacked with a nucleic acid sequence providing other useful or valuable traits such as a nucleic acid sequence from  Bacillus thuringensis  that confers resistance to hemiopteran, homopteran, lepidopteran, coliopteran or other insects or pests. 
     Thus, the disclosed sequences and closely related, functionally related sequences may be identified that, when ectopically expressed or overexpressed in plants, confer one or more characteristics that lead to greater photosynthetic resource use efficiency. These characteristics include, but are not limited to, the embodiments listed below. 
     1. A dicot or monocot transgenic plant that has greater or increased photosynthetic resource use efficiency †  relative to a control plant; 
     wherein the transgenic plant comprises an exogenous recombinant polynucleotide comprising a promoter selected from the group consisting of: 
     a constitutive promoter, a non-constitutive promoter, an inducible promoter, a tissue-enhanced promoter, and a photosynthetic tissue-enhanced promoter; 
     wherein the promoter regulates expression of a polypeptide having a percentage identity to an amino acid sequence comprising an AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide in a photosynthetic or green tissue of the transgenic plant; 
     wherein the percentage identity is at least:
         26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identity to the entire length of any of SEQ ID NOs: 2n, where n=1-241; and/or   at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identity to a domain of any of SEQ ID NOs: 483 to 841; and/or   at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to a consensus sequence of any of SEQ ID NO: 842-861; and/or   the exogenous recombinant polynucleotide hybridizes with any of SEQ ID NO: 1, 41, 85, 107, 125, 155, 191, 245, 277, 317, 355, 387, 409, or 443 under stringent hybridization conditions followed by one, two, or more wash steps of 6×SSC and 65° C. for ten to thirty minutes per step;       

     wherein expression of the polypeptide under the regulatory control of the promoter confers greater or increased photosynthetic resource use efficiency in the transgenic plant relative to the control plant; 
     wherein the control plant does not comprise the recombinant polynucleotide; and/or 
     2. The transgenic plant of embodiment 1, wherein the photosynthetic tissue-enhanced promoter is an RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an Os02g09720 promoter, an Os05g34510 promoter, an Os11g08230 promoter, an Os01g64390 promoter, an Os06g15760 promoter, an Os12g37560 promoter, an Os03g17420 promoter, an Os04g51000 promoter, an Os01g01960 promoter, an Os05g04990 promoter, an Os02g44970 promoter, an Os01g25530 promoter, an Os03g30650 promoter, an Os01g64910 promoter, an Os07g26810 promoter, an Os07g26820 promoter, an Os09g11220 promoter, an Os04g21800 promoter, an Os10g23840 promoter, an Os08g13850 promoter, an Os12g42980 promoter, an Os03g29280 promoter, an Os03g20650 promoter, or an Os06g43920 promoter (SEQ ID NO: 862-888, respectively), or a functional variant thereof, or a functional fragment thereof, or a promoter sequence that is at least 80% identical to SEQ ID NO: 862-888; and/or
 
3. The transgenic plant of embodiments 1 or 2, wherein:
 
     the recombinant polynucleotide encodes the polypeptide which comprises any of SEQ ID NOs: 2n, where n=1-241; and/or 
     any of SEQ ID NOs: 483, 490, 510, 538, 566, 588, 599, 608, 623, 629, 659, 686, 702, 721, 741, 760, 769, 786, 813; and/or 
     any of SEQ ID NO: 842-861; and/or 
     4. The transgenic plant of any of embodiments 1 to 3, wherein the polypeptide is encoded by 
     (a) the exogenous recombinant polynucleotide, or 
     (b) a second exogenous recombinant polynucleotide and expression of the polypeptide is regulated by a trans-regulatory element; and/or 
     5. The transgenic plant of any of embodiments 1 to 4, wherein a plurality of the transgenic plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density; and/or
 
