# Patent

## Title
Plants having enhanced yield-related traits and a method for making the same

## Abstract

The present invention relates generally to the field of molecular biology and concerns a method for enhancing yield related traits by modulating expression in a plant of a nucleic acid encoding a BET1-like polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding this BET1-like polypeptide, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants. The invention also provides constructs useful in the methods of the invention.
The present invention relates generally to the field of molecular biology and concerns a method for improving various plant growth characteristics by modulating expression in a plant of a nucleic acid encoding a CRT (Calreticulin). The present invention also concerns plants having modulated expression of a nucleic acid encoding a Calreticulin, which plants have improved growth characteristics relative to corresponding wild type plants or other control plants. The invention also provides hereto unknown Calreticulin polynucleotides, polypeptides and constructs useful in the methods of the invention.
The present invention relates generally to the field of molecular biology and concerns a method for increasing various plant yield-related traits by increasing expression in a plant of a nucleic acid sequence encoding a tRNA dihydrouridine synthase 1-like (DUS1L) polypeptide. The present invention also concerns plants having increased expression of a nucleic acid sequence encoding a DUS1L polypeptide, which plants have increased yield-related traits relative to control plants. The invention additionally relates to nucleic acid sequences, nucleic acid constructs, vectors and plants containing said nucleic acid sequences.
The present invention relates generally to the field of molecular biology and concerns a method for enhancing yield-related traits by modulating expression in a plant of a nucleic acid encoding an ES43-like polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding an ES43_like polypeptide, which plants have improved growth characteristics relative to corresponding wild type plants or other control plants. The invention also provides hereto unknown ES43-like polynucleotides and polypeptides and constructs useful in the methods of the invention.
The present invention relates generally to the field of molecular biology and concerns a method for enhancing various economically important yield-related traits in plants. More specifically, the present invention concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding an HON5-like polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding an HON5-like polypeptide, which plants have enhanced yield-related traits relative to control plants. The invention also provides hitherto unknown HON5-like-encoding nucleic acids, and constructs comprising the same, useful in performing the methods of the invention.
The present invention relates generally to the field of molecular biology and concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding a glutamate-1-semialdehyde aminotransferase (GSA1) polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding a GSA1, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants. The invention also provides constructs useful in the methods of the invention.

## Background
RELATED APPLICATIONS
This application is a national stage application (under 35 U.S.C. §371) of PCT/EP2010/052122 , filed Feb. 19, 2010, which claims benefit of U.S. Provisional Application 61/155,182, filed Feb. 25, 2009 ; U.S. Provisional Application 61/155,180, filed Feb. 25, 2009; U.S. Provisional Application 61/155,192, filed Feb. 25, 2009; U.S. Provisional Application 61/155,179, filed Feb. 25, 2009; U.S. Provisional Application 61/155,177, filed Feb. 25, 2009; U.S. Provisional Application 61/155,185, filed Feb. 25, 2009; European application 09100150.3, filed Feb. 25, 2009; European application 09100148.7, filed Feb. 25, 2009; European application 09100151.1, filed Feb. 25, 2009; European application 09100147.9, filed Feb. 25, 2009; European application 09156049.0, filed Mar. 24, 2009; U.S. Provisional Application 61/162,733, filed Mar. 24, 2009; European application 09004255.7, filed Mar. 25, 2009; and U.S. Provisional Application 61/163,469, filed Mar. 26, 2009.


SUBMISSION OF SEQUENCE LISTING
The Sequence Listing associated with this application is filed in electronic format via EFS-Web and hereby incorporated by reference into the specification in its entirety. The name of the text file containing the Sequence Listing is Revised_Sequence_List—13987—00150_US. The size of the text file is 962 KB, and the text file was created on Dec. 12, 2011.
The present invention relates generally to the field of molecular biology and concerns a method for enhancing yield related traits by modulating expression in a plant of a nucleic acid encoding a BET1-like polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding this BET1-like polypeptide, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants. The invention also provides constructs useful in the methods of the invention.
The present invention relates generally to the field of molecular biology and concerns a method for improving various plant growth characteristics by modulating expression in a plant of a nucleic acid encoding a CRT (Calreticulin). The present invention also concerns plants having modulated expression of a nucleic acid encoding a Calreticulin, which plants have improved growth characteristics relative to corresponding wild type plants or other control plants. The invention also provides hereto unknown Calreticulin polynucleotides, polypeptides and constructs useful in the methods of the invention.
The present invention relates generally to the field of molecular biology and concerns a method for increasing various plant yield-related traits by increasing expression in a plant of a nucleic acid sequence encoding a tRNA dihydrouridine synthase 1-like (DUS1L) polypeptide. The present invention also concerns plants having increased expression of a nucleic acid sequence encoding a DUS1L polypeptide, which plants have increased yield-related traits relative to control plants. The invention additionally relates to nucleic acid sequences, nucleic acid constructs, vectors and plants containing said nucleic acid sequences.
The present invention relates generally to the field of molecular biology and concerns a method for enhancing yield-related traits by modulating expression in a plant of a nucleic acid encoding an ES43-like polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding an ES43_like polypeptide, which plants have improved growth characteristics relative to corresponding wild type plants or other control plants. The invention also provides hereto unknown ES43-like polynucleotides and polypeptides and constructs useful in the methods of the invention.
The present invention relates generally to the field of molecular biology and concerns a method for enhancing various economically important yield-related traits in plants. More specifically, the present invention concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding an HON5-like polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding an HON5-like polypeptide, which plants have enhanced yield-related traits relative to control plants. The invention also provides hitherto unknown HON5-like-encoding nucleic acids, and constructs comprising the same, useful in performing the methods of the invention.
The present invention relates generally to the field of molecular biology and concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding a glutamate-1-semialdehyde aminotransferase (GSA1) polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding a GSA1, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants. The invention also provides constructs useful in the methods of the invention.
The ever-increasing world population and the dwindling supply of arable land available for agriculture fuels research towards increasing the efficiency of agriculture. Conventional means for crop and horticultural improvements utilise selective breeding techniques to identify plants having desirable characteristics. However, such selective breeding techniques have several drawbacks, namely that these techniques are typically labour intensive and result in plants that often contain heterogeneous genetic components that may not always result in the desirable trait being passed on from parent plants. Advances in molecular biology have allowed mankind to modify the germplasm of animals and plants. Genetic engineering of plants entails the isolation and manipulation of genetic material (typically in the form of DNA or RNA) and the subsequent introduction of that genetic material into a plant. Such technology has the capacity to deliver crops or plants having various improved economic, agronomic or horticultural traits.
A trait of particular economic interest is increased yield. Yield is normally defined as the measurable produce of economic value from a crop. This may be defined in terms of quantity and/or quality. Yield is directly dependent on several factors, for example, the number and size of the organs, plant architecture (for example, the number of branches), seed production, leaf senescence and more. Root development, nutrient uptake, stress tolerance and early vigour may also be important factors in determining yield. Optimizing the abovementioned factors may therefore contribute to increasing crop yield.
Seed yield is a particularly important trait, since the seeds of many plants are important for human and animal nutrition. Crops such as corn, rice, wheat, canola and soybean account for over half the total human caloric intake, whether through direct consumption of the seeds themselves or through consumption of meat products raised on processed seeds. They are also a source of sugars, oils and many kinds of metabolites used in industrial processes. Seeds contain an embryo (the source of new shoots and roots) and an endosperm (the source of nutrients for embryo growth during germination and during early growth of seedlings). The development of a seed involves many genes, and requires the transfer of metabolites from roots, leaves and stems into the growing seed. The endosperm, in particular, assimilates the metabolic precursors of carbohydrates, oils and proteins and synthesizes them into storage macromolecules to fill out the grain.
Plant biomass is yield for forage crops like alfalfa, silage corn and hay. Many proxies for yield have been used in grain crops. Chief amongst these are estimates of plant size. Plant size can be measured in many ways depending on species and developmental stage, but include total plant dry weight, above-ground dry weight, above-ground fresh weight, leaf area, stem volume, plant height, rosette diameter, leaf length, root length, root mass, tiller number and leaf number. Many species maintain a conservative ratio between the size of different parts of the plant at a given developmental stage. These allometric relationships are used to extrapolate from one of these measures of size to another (e.g. Tittonell et al 2005 Agric Ecosys & Environ 105: 213). Plant size at an early developmental stage will typically correlate with plant size later in development. A larger plant with a greater leaf area can typically absorb more light and carbon dioxide than a smaller plant and therefore will likely gain a greater weight during the same period (Fasoula & Tollenaar 2005 Maydica 50:39). This is in addition to the potential continuation of the micro-environmental or genetic advantage that the plant had to achieve the larger size initially. There is a strong genetic component to plant size and growth rate (e.g. ter Steege et al 2005 Plant Physiology 139:1078), and so for a range of diverse genotypes plant size under one environmental condition is likely to correlate with size under another (Hittalmani et al 2003 Theoretical Applied Genetics 107:679). In this way a standard environment is used as a proxy for the diverse and dynamic environments encountered at different locations and times by crops in the field.
Another important trait for many crops is early vigour. Improving early vigour is an important objective of modern rice breeding programs in both temperate and tropical rice cultivars. Long roots are important for proper soil anchorage in water-seeded rice. Where rice is sown directly into flooded fields, and where plants must emerge rapidly through water, longer shoots are associated with vigour. Where drill-seeding is practiced, longer mesocotyls and coleoptiles are important for good seedling emergence. The ability to engineer early vigour into plants would be of great importance in agriculture. For example, poor early vigour has been a limitation to the introduction of maize (Zea mays L.) hybrids based on Corn Belt germplasm in the European Atlantic.
Harvest index, the ratio of seed yield to aboveground dry weight, is relatively stable under many environmental conditions and so a robust correlation between plant size and grain yield can often be obtained (e.g. Rebetzke et al 2002 Crop Science 42:739). These processes are intrinsically linked because the majority of grain biomass is dependent on current or stored photosynthetic productivity by the leaves and stem of the plant (Gardener et al 1985 Physiology of Crop Plants. Iowa State University Press, pp 68-73). Therefore, selecting for plant size, even at early stages of development, has been used as an indicator for future potential yield (e.g. Tittonell et al 2005 Agric Ecosys & Environ 105: 213). When testing for the impact of genetic differences on stress tolerance, the ability to standardize soil properties, temperature, water and nutrient availability and light intensity is an intrinsic advantage of greenhouse or plant growth chamber environments compared to the field. However, artificial limitations on yield due to poor pollination due to the absence of wind or insects, or insufficient space for mature root or canopy growth, can restrict the use of these controlled environments for testing yield differences. Therefore, measurements of plant size in early development, under standardized conditions in a growth chamber or greenhouse, are standard practices to provide indication of potential genetic yield advantages.
A further important trait is that of improved abiotic stress tolerance. Abiotic stress is a primary cause of crop loss worldwide, reducing average yields for most major crop plants by more than 50% (Wang et al., Planta (2003) 218: 1-14). Abiotic stresses may be caused by drought, salinity, extremes of temperature, chemical toxicity, excess or deficiency of nutrients (macroelements and/or microelements), radiation and oxidative stress. The ability to improve plant tolerance to abiotic stress would be of great economic advantage to farmers worldwide and would allow for the cultivation of crops during adverse conditions and in territories where cultivation of crops may not otherwise be possible.
Crop yield may therefore be increased by optimising one of the above-mentioned factors.
Depending on the end use, the modification of certain yield traits may be favoured over others. For example for applications such as forage or wood production, or bio-fuel resource, an increase in the vegetative parts of a plant may be desirable, and for applications such as flour, starch or oil production, an increase in seed parameters may be particularly desirable. Even amongst the seed parameters, some may be favoured over others, depending on the application. Various mechanisms may contribute to increasing seed yield, whether that is in the form of increased seed size or increased seed number.
One approach to increasing yield (seed yield and/or biomass) in plants may be through modification of the inherent growth mechanisms of a plant, such as the cell cycle or various signalling pathways involved in plant growth or in defense mechanisms.
It has now been found that various yield-related traits may be improved in plants by modulating expression in a plant of a nucleic acid encoding a BET1-like polypeptide in a plant.
It has now also been found that various growth characteristics may be improved in plants by modulating expression in a plant of a nucleic acid encoding a Calreticulin (a CRT polypeptide) in a plant.
It has now also been found that various yield-related traits may be increased in plants relative to control plants by increasing expression in a plant of a nucleic acid sequence encoding a tRNA dihydrouridine synthase 1-like (DUS1L) polypeptide. The increased yield-related traits comprise one or more of: increased aboveground biomass, increased seed yield per plant, increased number of filled seeds, and increased total number of seeds.
It has now also been found that various growth characteristics may be improved in plants by modulating expression in a plant of a nucleic acid encoding an ES43-like polypeptide in a plant.
It has now also been found that various yield-related traits may be improved in plants by modulating expression in a plant of a nucleic acid encoding a HON5-like polypeptide in a plant.
It has now also been found that various growth characteristics may be improved in plants by modulating expression in a plant of a nucleic acid encoding a GSA1 polypeptide in a plant.
BACKGROUND
1. BET1-Like Polypeptides
Gregorio Hueros et. al. (Plant Cell, Vol. 7, 747-757, 6/1995 Am. Soc. Plant Physiol.) disclosed a cDNA clone, BET1 (for basal endosperm transfer layer), isolated from a cDNA bank prepared from 10-days after pollination (DAP) maize endosperm mRNA. BET1 mRNA showed to encode a 7-kD cell wall polypeptide. Both the mRNA and protein were restricted in their distribution to the basal endosperm transfer layer and were not expressed elsewhere in the plant. BET1 expression commenced at 9 DAP, reached a maximum between 12 and 16 DAP, and declined after 16 DAP. The initial accumulation of the BET1 polypeptide reached a plateau by 16 DAP and declined thereafter, becoming undetectable by 20 DAP. The antibody raised against the BET1 protein reacted with a number of polypeptides of higher molecular mass than the BET1 monomer. Most of these were present in cytosolic fractions and were found in nonbasal cell endosperm extracts, but three species appeared to be basal cell specific. This result and the reactivity of exhaustively extracted cell wall material with the BET1 antibody suggest that a fraction of the protein is deposited in a covalently bound form in the extracellular matrix. It was proposed that BET1 protein plays a role in the structural specialization of the transfer cells. In addition, BET1 provides a new molecular marker for the development of this endosperm domain.
2. Calreticulin Polypeptides
Calcium plays an essential role in multiple signal transduction pathways both in plants and in animals. Cytoplasmic calcium concentrations are tightly regulated at 100-200 nM but higher levels, in the range of micro- and milli-molar are found in subcellular organelles. In plants calcium is an also a micronutrient.
Calreticulin (CRT), a protein involved in the modulation of the ER (endoplasmic reticulum) Ca2+(Calcium)-ATPase, is found in all eukaryotes. Studies in mammalians filed have elucidated the structure of the CRT proteins and a number of key physiological functions, including control of cell adhesion and signal transduction through calcium-binding and quality control of protein folding and posttranscriptional modifications (Michalak. Biochem J. 2009 417(3):651-66).
Structurally CRT proteins are characterized by three distinct domains: a globular neutral N-domain, a proline-rich P-domain, and a polyacidic C-domain. CRT also has an N-terminal signal peptide sequence and an ER retention motif in the C-domain. The P-domain is responsible for the high-affinity (in the order of Kd 1.6 micromolar) and low-capacity Ca2+ binding while the C-domain is responsible for the low-affinity (in the order of Kd 0.3-2 mM) and high-capacity Ca2+ binding. CRT polypeptides include an N-terminal signal sequence and an ER-retention motif in the C-domain. Within the P-domain, there are two types of triplicate repeated motifs that are highly conserved among various animal species. However, the C-domain is less conserved than other domains of CRT. Four amino acid residues at the tip of the “extended arm” of the P-domain are critical in the chaperone function of CRT. The C-domain is involved n the Ca2+ storage in the lumen of the ER (Michalak. Biochem J. 1992, 285 (Pt 3):681-92.).
In plants, CRT proteins share same structural features and similar Ca2+ binding proteins as their animal counterparts. Phylogenetic studies revealed that plant CRT fall into two evolutionary related groups, the so called CRT1/2 and CRT3. CRT1/2 are often localized to the plasmodesmata of the cell. Plant CRT have been proposed to play a role in regeneration, gravitropism, signal transduction, and regulation of stress tolerance (Christensen et al. 2008, Plant Cell Physiol. 49(6): 912-924).
BrCRT1, a CRT form Brassica rapa when expressed in transgenic tobacco plants displayed no obvious phenotypic differences in appearance, time of flowering, or seed production when grown to maturity in soil and a weak growth inhibition of seedlings (Jin at al. 2005 Transgenic Res. 14(5):619-26).
3. tRNA Dihydrouridine Synthase 1-Like Polypeptides (DUS1L Polypeptides)
In translation, transfer RNA is the central adapter molecule as it physically links the genetic information of messenger RNA, and the addition of correctly ordered amino acids to a growing polypeptide chain. One of the structural features of tRNA is the presence of a wide variety of post-transcriptionally modified RNA bases. Dihydrouridine is one of the most abundant modified tRNA bases in prokaryotes and eukaryotes. It differs from uridine only by the reduction of uridine's carbon-carbon double bond (non-aromatic base), and is found almost exclusively at preferred positions in the D-loop of tRNA, which can further contain varying numbers of dihydrouridine residues (Bishop et al. (2002) 277(28): 25090-25095). The most likely chemical role of dihydrouridine is to enhance the conformational flexibility of tRNA, and thus improve the translational efficiencies.
The family of dihydrouridine synthase (DUS) enzymes, which catalyze the modification of uridine to dihydrouridine, has been identified in Saccharomyces cerevisiae and E. coli (Bishop et al, supra). DUSs comprise a discrete gene family (3 members in E. coli YjbN, YhdG, and Yohl, at least 4 members in yeast YML080w or DUS1, YNR015w, YLR405w, and YLR401c), allowing putative DUS genes from other organisms to be proposed based on sequence homology. Such homologs have been found for example in human, chimpanzee, dog, cow, mouse, hicken, zebrafish, fruit fly, mosquito, C. elegans, rice, and P. falciparum. In the Arabidopsis genome, at least 3 genes have been identified as potentially encoding DUS enzymes (AT3G49640, AT4G38890, AT5G67220 or DUS1 like). One of these genes encodes a polypepyide with higher similarity to the DUS1 enzyme, and is therefore called DUS1 like (DUS1L) enzyme.
In international application WO 02/66660 “Method for identifying herbicidally active substances” a nucleic acid sequence is described encoding a DUS1L polypeptide (SEQ ID NO: 84), and constructs comprising this sequence. Transgenic plants lacking the gene product present significantly delayed growth and/or completely stunted growth at the embryonic stage of Arabidopsis thaliana. The invention relates to the use of said genes and the gene products coded thereby for discovering novel herbicides.
Surprisingly, it has now been found that increasing expression in a plant of a nucleic acid sequence encoding a DUS1L polypeptide as defined herein, gives plants having increased yield-related traits relative to control plants.
According to one embodiment, there is provided a method for increasing yield-related traits in plants relative to control plants, comprising increasing expression in a plant of a nucleic acid sequence encoding a DUS1L polypeptide as defined herein. The increased yield-related traits comprise one or more of: increased aboveground biomass, increased seed yield per plant, increased number of filled seeds, and increased total number of seeds.
4. ES43-Like Polypeptides
The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation (FEBS Lett. 1999 March 5; 446(1):189-93).
PHD domains are protein Zinc finger domains that fold into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains (Pascual et al. J Mol Biol 2000; 304:723-729). Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
The PHD (homeodomain) zinc finger domain which is a C4HC3 zinc-finger-like motif found in nuclear proteins is thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger (Aasland et al. Trends Biochem Sci. 1995 February; 20(2):56-9).
A number of plant proteins comprising both BAH and PHD finger domains have been described. For Example the ES43 protein of Balery (Speulman and Salamini Plant Sci.
106, 91-98 (1995), SHL (Mussig et al. Mol Gen Genet. 2000 November; 264(4):363-70) and EBS (Pi{umlaut over (n)}eiro et al. Plant Cell. 2003 July; 15(7):1552-62) of Arabidopsis thaliana. EBS has been implicated in the transcriptional repressor complex that modulates chromatin structure and is required to repress the initiation of flowering in short days. Overexpression of EBS caused early flowering in Arabidopsis thaliana plants (Pi{umlaut over (n)}eiro et al. 2003).
5. HON5-Like Polypeptides
High-mobility-group (HMG) proteins are small and relatively abundant chromatin-associated proteins, biochemically defined as small proteins typically around 30 KDa, having a relatively high proportion of basic and acidic amino acids, and capable of solubilising in dilute perchloric or trichloroacetic acid.
Plants and animals possess a family of HMG proteins that are similar on the basis of a shared motif known as the AT-hook, a domain that preferentially recognizes and binds to DNA with certain structural features, such as those imparted by AT-rich DNA. Since these proteins recognize chromatin and/or DNA structure (such as the structure imparted by AT-rich DNA) rather than as specific DNA sequence, they have been named architectural transcription factors.
Much of the information available on the function of the animal HMGA family has been inferred to the plant HMG-1/Y family of AT-hook proteins.
In plants, two groups of chromosomal HMG proteins have been identified, namely the HMGA family, typically containing four A/T-hook DNA-binding motifs, and the HMGB family, containing a single HMG-box DNA-binding domain. Both plant and animal AT hook proteins bind AT-rich tracts of DNA in the minor groove, induce DNA bending, and function in the regulation of gene expression. By orchestrating multiple protein-protein and protein-DNA interactions, the HMGA proteins assist the formation of higher-order transcription factor complexes, regulating gene expression (Klosterman et al; Plant Science 162 (2002) 855—866).
SUMMARY
1. BET1-Like Polypeptides
Surprisingly, it has now been found that modulating expression of a nucleic acid encoding a BET1-like polypeptide gives plants enhanced yield-related traits, in particular increased yield relative to control plants.
According one embodiment, there is provided a method for increasing plant yield relative to control plants, comprising modulating expression of a nucleic acid encoding a BET1-like polypeptide in a plant.
2. Calreticulin Polypeptides
Surprisingly, it has now been found that modulating expression of a nucleic acid encoding a Calreticulin polypeptide gives plants having enhanced yield-related traits relative to control plants.
According one embodiment, there is provided a method for enhancing yield related traits of a plant relative to control plants, comprising modulating expression of a nucleic acid encoding a Calreticulin polypeptide in a plant.
3. ES43-Like Polypeptides
Surprisingly, it has now been found that modulating expression of a nucleic acid encoding an ES43-like polypeptide gives plants having enhanced yield-related traits in particular increased yield relative to control plants.
According one embodiment, there is provided a method for enhancing yield-related traits of a plant relative to control plants, comprising modulating expression of a nucleic acid encoding an ES43-like polypeptide in a plant.
4. HON5-Like Polypeptides
Surprisingly, it has now been found that modulating expression of a nucleic acid encoding a HON5-like polypeptide gives plants having enhanced yield-related traits, relative to control plants.
According one embodiment, there is provided a method for enhancing yield-related traits of a plant relative to control plants, comprising modulating expression of a nucleic acid encoding a HON5-like polypeptide in a plant.
5. glutamate-1-semialdehyde aminotransferase polypeptides (GSA1 polypeptides)
Surprisingly, it has now been found that modulating expression of a nucleic acid encoding a GSA1 polypeptide gives plants having enhanced yield-related traits, in particular (increased seed yield) relative to control plants.
According one embodiment, there is provided a method for enhancing yield related traits of a plant relative to control plants, comprising modulating expression of a nucleic acid encoding a GSA1 polypeptide in a plant.
Definitions
Polypeptide(s)/Protein(s)
The terms “polypeptide” and “protein” are used interchangeably herein and refer to amino acids in a polymeric form of any length, linked together by peptide bonds.
Polynucleotide(s)/Nucleic Acid(s)/Nucleic Acid Sequence(s)/Nucleotide Sequence(s)
The terms “polynucleotide(s)”, “nucleic acid sequence(s)”, “nucleotide sequence(s)”, “nucleic acid(s)”, “nucleic acid molecule” are used interchangeably herein and refer to nucleotides, either ribonucleotides or deoxyribonucleotides or a combination of both, in a polymeric unbranched form of any length.
Homologue(s)
“Homologues” of a protein encompass peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived.
A deletion refers to removal of one or more amino acids from a protein.
An insertion refers to one or more amino acid residues being introduced into a predetermined site in a protein. Insertions may comprise N-terminal and/or C-terminal fusions as well as intra-sequence insertions of single or multiple amino acids. Generally, insertions within the amino acid sequence will be smaller than N- or C-terminal fusions, of the order of about 1 to 10 residues. Examples of N- or C-terminal fusion proteins or peptides include the binding domain or activation domain of a transcriptional activator as used in the yeast two-hybrid system, phage coat proteins, (histidine)-6-tag, glutathione S-transferase-tag, protein A, maltose-binding protein, dihydrofolate reductase, Tag•100 epitope, c-myc epitope, FLAG®-epitope, lacZ, CMP (calmodulin-binding peptide), HA epitope, protein C epitope and VSV epitope.
A substitution refers to replacement of amino acids of the protein with other amino acids having similar properties (such as similar hydrophobicity, hydrophilicity, antigenicity, propensity to form or break α-helical structures or β-sheet structures). Amino acid substitutions are typically of single residues, but may be clustered depending upon functional constraints placed upon the polypeptide and may range from 1 to 10 amino acids; insertions will usually be of the order of about 1 to 10 amino acid residues. The amino acid substitutions are preferably conservative amino acid substitutions. Conservative substitution tables are well known in the art (see for example Creighton (1984) Proteins. W.H. Freeman and Company (Eds) and Table 1 below).







TABLE 1







Examples of conserved amino acid substitutions










Residue
Conservative 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



Ser
Thr; Gly



Thr
Ser; Val



Trp
Tyr



Tyr
Trp; Phe



Val
Ile; Leu










Amino acid substitutions, deletions and/or insertions may readily be made using peptide synthetic techniques well known in the art, such as solid phase peptide synthesis and the like, or by recombinant DNA manipulation. Methods for the manipulation of DNA sequences to produce substitution, insertion or deletion variants of a protein are well known in the art. For example, techniques for making substitution mutations at predetermined sites in DNA are well known to those skilled in the art and include M13 mutagenesis, T7-Gen in vitro mutagenesis (USB, Cleveland, Ohio), QuickChange Site Directed mutagenesis (Stratagene, San Diego, Calif.), PCR-mediated site-directed mutagenesis or other site-directed mutagenesis protocols.
Derivatives
“Derivatives” include peptides, oligopeptides, polypeptides which may, compared to the amino acid sequence of the naturally-occurring form of the protein, such as the protein of interest, comprise substitutions of amino acids with non-naturally occurring amino acid residues, or additions of non-naturally occurring amino acid residues. “Derivatives” of a protein also encompass peptides, oligopeptides, polypeptides which comprise naturally occurring altered (glycosylated, acylated, prenylated, phosphorylated, myristoylated, sulphated etc.) or non-naturally altered amino acid residues compared to the amino acid sequence of a naturally-occurring form of the polypeptide. A derivative may also comprise one or more non-amino acid substituents or additions compared to the amino acid sequence from which it is derived, for example a reporter molecule or other ligand, covalently or non-covalently bound to the amino acid sequence, such as a reporter molecule which is bound to facilitate its detection, and non-naturally occurring amino acid residues relative to the amino acid sequence of a naturally-occurring protein. Furthermore, “derivatives” also include fusions of the naturally-occurring form of the protein with tagging peptides such as FLAG, HIS6 or thioredoxin (for a review of tagging peptides, see Terpe, Appl. Microbiol. Biotechnol. 60, 523-533, 2003).
Orthologue(s)/Paralogue(s)
Orthologues and paralogues encompass evolutionary concepts used to describe the ancestral relationships of genes. Paralogues are genes within the same species that have originated through duplication of an ancestral gene; orthologues are genes from different organisms that have originated through speciation, and are also derived from a common ancestral gene.
Domain, Motif/Consensus Sequence/Signature
The term “domain” refers to a set of amino acids conserved at specific positions along an alignment of sequences of evolutionarily related proteins. While amino acids at other positions can vary between homologues, amino acids that are highly conserved at specific positions indicate amino acids that are likely essential in the structure, stability or function of a protein. Identified by their high degree of conservation in aligned sequences of a family of protein homologues, they can be used as identifiers to determine if any polypeptide in question belongs to a previously identified polypeptide family.
The term “motif” or “consensus sequence” or “signature” refers to a short conserved region in the sequence of evolutionarily related proteins. Motifs are frequently highly conserved parts of domains, but may also include only part of the domain, or be located outside of conserved domain (if all of the amino acids of the motif fall outside of a defined domain).
Specialist databases exist for the identification of domains, for example, SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244), InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318), Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation. (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAI Press, Menlo Park; Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004)), or Pfam (Bateman et al., Nucleic Acids Research 30(1): 276-280 (2002)). A set of tools for in silico analysis of protein sequences is available on the ExPASy proteomics server (Swiss Institute of Bioinformatics (Gasteiger et al., ExPASy: the proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Res. 31:3784-3788 (2003)). Domains or motifs may also be identified using routine techniques, such as by sequence alignment.
Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the global (i.e. spanning the complete sequences) alignment of two sequences that maximizes the number of matches and minimizes the number of gaps. The BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology Information (NCBI). Homologues may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1.83), with the default pairwise alignment parameters, and a scoring method in percentage. Global percentages of similarity and identity may also be determined using one of the methods available in the MatGAT software package (Campanella et al., BMC Bioinformatics. 2003 July 10; 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.). Minor manual editing may be performed to optimise alignment between conserved motifs, as would be apparent to a person skilled in the art. Furthermore, instead of using full-length sequences for the identification of homologues, specific domains may also be used. The sequence identity values may be determined over the entire nucleic acid or amino acid sequence or over selected domains or conserved motif(s), using the programs mentioned above using the default parameters. For local alignments, the Smith-Waterman algorithm is particularly useful (Smith T F, Waterman Miss. (1981) J. Mol. Biol. 147(1); 195-7).
Reciprocal BLAST
Typically, this involves a first BLAST involving BLASTing a query sequence (for example using any of the sequences listed in Table A of the Examples section) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are generally used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived. The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence amongst the highest hits; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.
High-ranking hits are those having a low E-value. The lower the E-value, the more significant the score (or in other words the lower the chance that the hit was found by chance). Computation of the E-value is well known in the art. In addition to E-values, comparisons are also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In the case of large families, ClustalW may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues.
Hybridisation
The term “hybridisation” as defined herein is a process wherein substantially homologous complementary nucleotide sequences anneal to each other. The hybridisation process can occur entirely in solution, i.e. both complementary nucleic acids are in solution. The hybridisation process can also occur with one of the complementary nucleic acids immobilised to a matrix such as magnetic beads, Sepharose beads or any other resin. The hybridisation process can furthermore occur with one of the complementary nucleic acids immobilised to a solid support such as a nitro-cellulose or nylon membrane or immobilised by e.g. photolithography to, for example, a siliceous glass support (the latter known as nucleic acid arrays or microarrays or as nucleic acid chips). In order to allow hybridisation to occur, the nucleic acid molecules are generally thermally or chemically denatured to melt a double strand into two single strands and/or to remove hairpins or other secondary structures from single stranded nucleic acids.
The term “stringency” refers to the conditions under which a hybridisation takes place. The stringency of hybridisation is influenced by conditions such as temperature, salt concentration, ionic strength and hybridisation buffer composition. Generally, low stringency conditions are selected to be about 30° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. Medium stringency conditions are when the temperature is 20° C. below Tm, and high stringency conditions are when the temperature is 10° C. below Tm. High stringency hybridisation conditions are typically used for isolating hybridising sequences that have high sequence similarity to the target nucleic acid sequence. However, nucleic acids may deviate in sequence and still encode a substantially identical polypeptide, due to the degeneracy of the genetic code. Therefore medium stringency hybridisation conditions may sometimes be needed to identify such nucleic acid molecules.
The Tm is the temperature under defined ionic strength and pH, at which 50% of the target sequence hybridises to a perfectly matched probe. The Tm is dependent upon the solution conditions and the base composition and length of the probe. For example, longer sequences hybridise specifically at higher temperatures. The maximum rate of hybridisation is obtained from about 16° C. up to 32° C. below Tm. The presence of monovalent cations in the hybridisation solution reduce the electrostatic repulsion between the two nucleic acid strands thereby promoting hybrid formation; this effect is visible for sodium concentrations of up to 0.4M (for higher concentrations, this effect may be ignored). Formamide reduces the melting temperature of DNA-DNA and DNA-RNA duplexes with 0.6 to 0.7° C. for each percent formamide, and addition of 50% formamide allows hybridisation to be performed at 30 to 45° C., though the rate of hybridisation will be lowered. Base pair mismatches reduce the hybridisation rate and the thermal stability of the duplexes. On average and for large probes, the Tm decreases about 1° C. per % base mismatch. The Tm may be calculated using the following equations, depending on the types of hybrids:
1) DNA-DNA hybrids (Meinkoth and Wahl, Anal. Biochem., 138: 267-284, 1984):

Tm=81.5° C.+16.6×log10 [Na+]a+0.41×%[G/Cb]−500×[Lc]−1−0.61×% formamide

2) DNA-RNA or RNA-RNA hybrids:

Tm=79.8+18.5(log10 [Na+]a)+0.58(% G/Cb)+11.8(% G/Cb)2−820/Lc 

3) oligo-DNA or oligo-RNAs hybrids:

For <20 nucleotides: Tm=2(ln)

For 20-35 nucleotides: Tm=22+1.46(ln)

    
    
        a or for other monovalent cation, but only accurate in the 0.01-0.4 M range.
        b only accurate for % GC in the 30% to 75% range.
        cL=length of duplex in base pairs.
        d oligo, oligonucleotide; ln, =effective length of primer=2×(no. of G/C)+(no. of A/T).
    
    


Non-specific binding may be controlled using any one of a number of known techniques such as, for example, blocking the membrane with protein containing solutions, additions of heterologous RNA, DNA, and SDS to the hybridisation buffer, and treatment with Rnase. For non-homologous probes, a series of hybridizations may be performed by varying one of (i) progressively lowering the annealing temperature (for example from 68° C. to 42° C.) or (ii) progressively lowering the formamide concentration (for example from 50% to 0%). The skilled artisan is aware of various parameters which may be altered during hybridisation and which will either maintain or change the stringency conditions.
Besides the hybridisation conditions, specificity of hybridisation typically also depends on the function of post-hybridisation washes. To remove background resulting from non-specific hybridisation, samples are washed with dilute salt solutions. Critical factors of such washes include the ionic strength and temperature of the final wash solution: the lower the salt concentration and the higher the wash temperature, the higher the stringency of the wash. Wash conditions are typically performed at or below hybridisation stringency. A positive hybridisation gives a signal that is at least twice of that of the background. Generally, suitable stringent conditions for nucleic acid hybridisation assays or gene amplification detection procedures are as set forth above. More or less stringent conditions may also be selected. The skilled artisan is aware of various parameters which may be altered during washing and which will either maintain or change the stringency conditions.
For example, typical high stringency hybridisation conditions for DNA hybrids longer than 50 nucleotides encompass hybridisation at 65° C. in 1×SSC or at 42° C. in 1×SSC and 50% formamide, followed by washing at 65° C. in 0.3×SSC. Examples of medium stringency hybridisation conditions for DNA hybrids longer than 50 nucleotides encompass hybridisation at 50° C. in 4×SSC or at 40° C. in 6×SSC and 50% formamide, followed by washing at 50° C. in 2×SSC. The length of the hybrid is the anticipated length for the hybridising nucleic acid. When nucleic acids of known sequence are hybridised, the hybrid length may be determined by aligning the sequences and identifying the conserved regions described herein. 1×SSC is 0.15M NaCl and 15 mM sodium citrate; the hybridisation solution and wash solutions may additionally include 5×Denhardt's reagent, 0.5-1.0% SDS, 100 μg/ml denatured, fragmented salmon sperm DNA, 0.5% sodium pyrophosphate.
For the purposes of defining the level of stringency, reference can be made to Sambrook et al. (2001) Molecular Cloning: a laboratory manual, 3rd Edition, Cold Spring Harbor Laboratory Press, CSH, New York or to Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989 and yearly updates).
Splice Variant
The term “splice variant” as used herein encompasses variants of a nucleic acid sequence in which selected introns and/or exons have been excised, replaced, displaced or added, or in which introns have been shortened or lengthened. Such variants will be ones in which the biological activity of the protein is substantially retained; this may be achieved by selectively retaining functional segments of the protein. Such splice variants may be found in nature or may be manmade. Methods for predicting and isolating such splice variants are well known in the art (see for example Foissac and Schiex (2005) BMC Bioinformatics 6: 25).
Allelic Variant
Alleles or allelic variants are alternative forms of a given gene, located at the same chromosomal position. Allelic variants encompass Single Nucleotide Polymorphisms (SNPs), as well as Small Insertion/Deletion Polymorphisms (INDELs). The size of INDELs is usually less than 100 bp. SNPs and INDELs form the largest set of sequence variants in naturally occurring polymorphic strains of most organisms.
Endogenous Gene
Reference herein to an “endogenous” gene not only refers to the gene in question as found in a plant in its natural form (i.e., without there being any human intervention), but also refers to that same gene (or a substantially homologous nucleic acid/gene) in an isolated form subsequently (re)introduced into a plant (a transgene). For example, a transgenic plant containing such a transgene may encounter a substantial reduction of the transgene expression and/or substantial reduction of expression of the endogenous gene. The isolated gene may be isolated from an organism or may be manmade, for example by chemical synthesis.
Gene Shuffling/Directed Evolution
Gene shuffling or directed evolution consists of iterations of DNA shuffling followed by appropriate screening and/or selection to generate variants of nucleic acids or portions thereof encoding proteins having a modified biological activity (Castle et al., (2004) Science 304(5674): 1151-4; U.S. Pat. Nos. 5,811,238 and 6,395,547).
Construct
Additional regulatory elements may include transcriptional as well as translational enhancers. Those skilled in the art will be aware of terminator and enhancer sequences that may be suitable for use in performing the invention. An intron sequence may also be added to the 5′ untranslated region (UTR) or in the coding sequence to increase the amount of the mature message that accumulates in the cytosol, as described in the definitions section. Other control sequences (besides promoter, enhancer, silencer, intron sequences, 3′UTR and/or 5′UTR regions) may be protein and/or RNA stabilizing elements. Such sequences would be known or may readily be obtained by a person skilled in the art.
The genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type. One example is when a genetic construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to, the f1-ori and colE1.
For the detection of the successful transfer of the nucleic acid sequences as used in the methods of the invention and/or selection of transgenic plants comprising these nucleic acids, it is advantageous to use marker genes (or reporter genes). Therefore, the genetic construct may optionally comprise a selectable marker gene. Selectable markers are described in more detail in the “definitions” section herein. The marker genes may be removed or excised from the transgenic cell once they are no longer needed. Techniques for marker removal are known in the art, useful techniques are described above in the definitions section.
Regulatory Element/Control Sequence/Promoter
The terms “regulatory element”, “control sequence” and “promoter” are all used interchangeably herein and are to be taken in a broad context to refer to regulatory nucleic acid sequences capable of effecting expression of the sequences to which they are ligated. The term “promoter” typically refers to a nucleic acid control sequence located upstream from the transcriptional start of a gene and which is involved in recognising and binding of RNA polymerase and other proteins, thereby directing transcription of an operably linked nucleic acid. Encompassed by the aforementioned terms are transcriptional regulatory sequences derived from a classical eukaryotic genomic gene (including the TATA box which is required for accurate transcription initiation, with or without a CCAAT box sequence) and additional regulatory elements (i.e. upstream activating sequences, enhancers and silencers) which alter gene expression in response to developmental and/or external stimuli, or in a tissue-specific manner. Also included within the term is a transcriptional regulatory sequence of a classical prokaryotic gene, in which case it may include a −35 box sequence and/or −10 box transcriptional regulatory sequences. The term “regulatory element” also encompasses a synthetic fusion molecule or derivative that confers, activates or enhances expression of a nucleic acid molecule in a cell, tissue or organ.
A “plant promoter” comprises regulatory elements, which mediate the expression of a coding sequence segment in plant cells. Accordingly, a plant promoter need not be of plant origin, but may originate from viruses or micro-organisms, for example from viruses which attack plant cells. The “plant promoter” can also originate from a plant cell, e.g. from the plant which is transformed with the nucleic acid sequence to be expressed in the inventive process and described herein. This also applies to other “plant” regulatory signals, such as “plant” terminators. The promoters upstream of the nucleotide sequences useful in the methods of the present invention can be modified by one or more nucleotide substitution(s), insertion(s) and/or deletion(s) without interfering with the functionality or activity of either the promoters, the open reading frame (ORF) or the 3′-regulatory region such as terminators or other 3′ regulatory regions which are located away from the ORF. It is furthermore possible that the activity of the promoters is increased by modification of their sequence, or that they are replaced completely by more active promoters, even promoters from heterologous organisms. For expression in plants, the nucleic acid molecule must, as described above, be linked operably to or comprise a suitable promoter which expresses the gene at the right point in time and with the required spatial expression pattern.
For the identification of functionally equivalent promoters, the promoter strength and/or expression pattern of a candidate promoter may be analysed for example by operably linking the promoter to a reporter gene and assaying the expression level and pattern of the reporter gene in various tissues of the plant. Suitable well-known reporter genes include for example beta-glucuronidase or beta-galactosidase. The promoter activity is assayed by measuring the enzymatic activity of the beta-glucuronidase or beta-galactosidase. The promoter strength and/or expression pattern may then be compared to that of a reference promoter (such as the one used in the methods of the present invention). Alternatively, promoter strength may be assayed by quantifying mRNA levels or by comparing mRNA levels of the nucleic acid used in the methods of the present invention, with mRNA levels of housekeeping genes such as 18S rRNA, using methods known in the art, such as Northern blotting with densitometric analysis of autoradiograms, quantitative real-time PCR or RT-PCR (Heid et al., 1996 Genome Methods 6: 986-994). Generally by “weak promoter” is intended a promoter that drives expression of a coding sequence at a low level. By “low level” is intended at levels of about 1/10,000 transcripts to about 1/100,000 transcripts, to about 1/500,0000 transcripts per cell. Conversely, a “strong promoter” drives expression of a coding sequence at high level, or at about 1/10 transcripts to about 1/100 transcripts to about 1/1000 transcripts per cell. Generally, by “medium strength promoter” is intended a promoter that drives expression of a coding sequence at a lower level than a strong promoter, in particular at a level that is in all instances below that obtained when under the control of a 35S CaMV promoter.
Operably Linked
The term “operably linked” as used herein refers to a functional linkage between the promoter sequence and the gene of interest, such that the promoter sequence is able to initiate transcription of the gene of interest.
Constitutive Promoter
A “constitutive promoter” refers to a promoter that is transcriptionally active during most, but not necessarily all, phases of growth and development and under most environmental conditions, in at least one cell, tissue or organ. Table 2a below gives examples of constitutive promoters.







