Patent Publication Number: US-10323252-B2

Title: Plant biomass yield increase by modified SWAM1 gene expression

Description:
CLAIM OF PRIORITY 
     This application claims the benefit of priority of U.S. Provisional Patent Application No. 62/186,801, filed 30 Jun. 2015, the benefit of priority of which is claimed hereby, and which is incorporated by reference herein in its entirety. 
    
    
     GOVERNMENT GRANT SUPPORT 
     This invention was made with government support under DE-FG02-08ER64700DE and DE-SC0006641 awarded by the Office of Science, Biological and Environmental Research, Department of Energy. The government has certain rights in the invention. 
    
    
     SEQUENCE LISTING 
     This document incorporates by reference herein an electronic sequence listing text file, which is filed in electronic format via EFS-Web. The text file is named “1593751.txt,” is 86,016 bytes, and was created on Jun. 28, 2016. 
     BACKGROUND 
     Plant biomass offers a sustainable low cost alternative to fossil fuels and grasses such as miscanthus, sorghum and switchgrass can provide biofuel feedstocks. 
     SUMMARY OF THE INVENTION 
     One embodiment provides a transgenic plant, including, but not limited to, transgenic miscanthus, switchgrass, sorghum, poplar, wheat, lye, corn, barley, oat, rapeseed, potatoes, rice, soybean,  Brachypoclium distachyon  plant, plant cell, plant part or seed, wherein the transgenic plant, plant cell, plant part or seed comprises a heterologous promoter which increases expression of SWAM1, other genes related to SWAM1 (see  FIG. 7 ), or GNRF, as compared to a non-transgenic plant. 
     Another embodiment provides a method to increase plant biomass, with respect to a control plant, the method comprising transforming a plant, including, but not limited to, miscanthus, switchgrass, sorghum, poplar, wheat, rye, corn, barley, oat, rapeseed, potatoes, rice, soybean,  Brachypodium distachyon  plant with a recombinant polynucleotide that encodes a heterologous promoter that increases the expression of SWAM1, other genes related to SWAM1 (see  FIG. 7 ), or GNRF, wherein increased expression of SWAM1, other genes related to SWAM1 (see  FIG. 7 ), or GNRF in the transgenic plant, results in a transgenic plant with increased biomass. 
     Another embodiment provides a method to produce a transgenic plant with increased biomass comprising introducing a nucleic acid encoding a SWAM1 transcription factor, other genes related to SWAM1 (see  FIG. 7 ), or GNRF under the control of a heterologous promoter into a plant cell including, but not limited to, transgenic miscanthus, switchgrass, sorghum, poplar, wheat, rye, corn, barley, oat, rapeseed, potatoes, rice, soybean,  Brachypodium distachyon  plant cell. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIGS. 1A-C . Phylogenetic analysis of SWAM1 and related sequences suggests that the SWAM clade is present in diverse dicots, but absent from the Brassicaceae. Relative transcript abundance of SWAM1 in leaf, root and stem tissue measured with a microarray. Mean±standard deviation of three biological replicates (A). RNA in situ hybridization illustrating SWAM1 transcript localization in stem cross sections six weeks post germination (B) Sections were taken through the first internode and probed with anti-sense probes and imaged at 20× magnification. ep; epidermis, if; interfascicular fiber cells, xy; xylem, ph; phloem, pi; pith. A subclade of the MYB family illustrating amino acid sequence similarity between  Arabidopsis thaliana  (red), rice (blue) and  Brachypodium distachyon  (black). Red labels represent monocot species, including  Brachypodium dystachyon  (Bradi), rice ( Oryza sativa , Os) and switchgrass ( Panicum virgatum , Pavir). The black labels represent Brassicaceae species, including  Arabidopsis thaliana  (At),  Arabidopsis lyrata  (Alyrata), and  Capsella rubella  (Crubella). The blue labels represent other dicotyledonous species, including poplar (Potri), potato (Ltuber), peach (Ppersica), papaya (Cpapaya), and  Medicago truneatula  (Medtr). We constructed the phylogeny using MrBayes v3.2. The MYB46/83 clade members from all the species were chosen as the outgroup. 
         FIGS. 2A-F . SWAM1 is an activator of plant above ground biomass accumulation. Vector control (left), SWAM1-OE (center), and SWAM1-DR (right) plants were planted at the same time. All three lines appeared similar two weeks following germination (A). When completely senesced, SWAM1-DR lines remained dwarf (B). Number of days before the first inflorescence was visible (C). Total above ground biomass (D), plant height (E), and stem cross section area of the first internode (F) at complete senescence. Twelve to sixteen individuals from three independent events were analyzed for each trait. *p&lt;0.05. 
         FIGS. 3A-E . SWAM1-DR plants are dwarf due to non-elongated stem cells. Longitudinal stem sections illustrating the cell length of control (A), SWAM1-OE (B), and SWAM1-DR (C). Confocal images of propidium iodide stained longitudinal stem sections of the first internode of flowering stems. Scale bar=50 μm. Stem internode epidermal cell count (D), and Stem epidermal cell length (E) of the first internode of flowering stems. 
         FIGS. 4A-E . SWAM1 is an activator of stem lignin accumulation. First internodes of fully senesced plants were hand sectioned and stained with phloroglucinol-HCl and representative images are illustrated (A-C). Compared to the control (A) SWAM1-OE stem sections (B) stained a dark orange red color and SWAM1-DR stem sections (C) were stained yellow in the interfascicular region and a less intense red color in the vascular bindles. Scale bar=0.1 mm. Acetyl bromide soluble lignin content (D) and Ethanol yield (E) of completely senesced stem tissue. Pulverized stem tissue from six to sixteen individuals from three independent events were analyzed for each line. *p&lt;0.05. 
         FIGS. 5A-F . SWAM1 is an activator of interfascicular fibers secondary cell wall thickening. Representative transmission electron micrographs illustrating the cell wall thickness of cells in the interfascicular fiber region of the first internode of inflorescence stems of control (A,D), SWAM1-OE (B,E) and SWAM1-DR (C,F). D-F are 5× magnified images of A-C. Black and white lines indicate the thickness of secondary and primary walls, respectively. Scale bars=5 μm (A-C) and 1 μm (D-F). 
         FIGS. 6A-D . SWAM1 directly interacts with an AC-like sequence motif to activate cell wall gene expression. Relative expression of SWAM1 (A) and secondary cell wall genes (B) in control, SWAM1-OE and SWAM1-DR stems. The tallest stem was collected from developmentally equivalent plants when the inflorescence was first visible from the flag leaf Nine individuals from three independent events were analyzed in triplicate using QRT-PCR and normalized relative to two housekeeping genes, BdUBC18 and BdGctpDH, β-galactosidase activity illustrating a preferential interaction between the AC-II element and SWAM1 protein in yeast (C). Values are mean of three independent yeast transformations. Relative fold enrichment of cell wall promoter fragments (D). Three biological samples were analyzed for control and SWAM1:GFP in triplicate using QRT-PCR and normalized to input DNA. *p&lt;0.05. 
         FIG. 7A . Group of genes related to SWAM1 are depicted. 
         FIGS. 7B-L . Provides the gene names and the predicted protein sequences of those genes listed in  7 A (SEQ ID NOs: 2-31). 
         FIG. 8 . Synteny analysis of the SWAM1 regions of papaya (Papaya.sugercontig110) and poplar (Potri Chr 15) suggests loss of this and two adjacent loci in  Arabidopsis thaliana . Syntenically conserved papaya and poplar loci in the region are marked, with the prefixes Papaya.supercontig and Potri. omitted for clarity. The figure was generated with SynFind, which is incorporated into CoGe (genomevolution.org/CoGe/). 
         FIG. 9 . Variants of the AC element are present in  Brachypodium distachyon  cellulose and lignin gene promoters. 1500 bp upstream of the transcription start site was analyzed for the presence of the AC-like elements. 
         FIG. 10 . A simplified model for flowering in  Arabidopsis thaliana . FLOWERING LOCUS T(FT) is activated by temperature, photoperiod, clock, hormones and aging. FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) are the main repressors of FT. FLC is activated by FRIGID A (FRI) and is repressed by the autonomous pathway and cold. When the timing is suitable for flowering FT protein moves through the phloem to the stem and interacts with the FD. FT-FD complex is responsible for activating the floral integrator gene SUPPRESSOR OF OVEREXPRESSION OF CONSIANSI (SOC1) and the floral meristem identity genes APETALA 1 (AP1), CAULIFLOWER (CAL), FRUITFUL (FUL) and LEAFY (LFY) which results in the vegetat8ive reproductive transition. 
         FIG. 11 . Proposed model for flowering in grasses. FLOWERING LOCUS T (FT) is activated by long days via PHOTOPERIOD1-H1 (PPD-H1) and is replaced by VERNALIZATION 2 (VRN2). During winter VRN1 is activated and represses VRN2 to initiate flowering in spring. Once activated FT moves through the phloem into the stem where it complexes with FLOWERING LOCUS D LIKE2 (FLDL2) to activate the floral meristem identity gene VRN1. 
         FIGS. 12A-B . Relative expression and phylogeny of Bradi2g4617. (A) Relative transcript abundance of Bradi2g4617 in leaf, root and stem tissue measured with a microarray. Mean±standard deviation of three biological replicates. (B) A subclade fo the NAC phylogeny illustrating amino acid sequence similarity between  Arabidopsis thaliana, Brachypodium distachyon, Oryza sativa, Zea maize, Populus trichocarpa  and  Sorghum biocolor . A rooted neighbor-joining phylogeny was constructed using MEGA5 with 1000 bootstrap permutations. Numbers on each branch indicate bootstrap support. Branches indicate in blue were used as an out group. 
         FIG. 13 . Plant phenotypes of control (left), gnrf-1 (center) and GNRF-OE (right) at flowering stage images were captured at the time of control plant flowering. Scale bar=1 cm. 
         FIGS. 14A-C . Whole plant phenotypes. (A) Days taken for the first flower to be visible from the flag leaf Fifteen to forty eight individuals were analyzed for each line. Note that GNRF-OE remained vegetative even after 75 days, (B) Plant height at complete maturity, (C) Total above ground biomass at complete senescence. Fifteen to twenty one individuals were analyzed for each line. *p&lt;0.05. 
         FIG. 15 . Transcript abundance of flowering pathway genes in stems. Relative expression of FUL1, FUL2, and RCN2 gene in control, gnrf-1 and GNRF-OE stems. Tallest stem was collected from developmentally equivalent plants when the inflorescence was first visible from the flag leaf. Eight to ten individuals from each line were analyzed in triplicate using QRT-PCR and normalized against two housekeeping genes. *p&lt;0.05. 
         FIGS. 16A-D . Relative expression of flowering pathway genes in leaves (A) FT, (B) MADS37, (C) ODDSOC1, and (D) ODDSOC2 Fourth leaf from the base of the tallest stem was collected from developmentally equivalent plants when the inflorescence was first visible from the flag leaf. Seven to nine individuals were analyzed in triplicate using QRT-PCR and normalized against two housekeeping genes. *p&lt;0.05. 
         FIG. 17 . Transcript abundance of GNRF in control and GNRF-OE stems. Relative expression of GNRF was measured in the stem tissue of the tallest stem when the inflorescence was just visible from the flag leaf of the control plants. Ten individuals were analyzed in triplicate using QRT-PCR and normalized against two housekeeping genes. *p&lt;0.05. 
         FIG. 18 . Target cell wall gene expression in stems. Relative expression of secondary cell wall genes in control, gnrf-1 and GNRF-OE stems. Tallest stem was collected from developmentally equivalent plants when the inflorescence was first visible form the flag leaf. Eight to ten individuals were analyzed in triplicate using QRT-PCR and normalized against two housekeeping genes. 
         FIGS. 19A-B . Histo-chemical and compositional analysis of stem lignification. (A) Lignin staining of stem cross sections. First internodes of fully senesced plants were hand sectioned and stained with phloroglucinol-HCl to visualize lignin. Representative images were illustrated. Scale bar=50 μm. (B) Acetyl bromide soluble lignin content in senesced stems. Three to six individuals from each line were analyzed for the ASBL lignin content. *p&lt;0.05. 
     