6. The transgenic plant of any of embodiments 1 to 5, wherein the transgenic plant produces a greater yield than the control plant, including, but not limited to, a greater yield of: vegetative biomass, plant parts, whole plants, shoot vegetative organs/structures (for example, leaves, stems and tubers), roots, flowers and floral organs/structures (for example, bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (for example, vascular tissue, ground tissue, pulped, pureed, ground-up, macerated or broken-up tissue, and the like) and cells (for example, guard cells, egg cells, and the like); and/or
 
7. The transgenic plant of any of embodiments 1 to 6, wherein the transgenic plant is selected from the group consisting of a corn, wheat, rice,  Setaria, Miscanthus , switchgrass, ryegrass, sugarcane, miscane, barley, sorghum, turfgrass, soy, cotton, canola, rapeseed,  Crambe, Camelina , sugar beet, alfalfa, tomato,  Eucalyptus , poplar, willow, pine, birch and a woody plant; and/or
 
8. The transgenic plant of any of embodiments 1 to 7, wherein the transgenic plant is morphologically similar to the control plant at one or more stages of growth, and/or developmentally similar to the control plant.
 
9. A method for increasing photosynthetic resource use efficiency †  in a dicot or monocot plant, the method comprising:
 
     (a) providing one or more dicot or monocot plants that comprise an exogenous recombinant polynucleotide comprising a promoter selected from the group consisting of: 
     a constitutive promoter, a non-constitutive promoter, an inducible promoter, a tissue-enhanced promoter, and a photosynthetic tissue-enhanced promoter; 
     wherein the promoter regulates expression of a polypeptide having a percentage identity to an amino acid sequence comprising an AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide in a photosynthetic or green tissue of the dicot or monocot plant; 
     wherein the percentage identity is at least:
         26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identity to the entire length of any of SEQ ID NOs: 2n, where n=1-241; and/or   at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identity to a domain of any of SEQ ID NOs: 483 to 841; and/or   at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to a consensus sequence of any of SEQ ID NO: 842-861; and/or   the exogenous recombinant polynucleotide hybridizes with any of SEQ ID NO: 1, 41, 85, 107, 125, 155, 191, 245, 277, 317, 355, 387, 409, or 443 under stringent hybridization conditions followed by one, two, or more wash steps of 6×SSC and 65° C. for ten to thirty minutes per step;   wherein expression of the polypeptide in the one or more dicot or monocot plants confers greater or increased photosynthetic resource use efficiency relative to a control plant that does not comprise the recombinant polynucleotide; and       

     (b) growing the one or more dicot or monocot plants; and/or 
     10. The method of embodiment 9, wherein the photosynthetic tissue-enhanced promoter is an RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an Os02g09720 promoter, an Os05g34510 promoter, an Os11g08230 promoter, an Os01g64390 promoter, an Os06g15760 promoter, an Os12g37560 promoter, an Os03g17420 promoter, an Os04g51000 promoter, an Os01g01960 promoter, an Os05g04990 promoter, an Os02g44970 promoter, an Os01g25530 promoter, an Os03g30650 promoter, an Os01g64910 promoter, an Os07g26810 promoter, an Os07g26820 promoter, an Os09g11220 promoter, an Os04g21800 promoter, an Os10g23840 promoter, an Os08g13850 promoter, an Os12g42980 promoter, an Os03g29280 promoter, an Os03g20650 promoter, or an Os06g43920 promoter (SEQ ID NO: 862-888, respectively), or a functional variant thereof, or a functional fragment thereof, or a promoter sequence that is at least 80% identical to SEQ ID NO: 862-888; and/or
 
11. The method of embodiments 9 or 10, wherein an expression cassette comprising the recombinant polynucleotide is introduced into a target plant to produce the dicot or monocot plant comprising the exogenous recombinant polynucleotide; and/or
 