TABLE 2a







Examples of constitutive promoters








Gene Source
Reference





Actin
McElroy et al, Plant Cell, 2: 163-171, 1990


HMGP
WO 2004/070039


CAMV 35S
Odell et al, Nature, 313: 810-812, 1985


CaMV 19S
Nilsson et al., Physiol. Plant. 100: 456-462, 1997


GOS2
de Pater et al, Plant J Nov; 2(6): 837-44, 1992,



WO 2004/065596


Ubiquitin
Christensen et al, Plant Mol. Biol. 18: 675-689,



1992


Rice cyclophilin
Buchholz et al, Plant Mol Biol. 25(5): 837-43, 1994


Maize H3 histone
Lepetit et al, Mol. Gen. Genet. 231: 276-285, 1992


Alfalfa H3 histone
Wu et al. Plant Mol. Biol. 11: 641-649, 1988


Actin 2
An et al, Plant J. 10(1); 107-121, 1996


34S FMV
Sanger et al., Plant. Mol. Biol., 14, 1990: 433-443


Rubisco small
U.S. Pat. No. 4,962,028


subunit


OCS
Leisner (1988) Proc Natl Acad Sci USA 85(5): 2553


SAD1
Jain et al., Crop Science, 39 (6), 1999: 1696


SAD2
Jain et al., Crop Science, 39 (6), 1999: 1696


nos
Shaw et al. (1984) Nucleic Acids Res.



12(20): 7831-7846


V-ATPase
WO 01/14572


Super promoter
WO 95/14098


G-box proteins
WO 94/12015









Ubiquitous Promoter

A ubiquitous promoter is active in substantially all tissues or cells of an organism.
Developmentally-Regulated Promoter
A developmentally-regulated promoter is active during certain developmental stages or in parts of the plant that undergo developmental changes.
Inducible Promoter
An inducible promoter has induced or increased transcription initiation in response to a chemical (for a review see Gatz 1997, Annu. Rev. Plant Physiol. Plant Mol. Biol., 48:89-108), environmental or physical stimulus, or may be “stress-inducible”, i.e. activated when a plant is exposed to various stress conditions, or a “pathogen-inducible” i.e. activated when a plant is exposed to exposure to various pathogens.
Organ-Specific/Tissue-Specific Promoter
An organ-specific or tissue-specific promoter is one that is capable of preferentially initiating transcription in certain organs or tissues, such as the leaves, roots, seed tissue etc. For example, a “root-specific promoter” is a promoter that is transcriptionally active predominantly in plant roots, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts. Promoters able to initiate transcription in certain cells only are referred to herein as “cell-specific”.
Examples of root-specific promoters are listed in Table 2b below:







TABLE 2b







Examples of root-specific promoters








Gene Source
Reference





RCc3
Plant Mol Biol. 1995 Jan; 27(2): 237-48


Arabidopsis PHT1
Kovama et al., 2005; Mudge et al.



(2002, Plant J. 31: 341)


Medicago phosphate
Xiao et al., 2006


transporter


Arabidopsis Pyk10
Nitz et al. (2001) Plant Sci 161(2): 337-346


root-expressible genes
Tingey et al., EMBO J. 6: 1, 1987.


tobacco auxin-inducible
Van der Zaal et al., Plant Mol. Biol. 16,


gene
983, 1991.


β-tubulin
Oppenheimer, et al., Gene 63: 87, 1988.


tobacco root-specific
Conkling, et al., Plant Physiol. 93: 1203, 1990.


genes


B. napus G1-3b gene
U.S. Pat. No. 5,401,836


SbPRP1
Suzuki et al., Plant Mol. Biol. 21: 109-119,



1993.


LRX1
Baumberger et al. 2001, Genes & Dev. 15:



1128


BTG-26 Brassica napus
US 20050044585


LeAMT1 (tomato)
Lauter et al. (1996, PNAS 3: 8139)


The LeNRT1-1 (tomato)
Lauter et al. (1996, PNAS 3: 8139)


class I patatin gene
Liu et al., Plant Mol. Biol. 153: 386-395, 1991.


(potato)


KDC1 (Daucus carota)
Downey et al. (2000, J. Biol. Chem. 275:



39420)


TobRB7 gene
W Song (1997) PhD Thesis, North Carolina



State University, Raleigh, NC USA


OsRAB5a (rice)
Wang et al. 2002, Plant Sci. 163: 273


ALF5 (Arabidopsis)
Diener et al. (2001, Plant Cell 13: 1625)


NRT2; 1Np
Quesada et al. (1997, Plant Mol. Biol. 34: 265)


(N. plumbaginifolia)









A seed-specific promoter is transcriptionally active predominantly in seed tissue, but not necessarily exclusively in seed tissue (in cases of leaky expression). The seed-specific promoter may be active during seed development and/or during germination. The seed specific promoter may be endosperm/aleurone/embryo specific. Examples of seed-specific promoters (endosperm/aleurone/embryo specific) are shown in Table 2c to Table 2f below. Further examples of seed-specific promoters are given in Qing Qu and Takaiwa (Plant Biotechnol. J. 2, 113-125, 2004), which disclosure is incorporated by reference herein as if fully set forth.







TABLE 2c







Examples of seed-specific promoters








Gene source
Reference





seed-specific genes
Simon et al., Plant Mol. Biol. 5: 191, 1985;



Scofield et al., J. Biol. Chem. 262: 12202, 1987.;



Baszczynski et al., Plant Mol. Biol. 14: 633, 1990.


Brazil Nut albumin
Pearson et al., Plant Mol. Biol. 18: 235-245, 1992.


legumin
Ellis et al., Plant Mol. Biol. 10: 203-214, 1988.


glutelin (rice)
Takaiwa et al., Mol. Gen. Genet. 208: 15-22, 1986;



Takaiwa et al., FEBS Letts. 221: 43-47, 1987.


zein
Matzke et al Plant Mol Biol, 14(3): 323-32 1990


napA
Stalberg et al, Planta 199: 515-519, 1996.


wheat LMW and HMW
Mol Gen Genet 216: 81-90, 1989; NAR 17: 461-2, 1989


glutenin-1


wheat SPA
Albani et al, Plant Cell, 9: 171-184, 1997


wheat α, β, γ-gliadins
EMBO J. 3: 1409-15, 1984


barley Itr1 promoter
Diaz et al. (1995) Mol Gen Genet 248(5): 592-8


barley B1, C, D, hordein
Theor Appl Gen 98: 1253-62, 1999; Plant J 4: 343-55,



1993; Mol Gen Genet 250: 750-60, 1996


barley DOF
Mena et al, The Plant Journal, 116(1): 53-62, 1998


blz2
EP99106056.7


synthetic promoter
Vicente-Carbajosa et al., Plant J. 13: 629-640, 1998.


rice prolamin NRP33
Wu et al, Plant Cell Physiology 39(8) 885-889, 1998


rice a-globulin Glb-1
Wu et al, Plant Cell Physiology 39(8) 885-889, 1998


rice OSH1
Sato et al, Proc. Natl. Acad. Sci. USA, 93: 8117-8122,



1996


rice α-globulin REB/OHP-1
Nakase et al. Plant Mol. Biol. 33: 513-522, 1997


rice ADP-glucose pyrophosphorylase
Trans Res 6: 157-68, 1997


maize ESR gene family
Plant J 12: 235-46, 1997


sorghum α-kafirin
DeRose et al., Plant Mol. Biol 32: 1029-35, 1996


KNOX
Postma-Haarsma et al, Plant Mol. Biol. 39: 257-71, 1999


rice oleosin
Wu et al, J. Biochem. 123: 386, 1998


sunflower oleosin
Cummins et al., Plant Mol. Biol. 19: 873-876, 1992


PRO0117, putative rice 40S
WO 2004/070039


ribosomal protein


PRO0136, rice alanine
unpublished


aminotransferase


PRO0147, trypsin inhibitor
unpublished


ITR1 (barley)


PRO0151, rice WSI18
WO 2004/070039


PRO0175, rice RAB21
WO 2004/070039


PRO005
WO 2004/070039


PRO0095
WO 2004/070039


α-amylase (Amy32b)
Lanahan et al, Plant Cell 4: 203-211, 1992; Skriver et al,



Proc Natl Acad Sci USA 88: 7266-7270, 1991


cathepsin β-like gene
Cejudo et al, Plant Mol Biol 20: 849-856, 1992


Barley Ltp2
Kalla et al., Plant J. 6: 849-60, 1994


Chi26
Leah et al., Plant J. 4: 579-89, 1994


Maize B-Peru
Selinger et al., Genetics 149; 1125-38, 1998
















TABLE 2d







examples of endosperm-specific promoters








Gene source
Reference





glutelin (rice)
Takaiwa et al. (1986) Mol Gen Genet 208: 15-22;



Takaiwa et al. (1987) FEBS Letts. 221: 43-47


zein
Matzke et al., (1990) Plant Mol Biol 14(3): 323-32


wheat LMW and
Colot et al. (1989) Mol Gen Genet 216: 81-90,


HMW glutenin-1
Anderson et al. (1989) NAR 17: 461-2


wheat SPA
Albani et al. (1997) Plant Cell 9: 171-184


wheat gliadins
Rafalski et al. (1984) EMBO 3: 1409-15


barley Itr1 promoter
Diaz et al. (1995) Mol Gen Genet 248(5): 592-8


barley B1, C, D,
Cho et al. (1999) Theor Appl Genet 98: 1253-62;


hordein
Muller et al. (1993) Plant J 4: 343-55;



Sorenson et al. (1996) Mol Gen Genet 250: 750-60


barley DOF
Mena et al, (1998) Plant J 116(1): 53-62


blz2
Onate et al. (1999) J Biol Chem 274(14): 9175-82


synthetic promoter
Vicente-Carbajosa et al. (1998) Plant J 13: 629-640


rice prolamin
Wu et al, (1998) Plant Cell Physiol 39(8) 885-889


NRP33


rice globulin Glb-1
Wu et al. (1998) Plant Cell Physiol 39(8) 885-889


rice globulin
Nakase et al. (1997) Plant Molec Biol 33: 513-522


REB/OHP-1


rice ADP-glucose
Russell et al. (1997) Trans Res 6: 157-68


pyrophosphorylase


maize ESR gene
Opsahl-Ferstad et al. (1997) Plant J 12: 235-46


family


sorghum kafirin
DeRose et al. (1996) Plant Mol Biol 32: 1029-35
















TABLE 2e







Examples of embryo specific promoters:








Gene



source
Reference





rice OSH1
Sato et al, Proc. Natl. Acad. Sci. USA, 93: 8117-8122, 1996


KNOX
Postma-Haarsma et al, Plant Mol. Biol. 39: 257-71, 1999


PRO0151
WO 2004/070039


PRO0175
WO 2004/070039


PRO005
WO 2004/070039


PRO0095
WO 2004/070039
















TABLE 2f







Examples of aleurone-specific promoters:








Gene source
Reference





α-amylase (Amy32b)
Lanahan et al, Plant Cell 4: 203-211, 1992;



Skriver et al, Proc Natl Acad Sci USA 88:



7266-7270, 1991


cathepsin β-like gene
Cejudo et al, Plant Mol Biol 20: 849-856, 1992


Barley Ltp2
Kalla et al., Plant J. 6: 849-60, 1994


Chi26
Leah et al., Plant J. 4: 579-89, 1994


Maize B-Peru
Selinger et al., Genetics 149; 1125-38, 1998









A green tissue-specific promoter as defined herein is a promoter that is transcriptionally active predominantly in green tissue, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts.
Examples of green tissue-specific promoters which may be used to perform the methods of the invention are shown in Table 2g below.







TABLE 2g







Examples of green tissue-specific promoters









Gene
Expression
Reference





Maize Orthophosphate dikinase
Leaf specific
Fukavama et al., 2001


Maize Phosphoenolpyruvate
Leaf specific
Kausch et al., 2001


carboxylase


Rice Phosphoenolpyruvate
Leaf specific
Liu et al., 2003


carboxylase


Rice small subunit Rubisco
Leaf specific
Nomura et al., 2000


rice beta expansin EXBP9
Shoot specific
WO 2004/070039


Pigeonpea small subunit Rubisco
Leaf specific
Panguluri et al., 2005


Pea RBCS3A
Leaf specific









Another example of a tissue-specific promoter is a meristem-specific promoter, which is transcriptionally active predominantly in meristematic tissue, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts. Examples of green meristem-specific promoters which may be used to perform the methods of the invention are shown in Table 2h below.







TABLE 2h







Examples of meristem-specific promoters









Gene source
Expression pattern
Reference





rice OSH1
Shoot apical meristem,
Sato et al. (1996)



from embryo globular stage
Proc. Natl. Acad. Sci.



to seedling stage
USA, 93: 8117-8122


Rice metallothionein
Meristem specific
BAD87835.1


WAK1 & WAK 2
Shoot and root apical
Wagner & Kohorn



meristems, and in
(2001) Plant Cell



expanding leaves and
13(2): 303-318



sepals









Terminator

The term “terminator” encompasses a control sequence which is a DNA sequence at the end of a transcriptional unit which signals 3′ processing and polyadenylation of a primary transcript and termination of transcription. The terminator can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. The terminator to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.
Selectable Marker (Gene)/Reporter Gene
“Selectable marker”, “selectable marker gene” or “reporter gene” includes any gene that confers a phenotype on a cell in which it is expressed to facilitate the identification and/or selection of cells that are transfected or transformed with a nucleic acid construct of the invention. These marker genes enable the identification of a successful transfer of the nucleic acid molecules via a series of different principles. Suitable markers may be selected from markers that confer antibiotic or herbicide resistance, that introduce a new metabolic trait or that allow visual selection. Examples of selectable marker genes include genes conferring resistance to antibiotics (such as nptII that phosphorylates neomycin and kanamycin, or hpt, phosphorylating hygromycin, or genes conferring resistance to, for example, bleomycin, streptomycin, tetracyclin, chloramphenicol, ampicillin, gentamycin, geneticin (G418), spectinomycin or blasticidin), to herbicides (for example bar which provides resistance to Basta®; aroA or gox providing resistance against glyphosate, or the genes conferring resistance to, for example, imidazolinone, phosphinothricin or sulfonylurea), or genes that provide a metabolic trait (such as manA that allows plants to use mannose as sole carbon source or xylose isomerase for the utilisation of xylose, or antinutritive markers such as the resistance to 2-deoxyglucose). Expression of visual marker genes results in the formation of colour (for example β-glucuronidase, GUS or β-galactosidase with its coloured substrates, for example X-Gal), luminescence (such as the luciferin/luceferase system) or fluorescence (Green Fluorescent Protein, GFP, and derivatives thereof). This list represents only a small number of possible markers. The skilled worker is familiar with such markers. Different markers are preferred, depending on the organism and the selection method.
It is known that upon stable or transient integration of nucleic acids into plant cells, only a minority of the cells takes up the foreign DNA and, if desired, integrates it into its genome, depending on the expression vector used and the transfection technique used. To identify and select these integrants, a gene coding for a selectable marker (such as the ones described above) is usually introduced into the host cells together with the gene of interest.
These markers can for example be used in mutants in which these genes are not functional by, for example, deletion by conventional methods. Furthermore, nucleic acid molecules encoding a selectable marker can be introduced into a host cell on the same vector that comprises the sequence encoding the polypeptides of the invention or used in the methods of the invention, or else in a separate vector. Cells which have been stably transfected with the introduced nucleic acid can be identified for example by selection (for example, cells which have integrated the selectable marker survive whereas the other cells die).
Since the marker genes, particularly genes for resistance to antibiotics and herbicides, are no longer required or are undesired in the transgenic host cell once the nucleic acids have been introduced successfully, the process according to the invention for introducing the nucleic acids advantageously employs techniques which enable the removal or excision of these marker genes. One such a method is what is known as co-transformation. The co-transformation method employs two vectors simultaneously for the transformation, one vector bearing the nucleic acid according to the invention and a second bearing the marker gene(s). A large proportion of transformants receives or, in the case of plants, comprises (up to 40% or more of the transformants), both vectors. In case of transformation with Agrobacteria, the transformants usually receive only a part of the vector, i.e. the sequence flanked by the T-DNA, which usually represents the expression cassette. The marker genes can subsequently be removed from the transformed plant by performing crosses. In another method, marker genes integrated into a transposon are used for the transformation together with desired nucleic acid (known as the Ac/Ds technology). The transformants can be crossed with a transposase source or the transformants are transformed with a nucleic acid construct conferring expression of a transposase, transiently or stable. In some cases (approx. 10%), the transposon jumps out of the genome of the host cell once transformation has taken place successfully and is lost. In a further number of cases, the transposon jumps to a different location. In these cases the marker gene must be eliminated by performing crosses. In microbiology, techniques were developed which make possible, or facilitate, the detection of such events. A further advantageous method relies on what is known as recombination systems; whose advantage is that elimination by crossing can be dispensed with. The best-known system of this type is what is known as the Cre/lox system. Cre1 is a recombinase that removes the sequences located between the loxP sequences. If the marker gene is integrated between the loxP sequences, it is removed once transformation has taken place successfully, by expression of the recombinase. Further recombination systems are the HIN/HIX, FLP/FRT and REP/STB system (Tribble et al., J. Biol. Chem., 275, 2000: 22255-22267; Velmurugan et al., J. Cell Biol., 149, 2000: 553-566). A site-specific integration into the plant genome of the nucleic acid sequences according to the invention is possible. Naturally, these methods can also be applied to microorganisms such as yeast, fungi or bacteria.
Transgenic/Transgene/Recombinant
For the purposes of the invention, “transgenic”, “transgene” or “recombinant” means with regard to, for example, a nucleic acid sequence, an expression cassette, gene construct or a vector comprising the nucleic acid sequence or an organism transformed with the nucleic acid sequences, expression cassettes or vectors according to the invention, all those constructions brought about by recombinant methods in which either

    
    
        (a) the nucleic acid sequences encoding proteins useful in the methods of the invention, or
        (b) genetic control sequence(s) which is operably linked with the nucleic acid sequence according to the invention, for example a promoter, or
        (c) a) and b)

are not located in their natural genetic environment or have been modified by recombinant methods, it being possible for the modification to take the form of, for example, a substitution, addition, deletion, inversion or insertion of one or more nucleotide residues. The natural genetic environment is understood as meaning the natural genomic or chromosomal locus in the original plant or the presence in a genomic library. In the case of a genomic library, the natural genetic environment of the nucleic acid sequence is preferably retained, at least in part. The environment flanks the nucleic acid sequence at least on one side and has a sequence length of at least 50 bp, preferably at least 500 bp, especially preferably at least 1000 bp, most preferably at least 5000 bp. A naturally occurring expression cassette—for example the naturally occurring combination of the natural promoter of the nucleic acid sequences with the corresponding nucleic acid sequence encoding a polypeptide useful in the methods of the present invention, as defined above—becomes a transgenic expression cassette when this expression cassette is modified by non-natural, synthetic (“artificial”) methods such as, for example, mutagenic treatment. Suitable methods are described, for example, in U.S. Pat. No. 5,565,350 or WO 00/15815.

    
    


A transgenic plant for the purposes of the invention is thus understood as meaning, as above, that the nucleic acids used in the method of the invention are not at their natural locus in the genome of said plant, it being possible for the nucleic acids to be expressed homologously or heterologously. However, as mentioned, transgenic also means that, while the nucleic acids according to the invention or used in the inventive method are at their natural position in the genome of a plant, the sequence has been modified with regard to the natural sequence, and/or that the regulatory sequences of the natural sequences have been modified. Transgenic is preferably understood as meaning the expression of the nucleic acids according to the invention at an unnatural locus in the genome, i.e. homologous or, preferably, heterologous expression of the nucleic acids takes place. Preferred transgenic plants are mentioned herein.
Modulation
The term “modulation” means in relation to expression or gene expression, a process in which the expression level is changed by said gene expression in comparison to the control plant, the expression level may be increased or decreased. The original, unmodulated expression may be of any kind of expression of a structural RNA (rRNA, tRNA) or mRNA with subsequent translation. The term “modulating the activity” shall mean any change of the expression of the inventive nucleic acid sequences or encoded proteins, which leads to increased yield and/or increased growth of the plants.
Expression
The term “expression” or “gene expression” means the transcription of a specific gene or specific genes or specific genetic construct. The term “expression” or “gene expression” in particular means the transcription of a gene or genes or genetic construct into structural RNA (rRNA, tRNA) or mRNA with or without subsequent translation of the latter into a protein. The process includes transcription of DNA and processing of the resulting mRNA product.
Increased Expression/Overexpression
The term “increased expression” or “overexpression” as used herein means any form of expression that is additional to the original wild-type expression level.
Methods for increasing expression of genes or gene products are well documented in the art and include, for example, overexpression driven by appropriate promoters, the use of transcription enhancers or translation enhancers. Isolated nucleic acids which serve as promoter or enhancer elements may be introduced in an appropriate position (typically upstream) of a non-heterologous form of a polynucleotide so as to upregulate expression of a nucleic acid encoding the polypeptide of interest. For example, endogenous promoters may be altered in vivo by mutation, deletion, and/or substitution (see, Kmiec, U.S. Pat. No. 5,565,350; Zarling et al., WO9322443), or isolated promoters may be introduced into a plant cell in the proper orientation and distance from a gene of the present invention so as to control the expression of the gene.
If polypeptide expression is desired, it is generally desirable to include a polyadenylation region at the 3′-end of a polynucleotide coding region. The polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. The 3′ end sequence to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.
An intron sequence may also be added to the 5′ untranslated region (UTR) or the coding sequence of the partial coding sequence to increase the amount of the mature message that accumulates in the cytosol. Inclusion of a spliceable intron in the transcription unit in both plant and animal expression constructs has been shown to increase gene expression at both the mRNA and protein levels up to 1000-fold (Buchman and Berg (1988) Mol. Cell. biol. 8: 4395-4405; Callis et al. (1987) Genes Dev 1:1183-1200). Such intron enhancement of gene expression is typically greatest when placed near the 5′ end of the transcription unit. Use of the maize introns Adh1-S intron 1, 2, and 6, the Bronze-1 intron are known in the art. For general information see: The Maize Handbook, Chapter 116, Freeling and Walbot, Eds., Springer, N.Y. (1994).
Decreased Expression
Reference herein to “decreased expression” or “reduction or substantial elimination” of expression is taken to mean a decrease in endogenous gene expression and/or polypeptide levels and/or polypeptide activity relative to control plants. The reduction or substantial elimination is in increasing order of preference at least 10%, 20%, 30%, 40% or 50%, 60%, 70%, 80%, 85%, 90%, or 95%, 96%, 97%, 98%, 99% or more reduced compared to that of control plants.
For the reduction or substantial elimination of expression an endogenous gene in a plant, a sufficient length of substantially contiguous nucleotides of a nucleic acid sequence is required. In order to perform gene silencing, this may be as little as 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10 or fewer nucleotides, alternatively this may be as much as the entire gene (including the 5′ and/or 3′ UTR, either in part or in whole). The stretch of substantially contiguous nucleotides may be derived from the nucleic acid encoding the protein of interest (target gene), or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest. Preferably, the stretch of substantially contiguous nucleotides is capable of forming hydrogen bonds with the target gene (either sense or antisense strand), more preferably, the stretch of substantially contiguous nucleotides has, in increasing order of preference, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100% sequence identity to the target gene (either sense or antisense strand). A nucleic acid sequence encoding a (functional) polypeptide is not a requirement for the various methods discussed herein for the reduction or substantial elimination of expression of an endogenous gene.
This reduction or substantial elimination of expression may be achieved using routine tools and techniques. A preferred method for the reduction or substantial elimination of endogenous gene expression is by introducing and expressing in a plant a genetic construct into which the nucleic acid (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of any one of the protein of interest) is cloned as an inverted repeat (in part or completely), separated by a spacer (non-coding DNA).
In such a preferred method, expression of the endogenous gene is reduced or substantially eliminated through RNA-mediated silencing using an inverted repeat of a nucleic acid or a part thereof (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest), preferably capable of forming a hairpin structure. The inverted repeat is cloned in an expression vector comprising control sequences. A non-coding DNA nucleic acid sequence (a spacer, for example a matrix attachment region fragment (MAR), an intron, a polylinker, etc.) is located between the two inverted nucleic acids forming the inverted repeat. After transcription of the inverted repeat, a chimeric RNA with a self-complementary structure is formed (partial or complete). This double-stranded RNA structure is referred to as the hairpin RNA (hpRNA). The hpRNA is processed by the plant into siRNAs that are incorporated into an RNA-induced silencing complex (RISC). The RISC further cleaves the mRNA transcripts, thereby substantially reducing the number of mRNA transcripts to be translated into polypeptides. For further general details see for example, Grierson et al. (1998) WO 98/53083; Waterhouse et al. (1999) WO 99/53050).
Performance of the methods of the invention does not rely on introducing and expressing in a plant a genetic construct into which the nucleic acid is cloned as an inverted repeat, but any one or more of several well-known “gene silencing” methods may be used to achieve the same effects.
One such method for the reduction of endogenous gene expression is RNA-mediated silencing of gene expression (downregulation). Silencing in this case is triggered in a plant by a double stranded RNA sequence (dsRNA) that is substantially similar to the target endogenous gene. This dsRNA is further processed by the plant into about 20 to about 26 nucleotides called short interfering RNAs (siRNAs). The siRNAs are incorporated into an RNA-induced silencing complex (RISC) that cleaves the mRNA transcript of the endogenous target gene, thereby substantially reducing the number of mRNA transcripts to be translated into a polypeptide. Preferably, the double stranded RNA sequence corresponds to a target gene.
Another example of an RNA silencing method involves the introduction of nucleic acid sequences or parts thereof (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest) in a sense orientation into a plant. “Sense orientation” refers to a DNA sequence that is homologous to an mRNA transcript thereof. Introduced into a plant would therefore be at least one copy of the nucleic acid sequence. The additional nucleic acid sequence will reduce expression of the endogenous gene, giving rise to a phenomenon known as co-suppression. The reduction of gene expression will be more pronounced if several additional copies of a nucleic acid sequence are introduced into the plant, as there is a positive correlation between high transcript levels and the triggering of co-suppression.
Another example of an RNA silencing method involves the use of antisense nucleic acid sequences. An “antisense” nucleic acid sequence comprises a nucleotide sequence that is complementary to a “sense” nucleic acid sequence encoding a protein, i.e. complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA transcript sequence. The antisense nucleic acid sequence is preferably complementary to the endogenous gene to be silenced. The complementarity may be located in the “coding region” and/or in the “non-coding region” of a gene. The term “coding region” refers to a region of the nucleotide sequence comprising codons that are translated into amino acid residues. The term “non-coding region” refers to 5′ and 3′ sequences that flank the coding region that are transcribed but not translated into amino acids (also referred to as 5′ and 3′ untranslated regions).
Antisense nucleic acid sequences can be designed according to the rules of Watson and Crick base pairing. The antisense nucleic acid sequence may be complementary to the entire nucleic acid sequence (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest), but may also be an oligonucleotide that is antisense to only a part of the nucleic acid sequence (including the mRNA 5′ and 3′ UTR). For example, the antisense oligonucleotide sequence may be complementary to the region surrounding the translation start site of an mRNA transcript encoding a polypeptide. The length of a suitable antisense oligonucleotide sequence is known in the art and may start from about 50, 45, 40, 35, 30, 25, 20, 15 or 10 nucleotides in length or less. An antisense nucleic acid sequence according to the invention may be constructed using chemical synthesis and enzymatic ligation reactions using methods known in the art. For example, an antisense nucleic acid sequence (e.g., an antisense oligonucleotide sequence) may be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acid sequences, e.g., phosphorothioate derivatives and acridine substituted nucleotides may be used. Examples of modified nucleotides that may be used to generate the antisense nucleic acid sequences are well known in the art. Known nucleotide modifications include methylation, cyclization and ‘caps’ and substitution of one or more of the naturally occurring nucleotides with an analogue such as inosine. Other modifications of nucleotides are well known in the art.
The antisense nucleic acid sequence can be produced biologically using an expression vector into which a nucleic acid sequence has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest). Preferably, production of antisense nucleic acid sequences in plants occurs by means of a stably integrated nucleic acid construct comprising a promoter, an operably linked antisense oligonucleotide, and a terminator.
The nucleic acid molecules used for silencing in the methods of the invention (whether introduced into a plant or generated in situ) hybridize with or bind to mRNA transcripts and/or genomic DNA encoding a polypeptide to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid sequence which binds to DNA duplexes, through specific interactions in the major groove of the double helix. Antisense nucleic acid sequences may be introduced into a plant by transformation or direct injection at a specific tissue site. Alternatively, antisense nucleic acid sequences can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense nucleic acid sequences can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid sequence to peptides or antibodies which bind to cell surface receptors or antigens. The antisense nucleic acid sequences can also be delivered to cells using the vectors described herein.
According to a further aspect, the antisense nucleic acid sequence is an a-anomeric nucleic acid sequence. An a-anomeric nucleic acid sequence forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual b-units, the strands run parallel to each other (Gaultier et al. (1987) Nucl Ac Res 15: 6625-6641). The antisense nucleic acid sequence may also comprise a 2′-o-methylribonucleotide (Inoue et al. (1987) Nucl Ac Res 15, 6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215, 327-330).
The reduction or substantial elimination of endogenous gene expression may also be performed using ribozymes. Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid sequence, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334, 585-591) can be used to catalytically cleave mRNA transcripts encoding a polypeptide, thereby substantially reducing the number of mRNA transcripts to be translated into a polypeptide. A ribozyme having specificity for a nucleic acid sequence can be designed (see for example: Cech et al. U.S. Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742). Alternatively, mRNA transcripts corresponding to a nucleic acid sequence can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules (Bartel and Szostak (1993) Science 261, 1411-1418). The use of ribozymes for gene silencing in plants is known in the art (e.g., Atkins et al. (1994) WO 94/00012; Lenne et al. (1995) WO 95/03404; Lutziger et al. (2000) WO 00/00619; Prinsen et al. (1997) WO 97/13865 and Scott et al. (1997) WO 97/38116).
Gene silencing may also be achieved by insertion mutagenesis (for example, T-DNA insertion or transposon insertion) or by strategies as described by, among others, Angell and Baulcombe ((1999) Plant J 20(3): 357-62), (Amplicon VIGS WO 98/36083), or Baulcombe (WO 99/15682).
Gene silencing may also occur if there is a mutation on an endogenous gene and/or a mutation on an isolated gene/nucleic acid subsequently introduced into a plant. The reduction or substantial elimination may be caused by a non-functional polypeptide. For example, the polypeptide may bind to various interacting proteins; one or more mutation(s) and/or truncation(s) may therefore provide for a polypeptide that is still able to bind interacting proteins (such as receptor proteins) but that cannot exhibit its normal function (such as signalling ligand).
A further approach to gene silencing is by targeting nucleic acid sequences complementary to the regulatory region of the gene (e.g., the promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells. See Helene, C., Anticancer Drug Res. 6, 569-84, 1991; Helene et al., Ann. N.Y. Acad. Sci. 660, 27-36 1992; and Maher, L. J. Bioassays 14, 807-15, 1992.
Other methods, such as the use of antibodies directed to an endogenous polypeptide for inhibiting its function in planta, or interference in the signalling pathway in which a polypeptide is involved, will be well known to the skilled man. In particular, it can be envisaged that manmade molecules may be useful for inhibiting the biological function of a target polypeptide, or for interfering with the signalling pathway in which the target polypeptide is involved.
Alternatively, a screening program may be set up to identify in a plant population natural variants of a gene, which variants encode polypeptides with reduced activity. Such natural variants may also be used for example, to perform homologous recombination.
Artificial and/or natural microRNAs (miRNAs) may be used to knock out gene expression and/or mRNA translation. Endogenous miRNAs are single stranded small RNAs of typically 19-24 nucleotides long. They function primarily to regulate gene expression and/or mRNA translation. Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their target sequences. However, there are natural targets with up to five mismatches. They are processed from longer non-coding RNAs with characteristic fold-back structures by double-strand specific RNases of the Dicer family. Upon processing, they are incorporated in the RNA-induced silencing complex (RISC) by binding to its main component, an Argonaute protein. mRNAs serve as the specificity components of RISC, since they base-pair to target nucleic acids, mostly mRNAs, in the cytoplasm. Subsequent regulatory events include target mRNA cleavage and destruction and/or translational inhibition. Effects of miRNA overexpression are thus often reflected in decreased mRNA levels of target genes.
Artificial microRNAs (amiRNAs), which are typically 21 nucleotides in length, can be genetically engineered specifically to negatively regulate gene expression of single or multiple genes of interest. Determinants of plant microRNA target selection are well known in the art. Empirical parameters for target recognition have been defined and can be used to aid in the design of specific amiRNAs, (Schwab et al., Dev. Cell 8, 517-527, 2005). Convenient tools for design and generation of amiRNAs and their precursors are also available to the public (Schwab et al., Plant Cell 18, 1121-1133, 2006).
For optimal performance, the gene silencing techniques used for reducing expression in a plant of an endogenous gene requires the use of nucleic acid sequences from monocotyledonous plants for transformation of monocotyledonous plants, and from dicotyledonous plants for transformation of dicotyledonous plants. Preferably, a nucleic acid sequence from any given plant species is introduced into that same species. For example, a nucleic acid sequence from rice is transformed into a rice plant. However, it is not an absolute requirement that the nucleic acid sequence to be introduced originates from the same plant species as the plant in which it will be introduced. It is sufficient that there is substantial homology between the endogenous target gene and the nucleic acid to be introduced.
Described above are examples of various methods for the reduction or substantial elimination of expression in a plant of an endogenous gene. A person skilled in the art would readily be able to adapt the aforementioned methods for silencing so as to achieve reduction of expression of an endogenous gene in a whole plant or in parts thereof through the use of an appropriate promoter, for example.
Transformation
The term “introduction” or “transformation” as referred to herein encompasses the transfer of an exogenous polynucleotide into a host cell, irrespective of the method used for transfer. Plant tissue capable of subsequent clonal propagation, whether by organogenesis or embryogenesis, may be transformed with a genetic construct of the present invention and a whole plant regenerated there from. The particular tissue chosen will vary depending on the clonal propagation systems available for, and best suited to, the particular species being transformed. Exemplary tissue targets include leaf disks, pollen, embryos, cotyledons, hypocotyls, megagametophytes, callus tissue, existing meristematic tissue (e.g., apical meristem, axillary buds, and root meristems), and induced meristem tissue (e.g., cotyledon meristem and hypocotyl meristem). The polynucleotide may be transiently or stably introduced into a host cell and may be maintained non-integrated, for example, as a plasmid. Alternatively, it may be integrated into the host genome. The resulting transformed plant cell may then be used to regenerate a transformed plant in a manner known to persons skilled in the art.
The transfer of foreign genes into the genome of a plant is called transformation. Transformation of plant species is now a fairly routine technique. Advantageously, any of several transformation methods may be used to introduce the gene of interest into a suitable ancestor cell. The methods described for the transformation and regeneration of plants from plant tissues or plant cells may be utilized for transient or for stable transformation. Transformation methods include the use of liposomes, electroporation, chemicals that increase free DNA uptake, injection of the DNA directly into the plant, particle gun bombardment, transformation using viruses or pollen and microprojection. Methods may be selected from the calcium/polyethylene glycol method for protoplasts (Krens, F. A. et al., (1982) Nature 296, 72-74; Negrutiu I et al. (1987) Plant Mol Biol 8: 363-373); electroporation of protoplasts (Shillito R. D. et al. (1985) Bio/Technol 3, 1099-1102); microinjection into plant material (Crossway A et al., (1986) Mol. Gen. Genet. 202: 179-185); DNA or RNA-coated particle bombardment (Klein T M et al., (1987) Nature 327: 70) infection with (non-integrative) viruses and the like. Transgenic plants, including transgenic crop plants, are preferably produced via Agrobacterium-mediated transformation. An advantageous transformation method is the transformation in planta. To this end, it is possible, for example, to allow the agrobacteria to act on plant seeds or to inoculate the plant meristem with agrobacteria. It has proved particularly expedient in accordance with the invention to allow a suspension of transformed agrobacteria to act on the intact plant or at least on the flower primordia. The plant is subsequently grown on until the seeds of the treated plant are obtained (Clough and Bent, Plant J. (1998) 16, 735-743). Methods for Agrobacterium-mediated transformation of rice include well known methods for rice transformation, such as those described in any of the following: European patent application EP 1198985 A1, Aldemita and Hodges (Planta 199: 612-617, 1996); Chan et al. (Plant Mol Biol 22 (3): 491-506, 1993), Hiei et al. (Plant J 6 (2): 271-282, 1994), which disclosures are incorporated by reference herein as if fully set forth. In the case of corn transformation, the preferred method is as described in either Ishida et al. (Nat. Biotechnol 14(6): 745-50, 1996) or Frame et al. (Plant Physiol 129(1): 13-22, 2002), which disclosures are incorporated by reference herein as if fully set forth. Said methods are further described by way of example in B. Jenes et al., Techniques for Gene Transfer, in: Transgenic Plants, Vol. 1, Engineering and Utilization, eds. S. D. Kung and R. Wu, Academic Press (1993) 128-143 and in Potrykus Annu. Rev. Plant Physiol. Plant Molec. Biol. 42 (1991) 205-225). The nucleic acids or the construct to be expressed is preferably cloned into a vector, which is suitable for transforming Agrobacterium tumefaciens, for example pBin19 (Bevan et al., Nucl. Acids Res. 12 (1984) 8711). Agrobacteria transformed by such a vector can then be used in known manner for the transformation of plants, such as plants used as a model, like Arabidopsis (Arabidopsis thaliana is within the scope of the present invention not considered as a crop plant), or crop plants such as, by way of example, tobacco plants, for example by immersing bruised leaves or chopped leaves in an agrobacterial solution and then culturing them in suitable media. The transformation of plants by means of Agrobacterium tumefaciens is described, for example, by Höfgen and Willmitzer in Nucl. Acid Res. (1988) 16, 9877 or is known inter alia from F. F. White, Vectors for Gene Transfer in Higher Plants; in Transgenic Plants, Vol. 1, Engineering and Utilization, eds. S. D. Kung and R. Wu, Academic Press, 1993, pp. 15-38.
In addition to the transformation of somatic cells, which then have to be regenerated into intact plants, it is also possible to transform the cells of plant meristems and in particular those cells which develop into gametes. In this case, the transformed gametes follow the natural plant development, giving rise to transgenic plants. Thus, for example, seeds of Arabidopsis are treated with agrobacteria and seeds are obtained from the developing plants of which a certain proportion is transformed and thus transgenic [Feldman, K A and Marks M D (1987). Mol Gen Genet. 208:274-289; Feldmann K (1992). In: C Koncz, N-H Chua and J Shell, eds, Methods in Arabidopsis Research. Word Scientific, Singapore, pp. 274-289]. Alternative methods are based on the repeated removal of the inflorescences and incubation of the excision site in the center of the rosette with transformed agrobacteria, whereby transformed seeds can likewise be obtained at a later point in time (Chang (1994). Plant J. 5: 551-558; Katavic (1994). Mol Gen Genet, 245: 363-370). However, an especially effective method is the vacuum infiltration method with its modifications such as the “floral dip” method. In the case of vacuum infiltration of Arabidopsis, intact plants under reduced pressure are treated with an agrobacterial suspension [Bechthold, N (1993). C R Acad Sci Paris Life Sci, 316: 1194-1199], while in the case of the “floral dip” method the developing floral tissue is incubated briefly with a surfactant-treated agrobacterial suspension [Clough, S J and Bent A F (1998) The Plant J. 16, 735-743]. A certain proportion of transgenic seeds are harvested in both cases, and these seeds can be distinguished from non-transgenic seeds by growing under the above-described selective conditions. In addition the stable transformation of plastids is of advantages because plastids are inherited maternally is most crops reducing or eliminating the risk of transgene flow through pollen. The transformation of the chloroplast genome is generally achieved by a process which has been schematically displayed in Klaus et al., 2004 [Nature Biotechnology 22 (2), 225-229]. Briefly the sequences to be transformed are cloned together with a selectable marker gene between flanking sequences homologous to the chloroplast genome. These homologous flanking sequences direct site specific integration into the plastome. Plastidal transformation has been described for many different plant species and an overview is given in Bock (2001) Transgenic plastids in basic research and plant biotechnology. J Mol. Biol. 2001 Sep. 21; 312 (3):425-38 or Maliga, P (2003) Progress towards commercialization of plastid transformation technology. Trends Biotechnol. 21, 20-28. Further biotechnological progress has recently been reported in form of marker free plastid transformants, which can be produced by a transient co-integrated maker gene (Klaus et al., 2004, Nature Biotechnology 22(2), 225-229).
The genetically modified plant cells can be regenerated via all methods with which the skilled worker is familiar. Suitable methods can be found in the above-mentioned publications by S. D. Kung and R. Wu, Potrykus or Höfgen and Willmitzer.
Generally after transformation, plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant. To select transformed plants, the plant material obtained in the transformation is, as a rule, subjected to selective conditions so that transformed plants can be distinguished from untransformed plants. For example, the seeds obtained in the above-described manner can be planted and, after an initial growing period, subjected to a suitable selection by spraying. A further possibility consists in growing the seeds, if appropriate after sterilization, on agar plates using a suitable selection agent so that only the transformed seeds can grow into plants. Alternatively, the transformed plants are screened for the presence of a selectable marker such as the ones described above.
Following DNA transfer and regeneration, putatively transformed plants may also be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, both techniques being well known to persons having ordinary skill in the art.
The generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1) transformed plant may be selfed and homozygous second-generation (or T2) transformants selected, and the T2 plants may then further be propagated through classical breeding techniques. The generated transformed organisms may take a variety of forms. For example, they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g., all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion).
T-DNA Activation Tagging
T-DNA activation tagging (Hayashi et al. Science (1992) 1350-1353), involves insertion of T-DNA, usually containing a promoter (may also be a translation enhancer or an intron), in the genomic region of the gene of interest or 10 kb up- or downstream of the coding region of a gene in a configuration such that the promoter directs expression of the targeted gene. Typically, regulation of expression of the targeted gene by its natural promoter is disrupted and the gene falls under the control of the newly introduced promoter. The promoter is typically embedded in a T-DNA. This T-DNA is randomly inserted into the plant genome, for example, through Agrobacterium infection and leads to modified expression of genes near the inserted T-DNA. The resulting transgenic plants show dominant phenotypes due to modified expression of genes close to the introduced promoter.
Tilling
The term “TILLING” is an abbreviation of “Targeted Induced Local Lesions In Genomes” and refers to a mutagenesis technology useful to generate and/or identify nucleic acids encoding proteins with modified expression and/or activity. TILLING also allows selection of plants carrying such mutant variants. These mutant variants may exhibit modified expression, either in strength or in location or in timing (if the mutations affect the promoter for example). These mutant variants may exhibit higher activity than that exhibited by the gene in its natural form, TILLING combines high-density mutagenesis with high-throughput screening methods. The steps typically followed in TILLING are: (a) EMS mutagenesis (Redei G P and Koncz C (1992) In Methods in Arabidopsis Research, Koncz C, Chua N H, Schell J, eds. Singapore, World Scientific Publishing Co, pp. 16-82; Feldmann et al., (1994) In Meyerowitz E M, Somerville C R, eds, Arabidopsis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp 137-172; Lightner J and Caspar T (1998) In J Martinez-Zapater, J Salinas, eds, Methods on Molecular Biology, Vol. 82. Humana Press, Totowa, N.J., pp 91-104); (b) DNA preparation and pooling of individuals; (c) PCR amplification of a region of interest; (d) denaturation and annealing to allow formation of heteroduplexes; (e) DHPLC, where the presence of a heteroduplex in a pool is detected as an extra peak in the chromatogram; (f) identification of the mutant individual; and (g) sequencing of the mutant PCR product. Methods for TILLING are well known in the art (McCallum et al., (2000) Nat Biotechnol 18: 455-457; reviewed by Stemple (2004) Nat Rev Genet. 5(2): 145-50).
Homologous Recombination
Homologous recombination allows introduction in a genome of a selected nucleic acid at a defined selected position. Homologous recombination is a standard technology used routinely in biological sciences for lower organisms such as yeast or the moss Physcomitrella. Methods for performing homologous recombination in plants have been described not only for model plants (Offring a et al. (1990) EMBO J. 9(10): 3077-84) but also for crop plants, for example rice (Terada et al. (2002) Nat Biotech 20(10): 1030-4; lida and Terada (2004) Curr Opin Biotech 15(2): 132-8), and approaches exist that are generally applicable regardless of the target organism (Miller et al, Nature Biotechnol. 25, 778-785, 2007).
Yield Related Traits
Yield related traits comprise one or more of yield, biomass, seed yield, early vigour, greenness index, increased growth rate, improved agronomic traits (such as improved Water Use Efficiency (WUE), Nitrogen Use Efficiency (NUE), etc.).
Yield
The term “yield” in general means a measurable produce of economic value, typically related to a specified crop, to an area, and to a period of time. Individual plant parts directly contribute to yield based on their number, size and/or weight, or the actual yield is the yield per square meter for a crop and year, which is determined by dividing total production (includes both harvested and appraised production) by planted square meters. The term “yield” of a plant may relate to vegetative biomass (root and/or shoot biomass), to reproductive organs, and/or to propagules (such as seeds) of that plant.
Taking corn as an example, a yield increase may be manifested as one or more of the following: increase in the number of plants established per square meter, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), among others. Taking rice as an example, a yield increase may manifest itself as an increase in one or more of the following: number of plants per square meter, number of panicles per plant, panicle length, number of spikelets per panicle, number of flowers (florets) per panicle, increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), increase in thousand kernel weight, among others. In rice, submergence tolerance may also result in increased yield.
Early Vigour
“Early vigour” refers to active healthy well-balanced growth especially during early stages of plant growth, and may result from increased plant fitness due to, for example, the plants being better adapted to their environment (i.e. optimizing the use of energy resources and partitioning between shoot and root). Plants having early vigour also show increased seedling survival and a better establishment of the crop, which often results in highly uniform fields (with the crop growing in uniform manner, i.e. with the majority of plants reaching the various stages of development at substantially the same time), and often better and higher yield. Therefore, early vigour may be determined by measuring various factors, such as thousand kernel weight, percentage germination, percentage emergence, seedling growth, seedling height, root length, root and shoot biomass and many more.
Increased Growth Rate
The increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. Plants having an increased growth rate may have a shorter life cycle. The life cycle of a plant may be taken to mean the time needed to grow from a dry mature seed up to the stage where the plant has produced dry mature seeds, similar to the starting material. This life cycle may be influenced by factors such as speed of germination, early vigour, growth rate, greenness index, flowering time and speed of seed maturation. The increase in growth rate may take place at one or more stages in the life cycle of a plant or during substantially the whole plant life cycle. Increased growth rate during the early stages in the life cycle of a plant may reflect enhanced vigour. The increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible (a similar effect may be obtained with earlier flowering time). If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soybean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible. Altering the harvest cycle of a plant may lead to an increase in annual biomass production per square meter (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested). An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened. The growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.
Stress Resistance
An increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stresses compared to control plants. Plants typically respond to exposure to stress by growing more slowly. In conditions of severe stress, the plant may even stop growing altogether. Mild stress on the other hand is defined herein as being any stress to which a plant is exposed which does not result in the plant ceasing to grow altogether without the capacity to resume growth. Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35%, 30% or 25%, more preferably less than 20% or 15% in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture. Mild stresses are the everyday biotic and/or abiotic (environmental) stresses to which a plant is exposed. Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures. The abiotic stress may be an osmotic stress caused by a water stress (particularly due to drought), salt stress, oxidative stress or an ionic stress. Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi, nematodes and insects.
In particular, the methods of the present invention may be performed under non-stress conditions or under conditions of mild drought to give plants having increased yield relative to control plants. As reported in Wang et al. (Planta (2003) 218: 1-14), abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity. Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes a particularly high degree of “cross talk” between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signalling pathways and cellular responses, such as the production of stress proteins, up-regulation of anti-oxidants, accumulation of compatible solutes and growth arrest. The term “non-stress” conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given location. Plants with optimal growth conditions, (grown under non-stress conditions) typically yield in increasing order of preference at least 97%, 95%, 92%, 90%, 87%, 85%, 83%, 80%, 77% or 75% of the average production of such plant in a given environment. Average production may be calculated on harvest and/or season basis. Persons skilled in the art are aware of average yield productions of a crop.
Nutrient deficiency may result from a lack of nutrients such as nitrogen, phosphates and other phosphorous-containing compounds, potassium, calcium, magnesium, manganese, iron and boron, amongst others.
The term salt stress is not restricted to common salt (NaCl), but may be any one or more of: NaCl, KCl, LiCl, MgCl2, CaCl2, amongst others.
Increase/Improve/Enhance
The terms “increase”, “improve” or “enhance” are interchangeable and shall mean in the sense of the application at least a 3%, 4%, 5%, 6%, 7%, 8%, 9% or 10%, preferably at least 15% or 20%, more preferably 25%, 30%, 35% or 40% more yield and/or growth in comparison to control plants as defined herein.
Seed Yield
Increased seed yield may manifest itself as one or more of the following: a) an increase in seed biomass (total seed weight) which may be on an individual seed basis and/or per plant and/or per square meter; b) increased number of flowers per plant; c) increased number of (filled) seeds; d) increased seed filling rate (which is expressed as the ratio between the number of filled seeds divided by the total number of seeds); e) increased harvest index, which is expressed as a ratio of the yield of harvestable parts, such as seeds, divided by the total biomass; and f) increased thousand kernel weight (TKW), which is extrapolated from the number of filled seeds counted and their total weight. An increased TKW may result from an increased seed size and/or seed weight, and may also result from an increase in embryo and/or endosperm size.
An increase in seed yield may also be manifested as an increase in seed size and/or seed volume. Furthermore, an increase in seed yield may also manifest itself as an increase in seed area and/or seed length and/or seed width and/or seed perimeter. Increased yield may also result in modified architecture, or may occur because of modified architecture.
Greenness Index
The “greenness index” as used herein is calculated from digital images of plants. For each pixel belonging to the plant object on the image, the ratio of the green value versus the red value (in the RGB model for encoding color) is calculated. The greenness index is expressed as the percentage of pixels for which the green-to-red ratio exceeds a given threshold. Under normal growth conditions, under salt stress growth conditions, and under reduced nutrient availability growth conditions, the greenness index of plants is measured in the last imaging before flowering. In contrast, under drought stress growth conditions, the greenness index of plants is measured in the first imaging after drought.
Marker Assisted Breeding
Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a collection of allelic variants of so called “natural” origin caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants in which the superior allelic variant was identified with another plant. This could be used, for example, to make a combination of interesting phenotypic features.
Use as Probes in (Gene Mapping)
Use of nucleic acids encoding the protein of interest for genetically and physically mapping the genes requires only a nucleic acid sequence of at least 15 nucleotides in length. These nucleic acids may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch E F and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with the nucleic acids encoding the protein of interest. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1: 174-181) in order to construct a genetic map. In addition, the nucleic acids may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the nucleic acid encoding the protein of interest in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331).
The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4: 37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.
The nucleic acid probes may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).
In another embodiment, the nucleic acid probes may be used in direct fluorescence in situ hybridisation (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favour use of large clones (several kb to several hundred kb; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.
A variety of nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.
Plant
The term “plant” as used herein encompasses whole plants, ancestors and progeny of the plants and plant parts, including seeds, shoots, stems, leaves, roots (including tubers), flowers, and tissues and organs, wherein each of the aforementioned comprise the gene/nucleic acid of interest. The term “plant” also encompasses plant cells, suspension cultures, callus tissue, embryos, meristematic regions, gametophytes, sporophytes, pollen and microspores, again wherein each of the aforementioned comprises the gene/nucleic acid of interest.
Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs selected from the list comprising Acer spp., Actinidia spp., Abelmoschus spp., Agave sisalana, Agropyron spp., Agrostis stolonifera, Allium spp., Amaranthus spp., Ammophila arenaria, Ananas comosus, Annona spp., Apium graveolens, Arachis spp, Artocarpus spp., Asparagus officinalis, Avena spp. (e.g. Avena sativa, Avena fatua, Avena byzantina, Avena fatua var. sativa, Avena hybrida), Averrhoa carambola, Bambusa sp., Benincasa hispida, Bertholletia excelsea, Beta vulgaris, Brassica spp. (e.g. Brassica napus, Brassica rapa ssp. [canola, oilseed rape, turnip rape]), Cadaba farinosa, Camellia sinensis, Canna indica, Cannabis sativa, Capsicum spp., Carex elata, Carica papaya, Larissa macrocarpa, Carya spp., Carthamus tinctorius, Castanea spp., Ceiba pentandra, Cichorium endivia, Cinnamomum spp., Citrullus lanatus, Citrus spp., Cocos spp., Coffea spp., Colocasia esculenta, Cola spp., Corchorus sp., Coriandrum sativum, Corylus spp., Crataegus spp., Crocus sativus, Cucurbita spp., Cucumis spp., Cynara spp., Daucus carota, Desmodium spp., Dimocarpus longan, Dioscorea spp., Diospyros spp., Echinochloa spp., Elaeis (e.g. Elaeis guineensis, Elaeis oleifera), Eleusine coracana, Eragrostis tef, Erianthus sp., Eriobotrya japonica, Eucalyptus sp., Eugenia unifiora, Fagopyrum spp., Fagus spp., Festuca arundinacea, Ficus carica, Fortunella spp., Fragaria spp., Ginkgo biloba, Glycine spp. (e.g. Glycine max, Soja hispida or Soja max), Gossypium hirsutum, Helianthus spp. (e.g. Helianthus annuus), Hemerocallis fulva, Hibiscus spp., Hordeum spp. (e.g. Hordeum vulgare), Ipomoea batatas, Juglans spp., Lactuca sativa, Lathyrus spp., Lens culinaris, Linum usitatissimum, Litchi chinensis, Lotus spp., Luffa acutangula, Lupinus spp., Luzula sylvatica, Lycopersicon spp. (e.g. Lycopersicon esculentum, Lycopersicon lycopersicum, Lycopersicon pyriforme), Macrotyloma spp., Malus spp., Malpighia emarginata, Mammea americana, Mangifera indica, Manihot spp., Manilkara zapota, Medicago sativa, Melilotus spp., Mentha spp., Miscanthus sinensis, Momordica spp., Morus nigra, Musa spp., Nicotiana spp., Olea spp., Opuntia spp., Ornithopus spp., Oryza spp. (e.g. Oryza sativa, Oryza latifolia), Panicum miliaceum, Panicum virgatum, Passiflora edulis, Pastinaca sativa, Pennisetum sp., Persea spp., Petroselinum crispum, Phalaris arundinacea, Phaseolus spp., Phleum pratense, Phoenix spp., Phragmites australis, Physalis spp., Pinus spp., Pistacia vera, Pisum spp., Poa spp., Populus spp., Prosopis spp., Prunus spp., Psidium spp., Punica granatum, Pyrus communis, Quercus spp., Raphanus sativus, Rheum rhabarbarum, Ribes spp., Ricinus communis, Rubus spp., Saccharum spp., Salix sp., Sambucus spp., Secale cereale, Sesamum spp., Sinapis sp., Solanum spp. (e.g. Solanum tuberosum, Solanum integrifolium or Solanum lycopersicum), Sorghum bicolor, Spinacia spp., Syzygium spp., Tagetes spp., Tamarindus indica, Theobroma cacao, Trifolium spp., Tripsacum dactyloides, Triticosecale rimpaui, Triticum spp. (e.g. Triticum aestivum, Triticum durum, Triticum turgidum, Triticum hybernum, Triticum macha, Triticum sativum, Triticum monococcum or Triticum vulgare), Tropaeolum minus, Tropaeolum majus, Vaccinium spp., Vida spp., Vigna spp., Viola odorata, Vitis spp., Zea mays, Zizania palustris, Ziziphus spp., amongst others.
Control Plant(s)
The choice of suitable control plants is a routine part of an experimental setup and may include corresponding wild type plants or corresponding plants without the gene of interest. The control plant is typically of the same plant species or even of the same variety as the plant to be assessed. The control plant may also be a nullizygote of the plant to be assessed. Nullizygotes are individuals missing the transgene by segregation. A “control plant” as used herein refers not only to whole plants, but also to plant parts, including seeds and seed parts.