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     Several MYB proteins have been reported to regulate plant cell wall synthesis, but none has been shown to function as an activator in a grass.  Brachypodium distachyon  SECONDARY WALL ASSOCIATED MYB1 (SWAM1) was identified herein as a regulator of secondary cell wall biosynthesis based on gene expression and phylogeny. SWAM1 protein interacts with cellulose and lignin gene promoters in vitro and in vivo with preferential binding to AC-rich sequence motifs commonly found in cell wall gene promoters. Gain-of-function lines had greater above ground biomass without a change in flowering time while SWAM1-DR plants were severely dwarfed with a striking reduction in schierenchyma fiber lignin. Cellulose, hemicellulose, and lignin genes were significantly down-regulated in SWAM1-DR plants and up-regulated in SWAM1-OE plants. Considering lignin is inversely correlated with bioconversion efficiency phenotypes, ethanol yield was measured after culturing stems with  Clostridium phytolermentans . While no effect in ethanol yield was observed for SWAM1-OE, yield was and a significantly increase for SWAM1-DR samples. Interestingly, the analysis of phylogeny and synteny strongly suggests that the SWAM1 clade was present in the last common ancestor between eudicots and grasses, but is no longer present in the Brassicaceae. Collectively the data suggests that SWAM1 a transcriptional activator of secondary cell wall thickening and biomass accumulation in  B. distachyon  and potentially in food and energy crop species. 
     Thus, the present invention provides for the production of plants with increased biomass and their use in bio-ethanol or other biofuel production or as animal feed (e.g., as a silage or silage-type feed for animals, such as ruminants). 
     In describing and claiming the invention, the following terminology will be used in accordance with the definitions set forth below. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention. Specific and preferred values listed below for radicals, substituents, and ranges are for illustration only; they do not exclude other defined values or other values within defined ranges for the radicals and substituents. 
     As used herein, the articles “a” and “an” refer to one or to more than one, i.e., to at least one, of the grammatical object of the article. By way of example, “an element” means one element or more than one element. 
     The term “about,” as used herein, means approximately, in the region of, roughly, or around. When the term “about” is used in conjunction with a numerical range, it modifies that range by extending the boundaries above and below the numerical values set forth. In general, the term “about” is used herein to modify a numerical value above and below the stated value by a variance of 20%. 
     As used herein, “heterologous” in reference to a nucleic acid is a nucleic acid that originates from a foreign species, or, if from the same species, is modified from its native form in composition and/or genomic locus by deliberate intervention. For example, a promoter operably linked to a heterologous structural gene is from a species different from that from which the structural gene was derived or, if from the same species, one or both are modified from their original form. A heterologous protein may originate from a foreign species or, if from the same species, is modified from its original form by deliberate intervention. 
     Any method to increase expression/activity of the target gene is contemplated in the methods described herein. The term “introduced” in the context of inserting a nucleic acid into a cell, means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed. 
     The term “isolated” refers to a factor(s), cell or cells which are not associated with one or more factors, cells or one or more cellular components that are associated with the factor(s), cell or cells in vivo. 
     As used herein, “nucleic acid” includes reference to a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form, and unless otherwise stated, encompasses known analogues having the essential nature of natural nucleotides in that they hybridize to single-stranded nucleic acids in a manner similar to naturally occurring nucleotides (e.g., peptide nucleic acids). Unless otherwise indicated, the term includes reference to the specified sequence as well as the complementary sequence thereof. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are “polynucleotides” as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples, are “polynucleotides” as the term is used herein. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art. The term polynucleotide as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides. 
     The term “residue” or “amino acid residue” or “amino acid” are used interchangeably herein to refer to an amino acid that is incorporated into a protein, polypeptide, or peptide (collectively “protein”). The amino acid may be a naturally occurring amino acid and, unless otherwise limited, may encompass known analogs of natural amino acids that can function in a similar manner as naturally occurring amino acids. 
     The terms “polypeptide,” “peptide,” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers. 
     As used herein “operably linked” includes reference to a functional linkage between a first sequence, such as a promoter and a second sequence, wherein the promoter sequence initiates and mediates transcription of the DNA sequence corresponding to the second sequence. Generally, operably linked means that the nucleic acid sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame. 
     As used herein “promoter” includes reference to a region of DNA upstream from the start of transcription and involved in recognition and binding of RNA polymerase and other proteins to initiate transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells. Exemplary plant promoters include, but are not limited to those that are obtained from plants, plant viruses, and bacteria which comprise genes expressed in plant cells such  Agrobacterium  or  Rhizobium . Examples are promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, seeds, fibers, xylem vessels, tracheids, or sclerenchyma. Such promoters are referred to as “tissue preferred.” A “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. An “inducible” or “regulatable” promoter is a promoter, which is under environmental/external signal control (e.g., chemically inducible promoter, such as alcohol inducible promoter). Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions or the presence of light. Additional examples of inducible promoters are the Adh1 promoter, which is inducible by hypoxia or cold stress, the Hsp70 promoter, which is inducible by heat stress, the PPDK promoter, which is inducible by light, and the promoter inducible by alcohol. Another type of promoter is a developmentally regulated promoter, for example, a promoter that drives expression during pollen development or senescence (see, for example,  FIG. 6 ). Tissue preferred, cell type specific, developmentally regulated, and inducible promoters constitute “non-constitutive” promoters. A “constitutive” promoter is a promoter, which is active under most environmental conditions. 
     As used herein “recombinant” includes reference to a cell or vector, that has been modified by the introduction of a heterologous nucleic acid or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found in identical form within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all as a result of deliberate intervention. 
     As used herein, “vector” or “plasmid” includes reference to a nucleic acid used in transfection of a host cell and into which can be inserted a polynucleotide. Vectors are often replicons. Expression vectors permit transcription of a nucleic acid inserted therein. Typical vectors useful for expression of genes in higher plants are well known in the art and include vectors derived from the tumor-inducing (Ti) plasmid of  Agrobacterium tumefaciens  described by Rogers, et al., (1987) Meth. Enzymol. 153:253-77. These vectors are plant integrating vectors in that on transformation, the vectors integrate a portion of vector DNA into the genome of the host plant. Exemplary  A. tumefaciens  vectors are plasmids pKYLX6 and pKYLX7 of Schardl, et al., (1987) Gene 611-11, and Berger, et al., (1989) Proc. Natl. Acad. Sci. USA, 86:8402-6. 
     As used herein, a “recombinant expression cassette” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements, which permit transcription of a particular nucleic acid in a target cell. The recombinant expression cassette can be incorporated into a plasmid, chromosome, mitochondrial DNA, plastid DNA, virus, or nucleic acid fragment. Typically, the recombinant expression cassette portion of an expression vector includes, among other sequences, a nucleic acid to be transcribed, and a promoter. For example, plant expression vectors may include (1) a pre-selected sequence under the transcriptional control of 5° and 3′ regulatory sequences and (2) a dominant selectable marker. Such plant expression vectors may also contain, if desired, a promoter regulatory region (e.g., one conferring inducible or constitutive, environmentally- or developmentally-regulated, or cell- or tissue-specific/selective expression), a transcription initiation start site, a ribosome binding site, an RNA processing signal, a transcription termination site, and/or a polyadenylation signal. 
     Expression cassettes, vectors and in vitro culture methods for plant cell or tissue transformation and regeneration of plants are known and available to the art. See, e.g., Gruber, et al., “Vectors for Plant Transformation,” in METHODS IN PLANT MOLECULAR BIOLOGY AND BIOTECHNOLOGY, supra, pp. 89-119. 
     As used herein, the term “plant” includes reference to whole plants, plant organs (e.g., leaves, stems, roots, etc.), seeds and plant cells and progeny of same. Plant cell, as used herein includes, without limitation, seeds, cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and/or microspores. 
     As used herein, “transgenic plant” includes reference to a plant, which comprises within its genome a heterologous polynucleotide. Generally, the heterologous polynucleotide is stably integrated within the genome such that the polynucleotide is passed on to successive generations. The heterologous polynucleotide may be integrated into the genome alone or as part of a recombinant expression cassette. “Transgenic” is used herein to include any cell, cell line, callus, tissue, plant part or plant, the genotype of which has been altered by the presence of heterologous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic. 
     “Bio-alcohols,” such as “bio-ethanol,” are biologically produced alcohols, most commonly ethanol, and less commonly propanol, butanol and methyl butenol, which are generally produced by the action of microorganisms and enzymes through the fermentation of sugars or starches, or cellulose. Ethanol fuel is the most common biofuel worldwide. Alcohol fuels are produced by fermentation of sugars derived from wheat, corn, sugar beets, sugar cane, molasses and any sugar or starch that alcoholic beverages can be made from (like potato and fruit waste, etc.). The ethanol production methods used are enzyme digestion (to release sugars from stored starches), fermentation of the sugars, distillation and drying. The distillation process requires energy input for heat (often unsustainable natural gas fossil fuel, but cellulosic biomass, such as the waste left after sugar cane is pressed to extract its juice, can also be used more sustainably). Ethanol can be used in engines as a replacement for gasoline. 
     “Biomass” or “biofuel” is material derived from recently living organisms. This includes plants, animals and their by-products. For example, manure, garden waste and crop residues are all sources of biomass. It is a renewable energy source based on the carbon cycle, unlike other natural resources such as petroleum, coal, and nuclear fuels. It is used to produce power, heat and steam and fuel, through a number of different processes. “Agrofuels” are “biofuels” which are produced from crops. There are two common strategies of producing liquid and gaseous agrofuels. One is to grow crops high in sugar (sugar cane, sugar beet, and sweet sorghum) or starch (corn/maize), and then use yeast fermentation to produce alcohol (e.g., ethanol). The second is to grow plants that contain high amounts of vegetable oil, such as oil palm, soybean, algae, jatropha, or pongamia pinnata. When these oils are heated, their viscosity is reduced, and they can be burned directly in a diesel engine, or they can be chemically processed to produce fuels such as biodiesel. Wood and its byproducts can also be converted into biofuels such as woodgas, methanol or ethanol fuel. It is also possible to make cellulosic ethanol from non-edible plant parts. 
     Numerous methods for introducing foreign genes into plants (e.g., plant cells) are available to an art worker, including biological and physical plant transformation protocols. See, e.g., Miki, et al., “Procedure for Introducing Foreign DNA into Plants,” in METHODS IN PLANT MOLECULAR BIOLOGY AND BIOTECHNOLOGY, Glick and Thompson, eds., CRC Press, Inc., Boca Raton, pp. 67-88 (1993). The methods chosen vary with the host plant, and include chemical transfection methods such as calcium phosphate, microorganism-mediated gene transfer such as  Agrobacterium  mediated transformation (Horsch, et al., (1985) Science 227:1229-31), microprojectile-mediated transformation, electroporation (Riggs, et al., (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606), micro-injection (Crossway, et al., (1986) Biotechniques 4:320-334; and U.S. Pat. No. 6,300,543), direct gene transfer (Paszkowski, et al., (1984) EMBO J. 3:2717-2722), sonication (Zang, et al., (1991) BioTechnology 9:996), liposome or spheroplast fusions (Deshayes, et al., (1985) EMBO J. 4:2731; and Christou, et al., (1987) Proc. Natl. Acad. Sci. USA 84:3962), protoplast transformation, macroinjection, DNA uptake by germinating pollen and DNA uptake in embryos by swelling (Potrykus,  Physiol. Plant  (1990), 269-273), and biolistic bombardment (see, for example, Sanford, et al., U.S. Pat. No. 4,945,050; WO 91/10725; and McCabe, et al., (1988) Biotechnology 6:923-926; Tomes, et al., Direct DNA Transfer into Intact Plant Cells Via Microprojectile Bombardment. pp. 197-213 in Plant Cell, Tissue and Organ Culture, Fundamental Methods eds. O. L. Gamborg &amp; G. C. Phillips, Springer-Verlag Berlin Heidelberg New York, 1995). 
     Once the DNA introduced is integrated into the genome of the plant cell, it is generally considered stable and is also retained in the progeny of the originally transformed cell. It can contain a selection marker Which mediates, for example, resistance to a biocide such as phosphinothricin or an antibiotic such as kanamycin, G 418, bleomycin or hygromycin, to the transformed plant cells or which permits selection via the presence or absence of certain sugars or amino acids. The marker chosen should therefore allow the selection of transformed cells over cells which lack the DNA introduced. 
     Once transformed, these cells can be used to regenerate transgenic plants in any manner available to the art. Seeds may be obtained from the plant cells. Two or more generations can be grown in order to ensure that the phenotype characteristic is stably retained and inherited. Also, seeds can be harvested in order to ensure that the phenotype in question or other characteristics have been retained. 
     The invention also relates to propagation material of the plants according to the invention, for example fruits, seeds, tubers, rootstocks, seedlings, cuttings, calli, protoplasts, cell cultures, tissues and the like. 
     As used herein, “an increase” in yield or growth is about 1% to about 10%, or less than about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about 20%, about 21%, about 22%, about 23%, about 24%, about 25%, about 26%, about 27%, about 28%, about 29%, or about 30% or higher such as less than about 35%, about 40% about 45%, or about 50% increase in yield (e.g., grain/crop yield) or growth, as compared to a wild-type plant. 
     “Increase expression” refers to an increase in expression of protein or RNA. This increase can be from about 0.5% to 100% increase of expression of the gene, including about 1% to about 10%, or about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100% as compared to a wild-type plant. 
     In one embodiment, the sequences mentioned herein also comprise variations that are at least about 50% or about 60% or about 70%, about T1%, about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, or about 79%, or at least about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, or about 89%, or at least about 90%, about 91%, about 92%, about 93%, or about 94%, or at least about 95%, about 96%, about 97%, about 98%, or about 99% sequence identity, compared to the sequences provided herein using one of alignment programs available in the art using standard parameters. In one embodiment, the differences in sequence are due to conservative amino acid. changes. In another embodiment, the protein sequence has at least 80%, or at least 85%, at least 90% or at least 95% sequence identity with the sequences provided herein and can be bioactive. 
     Methods of alignment of sequences for comparison are available in the art. Thus, the determination of percent identity between any two sequences can be accomplished using a mathematical algorithm. Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 8 (available from Genetics Computer Group (GCG), 575 Science Drive, Madison, Wis., USA). Alignments using these programs can be performed using the default parameters. 
     The terms “comprises,” “comprising,” and the like can have the meaning ascribed to them in U.S. Patent Law and can mean “includes,” “including” and the like. As used herein, “including” or “includes” or the like means including, without limitation. 
     The following examples are intended to further illustrate certain particularly preferred embodiments of the invention and are not intended to limit the scope of the invention in any way. 
     EXAMPLES 
     Example I 
       Brachypodium distachyon  SWAM1 is a positive regulator of secondary cell wall synthesis and biofuel feedstock attributes and is not found in the Brassicaceae 
     Introduction 