12. The method of any of embodiments 9 to 11, wherein the polypeptide is encoded by
 
     (a) the exogenous recombinant polynucleotide, or 
     (b) a second exogenous recombinant polynucleotide and expression of the polypeptide is regulated by a trans-regulatory element; and/or 
     13. The method of any of embodiments 9 to 12, wherein the dicot or monocot plant is selected for having the increased photosynthetic resource use efficiency relative to the control plant; and/or
 
14. The method of any of embodiments 9 to 13, wherein the dicot or monocot plant produces a greater yield relative to the control plant; and/or
 
15. The method of any of embodiments 9 to 14, wherein the dicot or monocot plant is selected for having the greater yield relative to the control plant; and/or
 
16. The method of any of embodiments 9 to 15, wherein a plurality of the dicot or monocot plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density; and/or
 
17. The method of any of embodiments 9 to 16, wherein the dicot or monocot plant is selected from the group consisting of a corn, wheat, rice,  Setaria, Miscanthus , switchgrass, ryegrass, sugarcane, miscane, barley, sorghum, turfgrass, soy, cotton, canola, rapeseed,  Crambe, Camelina , sugar beet, alfalfa, tomato,  Eucalyptus , poplar, willow, pine, birch and a woody plant; and/or
 
18. The method of any of embodiments 9 to 17, the method steps further including:
 
     crossing the dicot or monocot plant with itself, a second plant from the same line as the dicot or monocot plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed. 
     19. A method for producing and selecting a dicot or monocot crop plant with greater yield or greater photosynthetic resource use efficiency †  than a control plant, the method comprising:
         (a) providing one or more dicot or monocot transgenic plants that comprise an exogenous recombinant polynucleotide comprising a promoter selected from the group consisting of:
           a constitutive promoter, a non-constitutive promoter, an inducible promoter, a tissue-enhanced promoter, and a photosynthetic tissue-enhanced promoter;   wherein the promoter regulates expression of a polypeptide having a percentage identity to an amino acid sequence comprising an AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide in a photosynthetic or green tissue of the dicot or monocot transgenic plant;   wherein the percentage identity is:   at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identity to the entire length of any of SEQ ID NOs: 2n, where n=1-241; and/or   at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identity to a domain of any of SEQ ID NOs: 483 to 841; and/or   at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to a consensus sequence of any of SEQ ID NO: 842-861; and/or   
           the exogenous recombinant polynucleotide hybridizes with any of SEQ ID NO: 1, 41, 85, 107, 125, 155, 191, 245, 277, 317, 355, 387, 409, or 443 under stringent hybridization conditions followed by one, two, or more wash steps of 6×SSC and 65° C. for ten to thirty minutes per step;
           wherein the photosynthetic tissue-enhanced promoter does not regulate protein expression in a constitutive manner;   
           (b) growing a plurality of the dicot or monocot transgenic plants; and   (c) selecting a dicot or monocot transgenic plant that:
           has greater photosynthetic resource use efficiency than the control plant, wherein the control plant does not comprise the recombinant polynucleotide; and/or   comprises the recombinant polynucleotide;   
           wherein expression of the polypeptide in the selected dicot or monocot transgenic plant confers the greater photosynthetic resource use efficiency or the greater yield relative to the control plant; and/or
 
20. The method of embodiment 19, the method steps further including:
   (d) crossing the selected dicot or monocot transgenic plant with itself, a second plant from the same line as the selected transgenic plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed; and/or
 
21. The method of embodiment 19 or 20, wherein the dicot or monocot transgenic plant is selected for having the increased photosynthetic resource use efficiency relative to the control plant; and/or
 
22. The method of any of embodiments 19 to 21, wherein a plurality of the selected dicot or monocot transgenic plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density; and/or
 
23. The method of any of embodiments 19 to 22, wherein the selected dicot or monocot transgenic plant has an altered trait that confers the greater photosynthetic resource use efficiency.
 