DETAILED DESCRIPTION OF THE INVENTION
Surprisingly, it has now been found that modulating expression in a plant of a nucleic acid encoding a BET1-like polypeptide gives plants having enhanced yield-related traits relative to control plants. According to a first embodiment, the present invention provides a method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a BET1-like polypeptide and optionally selecting for plants having enhanced yield-related traits.
The invention also provides hitherto unknown BET1-like-encoding nucleic acids and BET1-like polypeptides.
According to a further embodiment of the present invention, there is therefore provided an isolated nucleic acid molecule selected from:

    
    
        (i) a nucleic acid represented by any one of SEQ ID NO: 11 and 95;
        (ii) the complement of a nucleic acid represented by any one of SEQ ID NO: 11 and 95;
        (iii) a nucleic acid encoding the polypeptide as represented by any one of SEQ ID NO: 12 and 96 preferably as a result of the degeneracy of the genetic code, said isolated nucleic acid can be derived from a polypeptide sequence as represented by any one of SEQ ID NO: 12 and 96 and further preferably confers enhanced yield-related traits relative to control plants;
        (iv) a nucleic acid having, in increasing order of preference 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%, 96%, 97%, 98%, or 99% sequence identity with any of the nucleic acid sequences of Table A1 and further preferably conferring enhanced yield-related traits relative to control plants;
        (v) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iv) under stringent hybridization conditions and preferably confers enhanced yield-related traits relative to control plants;
        (vi) a nucleic acid encoding a BET1-like polypeptide having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 12 and 96 and to any of the other amino acid sequences in Table A1 and preferably conferring enhanced yield-related traits relative to control plants.
    
    


According to a further embodiment of the present invention, there is also provided an isolated polypeptide selected from:

    
    
        (i) an amino acid sequence represented by any one of SEQ ID NO: 12 and 96;
        (ii) an amino acid sequence having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 12 and 96 and any of the other amino acid sequences in Table A1 and preferably conferring enhanced yield-related traits relative to control plants.
        (iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.
    
    


Furthermore, it has now surprisingly been found that modulating expression in a plant of a nucleic acid encoding a Calreticulin polypeptide gives plants having enhanced yield-related traits relative to control plants. According to a first embodiment, the present invention provides a method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a Calreticulin polypeptide and optionally selecting for plants having enhanced yield-related traits.
The invention also provides hitherto unknown Calreticulin-encoding nucleic acids and Calreticulin polypeptides.
According to a further embodiment of the present invention, there is therefore provided an isolated nucleic acid molecule selected from:

    
    
        (i) a nucleic acid represented by any one of SEQ ID NO: 116, 130, 140, 198 and 228;
        (ii) the complement of a nucleic acid represented by any one of SEQ ID NO: 116, 130, 140, 198 and 228;
        (iii) a nucleic acid encoding the polypeptide as represented by any one of SEQ ID NO: 117, 131, 141, 199 and 229 preferably as a result of the degeneracy of the genetic code, said isolated nucleic acid can be derived from a polypeptide sequence as represented by any one of SEQ ID NO: 117, 131, 141, 199 and 229 and further preferably confers enhanced yield-related traits relative to control plants;
        (iv) a nucleic acid having, in increasing order of preference 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%, 96%, 97%, 98%, or 99% sequence identity with any of the nucleic acid sequences of Table A2 and further preferably conferring enhanced yield-related traits relative to control plants;
        (v) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iv) under stringent hybridization conditions and preferably confers enhanced yield-related traits relative to control plants;
        (vi) a nucleic acid encoding a Calreticulin polypeptide having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 117, 131, 141, 199 and 229 and any of the other amino acid sequences in Table A2 and preferably conferring enhanced yield-related traits relative to control plants.
    
    


According to a further embodiment of the present invention, there is also provided an isolated polypeptide selected from:

    
    
        (i) an amino acid sequence represented by any one of SEQ ID NO: 117, 131, 141, 199 and 229;
        (ii) an amino acid sequence having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 117, 131, 141, 199 and 229 and any of the other amino acid sequences in Table A2 and preferably conferring enhanced yield-related traits relative to control plants.
        (iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.
    
    


Furthermore, it has now surprisingly been found that increasing expression in a plant of a nucleic acid sequence encoding a DUS1L polypeptide as defined herein, gives plants having increased yield-related traits relative to control plants. According to a first embodiment, the present invention provides a method for increasing yield-related traits in plants relative to control plants, comprising increasing expression in a plant of a nucleic acid sequence encoding a DUS1L polypeptide.
The invention also provides hitherto unknown nucleic acid sequences encoding DUS1L polypeptides, and DUS1L polypeptides.
According to one embodiment of the present invention, there is therefore provided an isolated nucleic acid molecule selected from:

    
    
        (i) a nucleic acid sequence as represented by SEQ ID NO: 264 or by SEQ ID NO: 292;
        (ii) the complement of a nucleic acid sequence as represented by SEQ ID NO: 264 or by SEQ ID NO: 292;
        (iii) a nucleic acid sequence encoding a DUS1L polypeptide having, in increasing order of preference, at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more amino acid sequence identity to the polypeptide sequence represented by SEQ ID NO: 265 or by SEQ ID NO: 293.
    
    


According to a further embodiment of the present invention, there is also provided an isolated polypeptide selected from:

    
    
        (i) a polypeptide sequence as represented by SEQ ID NO: 265 or by SEQ ID NO: 293;
        (ii) a polypeptide sequence having, in increasing order of preference, at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more amino acid sequence identity to a polypeptide sequence as represented by SEQ ID NO: 265 or by SEQ ID NO: 293;
        (iii) derivatives of any of the polypeptide sequences given in (i) or (ii) above.
    
    


Furthermore, it has now surprisingly been found that modulating expression in a plant of a nucleic acid encoding an ES43-like polypeptide gives plants having enhanced yield-related traits relative to control plants. According to a first embodiment, the present invention provides a method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding an ES43-like polypeptide and optionally selecting for plants having enhanced yield-related traits.
The invention also provides hitherto unknown ES43-like-encoding nucleic acids and ES43-like polypeptides.
According to a further embodiment of the present invention, there is therefore provided an isolated nucleic acid molecule selected from:

    
    
        (i) a nucleic acid represented by any one of SEQ ID NO: 308, 370, and 372;
        (ii) the complement of a nucleic acid represented by any one of SEQ ID NO: 308, 370, and 372;
        (iii) a nucleic acid encoding the polypeptide as represented by any one of SEQ ID NO: 309, 371 and 373 preferably as a result of the degeneracy of the genetic code, said isolated nucleic acid can be derived from a polypeptide sequence as represented by any one of SEQ ID NO: 309, 371 and 373 and further preferably confers enhanced yield-related traits relative to control plants;
        (iv) a nucleic acid having, in increasing order of preference 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%, 96%, 97%, 98%, or 99% sequence identity with any of the nucleic acid sequences of Table A4 and further preferably conferring enhanced yield-related traits relative to control plants;
        (v) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iv) under stringent hybridization conditions and preferably confers enhanced yield-related traits relative to control plants;
        (vi) a nucleic acid encoding a ES43-like polypeptide having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 309, 371 and 373 and any of the other amino acid sequences in Table A4 and preferably conferring enhanced yield-related traits relative to control plants.
    
    


According to a further embodiment of the present invention, there is also provided an isolated polypeptide selected from:

    
    
        (i) an amino acid sequence represented by any one of SEQ ID NO: 309, 371 and 373;
        (ii) an amino acid sequence having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 309, 371 and 373 and any of the other amino acid sequences in Table A4 and preferably conferring enhanced yield-related traits relative to control plants.
        (iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.
    
    


Furthermore, it has now surprisingly been found that modulating expression in a plant of a nucleic acid encoding a HON5-like polypeptide gives plants having enhanced yield-related traits relative to control plants. According to a first embodiment, the present invention provides a method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a HON5-like polypeptide and optionally selecting for plants having enhanced yield-related traits.
The invention also provides hitherto unknown HON5-like-encoding nucleic acids and HON5-like polypeptides.
According to a further embodiment of the present invention, there is therefore provided an isolated nucleic acid molecule selected from:

    
    
        (i) a nucleic acid represented by any one of SEQ ID NO: 393 and 395;
        (ii) the complement of a nucleic acid represented by any one of SEQ ID NO: 393 and 395;
        (iii) a nucleic acid encoding the polypeptide as represented by any one of SEQ ID NO: 393 and 395 preferably as a result of the degeneracy of the genetic code, said isolated nucleic acid can be derived from a polypeptide sequence as represented by any one of SEQ ID NO: 394 and 396 and further preferably confers enhanced yield-related traits relative to control plants;
        (iv) a nucleic acid having, in increasing order of preference 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%, 96%, 97%, 98%, or 99% sequence identity with any of the nucleic acid sequences of Table A5 and further preferably conferring enhanced yield-related traits relative to control plants;
        (v) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iv) under stringent hybridization conditions and preferably confers enhanced yield-related traits relative to control plants;
        (vi) a nucleic acid encoding a HON5-like polypeptide having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 394 and 396 and any of the other amino acid sequences in Table A5 and preferably conferring enhanced yield-related traits relative to control plants.
    
    


According to a further embodiment of the present invention, there is also provided an isolated polypeptide selected from:

    
    
        (i) an amino acid sequence represented by any one of SEQ ID NO: 394 and 396;
        (ii) an amino acid sequence having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 394 and 396 and any of the other amino acid sequences in Table A5 and preferably conferring enhanced yield-related traits relative to control plants.
        (iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.
    
    


Furthermore, it has now surprisingly been found that modulating expression in a plant of a nucleic acid encoding a GSA1 polypeptide gives plants having enhanced yield-related traits relative to control plants. According to a first embodiment, the present invention provides a method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a GSA1 polypeptide and optionally selecting for plants having enhanced yield-related traits.
A preferred method for modulating (preferably, increasing) expression of a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, is by introducing and expressing in a plant a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide.
Concerning BET1-like polypeptides, any reference hereinafter to a “protein useful in the methods of the invention” is taken to mean a BET1-like polypeptide as defined herein. Any reference hereinafter to a “nucleic acid useful in the methods of the invention” is taken to mean a nucleic acid capable of encoding such a BET1-like polypeptide. The nucleic acid to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid encoding the type of protein which will now be described, hereafter also named “BET1-like nucleic acid” or “BET1-like gene”.
Concerning Calreticulin polypeptides, any reference hereinafter to a “protein useful in the methods of the invention” is taken to mean a Calreticulin polypeptide as defined herein. Any reference hereinafter to a “nucleic acid useful in the methods of the invention” is taken to mean a nucleic acid capable of encoding such a Calreticulin polypeptide. The nucleic acid to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid encoding the type of protein which will now be described, hereafter also named “Calreticulin nucleic acid” or “Calreticulin gene”.
Concerning DUS1L polypeptides, any reference hereinafter to a “protein useful in the methods of the invention” is taken to mean a DUS1L polypeptide as defined herein. Any reference hereinafter to a “nucleic acid sequence useful in the methods of the invention” is taken to mean a nucleic acid sequence capable of encoding such a DUS1L polypeptide. The nucleic acid sequence to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid sequence encoding the type of polypeptide, which will now be described, hereafter also named “DUS1L nucleic acid sequence” or “DUS1L gene”.
Concerning ES43-like polypeptide, any reference hereinafter to a “protein useful in the methods of the invention” is taken to mean an ES43-like polypeptide as defined herein. Any reference hereinafter to a “nucleic acid useful in the methods of the invention” is taken to mean a nucleic acid capable of encoding such an ES43-like polypeptide. The nucleic acid to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid encoding the type of protein which will now be described, hereafter also named “ES43-like nucleic acid” or “ES43-like gene”.
Concerning HON5-like polypeptides, any reference hereinafter to a “protein useful in the methods of the invention” is taken to mean a HON5-like polypeptide as defined herein. Any reference hereinafter to a “nucleic acid useful in the methods of the invention” is taken to mean a nucleic acid capable of encoding such a HON5-like polypeptide. The nucleic acid to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid encoding the type of protein which will now be described, hereafter also named “HON5-like nucleic acid” or “HON5-like gene”.
Concerning GSA1 polypeptides, any reference hereinafter to a “protein useful in the methods of the invention” is taken to mean a GSA1 polypeptide as defined herein. Any reference hereinafter to a “nucleic acid useful in the methods of the invention” is taken to mean a nucleic acid capable of encoding such a GSA1 polypeptide. The nucleic acid to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid encoding the type of protein which will now be described, hereafter also named “GSA1 nucleic acid” or “GSA1 gene”.
A “BET1-like polypeptide” as defined herein refers to any polypeptide comprising a CC domain as defined by SEQ ID No 97: C(X1)a C(X2)c (Y)c G(X3)d C(X4) C, wherein:

    
    
        X1, X2, X3 and X4 may be any amino acid,
        Y may be any amino acid or none (no amino acid),
        
            a means up to 3 times X1,
            b means up to 7 times X2,
            c means up to 2 times Y,
            d means up to 15 times X3 
        
        
    
    


In a further embodiment of the present invention, d is preferably 8, 10 or 11 times of the amino acids represented by X3.
A preferred CC domain according the present invention is a domain having at least 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%, 96%, 97%, 98%, or 99% sequence identity to the domain represented by SEQ ID NO 98: CRLICSSKGFKDGG WCDESVEHKVCCC
Additionally, another preferred embodiment of the present invention refers to a BET1-like polypeptide comprising the CC domain, as defined above, and the following motifs Motif 1 and/or Motif 2:










Motif 1: G(W/Y)CD(E/K);
(SEQ ID NO: 99)



 



Motif 2: EGF
(SEQ ID NO: 100)






The most preferable embodiment of the present invention refers to a BET1-like polypeptide comprising the CC domain, as defined above, and the motif 1 (which is present in SEQ ID NO: 2), also as defined above.
In another preferably embodiment of the present invention, the BET1-like polypeptide comprises a sequence such as SEQ ID NO: 2:







SEQ ID NO: 2:


MAVMKSSTMVALLLAVAILSSLSPCYEAGGCIGKPKKSPPPPRKPYFSS


 


YSEDHQNCRLICSSKGFKDGGWCDESVEHKVCCCSH.






Alternatively, the homologue of a BET1-like polypeptide has in increasing order of preference at least 25%, 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%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by any of the polypeptides of Table A1, preferably by SEQ ID NO: 2, provided that the homologous protein comprises the conserved motifs as outlined above. The overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides). Compared to overall sequence identity, the sequence identity will generally be higher when only conserved domains or motifs are considered.
Calreticulin polypeptides are well known in the art. (Christianssen et al 2008. Plant Cell Physiol. 2008 June; 49(6):912-24). A Calreticulin polypeptide typically refers to any polypeptide comprising three distinct structural and functional domains with loosely defined boundaries: the nearly neutral N-domain, the proline-rich P-domain, and the polyacidic C-domain (FIG. 4).
A preferred Calreticulin polypeptide useful in the methods of the invention is a polypeptide comprising one or more of the following motifs:

    
    
        (i) Motif 3: PXXIXDPXXKKPEXWDD (SEQ ID NO: 246),
        (ii) Motif 4: GXWXXXXIXNPXYK (SEQ ID NO: 247),
        (iii) Motif 5: E[VL]WQVK (SEQ ID NO: 248),
        (iv) Motif 6: TLV[FL]QFSVKHEQKLDCGGGY[MV]KLLSGDVDQKKFGG[DE]PYSI MFGPDICGY (SEQ ID NO: 249) which represents typical CRT plant polypeptides of the CRT1/2 group;
        (v) Motif 7: TPYS[LF]MFGPD[IL]CGTQTKKLH[VL]ILSYQGQNYPIKKDL[QE]CETD KLTH[FV]YTFI (SEQ ID NO: 250) which represents typical CRT plant polypeptides of the CRT3 group;
        (vi) Motif 8: N[HY][LP]IKK[DE][VL]PCETD[QK]LTH[VF]YTFI[LI]RPDA[TS]YSILIDN[VR]E[KR][QE][TS]GS[LM]Y[TS]DWD[IL]L (SEQ ID NO: 251) which represents typical CRT polypeptides of the viridiplantae kingdom;
        (vii) Motif 9: QKKFGGDTPYSIMFGPDICGY[SQ]TKK[VL]H[AV]I] (SEQ ID NO: 252), which represents typical CRT polypeptides of the eukaryotic origin,
        (viii) a motif having at least 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%, 96%, 97%, 98%, or 99% overall sequence identity to any one of the motifs (i) to (vii);
    
    


Wherein “X” represents any amino acid and wherein amino acids indicated between brackets “[ ]” represent alternative amino acids at that location.
Preferred Calreticulin polypeptides of the invention comprise a signal peptide in N term and a ER retention signal ((H/K)DEL) in C term, preferably any of those disclosed in Christianssen et al 2008.
A preferred polypeptide of the invention refers in increasing order of preference to any polypeptide of Table A2, an orthologue or a homologue of any of the Calreticulin polypeptides given in Table A2.
Alternatively, the homologue of a Calreticulin protein has in increasing order of preference at least 25%, 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%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by SEQ ID NO: 105, provided that the homologous protein comprises the conserved motifs as outlined above. The overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides). Compared to overall sequence identity, the sequence identity will generally be higher when only conserved domains or motifs are considered.
Preferably, the polypeptide sequence which when used in the construction of a phylogenetic tree, such as the one depicted in Christensen et al. 2008-FIG. 1 and herein reproduced in FIG. 5, clusters with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b, and Os_CRT3 or At_CRT3 polypeptides, preferably with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b. Alternatively, the polypeptide sequence which when used in the construction of a phylogenetic tree, such as the one described in Example 2 cluster with any one of the polypeptide within in the following phylogenetic classes: class 1-CRT1,2-CRT3,3-algae, 4-animal and 5-protist of Example 2, preferably with class 1-CRT1.
A “DUS1L polypeptide” as defined herein refers to any polypeptide comprising (i) a tRNA-dihydrouridine synthase domain with an InterPro entry IPR001269; (ii) an aldolase-type TIM barrel domain with an InterPro entry IPR013785; and (iii) a tRNA-dihydrouridine synthase conserved site with an InterPro entry IPR018517.
Alternatively or additionally, “DUS1L polypeptide” as defined herein refers to any polypeptide comprising in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to a tRNA-dihydrouridine synthase domain as represented by SEQ ID NO: 294.
Alternatively or additionally, a “DUS1L polypeptide” as defined herein refers to any polypeptide sequence comprising in increasing order of preference at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to a polypeptide as represented by SEQ ID NO: 259.
Alternatively or additionally, a “DUS1L polypeptide” as defined herein refers to any polypeptide comprising in increasing order of preference at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to any of the polypeptide sequences given in Table A3 herein.
Additionally, a “DUS1L polypeptide” as defined herein can functionally complement an E. coli strain deficient in tRNA dihydrouridine synthase activity, thereby increasing tRNA dihydrouridine content.
An “ES43-like polypeptide” as defined herein refers to any polypeptide comprising a comprising a BAH domain (Pfam accession number: PF01426) and a PHD domain (Pfam accession number: PF00628).
A BAH domain is well known in the art (Callebaut et al. FEBS letts 1999; 446:189-193). A PHD domain is well known in the art (Aasland R, et al. Trends Biochem Sci 1995; 20:56-59). Methods to identify a BAH domain and a PHD domain are well known in the art, for example identification by consulting Structural domain databases and/or Sequence domain databases.
Examples of Structural Databases:

    
    
        CATH (Orengo et al. (1997). Structure, 5, 1093-1108; Alison et al. Nucleic Acids Research, 2009, Vol. 37).
        DALI (Holm, 2008. Bioinformatics 24, 2780-2781)°
        SCOP (Murzin et al. J. Mol. Biol. 247, 536-540; Andreeva et al. Nucl. Acid Res. 36: D419-D425)
    
    


Examples of Sequence Domain Databases:

    
    
        InterPro (Hunters et al. 2009 Nucleic Acids Res. 37 (Database Issue):D224-228; Quevillon et al. 2005 Nucleic Acids Res. 33 (Web Server issue):W116-W120).
        Pfam (Finn Nucleic Acids Research (2008) Database Issue 36:D281-D288).
        SMART (Schultz et al. (1998) PNAS 95: 5857-5864; Letunic et al. 2004, NAR 32, D142-D144).
        NCBI Conserved Domain Database (Marchler-Bauer et al. Nucleic Acids Res. 2007; 35 (Database Issue):D237-40).
        SUPERFAMILY Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms (Gough et al. J. Mol. Biol., 313(4), 903-919).
    
    


Further details on method to consult specific protein domain databases are provided in the Examples section.
A preferred ES43-like polypeptide according to the invention is a polypeptide comprising a domain having an amino acid sequence in increasing order of preference at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence of SEQ ID NO: 374 (BAH domain of SEQ ID NO: 299) or to the amino acid sequence of SEQ ID NO: 375 (PHD domain of SEQ ID NO: 299.
Further preferably the ES43-like polypeptide according to the invention comprises any one or more of the following protein motifs:











(i)
Motif 10: VRVRVRWYY;
(SEQ ID NO: 376)



 



(ii)
Motif 11: RPEE;
(SEQ ID NO: 377)



 



(iii)
Motif 12: TIEGKC;
(SEQ ID NO: 378)



 



(iv)
Motif 13: GDCVLMR;
(SEQ ID NO: 379)



 



(v)
Motif 14: YVAR;
(SEQ ID NO: 380)



 



(vi)
Motif 15: GAKE;
(SEQ ID NO: 381)



 



(vii)
Motif 16: CRFEY;
(SEQ ID NO: 382)



 



(viii)
Motif 17: HEAT
(SEQ ID NO: 383)






A yet further preferable ES43-like polypeptide is a homologue, preferably a paralogue or an orthologue of the ES43-like polypeptide represented by SEQ ID NO: 299.
Preferably the BAH domain is located the N-terminus of the ES43-like polypeptide while the PHD domain is located at the C-terminus.
Alternatively, the homologue of an ES43-like protein has in increasing order of preference at least 25%, 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%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by SEQ ID NO: 299, provided that the homologous protein comprises the conserved domains as outlined above. The overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides). Compared to overall sequence identity, the sequence identity will generally be higher when only conserved domains or motifs are considered. For local alignments, the Smith-Waterman algorithm is particularly useful (Smith T F, Waterman Miss. (1981) J. Mol. Biol. 147(1); 195-7).
A “HON5-like polypeptide” as defined herein refers to any polypeptide comprising a histone H1/H5 domain (Pfam: PF00538; Interpro: IPR005818) and at least two, preferably two, three, four, five, six or seven AT-hook domains (Pfam: PF02178; InterPro: IPR000637).
Histone H1/H5 protein domains (Pfam: PF00538; Interpro: IPR005818) are well known in the art. Histone H1/H5 protein domain may be represented by the consensus sequence: HPPYAEMIAIAALKEDGSSKAIAKYIERYTGLPPHSALLTHHLKRLKSSGLLVMVKKSYKLA S (SEQ ID NO: 411). The consensus sequence shows which residues are most conserved (abundant) at each position in the histone H1/H5 domain in H1 or H5 proteins of different origin. The skilled in the art will recognize that histone H1/H5 domain in specific H1 polypeptide may differ from that specified in the consensus, while the overall homology along the domain remains.
A preferred histone H1/H5 domain present in HON5-like polypeptides refers to a domain having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the consensus sequence of the H1/H5 protein domain as represented by SEQ ID NO: 410. A further preferred H1/H5 histone domain is any one of the H1/H5 histone domains as present in the polypeptides of Table A5, most preferably in SEQ ID NO: 388.
AT hook domains also known as AT hook motifs are well known in the art. AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins (Reeves and Beckerbauer .Biochim. Biophys. Acta 1519 13-29 2001. The ATHook domain is registered in Interporo database with reference accession number: InterPro: IPR017956 under the name AT hook, DNA-binding, conserved site (Hunter et al; 2009, Nucleic Acids Res. 37 Database Issue: D224-228), and in the pfam database (Finn et al. Nucleic Acids Research (2008) Database Issue 36:D281-D288) under the reference accession number PF02178 with the name “AT hook motif”. A preferred AT hook domain present in HON5-like polypeptides refers to a domain having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any of the AT hook motifs present in the polypeptides of Table A5, more preferably in SEQ ID NO: 388.
Additionally or alternatively and preferably, a HON5-like polypeptide comprises one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one of the following Motifs:








Motif I:



(SEQ ID NO: 411)



Y[ASK]EMI[YC]TAI[AGT]AL[KN][ED][PK]DGSS[KR]RAI[AS][KR]YIERA[YF][TP][GD]



 


LP[PS]AH[SD][AD]LLTHHLK[RT]L[KR]


 


Motif II:


(SEQ ID NO: 412)



GLLV[ML]VK[KH]SYKL[AP][RS]S



 


Motif III:


(SEQ ID NO: 413)



SA[PS][PQS]GQKRGRGRPPKPK







wherein amino acids between brackets represent alternative amino acids at that position.