     A large portion of plant biomass consists of secondary cell walls rich in cellulose, hemicelluloses, and lignin. It was the innovation of such walls and vascular cells that allowed plants to grow large and colonize areas further inland away from bodies of water. Diversification of vascular systems included the appearance of numerous arrangements of vasculature and the most advanced and varied are the angiosperms (Worsdell, 1902). Among the many distinctions between eudicotyledons and grasses are vascular patterning and the function and composition of cells with secondary walls (Esau, 1977; Kellogg, 2001; Vogel, 2008). Those aspects profoundly influence plant form and function as a food source for humans and animals, a raw material in the pulp and paper industry, and a biofuel feedstock. As with agronomic food crops, yield is the foremost energy crop trait and cultivation should demand few inputs (Jessup, 2009). Energy crop quality can be gauged by the type and relative quantity of fuel that can be derived from a unit of raw material. The transcriptional regulation of each secondary wall polymer and the manner in which they interact influences function as well as industrial feedstock quality (Carroll and Somerville, 2009). 
     The transcriptional network that governs the regulation of secondary cell wall thickening in eudicots consists of numerous MYB family transcription factors (Zhong et al., 2010; Hussey et al., 2013; Schuetz et al., 2013). MYB proteins are present in all eukaryotes and are generally encoded by large gene families (Katiyar et al., 2012; Du et al., 2013). For example,  Arahidopsis thaliana  and rice ( Oryza sativa ) have an estimated 197 and 155 MYBs, respectively. In addition to overall sequence similarity, the sub-families are categorized based on the number and type of DNA-binding domains in each protein, which ranges from one to four copies. The majority of plant MYB proteins harbor two DNA-binding domains and the so called R2R3-MYB group is extensively described in several plant species including  A. thaliana, Populus , orange ( Citrus sinensis ), maize ( Zea mays ), and rice (Wilkins et al., 2009; Katiyar et al., 2012; Du et al., 2013; Liu et al., 2014). The  A. thaliana  MYB proteins known to regulate the cell wall transcription network include AtMYB46/83/58/63/85/20/52/54/69/103/4/32/75 (Hussey et al., 2013; Zhao and Bartley, 2014). Among these, AtMYB46 and AtMYB83 are regulators capable of activating downstream transcription factors and cell wall genes (Ko et al., 2014). Over-expression of AtMYB46 or AtMYB83 resulted in thicker secondary cell walls in the xylem vessels and dominant repression resulted in thinner walls (Thong et al., 2007; McCarthy et al., 2009). Other proteins specifically regulate the biosynthesis of a single component of the cell wall. For instance, AtMYB58 and AtMYB63 directly bind the promoters of lignin genes to activate lignin biosynthesis (Zhou et al., 2009). Dominant repression of these two proteins resulted in a reduction of secondary wall thickening and lignin content. As a result, these plants were unable to grow upright. On the other hand, over-expression resulted in increased lignin pathway gene expression and ectopic deposition of lignin in cells that are normally not lignified. However, over-expression of either AtMYB58 or AtMYB63 did not result in thicker secondary cell walls (Zhou et al., 2009). Several other MYBs including AtMYB20/54/69/85/103 are highly expressed in stem tissue and activate secondary wall thickening (Hussey et al., 2013). AtMYB85 can activate genes in the lignin pathway and dominant repression resulted in a significant reduction in thickness of interfascicular and xylary fiber walls and over-expression resulted in ectopic deposition of secondary cell walls in stem epidermis and cortex (Zhong et al., 2008). Dominant repression AtMYB103/52/54/69 transgenes also reduced secondary wall thickening in interfascicular and xylary fiber cells; however, none had a significant effect on the vessels (Zhong et al., 2008). The research conducted on  A. thaliana  MYB proteins implies they play crucial regulatory roles as activators and repressors of cell wall biosynthesis. 
     The three variants of the AC element, AC-I (ACCTACC), AC-II (ACCAACC), and AC-III (ACCTAAC), present in promoters of many lignin pathway genes have been shown to interact with MYB protein to influence transcription (Lois et al., 1989; Hatton et al., 1995; Raes et al., 2003). The AC element was further described to have four more variations by interchanging the T with a C at the last base position, ACC(T/A)A(A/C)(C/T) and named the secondary wall MYB responsive element (SMRE) or the AtMYB46 responsive cis-element (M46RE) (Kim et al., 2012; Zhong and Ye, 2012). This element was over represented in the promoters of genes up regulated by the over-expression of AtMYB46 under an inducible promoter. The representation was greatest among cellulose, hemicellulose, and lignin genes associated with AtMYB46 regulated secondary cell wall biosynthesis (Kim et al., 2012; Kim et al., 2013). Interestingly, interactions between MYB proteins and AC element like motifs can result in either transcriptional activation or repression (Rats et al., 2003). 
     Unlike  A. thaliana  and  Populus , the current transcriptional regulatory network for grass secondary cell wall biosynthesis is rather lacking (Handakumbura and Hazen, 2012). To date, the function of two MYB transcription factors has been demonstrated in a grass. ZmMYB31 and PvMYB4 are two transcriptional repressors characterized in maize and switchgrass, respectively. Like their close homologs in  A. thaliana  (AtMYB4) and  Eucalyptus gunnii  (EgMYB1) they directly repress lignin gene expression by binding to the AC elements found in the promoters of these genes and subsequently regulate cell wall biosynthesis (Jin et al., 2000; Legay et al., 2007; Fornalé et al., 2010; Shen et al., 2012). Rice and maize orthologs of AtMYB46 and AtMYB83 are the only grass MYB activators characterized thus far. These proteins are capable of activating secondary cell wall biosynthetic pathways when over-expressed in  A. thaliana  (Thong et al., 2011). However, no MYB activators have been functionally characterized and shown to directly activate cell wall genes in grasses. Herein candidate genes are identified for the positive regulation of secondary cell wall biosynthesis based on co-expression analysis and protein phylogenies in the model monocot  Brachypodium distachyon . The function of a MYB transcription factor that has no orthologous counterpart in  A. thaliana  and other Brassicaceae, SECONDARY WALL ASSOCIATED MYB1 (Bradi2g47590), is demonstrated herein via overexpression and dominant repressor lines. In addition, it is shown that SWAM1 protein directly activates cell wall gene promoters to regulate wall thickening. 
     Materials and Methods 
     Phylogenetic Analysis 
     The following genome annotation versions were mined, which were current at the time of this analysis:  S. lycopersicum , iTAG 2.3,  P. persica , v1.0,  M. truncatula , Phytozome v4.1,  P. trichocarpa , Phytozome v3.0,  C. rubella , Phytozome v1.0,  A. thaliana , TAIR10,  A. lyrata , Phytozome v1.0,  C. papaya  ASGPBv0.4, rice,  B. distachyon , Phytozome v2.1, MSU v7.0  P. virgatum , Phytozome v1.1. Two different processes were used to identify SWAM1 homologs and related proteins from different genomes. To establish BLASTP criteria for quickly identifying specific proteins from diverse genomes, a global analysis was conducted with a small number of species using HMMFR 3.0 (Finn et al., 2011) to identify the putative R2R3 MYB protein sequences in  O. sativa, S. lycopersicum, P. persica  and  M. truncatula  with an in-house Hidden Markov Model profile based on the 126 R2R3 MYB proteins in  A. thaliana  (Dubos et al., 2010). From these five species and the  B. distachyon  MYBs, identified previously (International  Brachypodium  Initiative, 2010), a phylogenetic tree was built with the whole R2R3-type MYB family using a Neighbor-joining algorithm and 500 bootstraps in MEGA v.5.2.2 (Tamura et al., 2011). Homologs of SWAM1 were selected if they were included in the same clade and supported by a bootstrap score≥50. To identify the homologs of SWAM1 in more species, BLASTP was used to search the following species:  P. virgatum, P. trichocarpa, A. Lyrata, C. papaya  and  C. rubella . Sequences were included with E values≤E-60, which recalled all of the SWAM1 homologs identified based on the topology of the R2R3-type MYB phylogeny described above. Then the SWAM1 homologs were finalized from all species by further phylogenetic analysis with MrBayes. To identify homologs of AtMYB50, AtMYB61, AtMYB46 and AtMYB83 in poplar, rice and switchgrass, the recent publication of Zhao (2014) was used. To identify these proteins in the other species, the best BLASTP hit was included for AtMYB50, AtMYB61, AtMYB46 and AtMYB83. There was no evidence of gene family expansion in these groups, since the top two BLASTP hits for each target had obviously lower E values. Supplementary Table 2 contains the names and protein sequences used for the phylogenetic study of SWAM1. The protein sequences were aligned with MAFFT with the L-INS-I model, which allows local iterative refinement and shows better performance than CLUSTAL or MUSCLE, in general (Katoh et al., 2002; Thompson et al., 2011). To calculate the protein sequence similarity, the MUSCLE alignment incorporated into Geneious v.6 (Biomatters, Aukland, NZ) was used. The phylogeny for SWAM1 and related sequences in the AtMYB50 clade with the AtMYB83 clade as the outgroup was constructed using MrBayes v3.2. Two million generations yielded an average standard deviation of the split frequency of 0.0128, which indicates a relatively high confidence topology (Ronquist et al., 2012). 
     Synteny Analysis 
     The syntenic region of the Swam1 in the genomes of papaya, poplar, and  A. thaliana  was analyzed with the SynFind, which is incorporated within CoGe: Comparative Genomics (genomevolution.org/CoGe/) (Lyons et al., 2008). 
     Yeast One-Hybrid Screens 
     Yeast one-hybrid screens were conducted as previously reported (Pruneda-Paz et al., 2009). Two synthetic promoters were generated for the AC-like element (ACCAAC) and the mutated AC-like element (TTTAAC) by fusing four copies of the sequence in tandem. A spacer sequence of tttagatatcataa (SEQ ID NO: 1) was included at the 3′end of the synthetic promoters. Sequence confirmed clones were recombined with pLacZi plasmid (Clonetech) containing the LacZ reporter gene and stably integrated into the YM4271 yeast strain. SWAM1 was fused in frame with GAL4 activation domain in pDEST22 destination vector. 
     Plant Material and Growth Conditions 
       B. distachyon  (L.) line Bd21-3 was used as the genetic background. Wild type, control, and mutant seeds were imbibed on moist paper towels for seven days at 4° C. and planted in potting mix (#2; Conrad Fafard Inc. Agawam, Mass.). Plants were grown at control conditions in a growth chamber at 20° C. in 20 h: 4 h light: dark cycles at a fluence rate of 220 μmol·m −2 s −1  and relative humidity of 68%. 
     Plasmid Construction and Plant Transformation 
     The full-length coding region of SWAM1 (Bradi2g47590) was PCR amplified from Bd21-3 stem cDNA to include the stop codon using Phusion high-fidelity DNA polymerase (New England BioLabs) and cloned into pENTR/D-TOPO vector (Invitrogen). Sequence confirmed plasmid was recombined with pOL001 ubigate ori1 destination vector (modified from pOL001, described in (Vogel et al., 2006)) to generate the MYB48 gain-of-function construct (SWAM1-OE). A 39 nucleotide dominant repressor CRES sequence (Mitsuda et al., 2011) was synthesized using overlapping oligonucleotides with attB2 and attB5 flanking sites and cloned into pDONR 221 P5-P2. Full-length coding region of SWAM1 without the stop codon (MYB48NS) was cloned into pDONR 221 P1-P5r. CRES and MYB48NS entry clones were recombined with pOL001 ubigate ori1 destination vector to generate the MYB48 dominant repressor construct (SWAM1-DR). All constructs were transformed into  Agrobaterium tumefaciens  strain AGL1 via electroporation for calli transformations.  Brachypodium distachyon  calli transformations were carried out with minor modifications as previously described (Handakumbura et al., 2013). Primary transgenic were PCR confirmed for the hygromycin resistance gene and propagated for three subsequent generations and the resulting T 4  progeny were PCR confirmed for presence of the hygromycin phosphotransferase II gene using a Phire Plant Direct PCR Kit (Thermo Scientific) according to manufactures specifications. PCR confirmed transgenics were used for subsequent experiments. 
     Measurements of Transcript Abundance and Localization 
     Total RNA was extracted using a kit (Plant RNaeasy, Qiagen, Valencia, Calif.) according to the manufactures instructions. First, second, and third nodes and internodes of the tallest stem were frozen in liquid nitrogen from developmentally comparable individuals at inflorescence immergence, stage 51 on the  B. distachyon  BBCH-scale (Hong et al., 2011). On-column DNA digestions were performed using RNase-free DNase I (Qiagen). First strand cDNA was synthesized using oligo dT primers (Invitrogen) and QRT-PCR reactions were performed in triplicate as previously described (Handakumbura et al., 2013). Values were normalized against two housekeeping genes, BdUBC18 (UBIQUITIN-CONJUGATING ENZYME 18) and BdGapDH (Hong et al., 2008). Primers were designed using QuantiPrime primer design tool (Arvidsson et al., 2008). 
     RNA in situ hybridization was performed as previously described (Handakumbura et al., 2013) using stem cross sections of the first internode of the tallest stem at the completion of flowering, stage 65 on the  B. distachyon  BBCH-scale. 
     Microscopy 
     First internode of the tallest stem at complete senescence was used for histochemical analysis. Hand-cut stem cross sections were stained with phloroglucinol-HCl and observed under an Eclipse E200MV R microscope (Nikon) and imaged using a PixeLINK 3 MP camera. Images captured at 4× magnification were used for area measurements by freehand tracing of a perimeter in ImageJ (rsb.info.nih.gov/ij/). First internode of the tallest stem of mutant and vector control plants were excised when the inflorescence was first visible from the flag leaf and fixed in 2% glutaraldehyde in 50 mM phosphate buffer (33 mM Na2HPO4, 1.8 mM NaH2PO4 and 140 mM NaCl, pH 7.2) at room temperature for 2 hours. Next, samples were post-fixed in phosphate buffered OsO4 under same conditions. Samples were rinsed thrice with water and dehydrated in a graded ethanol series. Fixed tissue was infiltrated with 30%, 50%, 70% and 10 0% Spurr&#39;s resin for 1 hour each. Samples were infiltrated overnight in 100% resin, embedded in fresh resin and allowed to solidify in an oven. Embedded samples were sectioned using an ultra-cut microtome; post-fixed with uranyl acetate and lead citrate, and observed with an electron microscope. 
     Acetyle Bromide Soluble Lignin Measurements 
     Acetyl bromide soluble lignin content was measured as previously described (Foster et al., 2010). Briefly, 1.5 mg of senesced ground stem tissue was incubates with 100 μl of freshly made acetyl bromide solution (25% v/v acetyl bromide in glacial acetic acid) and incubated at 50° C. for 2 hours followed by an additional hour of incubation with vortexing every 15 min. Next, samples were cooled on ice to room temperature, and mixed with 400 μl of 2 M HaOH and 70 μl of freshly prepared 0.5 M hydroxylamine hydrochloride. A total volume of 2 ml was obtained by adding 1.43 ml glacial acetic acid. Absorbance was measured at 280 nm wavelength using a plate reader. Six to sixteen individuals from three events were analyzed for each transgene and percent acetyl bromide soluble lignin was calculated as previously described (Foster et al., 2010). 
     Cell Wall Digestibility Measurements 
     Fully senesced stems were washed with 70% ethanol at 70° C. for 1 h to remove soluble cell wall material and was air dried overnight. Next they were ground using a ball mill and weighed into individual wells in 20 mg duplicated and fermented with  Clostridium phytophementans  as previously described (Lee et al., 2012; Lee et al., 2012). Nine individuals from three independent events were analyzed in duplicate for each transgene. 
     Chromatin Immunoprecipitation 
     About 2 g of whole stems tissue was harvested from three week old plants and treated for 15 min under vacuum with cross-linking buffer (10 mM Tris, pH 8.0, 1 mM EDTA, 250 mM sucrose, 1 mM PMSF and 1% formaldehyde). Cross-linking was quenched using 125 mM glycine, pH 8.0, under vacuum for 5 min, followed by three washing steps in double-distilled water. Next the tissue was rapidly frozen in liquid nitrogen, ground to a fine power using a mortar and pestle and stored at −80° C. Chromatin was extracted using a kit (Zymo-spin) according to the manufacturer specification. Cross-linked samples were washed with the provided Nuclei prep buffer, resuspended in chromatin shearing buffer and sonicated on ice for four cycles using 40% amptitude. 100 μl of the sheared chromatin was incubated with the anti-GFP antibody overnight at 4° C. Samples were recovered using ZymoMag Protein A beads, washed thrice with the chromatin wash buffers and eluted using the chromatin elusion buffer. Eluted DNA was treated with 5M NaCl at 75° C. for 5 min and incubated with Proteinase K at 65° C. for 30 min, ChiP DNA was purified using the provide columns and eluted using 8 μl of elusion buffer. Triplicate QRT-PCR reactions were performed for three biological replicates using Quantifast SYBR Green PCR Kit (QIAGEN), with 2 ng of DNA with the following cycler conditions: 2 min at 95° C., followed by 40 cycles of 15 s at 95° C., 20 s at 55° C. and 20 s at 68° C. Results were normalized to the input DNA, using the following equation: 100×2 (Ct input·3.32-Ct ChIP) . 
     Statistical Analysis 
     For each measurement three different T 4  families were analyzed for each transgene. Student&#39;s t-tests were performed in R v2.15.0. Significance was set a P&lt;0.05. 
     Accession Numbers 
     AS1 (At2G37630), AtMYB1 (At3G09230), AtMYB3R4 (At5g11510), AtMYB3R-1 (At4g32730), AtMYB4 (At4G38620), AtMYB7 (At2G16720), AtMYB16 (At5G15310), AtMYB20 (At1G66230), AtMYB32 (At4G34990), AtMYB36 (At5G57620), AtMYB37 (At5G23000), AtMYB42 (At4G12350), AtMYB43 (At5G16600), AtMYB46 (At5G12870), AtMYB48 (At3G46130), AtMYB50 (At1G57560), AtMYB55 (At4G01680), AtMYB58 (At1G16490), AtMYB59 (At5G59780), AtMYB61 (At1G09540), AtMYB63 (At1G79180), AtMYB71 (AT3G24310), AtMYB79 (AT4G13480), AtMYB83 (At3G08500), AtMYB85 (At4G22680), AtMYB86 (At5G26660), AtMYB91 (At2G37630), AtMYB103 (At1G63910), AtMYB106 (At3G01140), AtMYB109 (At3G55730), BdCAD1 (Bradi3g17920), BdCESA4 (Bradi4g28350), BdCESA7 (Bradi2g30540), BdCESA8 (Bradi2g49912), BdCOMT4 (Bradi3g16530) BdGapDH (Bradi3g14120), BdGT47D3 (Bradi2g59400), BdUBC18 (Bd4G00660), EgMYB1 (CAE09058), OsMYB46 (Os12g33070), PvMYB4 (JF299185), ZmMYB31 (GRMZM2G050305), ZmMY1346 (GRMZM2G052606). See Table 1 for BdMYB accession numbers. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Secondary cell wall associated R2R3-type MYB transcription factors.  Brachypodium distachyon  MYBs co-regulated with 
               