24. A method for producing a dicot or monocot crop plant with greater photosynthetic resource use efficiency †  than a control plant, the method comprising:
   (a) providing a dicot or monocot transgenic plant that comprises an exogenous recombinant polynucleotide that comprises a promoter selected from the group consisting of:
           a constitutive promoter, a non-constitutive promoter, an inducible promoter, a tissue-enhanced promoter, or a photosynthetic tissue-enhanced promoter;   wherein the promoter regulates expression of a polypeptide comprising SEQ ID NO: 2, 42, 86, 108, 126, 156, 192, 246, 278, 318, 356, 388, 410, or 444 in a photosynthetic or green tissue of the transgenic plant to a level that is effective in conferring greater photosynthetic resource use efficiency in the transgenic plant relative to the control plant; and   
           (b) measuring an altered trait that confers the greater photosynthetic resource use efficiency,
           wherein expression of the polypeptide in the selected dicot or monocot transgenic plant confers the greater photosynthetic resource use efficiency of the transgenic plant relative to the control plant, thereby producing the crop plant with greater photosynthetic resource use efficiency than the control plant; and/or
 
25. The method of embodiment 24, wherein the transgenic dicot or monocot plant is selected for having the increased photosynthetic resource use efficiency relative to the control plant.
 
26. A method for producing a monocot plant with increased grain yield, said method including:
   
           (a) providing a monocot plant cell or plant tissue with stably integrated, exogenous recombinant polynucleotide comprising a promoter (for example, a constitutive, a non-constitutive, an inducible, a tissue-enhanced, or a photosynthetic tissue-enhanced promoter) that is functional in plant cells and that is operably linked to an exogenous or an endogenous nucleic acid sequence that encodes a polypeptide that has a percentage identity to an amino acid sequence comprising an AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide, wherein the percentage identity is:
           at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identity to the entire length of any of SEQ ID NOs: 2n, where n=1-241; and/or   at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identity to a domain of any of SEQ ID NOs: 483 to 841; and/or   at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to a consensus sequence of any of SEQ ID NO: 842-861; and/or   the exogenous recombinant polynucleotide hybridizes with any of SEQ ID NO: 1, 41, 85, 107, 125, 155, 191, 245, 277, 317, 355, 387, 409, or 443 under stringent hybridization conditions followed by one, two, or more wash steps of 6×SSC and 65° C. for ten to thirty minutes per step;   
           (b) generating a monocot plant from the plant cell or the plant tissue, wherein the monocot plant comprises the exogenous recombinant polynucleotide, wherein the polypeptide is expressed in a photosynthetic or green tissue of the monocot plant to a level that is effective in conferring greater photosynthetic resource use efficiency† in the monocot plant relative to a control plant that does not contain the recombinant polynucleotide;   (c) growing the monocot plant; and   (d) measuring an increase in photosynthetic resource use efficiency of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 2%, 28%, 29%, or 30% relative to the control plant, or an increase in grain yield of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 2%, 28%, 29%, or 30% or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 bushels per acre;   thereby producing the monocot plant with increased grain yield relative to the control plant; and/or
 
27. The method of embodiment 26, wherein the AtMYB27, RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide comprises a consensus sequence of one or more of any of SEQ ID NOs: 842-861; and/or
 
28. A transgenic monocot plant produced by the method of embodiment 26; and/or
 
29. The transgenic monocot plant of embodiment 28, wherein transgenic monocot plant is a corn, wheat, rice,  Miscanthus, Setaria , switchgrass, ryegrass, sugarcane, miscane, barley, sorghum or turfgrass plant; and/or
 
30. The method of embodiment 26, wherein the promoter is an RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an Os02g09720 promoter, an Os05g34510 promoter, an Os11g08230 promoter, an Os01g64390 promoter, an Os06g15760 promoter, an Os12g37560 promoter, an Os03g17420 promoter, an Os04g51000 promoter, an Os01g01960 promoter, an Os05g04990 promoter, an Os02g44970 promoter, an Os01g25530 promoter, an Os03g30650 promoter, an Os01g64910 promoter, an Os07g26810 promoter, an Os07g26820 promoter, an Os09g11220 promoter, an Os04g21800 promoter, an Os10g23840 promoter, an Os08g13850 promoter, an Os12g42980 promoter, an Os03g29280 promoter, an Os03g20650 promoter, or an Os06g43920 promoter (SEQ ID NO: 862-888, respectively) or a Cauliflower Mosaic 35S promoter, or a functional variant thereof, or a functional fragment thereof, or a promoter sequence that is at least 80% identical to SEQ ID NO: 862-888; and/or
 