Motif I and Motif II are typically located within the H1/H5 domain, while Motif III typically overlaps with AT-hook domains.
Alternatively, the homologue of a HON5-like protein has in increasing order of preference at least 25%, 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%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by any of the polypeptides in Table A5 preferably by SEQ ID NO: 388 and preferably comprises Motif I, II and III as defined above.
The overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides). Compared to overall sequence identity, the sequence identity will generally be higher when only conserved domains or motifs are considered. For local alignments, the Smith-Waterman algorithm is particularly useful (Smith T F, Waterman Miss. (1981) J. Mol. Biol. 147(1); 195-7).
A “GSA1 polypeptide” as defined herein refers to any polypeptide comprising any one or more of:








Domain 1:



(SEQ ID NO: 487)



VPS[IV]EMVRFVNSGTEAC[ML][GS][VA]LRL[AM]RA[FY]TGREK[IV][IL]K



 


FEGCYHGHAD[PS]FLVK


Domain 2:


(SEQ ID NO: 488)



NSPVRAFKSVGGQP[IV]V[FI]D[SR]VKG[SA][HRY][MA]WD[IV]DGN[EK]



 


Y[IV]DYVGSWGPAIIGHADD


Domain 3:


(SEQ ID NO: 489)



AQEYFGITPD[LV]TT[LM]GK[IV]IGGGLPVGAYGG[RK][RK][ED]IMEMVAP



 


AGPMYQAGTLS






or a domain having in increasing order of preference at least 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%, 96%, 97%, 98%, or 99% overall sequence identity to any one or more of domains 1 to 3.

Alternatively, the homologue of a GSA1 protein has in increasing order of preference at least 25%, 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%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by SEQ ID NO: 418, provided that the homologous protein comprises the conserved motifs as outlined above.
The overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides). Compared to overall sequence identity, the sequence identity will generally be higher when only conserved domains or motifs are considered. For local alignments, the Smith-Waterman algorithm is particularly useful (Smith T F, Waterman Miss. (1981) J. Mol. Biol. 147(1); 195-7).
Preferably, the polypeptide sequence which when used in the construction of a phylogenetic tree, such as the one depicted in FIG. 17, clusters with the group of GSA1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 418 rather than with any other group.
The terms “domain”, “signature” and “motif” are defined in the “definitions” section herein. Specialist databases exist for the identification of domains, for example, SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244), InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31, 315-318), Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation. (In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp 53-61, AAAI Press, Menlo Park; Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004)), or Pfam (Bateman et al., Nucleic Acids Research 30(1): 276-280 (2002)). A set of tools for in silico analysis of protein sequences is available on the ExPASy proteomics server (Swiss Institute of Bioinformatics (Gasteiger et al., ExPASy: the proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Res. 31:3784-3788 (2003)). Domains or motifs may also be identified using routine techniques, such as by sequence alignment.
Concerning DUS1L polypeptides, an alignment of the polypeptides of Table A3 herein, is shown in FIG. 9. Such alignments are useful for identifying the most conserved domains or motifs between the DUS1L polypeptides as defined herein. One such domain is a tRNA-dihydrouridine synthase domain with an InterPro entry IPR001269 (integrating the PFAM PF01207 entry (marked by X's in FIG. 9)). One such motif is the tRNA-dihydrouridine synthase conserved site with an InterPro entry IPR018517 (integrating the PROSITE PS01136 (marked by X's in FIG. 9). Conserved residues are boxed in FIG. 9, in particular a Cys residue which is in other organisms a key general-acid/base catalyst.
Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the global (i.e. spanning the complete sequences) alignment of two sequences that maximizes the number of matches and minimizes the number of gaps. The BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology Information (NCBI). Homologues may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1.83), with the default pairwise alignment parameters, and a scoring method in percentage. Global percentages of similarity and identity may also be determined using one of the methods available in the MatGAT software package (Campanella et al., BMC Bioinformatics. 2003 Jul. 10; 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.). Minor manual editing may be performed to optimise alignment between conserved motifs, as would be apparent to a person skilled in the art. Furthermore, instead of using full-length sequences for the identification of homologues, specific domains may also be used. The sequence identity values may be determined over the entire nucleic acid or amino acid sequence or over selected domains or conserved motif(s), using the programs mentioned above using the default parameters. For local alignments, the Smith-Waterman algorithm is particularly useful (Smith T F, Waterman Miss. (1981) J. Mol. Biol. 147(1); 195-7).
Concerning DUS1L polypeptides, Example 3 herein describes in Table C2 the percentage identity between the DUS1L polypeptide as represented by SEQ ID NO: 259 and the DUS1L polypeptides listed in Table A3, which can be as low as 32% amino acid sequence identity. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example using BLAST, the statistical significance threshold (called “expect” value) for reporting matches against database sequences may be increased to show less stringent matches. This way, short nearly exact matches may be identified.
BET1-like polypeptides, when expressed in rice according to the methods of the present invention as outlined in the Examples section, give plants having increased yield related traits, in particular seed yield.
Additionally, BET1-like polypeptides may display a preferred subcellular localization, typically one or more of nuclear, cytoplasmic, chloroplastic, or mitochondrial. The task of protein subcellular localisation prediction is important and well studied. Knowing a protein's localisation helps elucidate its function. Experimental methods for protein localization range from immunolocalization to tagging of proteins using green fluorescent protein (GFP) or beta-glucuronidase (GUS). Such methods are accurate although labor-intensive compared with computational methods. Recently much progress has been made in computational prediction of protein localisation from sequence data. Among algorithms well known to a person skilled in the art are available at the ExPASy Proteomics tools hosted by the Swiss Institute for Bioinformatics, for example, PSort, TargetP, ChloroP, LocTree, Predotar, LipoP, MITOPROT, PATS, PTS1, SignalP, TMHMM, and others.
BET1-like polypeptide preferably comprises a transmembrane signal peptide which is typically located at the N-terminus. Transmembrane signal peptides are known in the art. Preferably BET1-like polypeptides are preferably localized in a membranous structure of the cell, most preferably at the endosperm transfer layer. Methods to determine the cellular subcelullar location of a protein are well known in the art.
Furthermore, CRT polypeptides typically have calcium (Ca2+) binding activity. Tools and techniques for measuring calcium (Ca2+) binding activity are well known in the art. For example the binding of a protein to calcium (Ca2+) may be determined in 45Ca2+ overlays of protein blots or by means of (3H)Bradykinin binding assay and/or fluorescence Ca2+ measurements of mouse embryonic fibroblasts assays as described by Christensen et al Plant Cell Phys. 2008, 49(6)912-24. Alternatively CRT polypeptide activity may be assay in complementation of the Atcrt1a mutant as described by Christiansen et al. 2008. In addition, CRT polypeptides, when expressed in rice according to the methods of the present invention as outlined in the Example section, give plants having increased yield related traits, in particular.
Concerning DUS1L polypeptides, the task of protein subcellular localisation prediction is important and well studied. Knowing a protein's localisation helps elucidate its function. Experimental methods for protein localization range from immunolocalization to tagging of proteins using green fluorescent protein (GFP) or beta-glucuronidase (GUS). Such methods are accurate although labor-intensive compared with computational methods. Recently much progress has been made in computational prediction of protein localisation from sequence data. Among algorithms well known to a person skilled in the art are available at the ExPASy Proteomics tools hosted by the Swiss Institute for Bioinformatics, for example, PSort, TargetP, ChloroP, LocTree, Predotar, LipoP, MITOPROT, PATS, PTS1, SignalP, TMHMM, and others. The predicted subcellular localisation of SEQ ID NO: 259 using the PSort algorithm is the mitochondrial compartment (see Example 5).
Furthermore, ES43-like polypeptides typically have protein-protein interaction activity. Tools and techniques for measuring protein-protein interaction activity are well known in the art such as Co-immunoprecipitation, Bimolecular Fluorescence Complementation (BiFC), Fluorescence resonance energy transfer (FRET), Pull-down assays, Label transfer, theyeast two-hybrid screen, In-vivo crosslinking, Tandem affinity purification (TAP), Chemical crosslinking, Quantitative immunoprecipitation combined with knock-down (QUICK), Dual Polarisation Interferometry (DPI), Protein-protein docking, # Static Light Scattering (SLS), Chemical crosslinking followed by high mass MALDI mass spectrometry, SPINE (Strep-protein interaction experiment) and Surface plasmon resonance (Wikipedia).
In addition, ES43-like polypeptides, when expressed in rice according to the methods of the present invention as outlined in the Examples section, give plants having increased yield related traits, in particular increased seed filing rate.
Furthermore, HON5-like polypeptides typically have DNA binding and/or protein binding activity. Tools and techniques for measuring DNA binding, chromatin interaction and/or protein binding activity are well known in the art, including for example electrophoretic mobility shift assays and footprinting studies of the interaction with A/T-rich stretch frequently occurring in plant promoter regions (Gasser 2003, Plant Mol Biol. 53(3):281-95 and references therein; Pedersen et al., 1991; Nieto-Sotelo et al. 1994 Plant Cell 6: 287-301; Zhang et al. 2003 Biochemistry 42: 6596-6607; Klosterman 2002 Plant Science 162, 855-866).
In addition, HON5-like polypeptides, when expressed in rice according to the methods of the present invention as outlined in the Examples section give plants having increased yield related traits, in particular an increase in any one or more of total seed weight, number of filled seeds, increase of seed filling rate and harvest index.
Additionally, HON5-like polypeptides may display a preferred subcellular localization, typically one or more of nuclear, citoplasmic, chloroplastic, or mitochondrial. The task of protein subcellular localisation prediction is important and well studied. Knowing a protein's localisation helps elucidate its function. Experimental methods for protein localization range from immunolocalization to tagging of proteins using green fluorescent protein (GFP) or beta-glucuronidase (GUS). Such methods are accurate although labor-intensive compared with computational methods. Recently much progress has been made in computational prediction of protein localisation from sequence data. Among algorithms well known to a person skilled in the art are available at the ExPASy Proteomics tools hosted by the Swiss Institute for Bioinformatics, for example, PSort, TargetP, ChloroP, LocTree, Predotar, LipoP, MITOPROT, PATS, PTS1, SignalP, TMHMM, and others.
GSA1 polypeptides, when expressed in rice according to the methods of the present invention as outlined in the Examples section, give plants having increased yield related traits, in particular increased seed yield.
Concerning BET1-like polypeptides, the present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ ID NO: 1, encoding the polypeptide sequence of SEQ ID NO: 2. However, performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any BET1-like-encoding nucleic acid or BET1-like polypeptide as defined herein.
Examples of nucleic acids encoding BET1-like polypeptides are given in Table A1 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention. The amino acid sequences given in Table A1 of the Examples section are example sequences of orthologues and paralogues of the BET1-like polypeptide represented by SEQ ID NO: 2, the terms “orthologues” and “paralogues” being as defined herein. Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search. Typically, this involves a first BLAST involving BLASTing a query sequence (for example using any of the sequences listed in Table A1 of the Examples section) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are generally used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 1 or SEQ ID NO: 2, the second BLAST would therefore be against corn sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence amongst the highest hits; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.
Concerning Calreticulin polypeptides, the present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ ID NO: 104, encoding the polypeptide sequence of SEQ ID NO: 105. However, performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any Calreticulin-encoding nucleic acid or Calreticulin polypeptide as defined herein.
Examples of nucleic acids encoding Calreticulin polypeptides are given in Table A2 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention. The amino acid sequences given in Table A2 of the Examples section are example sequences of orthologues and paralogues of the Calreticulin polypeptides represented by SEQ ID NO: 105, the terms “orthologues” and “paralogues” being as defined herein. Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search. Typically, this involves a first BLAST involving BLASTing a query sequence (for example using any of the sequences listed in Table A2 of the Examples section) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are generally used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 104 or SEQ ID NO: 105, the second BLAST would therefore be against Solanum lycopersicum sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence amongst the highest hits; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.
Concerning DUS1L polypeptides, the present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ ID NO: 258, encoding the DUS1L polypeptide sequence of SEQ ID NO: 259. However, performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any nucleic acid sequence encoding a DUS1L polypeptide as defined herein.
Examples of nucleic acid sequences encoding DUS1L polypeptides are given in Table A3 of the Examples section herein. Such nucleic acid sequences are useful in performing the methods of the invention. The polypeptide sequences given in Table A3 of the Examples section are example sequences of orthologues and paralogues of the DUS1L polypeptide represented by SEQ ID NO: 259, the terms “orthologues” and “paralogues” being as defined herein. Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search. Typically, this involves a first BLAST involving BLASTing a query sequence (for example using any of the sequences listed in Table A3 of the Examples section) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are generally used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 258 or SEQ ID NO: 259, the second BLAST would therefore be against Saccharum officinarum sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence amongst the highest hits; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.
Concerning ES43-like polypeptides, the present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ ID NO: 298, encoding the polypeptide sequence of SEQ ID NO: 299. However, performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any ES43-like-encoding nucleic acid or ES43-like polypeptide as defined herein.
Examples of nucleic acids encoding ES43-like polypeptides are given in Table A4 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention. The amino acid sequences given in Table A4 of the Examples section are example sequences of orthologues and paralogues of the ES43-like polypeptide represented by SEQ ID NO: 299, the terms “orthologues” and “paralogues” being as defined herein. Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search. Typically, this involves a first BLAST involving BLASTing a query sequence (for example using any of the sequences listed in Table A4 of the Examples section) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are generally used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 298 or SEQ ID NO: 299, the second BLAST would therefore be against rice sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence amongst the highest hits; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.
Concerning HON5-like polypeptides, the present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ ID NO: 387, encoding the polypeptide sequence of SEQ ID NO: 388. However, performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any HON5-like-encoding nucleic acid or HON5-like polypeptide as defined herein.
Examples of nucleic acids encoding HON5-like polypeptides are given in Table A5 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention. The amino acid sequences given in Table A5 of the Examples section are example sequences of orthologues and paralogues of the HON5-like polypeptide represented by SEQ ID NO: 388, the terms “orthologues” and “paralogues” being as defined herein. Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search. Typically, this involves a first BLAST involving BLASTing a query sequence (for example using any of the sequences listed in Table A5 of the Examples section) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are generally used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 387 or SEQ ID NO: 388, the second BLAST would therefore be against Populus trichocarpa sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence amongst the highest hits; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.
Concerning HON5-like polypeptides, the present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ ID NO: 417, encoding the polypeptide sequence of SEQ ID NO: 418. However, performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any GSA1-encoding nucleic acid or GSA1 polypeptide as defined herein.
Examples of nucleic acids encoding GSA1 polypeptides are given in Table A6 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention. The amino acid sequences given in Table A6 of the Examples section are example sequences of orthologues and paralogues of the GSA1 polypeptide represented by SEQ ID NO: 418, the terms “orthologues” and “paralogues” being as defined herein. Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search. Typically, this involves a first BLAST involving BLASTing a query sequence (for example using any of the sequences listed in Table A6 of the Examples section) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are generally used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived (where the query sequence is SEQ ID NO: 417 or SEQ ID NO: 418, the second BLAST would therefore be against Populus sequences). The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence amongst the highest hits; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.
High-ranking hits are those having a low E-value. The lower the E-value, the more significant the score (or in other words the lower the chance that the hit was found by chance). Computation of the E-value is well known in the art. In addition to E-values, comparisons are also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In the case of large families, Clustal W may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues.
Nucleic acid variants may also be useful in practising the methods of the invention. Examples of such variants include nucleic acids encoding homologues and derivatives of any one of the amino acid sequences given in Table A1 to A6 of the Examples section, the terms “homologue” and “derivative” being as defined herein. Also useful in the methods of the invention are nucleic acids encoding homologues and derivatives of orthologues or paralogues of any one of the amino acid sequences given in Table A1 to A6 of the Examples section. Homologues and derivatives useful in the methods of the present invention have substantially the same biological and functional activity as the unmodified protein from which they are derived.
Further nucleic acid variants useful in practising the methods of the invention include portions of nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, nucleic acids hybridising to nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, splice variants of nucleic acids encoding BET1-like polypeptides, allelic variants of nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, and variants of nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, obtained by gene shuffling. The terms hybridising sequence, splice variant, allelic variant and gene shuffling are as described herein.
Nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, need not be full-length nucleic acids, since performance of the methods of the invention does not rely on the use of full-length nucleic acid sequences. According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a portion of any one of the nucleic acid sequences given in Table A1 to A6 of the Examples section, or a portion of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A1 to A6 of the Examples section.
A portion of a nucleic acid may be prepared, for example, by making one or more deletions to the nucleic acid. The portions may be used in isolated form or they may be fused to other coding (or non-coding) sequences in order to, for example, produce a protein that combines several activities. When fused to other coding sequences, the resultant polypeptide produced upon translation may be bigger than that predicted for the protein portion.
Concerning BET1-like polypeptides, portions useful in the methods of the invention, encode a BET1-like polypeptide as defined herein, and have substantially the same biological activity as the amino acid sequences given in Table A1 of the Examples section. Preferably, the portion is a portion of any one of the nucleic acids given in Table A1 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A1 of the Examples section. Preferably the portion is at least 50, 75, 100, 150, 200, or more consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A1 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A1 of the Examples section. Most preferably the portion is a portion of the nucleic acid of SEQ ID NO: 1. Preferably, the portion encodes a fragment of an amino acid sequence comprising domain CC, preferably motif1 and/or 2 as defined above and having preferably at least 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%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 2.
Concerning Calreticulin polypeptides, portions useful in the methods of the invention, encode a Calreticulin polypeptide as defined herein, and have substantially the same biological activity as the amino acid sequences given in Table A2 of the Examples section. Preferably, the portion is a portion of any one of the nucleic acids given in Table A2 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A2 of the Examples section. Preferably the portion is at least 100, 200, 300, 400, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, or more consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A2 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A2 of the Examples section. Most preferably the portion is a portion of the nucleic acid of SEQ ID NO: 104. Preferably, the portion encodes a fragment of an amino acid sequence which, when used in the construction of a phylogenetic tree, such as the one depicted in Christensen et al. 2008-FIG. 1 and herein reproduced in FIG. 5, clusters with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b, and Os_CRT3 or At_CRT3 polypeptides, preferably with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b. Alternatively, the portion encodes a fragment of an amino acid sequence which, when used in the construction of a phylogenetic tree, such as the one described in Example 2 cluster with any one of the polypeptide within the following phylogenetic classes: class 1-CRT1,2-CRT3,3-algae, 4-animal and 5-protist of Example 2, preferably with the class 1-CRT1 polypeptides.
Concerning DUS1L polypeptides, portions useful in the methods of the invention, encode a DUS1L polypeptide as defined herein, and have substantially the same biological activity as the polypeptide sequences given in Table A3 of the Examples section. Preferably, the portion is a portion of any one of the nucleic acid sequences given in Table A3 of the Examples section, or is a portion of a nucleic acid sequence encoding an orthologue or paralogue of any one of the polypeptide sequences given in Table A3 of the Examples section. Preferably the portion is, in increasing order of preference at least 700, 800, 900, 1000, 1100, 1150, 1200, 1250, 1300, 1350, 1400 or more consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A3 of the Examples section, or of a nucleic acid sequence encoding an orthologue or paralogue of any one of the polypeptide sequences given in Table A3 of the Examples section. Preferably, the portion is a portion of a nucleic sequence encoding a polypeptide sequence comprising in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to a tRNA-dihydrouridine synthase domain as represented by SEQ ID NO: 294. More preferably, the portion is a portion of a nucleic sequence encoding a polypeptide sequence comprising in increasing order of preference at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to the DUS1L polypeptide as represented by SEQ ID NO: 259 or to any of the polypeptide sequences given in Table A3 herein. Most preferably, the portion is a portion of the nucleic acid sequence of SEQ ID NO: 258.
Concerning ES43-like polypeptides, portions useful in the methods of the invention, encode an ES43-like polypeptide as defined herein, and have substantially the same biological activity as the amino acid sequences given in Table A4 of the Examples section. Preferably, the portion is a portion of any one of the nucleic acids given in Table A4 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A4 of the Examples section. Preferably the portion is at least 100, 200, 300, 400, 500, 550, 600, 650, 700, or more consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A4 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A4 of the Examples section. Most preferably the portion is a portion of the nucleic acid of SEQ ID NO: 298. Preferably, the portion encodes a fragment of an amino acid sequence which comprises a BAH domain or a PHD domain or both.
Concerning HON5-like polypeptides, portions useful in the methods of the invention, encode a HON5-like polypeptide as defined herein, and have substantially the same biological activity as the amino acid sequences given in Table A5 of the Examples section. Preferably, the portion is a portion of any one of the nucleic acids given in Table A5 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A5 of the Examples section. Preferably the portion is at least 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, or more consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A5 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A5 of the Examples section. Most preferably the portion is a portion of the nucleic acid of SEQ ID NO: 387. Preferably, the portion encodes a fragment of an amino acid sequence which comprises any one or more of the Motifs I, II or III as outline above.
Concerning GSA1 polypeptides, portions useful in the methods of the invention, encode a GSA1 polypeptide as defined herein, and have substantially the same biological activity as the amino acid sequences given in Table A6 of the Examples section. Preferably, the portion is a portion of any one of the nucleic acids given in Table A6 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A6 of the Examples section. Preferably the portion is at least 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, or more consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A6 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A6 of the Examples section. Most preferably the portion is a portion of the nucleic acid of SEQ ID NO: 417. Preferably, the portion encodes a fragment of an amino acid sequence which, when used in the construction of a phylogenetic tree, such as the one depicted in FIG. 17, clusters with the group of GSA1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 418 rather than with any other group.
Another nucleic acid variant useful in the methods of the invention is a nucleic acid capable of hybridising, under reduced stringency conditions, preferably under stringent conditions, with a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, as defined herein, or with a portion as defined herein.
According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a nucleic acid capable of hybridizing to any one of the nucleic acids given in Table A1 to A6 of the Examples section, or comprising introducing and expressing in a plant a nucleic acid capable of hybridising to a nucleic acid encoding an orthologue, paralogue or homologue of any of the nucleic acid sequences given in Table A1 to A6 of the Examples section.
Concerning BET1-like polypeptides, hybridising sequences useful in the methods of the invention encode a BET1-like polypeptide as defined herein, having substantially the same biological activity as the amino acid sequences given in Table A1 of the Examples section. Preferably, the hybridising sequence is capable of hybridising to the complement of any one of the nucleic acids given in Table A1 of the Examples section, or to a portion of any of these sequences, a portion being as defined above, or the hybridising sequence is capable of hybridising to the complement of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A1 of the Examples section. Most preferably, the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ ID NO: 1 or to a portion thereof.
Another nucleic acid variant useful in the methods of the invention is a splice variant encoding a BET1-like polypeptide as defined hereinabove, a splice variant being as defined herein.
Concerning Calreticulin polypeptides, hybridising sequences useful in the methods of the invention encode a Calreticulin polypeptide as defined herein, having substantially the same biological activity as the amino acid sequences given in Table A2 of the Examples section. Preferably, the hybridising sequence is capable of hybridising to the complement of any one of the nucleic acids given in Table A2 of the Examples section, or to a portion of any of these sequences, a portion being as defined above, or the hybridising sequence is capable of hybridising to the complement of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A2 of the Examples section. Most preferably, the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ ID NO: 104 or to a portion thereof.
Preferably, the hybridising sequence encodes a polypeptide with an amino acid sequence which, when full-length and used in the construction of a phylogenetic tree, such as the one depicted in Christensen et al. 2008-FIG. 1 and herein reproduced in FIG. 5, clusters with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b, and Os_CRT3 or At_CRT3 polypeptides, preferably with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b. Alternatively, the hybridising sequence encodes a polypeptide sequence which, when used in the construction of a phylogenetic tree, such as the one described in Example 2 clusters with any one of the polypeptides within the following phylogenetic classes: class 1-CRT1,2-CRT3,3-algae, 4-animal and 5-protist of Example 2, preferably with the class 1-CRT1 polypeptides.
Concerning DUSL1 polypeptides, hybridising sequences useful in the methods of the invention encode a DUS1L polypeptide as defined herein, and have substantially the same biological activity as the polypeptide sequences given in Table A3 of the Examples section. Preferably, the hybridising sequence is capable of hybridising to any one of the nucleic acid sequences given in Table A3 of the Examples section, or to a complement thereof, or to a portion of any of these sequences, a portion being as defined above, or wherein the hybridising sequence is capable of hybridising to a nucleic acid sequence encoding an orthologue or paralogue of any one of the polypeptide sequences given in Table A3 of the Examples section, or to a complement thereof. Preferably, the hybridising sequence is capable of hybridising to a nucleic acid sequence encoding a polypeptide sequence comprising in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to a tRNA-dihydrouridine synthase domain as represented by SEQ ID NO: 294. More preferably, the hybridising sequence is capable of hybridising to a nucleic acid sequence encoding a polypeptide sequence comprising in increasing order of preference at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to the DUS1L polypeptide as represented by SEQ ID NO: 259 or to any of the polypeptide sequences given in Table A3 herein. Most preferably, the hybridising sequence is capable of hybridising to a nucleic acid sequence as represented by SEQ ID NO: 258 or to a portion thereof.
Concerning ES43-like polypeptides, hybridising sequences useful in the methods of the invention encode an ES43-like polypeptide as defined herein, having substantially the same biological activity as the amino acid sequences given in Table A4 of the Examples section. Preferably, the hybridising sequence is capable of hybridising to the complement of any one of the nucleic acids given in Table A4 of the Examples section, or to a portion of any of these sequences, a portion being as defined above, or the hybridising sequence is capable of hybridising to the complement of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A4 of the Examples section. Most preferably, the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ ID NO: 298 or to a portion thereof.
Preferably, the hybridising sequence encodes a polypeptide with an amino acid sequence which comprises a BAH or a PHD domain or both domains.
Concerning HON5-like polypeptides, hybridising sequences useful in the methods of the invention encode a HON5-like polypeptide as defined herein, having substantially the same biological activity as the amino acid sequences given in Table A5 of the Examples section. Preferably, the hybridising sequence is capable of hybridising to the complement of any one of the nucleic acids given in Table A5 of the Examples section, or to a portion of any of these sequences, a portion being as defined above, or the hybridising sequence is capable of hybridising to the complement of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A5 of the Examples section. Most preferably, the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ ID NO: 387 or to a portion thereof.
Preferably, the hybridising sequence encodes a polypeptide with an amino acid sequence which comprises any one or more of the Motifs I, II or III as outline above.
Concerning GSA1 polypeptides, hybridising sequences useful in the methods of the invention encode a GSA1 polypeptide as defined herein, having substantially the same biological activity as the amino acid sequences given in Table A6 of the Examples section. Preferably, the hybridising sequence is capable of hybridising to the complement of any one of the nucleic acids given in Table A6 of the Examples section, or to a portion of any of these sequences, a portion being as defined above, or the hybridising sequence is capable of hybridising to the complement of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A6 of the Examples section. Most preferably, the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ ID NO: 417 or to a portion thereof.
Preferably, the hybridising sequence encodes a polypeptide with an amino acid sequence which, when full-length and used in the construction of a phylogenetic tree, such as the one depicted in FIG. 17, clusters with the group of GSA1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 418 rather than with any other group.
Another nucleic acid variant useful in the methods of the invention is a splice variant encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, as defined hereinabove, a splice variant being as defined herein.
According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a splice variant of any one of the nucleic acid sequences given in Table A1 to A6 of the Examples section, or a splice variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A1 to A6 of the Examples section.
Concerning BET1-like polypeptides, preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 1, or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 2 and/or any polypeptide having an amino acid sequence of a BET1-like polypeptide as defined above.
Concerning Calreticulin polypeptides, preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 104, or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 105. Preferably, the amino acid sequence encoded by the splice variant, when used in the construction of a phylogenetic tree, such as the one depicted in Christensen et al. 2008-FIG. 1 and herein reproduced in FIG. 5, clusters with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b, and Os_CRT3 or At_CRT3 polypeptides, preferably with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b. Alternatively, the spliced variant encodes a polypeptide which, when used in the construction of a phylogenetic tree, such as the one described in Example 2 clusters with any one of the polypeptides within the following phylogenetic classes: class 1-CRT1,2-CRT3,3-algae, 4-animal and 5-protist of Example 2, preferably with the class 1-CRT1 polypeptides.
Concerning DUSL1 polypeptides, preferred splice variants are splice variants of a nucleic acid sequence represented by SEQ ID NO: 258, or a splice variant of a nucleic acid sequence encoding an orthologue or paralogue of SEQ ID NO: 259. Preferably, the splice variant is a splice variant of a nucleic acid sequence encoding a polypeptide sequence comprising in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to a tRNA-dihydrouridine synthase domain as represented by SEQ ID NO: 294. More preferably, the splice variant is a splice variant of a nucleic acid sequence encoding a polypeptide sequence comprising in increasing order of preference at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to the DUS1L polypeptide as represented by SEQ ID NO: 259 or to any of the polypeptide sequences given in Table A3 herein. Most preferably, the splice variant is a splice variant of a nucleic acid sequence as represented by SEQ ID NO: 258, or of a nucleic acid sequence encoding a polypeptide sequence as represented by SEQ ID NO: 259.
Concerning ES43-like polypeptides, preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 298, or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 299. Preferably, the amino acid sequence encoded by the splice variant preferably comprises a BAH or a PHD domain or both domains.
Concerning HON5-like polypeptides, preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 387, or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 388. Preferably, the amino acid sequence encoded by the splice variant comprises any one or more of the Motifs I, II or III as outline above.
Concerning GSA1 polypeptides, preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 417, or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 418. Preferably, the amino acid sequence encoded by the splice variant, when used in the construction of a phylogenetic tree, such as the one depicted in FIG. 17, clusters with the group of GSA1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 418 rather than with any other group.
Another nucleic acid variant useful in performing the methods of the invention is an allelic variant of a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, as defined hereinabove, an allelic variant being as defined herein.
According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant an allelic variant of any one of the nucleic acids given in Table A of the Examples section, or comprising introducing and expressing in a plant an allelic variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of the Examples section.
Concerning BET1-like polypeptides, the polypeptides encoded by allelic variants useful in the methods of the present invention have substantially the same biological activity as the BET1-like polypeptide of SEQ ID NO: 2 and any of the amino acids depicted in Table A1 of the Examples section. Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles. Preferably, the allelic variant is an allelic variant of SEQ ID NO: 1 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 2.
Concerning Calreticulin polypeptides, the polypeptides encoded by allelic variants useful in the methods of the present invention have substantially the same biological activity as the Calreticulin polypeptide of SEQ ID NO: 105 and any of the amino acids depicted in Table A2 of the Examples section. Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles. Preferably, the allelic variant is an allelic variant of SEQ ID NO: 104 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 105. Preferably, the amino acid sequence encoded by the allelic variant, when used in the construction of a phylogenetic tree, such as the one depicted in Christensen et al. 2008-FIG. 1 and herein reproduced in FIG. 5, clusters with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b, and Os_CRT3 or At_CRT3 polypeptides, preferably with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b. Alternatively, the allelic variant encodes a polypeptide which, when used in the construction of a phylogenetic tree, such as the one described in Example 2 clusters with any one of the polypeptides within the following phylogenetic classes: class 1-CRT1,2-CRT3,3-algae, 4-animal and 5-protist of Example 2, preferably with the class 1-CRT1 polypeptides.
Concerning DUSL1 polypeptides, the allelic variants useful in the methods of the present invention have substantially the same biological activity as the DUS1L polypeptide of SEQ ID NO: 259 and any of the polypeptide sequences depicted in Table A3 of The Examples section. Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles. Preferably, the allelic variant is an allelic variant of a polypeptide sequence comprising in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to a tRNA-dihydrouridine synthase domain as represented by SEQ ID NO: 294. More preferably the allelic variant is an allelic variant encoding a polypeptide sequence comprising in increasing order of preference at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to the DUS1L polypeptide as represented by SEQ ID NO: 259 or to any of the polypeptide sequences given in Table A3 herein. Most preferably, the allelic variant is an allelic variant of SEQ ID NO: 258 or an allelic variant of a nucleic acid sequence encoding an orthologue or paralogue of SEQ ID NO: 259.
Concerning ES43-like polypeptides, the polypeptides encoded by allelic variants useful in the methods of the present invention have substantially the same biological activity as the ES43-like polypeptide of SEQ ID NO: 299 and any of the amino acids depicted in Table A4 of the Examples section. Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles. Preferably, the allelic variant is an allelic variant of SEQ ID NO: 298 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 299. Preferably, the amino acid sequence encoded by the allelic variant comprises a BAH or a PHD domain or both domains.
Concerning HON5-like polypeptides, the polypeptides encoded by allelic variants useful in the methods of the present invention have substantially the same biological activity as the HON5-like polypeptide of SEQ ID NO: 388 and any of the amino acids depicted in Table A5 of the Examples section. Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles. Preferably, the allelic variant is an allelic variant of SEQ ID NO: 387 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 388. Preferably, the amino acid sequence encoded by the allelic variant comprises any one or more of the Motifs I, II or III as outline above.
Concerning GSA1 polypeptides, the polypeptides encoded by allelic variants useful in the methods of the present invention have substantially the same biological activity as the GSA1 polypeptide of SEQ ID NO: 418 and any of the amino acids depicted in Table A6 of the Examples section. Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles. Preferably, the allelic variant is an allelic variant of SEQ ID NO: 417 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 418. Preferably, the amino acid sequence encoded by the allelic variant, when used in the construction of a phylogenetic tree, such as the one depicted in FIG. 17, clusters with the GSA1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 418 rather than with any other group.
Gene shuffling or directed evolution may also be used to generate variants of nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, as defined above; the term “gene shuffling” being as defined herein.
According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a variant of any one of the nucleic acid sequences given in Table A1 to A6 of the Examples section, or comprising introducing and expressing in a plant a variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A1 to A6 of the Examples section, which variant nucleic acid is obtained by gene shuffling.
Concerning BET1-like polypeptides, preferably, the amino acid sequence encoded by the variant nucleic acid is obtained by gene shuffling.
Concerning Calreticulin polypeptides, preferably, the amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling, when used in the construction of a phylogenetic tree, such as the one depicted in Christensen et al. 2008-FIG. 1 and herein reproduced in FIG. 5, clusters with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b, and Os_CRT3 or At_CRT3 polypeptides, preferably with the group of At_CRT1a or At_CRT1b, Os_CRT1a or Os_CRT1b. Alternatively, the variant nucleic acid encodes a polypeptide which, when used in the construction of a phylogenetic tree, such as the one described in Example 2 clusters with any one of the polypeptides within the following phylogenetic classes: class 1-CRT1,2-CRT3,3-algae, 4-animal and 5-protist of Example 2, preferably with the class 1-CRT1 polypeptides.
Concerning DUSL1 polypeptides, preferably, the variant nucleic acid sequence obtained by gene shuffling encodes a polypeptide sequence comprising in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to a tRNA-dihydrouridine synthase domain as represented by SEQ ID NO: 294. More preferably, the variant nucleic acid sequence obtained by gene shuffling encodes a polypeptide sequence comprising in increasing order of preference at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to the DUS1L polypeptide as represented by SEQ ID NO: 259 or to any of the polypeptide sequences given in Table A3 herein. Most preferably, the nucleic acid sequence obtained by gene shuffling encodes a polypeptide sequence as represented by SEQ ID NO: 259.
Concerning ES43-like polypeptides, preferably, the amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling, which preferably encode a protein which comprises a BAH or a PHD domain or both domains.
Concerning HONE-like polypeptides, preferably, the amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling comprises any one or more of the Motifs I, II or III as outline above.
Concerning GSA1 polypeptides, preferably, the amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling, when used in the construction of a phylogenetic tree such as the one depicted in FIG. 17, clusters with the group of GSA1 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 418 rather than with any other group.
Furthermore, nucleic acid variants may also be obtained by site-directed mutagenesis. Several methods are available to achieve site-directed mutagenesis, the most common being PCR based methods (Current Protocols in Molecular Biology. Wiley Eds.).
Nucleic acids encoding BET1-like polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the BET1-like polypeptide-encoding nucleic acid is from a plant, further preferably from a monocotyledonous plant, more preferably from the family Poaceae, most preferably the nucleic acid is from Zea mays. 
Nucleic acids encoding Calreticulin polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the Calreticulin polypeptides-encoding nucleic acid is from a plant, further preferably from a dicotyledonous plant, more preferably from the family Solanaceae or from the family Salicaceae, in particular from Populus species, most preferably the nucleic acid is from Solanum lycopersicum or from Populus trichocarpa. 
Nucleic acid sequences encoding DUS1L polypeptides may be derived from any natural or artificial source. The nucleic acid sequence may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. The nucleic acid sequence encoding a DUS1L polypeptide is from an algae. The nucleic acid sequence encoding a DUS1L polypeptide is from a plant, further preferably from a monocotyledonous plant, more preferably from the family Poaceae, most preferably the nucleic acid sequence is from Saccharum officinarum. 
Nucleic acids encoding ES43-like polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the ES43-like polypeptide-encoding nucleic acid is from a plant, further preferably from a monocotyledonous plant, more preferably from the family Poaceae, most preferably the nucleic acid is from Oryza sativa. 
Nucleic acids encoding HON5-like polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the HON5-like polypeptide-encoding nucleic acid is from a plant, further preferably from a dicotyledonous plant, more preferably from the family Salicaceae, most preferably the nucleic acid is from Populus trichocarpa. 
Nucleic acids encoding GSA1 polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the GSA1 polypeptide-encoding nucleic acid is from a plant, further preferably from a monocotyledonous or dicotyledonous plant, more preferably from Populus. 
Performance of the methods of the invention gives plants having enhanced yield-related traits. In particular performance of the methods of the invention gives plants having increased yield, especially increased seed yield relative to control plants. The terms “yield” and “seed yield” are described in more detail in the “definitions” section herein.
Reference herein to enhanced yield-related traits is taken to mean an increase in biomass (weight) of one or more parts of a plant, which may include aboveground (harvestable) parts and/or (harvestable) parts below ground. In particular, such harvestable parts are seeds, and performance of the methods of the invention results in plants having increased seed yield relative to the seed yield of control plants.
Taking corn as an example, a yield increase may be manifested as one or more of the following: increase in the number of plants established per square meter, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), among others. Taking rice as an example, a yield increase may manifest itself as an increase in one or more of the following: number of plants per square meter, number of panicles per plant, number of spikelets per panicle, number of flowers (florets) per panicle (which is expressed as a ratio of the number of filled seeds over the number of primary panicles), increase in the seed filling rate (which is the number of filled seeds divided by the total number of seeds and multiplied by 100), increase in thousand kernel weight, among others.
The present invention provides a method for increasing yield, especially seed yield of plants, relative to control plants, which method comprises modulating expression in a plant of a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, as defined herein.
Since the transgenic plants according to the present invention have increased yield and/or yield-related traits, it is likely that these plants exhibit an increased growth rate (during at least part of their life cycle), relative to the growth rate of control plants at a corresponding stage in their life cycle.
The increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. Plants having an increased growth rate may have a shorter life cycle. The life cycle of a plant may be taken to mean the time needed to grow from a dry mature seed up to the stage where the plant has produced dry mature seeds, similar to the starting material. This life cycle may be influenced by factors such as early vigour, growth rate, greenness index, flowering time and speed of seed maturation. The increase in growth rate may take place at one or more stages in the life cycle of a plant or during substantially the whole plant life cycle. Increased growth rate during the early stages in the life cycle of a plant may reflect increased (early) vigour. The increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible (a similar effect may be obtained with earlier flowering time; delayed flowering is usually not a desirede trait in crops). If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soybean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible. Altering the harvest cycle of a plant may lead to an increase in annual biomass production per acre (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested). An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened. The growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.
According to a preferred feature of the present invention, performance of the methods of the invention gives plants having an increased growth rate relative to control plants. Therefore, according to the present invention, there is provided a method for increasing the growth rate of plants, which method comprises modulating expression in a plant of a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, as defined herein.
An increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stresses compared to control plants. Plants typically respond to exposure to stress by growing more slowly. In conditions of severe stress, the plant may even stop growing altogether. Mild stress on the other hand is defined herein as being any stress to which a plant is exposed which does not result in the plant ceasing to grow altogether without the capacity to resume growth. Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35%, 30% or 25%, more preferably less than 20% or 15% in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture. Mild stresses are the everyday biotic and/or abiotic (environmental) stresses to which a plant is exposed. Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures. The abiotic stress may be an osmotic stress caused by a water stress (particularly due to drought), salt stress, oxidative stress or an ionic stress. Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi, nematodes and insects. Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi, nematodes, and insects. The term “non-stress” conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given location. The term non-stress conditions as used herein, encompasses the occasional or everyday mild stresses to which a plant is exposed, as defined herein, but does not encompass severe stresses.
In particular, the methods of the present invention may be performed under non-stress conditions or under conditions of mild drought to give plants having increased yield relative to control plants. As reported in Wang et al. (Planta (2003) 218: 1-14), abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity. Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes a particularly high degree of “cross talk” between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signalling pathways and cellular responses, such as the production of stress proteins, up-regulation of anti-oxidants, accumulation of compatible solutes and growth arrest. The term “non-stress” conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given location. Plants with optimal growth conditions, (grown under non-stress conditions) typically yield in increasing order of preference at least 97%, 95%, 92%, 90%, 87%, 85%, 83%, 80%, 77% or 75% of the average production of such plant in a given environment. Average production may be calculated on harvest and/or season basis. Persons skilled in the art are aware of average yield productions of a crop.
The term “abiotic stress” as defined herein is taken to mean any one or more of: water stress (due to drought or excess water), anaerobic stress, salt stress, temperature stress (due to hot, cold or freezing temperatures), chemical toxicity stress and oxidative stress. According to one aspect of the invention, the abiotic stress is an osmotic stress, selected from water stress, salt stress, oxidative stress and ionic stress. Preferably, the water stress is drought stress. The term salt stress is not restricted to common salt (NaCl), but may be any stress caused by one or more of: NaCl, KCl, LiCl, MgCl2, CaCl2, amongst others.
Performance of the methods of the invention gives plants grown under non-stress conditions or under mild drought conditions increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield and/yield-related traits in plants grown under non-stress conditions or under mild drought conditions, which method comprises modulating expression in a plant of a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide.
Concerning DUSL1 polypeptides, performance of the methods of the invention gives plants having increased yield-related traits, under abiotic stress conditions relative to control plants grown in comparable stress conditions. Therefore, according to the present invention, there is provided a method for increasing yield-related traits, in plants grown under abiotic stress conditions, which method comprises increasing expression in a plant of a nucleic acid sequence encoding a DUS1L polypeptide. According to one aspect of the invention, the abiotic stress is an osmotic stress, selected from one or more of the following: water stress, salt stress, oxidative stress and ionic stress.
Another example of abiotic environmental stress is the reduced availability of one or more nutrients that need to be assimilated by the plants for growth and development. Because of the strong influence of nutrition utilization efficiency on plant yield and product quality, a huge amount of fertilizer is poured onto fields to optimize plant growth and quality. Productivity of plants ordinarily is limited by three primary nutrients, phosphorous, potassium and nitrogen, which is usually the rate-limiting element in plant growth of these three. Therefore the major nutritional element required for plant growth is nitrogen (N). It is a constituent of numerous important compounds found in living cells, including amino acids, proteins (enzymes), nucleic acids, and chlorophyll. 1.5% to 2% of plant dry matter is nitrogen and approximately 16% of total plant protein. Thus, nitrogen availability is a major limiting factor for crop plant growth and production (Frink et al. (1999) Proc Natl Acad Sci USA 96(4): 1175-1180), and has as well a major impact on protein accumulation and amino acid composition. Therefore, of great interest are crop plants with increased yield-related traits, when grown under nitrogen-limiting conditions.
Performance of the methods of the invention gives plants grown under conditions of nutrient deficiency, particularly under conditions of nitrogen deficiency, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of nutrient deficiency, which method comprises modulating expression in a plant of a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide. Nutrient deficiency may result from a lack of nutrients such as nitrogen, phosphates and other phosphorous-containing compounds, potassium, calcium, magnesium, manganese, iron and boron, amongst others.
Performance of the methods of the invention gives plants grown under conditions of salt stress, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of salt stress, which method comprises modulating expression in a plant of a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide. The term salt stress is not restricted to common salt (NaCl), but may be any one or more of: NaCl, KCl, LiCl, MgCl2, CaCl2, amongst others.
The present invention encompasses plants or parts thereof (including seeds) obtainable by the methods according to the present invention. The plants or parts thereof comprise a nucleic acid transgene encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, as defined above, operably linked to a promoter functioning in plants.
The invention also provides genetic constructs and vectors to facilitate introduction and/or expression in plants of nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides. The gene constructs may be inserted into vectors, which may be commercially available, suitable for transforming into plants and suitable for expression of the gene of interest in the transformed cells. The invention also provides use of a gene construct as defined herein in the methods of the invention.
More specifically, the present invention provides a construct comprising:

    
    
        (a) a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, as defined above;
        (b) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally
        (c) a transcription termination sequence.
    