               
                 BdCESA4/7/8 and BdCAD1, and BdCOMT4 were identified based on a correlation coefficient cut off of 0.8 for either BdCESA4/7/8 or BdCAD1 
               
               
                 and BdCOMT4. Orthologs of the majority of the tightly co-regulated MYB transcription factors have already been implicated in secondary cell 
               
               
                 wall processes in  A. thaliana  and are listed below. 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                   
                   
                 CESA4/7/8 
                 CAD1/COMT4 
                   
               
               
                   
                   
                 Most similar  A. thaliana   
                 correlation 
                 correlation 
               
               
                 Locus 
                 Name 
                 proteins 
                 coefficient 
                 coefficient 
                 References describing function in  A. thaliana   
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 Bradi4g06317 
                 BdMYB1 
                 AtMYB46/83 
                 0.99 
                 0.92 
                 (Zhong et al., 2007; McCarthy et al., 2009) 
               
               
                 Bradi2g47590 
                 BdMYB48 
                 AtMYB50/61 
                 0.99 
                 0.96 
               
               
                 Bradi3g17165 
                 BdMYB110 
                 AtMYB103 
                 0.99 
                 0.92 
                 (Öhman et al., 2013) 
               
               
                 Bradi2g17982 
                 BdMYB31 
                 AtMYB50/61 
                 0.99 
                 0.87 
               
               
                 Bradi5g20130 
                 BdMYB104 
                 AtMYB58/63 
                 0.97 
                 0.95 
                 (Zhou et al., 2009) 
               
               
                 Bradi1g10470 
                 BdMYB2 
                 AtMYB52/54 
                 0.97 
                 0.89 
                 (Cassan-Wang et al., 2013) 
               
               
                 Bradi3g56917 
                 BdMYB76 
                 AtMYB20/43 
                 0.96 
                 0.95 
                 (Ehlting et al., 2005; Zhong et al., 2008; Cui et al., 2013) 
               
               
                 Bradi3g42430 
                 BdMYB69 
                 AtMYB42/85 
                 0.96 
                 0.88 
                 (Zhong et al., 2008) 
               
               
                 Bradi5g15246 
                 BdMYB101 
                 AtMYB71/79 
                 0.95 
                 0.92 
               
               
                 Bradi2g28910 
                 BdMYB39 
                 AtMYB71/79 
                 0.95 
                 0.82 
               
               
                 Bradi2g17280 
                 BdMYB30 
                 AtMYB36/37 
                 0.94 
                 0.85 
                 (Muller et al., 2006) 
               
               
                 Bradi3g36660 
                 BdMYB64 
                 AtMYB16/106 
                 0.93 
                 0.75 
                 (Folkers et al., 1997; Oshima et al., 2013) 
               
               
                 Bradi4g29796 
                 BdMYB90 
                 AtMYB20/43 
                 0.92 
                 0.92 
                 (Ehlting et al., 2005; Zhong et al., 2008; Cui et al., 2013) 
               
               
                 Bradi2g40620 
                 BdMYB44 
                 AtMYB50/61 
                 0.92 
                 0.72 
               
               
                 Bradi4g04050 
                 BdMYB80 
                 AtMYB48/59 
                 0.91 
                 0.73 
                 (Mu et al., 2009) 
               
               
                 Bradi4g36210 
                 BdMYB93 
                 AtMYB42/85 
                 0.90 
                 0.79 
                 (Zhong et al., 2008) 
               
               
                 Bradi1g61397 
                 BdMYB18 
                 AtMYB50/61 
                 0.90 
                 0.68 
                 (Liang et al., 2005) 
               
               
                 Bradi2g36730 
                 BdMYB41 
                 AtMYB50/61 
                 0.89 
                 0.98 
                 (Liang et al., 2005) 
               
               
                 Bradi4g23967 
                 BdMYB109 
                 AtMYB4/7/32 
                 0.88 
                 0.99 
                 (Jin et al., 2000; Preston et al., 2004; Fornalé et al., 2014) 
               
               
                 Bradi4g36460 
                 BdMYB94 
                 AtMYB4/7/32 
                 0.84 
                 0.97 
                 (Jin et al., 2000; Preston et al., 2004; Fornalé et al., 2014) 
               
               
                 Bradi2g31887 
                 BdMYB40 
                 AtMYB3R4/3R-1 
                 0.81 
                 0.94 
                 (Haga et al., 2007; Haga et al., 2011) 
               
               
                 Bradi1g51961 
                 BdMYB15 
                 AtMYB92 
                 0.80 
                 0.56 
               
               
                 Bradi2g07677 
                 BdMYB25 
                 AtMYB3R4/3R-1 
                 0.80 
                 0.94 
                 (Haga et al., 2007; Haga et al., 2011) 
               
               
                 Bradi4g03970 
                 BdMYB79 
                 AtMYB91; AS1 
                 0.77 
                 0.86 
                 (Ori et al., 2000) 
               
               
                 Bradi2g37377 
                 BdMYB111 
                 AtMYB48/59 
                 0.74 
                 0.91 
                 (Mu et al., 2009) 
               
               
                 Bradi2g55040 
                 BdMYB53 
                 AtMYB1/109 
                 0.71 
                 0.91 
               
               
                 Bradi1g44070 
                 BdMYB12 
                 AtMYB20/43 
                 0.71 
                 0.86 
                 (Ehlting et al., 2005; Zhong et al., 2008; Cui et al., 2013) 
               
               
                 Bradi1g20250 
                 BdMYB4 
                 AtMYB55/86 
                 0.69 
                 0.81 
               
               
                 Bradi3g10067 
                 BdMYB112 
                 AtMYBR4/3R-1 
                 0.62 
                 0.80 
                 (Haga et al., 2007; Haga et al., 2011) 
               
               
                   
               
            
           
         
       
     
                     TABLE S3                  List of oligonucleotides used                     Primer Name   Sequence               attB1MYB48_F   ACAAGTTTGTACAAAAAAGCAGGCTCTATGGGGCGGCACGCGGGCACT           SEQ ID NO: 32)               attB2MYB48_R   ACCACTTTGTACAAGAAAGCTGGGTATCAAAAGTACTCGAGGTTGAAG           (SEQ ID NO: 33)               attB5rMYB48_NSR   ACAACTTTTGTATACAAAGTTGTAAAGTACTCGAGGTTGAAGTC           (SEQ ID NO: 34)               attB5CRES_F   GgggACAACTTTGTATACAAAAGTTGCTGTTGATCTTGATCTTGAATTGAGATTGGGT           (SEQ ID NO: 35)               attB2CRES_R   GgggACCACTTTGTACAAGAAAGCTGGGTATCAAGCAAAACCCAATCT           (SEQ ID NO: 36)               attB5GFP_F   ggggACAACTTTGTATACAAAAGTTGCTATG GTG AGC AAG GGC GAG GAG           (SEQ ID NO: 37)               attB2GFP_R   ggggACCACTTTGTACAAGAAAGCTGGGTATCA CTT GTA CAG CTC GTC CAT GCC           (SEQ ID NO: 38)               attB1GFP_F   GgggACAAGTTTGTACAAAAAAGCAGGCTCTATGGTGAGCAAGGGCGAGG           (SEQ ID NO: 39)               qPCRGT47-1_F   AATATAGCGCGCTGCATGTCCTC           (SEO ID NO: 40)               qPCRGT47-1_R   AATATAGCGCGCTGCATGTCCTC           (SEQ ID NO: 41)               qPCRMYB48CDS_F   AGGAAACAGGTGGTCGCAGATTG           (SEQ ID NO: 42)               qPCRMYB48CDS_R   GCTTCTTCTTGAGGCAGCTGTTCC           (SEQ ID NO: 43)               qPCRUBC18_F   GGAGGCACCTCAGGTCATTT           (SEQ ID NO: 44)               qPCRUBC18_R   ATAGCGGTCATTGTCTTGCG           (SEQ ID NO: 45)               qPCRGAPDH_F   TTGCTCTCCAGAGCGATGAC           (SEQ ID NO: 46               qPCRGAPDH_R   CTCCACGACATAATCGGCAC           (SEQ ID NO: 47)               qPCRCAD1_F   AGGATAGAATGGGCAGCATCGC           (SEQ ID NO: 48)               qPCRCAD1_R   ATCTTCAGGGCCTGTCTTCCTGAG           (SEQ ID NO: 49)               qPCRCOMT4_F   TGGAGAGCTGGTACTACCTGAAG           (SEQ ID NO: 50)               qPCRCOMT4_R   CGACATCCCGTATGCCTTGTTG           (SEQ ID NO: 51)               qPCRCESA4_F   GCGTTTCGCATACACCAACACC           (SEQ ID NO: 52)               qPCRCESA4_R   ACTCGCTAGGTTGTTCAGTGTGG           (SEQ ID NO: 53)               qPCRCESA7_F   GCGATTCGCCTACATCAACACC           (SEQ ID NO: 54)               qPCRCESA7_R   GGCTGGCAAATGTGCTAATCGG           (SEQ ID NO: 55)               qPCRCESA8_F   CAAAGCACAAGTTCCGCCTGTG           (SEQ ID NO: 56)               qPCRCESA8_R   TGGCTCGTATGCATCTGTCAAATC           (SEQ ID NO: 57)               qUBC18p_F   AAGGCTTGAACATGACAGCA           (SEQ ID NO: 58)               qUBC18p_R   ATGAAATGGGCACCTGAAAA           (SEQ ID NO: 59)               qCESA4p-1_F   TGCAAAAGGCCTCAGCTAAT           (SEQ ID NO: 60)               qCESA4p-1_R   TGGTGGCATACAAAACCTCA           (SEQ ID NO: 61)               qCESA4p-2_F   CTTCACGCTCACTCACCATC           (SEQ ID NO: 62)               qCESA4p-2_R   CGGAAGACCAAGAATGAAGC           (SEQ ID NO: 63)               qCESA8p-2_F   CTTGCTCTCACCGTCCTGA           (SEQ ID NO: 64)               qCESA8p-2_R   GGTTTCGAAGCGAAGGTGAC           (SEQ ID NO: 65)               qCADp-1_F   TTCCTATTGCAAGTACATCATGC           (SEQ ID NO: 66)               qCADp-1_R   TATCGTGTGCTGCCCATCTA           (SEQ ID NO: 67)               qCADp-3_F   AAACTGTTTGAAAATCAAATCTGC           (SED ID NO: 68)               qCADp-3_R   GGAAGTTGTCGTGGGATCAG           (SEQ ID NO: 69)               qCOMTp-2_F   TCGAGAAATAATGGTTCAGACG           (SEQ ID NO: 70)               qCOMTp-2_R   AGATATACTTGTTGTCGCGAAG           (SEQ ID NO: 71)               Hpt_F   AGAATCTCGTGCTTTCAGCTTCGA           (SEQ ID NO: 72)               Hpt_R   TCAAGACCAATGCGGAGCATATAC           (SEQ ID NO: 73)               Myb48_probe_aF   GCATGGCGCATTTTGACTTCAACC           (SEQ ID NO: 74)               Myb48_probe_aR   CTA CAC AAT GTT CAC ATT CCT ATA CC           (SEQ ID NO: 75)                    
Results
 