31. The method of embodiment 28, wherein the clade polypeptide comprises any of SEQ ID NO: 2, 42, 86, 108, 126, 156, 192, 246, 278, 318, 356, 388, 410, or 444. † In the above embodiments 1, 9, 19, 24, and 26, greater photosynthetic resource use efficiency may be characterized by or measured as, but is not limited to, any one or more of following measurements or characteristics relative to a control plant. The measured or altered trait may be selected from the group consisting of:(a) increased photosynthetic capacity, measured as an increase in the rate of light-saturated photosynthesis of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, or 40% when compared to the rate of light-saturated photosynthesis of a control leaf at the same leaf-internal CO 2  concentration. Optionally, measurements are made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; and/or(b) increased photosynthetic rate, measured as an increase in the rate of light-saturated photosynthesis of at least 5%, 10%, 15%, 19%, 20%, 22%, 23%, 25%, 30%, 32%, 35%, or 40%. Optionally, measurements are made after 40 minutes of acclimation to a light intensity known to be saturating for photosynthesis; and/or(c) a decrease in the chlorophyll content of the leaf of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, or 40%, observed in the absence of a decrease in photosynthetic capacity; and/or(d) a decrease in the percentage of the leaf dry weight that is nitrogen of at least 0.5%, 1.0%, 1.5%, 2.0%, 2.5%, 3.0%, 3.5%, or 4.0% observed in the absence of a decrease in photosynthetic capacity or increase in dry weight; and/or(e) increased transpiration efficiency, measured as an increase in the rate of light-saturated photosynthesis relative to water loss via transpiration from the leaf, of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, or 40%; optionally, measurements are made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m −2  s −1 ; and/or(f) an increase in the resistance to water vapor diffusion out of the leaf that is exerted by the stomata, measured as a decrease in stomatal conductance to H 2 O loss from the leaf of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, or 40%; optionally, measurements were are after 40 minutes of acclimation to a light intensity of 700 μmol PAR m-2 s-1; and/or(g) a decrease in the resistance to carbon dioxide diffusion into the leaf that is exerted by the stomata, measured as an increase in stomatal conductance of at least 5%, 10%, 13%, 15%, 20%, 25%, 27%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, or 68%; optionally, measurements were are after 40 minutes of acclimation to a light intensity of 700 μmol PAR m-2 s-1; and/or(h) a decrease in non-photochemical quenching of at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, or at least 10%, for leaf measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m −2  s −1 ; and/or(i) a decrease in the ratio of the carbon isotope  12 C to  13 C found in either all the dried above-ground biomass, or specific components of the above-ground biomass, e.g., leaves or reproductive structures, of at least 0.5‰ (0.5 per mille), or at least 1.0‰, 1.5‰, 2.0‰, 2.5‰, 3.0‰, 3.5‰, or 4.0‰ measured as a decrease in the ratio of  12 C to  13 C relative to the controls with both ratio being expressed relative to the same standard; and/or(j) an increase in the total dry weight of above-ground plant material of at least 5%, 10%, 15%, 20%, 23%, 25%, 30%, 32%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, or 75%.
       

     All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference. 
     The present invention is not limited by the specific embodiments described herein. The invention now being fully described, it will be apparent to one of ordinary skill in the art that many changes and modifications can be made thereto without departing from the spirit or scope of the appended claims. Modifications that become apparent from the foregoing description and accompanying figures fall within the scope of the claims.