    


Preferably, the nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, is as defined above. The term “control sequence” and “termination sequence” are as defined herein.
Concerning DUS1L polypeptides, one of the control sequences of a construct is preferably a consitituve promoter isolated from a plant genome. An example of a constitutive promoter is a GOS2 promoter, preferably a GOS2 promoter from rice, most preferably a GOS2 sequence as represented by SEQ ID NO: 295.
Plants are transformed with a vector comprising any of the nucleic acids described above. The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells containing the sequence of interest. The sequence of interest is operably linked to one or more control sequences (at least to a promoter).
Advantageously, any type of promoter, whether natural or synthetic, may be used to drive expression of the nucleic acid sequence, but preferably the promoter is of plant origin. A constitutive promoter is particularly useful in the methods. Preferably the constitutive promoter is also a ubiquitous promoter of medium strength. See the “Definitions” section herein for definitions of the various promoter types.
Concerning DUS1L polypeptides, advantageously, any type of promoter, whether natural or synthetic, may be used to increase expression of the nucleic acid sequence. A constitutive promoter is particularly useful in the methods, preferably a constitutive promoter isolated from a plant genome. The plant constitutive promoter drives expression of a coding sequence at a level that is in all instances below that obtained under the control of a 35S CaMV viral promoter. An example of such a promoter is a GOS2 promoter as represented by SEQ ID NO: 295.
Concerning DUS1L polypeptides, organ-specific promoters, for example for preferred expression in leaves, stems, tubers, meristems, seeds, are useful in performing the methods of the invention. Developmentally-regulated and inducible promoters are also useful in performing the methods of the invention. See the “Definitions” section herein for definitions of the various promoter types.
Concerning BET1-like polypeptides, it should be clear that the applicability of the present invention is not restricted to the BET1-like polypeptide-encoding nucleic acid represented by SEQ ID NO: 1, nor is the applicability of the invention restricted to expression of a BET1-like polypeptide-encoding nucleic acid when driven by a constitutive promoter.
The constitutive promoter is preferably a medium strength promoter, more preferably selected from a plant derived promoter, such as a GOS2 promoter, more preferably is the promoter GOS2 promoter from rice. Further preferably the constitutive promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 103, most preferably the constitutive promoter is as represented by SEQ ID NO: 103. See the “Definitions” section herein for further examples of constitutive promoters.
Optionally, one or more terminator sequences may be used in the construct introduced into a plant. Preferably, the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 103, and the nucleic acid encoding the BET1-like polypeptide.
Concerning Calreticulin polypeptides, it should be clear that the applicability of the present invention is not restricted to the Calreticulin polypeptide-encoding nucleic acid represented by SEQ ID NO: 104, nor is the applicability of the invention restricted to expression of a Calreticulin polypeptide-encoding nucleic acid when driven by a constitutive promoter.
The constitutive promoter is preferably a medium strength promoter, more preferably selected from a plant derived promoter, such as a GOS2 promoter, more preferably is the promoter GOS2 promoter from rice. Further preferably the constitutive promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 257, most preferably the constitutive promoter is as represented by SEQ ID NO: 257. See the “Definitions” section herein for further examples of constitutive promoters.
Optionally, one or more terminator sequences may be used in the construct introduced into a plant. Preferably, the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 257, and the nucleic acid encoding the Calreticulin polypeptide.
Concerning DUS1L polypeptides, it should be clear that the applicability of the present invention is not restricted to a nucleic acid sequence encoding the DUS1L polypeptide, as represented by SEQ ID NO: 258, nor is the applicability of the invention restricted to expression of a DUS1L polypeptide-encoding nucleic acid sequence when driven by a constitituve promoter.
Optionally, one or more terminator sequences may be used in the construct introduced into a plant.
Concerning ES43-like polypeptides, it should be clear that the applicability of the present invention is not restricted to the ES43-like polypeptide-encoding nucleic acid represented by SEQ ID NO: 298, nor is the applicability of the invention restricted to expression of an ES43-like polypeptide-encoding nucleic acid when driven by a constitutive promoter.
The constitutive promoter is preferably a medium strength promoter, more preferably selected from a plant derived promoter, such as a GOS2 promoter, more preferably is the promoter GOS2 promoter from rice. Further preferably the constitutive promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 386, most preferably the constitutive promoter is as represented by SEQ ID NO: 386. See the “Definitions” section herein for further examples of constitutive promoters.
Optionally, one or more terminator sequences may be used in the construct introduced into a plant. Preferably, the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 386, and the nucleic acid encoding the ES43-like polypeptide.
Concerning HON5-like polypeptides, it should be clear that the applicability of the present invention is not restricted to the HON5-like polypeptide-encoding nucleic acid represented by SEQ ID NO: 387, nor is the applicability of the invention restricted to expression of a HON5-like polypeptide-encoding nucleic acid when driven by a constitutive promoter, or when driven by a root-specific promoter.
The constitutive promoter is preferably a medium strength promoter, more preferably selected from a plant derived promoter, such as a GOS2 promoter, more preferably is the promoter GOS2 promoter from rice. Further preferably the constitutive promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 416, most preferably the constitutive promoter is as represented by SEQ ID NO: 416. See the “Definitions” section herein for further examples of constitutive promoters.
Optionally, one or more terminator sequences may be used in the construct introduced into a plant. Preferably, the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 416, and the nucleic acid encoding the HON5-like polypeptide.
Concerning GSA1 polypeptides, it should be clear that the applicability of the present invention is not restricted to the GSA1 polypeptide-encoding nucleic acid represented by SEQ ID NO: 417, nor is the applicability of the invention restricted to expression of a GSA1 polypeptide-encoding nucleic acid when driven by a constitutive promoter.
The constitutive promoter is preferably a medium strength promoter, more preferably selected from a plant derived promoter, such as a GOS2 promoter, more preferably is the promoter GOS2 promoter from rice. Further preferably the constitutive promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 492, most preferably the constitutive promoter is as represented by SEQ ID NO: 492. See the “Definitions” section herein for further examples of constitutive promoters.
Optionally, one or more terminator sequences may be used in the construct introduced into a plant. Preferably, the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 492, and the nucleic acid encoding the GSA1 polypeptide.
Additional regulatory elements may include transcriptional as well as translational enhancers. Those skilled in the art will be aware of terminator and enhancer sequences that may be suitable for use in performing the invention. An intron sequence may also be added to the 5′ untranslated region (UTR) or in the coding sequence to increase the amount of the mature message that accumulates in the cytosol, as described in the definitions section. Other control sequences (besides promoter, enhancer, silencer, intron sequences, 3′UTR and/or 5′UTR regions) may be protein and/or RNA stabilizing elements. Such sequences would be known or may readily be obtained by a person skilled in the art.
The genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type. One example is when a genetic construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to, the f1-ori and colE1.
For the detection of the successful transfer of the nucleic acid sequences as used in the methods of the invention and/or selection of transgenic plants comprising these nucleic acids, it is advantageous to use marker genes (or reporter genes). Therefore, the genetic construct may optionally comprise a selectable marker gene. Selectable markers are described in more detail in the “definitions” section herein. The marker genes may be removed or excised from the transgenic cell once they are no longer needed. Techniques for marker removal are known in the art, useful techniques are described above in the definitions section.
It is known that upon stable or transient integration of nucleic acid sequences into plant cells, only a minority of the cells takes up the foreign DNA and, if desired, integrates it into its genome, depending on the expression vector used and the transfection technique used. To identify and select these integrants, a gene coding for a selectable marker (such as the ones described above) is usually introduced into the host cells together with the gene of interest. These markers can for example be used in mutants in which these genes are not functional by, for example, deletion by conventional methods. Furthermore, nucleic acid sequence molecules encoding a selectable marker can be introduced into a host cell on the same vector that comprises the sequence encoding the polypeptides of the invention or used in the methods of the invention, or else in a separate vector. Cells which have been stably transfected with the introduced nucleic acid sequence can be identified for example by selection (for example, cells which have integrated the selectable marker survive whereas the other cells die). The marker genes may be removed or excised from the transgenic cell once they are no longer needed. Techniques for marker gene removal are known in the art, useful techniques are described above in the definitions section.
The invention also provides a method for the production of transgenic plants having enhanced yield-related traits relative to control plants, comprising introduction and expression in a plant of any nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, as defined hereinabove.
More specifically, the present invention provides a method for the production of transgenic plants having enhanced yield-related traits, particularly increased (seed) yield, which method comprises:

    
    
        (i) introducing and expressing in a plant or plant cell a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide; and
        (ii) cultivating the plant cell under conditions promoting plant growth and development.
    
    


The nucleic acid of (i) may be any of the nucleic acids capable of encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, as defined herein.
The nucleic acid may be introduced directly into a plant cell or into the plant itself (including introduction into a tissue, organ or any other part of a plant). According to a preferred feature of the present invention, the nucleic acid is preferably introduced into a plant by transformation. The term “transformation” is described in more detail in the “definitions” section herein.
The genetically modified plant cells can be regenerated via all methods with which the skilled worker is familiar. Suitable methods can be found in the above-mentioned publications by S. D. Kung and R. Wu, Potrykus or Hofgen and Willmitzer.
Generally after transformation, plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant. To select transformed plants, the plant material obtained in the transformation is, as a rule, subjected to selective conditions so that transformed plants can be distinguished from untransformed plants. For example, the seeds obtained in the above-described manner can be planted and, after an initial growing period, subjected to a suitable selection by spraying. A further possibility consists in growing the seeds, if appropriate after sterilization, on agar plates using a suitable selection agent so that only the transformed seeds can grow into plants. Alternatively, the transformed plants are screened for the presence of a selectable marker such as the ones described above.
Following DNA transfer and regeneration, putatively transformed plants may also be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, both techniques being well known to persons having ordinary skill in the art.
The generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1) transformed plant may be selfed and homozygous second-generation (or T2) transformants selected, and the T2 plants may then further be propagated through classical breeding techniques. The generated transformed organisms may take a variety of forms. For example, they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g., all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion).
The present invention clearly extends to any plant cell or plant produced by any of the methods described herein, and to all plant parts and propagules thereof. The present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced by the parent in the methods according to the invention.
The invention also includes host cells containing an isolated nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, as defined hereinabove. Preferred host cells according to the invention are plant cells. Host plants for the nucleic acids or the vector used in the method according to the invention, the expression cassette or construct or vector are, in principle, advantageously all plants, which are capable of synthesizing the polypeptides used in the inventive method.
The methods of the invention are advantageously applicable to any plant. Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs. According to a preferred embodiment of the present invention, the plant is a crop plant. Examples of crop plants include soybean, sunflower, canola, alfalfa, rapeseed, linseed, cotton, tomato, potato and tobacco. Further preferably, the plant is a monocotyledonous plant. Examples of monocotyledonous plants include sugarcane. More preferably the plant is a cereal. Examples of cereals include rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo and oats.
The invention also extends to harvestable parts of a plant such as, but not limited to seeds, leaves, fruits, flowers, stems, roots, rhizomes, tubers and bulbs, which harvestable parts comprise a recombinant nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide. The invention furthermore relates to products derived, preferably directly derived, from a harvestable part of such a plant, such as dry pellets or powders, oil, fat and fatty acids, starch or proteins.
According to a preferred feature of the invention, the modulated expression is increased expression. Methods for increasing expression of nucleic acids or genes, or gene products, are well documented in the art and examples are provided in the definitions section.
As mentioned above, a preferred method for modulating expression of a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, is by introducing and expressing in a plant a nucleic acid encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide; however the effects of performing the method, i.e. enhancing yield-related traits may also be achieved using other well known techniques, including but not limited to T-DNA activation tagging, TILLING, homologous recombination. A description of these techniques is provided in the definitions section.
The present invention also encompasses use of nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, as described herein and use of these BET1-like polypeptides, or Calreticulin polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, in enhancing any of the aforementioned yield-related traits in plants.
The present invention also encompasses use of nucleic acid sequences encoding DUS1L polypeptides as described herein and use of these DUS1L polypeptides in increasing any of the aforementioned yield-related traits in plants, under normal growth conditions, under abiotic stress growth (preferably osmotic stress growth conditions) conditions, and under growth conditions of reduced nutrient availability, preferably under conditions of reduced nitrogen availability.
Nucleic acids encoding BET1-like polypeptide, or Calreticulin polypeptide, or DUS1L polypeptide, or ES43-like polypeptide, or HON5-like polypeptide, or GSA1 polypeptide, described herein, or the BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, themselves, may find use in breeding programmes in which a DNA marker is identified which may be genetically linked to a BET1-like polypeptide-encoding gene. The nucleic acids/genes, or the BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, themselves may be used to define a molecular marker. This DNA or protein marker may then be used in breeding programmes to select plants having enhanced yield-related traits as defined hereinabove in the methods of the invention.
Allelic variants of a nucleic acid/gene encoding a BET1-like polypeptide, or a Calreticulin polypeptide, or a DUS1L polypeptide, or an ES43-like polypeptide, or a HON5-like polypeptide, or a GSA1 polypeptide, may also find use in marker-assisted breeding programmes. Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a collection of allelic variants of so called “natural” origin caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants in which the superior allelic variant was identified with another plant. This could be used, for example, to make a combination of interesting phenotypic features.
Nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. Such use of nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, requires only a nucleic acid sequence of at least 15 nucleotides in length. The nucleic acids encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch E F and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with the POI-encoding nucleic acids. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1: 174-181) in order to construct a genetic map. In addition, the nucleic acids may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the nucleic acid encoding BET1-like polypeptides, or Calreticulin polypeptides, or DUS1L polypeptides, or ES43-like polypeptides, or HON5-like polypeptides, or GSA1 polypeptides, in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331).
The production and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4: 37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.
The nucleic acid probes may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).
In another embodiment, the nucleic acid probes may be used in direct fluorescence in situ hybridisation (FISH) mapping (Trask (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favour use of large clones (several kb to several hundred kb; see Laan et al. (1995) Genome Res. 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes.
A variety of nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.
The methods according to the present invention result in plants having enhanced yield-related traits, as described hereinbefore. These traits may also be combined with other economically advantageous traits, such as further yield-enhancing traits, tolerance to abiotic and biotic stresses, tolerance to herbicides, insectides, traits modifying various architectural features and/or biochemical and/or physiological features.
Description of Figures
The present invention will now be described with reference to the following figures in which:
FIG. 1 represents (domain structure, sequence of SEQ ID No: 2 with conserved CC domain (bold) and Motif 1 (underlined) are highlighted.
FIG. 2 represents a multiple alignment of BET1-like polypeptides. Sequences shown are: A.arenosa_x—thaliana_TA52—378006—1 (SEQ ID NO: 4); B.napus_BN06MS42331943.f_k04—1—40488—1 (SEQ ID NO: 12); V.corymbosum_CV091429—1 (SEQ ID NO: 80); V.corymbosum_TA638—69266—1 (SEQ ID NO:82); B.vulgaris_DV501764—1 (SEQ ID NO: 18); B.pendula_CD278481—1 (SEQ ID NO: 16); C.reticulata_x_temple_DN795225—1 (SEQ ID NO: 20); P.dulcis_TA313—3755—1 (SEQ ID NO: 50); V.riparia_TA839—96939—1 (SEQ ID NO: 84 ); L.serriola_TA5233—75943—1 (SEQ ID NO: 30); S.indicum_TA1114—4182—1(SEQ ID NO: 78); G.biloba_DR064764—1(SEQ ID NO: 26); P.abies_TA1522—3329—1 (SEQ ID NO: 36); P.sitchensis_TA10405—3332—1 (SEQ ID NO: 66); P.abies_TA1523—3329—1 (SEQ ID NO: 38); P.engelmannii_x_glauca_CO203682—1(SEQ ID NO: 52); P.pinaster_BX678743—1 (SEQ ID NO: 56); P.taeda _TA16676—3352—1(SEQ ID NO: 70); P.pinaster_TA4882—71647—1 (SEQ ID NO: 64); P.taeda_TA3629—3352—1 (SEQ ID NO: 74); P.abies_TA2417—3329—1 (SEQ ID NO: 40); P.menziesii_TA1952—3357—1 (SEQ ID NO: 54); P.pinaster_BX682074—1 (SEQ ID NO: 58); P.taeda _TA22888—3352—1 (SEQ ID NO: 72); P.pinaster_CR392675—1 (SEQ ID NO: 60); P.pinaster_TA4836—71647—1 (SEQ ID NO: 62); P.taeda_CO162523—1 (SEQ ID NO: 68); P.taeda_TA4949—3352—1 (SEQ ID NO: 76); T----M---—25296 (SEQ ID NO: 2); Z.mays_DR787277—1 (SEQ ID NO: 92); Z.mays_ZM07MC13625—57676372—13595—1 (SEQ ID NO: 96); Z.mays_c62091609gm030403—7698—1 (SEQ ID NO: 88); mays_DQ245377—1 (SEQ ID NO: 90); Z.mays_EC364520—1 (SEQ ID NO: 94); Z.mays_c57759235gm030403—14494—1 (SEQ ID NO: 86); A.majus_AJ789814—1 (SEQ ID NO: 8); P.coccineus_TA3810—3886—1 (SEQ ID NO: 48); C.tetragonoloba_EG981304—1 (SEQ ID NO: 22); M.truncatula_AC169182—23.5—1 (SEQ ID NO: 32; ); G.max_TA67390—3847—1 (SEQ ID NO: 28); C.tetragonoloba_EG987480—1 (SEQ ID NO: 24); M.truncatula_AC16918239.5—1 (SEQ ID NO: 34); A.hypogaea_EE124570—1 (SEQ ID NO: 6); P.coccineus_CA908259—1 (SEQ ID NO: 42); P.coccineus_CA908272—1 (SEQ ID NO: 44); P.coccineus_TA26993886—1 (SEQ ID NO: 46); A.thaliana_AT1G56233.1—1 (SEQ ID NO: 10); and B.napus_CD815839—1 (SEQ ID NO: 14).
FIG. 3 represents the binary vector used for increased expression in rice of a BET1like-encoding nucleic acid under the control of a rice GOS2 promoter (pGOS2).
FIG. 4 represents a multiple alignment of Calreticulin polypeptides. Structural characteristic elements of Calreticulin polypeptides are indicated over the consensus sequence. Sequences shown are: A.formosa_TA8804 (SEQ ID NO: 195); C.maculosa_TA223 (SEQ ID NO: 201); P.trifoliata_TA7309 (SEQ ID NO: 221); E.esula_TA10075 (SEQ ID NO: 203); M.domestica_TA28184 (SEQ ID NO: 209); M.truncatula_TA23636 (SEQ ID NO: 211); V.vinifera_GSVIVT00025039001 (SEQ ID NO: 227); A.thaliana_AT1G08450_CRT3 (SEQ ID NO: 197); B.napus_BPS—33882 (SEQ ID NO: 199); G.raimondii_TA11257 (SEQ ID NO:205) P.trichocarpa_VII.148 (SEQ ID NO: 219); H.vulgare_TA32081 (SEQ ID NO: 207); T.aestivum_TA53764 (SEQ ID NO: 225); O.sativa_Os01g67054.1 (SEQ ID NO: 213); Z.mays_TA15627 (SEQ ID NO: 231); O.sativa_Os05g43170.1 (SEQ ID NO: 215); S.bicolor_TA24664 (SEQ ID NO: 223); Z.mays_BPS—22383 (SEQ ID NO: 229); P.patens—164102 (SEQ ID NO: 217); C.reinhardtii_TA11983 (SEQ ID NO: 233); P.pinaster_TA4383 (SEQ ID NO: 163); P.taeda_TA5639 (SEQ ID NO: 167); W.mirabilis_TA538 (SEQ ID NO: 191); P.sitchensis_TA20930 (SEQ ID NO: 165); B.distachyon_TA448 (SEQ ID NO: 115); O.sativa_Os03g0832200 (SEQ ID NO: 157); H.vulgare_TA38555 (SEQ ID NO: 143); T.aestivum_TA74192 (SEQ ID NO: 187); S.bicolor_TA25211 (SEQ ID NO: 179); H.vulgare_BPS—7785(SEQ ID NO: 141); T.aestivum_TA50840 (SEQ ID NO: 185); S.bicolor_TA20922 (SEQ ID NO: 177); Z.mays_TA170881 (SEQ ID NO: 193); O.sativa_Os07g0246200 (SEQ ID NO:159); A.trichopoda_TA1102 (SEQ ID NO: 113); A.thaliana_AT1G09210_CRT2 (SEQ ID NO:109); B.napus_BPS—28478 (SEQ ID NO: 117); A.thaliana_AT1G56340_CRT1 (SEQ ID NO: 111); B.napus_TA20659 (SEQ ID NO: 119); A.formosa_TA9419 (SEQ ID NO: 107); C.annuum_TA4292 (SEQ ID NO: 123); S.habrochaites_TA1435 (SEQ ID NO: 181); S.lycopersicum_TA36564 (SEQ ID NO: 105); S.tuberosum_TA24720 (SEQ ID NO: 183); G.hirsutum_TA20990 (SEQ ID NO: 129); G.raimondii_TA8857 (SEQ ID NO: 133); G.raimondii_TA8860 (SEQ ID NO: 135); I.nil_TA5002 (SEQ ID NO: 145); C.endivia_TA1106 (SEQ ID NO: 125); C.solstitialis_TA9 (SEQ ID NO: 127); H.annuus_TA7525 (SEQ ID No: 137); H.argophyllus_TA1300 (SEQ ID NO: 139); L.serriola_TA711 (SEQ ID NO: 149); O.basilicum_TA646 (SEQ ID NO: 155); B.vulgaris_TA7257 (SEQ ID NO: 121); M.domestica_TA24948 (SEQ ID NO: 151); P.persica_TA3474 (SEQ ID NO: 161); G.max_BPS—38275 (SEQ ID NO: 131); P.vulgaris_TA3122 (SEQ ID NO: 173); L.japonicus_TA548 (SEQ ID NO: 147); M.truncatula_AC149474 (SEQ ID NO: 153); P.trichocarpa—133.107 (SEQ ID NO: 169); P.trichocarpa—729432 (SEQ ID NO: 171); R.communis_U74630 (SEQ ID NO: 175); and V.vinifera_TA38405 (SEQ ID NO: 189).
FIG. 5 shows phylogenetic tree as described by Christensen et al. 2008 FIG. 1A.
FIG. 6 represents the binary vector used for increased expression in Oryza sativa of a Calreticulin-encoding nucleic acid under the control of a rice GOS2 promoter (pGOS2). The term “calreticulin” in this figure is taken to mean any one of the nucleic acid sequences of Table A2, S.lycopersicum_TA36564 or P.trichocarpa—133.107.
FIG. 7 represents the chemical reaction catalyzed by a DUS enzyme (according to Bishop et al. (2002) J Biol Chem 277(28):25000-25006).
FIG. 8 is a two-dimensional representation of a generic E. coli tRNA with the D-loop nucleotides shown, Conserved D-loop bases are shown (R, purine). Positions that may contain D are shown as X and pointed out with arrows enzyme (according to Bishop et al. (2002) J Biol Chem 277(28): 25000-25006).
FIG. 9 shows an AlignX (from Vector NTI 10.3, Invitrogen Corporation) multiple sequence alignment of the DUS1L polypeptides from Table A3. One important domain is a tRNA-dihydrouridine synthase domain with an InterPro entry IPR001269 (integrating the PFAM PF01207 entry (marked by X's). One important motif is the tRNA-dihydrouridine synthase conserved site with an InterPro entry IPR018517 (integrating the PROSITE PSO1136 (marked by X's, in bold in SEQ ID NO: Sacof_DUS1L). Conserved residues are heavily boxed, in particular a Cys residue which is in other organisms a key general-acid/base catalyst. Sequences shown are: A.thaliana_AT5G67220.1 (SEQ ID NO: 261); B.napus_BN06MC20455 (SEQ ID NO: 265); B.napus_TC79818 (SEQ ID NO: 263); P.patens—149014 (SEQ ID NO: 277); S.moellendorffii—443602 (SEQ ID NO: 283); P.taeda_TA13257—3352 (SEQ ID NO: 279); O.sativa_LOC_Os06g49870.1 (SEQ ID NO: 275); Sacof_DuS1L (SEQ ID NO: 259); S.bicolor_Sb10g029830.1 (SEQ ID NO: 287); Z.mays_ZM07MC04636 (SEQ ID NO: 293); G.max_Glyma05g20510.1 (SEQ ID NO: 273); G.max_Glyma17g18490.1 (SEQ ID NO: 271); R.communis_TA2745—3988 (SEQ ID NO: 281); S.lycopersicum_TC206234 (SEQ ID NO: 285); V.vinifera_GSVIVT0001954 (SEQ ID NO: 289); C.vulgaris—36290 (SEQ ID NO: 267); V.carteri—80128 (SEQ ID NO: 291); and E.huxleyi—437158 (SEQ ID NO: 269).
FIG. 10 shows the binary vector for increased expression in Oryza sativa plants of a nucleic acid sequence encoding a DUS1L polypeptide under the control of a promoter functioning in plants.
FIG. 11 represents the amino acid sequence of the ES43-like polypeptide represented SEQ ID NO: 299 with the BAH domain in bold and the PHD domain underlined.
FIG. 12 represents a multiple alignment of ES43-like polypeptides. Sequences shown are: O.sativa_Os07g0186400#1 (SEQ ID NO: 325); T_M_---—29382_---4312—116 (SEQ ID NO: 299); O.sativa_AK061201#1 (SEQ ID NO: 327); Z.mays_TA12947—4577999#1 (SEQ ID NO: 369); Z.mays_ZM07MC24083_BFb0146O24@(SEQ ID NO: 293); H.vulgare_TA40508—4513#1 (SEQ ID NO: 317); H.vulgare_TA35269—4513#1 (SEQ ID NO: 311); O.sativa_Os03g0799600#1 (SEQ ID NO: 329); A.thaliana_AT4G39100.1#1 (SEQ ID NO: 305); T_M_---—2176_---0490—46—8 (SEQ ID NO: 357); B.napus_BN06MC06825—42494234@6 (SEQ ID NO: 309); P.trichocarpa_scaff_IV.1226#1 (SEQ ID NO: 341); S.lycopersicum_TA42220—4081#1 (SEQ ID NO: 353); A.thaliana_AT4G22140.1#1 (SEQ ID NO: 301); A.thaliana_AT4G22140.2#1 (SEQ ID NO: 303); A.thaliana_AT4G04260.1#1 (SEQ ID NO: 307); P.trichocarpa_scaff_XI.104#1 (SEQ ID NO: 345); .trichocarpa_scaff—166.34#1 (SEQ ID NO: 349); H.vulgare_TA42493—4513#1 (SEQ ID NO: 313); T.aestivum_c54968390@13747#1 (SEQ ID NO: 365); T—M_---—14367_---4367—137 (SEQ ID NO: 359); T.aestivum_TA54637—4565#1 (SEQ ID NO: 361); H.vulgare_BF623189#1 (SEQ ID NO: 315); O.sativa_Os09g0386500#1 (SEQ ID NO: 321); Z.mays_TA19459—4577999#1 (SEQ ID NO: 367); Z.mays_ZMO7MC24174_BFb0045F09@(SEQ ID NO: 373); O.sativa_Os08g0421900#1 (SEQ ID NO: 323); P.trichocarpa_scaff_II.2065#1 (SEQ ID NO: 351); S.lycopersicum_TA40478—4081#1 (SEQ ID NO: 355); P.trichocarpa_scaff_XIV.1045#1 (SEQ ID NO: 343); P.trichocarpa—scaff 1247.1#1 (SEQ ID NO: 347); P.patens—149469#1 (SEQ ID NO: 333); P.patens—108696#1 (SEQ ID NO: 335); P.patens—153027#1 (SEQ ID NO: 331); P.patens—59496#1 (SEQ ID NO: 337); P.patens—213413#1 (SEQ ID NO: 339); T.aestivum_CK201479#1 (SEQ ID NO: 363); and L.usitatissimum_LUO4MC11049—62 (SEQ ID NO: 319).
FIG. 13 represents the binary vector used for increased expression in Oryza sativa of a ES43-like-encoding nucleic acid under the control of a rice GOS2 promoter (pGOS2).
FIG. 14 represents a multiple alignment of HON5-like polypeptides. HI/H5 domain is indicated between brackets and AThook domains are indicated by rectangles. Sequences shown are; Arath_HMGA2 (SEQ ID NO: 390); Arath_Hon4 (SEQ ID NO: 392); Brana_Hon5 like (SEQ ID NO: 394); Glyma_HON5 like (SEQ ID NO: 396); Lotja_HMGA1701 (SEQ ID NO: 402); Poptr_HMGA905 (SEQ ID NO: 388); Poptr_HMGA906 (SEQ ID NO: 406); Vitvi_hon5 like (SEQ ID NO: 409); Gosar_HMGA10101 (SEQ ID NO: 398); Gosar_HMGA14201 (SEQ ID NO: 400); Orysa_HMGA2201 (SEQ ID NO: 404); and Sacof_HMGA2503 (SEQ ID NO: 408).
FIG. 15 represents the binary vector used for increased expression in Oryza sativa of a HON5-like-encoding nucleic acid represented by SEQ ID NO: 387 under the control of a rice GOS2 promoter (pGOS2)
FIG. 16 represents a multiple alignment of GSA1-like sequences. Sequences shown are: ===5613 (SEQ ID NO: 418); P—tremuloides—575404 (SEQ ID NO: 468); R—communis_TA2570—3988 (SEQ ID NO: 472); A—thaliana _AT3G48730—1 (SEQ ID NO: 420); A—thaliana_AT5G63570—1 (SEQ ID NO: 422); B—napus_TC63445 (SEQ ID NO: 426); B—napus_TC63450 (SEQ ID NO: 428); N—benthamiana_TC14122 (SEQ ID NO: 450); N—tabacum_TC18263 (SEQ ID NO: 452); N—tabacum_TC18710 (SEQ ID NO: 454); S—lycopersicum_TC191683 (SEQ ID NO: 474); Aquilegia_sp_TC22821 (SEQ ID NO: 424); C—reinhardtii—138524 (SEQ ID NO: 430); V—carteri—74470 (SEQ ID NO: 482); Chlorella—37143 (SEQ ID NO: 434); O—lucimarinus—28523 (SEQ ID NO: 456); _RCC809—53004 (SEQ ID NO: 458); O—taurii—24711 (SEQ ID NO: 462); C—vulgaris—43392 (SEQ ID NO: 432); E—huxleyi—437052 (SEQ ID NO: 436); P—tricornutum—36347 (SEQ ID NO: 470); Tpseudonana—575 (SEQ ID NO: 480); P—patens—116325 (SEQ ID NO: 464); P—patens—181992 (SEQ ID NO: 466); S—moellendorffii—183248 (SEQ ID NO: 476); F—arundinacea_TC6452 (SEQ ID NO: 438); H—vulgare_TC162130 (SEQ ID NO: 446); T—aestivum_TA06MC00384—60074805—384 (SEQ ID NO: 478); O—sativa_LOC_Os08g41990—1 (SEQ ID NO: 460); Z—mays_ZM07MC17771_BFb0062K01—17727 (SEQ ID NO: 486); F—vesca_TA11529—57918 (SEQ ID NO: 440); G—max_Glyma04g00420—1 (SEQ ID NO: 442); G—max_Glyma06g00510—1 (SEQ ID NO: 444); M—truncatula_CU024868—27—4 (SEQ ID NO: 448); and V—shuttleworthii_TA2337—246827 (SEQ ID NO: 484).
FIG. 17 shows a phylogenetic tree of GSA1-like sequences.
FIG. 18 represents the binary vector used for increased expression in Oryza sativa of a GSA1-encoding nucleic acid under the control of a rice GOS2 promoter (pGOS2).
Items
1. BET1-Like Polypeptides


    1. A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding BET1-like polypeptide, wherein said BET1-like polypeptide comprises a CC domain:
    
        (i) as represented by SEQ. ID NO: 97; and/or
        (ii) preferably having at least 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%, 96%, 97%, 98%, or 99% sequence identity to the CC domain represented by SEQ ID NO: 98.
    
    
    2. Method according to item 1, wherein the CC domain comprises one or more of the following motifs:











(i)
Motif 1: G(W/Y)CD(E/K);
(SEQ ID NO: 99)


 


(ii)
Motif 2: EGF,
(SEQ ID NO: 100)






    3. Method according to item 1 or 2, wherein said modulated expression is effected by introducing and expressing in a plant a nucleic acid encoding a BET1-like polypeptide.
    4. Method according to any one of items 1 to 3, wherein said nucleic acid encoding a BET1-like polypeptide encodes any one of the proteins listed in Table A1 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
    5. Method according to any one of items 1 to 4, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the proteins given in Table A1.
    6. Method according to any preceding item, wherein said enhanced yield-related traits comprise increased yield, such as increased biomass and/or increased seed yield relative to control plants.
    7. Method according to any one of items 1 to 6, wherein said enhanced yield-related traits are obtained under non-stress conditions.
    8. Method according to any one of items 1 to 6, wherein said enhanced yield-related traits are obtained under conditions of drought stress and/or nitrogen deficiency.
    9. Method according to any one of items 3 to 8, wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
    10. Method according to any one of items 1 to 9, wherein said nucleic acid encoding a BET1-like polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Poaceae, more preferably from the genus Zea, most preferably from Zea mays. 
    11. Plant or part thereof, including seeds, obtainable by a method according to any one of items 1 to 10, wherein said plant or part thereof comprises a recombinant nucleic acid encoding a BET1-like polypeptide.
    12. Construct comprising:
    
        (a) nucleic acid encoding a BET1-like polypeptide as defined in items 1 or 2;
        (b) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally
        (c) a transcription termination sequence.
    
    
    13. Construct according to item 12, wherein one of said control sequences is a constitutive promoter, preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
    14. Use of a construct according to item 12 or 13 in a method for making plants having increased yield, particularly increased biomass and/or increased seed yield relative to control plants.
    15. Plant, plant part or plant cell transformed with a construct according to item 12 or 13.
    16. Method for the production of a transgenic plant having increased yield, particularly increased biomass and/or increased seed yield relative to control plants, comprising:
    
        (i) introducing and expressing in a plant a nucleic acid encoding a BET1-like polypeptide as defined in item 1 or 2; and
        (ii) cultivating the plant cell under conditions promoting plant growth and development.
    
    
    17. Transgenic plant having increased yield, particularly increased biomass and/or increased seed yield, relative to control plants, resulting from modulated expression of a nucleic acid encoding a BET1-like polypeptide as defined in item 1 or 2, or a transgenic plant cell derived from said transgenic plant.
    18. Transgenic plant according to item 11, 15 or 17, or a transgenic plant cell derived thereof, wherein said plant is a crop plant such as sugarbeet, or a monocot or a cereal, such as rice, maize, wheat, sugarcane, barley, millet, rye, triticale, sorghum emmer, spelt, secale, einkorn, teff, milo and oats.
    19. Harvestable parts of a plant according to item 18, wherein said harvestable parts are preferably shoot biomass and/or seeds.
    20. Products derived from a plant according to item 18 and/or from harvestable parts of a plant according to item 19.
    21. Use of a nucleic acid encoding a BET1-like polypeptide in increasing yield, particularly in increasing seed yield and/or shoot biomass in plants, relative to control plants.
    22. An isolated nucleic acid molecule selected from:
    
        (i) a nucleic acid represented by any one of SEQ ID NO: 11 and 95;
        (ii) the complement of a nucleic acid represented by any one of SEQ ID NO: 11 and 95;
        (iii) a nucleic acid encoding the polypeptide as represented by any one of SEQ ID NO: 12 and 96 preferably as a result of the degeneracy of the genetic code, said isolated nucleic acid can be derived from a polypeptide sequence as represented by any one of SEQ ID NO: 12 and 96 and further preferably confers enhanced yield-related traits relative to control plants;
        (iv) a nucleic acid having, in increasing order of preference 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%, 96%, 97%, 98%, or 99% sequence identity with any of the nucleic acid sequences of Table A1 and further preferably conferring enhanced yield-related traits relative to control plants;
        (v) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iv) under stringent hybridization conditions and preferably confers enhanced yield-related traits relative to control plants;
        (vi) a nucleic acid encoding a BET1-like polypeptide having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 12 and 96 and any of the other amino acid sequences in Table A1 and preferably conferring enhanced yield-related traits relative to control plants.
    
    
    23. An isolated polypeptide selected from:
    
        (i) an amino acid sequence represented by any one of SEQ ID NO: 12 and 96;
        (ii) an amino acid sequence having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 12 and 96 and any of the other amino acid sequences in Table A1 and preferably conferring enhanced yield-related traits relative to control plants.
        (iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.