Co-Expression Analyses Reveal a Suite of Secondary Cell Wall Associated MYB Transcription Factors
 
     Microarray and co-expression analyses have aided in the understanding of gene function in a variety or organisms both in terms of intraspecific as well as interspecific comparisons (Brown et al., 2005; Persson et al., 2005; Mutwil et al., 2011). Not surprisingly, regulators of secondary cell wall biosynthesis are commonly highly expressed in tissues containing secondary cell walls and are co-expressed with the downstream genes they activate. Therefore, co-expression analyses was performed with secondary cell wall related cellulose genes BdCESA4, BdCESA7, BdCESA8 and the lignin-related genes BdCAD1 and BdCOMT4 to identify candidate MYB transcription factors that putatively regulate secondary cell wall biosynthesis (Table 1) using a previously described microarray data set (d&#39;Yvoire et al., 2012; Dalmais et al., 2013; Handakumbura et al., 2013; Trabucco et al., 2013). 26 BdMYB transcription factors that are co-regulated with BdCESA4/7/8 and BdCAD1, and BdCOMT4 were identified. Many these are part of sub-clades described as having an association with secondary cell wall biosynthesis based on genes characterized in  A. thaliana  (Zhao and Bartley, 2014). BdMYB48 (Bradi2g47590), hereby referred to as SWAM1, was further characterized. 
     SWAM1 is Highly Expressed in Stein and is Localized to the Interfascicular Fibers 
     To investigate SWAM1 transcript abundance in leaf, stem and root, the previously described  B. distachyon  microarray data set (Handakumbura et al., 2013) was used. SWAM1 transcript abundance in stems was approximately six and three-fold greater relative to leaf and root, respectively ( FIG. 1A ). Grass stems are substantially enriched for secondary cell walls (Matos et al., 2013) and account for a larger proportion of above ground plant biomass. However, not all cell types in the stem undergo secondary wall development. To confirm that SWAM1 gene expression is associated with those cells undergoing secondary wall thickening, RNA in situ hybridization was carried out on stem cross sections at inflorescence immergence ( FIG. 1B ). Similar to what was reported for BdCESA4 and BdCESA7 (Handakumbura et al., 2013), SWAM1 transcripts were localized to cell types with thickened secondary walls at this stage of development. They were mainly localized to the epidermis, sclerenchyma fibers, and xylem cells in both small and large vascular bundles. No hybridization was detected in the parenchyma cells and phloem fibers. Hybridization with control SWAM1 sense probe showed no labeling as expected (data not shown). 
     SWAM1 Belongs to a Sub-Clade without Representation from the Brassicaceae Family 
     MYB proteins are involved in a variety of processes during growth and development including cell wall thickening, cell cycle, and defense. Many of the  A. thaliana  MYB proteins such as AtMYB46 and AtMYB83 directly regulate cell wall thickening. To determine the protein similarity between SWAM1 and functionally characterized MYBs, a phylogeny was reconstructed using MYB protein sequences from  A. thaliana, B. distachyon  and rice (data not shown). While the previously described OsMYB46 and BdMYB1 (Zhong et al., 2011; Valdivia et al., 2013) are orthologs of the well-characterized  A. thaliana  MYBs, AtMYB46 and AtMYB83, no  A. thaliana  protein was part of the SWAM1 clade that also includes Bradi2g17982 (SWAM2) and Bradi2g40620 (SWAM3). To evaluate if SWAM1 is indeed specific to grasses, the grass  Panicum virgatum , the asterid  Solanum tuberosum , and six more rosids were added to the phylogenetic analysis including two more members of the Brasicaceae family:  A. lyrata  and  Capsella rubella  ( FIG. 1C ). An outgroup of the phylogenetically distinct AtMYB46 and AtMYB83 clade was also included. While  A. thaliana  AtMYB50 and AtMYB61 proteins are the most similar to SWAM1/2/3, there is an additional clade more phylogenetically similar that includes proteins from the other eudicot species. However, this relationship between the eudicot and grass SWAM clades is not well resolved due to the relatively low likelihood. score support in the Bayesian tree. The dicot SWAM sequences are sister to the AtMYB50 and AtMYB61 clade in a Maximum-likelihood tree with 1000 bootstraps, but with week support (54%). However, based on the protein sequence alignment in MUSCLE, the eudicot SWAMs show higher similarity to the grass SWAMs than sequences included in the AtMYB50 and AtMYB61 clade. No protein from the represented species from the Bracicaceae family is part of the SWAM1 sub-clade. To further confirm that the SWAM1 gene lineage is missing from the Brassicaceae the local genome synteny was compared between  A. thaliana  and  Carica papaya , and a more distantly related rosid,  Populus trichocarpa . Using the SWAM1 clade genes, a region syntenic among  C. papaya  and  P. trichocarpa  was identified. The regions flanking the SWAM1 orthologs were used to identify a syntenic region in  A. thaliana . There is clear micro-synteny with no rearrangements between several consecutive ( FIG. 8 ). While the SWAM1 clade representative from each one of these species lies within this syntenic region, it is conspicuously absent in  A. thaliana . The analysis of phylogeny and synteny strongly suggest that the SWAM clade was present in the last common ancestor between eudicots and grasses, but was lost in the Brassicaceae during evolution. 
     Gain-of-Function and Dominant Repression of SWAM1 Results in Reciprocal Whole Plant Phenotypes 
     To investigate the function of SWAM1, gain-of-function lines were developed by over-expressing the full-length coding region under the maize ubiquitin promoter; SWAM1-OE. Similarly, dominant repressor lines were generated by over-expressing the full-length coding region fused to a 39-base pair dominant repressor sequence; SWAM1-DR. Multiple independent events were generated and tested for each transgene. In general, the SWAM1 gain-of-function and dominant repressor plants exhibited reciprocal phenotypes. Two weeks after germination, both lines had similar stature, but phenotypically diverged when stem internodes began to elongate ( FIG. 2A ). When the inflorescence emerged from the flag leaf, SWAM1-OE lines were slightly taller than the control lines and the dominant repressor lines were significantly shorter. These phenotypes persisted throughout development until plants completely senesced ( FIG. 2B ). Inflorescence emergence was significantly delayed by about 5 days in both lines compared to the controls ( FIG. 2C ). Moreover, they differed significantly in above ground biomass. At complete senescence, above ground biomass yield was significantly greater for SWAM1-OE plants and reduced for SWAM1-DR plants ( FIG. 2D ). While there was no significant difference in plant height between control and SWAM1-OE lines, SWAM1-DR lines were dramatically shorter ( FIG. 2E ). Leaf, stem node, and internode count were unchanged; however, the internodes were not fully elongated in SWAM1-DR plants. Possible explanations for a short internode include fewer cells, shorter cells, or both. To test these possibilities propidium iodide treated longitudinal sections of the first internode was examined using confocal microscopy ( FIG. 3A-C ). An equivalent number of long cells was observed among the three lines ( FIG. 3D ), but the SWAM1-DR long cells were not as elongated ( FIG. 3E ). In addition, the transverse stem cross section area differed among the three lines at senescence. Relative to control, SWAM1-OE plants had a larger transverse stem area and SWAM1-DR plants had a significantly smaller area ( FIG. 2F ). This observation may account for some of the differences observed in above ground biomass. 
     SWAM1 Regulates Secondary Cell Wall Lignification and Biofuel Conversion Efficiency 
     To further investigate the function of SWAM1, stem cross sections were analyzed using bright field light microscopy for changes in vascular patterning and composition. Vascular bundle shape and arrangement appeared similar in all three transgenic lines; however, a striking difference was observed in the cells between the vascular bundles when stained with a lignin-indicator dye, phloroglucinol-HCl ( FIG. 4A-C ). The interfascicular fiber regions of SWAM1-OE sections were bright red and the SWAM1-DR sections were yellow relative to the control sections indicating the presence of very little lignin. However, the color intensity of the vascular bundles was similar among the three transgenic lines. The striking change in histochemical staining led to the investigation of the lignin content in these lines. Fully senesced pulverized stem tissue was assayed for acetyl bromide soluble lignin content. There was a slight increase in lignin content in SWAM1-OE stems and a significant decrease in SWAM1-DR stems ( FIG. 4D ). Considering lignin content is generally inversely correlated with bioconversion efficiency phenotypes, ethanol yield was measured after culturing senesced stems with  Clostridium phytofermentans . As expected, a decrease in ethanol yield was observed for SWAM1-OE lines and conversely a significant increase for SWAM1-DR lines ( FIG. 4E ). 
     SWAM1 is an Activator of Secondary Cell Wall Biosynthesis and a Regulator of Cell Wall Thickening 
     The interfascicular fiber walls were examined in greater detail using transmission electron microscopy due to the striking changes observed in lignin staining and overall stem area. The first internode of the tallest stem when the inflorescence had just emerged from the flag leaf was fixed and sectioned using an ultra-cut microtome ( FIG. 5 ). In comparison to the cell wall thickness of the control samples, SWAM1-OE walls were thicker and SWAM1-DR walls noticeably thinner. These results suggest that changes in secondary wall thickness may account for the overall differences observed in stem area and the above ground biomass ( FIG. 5D-F ). Based on these results it is evident that SWAM1 plays an important role in activating secondary wall thickening. 
     SWAM1 Regulates Cellulose and Lignin Associated Gene Expression 
     To investigate the transcriptional function of SWAM1, gene expression was measured in SWAM1 transgenic mutants. The tallest stem from developmentally equivalent plants was collected and flash frozen when the inflorescence was just visible from the flag leaf. Quantitative real time PCR (QRT-PCR) was utilized to examine transcript abundance of the transgenes and cell wall genes. Presence of the SWAM1-OE transgene resulted in a slight increase in the abundance of the SWAM1 transcript and the SWAM1-DR transgene resulted in a significant increase in the total SWAM1 transcript ( FIG. 6A ). Three cellulose genes, two lignin genes and one hemicellulose gene was analyzed using QRT-PCR. Among the three CELLULOSE SYNTHASE A genes, BdCESA4 and BdCESA7 were significantly up regulated in SWAM1-OE plants. All three CESA genes were significantly down regulated in SWAM1-DR plants ( FIG. 6B ). A similar expression pattern was observed for the lignin gene, BdCOMT4, a significant up regulation in SWAM1-OE plants and a significant down regulation in SWAM1-DR plants. The second lignin gene BdCAD1 exhibited no significant change in the transcript level in SWAM1-OE plants however it was significantly down regulated in SWAM1-DR plants ( FIG. 6B ). The transcript levels of the hemicellulose gene BdGT47D3 was moderately increased in the SWAM1-OE plants and significantly decreased in SWAM1-DR plants. As demonstrated above, SWAM1 influences the expression of cellulose, hemicellulose and lignin gene expression. Changes in BdCESA4/7/8, BdGT47D3, BdCOMT4 and BdCAD1 transcript levels along with the changes observed in cell wall thickness and composition implies SWAM1 activates the transcription of secondary cell wall biosynthetic genes. It is reasonable to predict there will be transcriptional changes associated with other cell wall genes that are functional in a similar capacity in cellulose and lignin biosynthesis. The cis-regulatory regions of BdCESA4/7/8, BdCOMT4 and BdCAD1 were searched for known regulatory elements. A sequence similar to the AC-11 element (Hatton et al., 1995)(ACCAAC) is upstream of the lignin genes BdCAD1 and BdCOMT4 and the cellulose genes BdCESA4/7/8 ( FIG. 9 ). A heterologous system was used to test for an affinity between this common motif and SWAM1 protein. Four adjacent copies of the identified AC-II were fused to the GAL4 activation domain and stably integrated into the yeast genome. A similar strain was developed using a mutated motif (TTTAAC) as a negative control. SWAM1 preferentially bound the promoter containing the AC-II element, but not the mutated version ( FIG. 6C ). 
     SWAM1 Directly Interacts with Secondary Cell Wall Biosynthetic Genes In Vivo 
     Altogether these results support the notion that SWAM1 directly activates cellulose and lignin gene expression by direct interaction with their cis-regulatory regions. To investigate these interactions in vivo, transgenic lines were generated with a GFP-tagged SWAM1 (SWAM1-GFP-OE). These lines were used for chromatin immunoprecipitation along with control plants (GU-OE). Immunoprecipitated chromatin was used as template for QRT-PCR to assay for enrichment of specific cell wall gene cis-regulatory regions. The results revealed a SWAM1 specific enrichment of BdCESA4, BdCESA8, BdCAD1 and BdCOMT4 promoter fragments ( FIG. 6D ). Moreover, all the enriched fragments contain an AC-like element ( FIG. 9 ). This provides evidence for direct binding of SWAM1 to cell wall gene promoters. 
     Discussion 
     A co-transcriptional analysis coupled with protein phylogenies with a focus on MYB transcription factors was used and resulted in the identification of SWAM1 as a potential candidate regulator of cell wall thickening. The SWAM1 transcript was abundant in stem, mirroring the expression profile of characterized  A. thaliana  cell wall regulators involved in promoting secondary cell wall biosynthesis (Ko et al., 2004; Brown et al., 2005; Kubo et al., 2005; Persson et al., 2005). The SWAM1 transcript was mainly localized in the interfascicular fibers, xylem and somewhat to the epidermis. The SWAM1 protein shares some homology to AtMYB46 and AtMYB83, which are mainly expressed in xylem fibers (Zhong et al., 2007; McCarthy et al., 2009), but BdMYB1 is the closest ortholog (Valdivia et al., 2013). All of the characterized cell wall related  A. thaliana  MYB proteins are localized to the xylem and fibers and none have been reported with interfascicular fiber specific localization. Interestingly, SWAM1 has a strong localization pattern in the interfascicular fiber cells. The difference observed in tissue specific localization between SWAM1 and AtMYB46 and AtMYB83 could be attributed to the phylogenetic separation or species-specific differences. Indeed, SWAM1 is part of a phylogenetic clade that includes grasses and eudicots, but not the Brassicaceae, namely  A. thaliana, A. lyrata , and  C. rubella . As was observed in  B. distachyon , the poplar and potato SWAM1 clade genes are most highly expressed in the available gene expression dataset for potato and poplar (Winter et al., 2007), which suggests these genes may have a conserved function. 