2. Calreticulin Polypeptides

    
    
    1. A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a Calreticulin polypeptide.
    2. Method according to item 1, wherein said Calreticulin polypeptide comprises one or more of the following motifs:
    
        (i) Motif 3: PXXIXDPXXKKPEXWDD (SEQ ID NO: 246),
        (ii) Motif 4: GXWXXXXIXNPXYK (SEQ ID NO: 247),
        (iii) Motif 5: E[VL]WQVK (SEQ ID NO: 248),
        (iv) Motif 6: TLV[FL]QFSVKHEQKLDCGGGY[MV]KLLSGDVDQKKFGG[DE]TPYSI MFGPDICGY (SEQ ID NO: 249) which represents typical CRT plant polypeptides of the CRT1/2 group;
        (v) Motif 7: TPYS[LF]MFGPD[IL]CGTQTKKLH[VL]ILSYQGQNYPIKKDL[QE]CE TDKLTH[FV]YTFI (SEQ ID NO: 250) which represents typical CRT plant polypeptides of the CRT3 group;
        (vi) Motif 8: N[HY][LP]IKK[DE][VL]PCETD[QK]LTH[VF]YTFI[LI]RPDA[TS]YSILI DN[VR]E[KR][QE][TS]GS[LM]Y[TS]DWD[IL]L (SEQ ID NO: 251) which represents typical CRT polypeptides of the viridiplantae kingdom;
        (vii) Motif 9: QKKFGGDTPYSIMFGPDICGY[SQ]TKK[VL]H[AV]I (SEQ ID NO: 252), which represents typical CRT polypeptides of the eukaryotic origin,
        (viii) a motif having at least 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%, 96%, 97%, 98%, or 99% overall sequence identity to any one of the motifs (i) to (vii);
        Wherein “X” represents any amino acid and wherein amino acids indicated between brackets “[ ]” represent alternative amino acids at that location.
    
    
    3. Method according to item 1 or 2, wherein said modulated expression is effected by introducing and expressing in a plant a nucleic acid encoding a Calreticulin polypeptide.
    4. Method according to any one of items 1 to 3, wherein said nucleic acid encoding a Calreticulin polypeptide encodes any one of the proteins listed in Table A2 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
    5. Method according to any one of items 1 to 4, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the proteins given in Table A2.
    6. Method according to any preceding item, wherein said enhanced yield-related traits comprise increased yield, increased seed yield relative to control plants.
    7. Method according to any one of items 1 to 6, wherein said enhanced yield-related traits are obtained under non-stress conditions.
    8. Method according to any one of items 1 to 6, wherein said enhanced yield-related traits are obtained under conditions of drought stress, salt stress or nitrogen deficiency.
    9. Method according to any one of items 3 to 8, wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
    10. Method according to any one of items 1 to 9, wherein said nucleic acid encoding a Calreticulin polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Solanaceae, more preferably from the genus Solanum, most preferably from Solanum lycopersicum. 
    11. Plant or part thereof, including seeds, obtainable by a method according to any one of items 1 to 10, wherein said plant or part thereof comprises a recombinant nucleic acid encoding a Calreticulin polypeptide.
    12. Construct comprising:
    
        (i) nucleic acid encoding a Calreticulin polypeptide as defined in items 1 or 2;
        (ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally
        (iii) a transcription termination sequence.
    
    
    13. Construct according to item 12, wherein one of said control sequences is a constitutive promoter, preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
    14. Use of a construct according to item 12 or 13 in a method for making plants having increased yield, particularly increased seed yield relative to control plants.
    15. Plant, plant part or plant cell transformed with a construct according to item 12 or 13.
    16. Method for the production of a transgenic plant having increased yield, particularly increased seed yield relative to control plants, comprising:
    
        (i) introducing and expressing in a plant a nucleic acid encoding a Calreticulin polypeptide as defined in item 1 or 2; and
        (ii) cultivating the plant cell under conditions promoting plant growth and development.
    
    
    17. Transgenic plant having increased yield, particularly increased seed yield, relative to control plants, resulting from modulated expression of a nucleic acid encoding a Calreticulin polypeptide as defined in item 1 or 2, or a transgenic plant cell derived from said transgenic plant.
    18. Transgenic plant according to item 11, 15 or 17, or a transgenic plant cell derived thereof, wherein said plant is a crop plant such as sugarbeet, or a monocot or a cereal, such as rice, maize, wheat, sugarcane, barley, millet, rye, triticale, sorghum emmer, spelt, secale, einkorn, teff, milo and oats.
    19. Harvestable parts of a plant according to item 18, wherein said harvestable parts are preferably shoot biomass and/or seeds.
    20. Products derived from a plant according to item 18 and/or from harvestable parts of a plant according to item 19.
    21. Use of a nucleic acid encoding a Calreticulin polypeptide in increasing yield, particularly in increasing seed yield and/or shoot biomass in plants, relative to control plants.
    22. An isolated Calreticulin nucleic acid molecule selected from:
    
        (i) a nucleic acid represented by any one of SEQ ID NO: 116, 130, 140, 198 and 228;
        (ii) the complement of a nucleic acid represented by any one of SEQ ID NO: 116, 130, 140, 198 and 228;
        (iii) a nucleic acid encoding the polypeptide as represented by any one of SEQ ID NO: 117, 131, 141, 199 and 229 preferably as a result of the degeneracy of the genetic code, said isolated nucleic acid can be derived from a polypeptide sequence as represented by any one of SEQ ID NO: 117, 131, 141, 199 and 229 and further preferably confers enhanced yield-related traits relative to control plants;
        (iv) a nucleic acid having, in increasing order of preference 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%, 96%, 97%, 98%, or 99% sequence identity with any of the nucleic acid sequences of Table A2 and further preferably conferring enhanced yield-related traits relative to control plants;
        (v) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to
        (iv) under stringent hybridization conditions and preferably confers enhanced yield-related traits relative to control plants;
        (vi) a nucleic acid encoding a Calreticulin polypeptide having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 117, 131, 141, 199 and 229 and any of the other amino acid sequences in Table A2 and preferably conferring enhanced yield-related traits relative to control plants.
    
    
    23. An isolated Calreticulin polypeptide selected from:
    
        (i) an amino acid sequence represented by any one of SEQ ID NO: 117, 131, 141, 199 and 229;
        (ii) an amino acid sequence having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 117, 131, 141, 199 and 229 and any of the other amino acid sequences in Table A2 and preferably conferring enhanced yield-related traits relative to control plants.
        (iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.

3. tRNA Dihydrouridine Synthase 1-Like Polypeptides (DUS1L Polypeptides)

    
    
    1. A method for increasing yield-related traits in plants relative to control plants, comprising increasing expression in a plant of a nucleic acid sequence encoding a tRNA dihydrouridine synthase 1-like (DUS1L) polypeptide, which DUS1L polypeptide comprises (i) a tRNA-dihydrouridine synthase domain with an InterPro entry IPR001269; (ii) an aldolase-type TIM barrel domain with an InterPro entry IPR013785; and (iii) a tRNA-dihydrouridine synthase conserved site with an InterPro entry IPR018517, and optionally selecting for plants having increased yield-related traits.
    2. Method according to item 1, wherein said DUS1L polypeptide comprises (i) in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to a tRNA-dihydrouridine synthase domain as represented by SEQ ID NO: 294.
    3. Method according to item 2, wherein said DUS1L polypeptide further comprises in increasing order of preference at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to a polypeptide as represented by SEQ ID NO: 259.
    4. Method according to any preceding item, wherein said DUS1L polypeptide has in increasing order of preference at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity to any of the polypeptide sequences given in Table A3 herein.
    5. Method according to any preceding item, wherein said DUS1L polypeptide can functionally complement an E. coli strain deficient in tRNA dihydrouridine synthase activity, thereby increasing tRNA dihydrouridine content.
    6. Method according to any preceding item, wherein said nucleic acid sequence encoding a DUS1L polypeptide is represented by any one of the nucleic acid sequence SEQ ID NOs given in Table A3 or a portion thereof, or a sequence capable of hybridising with any one of the nucleic acid sequences SEQ ID NOs given in Table A3, or to a complement thereof.
    7. Method according to any preceding item, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the polypeptide sequence SEQ ID NOs given in Table A3.
    8. Method according to any preceding item, wherein said increased expression is effected by any one or more of: T-DNA activation tagging, TILLING, or homologous recombination.
    9. Method according to any preceding item, wherein said increased expression is effected by introducing and expressing in a plant a nucleic acid sequence encoding a DUS1L polypeptide.
    10. Method according to any preceding item, wherein said increased yield-related trait is one or more of: increased aboveground biomass, increased seed yield per plant, increased number of filled seeds, and increased total number of seeds.
    11. Method according to any preceding item, wherein said yield-related trait is increased in plants grown under grown under conditions of reduced nutrient availability, particularly under conditions of reduced nitrogen availability, relative to control plants.
    12. Method according to any preceding item, wherein said nucleic acid sequence is operably linked to a constitutive promoter.
    13. Method according to item 11, wherein said constitutive promoter is a GOS2 promoter, preferably a GOS2 promoter from rice, most preferably a GOS2 sequence as represented by SEQ ID NO: 295.
    14. Method according to any preceding item, wherein said nucleic acid sequence encoding a DUS1L polypeptide is from a plant, further preferably from a monocotyledonous plant, more preferably from the family Poaceae, most preferably the nucleic acid sequence is from Saccharum officinarum. 
    15. Plants, parts thereof (including seeds), or plant cells obtainable by a method according to any preceding item, wherein said plant, part or cell thereof comprises an isolated nucleic acid transgene encoding a DUS1L polypeptide.
    16. An isolated nucleic acid molecule selected from:
    
        (i) a nucleic acid sequence as represented by SEQ ID NO: 264 or by SEQ ID NO: 292;
        (ii) the complement of a nucleic acid sequence as represented by SEQ ID NO: 264 or by SEQ ID NO: 292;
        (iii) a nucleic acid sequence encoding a DUS1L polypeptide having, in increasing order of preference, at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more amino acid sequence identity to the polypeptide sequence represented by SEQ ID NO: 265 or by SEQ ID NO: 293.
    
    
    17. An isolated polypeptide selected from:
    
        (i) a polypeptide sequence as represented by SEQ ID NO: 265 or by SEQ ID NO: 293;
        (ii) a polypeptide sequence having, in increasing order of preference, at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more amino acid sequence identity to a polypeptide sequence as represented by any one of SEQ ID NO: 265 or by SEQ ID NO: 293;
        (iii) derivatives of any of the polypeptide sequences given in (i) or (ii) above.
    
    
    18. Construct comprising:
    
        (a) a nucleic acid sequence encoding a DUS1L polypeptide as defined in any one of items 1 to 7, or 16;
        (b) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally
        (c) a transcription termination sequence.
    
    
    19. Construct according to item 18 wherein said control sequence is a constitituve promoter.
    20. Construct according to item 19 wherein said constitituve promoter is a GOS2 promoter, preferably a GOS2 promoter from rice, most preferably a GOS2 sequence as represented by SEQ ID NO: 295.
    21. Use of a construct according to any one of items 18 to 20 in a method for making plants having increased yield-related traits relative to control plants, which increased yield-related traits are one or more of: increased aboveground biomass, increased seed yield per plant, increased number of filled seeds, and increased total number of seeds.
    22. Plant, plant part or plant cell transformed with a construct according to any one of items 18 to 20.
    23. Method for the production of transgenic plants having increased yield-related traits relative to control plants, comprising:
    
        (i) introducing and expressing in a plant, plant part, or plant cell, a nucleic acid sequence encoding a DUS1L polypeptide as defined in any one of items 1 to 7, or 16; and
        (ii) cultivating the plant cell, plant part, or plant under conditions promoting plant growth and development.
    
    
    24. Transgenic plant having increased yield-related traits relative to control plants, resulting from increased expression of an isolated nucleic acid sequence encoding a DUS1L polypeptide as defined in any one of items 1 to 7, or 16, or a transgenic plant cell or transgenic plant part derived from said transgenic plant.
    25. Transgenic plant according to item 15, 22, or 24, wherein said plant is a crop plant such as sugarbeet, or a monocot or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, teff, sugarcane, and oats, or a transgenic plant cell derived from said transgenic plant.
    26. Harvestable parts comprising an isolated nucleic acid sequence encoding a DUS1L polypeptide, of a plant according to item 25, wherein said harvestable parts are preferably seeds.
    27. Products derived from a plant according to item 25 and/or from harvestable parts of a plant according to item 26.
    28. Use of a nucleic acid sequence encoding a DUS1L polypeptide as defined in any one of items 1 to 7, or 16, in increasing yield-related traits, comprising one or more of: increased aboveground biomass, increased seed yield per plant, increased number of filled seeds, and increased total number of seeds.

4. ES43-Like Polypeptides

    1. A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding an ES43-like polypeptide, said polypeptide comprising a BAH domain and a PHD domain.
    2. Method according to item 1, wherein said ES43-like polypeptide comprises a domain having an amino acid sequence in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% identical to the amino acid sequence of SEQ ID NO: 374 (BAH domain of SEQ ID NO: 299) or to the amino acid sequence of SEQ ID NO: 375 (PHD domain of SEQ ID NO: 299).
    3. Method according to item 1 or 2, wherein said modulated expression is effected by introducing and expressing in a plant a nucleic acid encoding an ES43-like polypeptide.
    4. Method according to any one of items 1 to 3, wherein said nucleic acid encoding an ES43-like polypeptide encodes any one of the proteins listed in Table A4 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
    5. Method according to any one of items 1 to 4, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the proteins given in Table A4.
    6. Method according to any preceding item, wherein said enhanced yield-related traits comprise increased yield, preferably increased biomass and/or increased seed yield relative to control plants.
    7. Method according to any one of items 1 to 6, wherein said enhanced yield-related traits are obtained under non-stress conditions.
    8. Method according to any one of items 1 to 6, wherein said enhanced yield-related traits are obtained under conditions of drought stress and/or nitrogen deficiency.
    9. Method according to any one of items 3 to 8, wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
    10. Method according to any one of items 1 to 9, wherein said nucleic acid encoding an ES43-like polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Brassicaceae, more preferably from the genus Arabidopsis, most preferably from Arabidopsis thaliana. 
    11. Plant or part thereof, including seeds, obtainable by a method according to any one of items 1 to 10, wherein said plant or part thereof comprises a recombinant nucleic acid encoding an ES43-like polypeptide.
    12. Construct comprising:
    
        (a) nucleic acid encoding an ES43-like polypeptide as defined in items 1 or 2;
        (b) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally
        (c) a transcription termination sequence.
    
    
    13. Construct according to item 12, wherein one of said control sequences is a constitutive promoter, preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
    14. Use of a construct according to item 12 or 13 in a method for making plants having increased yield, particularly increased biomass and/or increased seed yield relative to control plants.
    15. Plant, plant part or plant cell transformed with a construct according to item 12 or 13.
    16. Method for the production of a transgenic plant having increased yield, particularly increased biomass and/or increased seed yield relative to control plants, comprising:
    
        (a) introducing and expressing in a plant a nucleic acid encoding an ES43-like polypeptide as defined in item 1 or 2; and
        (b) cultivating the plant cell under conditions promoting plant growth and development.
    
    
    17. Transgenic plant having increased yield, particularly increased biomass and/or increased seed yield, relative to control plants, resulting from modulated expression of a nucleic acid encoding an ES43-like polypeptide as defined in item 1 or 2, or a transgenic plant cell derived from said transgenic plant.
    18. Transgenic plant according to item 11, 15 or 17, or a transgenic plant cell derived thereof, wherein said plant is a crop plant such as sugarbeet, or a monocot or a cereal, such as rice, maize, wheat, sugarcane, barley, millet, rye, triticale, sorghum emmer, spelt, secale, einkorn, teff, milo and oats.
    19. Harvestable parts of a plant according to item 18, wherein said harvestable parts are preferably shoot biomass and/or seeds.
    20. Products derived from a plant according to item 18 and/or from harvestable parts of a plant according to item 19.
    21. Use of a nucleic acid encoding a an ES43-like polypeptide in increasing yield, particularly in increasing seed yield and/or shoot biomass in plants, relative to control plants.
    22. An isolated nucleic acid molecule selected from:
    
        (i) a nucleic acid represented by any one of SEQ ID NO: 308, 370, and 372;
        (ii) the complement of a nucleic acid represented by any one of SEQ ID NO: 308, 370, and 372;
        (iii) a nucleic acid encoding the polypeptide as represented by any one of SEQ ID NO: 309, 371 and 373 preferably as a result of the degeneracy of the genetic code, said isolated nucleic acid can be derived from a polypeptide sequence as represented by any one of SEQ ID NO: 309, 371 and 373 and further preferably confers enhanced yield-related traits relative to control plants;
        (iv) a nucleic acid having, in increasing order of preference 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%, 96%, 97%, 98%, or 99% sequence identity with any of the nucleic acid sequences of Table A4 and further preferably conferring enhanced yield-related traits relative to control plants;
        (v) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iv) under stringent hybridization conditions and preferably confers enhanced yield-related traits relative to control plants;
        (vi) a nucleic acid encoding a ES43-like polypeptide having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 309, 371 and 373 and any of the other amino acid sequences in Table A4 and preferably conferring enhanced yield-related traits relative to control plants.
    
    
    23. An isolated polypeptide selected from
    
        (i) an amino acid sequence represented by any one of SEQ ID NO: 309, 371 and 373;
        (ii) an amino acid sequence having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 309, 371 and 373 and any of the other amino acid sequences in Table A4 and preferably conferring enhanced yield-related traits relative to control plants.
        (iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.

5. HON5-Like Polypeptides

    
    
    1. A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a HON5-like polypeptide, wherein said HONE-like polypeptide comprises a histone H1/H5 domain (Pfam: PF00538; Interpro: IPR005818) and at least two, preferably two, three, four, five, six or seven AT-hook domains (Pfam: PF02178; InterPro: IPR000637).
    2. Method according to item 1, wherein said HON5-like polypeptide comprises one or more of the following motifs:









(i)


Motif I (SEQ ID NO: 411):


Y[ASK]EMI[YC]TAI[AGT]AL[KN][ED][PK]DGSS[KR]RAI


 


[AS][KR]YIERA[YF][TP][GD]LP[PS]AH[SD][AD]LLTHHLK


 


[RT]L[KR]


 


(ii)


Motif II (SEQ ID NO: 412):


GLLV[ML]VK[KH]SYKL[AP][RS]S


 


(iii)


Motif III (SEQ ID NO: 413):


SA[PS][PQS]GQKRGRGRPPKPK






    
    
        wherein amino acids between brackets represent alternative amino acids at that position.
    
    
    3. Method according to item 1 or 2, wherein said modulated expression is effected by introducing and expressing in a plant a nucleic acid encoding a HON5-like polypeptide.
    4. Method according to any one of items 1 to 3, wherein said nucleic acid encoding a HON5-like polypeptide encodes any one of the proteins listed in Table A5 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
    5. Method according to any one of items 1 to 4, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the proteins given in Table A5.
    6. Method according to any preceding item, wherein said enhanced yield-related traits comprise increased yield, preferably increased harvest index and/or increased seed yield relative to control plants.
    7. Method according to any one of items 1 to 6, wherein said enhanced yield-related traits are obtained under non-stress conditions.
    8. Method according to any one of items 1 to 6, wherein said enhanced yield-related traits are obtained under conditions of drought stress, salt stress or nitrogen deficiency.
    9. Method according to any one of items 3 to 8, wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
    10. Method according to any one of items 1 to 9, wherein said nucleic acid encoding a HON5-like polypeptide is of plant origin, preferably from a dicotyledonous plant, more preferably from the genus Populus, most preferably from Populus trichocarpa. 
    11. Plant or part thereof, including seeds, obtainable by a method according to any one of items 1 to 10, wherein said plant or part thereof comprises a recombinant nucleic acid encoding a HON5-like polypeptide.
    12. Construct comprising:
    
        (i) nucleic acid encoding a HON5-like polypeptide as defined in items 1 or 2;
        (ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally
        (iii) a transcription termination sequence.
    
    
    13. Construct according to item 12, wherein one of said control sequences is a constitutive promoter, preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
    14. Use of a construct according to item 12 or 13 in a method for making plants having increased yield, particularly increased harvest index and/or increased seed yield relative to control plants.
    15. Plant, plant part or plant cell transformed with a construct according to item 12 or 13.
    16. Method for the production of a transgenic plant having increased yield, particularly increased harvest index and/or increased seed yield relative to control plants, comprising:
    
        (i) introducing and expressing in a plant a nucleic acid encoding a HON5-like polypeptide as defined in item 1 or 2; and
        (ii) cultivating the plant cell under conditions promoting plant growth and development.
    
    
    17. Transgenic plant having increased yield, particularly increased harvest index and/or increased seed yield, relative to control plants, resulting from modulated expression of a nucleic acid encoding a HON5-like polypeptide as defined in item 1 or 2, or a transgenic plant cell derived from said transgenic plant.
    18. Transgenic plant according to item 11, 15 or 17, or a transgenic plant cell derived thereof, wherein said plant is a crop plant such as sugarbeet, or a monocot or a cereal, such as rice, maize, wheat, sugarcane, barley, millet, rye, triticale, sorghum emmer, spelt, secale, einkorn, teff, milo and oats.
    19. Harvestable parts of a plant according to item 18, wherein said harvestable parts are preferably shoot biomass and/or seeds.
    20. Products derived from a plant according to item 18 and/or from harvestable parts of a plant according to item 19.
    21. Use of a nucleic acid encoding a HON5-like polypeptide in increasing yield, particularly in increasing seed yield and/or harvest index in plants, relative to control plants.
    22. A isolated nucleic acid molecule selected from:
    
        (i) a nucleic acid represented by any one of SEQ ID NO: 393 and 395;
        (ii) the complement of a nucleic acid represented by any one of SEQ ID NO: 393 and 395;
        (iii) a nucleic acid encoding the polypeptide as represented by any one of SEQ ID NO: 394 and 396 preferably as a result of the degeneracy of the genetic code, said isolated nucleic acid can be derived from a polypeptide sequence as represented by any one of SEQ ID NO: 394 and 396 and further preferably confers enhanced yield-related traits relative to control plants;
        (iv) a nucleic acid having, in increasing order of preference 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%, 96%, 97%, 98%, or 99% sequence identity with any of the nucleic acid sequences of Table A5 and further preferably conferring enhanced yield-related traits relative to control plants;
        (v) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iv) under stringent hybridization conditions and preferably confers enhanced yield-related traits relative to control plants;
        (vi) a nucleic acid encoding a HON5-like polypeptide having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 394 and 396 and any of the other amino acid sequences in Table A5 and preferably conferring enhanced yield-related traits relative to control plants.
    
    
    23. An isolated polypeptide selected from:
    
        (i) an amino acid sequence represented by any one of SEQ ID NO: 394 and 396;
        (ii) an amino acid sequence having, in increasing order of preference, at least 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%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 394 and 396 and any of the other amino acid sequences in Table A5 and preferably conferring enhanced yield-related traits relative to control plants.
        (iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.

6. glutamate-1-semialdehyde aminotransferase polypeptides (GSA1 polypeptides)

    
    


1. A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a GSA1 polypeptide, wherein said GSA1 polypeptide comprises one or more of Domains 1 to 3:







(SEQ ID NO: 487)


Domain 1:


VPS[IV]EMVRFVNSGTEAC[ML][GS][VA]LRL[AM]RA[FY]TGREK


 


[IV][IL]KFEGCYHGHAD[PS]FLVK


 


(SEQ ID NO: 488)


Domain 2:


SPVRAFKSVGGQP[IV]V[FI]D[SR]VKG[SA][HRY][MA]WD[IV]D


 


GN[EK]Y[IV]DYVGSWGPAIIGHADD


 


(SEQ ID NO: 489)


Domain 3:


AQEYFGITPD[LV]TT[LM]GK[IV]IGGGLPVGAYGG[RK][RK][ED]


 


IMEMVAPAGPMYQAGTLS






or a domain having in increasing order of preference at least 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%, 96%, 97%, 98%, or 99% overall sequence identity to any one or more of Domains 1 to 3.

    2. Method according to item 1, wherein said modulated expression is effected by introducing and expressing in a plant a nucleic acid encoding a GSA1 polypeptide.
    3. Method according to item 1 or 2, wherein said nucleic acid encoding a GSA1 polypeptide encodes any one of the proteins listed in Table A6 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
    4. Method according to any one of items 1 to 3, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the proteins given in Table A6.
    5. Method according to any preceding item, wherein said enhanced yield-related traits comprise increased yield, preferably increased biomass and/or increased seed yield relative to control plants.
    6. Method according to any one of items 1 to 6, wherein said enhanced yield-related traits are obtained under conditions of drought stress.
    7. Method according to any one of items 2 to 6, wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
    8. Method according to any one of items 1 to 7, wherein said nucleic acid encoding a GSA1 polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Salicaceae, more preferably from the genus Populus, most preferably from Populus trichocarpa. 
    9. Plant or part thereof, including seeds, obtainable by a method according to any one of items 1 to 8, wherein said plant or part thereof comprises a recombinant nucleic acid encoding a GSA1 polypeptide.
    10. Construct comprising:
    
        (i) nucleic acid encoding a GSA1 polypeptide as defined in item 1;
        (ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally
        (iii) a transcription termination sequence.
    
    
    11. Construct according to item 10, wherein one of said control sequences is a constitutive promoter, preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
    12. Use of a construct according to item 10 or 11 in a method for making plants having increased yield, particularly increased biomass and/or increased seed yield relative to control plants.
    13. Plant, plant part or plant cell transformed with a construct according to item 10 or 11.
    14. Method for the production of a transgenic plant having increased yield, particularly increased biomass and/or increased seed yield relative to control plants, comprising:
    
        (i) introducing and expressing in a plant a nucleic acid encoding a GSA1 polypeptide as defined in item 1; and
        (ii) cultivating the plant cell under conditions promoting plant growth and development.
    
    
    15. Transgenic plant having increased yield, particularly increased biomass and/or increased seed yield, relative to control plants, resulting from modulated expression of a nucleic acid encoding a GSA1 polypeptide as defined in item 1, or a transgenic plant cell derived from said transgenic plant.
    16. Transgenic plant according to item 9, 13 or 15, or a transgenic plant cell derived thereof, wherein said plant is a crop plant such as sugarbeet, or a monocot or a cereal, such as rice, maize, wheat, sugarcane, barley, millet, rye, triticale, sorghum emmer, spelt, secale, einkorn, teff, milo and oats.
    17. Harvestable parts of a plant according to item 16, wherein said harvestable parts are preferably shoot biomass and/or seeds.
    18. Products derived from a plant according to item 16 and/or from harvestable parts of a plant according to item 17.
    19. Use of a nucleic acid encoding a GSA1 polypeptide in increasing yield, particularly in increasing seed yield and/or shoot biomass in plants, relative to control plants.


EXAMPLES
The present invention will now be described with reference to the following examples, which are by way of illustration alone. The following examples are not intended to completely define or otherwise limit the scope of the invention.
DNA manipulation: unless otherwise stated, recombinant DNA techniques are performed according to standard protocols described in (Sambrook (2001) Molecular Cloning: a laboratory manual, 3rd Edition Cold Spring Harbor Laboratory Press, CSH, New York) or in Volumes 1 and 2 of Ausubel et al. (1994), Current Protocols in Molecular Biology, Current Protocols. Standard materials and methods for plant molecular work are described in Plant Molecular Biology Labfax (1993) by R. D. D. Croy, published by BIOS Scientific Publications Ltd (UK) and Blackwell Scientific Publications (UK).
Example 1
Identification of Sequences Related to the Nucleic Acid Sequence Used in the Methods of the Invention
Sequences (full length cDNA, ESTs or genomic) related to the nucleic acid sequence used in the methods of the present invention were identified inter alia amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information (NCBI) using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches. For example, the polypeptide encoded by the nucleic acid used in the present invention was used for the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences set off. The output of the analysis was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflect the probability that a particular alignment occurs by chance (the lower the E-value, the more significant the hit). In addition to E-values, comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example the E-value may be increased to show less stringent matches. This way, short nearly exact matches may be identified.
1.1. BET1-Like Polypeptides
Table A1 provides a list of nucleic acid sequences related to the nucleic acid sequence used in the methods of the present invention.







TABLE A1







Examples of BET1-like polypeptides:










Nucleic




acid



SEQ
Polypeptide


BET1-like polypeptides
ID NO:
SEQ ID NO:












T----M---  25296
1
2


A. arenosa_x_thaliana_TA52_378006_1
3
4


A. hypogaea_EE124570_1
5
6


A. majus_AJ789814_1
7
8


A. thaliana_AT1G56233.1_1
9
10


B.
11
12


napus_BN06MS42331943.f_k04_1_40488_1


B. napus_CD815839_1
13
14


B. pendula_CD278481_1
15
16


B. vulgaris_DV501764_1
17
18


C. reticulata_x_temple_DN795225_1
19
20


C. tetragonoloba_EG981304_1
21
22


C. tetragonoloba_EG987480_1
23
24


G. biloba_DR064764_1
25
26


G. max_TA67390_3847_1
27
28


L. serriola_TA5233_75943_1
29
30


M. truncatula_AC169182_23.5_1
31
32


M. truncatula_AC169182_39.5_1
33
34


P. abies_TA1522_3329_1
35
36


P. abies_TA1523_3329_1
37
38


P. abies_TA2417_3329_1
39
40


P. coccineus_CA908259_1
41
42


P. coccineus_CA908272_1
43
44


P. coccineus_TA2699_3886_1
45
46


P. coccineus_TA3810_3886_1
47
48


P. dulcis_TA313_3755_1
49
50


P. engelmannii_x_glauca_CO203682_1
51
52


P. menziesii_TA1952_3357_1
53
54


P. pinaster_BX678743_1
55
56


P. pinaster_BX682074_1
57
58


P. pinaster_CR392675_1
59
60


P. pinaster_TA4836_71647_1
61
62


P. pinaster_TA4882_71647_1
63
64


P. sitchensis_TA10405_3332_1
65
66


P. taeda_CO162523_1
67
68


P. taeda_TA16676_3352_1
69
70


P. taeda_TA22888_3352_1
71
72


P. taeda_TA3629_3352_1
73
74


P. taeda_TA4949_3352_1
75
76


S. indicum_TA1114_4182_1
77
78


V. corymbosum_CV091429_1
79
80


V. corymbosum_DR068079_1
81
82


V. riparia_TA839_96939_1
83
84


Z. mays_c57759235gm030403_14494_1
85
86


Z. mays_c62091609gm030403_7698_1
87
88


Z. mays_DQ245377_1
89
90


Z. mays_DR787277_1
91
92


Z. mays_EC364520_1
93
94


Z. mays_ZM07MC13625_57676372_13595_1
95
96









1.2. Calreticulin Polypeptides

Table A2 provides a list of nucleic acid sequences related to the nucleic acid sequence used in the methods of the present invention.







TABLE A2







Examples of Calreticulin polypeptides:












Nucleic acid
Polypeptide



Name
SEQ ID NO:
SEQ ID NO:















S. lycopersicum_TA36564
104
105



A. formosa_TA9419
106
107



A. thaliana_AT1G09210_CRT2
108
109



A. thaliana_AT1G56340_CRT1
110
111



A. trichopoda_TA1102
112
113



B. distachyon_TA448
114
115



B. napus_BPS_28478
116
117



B. napus_TA20659
118
119



B. vulgaris_TA7257
120
121



C. annuum_TA4292
122
123



C. endivia_TA1106
124
125



C. solstitialis_TA9
126
127



G. hirsutum_TA20990
128
129



G. max_BPS_38275
130
131



G. raimondii_TA8857
132
133



G. raimondii_TA8860
134
135



H. annuus_TA7525
136
137



H. argophyllus_TA1300
138
139



H. vulgare_BPS_7785
140
141



H. vulgare_TA38555
142
143



I. nil_TA5002
144
145



L. japonicus_TA548
146
147



L. serriola_TA711
148
149



M. domestica_TA24948
150
151



M. truncatula_AC149474
152
153



O. basilicum_TA646
154
155



O. sativa_Os03g0832200
156
157



O. sativa_Os07g0246200
158
159



P. persica_TA3474
160
161



P. pinaster_TA4383
162
163



P. sitchensis_TA20930
164
165



P. taeda_TA5639
166
167



P. trichocarpa_133.107
168
169



P. trichocarpa_729432
170
171



P. vulgaris_TA3122
172
173



R. communis_U74630
174
175



S. bicolor_TA20922
176
177



S. bicolor_TA25211
178
179



S. habrochaites_TA1435
180
181



S. tuberosum_TA24720
182
183



T. aestivum_TA50840
184
185



T. aestivum_TA74192
186
187



V. vinifera_TA38405
188
189



W. mirabilis_TA538
190
191



Z. mays_TA170881
192
193



A. formosa_TA8804
194
195



A. thaliana_AT1G08450_CRT3
196
197



B. napus_BPS_33882
198
199



C. maculosa_TA223
200
201



E. esula_TA10075
202
203



G. raimondii_TA11257
204
205



H. vulgare_TA32081
206
207



M. domestica_TA28184
208
209



M. truncatula_TA23636
210
211



O. sativa_Os01g67054.1
212
213



O. sativa_Os05g43170.1
214
215



P. patens_164102
216
217



P. trichocarpa_VII.148
218
219



P. trifoliata_TA7309
220
221



S. bicolor_TA24664
222
223



T. aestivum_TA53764
224
225



V. vinifera_GSVIVT00025039001
226
227



Z. mays_BPS_22383
228
229



Z. mays_TA15627
230
231



C. reinhardtii_TA11983
232
233



V. carteri_76046
234
235



D. melanogaster_CRC
236
237



H. sapien_CALR3
238
239



H. sapien_CALRE
240
241



A. anophagefferens_21695
242
243



P. tricornutum_41172
244
245










1.3. tRNA Dihydrouridine Synthase 1-Like Polypeptides (DUS1L Polypeptides)

Table A3 provides a list of nucleic acid sequences related to the nucleic acid sequence used in the methods of the present invention.







TABLE A3







Examples of DUS1L polypeptide sequences, and encoding


nucleic acid sequences










Nucleic




acid



SEQ
Polypeptide


Name
ID NO
SEQ ID NO





Sacof_DUS1L
258
259


A. thaliana_AT5G67220.1
260
261


B. napus_TC79818
262
263


B. napus_BN06MC20455_46646511@20387
264
265


(P)


C. vulgaris_36290
266
267


E. huxleyi_437158
268
269


G. max_Glyma17g18490.1
270
271


G. max_Glyma05g20510.1
272
273


O. sativa_LOC_Os06g49870.1
274
275


P. patens_149014
276
277


P. taeda_TA13257_3352
278
279


R. communis_TA2745_3988
280
281


S. moellendorffii_443602
282
283


S. lycopersicum_TC206234
284
285


S. bicolor_Sb10g029830.1
286
287


V. vinifera_GSVIVT00019548001
288
289


V. carteri_80128
290
291


Z. mays_ZM07MC04636_BFb0070D07@4625
292
293


(P)









In some instances, related sequences have tentatively been assembled and publicly disclosed by research institutions, such as The Institute for Genomic Research (TIGR; beginning with TA). The Eukaryotic Gene Orthologs (EGO) database may be used to identify such related sequences, either by keyword search or by using the BLAST algorithm with the nucleic acid sequence or polypeptide sequence of interest. On other instances, special nucleic acid sequence databases have been created for particular organisms, such as by the Joint Genome Institute. Further, access to proprietary databases (P), has allowed the identification of novel nucleic acid and polypeptide sequences.
1.4. ES43-Like Polypeptides
Table A4 provides a list of nucleic acid sequences related to the nucleic acid sequence used in the methods of the present invention.







TABLE A4







Examples of ES43-like polypeptides:










Nucleic
Poly-



acid
peptide



SEQ
SEQ


Name ES43-like polypeptides
ID NO:
ID NO:





T  M  ---_29382; ---4312; 116; 772; 4530;
298
299


39#1


A. thaliana_AT4G22140.1#1
300
301


A. thaliana_AT4G22140.2#1
302
303


A. thaliana_AT4G39100.1#1
304
305


A. thaliana_AT4G04260.1#1
306
307


B. napus_BN06MC06825_42494234@6808#1
308
309


H. vulgare_TA35269_4513#1
310
311


H. vulgare_TA42493_4513#1
312
313


H. vulgare_BF623189#1
314
315


H. vulgare_TA40508_4513#1
316
317


L. usitatissimum_LU04MC11049_62370147@
318
319


11045#1


O. sativa_Os09g0386500#1
320
321


O. sativa_Os08g0421900#1
322
323


O. sativa_Os07g0186400#1
324
325


O. sativa_AK061201#1
326
327


O. sativa_Os03g0799600#1
328
329


P. patens_153027#1
330
331


P. patens_149469#1
332
333


P. patens_108696#1
334
335


P. patens_59496#1
336
337


P. patens_213413#1
338
339


P. trichocarpa_scaff_IV.1226#1
340
341


P. trichocarpa_scaff_XIV.1045#1
342
343


P. trichocarpa_scaff_XI.104#1
344
345


P. trichocarpa_scaff_1247.1#1
346
347


P. trichocarpa_scaff_166.34#1
348
349


P. trichocarpa_scaff_II.2065#1
350
351


S. lycopersicum_TA42220_4081#1
352
353


S. lycopersicum_TA40478_4081#1
354
355


T  M  ---_2176; ---0490; 46; 822; 3702; 32#1
356
357


T  M  ---_14367; ---4367; 137; 787; 4565;
358
359


23#1


T. aestivum_TA54637_4565#1
360
361


T. aestivum_CK201479#1
362
363


T. aestivum_c54968390@13747#1
364
365


Z. mays_TA19459_4577999#1
366
367


Z. mays_TA12947_4577999#1
368
369


Z. mays_ZM07MC24083_BFb0146O24@24016#1
370
371


Z. mays_ZM07MC24174_BFb0045F09@24106#1
372
373









In some instances, related sequences have tentatively been assembled and publicly disclosed by research institutions, such as The Institute for Genomic Research (TIGR; beginning with TA). The Eukaryotic Gene Orthologs (EGO) database may be used to identify such related sequences, either by keyword search or by using the BLAST algorithm with the nucleic acid sequence or polypeptide sequence of interest. On other instances, special nucleic acid sequence databases have been created for particular organisms, such as by the Joint Genome Institute. Further, access to proprietary databases, has allowed the identification of novel nucleic acid and polypeptide sequences.
1.5. HON5-Like Polypeptides
Table A5 provides a list of nucleic acid sequences related to the nucleic acid sequence used in the methods of the present invention.







TABLE A5







Examples of HON5-like polypeptides:












Nucleic





acid




SEQ
Polypeptide


Name
Organism name
ID NO:
SEQ ID NO:





Poptr_HMGA905
Populus trichocarpa
387
388


Arath_HMGA2
Arabidsopsis thaliana
389
390


Arath_Hon4
Arabidsopsis thaliana
391
392


Brana_Hon5\like
Brassica napus
393
394


Glyma_HON5\like
Glycine max
395
396


Gosar_HMGA10101
Gossypium arboretum
397
398


Alcep_HMGA14201
Allium cepa
399
400


Lotja_HMGA1701
Lotus japonica
401
402


Orysa_HMGA2201
Oryza sative
403
404


Poptr_HMGA906
Populus trichocarpa
405
406


Sacof_HMGA2503
Saccharum
407
408



officinarum


Vitvi_hon5\like
Vitis vinifera

409









In some instances, related sequences have tentatively been assembled and publicly disclosed by research institutions, such as The Institute for Genomic Research (TIGR; beginning with TA). The Eukaryotic Gene Orthologs (EGO) database may be used to identify such related sequences, either by keyword search or by using the BLAST algorithm with the nucleic acid sequence or polypeptide sequence of interest. On other instances, special nucleic acid sequence databases have been created for particular organisms, such as by the Joint Genome Institute. Further, access to proprietary databases, has allowed the identification of novel nucleic acid and polypeptide sequences.
1.6. glutamate-1-semialdehyde aminotransferase polypeptides (GSA1 polypeptides)
Table A6 provides a list of nucleic acid sequences related to the nucleic acid sequence used in the methods of the present invention.