     SWAM1 over-expression and dominant repression transgenes were used for in planta functional characterization. The timing of inflorescence emergence was the only trait that exhibited a similar and significant effect. The whole plant phenotypes were dramatically different; SWAM1-OE resulted in a larger plant with greater biomass. This has not been reported for the over-expression of AtMYB46/83/58 or 63 (Zhong et al., 2007; Ko et al., 2009; McCarthy et al., 2009; Zhou et al., 2009). The increase in above ground biomass appears to be in part the product of larger stems with thicker secondary cell walls. Thicker secondary cell walls were also observed in AtMYB46 and AtMYB83 over-expression lines (Zhong et al., 2007; McCarthy et al., 2009). Conversely, SWAM1-DR resulted in severely dwarf plants with significantly diminished above ground biomass. Dwarfism in SWAM1-DR plants was mainly attributed to the internode cell length, but not the cell count. SWAM1-DR stem cells were significantly shorter compared to the control stem cells resulting in a significantly dwarfed plant. These plants also had significantly smaller stems with thinner interfascicular fiber cell walls. AtMYB46 and AtMYB83 dominant repressors were also shown to have significantly thinner secondary cell walls in vessels and fibers resulting in a pendent phenotype (Zhong et al., 2007; McCarthy et al., 2009). However unlike SWAM1, dominant repression of AtMYB46 and AtMYB83 did not cause dwarfism. The difference seen between SWAM1 and AtMYB46 and AtMYB83 plant height phenotypes under dominant repression could be the result of a functional difference between these MYB proteins. 
     Another striking observation was the differences in lignification in stem cross sections. Senesced plants were used for histochemical analysis and lignin composition analysis. Over-expression of SWAM1 resulted in a moderate increase in the lignin content in whole stems and dominant repression resulted in a significant decrease. Based on phloroglucinol-HCl staining it is evident that SWAM1 has a profound impact on the interfascicular fiber cell wall lignification. SWAM1 transcripts were also localized to the same cell types in stem cross sections mainly to the interfascicular fibers and somewhat to the xylem and epidermis. Transcript localization and histochemical analysis of stems further supports an important role for SWAM1 in interfascicular fiber cell wall regulation. Reciprocal lignification patterns have been observed in histochemical studies performed on AtMYB46/83 transverse stem cross sections, where over expression of the genes resulted in ectopic lignification in parenchyma cells and dominant repression results in the absence of secondary cell wall lignification (Zhong et al., 2007; McCarthy et al., 2009). Even though reciprocal phenotypes for total stem lignin were observed, the prominent effect of SWAM1 dominant repression on interfascicular fiber cells is a unique observation. As expected, over-expression of SWAM1 upregulated secondary cell wall biosynthesis genes. Moreover, dominant repression resulted in a significant down regulation of the same cell wall genes. These findings argue that SWAM1 is an activator of secondary cell wall biosynthesis. Some MYB proteins are known to interact with AC-like elements and either activate or repress the transcription of downstream targets (Lois et al., 1989; Hatton et al., 1995; Raes et al., 2003; Kim et al., 2012; Zhong and Ye, 2012). Next, the promoters of genes involved in secondary cell wall biosynthesis for over represented cis-regulatory elements were investigated. As suspected BdCESA4/7/8. BdCAD1, and BdCOMT4 genes all harbor AC-like elements in their promoter regions. In yeast, SWAM1 preferentially bound the AC rich element relative to a mutated version. Therefore, it is plausible that SWAM1 activates the downstream secondary cell wall genes via a protein-DNA interaction facilitated through AC elements found in their promoter regions. This was further supported by the enrichment of cell wall gene promoters such as BdCESA4, BdCESA8 and BdCOMT4 in SWAM1 immunoprecipitated chromatin. This provides in planta evidence for a direct interaction between SWAM1 protein and the cell wall gene promoters. AtMYB46 has also been shown to interact with the AtCESA4/7/8 promoters in planta (Kim et al., 2013). Therefore, based on the in silico predictions, synthetic AC element analysis and chromatin immunoprecipitation, it is evident SWAM1 is a direct activator of secondary cell wall biosynthesis in  B. distachyon.    
     As might be expected for plants with a significant reduction in total lignin, a moderate reduction in ethanol yield was observed following incubation of pulverized SWAM1-DR stems with  Clostridium phytolermentans . On the other hand SWAM1-OE resulted in larger plants with greater above ground biomass without increasing recalcitrance making SWAM1 a candidate for energy crop improvement. In conclusion, it was herein demonstrated that SWAM1 is a activator capable of regulating secondary cell wall biosynthesis. This protein has a greater impact on the interfascicular fiber cell walls, which is ideal in manipulating energy crops without causing drastic effects to the vascular system. 
     Example 2 
     Grass NAC Repressor of Flowering Suppresses Floral Transition and Secondary Wall Synthesis in  Brachypodium Distachyon    
     Introduction 
     The large NAC (NAM, ATAF1/2, and CUC2) transcription factor family is comprised of plant-specific proteins. Several are well characterized with respect to the regulation of secondary cell wall biosynthesis and are thought of as key regulators in this process. SECONDARY WALL ASSOCIATED NAC DOMAIN PROTEIN1 (SND1; also known as NST3) is a fiber specific  Arabidopsis thaliana  secondary cell wall regulator. SND1 is the most extensively characterized among these NAC proteins that activate the expression of cellulose and lignin genes. Over-expression of SND1 results in ectopic deposition of secondary cell walls in parenchymatous cells. Conversely, dominant repression results in a significant reduction in secondary cell wall deposition in fibers (Zhong et al., 2006). NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 and 2 (NST1/2) regulate secondary cell wall deposition in  A. thaliana  anther endothecium (Mitsuda et al., 2005). NST1 and SND1 are thought to play redundant regulatory roles and the double mutant causes a drastic reduction in the expression of secondary cell wall genes and a significant reduction in cellulose, xylan and lignin biosynthesis (Mitsuda et al., 2007; Zhong et al., 2007). VASCULAR RELATED NAC DOMAIN6 and 7 (VND6/7) specifically expressed in protoxylem and metaxylem are required for vessel development in  A. thaliana  roots (Kubo et al., 2005; Demura and Fukuda, 2007). Moreover, over-expression of VND6/7 results in ectopic vessel development and dominant repression results in the loss of protoxylem and metaxylem development (Kubo et al., 2005). Collectively these five NAC proteins are considered master regulators capable of activating the entire secondary cell wall biosynthesis process by interacting and activating downstream transcription factors including SND2, SND3, MYB46, MYB54, MYB42, MYB103, MYB85, MYB52, MYB69 and KNAT7 (Zhong et al., 2007; Zhong et al., 2008). 
     To date, very little functional characterization has been done for the two wall biosynthesis associated NAC transcription factors SND2 and SND3. These two proteins are distantly related to the previously described proteins when considering DNA-binding and transcriptional activation domain sequences (Hu et al., 2010; Wang et al., 2011). Even though SND1, SND2, and SND3 share the same identifier, SND1 is closely related to NST1 and NST2 and distantly related to SND2 and SND3. In a recent study NAC protein from 19 plant species were analyzed to understand the evolutionary relationship among NST, SND and VND sub groups. In this comparison, SND2 orthologs were found in both dicot and monocot species. However, SND3 was only found within dicot species suggesting it is a dicot specific regulator (Yao et al., 2012). Both SND2 and SND3 are highly expressed in  A. thaliana  stems mirroring a similar expression profile of many characterized cell wall regulators (Yao et al., 2012). Over-expression of SND2 increases the secondary wall thickness in interfascicular and xylary fibers in  A. thaliana  (Zhong et al., 2008). Conversely, dominant repression results in a drastic reduction of secondary wall thickness in fibers. Moreover, SND2 has been shown to regulate cellulose, hemicellulose, and lignin biosynthesis genes (Hussey et al., 2011). SND2 orthologous proteins have also been characterized in poplar. Over-expression of the SND2 ortholog PopNAC154 in poplar reduced plant height; however, unlike in  A. thaliana , over-expression had no effect on secondary cell wall thickness (Grant et al., 2010). On the other hand, dominant repression of the SND2 ortholog (PtSND2) resulted in a significant reduction of secondary cell wall thickness in xylary fibers (Wang et al., 2013). These diverging results between  A. thaliana  and poplar suggest differing regulatory functions by the various SND2 orthologs in different plant species. This contrasts with SND1, where the rice and maize counterparts were able to complement the snd1/nst1 double mutant and cause similar over-expression phenotypes in  A. thaliana  (Zhong et al., 2011; Yoshida et al., 2013). 
     Secondary cell walls, by weight, represent the majority of biomass in stem tissue. While grasses can produce abundant stem before flowering,  A. thaliana  grows as a rosette of leaves and only elongates stem following floral induction. The transition from vegetative to reproductive growth is an important phenomenon that is achieved through the integration of developmental and environmental cues such as day length and temperature. The molecular mechanisms of flowering have been well characterized in the model dicot  A. thaliana . The mobile signal responsible for this transition is florigen, which is encoded by FLOWERING LOCUS T (FT). It moves from leaves to the shoot apical meristem to activate meristem identity genes, including APETALA1 (AP1), CAULIFLOWER (CAL) and FRUITFUL (FUL), to transition the shoot apical meristem into a flower bud ( FIG. 10 ) (Ream et al., 2014). FT is expressed following exposure to cold through epigenetic repression of repressors of flowering: FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) (Michaels and Amasino, 1999; Alexandre and Hennig, 2008; Gu et al., 2010). Long day photoperiod can also induce flowering through CONSTANS induction of FT expression (Imaizumi and Kay, 2006). Once activated, the mobile signal can complex with the bZIP transcription factor FD to form an FT-FD complex in the stem (Jaeger and Wigge, 2007). This complex is responsible for initiating the transcription of meristem identity genes. 
     Many of these same components have been identified as having a role in the control of flowering in grasses. Similar to  A. thaliana , FT (also known as VERNALIZATION3 in barley and wheat) is the main floral integrator of developmental and environmental cues and turning on floral meristem identity genes including VRN1 (Greenup et al., 2010; Wu et al., 2013; Lv et al., 2014; Ream et al., 2014). In temperate cereals, FT expression is induced under long days and VRN2 is repressed in response to vernalization (Greenup et al., 2010). VRN1 is the cereal AP1 ortholog, but contrary to  A. thaliana  AP1, VRN1 is expressed in both leaves and in the floral meristem (Trevaskis et al.; Alonso-Peral et al., 2011). VRN1 is activated by low temperatures and as a result represses VRN2 during winter allowing flowering in spring (Greenup et al., 2009). PHOTOPERIOD1-H1 (PPD-H)1 is another component responsible for activating FT under reduced levels of VRN2. Once activated, FT protein binds FLOWERING LOCUS D LIKE2 (FDL2), the FD ortholog found in cereals and initiates VRN1 transcription in the meristem (Li and Dubcovsky, 2008) triggering the transition to flowering ( FIG. 11 ). Regardless of the similarities and distinctions for the signal transduction pathways that govern floral induction between  A. thaliana  and grasses, fundamental differences in how that regulation relates to stem formation are expected. Here we describe the function of a NAC transcription factor, GRASS NAC REPRESSOR OF FLOWERING (GNRF), using over-expression and loss-of-function mutant lines. 
     Material and Methods 
     Phylogenetic Analysis 
     Amino acid sequences of  A. thaliana  NAC proteins SND2 and SND3 and the orthologous proteins from  O. sativa, Z. maize, P. trichocarpa  and  Sorghum biocolor  were downloaded from plant transcription factor data base (P1nTFDB; plntfdb.bio.uni-potsdam.de/v3.0).  B. distachyon  NAC sequences were downloaded from phytozome (phytozome.net/). A neighbor-joining phylogeny was constructed with 1000 bootstrap permutations using MEGA 5.0. An outgroup including  A. thaliana  NST1, NST2 and SND1 were also included in this analysis. 
     GNRF-OE Plasmid Construction 
     Full-length coding region of Bradi2g46197 (GNRF) was PCR amplified using Bd21-3 cDNA with the stop codon using Phusion high-fidelity DNA polymerase (New England Bio Labs) and cloned into pENTR/D-TOPO vector (Invitrogen). Sequence-confirmed entry clone was recombined with pOL001 ubigate ori1 destination vector (modified from pOL001, described in (Vogel et al., 2006) to generate the GNRF gain-of-function construct (GNRF-OE). Above construct was transformed into  Agrobacterium tumefaciens  strain AGL1 via electroporation for  B. distachyon  calli transformations. 
     Plant Material, Growth Conditions and Calli Transformation 
       Brachypodium distachyon  (L.) line Bd21-3 was used as the genetic background. Seeds were imbibed a week and planted as previously described by Handakumbura et al., 2013.  Brachypodium distachyon  calli transformation was carried out as described by (Vogel and Hill, 2008) with minor modifications described in Handakumbura et al., 2013. Once shoots and roots were established primary transgenics were transplanted to soil. Primary transgenic were PCR confirmed by the amplification of the hygromycin resistance gene and were propagated for two subsequent generations to obtain T3 individuals. 
     gnrf-1 Mutant Allele Isolation 
     A homozygous gnrf-1 mutant allele was isolated from the TILLING (Targeting Induced Local Lesions in Genomes) mutant population generated at INRA-Versailles by restriction enzyme digestions. Leaf genomic DNA was isolated from each individual using the method described by Handakumbura et al., 2013. A 614 bp fragment spanning the region with the mutations was PCR amplified using Taq DNA polymerase and the purified amplicons were digested with BaeGI at 37° C. The digestion results in two fragments of 141 bp and 473 bp for the wild-type allele and a single undigested fragment for the mutant allele. 
     Genotyping and Phenotyping 
     Genomic DNA was extracted from T3 generation GNRF-OE plants and M2 generation gnrf-1 plants as previously described (Handakumbura et al., 2013). GNRF-OE plants were PCR confirmed for the hygromycin selectable marker gene and were used in subsequent experiments. Flowering was induced in about five percent of the GNRF-OE plants with excessive fertilizer treatment with a N-P-K 10:30:20 fertilizer. Homozygous gnrf-1 mutants were confirmed by restriction enzyme digestion as described previously. Phenotypic data such as flowering time, plant height, above ground biomass at senescence were manually recorded. 
     RNA Extraction and QRT-PCR 
     Total RNA was extracted from the first, second, and third internodes of the tallest stem at BBCH stage 5 and from the fourth leaf from the base of the tallest stem at BBCH stage 4.5 (Hong et al.) (Plant RNaeasy, Qiagen, Valencia, Calif.) as previously described by Handakumbura et al., 2013. First strand cDNA was synthesized from 1 μg of DNase (Qiagen) treated total RNA using Superscript III reverse transcriptase with oligo dT primers (Invitrogen, Grand Island, N.Y.). Triplicate quantitative PCR reactions were performed as described in Chapter 3. BdUBC18 (ubiquitin-conjugating enzyme 18) and GapDH were used as reference genes for normalization (Hong et al., 2008). QuantiPrime primer design tool was used for qPCR primer design (Arvidsson et al., 2008). 
     Microarray Analysis 
     For the microarray analysis, three stem samples at BBCH stage 5 (Hong et al., 2011) were pooled for each biological replicate and hybridized in triplicate for each line. RNA was extracted using a kit (Plant RNaeasy, Qiagen, Valencia, Calif.) as described above. Samples were hybridized to a  B. distachyon  BradiAR1b520742 whole genome tiling array (Affymetrix, Santa Clara, Calif.). Based on the hybridization signals a significantly differentially expressed gene list was generated using a modified t-test (Tusher et al., 2001). 
     Histo-Chemical Analysis of Stem Lignification 
     Histo-chemical assays were performed on the first internode of tallest stem at complete maturity. Hand cut sections were stained with phloroglucinol-HCl as described in Chapter 3 for total lignin. Stained sections were observed under an Eclipse E200MV R microscope (Nikon) and imaged using a PixeLINK 3 MP camera. 
     Acetyl Bromide Soluble Lignin Measurement 
     Fully senesced pulverized stem tissue was used for acetyl bromide soluble lignin (ABSL) measurements as previously described (Foster et al., 2010) and briefly specified in Chapter 3. Three to six individuals were analyzed in triplicate for each line. 
     Results 
     Bradi2g46197 Transcript is Abundant in Stem Tissue 
     The secondary cell wall regulators characterized to date exhibit the signature expression profile of being highly expressed in tissues abundant in secondary cell walls relative to other tissues. To investigate Bradi2g46197 transcript abundance in leaf, stem, and root, a  B. distachyon  microarray data set was utilized (Handakumbura et al., 2013). Bradi2g46197 transcript abundance was approximately nine and three-fold greater in stem, relative to leaf and root, respectively ( FIG. 12A ). Grass stems are substantially enriched for secondary cell walls (Matos et al., 2013). Therefore, based on annotation and expression analysis, Bradi2g46197 is a potential candidate regulator of grass secondary cell wall biosynthesis. 
     Bradi2g46197 is the Closest Ortholog to SND2 
     Bradi2g46197 belongs to the plant specific NAC transcription factor family that is involved in a variety of processes. Some of the  A. thaliana  NAC proteins such as NST1/2, SND1/2/3 are specifically involved in the regulation of cell wall biosynthesis. To determine the protein similarity between Bradi2g46197 and the functionally characterized NACs, a phylogeny was constructed between the NAC protein sequences from  A. thaliana, B. distachyon, O. sativa, Z. maize, P. trichocarpa  and  Sorghum bicolor  using the MEGA 5.0 software. NST1, NST2 and SND1 were used as an out-group in order to better understand the relationship of Bradi2g46197 to the other dicot and monocot NAC orthologs ( FIG. 12B ). Based on protein similarity, Bradi2g46197 is a grass ortholog to both SND2 and SND3. Both dicots included in this analysis,  A. thaliana  and poplar, have two orthologous proteins in this clade while the grasses have only one. 
     Over-Expression of Bradi2g46197 Results in Persistent Vegetative Growth 
     To investigate the function of Bradi2g46197, gain-of-function lines were developed by over-expressing the full-length coding region under the maize Ubiqutin promoter. Multiple independent events were generated for this construct and at least three events were used in the subsequent experiments. A homozygous line with a nonsynonymous point mutation that modifies the fiftieth amino acid from a proline (P) to a leucine (L) was isolated from a TILLING (Targeting Induced Local Lesions in Genomes, (Dalmais et al., 2013) population to investigate the loss-of-function phenotypes. The aforementioned point mutation lies within the DNA binding domain in the N-terminus and predicted to alter protein function. Surprisingly, over-expression construct harboring transgenics remained vegetative until senescence ( FIG. 13 ). These plants exhibited a branched and bushy phenotype and did not transition from vegetative to reproductive growth. We therefore named the Bradi2g46197 locus GRASS NAC REPRESSOR OF FLOWERING (GNRF). From here on, the gain-of-function mutant will be referred to as GNRF-OE and the loss-of-function mutant gnrf-1. Unlike GNRF-OE plants, which did not flower and were considerably shorter than control plants, gnrf-1 plants flowered significantly earlier than the control plants by approximately 1.5 d ( FIG. 14A ) and were similar to control plants in stature ( FIG. 14B ). Moreover, the above ground biomass was significantly greater for GNRF-OE plants whereas no significant difference was observed between gnrf-1 plants and the controls ( FIG. 14C ). 
     GNRF is a Repressor of Genes Associated with Cell Wall, Transport, and Flowering 
     Considering the dramatic pleiotropic effects of the gain-of-function lines, a microarray experiment was performed using RNA from pooled stems from control, GNRF-OE and gnrf-1 plants in order to isolate the potential effected pathways. Samples were hybridized to the  B. distachyon  BradiAR1b520742 whole genome tiling arrays and differentially expressed genes were identified using a modified t-test. No significant differences in gene expression were detected between control and gnrf-1. Some rather dramatic changes were observed within the GNRF-OE plants. While only 23 genes were up-regulated by GNRF over-expression, 372 genes were significantly down-regulated. One of the largest categories of repressed genes was transporters of numerous substrates: amino acids, ammonium, arsenite, carboxylate, lipids, peptides, potassium, silicon, sucrose, and sulfate (Table 4.1). Polysaccharide synthesis genes, lignin and lignin related genes, and lipid transfer genes were also abundant among the repressed genes. The most striking observation was the &gt;50 fold repression of two floral meristem identity associated genes VRN1/FUL1/MADS33 (Bradi1g08340) and FUL2/MADS10 (Bradi1g59250). These two genes are the two closest orthologs to  A. thaliana  AP1 and FUL. Apart from the above two genes, several other MADS-box, bHLH, WRKY, HB, NAC and MYB transcription factors were repressed in GNRF-OE stems. Another interesting observation is the 3-fold reduction of BdMYB48 (Bradi2g47590). As previously described (Chapter 3) BdMYB48 is a direct activator of secondary cell wall biosynthesis genes. The repression of the cellulose genes CESA4, CESA7, and COMT4, 4CL1, 4CL3, CCoAMT lignin genes in the GNRF-OE stems could be an indirect effect due to the repression of BdMYB48. As a result of the repression of many cellulose and hemicellulose synthesis genes, GNRF-OE stems should show a significant reduction in the polysaccharide composition. Apart from lignin genes, many laccasses and peroxidases were also repressed in these mutants. These genes are necessary for the polymerization of lignin monomers and their subsequent polymerization within the cell wall (Boerjan et al., 2003). Moreover, several copper ion transporter genes were repressed. Copper ions act as a catalyst in the lignin polymerization process (Boerjan et al., 2003). Down regulation of many lignin and lignin associated genes along with the necessary catalysts should result in a significant reduction in cell wall lignification in GNRF-OE mutants. 
                     TABLE 4.1                  Genes repressed by GNRF in GNRF-OE stems                         Gene name   Gene description   Fold change                         Transcription factors                         Bradi1g08340   MADS33/VRN1/FUL1   53.8       Bradi1g59250   MADS10/FUL2   51.3       Bradi1g08326   MADS1   33.6       Bradi2g00280   WRKY47   7.7       Bradi3g26690   BEL-like Homeobox   7.0       Bradi1g48520   MADS7   6.1       Bradi1g69890   MADS11   5.7       Bradi1g26720   SBP family   4.6       Bradi1g57607   KNOX6 Homeobox   4.5       Bradi3g56290   bZip family   4.7       Bradi5g10640   NAC family, XND1-like   3.6       Bradi1g63690   MYB-like family   3.7       Bradi1g51960   MYB15   4.5       Bradi2g48690   MADS19   4.3       Bradi3g21480   Homeobox family   3.8       Bradi4g27720   bZIP70   4.4       Bradi3g34567   WRKY13   2.5       Bradi2g05700   NAC28   2.9       Bradi2g47590   MYB48/SWAM1   3.0       Bradi3g51800   MADS28   2.8       Bradi5g11270   MADS36   2.7       Bradi1g12690   KNOX4 Homeobox   3.0       Bradi1g10047   KNOX2 Homeobox   3.2       Bradi2g09720   C2C2-Dof family   3.4       Bradi1g73710   C2C2-Dof family   2.6       Bradi1g12780   bHLH family   3.4       Bradi1g71990   bHLH family   3.2       Bradi3g15440   bHLH family   2.7       Bradi3g16515   MYB59/LHY   2.9       Bradi3g03407   ARF family   3.1       Bradi4g33370   WRKY60   2.2       Bradi2g59110   SBP family   2.3       Bradi5g22920   bHLH family   2.2       Bradi2g23530   BEL-like Homeobox   2.3       Bradi5g17640   AP2 family   2.2                 Cell wall polysaccharide synthesis                         Bradi2g60557   Glycosylhydrolase, GH17, β-1,3-glucanase 1   12.4       Bradi2g34650   Fasciclin-like arabinogalactan protein   8.1       Bradi1g64560   Glycosyltransferase, GT34 family,   7.6           xylosyltransferase       Bradi2g08310   Glycosyltransferase, GT1 family, UDP-glucosyl   7.1           transferase       Bradi1g12290   Glycosyltransferase, GT47 family   6.8       Bradi4g13697   Glycosyltransferase, GT37 family fucosyltransferase 1   6.2       Bradi2g61230   Glycosyltransferase, GT61 family   5.5       Bradi1g25117   Cellulose synthase-like F   3.8       Bradi1g33827   Glycosylhydrolase, GH6, xyloglucan   4.9           endotransglycosylase 6       Bradi1g21990   Glycosyltransferase, GT75 family   4.8       Bradi1g12710   Glycosyl hydrolase, GH10 family   4.8       Bradi2g00220   Fasciclin-like arabinoogalactan protein   4.6       Bradi1g22030   COBRA   4.5       Bradi3g04080   Glycosylhydrolase, GH9 family glycosyl hydrolase   4.0           9B8       Bradi5g04120   Glycoside hydrolase, α-Expansin   3.9       Bradi2g53580   Glycoside hydrolase, α-Expansin   3.8       Bradi4g33490   Fasciclin-like arabinoogalactan protein   3.8       Bradi4g29640   Glycosylhydrolase, GH9 family   3.8       Bradi4g21240   Pfam: 04669 Polysaccharide biosynthesis   3.7       Bradi2g02320   Glycosylhydrolase, GH10 family   3.7       Bradi2g59410   Glycosyltransferase, GT47 family   3.6       Bradi1g59880   COBRA-like   3.6       Bradi3g33130   Glycoside hydrolase, β-Expansin   3.6       Bradi3g28350   Glycosyltransferase, GT2 family, CESA4   3.0       Bradi4g30540   Glycosyltransferase, GT2 family, CESA7   2.8       Bradi3g33140   Glycosylhydrolase, β-Expansin   2.7       Bradi3g19087   Glycosyltransferase, GT2 family, CSLC   2.6       Bradi4g28260   Glycosyltransferase, GT77 family, Extensin   2.5       Bradi1g10347   Glycosylhydrolase, GH17 family   2.3                 Lignin synthesis                         Bradi2g23370   Laccase   12.6       Bradi1g66720   Laccase   12.3       Bradi3g58560   Copper ion binding   11.6       Bradi1g27910   Peroxidase   11.3       Bradi2g09690   Peroxidase   6.9       Bradi2g20840   Peroxidase   5.9       Bradi1g27920   Peroxidase   5.3       Bradi3g30590   Ferulic acid 5-hydroxylase 1 (FAH1)   5.1       Bradi2g54680   Laccase   4.7       Bradi4g44810   Laccase   4.3       Bradi3g38540   Copper ion binding   4.5       Bradi1g24880   Laccase   4.3       Bradi4g11850   Laccase   4.3       Bradi4g28920   Copper transporter protein ATOX1-related   4.3       Bradi1g43680   Peroxidase   4.0       Bradi1g38297   Peroxidase   3.2       Bradi3g05750   4-coumarate-CoA ligase 3 (4CL3)   3.1       Bradi1g32870   Peroxidase   3.1       Bradi1g45790   Copper ion binding protein   2.9       Bradi1g68900   Peroxidase   2.9       Bradi3g39420   Caffeoyl CoA 3-O-methyltransferase (CCoAOMT)   2.8       Bradi3g16530   Caffeic acid O-methyltransferase (COMT4)   2.8       Bradi1g31320   4-coumarate-CoA ligase 1 (4CL1)   2.4       Bradi3g09240   Copper binding protein   2.3                 Lipid transfer                         Bradi2g17550   Lipid transfer protein   8.5       Bradi2g17530   Lipid transfer protein   7.8       Bradi2g30490   Lipid transfer protein   3.8       Bradi1g19470   Lipid transfer protein   6.1       Bradi2g54970   Lipid transfer protein   4.9       Bradi2g32950   Lipid transfer protein   4.7       Bradi2g17540   Lipid transfer protein   4.4       Bradi5g17930   Lipid transfer protein   4.2                 Transport                         Bradi3g39800   Dicarboxylate transporter   7.8       Bradi1g78100   Arsenite transport   6.5       Bradi1g45190   Amino acid transporter   6.3       Bradi3g05570   Potassium ion transporter   6.2       Bradi1g03500   Proton-dependent oligopeptide transporter   5.3       Bradi3g48950   Ammonium transporter   5.0       Bradi4g21790   Proton-dependent oligopeptide transporter   5.0       Bradi3g37850   Potassium ion transporter   4.7       Bradi1g21800   Sugar transporter   4.6       Bradi3g51280   Major facilitator superfamily   3.7       Bradi3g28920   UDP-glucuronic acid transporter   3.6       Bradi2g07830   Aquaporin transporter   3.6       Bradi1g69770   Aluminum activated citrate transporter   3.4       Bradi1g34140   ATPase-like zinc transporter   3.3       Bradi5g17990   ATP dependent copper transporter   3.2       Bradi1g25937   EamA-like transporter   3.1       Bradi4g28000   Sugar transporter   2.7       Bradi3g16130   ABC transporter   2.7       Bradi1g73170   Sucrose transporter   2.7       Bradi1g17830   Potassium transporter   2.6       Bradi3g39077   Oligopeptide transporter   2.6       Bradi4g34510   PINFORMED-Like auxin efflux carrier   2.5       Bradi2g24910   Amino acid transporter   2.5       Bradi3g32390   Tetracycline transporter   2.5       Bradi2g34560   ZIP Zinc transporter   2.5       Bradi5g24170   Sulfate transporter   2.4       Bradi3g51250   Mechanosensitive ion channel   2.4       Bradi1g59830   Amino acid transporter   2.3       Bradi1g34210   Cation transmembrane transporter   2.3       Bradi4g08130   ABC transporter   2.1                    
GNRF Represses Meristem Identity Genes and Floral Integrators
 