TABLE A6







Examples of GSA1 polypeptides:










Nucleic




acid



SEQ
Polypeptide


Name
ID NO:
SEQ ID NO:





===5613
417
418


A_thaliana_AT3G48730_1
419
420


A_thaliana_AT5G63570_1
421
422


Aquilegia_sp_TC22821
423
424


B_napus_TC63445
425
426


B_napus_TC63450
427
428


C_reinhardtii_138524
429
430


C_vulgaris_43392
431
432


Chlorella_37143
433
434


E_huxleyi_437052
435
436


F_arundinacea_TC6452
437
438


F_vesca_TA11529_57918
439
440


G_max_Glyma04g00420_1
441
442


G_max_Glyma06g00510_1
443
444


H_vulgare_TC162130
445
446


M_truncatula_CU024868_27_4
447
448


N_benthamiana_TC14122
449
450


N_tabacum_TC18263
451
452


N_tabacum_TC18710
453
454


O_lucimarinus_28523
455
456


O_RCC809_53004
457
458


O_sativa_LOC_Os08g41990_1
459
460


O_taurii_24711
461
462


P_patens_116325
463
464


P_patens_181992
465
466


P_tremuloides_575404
467
468


P_tricornutum_36347
469
470


R_communis_TA2570_3988
471
472


S_lycopersicum_TC191683
473
474


S_moellendorffii_183248
475
476


T_aestivum_TA06MC000384_60074805_384
477
478


T_pseudonana_575
479
480


V_carteri_74470
481
482


V_shuttleworthii_TA2337_246827
483
484


Z_mays_ZM07MC17771_BFb0062K01_17727
485
486









In some instances, related sequences have tentatively been assembled and publicly disclosed by research institutions, such as The Institute for Genomic Research (TIGR; beginning with TA). The Eukaryotic Gene Orthologs (EGO) database may be used to identify such related sequences, either by keyword search or by using the BLAST algorithm with the nucleic acid sequence or polypeptide sequence of interest. On other instances, special nucleic acid sequence databases have been created for particular organisms, such as by the Joint Genome Institute. Further, access to proprietary databases, has allowed the identification of novel nucleic acid and polypeptide sequences.
Example 2
Alignment of Sequences Related to the Polypeptide Sequences Used in the Methods of the Invention
2.1. BET1-Like Polypeptides
Alignment of polypeptide sequences was performed using the ClustalW 2.0 algorithm of progressive alignment (Thompson et al. (1997) Nucleic Acids Res 25:4876-4882; Chema et al. (2003). Nucleic Acids Res 31:3497-3500) with Blosum 62 matrix, gap opening penalty 10, gap extension penalty: 0.2). Minor manual editing was done to further optimise the alignment. The BET1-like polypeptides are aligned in FIG. 2.
Highly conserved amino acid residues are indicated in the consensus sequence.
2.2. Calreticulin Polypeptides
Alignment of polypeptide sequences of plant origin of Table A2 was performed using the ClustalW 2.0 algorithm of progressive alignment (Thompson et al. (1997) Nucleic Acids Res 25:4876-4882; Chema et al. (2003). Nucleic Acids Res 31:3497-3500) with standard setting (slow alignment, similarity matrix: Blosum 62 (gap opening penalty 10, gap extension penalty: 0.2). Minor manual editing was done to further optimise the alignment. The Calreticulin polypeptides are aligned in FIG. 4. Highly conserved amino acid residues are indicated in the consensus sequence.
A phylogenetic tree of Calreticulin polypeptides of plant origin is reproduced from Christensen et al. 2008 (FIG. 5).
A phylogenetic tree of the Calreticulin polypeptides of Table A2 was constructed using a neighbour-joining clustering algorithm as provided in the AlignX programme from the Vector NTI (Invitrogen). The Calreticulin polypeptides origin clustered in 5 distinct clades: 1-CRT1, comprising Calreticulin polypeptides of plant origin of the Group CRT1/2; 2-CRT3, comprising Calreticulin polypeptides of plant origin of the Group CRT3; 3-algae: comprising Calreticulin polypeptides of origating from algae; 4-animal: comprising Calreticulin polypeptides of originating from the animal kingdom. Table B1 shows the distribution of the polypeptides of Table A2 amongst the different clades.







TABLE B1







Phylogentic relationship of Calreticulin polypeptides.











Name
SEQ ID NO:
Clade







S. lycopersicum_TA36564
105
1-CRT1



A. formosa_TA9419
107
1-CRT1



A. thaliana_AT1G09210_CRT2
109
1-CRT1



A. thaliana_AT1G56340_CRT1
111
1-CRT1



A. trichopoda_TA1102
113
1-CRT1



B. distachyon_TA448
115
1-CRT1



B. napus_BPS_28478
117
1-CRT1



B. napus_TA20659
119
1-CRT1



B. vulgaris_TA7257
121
1-CRT1



C. annuum_TA4292
123
1-CRT1



C. endivia_TA1106
125
1-CRT1



C. solstitialis_TA9
127
1-CRT1



G. hirsutum_TA20990
129
1-CRT1



G. max_BPS_38275
131
1-CRT1



G. raimondii_TA8857
133
1-CRT1



G. raimondii_TA8860
135
1-CRT1



H. annuus_TA7525
137
1-CRT1



H. argophyllus_TA1300
139
1-CRT1



H. vulgare_BPS_7785
141
1-CRT1



H. vulgare_TA38555
143
1-CRT1



I. nil_TA5002
145
1-CRT1



L. japonicus_TA548
147
1-CRT1



L. serriola_TA711
149
1-CRT1



M. domestica_TA24948
151
1-CRT1



M. truncatula_AC149474
153
1-CRT1



O. basilicum_TA646
155
1-CRT1



O. sativa_Os03g0832200
157
1-CRT1



O. sativa_Os07g0246200
159
1-CRT1



P. persica_TA3474
161
1-CRT1



P. pinaster_TA4383
163
1-CRT1



P. sitchensis_TA20930
165
1-CRT1



P. taeda_TA5639
167
1-CRT1



P. trichocarpa_133.107
169
1-CRT1



P. trichocarpa_729432
171
1-CRT1



P. vulgaris_TA3122
173
1-CRT1



R. communis_U74630
175
1-CRT1



S. bicolor_TA20922
177
1-CRT1



S. bicolor_TA25211
179
1-CRT1



S. habrochaites_TA1435
181
1-CRT1



S. tuberosum_TA24720
183
1-CRT1



T. aestivum_TA50840
185
1-CRT1



T. aestivum_TA74192
187
1-CRT1



V. vinifera_TA38405
189
1-CRT1



W. mirabilis_TA538
191
1-CRT1



Z. mays_TA170881
193
1-CRT1



A. formosa_TA8804
195
2-CRT3



A. thaliana_AT1G08450_CRT3
197
2-CRT3



B. napus_BPS_33882
199
2-CRT3



C. maculosa_TA223
201
2-CRT3



E. esula_TA10075
203
2-CRT3



G. raimondii_TA11257
205
2-CRT3



H. vulgare_TA32081
207
2-CRT3



M. domestica_TA28184
209
2-CRT3



M. truncatula_TA23636
211
2-CRT3



O. sativa_Os01g67054.1
213
2-CRT3



O. sativa_Os05g43170.1
215
2-CRT3



P. patens_164102
217
2-CRT3



P. trichocarpa_VII.148
219
2-CRT3



P. trifoliata_TA7309
221
2-CRT3



S. bicolor_TA24664
223
2-CRT3



T. aestivum_TA53764
225
2-CRT3



V. vinifera_GSVIVT00025039001
227
2-CRT3



Z. mays_BPS_22383
229
2-CRT3



Z. mays_TA15627
231
2-CRT3



C. reinhardtii_TA11983
233
3-algae



V. carteri_76046
235
3-algae



D. melanogaster_CRC
237
4-animal



H. sapien_CALR3
239
4-animal



H. sapien_CALRE
241
4-animal



A. anophagefferens_21695
243
5-protist



P. tricornutum_41172
245
5-protist










2.3. tRNA Dihydrouridine Synthase 1-Like Polypeptides (DUS1L Polypeptides)

Multiple sequence alignment of all the DUS1L polypeptide sequences in Table A3 was performed using the AlignX algorithm (from Vector NTI 10.3, Invitrogen Corporation). Results of the alignment are shown in FIG. 9 of the present application. One important domain is a tRNA-dihydrouridine synthase domain with an InterPro entry IPR001269 (integrating the PFAM PF01207 entry (marked by X's). One important motif is the tRNA-dihydrouridine synthase conserved site with an InterPro entry IPR018517 (integrating the PROSITE PS01136 (marked by X's, in bold in SEQ ID NO: Sacof_DUS1L). Conserved residues are heavily boxed, in particular a Cys residue which is in other organisms a key general-acid/base catalyst.
2.4. ES43-Like Polypeptides
Alignment of polypeptide sequences was performed using the ClustalW 1.8 algorithm of progressive alignment (Thompson et al. (1997) Nucleic Acids Res 25:4876-4882; Chema et al. (2003). Nucleic Acids Res 31:3497-3500) with standard setting (slow alignment, similarity matrix: Gonnet, gap opening penalty 10, gap extension penalty: 0.2). Minor manual editing was done to further optimise the alignment. The ES43-like polypeptides are aligned in FIG. 12.
The sequence and location of the BAH and the PHD domains in the ES43-like polypeptides of Table A4 becomes apparent when looking at FIG. 11 and FIG. 12.
2.5. HON5-Like Polypeptides
Alignment of polypeptide sequences was performed using the ClustalW 2.0 algorithm of progressive alignment (Thompson et al. (1997) Nucleic Acids Res 25:4876-4882; Chema et al. (2003). Nucleic Acids Res 31:3497-3500) with standard setting and Blosum 62 matrix, gap opening penalty 10, gap extension penalty 0.2 as provided by the AlignX programme from Vector NTI (Invitrogen). Minor manual editing was done to further optimise the alignment. The HON5-like polypeptides are aligned in FIG. 14. Amino acid residues highly conserved are indicated in the consensus sequence. The HI/H5 domain and the AThook domains (6 in total) are indicated.
2.6. glutamate-1-semialdehyde aminotransferase polypeptides (GSA1 polypeptides)
Alignment of polypeptide sequences was performed using the ClustalW 2.0 algorithm of progressive alignment (Thompson et al. (1997) Nucleic Acids Res 25:4876-4882; Chema et al. (2003). Nucleic Acids Res 31:3497-3500) with standard setting (slow alignment, similarity matrix: Gonnet (or Blosum 62)., gap opening penalty 10, gap extension penalty: 0.2). Minor manual editing was done to further optimise the alignment. The GSA1 polypeptides are aligned in FIG. 16.
A phylogenetic tree of GSA1 polypeptides (FIG. 17) was constructed using a neighbour-joining clustering algorithm as provided in the AlignX programme from Vector NTI (Invitrogen).
Example 3
Calculation of Global Percentage Identity Between Polypeptide Sequences Useful in Performing the Methods of the Invention
3.1. BET1-Like Polypeptides
Global percentages of similarity and identity between full length polypeptide sequences useful in performing the methods of the invention were determined using one of the methods available in the art, the MatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 2003 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella J J, Bitincka L, Smalley J; software hosted by Ledion Bitincka). MatGAT software generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments using the Myers and Miller global alignment algorithm (with a gap opening penalty of 12, and a gap extension penalty of 2), calculates similarity and identity using for example Blosum 62 (for polypeptides), and then places the results in a distance matrix. Sequence similarity is shown in the bottom half of the dividing line and sequence identity is shown in the top half of the diagonal dividing line.
Parameters used in the comparison were:

    
    
        Scoring matrix: Blosum62
        First Gap: 12
        Extending gap: 2
    
    


Results of the software analysis are shown in Table C1 for the global similarity and identity over the full length of the polypeptide sequences. Percentage identity is given above the diagonal in bold and percentage similarity is given below the diagonal (normal face).
The percentage identity between the BET1-like polypeptide sequences useful in performing the methods of the invention can be as low as 25% % amino acid identity compared to SEQ ID No: 2 (Table C1).







TABLE C1







MatGAT results for global similarity and identity over the full length of the polypeptide sequences.
















BET1-like polypeptide
1
17
24
38
41
42
43
44
46



















 1. M. truncatula_AC169182_39.5_1

32.1
24.4
26.1
26.4
29
22.8
22.8
26.1


17. M. truncatula_AC169182_23.5_1
40.5

21.6
24.2
22
26
23.7
23.7
24.2


24. B. napus_BN06MS42331943.f_k04_1_40488_1
32.1
38.3

23.9
20.4
25
31.6
30.5
23.9


38. T----M---  25296
34.1
41.2
41.2

25
28.9
65.6
66.7
93.3


41. A. thaliana_AT1G56233.1_1
40.2
40.2
43.7
42.5

17.9
17.1
17.1
23.2


42. Z. mays_c57759235gm030403_14494_1
38.2
44.9
40.4
50.6
37.1

30.2
29.2
28.7


43. Z. mays_c62091609gm030403_7698_1
33.7
40.4
46.1
77.5
40.4
51.7

97.8
67


44. Z. mays_DQ245377_1
33.7
40.4
44.9
77.5
40.4
51.7
100

68.1


46. Z. mays_ZM07MC13625_57676372_13595_1
33.7
39.3
39.3
95.5
41.6
50.6
78.7
78.7









3.2. Calreticulin Polypeptides

Global percentages of similarity and identity between full length polypeptide sequences useful in performing the methods of the invention were determined using one of the methods available in the art, the MatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 2003 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella J J, Bitincka L, Smalley J; software hosted by Ledion Bitincka). MatGAT software generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments using the Myers and Miller global alignment algorithm (with a gap opening penalty of 12, and a gap extension penalty of 2), calculates similarity and identity using for example Blosum 62 (for polypeptides), and then places the results in a distance matrix. Sequence similarity is shown in the bottom half of the dividing line and sequence identity were shown in the top half of the diagonal dividing line.

    
    
        Scoring matrix: Blosum62
        First Gap: 12
        Extending gap: 2
    
    


The percentage identity between Calreticulin polypeptide sequences useful in performing the methods of the invention can be as low as 32% amino acid identity. The percentage identity between Calreticulin polypeptide sequences of the CRT1/2 is typically at least 64%. The percentage identity between Calreticulin polypeptide sequences of the CRT3 is typically at least 55%. The percentage identity of Calreticulin polypeptide sequences of the CRT1/2 group compared to Calreticulin polypeptide sequences of the CRT3 group is typically at least 49%.
3.3. tRNA Dihydrouridine Synthase 1-Like Polypeptides (DUS1L Polypeptides)
Global percentages of similarity and identity between full length polypeptide sequences useful in performing the methods of the invention were determined using one of the methods available in the art, the MatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 2003 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella J J, Bitincka L, Smalley J; software hosted by Ledion Bitincka). MatGAT software generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments using the Myers and Miller global alignment algorithm (with a gap opening penalty of 12, and a gap extension penalty of 2), calculates similarity and identity using for example Blosum 62 (for polypeptides), and then places the results in a distance matrix. Sequence similarity is shown in the bottom half of the dividing line and sequence identity is shown in the top half of the diagonal dividing line.
Parameters used in the comparison were:

    
    
        Scoring matrix: Blosum62
        First Gap: 12
        Extending gap: 2
    
    


Results of the software analysis are shown in Table C2 for the global similarity and identity over the full length of the polypeptide sequences (excluding the partial polypeptide sequences).
The percentage identity between the full length polypeptide sequences useful in performing the methods of the invention can be as low as 32% amino acid identity compared to SEQ ID NO: 259.







TABLE C2







MatGAT results for global similarity and identity over the full length of the polypeptide sequences of Table A3.


























1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18





























 1. Sacof_DuS1L

65
64
63
64
64
85
52
54
65
96
63
53
65
92
42
32
44


 2. A. thaliana_AT5G67220.1
77

83
85
68
68
64
52
52
68
65
67
51
70
65
38
28
40


 3. B. napus_BN06MC20455_46646511@20387
77
88

83
70
68
63
56
51
65
64
64
55
65
64
41
31
43


 4. B. napus_TC79818
77
93
87

67
67
63
52
52
66
63
66
51
66
65
38
28
39


 5. G. max_Glyma 05g20510.1
77
79
80
78

94
64
54
53
68
65
63
55
69
65
40
31
43


 6. G. max_Glyma 17g18490.1
75
78
79
78
96

65
54
53
69
65
64
55
69
66
41
31
43


 7. O. sativa_LOC_Os06g49870.1
92
78
75
77
75
75

53
52
66
84
63
52
64
83
42
32
45


 8. P. patens_149014
68
68
72
69
70
69
69

50
52
52
51
58
51
52
44
35
46


 9. P. taeda_TA13257_3352
67
66
62
66
64
62
67
65

54
55
52
51
54
53
36
28
40


10. R. communis_TA2745_3988
80
80
75
79
80
78
80
69
67

65
68
52
72
65
41
30
42


11. S. bicolor_Sb10g029830.1
98
79
77
78
76
75
92
69
68
80

64
53
65
94
42
32
45


12. S. lycopersicum_TC206234
78
79
75
78
77
75
76
69
68
81
78

51
70
64
39
30
40


13. S. moellendorffii_443602
69
68
72
68
69
69
68
73
63
68
69
66

51
53
44
32
45


14. V. vinifera_GSVIVT00019548001
81
83
78
81
82
81
80
71
64
84
79
79
68

65
40
30
41


15. Z. mays_ZM07MC04636_BFb0070D07@4625
95
79
76
78
77
76
90
69
67
78
95
79
69
81

42
31
44


16. C. vulgaris_36290
60
56
61
57
58
59
58
62
51
56
60
57
63
57
60

38
48


17. E. huxleyi_437158
49
48
49
47
48
48
50
53
41
47
49
47
50
48
50
53

33


18. V. carteri_80128
61
58
58
59
59
60
61
60
54
59
62
58
59
61
62
60
49









The percentage amino acid identity can be significantly increased if the most conserved region of the polypeptides is compared. For example, when comparing the amino acid sequence of a tRNA-dihydrouridine synthase domain as represented by SEQ ID NO: 294 with the respective corresponding domains of the polypeptides of Table A3, the percentage amino acid identity increases significantly (in order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more amino acid sequence identity).
3.4. ES43-Like Polypeptides
Global percentages of similarity and identity between full length polypeptide sequences useful in performing the methods of the invention is determined using one of the methods available in the art, the MatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 2003 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella J J, Bitincka L, Smalley J; software hosted by Ledion Bitincka). MatGAT software generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments using the Myers and Miller global alignment algorithm (with a gap opening penalty of 12, and a gap extension penalty of 2), calculates similarity and identity using for example Blosum 62 (for polypeptides), and then places the results in a distance matrix. Sequence similarity is shown in the bottom half of the dividing line and sequence identity is shown in the top half of the diagonal dividing line.
Parameters used in the comparison are:

    
    
        Scoring matrix: Blosum62
        First Gap: 12
        Extending gap: 2

3.5. HON5-Like Polypeptides

    
    


Global percentages of similarity and identity between full length polypeptide sequences useful in performing the methods of the invention were determined using one of the methods available in the art, the MatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 2003 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella J J, Bitincka L, Smalley J; software hosted by Ledion Bitincka). MatGAT software generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments using the Myers and Miller global alignment algorithm (with a gap opening penalty of 12, and a gap extension penalty of 2), calculates similarity and identity using for example Blosum 62 (for polypeptides), and then places the results in a distance matrix. Sequence similarity is shown in the bottom half of the dividing line and sequence identity is shown in the top half of the diagonal dividing line.
Parameters used in the comparison were:

    
    
        Scoring matrix: Blosum62
        First Gap: 12
        Extending gap: 2
    
    


Results of the software analysis are shown in Table C3 for the global similarity and identity over the full length of the polypeptide sequences of Table A5.







TABLE C3







MatGAT results for global similarity and identity over the full length of the polypeptide sequences.




















1
2
3
4
5
6
7
8
9
10
11
12























 1. HMGA905_Populus

35.9
31.0
31.8
38.9
29.1
17.6
26.7
32.3
25.4
23.3
59.0


 2. Vitvi_hon5\like
45.2

30.9
31.5
32.0
32.5
26.2
32.1
32.5
24.0
23.0
32.0


 3. Arath_Hon4
47.1
40.4

61.3
29.1
27.8
19.2
23.3
51.6
23.9
22.6
27.6


 4. Brana_Hon5\like
46.3
39.2
71.4

28.6
27.1
19.2
21.0
46.8
22.5
20.8
26.7


 5. Glyma_HON5\like
53.3
41.2
44.2
45.6

24.4
18.3
26.0
28.8
24.2
22.5
27.1


 6. HMGA10101_Gosar
36.8
44.2
35.8
33.7
33.3

29.3
32.0
27.9
21.9
19.8
38.4


 7. HMGA14201_Allce
24.3
33.8
25.6
26.5
24.9
38.8

30.8
18.2
18.4
17.9
24.4


 8. HMGA1701_Lotja
32.2
37.5
29.4
28.4
30.6
43.4
47.2

24.4
17.7
18.2
33.2


 9. HMGA2_Arath
50.3
43.4
65.8
63.5
44.0
37.2
25.3
30.5

23.2
21.9
26.2


10. HMGA2201_Orysa
37.2
32.5
39.8
38.5
36.8
31.6
24.7
23.2
39.2

38.2
23.7


11. HMGA2503_Sacof
38.6
30.4
39.5
38.6
35.3
27.3
22.6
23.1
37.0
49.7

22.5


12. HMGA906_Populus
65.1
45.3
39.6
37.1
38.3
50.1
33.9
42.3
37.4
32.3
32.8









3.6. glutamate-1-semialdehyde aminotransferase polypeptides (GSA1 polypeptides)

Global percentages of similarity and identity between full length polypeptide sequences useful in performing the methods of the invention were determined using one of the methods available in the art, the MatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 2003 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella J J, Bitincka L, Smalley J; software hosted by Ledion Bitincka). MatGAT software generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments using the Myers and Miller global alignment algorithm (with a gap opening penalty of 12, and a gap extension penalty of 2), calculates similarity and identity using for example Blosum 62 (for polypeptides), and then places the results in a distance matrix.
Parameters used in the comparison were:

    
    
        Scoring matrix: Blosum62
        First Gap: 12
        Extending gap: 2
    
    


Results of the software analysis are shown in Table C4 for the global similarity and identity over the full length of the polypeptide sequences. Percentage identity is given above the diagonal in bold and percentage similarity is given below the diagonal (normal face).
The percentage identity between the GSA1 polypeptide sequences useful in performing the methods of the invention can be as low as yy % amino acid identity compared to SEQ ID NO: 418.







TABLE C4





MatGAT results for global similarity and identity over the full length of the polypeptide sequences.




























1
2
3
4
5
6
7
8
9
10
11
12





 1. ===5613

81.8
80
78
81
81.4
62.2
63
64.5
63.7
75.9
83.5


 2. A_thaliana_AT3G48730_1
91

90.1
78.2
91.3
90.3
63.3
66.2
66.6
65.3
76.8
81.9


 3. A_thaliana_AT5G63570_1
89.1
95.4

76.4
96.6
95.1
63.5
65.6
65
63.5
77
81.5


 4. Aquilegia_sp_TC22821
89.1
88.2
86.3

77.1
77.1
63.5
66.3
65
63.5
76.6
79.4


 5. B_napus_TC63445
90.6
96
97.9
86.7

97
63
66
66.4
64.7
77.7
82.1


 6. B_napus_TC63450
90.8
96
97
88
98.5

64.1
66.1
65.5
65.1
76.6
81.7


 7. C_reinhardtii_138524
75.6
76.9
77.2
77
77
78.2

72.4
79.6
68.4
65.8
66.7


 8. C_vulgaris_43392
77.9
80.3
78.7
80
79.5
79.7
82.5

74.4
65.2
68.5
68.3


 9. Chlorella_37143
77.2
78.4
77.4
78.7
78.2
78.4
88.1
86.5

67.5
68.9
67


10. E_huxleyi_437052
78.7
80.3
80
80.2
80.3
80.5
82.3
78.6
79.7

64.9
65.8


11. F_arundinacea_TC6452
85.8
85.8
87.6
87.1
87.1
86.5
78
80.3
79.3
79.1

77.7


12. F_vesca_TA11529_57918
92.3
92.6
92
89
93
93.4
79.1
81
80.3
82.5
88.2



13. G_max_Glyma04g00420_1
90
89.2
87.8
88.8
88.4
89
76.2
79.4
75.7
80.9
86.3
89.4


14. G_max_Glyma06g00510_1
89.1
88.3
86.7
88.2
88.2
88.6
76.6
79.7
77.5
82.2
85.8
89


15. H_vulgare_TC162130
86.4
86.7
86.5
87.6
87.1
86.5
78.5
80.8
79.5
80.6
97.3
88.4


16. M_truncatula_CU024868_27_4
89.6
90.3
87.8
88.2
89
89.6
76.7
79.5
77.4
81
85.8
90.7


17. N_benthamiana_TC14122
90.5
88.6
88.6
87.6
88.8
89.8
75.7
79.3
79
79.3
86.1
89.6


18. N_tabacum_TC18263
89.8
90.2
88.9
89.1
89.7
90.8
74.9
78.2
77.4
77.8
85.4
90.2


19. N_tabacum_TC18710
89.1
89.5
88.7
88.7
89.5
90.6
74.9
78.2
77.4
78
85.4
89.5


20. O_lucimarinus_28523
75.6
77.3
77
75.5
77
76.7
83.4
80.6
81.9
80.8
77
78.2


21. O_RCC809_53004
71.8
74.4
74.3
72.2
74
74.2
81.6
77.8
81.5
78.6
73.8
75.1


22. O_sativa_LOC_Os08g41990_1
87.3
87.2
87.7
86.8
87.4
87.7
76.4
78.9
78.9
78.5
94.8
87.7


23. O_taurii_24711
71.4
73.7
73
72.2
73.4
73.6
80.6
76.3
79.1
77.6
73.4
74.6


24. P_patens_116325
82.3
83.1
84.3
82.5
83.9
83.5
80
78.7
80.6
79.7
83.9
84.6


25. P_patens_181992
82.1
83.5
83.7
82.9
83.5
84.2
79.2
78.8
79.2
78.4
82.5
83.1


26. P_tremuloides_575404
95.8
87.8
85.9
85.9
87.1
87.3
73.1
75.1
75.5
76.5
83.1
89


27. P_tricornutum_36347
71.6
75
73.8
72.2
74.2
74.6
74.7
72.4
74.3
76.9
73.6
73.4


28. R_communis_TA2570_3988
93.5
92
91.6
90.3
92.6
92.6
76.7
79.1
77.8
81.4
87.7
93


29. S_lycopersicum_TC191683
89.8
89.4
88.4
87.1
88.4
89.6
74.3
76.6
76.6
76.8
84.6
88.6


30. S_moellendorffii_183248
82.9
84.2
84.7
84.2
84.7
85.5
80.5
81.3
80
82.4
84.7
86.3


31. T_aestivum_TA06MC00384_60074805_384
80.4
80.3
81
81.6
81.6
80.8
74.1
75.2
75.6
76.3
90.9
81


32. T_pseudonana_575
71
73.5
73
71.9
73.4
73.6
73.4
72.6
74.3
77.6
72.7
72.9


33. V_carteri_74470
76.2
78.8
77.2
77.6
78
78.4
97
84.6
88.4
81.7
78.6
79.9


34. V_shuttleworthii_TA2337_246827
92.1
92.2
90.9
90.7
91.5
91.8
78.6
79.9
80.1
82
88.8
93.4


35. Z_mays_ZM07MC17771_BFb0062K01_17727
87.1
87.3
86.7
87.8
87.3
87.6
77
79.1
78.9
78.7
94.1
88.2






13
14
15
16
17
18
19
20
21
22
23
24





 1. ===5613
80.1
79.8
75.6
78.3
79.4
82.1
81.7
62.4
60.8
75.2
58.9
70


 2. A_thaliana_AT3G48730_1
78.7
78.7
77.2
80
82.1
82.9
83.1
65.1
62.9
76.4
59.5
70.3


 3. A_thaliana_AT5G63570_1
77.3
77.1
76.6
76.7
79.8
80.8
81
63.7
62.7
75.5
59.5
70.1


 4. Aquilegia_sp_TC22821
76.8
76.5
77
74.9
77.5
80
79.6
62.9
61.2
75.4
58.5
69.4


 5. B_napus_TC63445
77.7
77.9
77.2
78.7
80.8
81.6
82
63.7
62.8
76.5
59.5
70.1


 6. B_napus_TC63450
77.9
77.7
76.3
77.8
81.2
81.5
82.2
64.9
63.4
76
60.1
69.2


 7. C_reinhardtii_138524
63.8
63.8
66.1
63.5
63.5
61.2
60.7
73.9
71.9
63.8
71
66.6


 8. C_vulgaris_43392
65.2
65.7
68.2
65.7
66.2
64.7
64.7
67.8
66.2
66.7
65.1
66.8


 9. Chlorella_37143
64.1
64.9
68.1
65
67.8
64.9
64.6
73
72.8
66.5
69
67.9


10. E_huxleyi_437052
65.5
66.2
65.7
65.5
65.1
61.3
61.3
68.7
66.9
64.4
64.7
67.8


11. F_arundinacea_TC6452
77.9
77.5
95.6
76.1
77.2
76.6
77.2
65.5
62.8
91.6
62.2
73.7


12. F_vesca_TA11529_57918
80.7
80.4
78.2
79.1
81.5
82.7
82.5
65.2
63.4
76
61.3
73


13. G_max_Glyma04g00420_1

96.4
77.6
88.5
77.3
78.5
78.9
63.7
62.1
77
60.7
70.8


14. G_max_Glyma06g00510_1
98.1

78.2
89.4
77.7
77.3
78.3
64.4
62.7
76.6
61.9
70.5


15. H_vulgare_TC162130
87.7
86.4

76.5
78
77.4
77.6
65.3
63.5
90.4
61.9
73.1


16. M_truncatula_CU024868_27_4
93.2
93.8
87.4

78.1
78.3
78.3
63.6
62.2
75.4
61.5
69.2


17. N_benthamiana_TC14122
87.1
86.7
86.3
87.8
86.1
86.3
63.5
61.4
76.3
59.5
71.6


18. N_tabacum_TC18263
88.3
87.2
86.2
88.3
92.1

97.9
62.2
61.1
77
57.7
69.2


19. N_tabacum_TC18710
88.1
87.2
86
88.3
92.3
99.2

62
61.1
76.9
57.7
69.3


20. O_lucimarinus_28523
76
76.5
77
77.4
75.5
75.3
75.3

85.3
64.2
82.5
64.3


21. O_RCC809_53004
73.2
74
74.6
74.1
72.4
73
73
87.4

61.5
79.7
63.9


22. O_sativa_LOC_Os08g41990_1
86.8
85.8
93.9
85.8
87.6
87
86.6
75.9
73

60.7
73.2


23. O_taurii_24711
72.3
73.2
73.8
74.6
71.6
71.3
71.3
86.6
88.1
73

62.6


24. P_patens_116325
82.3
82.3
84.1
82.3
84.2
81.8
82.7
77.7
76.6
85
75.2



25. P_patens_181992
82.9
82.1
82.9
82.3
84
81.7
82.1
76.5
75.1
83.3
73.3
95.7


26. P_tremuloides_575404
86.7
85.9
84.1
86.3
87.8
86.9
86.3
73.3
69.7
85.3
69.7
80.1


27. P_tricornutum_36347
72.3
73.2
73.6
73.3
72.4
72.8
72.8
73.3
79.1
72.6
73.1
72.9


28. R_communis_TA2570_3988
91.1
90.7
88.6
91.8
90.2
89.7
89.3
77.4
73.4
88.5
73.4
83.5


29. S_lycopersicum_TC191683
86.5
85.9
84.2
86.7
91.9
95.9
95.9
74.1
72
85.1
70.3
81.5


30. S_moellendorffii_183248
82.8
82.8
84.9
83.6
84
84.3
84.1
77.5
75.2
83.9
73.3
86.8


31. T_aestivum_TA06MC00384_60074805_384
81.5
81.8
91.7
81.6
80.7
79.3
79.1
71.9
70.5
87.9
69.9
78.5


32. T_pseudonana_575
71.5
72.7
73.1
72.6
73
72.6
72.4
73.1
79.8
71.3
73.5
72.7


33. V_carteri_74470
76.8
76.6
78.9
77.4
76.6
76.4
76.4
84
82.1
77.6
81.3
80


34. V_shuttleworthii_TA2337_246827
89.6
89.6
88.4
92
90.9
91.2
90.8
78.6
74.2
88.5
74
83.9


35. Z_mays_ZM07MC17771_BFb0062K01_17727
87.6
86.5
94.5
86.5
86.7
86.6
86.6
76.6
73.6
95.8
73.6
85
























25
26
27
28
29
30
31
32
33
34
35







 1. ===5613
69
95.6
58.2
86.3
81.4
71.4
70
57.4
64.9
82.1
76.6



 2. A_thaliana_AT3G48730_1
69.1
79.3
62.3
83.4
80.9
74.1
70
59.3
64.8
80.9
77.8



 3. A_thaliana_AT5G63570_1
68.9
77.5
61
81
80.5
72.7
70.4
58
64.3
81.6
77



 4. Aquilegia_sp_TC22821
68.2
75.6
58.9
80.9
78.4
72.2
70.9
57.4
65.2
80.4
76.9



 5. B_napus_TC63445
68.9
78.1
61.7
81.8
80.7
72.5
70.9
58.8
64.1
82
78.3



 6. B_napus_TC63450
68.6
78.7
61.7
81.8
81.2
73.7
70.3
58.4
64.9
81.8
77.8



 7. C_reinhardtii_138524
66.3
60.6
60.9
63.4
61
67.2
60.8
61.3
92.5
63.8
63.8



 8. C_vulgaris_43392
67.1
61.6
59.8
66.6
64
68.3
62.7
59.2
72.8
66.5
66.5



 9. Chlorella_37143
66.3
63.5
61.7
66.4
65.1
66.6
63.1
62.3
80.7
64.5
66.7



10. E_huxleyi_437052
65.9
62
65.4
66.4
61.4
68.3
61.2
67.5
67.9
65.4
64.3



11. F_arundinacea_TC6452
72.8
73.9
62.2
78.6
76.8
76
87.9
59
66
77.9
89.9



12. F_vesca_TA11529_57918
70.3
80.7
61.3
84.5
80.3
73.7
71.3
60
67.2
84.7
78.3



13. G_max_Glyma04g00420_1
70.1
77.6
59.6
82.1
77.1
72.6
71.8
57.4
64.8
81.7
78.6



14. G_max_Glyma06g00510_1
69.7
77.3
60.5
80.8
76.7
72.1
71.6
58.2
64.9
81.4
78.4



15. H_vulgare_TC162130
72
73.3
62
78.9
76.1
76.4
88.8
59.7
66.7
77.7
90.5



16. M_truncatula_CU024868_27_4
69
76.3
61.1
81.7
77.1
72.5
70
59
64.5
82
76.7



17. N_benthamiana_TC14122
70.4
78.1
61
80.9
85.5
72.9
71.8
58.7
64.9
81.7
77



18. N_tabacum_TC18263
68.2
79.7
59.6
82.3
92.9
73.9
70.5
57.7
63.2
82.5
77.4



19. N_tabacum_TC18710
68.2
79.3
60
81.9
93.4
74.1
70.3
57.1
63
82.3
77.3



20. O_lucimarinus_28523
62.1
60.8
60.6
63.9
61.7
65.8
60.2
61.6
74.2
64.5
64.8



21. O_RCC809_53004
61.9
59
65.7
61.7
61
64.3
57.6
66.4
72.2
62.4
61.6



22. O_sativa_LOC_Os08g41990_1
73
73.7
61.3
77.6
75.8
74.6
83.3
58.2
64.8
76.2
92.1



23. O_taurii_24711
60.3
57.6
55.9
60.1
57.6
60.7
56.9
57
71
61.1
61.1



24. P_patens_116325
89.1
68.7
60.8
71.7
69.4
76.6
68
60.5
66.8
71.9
73.3



25. P_patens_181992

68.1
57.8
69.1
68.6
73.7
67.2
58.8
65.4
70.1
72.7



26. P_tremuloides_575404
81.1

56.4
83.8
80.1
69.9
68.1
55.6
63.3
79.4
74.3



27. P_tricornutum_36347
70.8
69.3

59.6
58.9
62.2
57
83.7
61.4
59.8
61.8



28. R_communis_TA2570_3988
82.1
90.2
72.9

81.2
72.8
72.9
57.9
64.4
85
78.6



29. S_lycopersicum_TC191683
81.7
87.8
71.4
88.8

73.1
69.5
56.6
62.4
81
76.1



30. S_moellendorffii_183248
85.8
79.7
74.4
84.2
83.2

70.5
60.9
67
72.9
74.5



31. T_aestivum_TA06MC00384_60074805_384
76.3
78.5
70.5
82.2
78.2
79.2

55.3
61.4
71.6
82.5



32. T_pseudonana_575
71
68.7
92.7
72.7
71.4
73.3
69.9

61.4
58.4
57.8



33. V_carteri_74470
79
74.1
74.8
78
75.7
80.9
74.6
73.3

65.5
65.3



34. V_shuttleworthii_TA2337_246827
84.4
89
74.2
93.9
90
85.7
82.2
73.8
79.7

77.9



35. Z_mays_ZM07MC17771_BFb0062K01_17727
83.3
84.5
73.4
89.5
84.2
84.5
87.6
71.9
77.4
89.9










A MATGAT table for local alignment of a specific domain, or data on % identity/similarity between specific domains may also be performed.
Example 4
Identification of Domains Comprised in Polypeptide Sequences Useful in Performing the Methods of the Invention
4.1. BET1-Like Polypeptides
The Integrated Resource of Protein Families, Domains and Sites (InterPro) database is an integrated interface for the commonly used signature databases for text- and sequence-based searches. The InterPro database combines these databases, which use different methodologies and varying degrees of biological information about well-characterized proteins to derive protein signatures. Collaborating databases include SWISS-PROT, PROSITE, TrEMBL, PRINTS, Propom and Pfam, Smart and TIGRFAMs. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. Pfam is hosted at the Sanger Institute server in the United Kingdom. Interpro is hosted at the European Bioinformatics Institute in the United Kingdom.
The results of the InterPro scan of the polypeptide sequence as represented by SEQ ID NO: 2 are presented in Table D1.











TABLE D1









Amino acid coordinates



Database
Name
on SEQ ID No 2









TMHMM
Transmembrane region
10-32







TMHMM was first described by Krogh. J Mol Biol. 2001 Jan 19; 305(3): 567-80






4.2. Calreticulin Polypeptides

The Integrated Resource of Protein Families, Domains and Sites (InterPro) database is an integrated interface for the commonly used signature databases for text- and sequence-based searches. The InterPro database combines these databases, which use different methodologies and varying degrees of biological information about well-characterized proteins to derive protein signatures. Collaborating databases include SWISS-PROT, PROSITE, TrEMBL, PRINTS, Propom and Pfam, Smart and TIGRFAMs. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. Pfam is hosted at the Sanger Institute server in the United Kingdom. Interpro is hosted at the European Bioinformatics Institute in the United Kingdom.
The results of the InterPro scan of the polypeptide sequence as represented by SEQ ID NO: 105 are presented in Table D2.







TABLE D2







InterPro scan results (major accession numbers) of the polypeptide sequence as represented by SEQ ID NO: 2.












Domain accession

Amino acid coordinates in



Database
number
Name domain
SEQ ID NO: 2
E-value





InterPro
IPR000886
Endoplasmic reticulum targeting sequence




ScanRegExp
PS00014
ER_TARGET
(406-409]


InterPro
IPR001580
Calreticulin/calnexin


BlastProDom
PD001866
CRTC_NICPL_Q40401;
(141-231]
1.00E−47


FPrintScan
PR00626
Calreticulin
(108-126]; (134-150]; (223-236];
2.9e−55; 2.9e−55;





(251-273]; (289-308]; (322-342]
2.9e−55;


HMMPanther
PTHR11073
Calreticulin AND CALNEXIN
 (66-409]
2.9e−233


HMMPfam
PF00262
Calreticulin
 (29-341]
5.4e−166


ScanRegExp
PS00803
Calreticulin_1
(106-121]
8.00E−05


ScanRegExp
PS00804
Calreticulin_2
(138-146]
8.00E−05


ScanRegExp
PS00805
Calreticulin_REPEAT
(216-228]; (251-263]
8.00E−05


InterPro
IPR008985
Concanavalin A-type lectin/glucanase
A-like
lectin/glucanase


superfamily
SSF49899
Concanavalin lectins/glucanases
 (20-234]; (320-358]
3.8e−80; 0.00015


InterPro
IPR009033
Calreticulin/calnexin,
P


superfamily
SSF63887
P-domain of clanexin/calreticulin
T(213-314]
6.8e−40


InterPro
IPR009169
Calreticulin


HMMPIR
PIRSF002356
Calreticulin
 (6-409]
4.3e−280


HMMPanther
PTHR11073: SF2
Calreticulin
 (66-409]
2.9e−233


InterPro
IPR010916
TonB box, conserved site


ScanRegExp
PS00430
TONB_DEPENDENT_REC_1
 (1-25]
NA


InterPro
IPR013320
Concanavalin A-type lectin/glucanase
A-like




subgroup


Gene3D
G3DSA:2.60.120.200
no description
 (20-239]; (243-368]
1.4e−66; 5.2e−16









When a given domain is present more than one time in the sequence of SEQ ID NO: 105 the amino acid position of the each domain is separated by symbol “;” in the column Amino acid coordinates in SEQ ID NO: 105. Accordingly the e-value for each domain. If only one e-value is indicated it is taken to mean that each of the domains has the same e-value.
4.3. tRNA Dihydrouridine Synthase 1-Like Polypeptides (DUS1L Polypeptides)
The Integrated Resource of Protein Families, Domains and Sites (InterPro) database is an integrated interface for the commonly used signature databases for text- and sequence-based searches. The InterPro database combines these databases, which use different methodologies and varying degrees of biological information about well-characterized proteins to derive protein signatures. Collaborating databases include SWISS-PROT, PROSITE, TrEMBL, PRINTS, Propom and Pfam, Smart and TIGRFAMs. Interpro is hosted at the European Bioinformatics Institute in the United Kingdom.
The results of the InterPro scan of the polypeptide sequence as represented by SEQ ID NO: 259 are presented in Table D3.