     Considering that GNRF-OE plants lacked the ability to transition from vegetative to reproductive growth, and many flowering associated genes were repressed as measured by microarray, flowering pathway genes were further investigated by QRT-PCR. I initially sought to validate the microarray results by analyzing the expression of FUL1, FUL2 and CENTRORADIALIS-LIKE1 HOMOLOGOUS TO TFL1 (RCN2) ( FIG. 15 ). The primary stem was collected and flash frozen from developmentally equivalent plants at BBCH stage 5 (Hong et al., 2011) when the inflorescence had just begun to emerge from the flag leaf sheath. Eight to ten plants were individually analyzed for transcript abundance. In agreement with the microarray data, FUL1, FUL2 and RCN2 were significantly down-regulated in GNRF-OE stems. The same genes were modestly, but not significantly up-regulated in the gnrf-1 stems. 
     Next relative transcript abundance of the mobile flowering signal was investigated. FLOWERING LOCUST, or florigen, is an activator of flowering and one of the terminal genes in this pathway (Higgins et al., 2010). The protein functions as a mobile signal that moves from the leaf to the shoot apex to initiate flowering. Accordingly, leaf tissue was used to investigate the relative abundance of FT transcripts. As might be expected, BdFT was undetectable in GNRF-OE leaves and significantly up-regulated in gnrf-1 leaves ( FIG. 16A ). In order to better understand this dynamic, I investigated several putative upstream repressors of FT. FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) act as immediate repressors of FT in  A. thaliana  and served as initial candidates in  B. distachyon  (Ruelens et al., 2013). While SVP expression was not altered in GNRF-OE (data not shown), expression of other FLC-like genes was altered ( FIG. 16B-D ). BdMADS37, BdODDSOC1 and BdODDSOC2 are  B. distachyon  orthologs of  A. thaliana  FLC and are collectively referred to as the FLC-like genes. BdMADS37 was down-regulated in GNRF-OE leaves and BbODDSOC1 and BdODDSOC2 were significantly up-regulated in GNRF-OE leaves. The expression of BdMADS37, BDODDSOC, and BdODDSOC2 were at similar levels to controls in gnrf-1 leaves. 
     GNRF Regulates Genes Associated with Cellulose, Xylan and Lignin Biosynthesis in Stem Tissue 
     Since NACs play a key regulatory role in secondary cell wall biosynthesis, the gene expression of several cell wall genes was measured in GNRF-OE and gnrf-1 plants to investigate the transcriptional function of GNRF. Quantitative real time PCR was utilized to examine transcript abundance of the transgenes and candidate cell wall genes using the same cDNA samples used for detecting flowering pathway genes. As expected, GNRF was significantly up-regulated in GNRF-OE stems ( FIG. 17 ). Three genes involved in cellulose biosynthesis namely BdCESA4/7/8 and two genes associated with lignin biosynthesis namely, BdCAD1 and BdCOMT4 and a gene with a predicted role in xylan biosynthesis BdGT47-1 were analyzed for changes in transcript abundance ( FIG. 18 ). All five cellulose and lignin genes were significantly down-regulated in GNRF-OE stems. The same genes were also found to be repressed in the microarray data set (Table 4.1). Conversely, the expression of BdCESA4/7, BdCAD1, and BdCOMT4 was significantly up-regulated in gnrf-1stems. While the putative xylan gene, BdGT47-1, was significantly up-regulated in the gnrf-1lines, no change was observed in GNRF-OE lines. Overall, these data suggest that GNRF is a repressor of cellulose and lignin gene expression. 
     GNRF Influences Cell Wall Composition 
     In order to correlate gene expression with levels of cellulose and lignin, histochemical assays were performed on stem tissue. First internodes of fully senesced stems were sectioned and stained with phloroglucinol-HCl to investigate possible changes in lignin content. While no visible changes in staining intensities were observed between control and gnrf-1 stem cross sections, GNRF-OE sclerenchyma fibers and vascular bundles exhibited a lighter shade of orange ( FIG. 19A ). Since phloroglucinol-HCl stains O-4-linked coniferyl and sinapyl aldehydes in lignified tissue in a concentration indicative manner, the lighter staining pattern observed in GNRF-OE is likely due to a decrease in total lignin. Fully senesced pulverized tissue was used to measure the acetyl bromide soluble lignin (ABSL) content to further investigate the function of GNRF on cell wall composition and lignification ( FIG. 19B ). As expected based on the phloroglucinol-HCL staining, the GNRF-OE stem was significantly reduced in ABSL content compared to the controls whereas no significant change was observed between the gnrf-1 and control samples. As many lignin and lignin related genes were repressed in the GNRF-OE stems it was expected to observe a reduction in lignin composition which is further demonstrated by the significant reduction in ABSL. 
     Discussion 
     Several NAC transcription factors have been shown to play crucial roles in secondary cell wall biosynthesis and overall plant growth and development. The  B. distachyon  NAC family is estimated to comprise 99 NAC proteins among which only one has been functionally characterized to date (International  Brachypodium  Initiative, 2010; Valdivia et al., 2013). GNRF was selected for functional characterization as it is highly expressed in stems mirroring an expression profile similar to that of characterized secondary cell wall regulators such as NST1, SND1 and SND2 (Mitsuda et al., 2005; Zhong et al., 2007). Moreover it is co-regulated with cell wall biosynthesis genes. 
     An over-expression construct was used to develop gain-of-function mutants with constitutive over-expression of GNRF. Simultaneously, a homozygous mutant allele harboring a nonsynonymous point mutation was isolated from a TILLING mutant collection to investigate the gnrf-1 loss-of-function phenotypes. Surprisingly, over-expression mutants demonstrated a persistent vegetative phenotype. GNRF-OE plants failed to flower and could not transition into the reproductive stage. Conversely the gnrf-1 mutants flowered significantly earlier than control plants. However apart from our observations, there are no known reports associating SND2 orthologs with flowering or floral transition. Over-expression of SND2 in  A. thaliana  had no adverse effects on flowering (Zhong et al., 2008). Additionally, no change in flowering time was observed with PtSND2 over-expression mutants (Wang et al., 2013). These observations warranted further investigation of the flowering pathway in  B. distachyon . I first confirmed the over-expression of the GNRF transgene and as expected GNRF transcripts were significantly up-regulated in both leaf and stem tissue in the GNRF-OE plants. FT is the key signal in the vegetative to reproductive transition, during which FT accumulates in  A. thaliana  leaves prior to flowering (Gu et al., 2010; Wu et al., 2013; Lv et al., 2014). In order to investigate the influence of GNRF on FT we analyzed FT expression in mutant leaves. As expected FT was not detectable in GNRF-OE leaves whereas it was significantly up-regulated in gnrf-1 leaves, in agreement with the flowering time phenotypes observed for these mutants. Unavailability of the mobile signal FT in GNRF-OE leaves is a possible cause for the persistant vegetative phenotype. Recently, FT was also shown to bind phospholipids to accelerate flowering (Nakamura et al., 2014). Another possibility is the repression of numerous lipid transporter genes, which in turn influence the availability of these phospholipids thus delaying the flowering process. 
     However the direct cause of the persistent vegetative growth of GNRF-OE is most likely due to the &gt;50 fold reduction of two MADS box transcription factors, FUL1 and FUL2. VRN1 is the closest ortholog to  A. thaliana  meristem identity gene AP1 in temperate cereals and is responsible for transitioning the meristem into a flower bud. Moreover FUL is another meristem identity gene homologous to AP1 (Ream et al., 2014). Even though BdMADS33/FUL1 and MADS10/FUL2 have not been functionally characterized, they are the closest orthologous proteins to AP1 and FUL, respectively, and therefore most likely regulate floral meristem identity in  B. distchyon . It is interesting to note that similar to the GNRF-OE phenotype, mutations in  A. thaliana  FUL gene along with mutations in AP1/CAT genes result in non-flowering leafy phenotypes (Ferrandiz et al., 2000). This provides strong support for the function of FUL1 and FUL2 as floral identity genes in  B. distachyon . AtAP1 is negatively regulated by the meristem identity gene TERMINAL FLOWER and the organ identity gene AGAMOUS. It is also regulated by the floral homeotic gene PISTILLATA and its interacting partner APETALA3 (Sundström et al., 2006). However, to date there is no indication of any involvement of a NAC transcription factor in the regulation of these redundant floral homeotic genes AP1/CAL/FUL. Furthermore, there are no known NAC transcription factors associated with dicot or monocot flowering pathways (Higgins et al., 2010). GNRF is the first NAC protein to be associated with the flowering pathway in  B. distachyon . The architecture of flowering pathways in  B. distachyon  and  A. thaliana  are similar in some aspects, for instance vegetative to reproductive transition is signaled by leaf localized FT expression (Corbesier et al.; Wu et al., 2013; Lv et al., 2014). In both species, activation of orthologous floral meristem identity genes results in flowering. Interestingly, the vernalization responses between these two species are significantly different. 
     GNRF is the closest ortholog to SND2. Very little is known about the function of SND2 in any plant system. To date it has only been shown to activate cell wall biosynthesis in  A. thaliana  and poplar (Zhong et al., 2008; Grant et al., 2010; Wang et al., 2013). Based on the protein similarity and the expression profile, GNRF likely has a similar function to SND2. In support of that, we have shown that GNRF is a regulator of cellulose, lignin and hemicellulose genes. Over-expression of GNRF resulted in a significant reduction of these genes in the GNRF-OE stems. Therefore, unlike SND2, GNRF appears to act as a repressor of cell wall biosynthesis. However, analysis of GNRF sequence revealed no apparent repression domains. Based on the microarray results, a handful of lignin genes, peroxidases, lacasses and copper ion transporters were repressed by GNRF. Since these components are essential for polymerization of lignin monomers, cell wall lignification should be effected in the GNRF-OE mutants. Complementing the expression analysis, histo-chemical analysis revealed a qualitative reduction in stem lignin in the GNRF-OE stems. This observation was further validated by the significantly lower levels of acetyl bromide soluble lignin content measured in GNRF-OE stems. 
     Based on the expression profiling and cell wall composition analysis it is evident that GNRF is involved in cell wall regulation. Unlike other classical cell wall regulators, GNRF has profound pleiotropic effects. Based on transcription profiling, GNRF is associated with cell wall, floral transition and transporters of numerous substrates. However using microarray expression analysis, direct and indirect regulation via GNRF over-expression is hard to decipher. Many different genes may be directly regulated by GNRF, including FUL1 and FUL2. Further experiments will be required to determine whether these genes are under direct regulation by GNRF as well as if these genes share common GNRF binding sites. 
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     The invention is described with reference to various specific and preferred embodiments and techniques. However, it should be understood that many variations and modifications may be made while remaining within its scope. All referenced publications, patents and patent documents are intended to be incorporated by reference, as though individually incorporated by reference.