TABLE D3







InterPro scan results of the polypeptide sequence as represented by SEQ ID


NO: 259










InterPro accession
Integrated database
Integrated database
Integrated database


number and name
name
accession number
accession name





IPR001269
PANTHER
PTHR11082
tRNA-dihydrouridine


tRNA-dihydrouridine


synthase


synthase family



PFam
PF01207
Dus


IPR013785 Aldolase-
GENE3D
G3DSA:3.20.20.70
No description


type TIM barrel


IPR018517
Prosite
PS01136
UPF0034


tRNA-dihydrouridine


synthase, conserved


site


noIPR unintegrated
Panther
PTHR11082:SF5
tRNA-dihydrouridine





synthase 1



SUPERFAMILY
SSF51395
FMN-linked





oxidoreductases









The TIM barrel is a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone. The structure is named after triosephosphate isomerase, a conserved glycolytic enzyme. TIM barrels are considered α/β protein folds because they include an alternating pattern of α-helices and β-strands in a single domain. In a TIM barrel the helices and strands (usually 8 of each) form a solenoid that curves around to close on itself in a toroid.
4.4. ES43-Like Polypeptides
Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. Pfam is hosted at the Sanger Institute server in the United Kingdom. In order to identify putative BAH and PHD domains in an ES43-like polypeptide, the Pfam database was searched using the amino acid sequence of SEQ ID NO: 299.
The results of the pfam scan of the polypeptide sequence as represented by SEQ ID NO: 299 are presented in Table D4.







TABLE D4







Pfam search results (major accession numbers) of the polypeptide


sequence as represented by SEQ ID NO: 299.















Amino acid







coordinates



Accession
Accession
on SEQ ID

Alignment


Database
number
name
NO 299
Evalue
method















Pfam
BAH domain
PF01426
 21-138
6.1e−4
ls


Pfam
PHD domain
PF00628
142-191
5.3e−17
fs









4.5. HON5-Like Polypeptides

The Integrated Resource of Protein Families, Domains and Sites (InterPro) database is an integrated interface for the commonly used signature databases for text- and sequence-based searches. The InterPro database combines these databases, which use different methodologies and varying degrees of biological information about well-characterized proteins to derive protein signatures. Collaborating databases include SWISS-PROT, PROSITE, TrEMBL, PRINTS, Propom and Pfam, Smart and TIGRFAMs. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. Pfam is hosted at the Sanger Institute server in the United Kingdom. Interpro is hosted at the European Bioinformatics Institute in the United Kingdom.
The results of the InterPro scan of the polypeptide sequence as represented by SEQ ID NO: 388 are presented in Table D5.







TABLE D5







InterPro scan results (major accession numbers) of the polypeptide sequence as represented by SEQ ID NO: 2.















Algorithm/


Location amino



Domain
Name
database
Accession number
Domain name
acid coordinates
E-value





InterPro IPR000637
HMG-I and HMG-Y,
SMART
SM00384
AT_hook
[153-165]T
0.0029



DNA-binding







[209-221]T
8.20E+11







[229-241]T
0.140000007







[244-256]T
0.149999998







[260-272]T
0.008099998







[301-313]T
0.014000001







[325-337]T
0.079000004







[347-359]T
0.0019


InterPro IPR005818
histone H1/H5
PFAM
PF00538
Linker_histone
[47-116]T
5.30E−14


InterPro IPR011991
Winged helix repressor
GENE3D
G3DSA 1.10.10.10
Wing_hlx_DNA_bd
[42-127]T
1.30E+03



DNA-binding









4.6. glutamate-1-semialdehyde aminotransferase polypeptides (GSA1 polypeptides)

The Integrated Resource of Protein Families, Domains and Sites (InterPro) database is an integrated interface for the commonly used signature databases for text- and sequence-based searches. The InterPro database combines these databases, which use different methodologies and varying degrees of biological information about well-characterized proteins to derive protein signatures. Collaborating databases include SWISS-PROT, PROSITE, TrEMBL, PRINTS, Propom and Pfam, Smart and TIGRFAMs. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. Pfam is hosted at the Sanger Institute server in the United Kingdom. Interpro is hosted at the European Bioinformatics Institute in the United Kingdom.
The results of the InterPro scan of the polypeptide sequence as represented by SEQ ID NO: 418 are presented in Table D6.







TABLE D6







InterPro scan results (major accession numbers) of the polypeptide sequence as


represented by SEQ ID NO: 418.











AA start
AA stop
















Gene3D
G3DSA:3.40.640.10
no description
123
371
2.7e−74 


HMMPanther
PTHR11986:SF5
glutamate-1-
75
479
7.2e−236




semialdehyde 2,1-




aminomutase


HMMPanther
PTHR11986
aminotransferase
75
479
7.2e−236




Class III


superfamily
SSF53383
PLP-dependent
53
479
3.3e−123




transferases


HMMPfam
PF00202
Aminotran_3
89
388
3.5e−71 


ScanRegExp
PS00600
AA_transfer_Class_3
288
324
8.00e−5  


HMMTigr
TIGR00713
hemL: glutamate-1-
57
479
1.8e−247




semialdehyde 2,1-




aminomut









Example 5
Topology Prediction of the Polypeptide Sequences Useful in Performing the Methods of the Invention
5.1. BET1-Like Polypeptides
TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal pre-sequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). Scores on which the final prediction is based are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class) may be an indication of how certain the prediction is. The reliability class (RC) ranges from 1 to 5, where 1 indicates the strongest prediction. TargetP is maintained at the server of the Technical University of Denmark.
For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted.
A number of parameters is selected, such as organism group (non-plant or plant), cutoff sets (none, predefined set of cutoffs, or user-specified set of cutoffs), and the calculation of prediction of cleavage sites (yes or no).
5.2. Calreticulin Polypeptides
TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal pre-sequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). Scores on which the final prediction is based are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class) may be an indication of how certain the prediction is. The reliability class (RC) ranges from 1 to 5, where 1 indicates the strongest prediction. TargetP is maintained at the server of the Technical University of Denmark.
For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted.
A number of parameters are selected, such as organism group (non-plant or plant), cutoff sets (none, predefined set of cutoffs, or user-specified set of cutoffs), and the calculation of prediction of cleavage sites (yes or no).
Many other algorithms can be used to perform such analyses, including:

    
    
        ChloroP 1.1 hosted on the server of the Technical University of Denmark;
        Protein Prowler Subcellular Localisation Predictor version 1.2 hosted on the server of the Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia;
        PENCE Proteome Analyst PA-GOSUB 2.5 hosted on the server of the University of Alberta, Edmonton, Alberta, Canada;
        TMHMM, hosted on the server of the Technical University of Denmark
        PSORT (URL: psort.org)
        PLOC (Park and Kanehisa, Bioinformatics, 19, 1656-1663, 2003).

5.3. ES43-Like Polypeptides

    
    


TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal pre-sequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). Scores on which the final prediction is based are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class) may be an indication of how certain the prediction is. The reliability class (RC) ranges from 1 to 5, where 1 indicates the strongest prediction. TargetP is maintained at the server of the Technical University of Denmark.
For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted.
A number of parameters is selected, such as organism group (non-plant or plant), cutoff sets (none, predefined set of cutoffs, or user-specified set of cutoffs), and the calculation of prediction of cleavage sites (yes or no).
5.4. HON5-Like Polypeptides
TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal pre-sequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). Scores on which the final prediction is based are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class) may be an indication of how certain the prediction is. The reliability class (RC) ranges from 1 to 5, where 1 indicates the strongest prediction. TargetP is maintained at the server of the Technical University of Denmark.
For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted.
A number of parameters is selected, such as organism group (non-plant or plant), cutoff sets (none, predefined set of cutoffs, or user-specified set of cutoffs), and the calculation of prediction of cleavage sites (yes or no).
Many other algorithms can be used to perform such analyses, including:

    
    
        ChloroP 1.1 hosted on the server of the Technical University of Denmark;
        Protein Prowler Subcellular Localisation Predictor version 1.2 hosted on the server of the Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia;
        PENCE Proteome Analyst PA-GOSUB 2.5 hosted on the server of the University of Alberta, Edmonton, Alberta, Canada;
        TMHMM, hosted on the server of the Technical University of Denmark
        PSORT (URL: psort.org)
        PLOC (Park and Kanehisa, Bioinformatics, 19, 1656-1663, 2003).

5.5. glutamate-1-semialdehyde aminotransferase polypeptides (GSA1 polypeptides)

    
    


TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal pre-sequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). Scores on which the final prediction is based are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class) may be an indication of how certain the prediction is. The reliability class (RC) ranges from 1 to 5, where 1 indicates the strongest prediction. TargetP is maintained at the server of the Technical University of Denmark.
For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted.
A number of parameters are selected, such as organism group (non-plant or plant), cutoff sets (none, predefined set of cutoffs, or user-specified set of cutoffs), and the calculation of prediction of cleavage sites (yes or no).
The results of TargetP 1.1 analysis of the polypeptide sequence as represented by SEQ ID NO: 418 are presented Table D7. The “plant” organism group has been selected, no cutoffs defined, and the predicted length of the transit peptide requested. The subcellular localization of the polypeptide sequence as represented by SEQ ID NO: 418 is predicted to be the chloroplast, no transit peptide is predicted.















TABLE D7





Name
Len
cTP
mTP
SP
other
Loc
RC
TPlen







CDS5613
479
0.880
0.257
0.050
0.031
C
2
43


cutoff

0.000
0.000
0.000
0.000









Many other algorithms can be used to perform such analyses, including:

    
    
        ChloroP 1.1 hosted on the server of the Technical University of Denmark;
        Protein Prowler Subcellular Localisation Predictor version 1.2 hosted on the server of the Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia;
        PENCE Proteome Analyst PA-GOSUB 2.5 hosted on the server of the University of Alberta, Edmonton, Alberta, Canada;
        TMHMM, hosted on the server of the Technical University of Denmark
        PSORT (URL: psort.org)
        PLOC (Park and Kanehisa, Bioinformatics, 19, 1656-1663, 2003).
    
    


Example 6
Subcellular Localisation Prediction of the Polypeptide Sequences Useful in Performing the Methods of the Invention
6.1 tRNA Dihydrouridine Synthase 1-Like Polypeptides (DUS1L Polypeptides)
Experimental methods for protein localization range from immunolocalization to tagging of proteins using green fluorescent protein (GFP) or beta-glucuronidase (GUS). Such methods to identify subcellular compartmentalisation of GRF polypeptides are well known in the art.
Computational prediction of protein localisation from sequence data was performed. Among algorithms well known to a person skilled in the art are available at the ExPASy Proteomics tools hosted by the Swiss Institute for Bioinformatics, for example, PSort, TargetP, ChloroP, LocTree, Predotar, LipoP, MITOPROT, PATS, PTS1, SignalP, TMHMM, TMpred, and others.
TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal pre-sequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). Scores on which the final prediction is based are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class) may be an indication of how certain the prediction is. The reliability class (RC) ranges from 1 to 5, where 1 indicates the strongest prediction. TargetP is maintained at the server of the Technical University of Denmark.
For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted.
A number of parameters were selected, such as organism group (non-plant or plant), cutoff sets (none, predefined set of cutoffs, or user-specified set of cutoffs), and the calculation of prediction of cleavage sites (yes or no).
The results of TargetP 1.1 analysis of the polypeptide sequence as represented by SEQ ID NO: 259 are presented Table E1. The “plant” organism group has been selected, and no cutoffs defined. The subcellular localization of the polypeptide sequence as represented by SEQ ID NO: 259 is mitochondria.







TABLE E1





TargetP 1.1 analysis of the polypeptide sequence as represented


by SEQ ID NO: 259


















Length (AA)
421



Chloroplastic transit peptide
0.026



Mitochondrial transit peptide
0.947



Secretory pathway signal peptide
0.008



Other subcellular targeting
0.075



Predicted Location
Mitochondria



Reliability class
1










Methods for targeting to mitochondria are well known in the art and include the use of mitochondrial transit peptides. Mitochondrial transit peptides which can be used to target any DUS1L polypeptide to a mitochondria, which DUS1L polypeptide is not, in its natural form, normally targeted to a mitochondria, or which DUS1L polypeptide in its natural form is targeted to mitochondria by virtue of a different transit peptide (for example, its natural transit peptide). For example, a nucleic acid sequence encoding a cyanobacterial or diatom DUS1L polypeptide may also be suitable for use in the methods of the invention so long as the polypeptide is targeted to mitochondria.
Example 7
Assay Related to the Polypeptide Sequences Useful in Performing the Methods of the Invention
7.1. tRNA Dihydrouridine Synthase 1-Like Polypeptides (DUS1L Polypeptides)
DUS1L polypeptides useful in the methods of the present invention (at least in their native form) typically, but not necessarily, have tRNA dihydrouridine synthase (DUS) activity. In vivo DUS-complementation assays are typically used, for example in bacteria or in yeast. An E. coli strain from which all three DUS genes have been deleted (D3dus), and, consequently, produces tRNA with no detectable dihydrouridine, is commonly used. The dihydrouridine-free strain thus acts as a “zero background” for testing the ability of DUS genes to catalyze dihydrouridine formation in living cells. By introducing into this strain plasmid-borne DUS genes, it is possible to measure reconstituted the tRNA's dihydrouridine content in tRNA purified from this strain (Bishop et al. (2002) supra).
Colorimetric measurement of tRNA dihyrouridine content is also possible, by an adaptation of the method of Jacobson and Hedgcoth ((1970) Anal Biochem 34, 459-469).
Example 8
Cloning of the Nucleic Acid Sequence Used in the Methods of the Invention
8.1. BET1-Like Polypeptides
The nucleic acid sequence used in the methods of the invention was amplified by PCR using as template a custom-made Arabidopsis thaliana seedlings cDNA library (in pCMV Sport 6.0; Invitrogen, Paisley, UK). PCR was performed using Hifi Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μl PCR mix.
The primers used were a first oligonucleotide as represented by SEQ ID NO: 101; for the sense orientation and a second oligonucleotide as represented by SEQ ID NO: 102 for the reverse, complementary strand which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombined in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pBET1_ike. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.
The entry clone comprising SEQ ID NO: 1 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ ID NO: 103) for constitutive specific expression was located upstream of this Gateway cassette.
After the LR recombination step, the resulting expression vector pGOS2:BET1-like (FIG. 3) was transformed into Agrobacterium strain LBA4044 according to methods well known in the art.
8.2. Calreticulin Polypeptides
The nucleic acid sequence used in the methods of the invention was amplified by PCR using as template a custom-made Lycopersicum esculentum or populus trichoparca seedlings cDNA library (in pCMV Sport 6.0; Invitrogen, Paisley, UK). PCR was performed using Hifi Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μl PCR mix. The primers used were
For S.lycopersicum_TA36564:








SEQ ID NO: 253 (sense, start codon in bold):



5′-ggggacaagtttgtacaaaaaagcaggcttaaacaatggctactcgacgaatgaaa-3′


and


 


SEQ ID NO: 254 (reverse, complementary):


5′-ggggaccactttgtacaagaaagctgggttgaatcaaaatgcttggctct-3′,






For P.trichocarpa—133.107:








SEQ ID NO: 255 (sense, start codon in bold):



5′-ggggacaagtttgtacaaaaaagcaggcttaaacaatgggaaaccctaaaactctc-3′


and


 


SEQ ID NO: 256 (reverse, complementary):


5′-ggggaccactttgtacaagaaagctgggtaagagtgcttcctcatcacag-3′;






which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombined in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pCalreticulin. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.

The entry clone comprising SEQ ID NO: 104 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ ID NO: 257) for constitutive specific expression was located upstream of this Gateway cassette.
After the LR recombination step, the resulting expression vector pGOS2::Calreticulin (FIG. 6) was transformed into Agrobacterium strain LBA4044 according to methods well known in the art.
8.3. tRNA Dihydrouridine Synthase 1-Like Polypeptides (DUS1L Polypeptides)
The Saccharum officinarum nucleic acid sequence encoding a DUS1L polypeptide sequence as represented by SEQ ID NO: 2 was amplified by PCR using as template a cDNA bank constructed using RNA from tomato plants at different developmental stages. The following primers, which include the AttB sites for Gateway recombination, were used for PCR amplification: prm08359 (SEQ ID NO: 296, sense): 5′-ggggacaagtttgtacaaaaaagcaggcttaaacaatgccactgcgcc-3′ and prm08360 (SEQ ID NO: 297, reverse, complementary): 5′-ggggaccactttgtacaagaaagctgggtcctgtcaggcattgc-3′
PCR was performed using Hifi Taq DNA polymerase in standard conditions. A PCR fragment of the expected length (including attB sites) was amplified and purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombined in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.
The entry clone comprising SEQ ID NO: 258 was subsequently used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ ID NO: 295) for constitutive expression was located upstream of this Gateway cassette.
After the LR recombination step, the resulting expression vector pGOS2::DUS1L (FIG. 10) for constitutive expression, was transformed into Agrobacterium strain LBA4044 according to methods well known in the art.
8.4. ES43-Like Polypeptides
The nucleic acid sequence used in the methods of the invention was amplified by PCR using as template a custom-made Oryza sativa seedlings cDNA library (in pCMV Sport 6.0; Invitrogen, Paisley, UK). PCR was performed using Hifi Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μl PCR mix. The primers used were (SEQ ID NO: 384; sense): 5′-ggggacaagtttgtacaaaaaagcaggcttaaacaatggcgaagtcgcgg-3′ and (SEQ ID NO: 385; reverse, complementary): 5′-ggggaccactttgtacaagaaagctgggttccaggtgtatctcgtcaatg-3′, which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombined in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pES43-like. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.
The entry clone comprising SEQ ID NO: 298 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ ID NO: 386) for constitutive specific expression was located upstream of this Gateway cassette.
After the LR recombination step, the resulting expression vector pGOS2::ES43-like (FIG. 13) was transformed into Agrobacterium strain LBA4044 according to methods well known in the art.
8.5. HON5-Like Polypeptides
The nucleic acid sequence used in the methods of the invention was amplified by PCR using as template a custom-made Populus trichocarpa seedlings cDNA library (in pCMV Sport 6.0; Invitrogen, Paisley, UK). PCR was performed using Hifi Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μl PCR mix. The primers used were (SEQ ID NO: 414; sense, start codon in bold): 5′-ggggacaagtttgtacaaaaaagcaggcttaaacaatg gacccaccacctcct-3′ and (SEQ ID NO: 415; reverse, complementary): 5′-ggggaccactttgtac aagaaagctgggtggaacaaattcatgatcctcg-3′, which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombined in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pHON5-like. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.
The entry clone comprising SEQ ID NO: 387 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ ID NO: 416) for constitutive specific expression was located upstream of this Gateway cassette.
After the LR recombination step, the resulting expression vector pGOS2::HON5-like (FIG. 15) was transformed into Agrobacterium strain LBA4044 according to methods well known in the art.
8.6. glutamate-1-semialdehyde aminotransferase polypeptides (GSA1 polypeptides)
The nucleic acid sequence used in the methods of the invention was amplified by PCR using as template a custom-made populus cDNA library (in pCMV Sport 6.0; Invitrogen, Paisley, UK). PCR was performed using Hifi Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μl PCR mix. The primers used were (SEQ ID NO: 490; sense, start codon in bold): prm(fwd) 5′-ggggacaagtttgtacaaaaaagcaggcttaaacaatggcttctacaa tcacagga-3′ and (SEQ ID NO: 491; reverse, complementary): prm(rev) 5′-ggggaccactttgtacaagaaagctgggtcaacaatcacacagcgagata-3′ which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombined in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an “entry clone”, pGSA1. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.
The entry clone comprising SEQ ID NO: 417 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ ID NO: 492) for constitutive specific expression was located upstream of this Gateway cassette.
After the LR recombination step, the resulting expression vector pGOS2::GSA1 (FIG. 18) was transformed into Agrobacterium strain LBA4044 according to methods well known in the art.
Example 9
Plant Transformation
Rice Transformation
The Agrobacterium containing the expression vector was used to transform Oryza sativa plants. Mature dry seeds of the rice japonica cultivar Nipponbare were dehusked. Sterilization was carried out by incubating for one minute in 70% ethanol, followed by 30 minutes in 0.2% HgCl2, followed by a 6 times 15 minutes wash with sterile distilled water. The sterile seeds were then germinated on a medium containing 2,4-D (callus induction medium). After incubation in the dark for four weeks, embryogenic, scutellum-derived calli were excised and propagated on the same medium. After two weeks, the calli were multiplied or propagated by subculture on the same medium for another 2 weeks. Embryogenic callus pieces were sub-cultured on fresh medium 3 days before co-cultivation (to boost cell division activity).
Agrobacterium strain LBA4404 containing the expression vector was used for co-cultivation. Agrobacterium was inoculated on AB medium with the appropriate antibiotics and cultured for 3 days at 28° C. The bacteria were then collected and suspended in liquid co-cultivation medium to a density (OD600) of about 1. The suspension was then transferred to a Petri dish and the calli immersed in the suspension for 15 minutes. The callus tissues were then blotted dry on a filter paper and transferred to solidified, co-cultivation medium and incubated for 3 days in the dark at 25° C. Co-cultivated calli were grown on 2,4-D-containing medium for 4 weeks in the dark at 28° C. in the presence of a selection agent. During this period, rapidly growing resistant callus islands developed. After transfer of this material to a regeneration medium and incubation in the light, the embryogenic potential was released and shoots developed in the next four to five weeks. Shoots were excised from the calli and incubated for 2 to 3 weeks on an auxin-containing medium from which they were transferred to soil. Hardened shoots were grown under high humidity and short days in a greenhouse.
Approximately 35 independent TO rice transformants were generated for one construct. The primary transformants were transferred from a tissue culture chamber to a greenhouse. After a quantitative PCR analysis to verify copy number of the T-DNA insert, only single copy transgenic plants that exhibit tolerance to the selection agent were kept for harvest of T1 seed. Seeds were then harvested three to five months after transplanting. The method yielded single locus transformants at a rate of over 50% (Aldemita and Hodges1996, Chan et al. 1993, Hiei et al. 1994).
Example 10
Transformation of Other Crops
Corn Transformation
Transformation of maize (Zea mays) is performed with a modification of the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. Transformation is genotype-dependent in corn and only specific genotypes are amenable to transformation and regeneration. The inbred line A188 (University of Minnesota) or hybrids with A188 as a parent are good sources of donor material for transformation, but other genotypes can be used successfully as well. Ears are harvested from corn plant approximately 11 days after pollination (DAP) when the length of the immature embryo is about 1 to 1.2 mm. Immature embryos are cocultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. Excised embryos are grown on callus induction medium, then maize regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to maize rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.
Wheat Transformation
Transformation of wheat is performed with the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. The cultivar Bobwhite (available from CIMMYT, Mexico) is commonly used in transformation. Immature embryos are co-cultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. After incubation with Agrobacterium, the embryos are grown in vitro on callus induction medium, then regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25° C. for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to rooting medium and incubated at 25° C. for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.
Soybean Transformation
Soybean is transformed according to a modification of the method described in the Texas A&M U.S. Pat. No. 5,164,310. Several commercial soybean varieties are amenable to transformation by this method. The cultivar Jack (available from the Illinois Seed foundation) is commonly used for transformation. Soybean seeds are sterilised for in vitro sowing. The hypocotyl, the radicle and one cotyledon are excised from seven-day old young seedlings. The epicotyl and the remaining cotyledon are further grown to develop axillary nodes. These axillary nodes are excised and incubated with Agrobacterium tumefaciens containing the expression vector. After the cocultivation treatment, the explants are washed and transferred to selection media. Regenerated shoots are excised and placed on a shoot elongation medium. Shoots no longer than 1 cm are placed on rooting medium until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.
Rapeseed/Canola Transformation
Cotyledonary petioles and hypocotyls of 5-6 day old young seedling are used as explants for tissue culture and transformed according to Babic et al. (1998, Plant Cell Rep 17: 183-188). The commercial cultivar Westar (Agriculture Canada) is the standard variety used for transformation, but other varieties can also be used. Canola seeds are surface-sterilized for in vitro sowing. The cotyledon petiole explants with the cotyledon attached are excised from the in vitro seedlings, and inoculated with Agrobacterium (containing the expression vector) by dipping the cut end of the petiole explant into the bacterial suspension. The explants are then cultured for 2 days on MSBAP-3 medium containing 3 mg/l BAP, 3% sucrose, 0.7% Phytagar at 23° C., 16 hr light. After two days of co-cultivation with Agrobacterium, the petiole explants are transferred to MSBAP-3 medium containing 3 mg/l BAP, cefotaxime, carbenicillin, or timentin (300 mg/l) for 7 days, and then cultured on MSBAP-3 medium with cefotaxime, carbenicillin, or timentin and selection agent until shoot regeneration. When the shoots are 5-10 mm in length, they are cut and transferred to shoot elongation medium (MSBAP-0.5, containing 0.5 mg/l BAP). Shoots of about 2 cm in length are transferred to the rooting medium (MSO) for root induction. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.
Alfalfa Transformation
A regenerating clone of alfalfa (Medicago sativa) is transformed using the method of (McKersie et al., 1999 Plant Physiol 119: 839-847). Regeneration and transformation of alfalfa is genotype dependent and therefore a regenerating plant is required. Methods to obtain regenerating plants have been described. For example, these can be selected from the cultivar Rangelander (Agriculture Canada) or any other commercial alfalfa variety as described by Brown D C W and A Atanassov (1985. Plant Cell Tissue Organ Culture 4: 111-112). Alternatively, the RA3 variety (University of Wisconsin) has been selected for use in tissue culture (Walker et al., 1978 Am J Bot 65:654-659). Petiole explants are cocultivated with an overnight culture of Agrobacterium tumefaciens C58C1 pMP90 (McKersie et al., 1999 Plant Physiol 119: 839-847) or LBA4404 containing the expression vector. The explants are cocultivated for 3 d in the dark on SH induction medium containing 288 mg/L Pro, 53 mg/L thioproline, 4.35 g/L K2SO4, and 100 μm acetosyringinone. The explants are washed in half-strength Murashige-Skoog medium (Murashige and Skoog, 1962) and plated on the same SH induction medium without acetosyringinone but with a suitable selection agent and suitable antibiotic to inhibit Agrobacterium growth. After several weeks, somatic embryos are transferred to BOi2Y development medium containing no growth regulators, no antibiotics, and 50 g/L sucrose. Somatic embryos are subsequently germinated on half-strength Murashige-Skoog medium. Rooted seedlings were transplanted into pots and grown in a greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.
Cotton Transformation
Cotton is transformed using Agrobacterium tumefaciens according to the method described in U.S. Pat. No. 5,159,135. Cotton seeds are surface sterilised in 3% sodium hypochlorite solution during 20 minutes and washed in distilled water with 500 μg/ml cefotaxime. The seeds are then transferred to SH-medium with 50 μg/ml benomyl for germination. Hypocotyls of 4 to 6 days old seedlings are removed, cut into 0.5 cm pieces and are placed on 0.8% agar. An Agrobacterium suspension (approx. 108 cells per ml, diluted from an overnight culture transformed with the gene of interest and suitable selection markers) is used for inoculation of the hypocotyl explants. After 3 days at room temperature and lighting, the tissues are transferred to a solid medium (1.6 g/l Gelrite) with Murashige and Skoog salts with B5 vitamins (Gamborg et al., Exp. Cell Res. 50:151-158 (1968)), 0.1 mg/l 2,4-D, 0.1 mg/l 6-furfurylaminopurine and 750 μg/ml MgCL2, and with 50 to 100 μg/ml cefotaxime and 400-500 μg/ml carbenicillin to kill residual bacteria. Individual cell lines are isolated after two to three months (with subcultures every four to six weeks) and are further cultivated on selective medium for tissue amplification (30° C., 16 hr photoperiod). Transformed tissues are subsequently further cultivated on non-selective medium during 2 to 3 months to give rise to somatic embryos. Healthy looking embryos of at least 4 mm length are transferred to tubes with SH medium in fine vermiculite, supplemented with 0.1 mg/l indole acetic acid, 6 furfurylaminopurine and gibberellic acid. The embryos are cultivated at 30° C. with a photoperiod of 16 hrs, and plantlets at the 2 to 3 leaf stage are transferred to pots with vermiculite and nutrients. The plants are hardened and subsequently moved to the greenhouse for further cultivation.
Example 11
Phenotypic Evaluation Procedure
11.1 Evaluation Setup
Approximately 35 independent TO corn transformants were generated. The primary transformants were transferred from a tissue culture chamber to a greenhouse for growing and harvest of T1 seed. Events, of which the T1 progeny segregated 3:1 for presence/absence of the transgene, were retained. For each of these events, approximately 10 T1 seedlings containing the transgene (hetero- and homo-zygotes) and approximately 10 T1 seedlings lacking the transgene (nullizygotes) were selected by monitoring visual marker expression. The transgenic plants and the corresponding nullizygotes were grown side-by-side at random positions. Greenhouse conditions were of shorts days (12 hours light), 28° C. in the light and 22° C. in the dark, and a relative humidity of 70%. Plants grown under non-stress conditions were watered at regular intervals to ensure that water and nutrients were not limiting and to satisfy plant needs to complete growth and development.
In some instances T1 events were further evaluated in the T2 generation following the same evaluation procedure as for the T1 generation but with more individuals per event. From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.
Drought Screen
Plants from T1 seeds were grown in potting soil under normal conditions until they approached the heading stage. They were then transferred to a “dry” section where irrigation was withheld. Humidity probes was inserted in randomly chosen pots to monitor the soil water content (SWC). When SWC went below certain thresholds, the plants were automatically re-watered continuously until a normal level was reached again. The plants were then re-transferred again to normal conditions. The rest of the cultivation (plant maturation, seed harvest) was the same as for plants not grown under abiotic stress conditions. Growth and yield parameters were recorded as detailed for growth under normal conditions.
Reduced Nutrient (Nitrogen) Availability Screen
Plants from six events (T2 seeds) were grown in potting soil under normal conditions except for the nutrient solution. The pots were watered from transplantation to maturation with a specific nutrient solution containing reduced N nitrogen (N) content, usually between 7 to 8 times less. The rest of the cultivation (plant maturation, seed harvest) was the same as for plants not grown under abiotic stress. Growth and yield parameters were recorded as detailed for growth under normal conditions.
Salt Stress Screen
Plants are grown on a substrate made of coco fibers and argex (3 to 1 ratio). A normal nutrient solution is used during the first two weeks after transplanting the plantlets in the greenhouse. After the first two weeks, 25 mM of salt (NaCl) is added to the nutrient solution, until the plants are harvested. Seed-related parameters are then measured.
11.2 Statistical Analysis: F Test
A two factor ANOVA (analysis of variants) was used as a statistical model for the overall evaluation of plant phenotypic characteristics. An F test was carried out on all the parameters measured of all the plants of all the events transformed with the gene of the present invention. The F test was carried out to check for an effect of the gene over all the transformation events and to verify for an overall effect of the gene, also known as a global gene effect. The threshold for significance for a true global gene effect was set at a 5% probability level for the F test. A significant F test value points to a gene effect, meaning that it is not only the mere presence or position of the gene that is causing the differences in phenotype.
Where two experiments with overlapping events were carried out, a combined analysis was performed. This is useful to check consistency of the effects over the two experiments, and if this is the case, to accumulate evidence from both experiments in order to increase confidence in the conclusion. The method used was a mixed-model approach that takes into account the multilevel structure of the data (i.e. experiment-event-segregants). P values were obtained by comparing likelihood ratio test to chi square distributions.
11.3 Parameters Measured
Biomass-Related Parameter Measurement
From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048×1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles.
The plant aboveground area (or leafy biomass) was determined by counting the total number of pixels on the digital images from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from the different angles and was converted to a physical surface value expressed in square mm by calibration. Experiments show that the aboveground plant area measured this way correlates with the biomass of plant parts above ground. The above ground area is the area measured at the time point at which the plant had reached its maximal leafy biomass. The early vigour is the plant (seedling) aboveground area three weeks post-germination. Increase in root biomass is expressed as an increase in total root biomass (measured as maximum biomass of roots observed during the lifespan of a plant); or as an increase in the root/shoot index (measured as the ratio between root mass and shoot mass in the period of active growth of root and shoot).
Early vigour was determined by counting the total number of pixels from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from different angles and was converted to a physical surface value expressed in square mm by calibration. The results described below are for plants three weeks post-germination.
Seed-Related Parameter Measurements
The mature primary panicles were harvested, counted, bagged, barcode-labelled and then dried for three days in an oven at 37° C. The panicles were then threshed and all the seeds were collected and counted. The filled husks were separated from the empty ones using an air-blowing device. The empty husks were discarded and the remaining fraction was counted again. The filled husks were weighed on an analytical balance. The number of filled seeds was determined by counting the number of filled husks that remained after the separation step. The total seed yield was measured by weighing all filled husks harvested from a plant. Total seed number per plant was measured by counting the number of husks harvested from a plant. Thousand Kernel Weight (TKW) is extrapolated from the number of filled seeds counted and their total weight. The Harvest Index (HI) in the present invention is defined as the ratio between the total seed yield and the above ground area (mm2), multiplied by a factor 106. The total number of flowers per panicle as defined in the present invention is the ratio between the total number of seeds and the number of mature primary panicles. The seed fill rate as defined in the present invention is the proportion (expressed as a %) of the number of filled seeds over the total number of seeds (or florets).
Example 12
Results of the Phenotypic Evaluation of the Transgenic Plants
12.1. BET1-Like Polypeptides
The results of the evaluation of transgenic rice plants in the T2 generation and expressing a nucleic acid comprising the longest Open Reading Frame in SEQ ID NO: 1 under non-stress conditions are presented below. See previous Examples for details on the generations of the transgenic plants.
The results of the evaluation of transgenic rice plants under non-stress conditions are presented below. An increase of more than 5% was observed for total seed yield per plant (totalwgseeds), number of filled seeds per plant (nrfilledseed), number of total seeds per plant (nrtotalseed), seed filing rate per plant (fillrate) and harvest index (harvestindex) (Table F1).







TABLE F1







Non-Stress conditions











% increase in transgenic



Yield related trait
compared to control plant














totalwgseeds
19.1



nrtotalseed
10.3



fillrate
11.5



harvestindex
13.3



nrfilledseed
23.6










The results of the evaluation of transgenic rice plants in T1 generation which are expressing a BET1-like nucleic acid according to SEQ ID NO: 1 under drought-stress conditions are presented hereunder. An increase was observed for total aboveground biomass (AreaMax) per plant, number of total seeds per plant (nrtotalseed) and seed filing rate per plat (fillrate) (Table F2).







TABLE F2







Drought Screen











% increase in transgenic



Yield related trait
compared to control plant














AreaMax
6.7



nrtotalseed
7.7



nrfilledseed
12.7










12.2. Calreticulin Polypeptides

The results of the evaluation of transgenic rice plants transformed with in the T1 generation and expressing a nucleic acid comprising the longest Open Reading Frame in SEQ ID NO: 104 under non-stress conditions are presented below. See previous Examples for details on the generations of the transgenic plants.
An increase of at least 5% was observed for the total seed yield (totalwgseeds), number of filled seeds (nrfilledseed), fill rate (fillrate), number of flowers per panicle (flowerperpan), harvest index (harvestindex), and of the total number of seeds (nrtotalseed) (Table F3).










TABLE F3







Parameters
Overall



















totalwgseeds
22.5



nrfilledseed
17.4



fillrate
10.6



flowerperpan
15.4



harvestindex
20.4



nrtotalseed
7.9










The results of the evaluation of transgenic rice plants transformed with in the T1 generation and expressing a nucleic acid comprising the longest Open Reading Frame in SEQ ID NO: 168 under non-stress conditions are presented below (Table F4). See previous Examples for details on the generations of the transgenic plants.
An increase of at least 5% was observed for the fill rate (fillrate).










TABLE F4







Parameters
Overall









fillrate
11.3










12.3. tRNA Dihydrouridine Synthase 1-Like Polypeptides (DUS1L Polypeptides)

The results of the evaluation of T2 generation transgenic rice plants expressing the nucleic acid sequence encoding a DUS1L polypeptide as represented by SEQ ID NO: 259, under the control of a constitutive promoter, and grown under nitrogen limiting conditions, are presented below.
There was a significant increase in aboveground biomass, seed yield per plant, number of filled seeds, and total number of seeds.







TABLE F5







Results of the evaluation of T2 generation transgenic rice plants expressing


the nucleic acid sequence encoding a DUS1L polypeptide as represented


by SEQ ID NO: 259, under the control of a promoter for constitutive


expression.











Overall average % increase in



Trait
4 events in the T2 generation














Plant aboveground biomass
6%



Total seed yield per plant
10%



Number of filled seeds
6%



Total number of seeds
10%










12.4. ES43-Like Polypeptides

The results of the evaluation of transgenic rice plants in the T2 generation and expressing a nucleic acid comprising the longest Open Reading Frame in SEQ ID NO: 298 under non-stress conditions are presented below. See previous Examples for details on the generations of the transgenic plants (Table F6).










TABLE F6








% increase in transgenic




plants compared to



Yield trait
control nullizygous plants









fillrate (seed filling rate)
7.0










Fillrate was calculated as a proportion (expressed as %) of the number of filled seeds over the number of seeds in the panicles of a plant.
12.5. HON5-Like Polypeptides
The results of the evaluation of transgenic rice plants in the T2 generation and expressing a nucleic acid comprising the longest Open Reading Frame in SEQ ID NO: 387 under non-stress conditions are presented below. See previous Examples for details on the generations of the transgenic plants.
The results of the evaluation of transgenic rice plants under non-stress conditions are presented below (Table F7). An increase of more than 5% was observed for total seed yield (totalwgseeds), number of filled seeds (nrfilledseed), fill rate (fillrate) harvest index (harvestindex), and of at least 2.5 for thousand kernel weight










TABLE F7








% increase in transgenic plant



Yield-related trait
compared to control plant



















totalwgseeds
10.6



nrfilledseed
8.9



fillrate
14.8



harvestindex
9.3










12.6. glutamate-1-semialdehyde aminotransferase polypeptides (GSA1 polypeptides)

The results of the evaluation of transgenic rice plants in the T1 and T2 generations and expressing a nucleic acid comprising the longest Open Reading Frame in SEQ ID NO: 417 under drought stress conditions is presented below.
T1:














Parameter
Overall



















Total weight seeds
20.9



Fill rate
26.3



Harvest index
22.7



Number filled seed
22.6










T2:















Parameter
Overall



















Total weight seeds
59.7



Fill rate
55.8



Harvest index
59.9



TKW
5.7



Number filled seed
50.6



Flower per pan
14.5



GravityY Max
6.4



Root Thick Max
5.0

## Claims

1. A method for enhancing a yield-related trait in a plant relative to a corresponding control plant, comprising transforming and expressing in the plant a nucleic acid encoding a Calreticulin polypeptide comprising the amino acid sequence of SEQ ID NO: 105, wherein the introduction of said nucleic acid results in an enhanced yield-related trait relative to a control plant.

2. The method of claim 1, wherein the nucleic acid comprises the nucleotide sequence of SEQ ID NO:104.

3. The method of claim 1, wherein said enhanced yield-related trait comprises increased yield, increased seed yield, increased seed yield per plant, increased number of filled seeds, increased total number of seeds, increased harvest index, increased biomass, and/or increased aboveground biomass relative to a corresponding control plant.

4. The method of claim 1, wherein said enhanced yield-related trait is obtained under non-stress conditions.

5. The method of claim 1, wherein said enhanced yield-related trait is obtained under conditions of drought stress, salt stress, nitrogen deficiency, or reduced nutrient availability.

6. The method of claim 1, wherein said nucleic acid is operably linked to a constitutive promoter, a GOS2 promoter, a GOS2 promoter from rice, or a promoter comprising the nucleotide sequence of SEQ ID NO: 295.

7. The method of claim 1, wherein the nucleic acid encoding a Calreticulin polypeptide is of plant origin, from a dicotyledonous plant, from a plant of the family Solanaceae, from a plant of the genus Solanum, or from a Solanum lycopersicum plant.

8. A method for making a pant having an increased yield-related trait relative to a corresponding control plant, comprising transforming a plant or a plant cell with a construct comprising (i) a nucleic acid sequence encoding a Calreticulin polypeptide comprising the amino acids sequence of SEQ ID NO: 105; (ii) one or more heterologous control sequences capable of driving expression of the nucleic acid sequence of (i); and optionally (iii) a transcription termination sequence, wherein the increased yield-related trait is one or more of increased yield, increased biomass, increased aboveground biomass, increased seed yield, increased seed yield per plant, increased number of filled seeds, increased total number of seeds, and increased harvest index.

9. A plant produced by the method of claim 8.

10. A method for the production of a transgenic plant having an enhanced yield-related trait relative to a corresponding control plant, comprising:
(i) introducing and expressing in a plant a nucleic acid encoding a Calreticulin polypeptide comprising the amino acid sequence of SEQ ID NO: 105; and
(ii) cultivating the plant under conditions promoting plant growth and development, wherein the enhanced yield-related trait is one or more of increased yield, increased seed yield, increased biomass, or increased harvest index.

11. The method of claim 8, further comprising selecting for a plant having an increased yield-related trait relative to a corresponding control plant.

12. The method of claim 10, further comprising selecting for a plant having an increased yield-related trait relative to a corresponding control plant.

13. The method of claim 10, wherein said nucleic acid comprises the nucleotide sequence of SEQ ID NO: 104.

14. The method of claim 8, wherein one of said control sequences is a constitutive promoter, a GOS2 promoter, a GOS2 promoter from rice, or a promoter comprising the nucleotide sequence of SEQ ID NO: 295.