Yield-related Polynucleotides And Polypeptides In Plants

  *US07635800B2*
  US007635800B2                                 
(12)United States Patent(10)Patent No.: US 7,635,800 B2
 Ratcliffe et al. (45) Date of Patent:Dec.  22, 2009

(54)Yield-related polynucleotides and polypeptides in plants 
    
(75)Inventors: Oliver Ratcliffe,  Oakland, CA (US); 
  Luc Adam,  Hayward, CA (US); 
  Jacqueline E. Heard,  Stonington, CT (US); 
  Cai-Zhong Jiang,  Fremont, CA (US); 
  T. Lynne Reuber,  San Mateo, CA (US); 
  Robert A. Creelman,  Castro Valley, CA (US) 
(73)Assignee:Mendel Biotechnology, Inc.,  Hayward, CA (US), Type: US Company 
(*)Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 64 days. 
(21)Appl. No.: 11/728,567 
(22)Filed: Mar.  26, 2007 
(65)Prior Publication Data 
 US 2007/0209086 A1 Sep.  6, 2007 
 Related U.S. Patent Documents 
(60) .
Division of application No. 10/225,066, filed on Aug.  9, 2002, now Pat. No. 7,238,860 , which is a continuation-in-part of application No. 10/171,468, filed on Jun.  14, 2002, now abandoned , which is a continuation-in-part of application No. 09/837,944, filed on Apr.  18, 2001, now abandoned .
 
(60)Provisional application No. 60/310,847, filed on Aug.  9, 2001.
 
 Provisional application No. 60/336,049, filed on Nov.  19, 2001.
 
 Provisional application No. 60/338,692, filed on Dec.  11, 2001.
 
(51)Int. Cl. C12N 015/82 (20060101); A01H 005/00 (20060101)
(52)U.S. Cl. 800/290; 800/298
(58)Field of Search  None

 
(56)References Cited
 
 U.S. PATENT DOCUMENTS
 5,792,929  A  8/1998    Mariani et al.     
 6,121,513  A  9/2000    Zhang et al.     
 6,664,446  B2  12/2003    Heard et al.     
 6,717,034  B2  4/2004    Jiang et al.     
 6,835,540  B2  12/2004    Broun     
 6,946,586  B1  9/2005    Fromm et al.     
 7,109,393  B2  9/2006    Gutterson et al.     
 7,135,616  B2  11/2006    Heard et al.     
 7,196,245  B2  3/2007    Jiang et al.     
 7,223,904  B2  5/2007    Heard et al.     
 7,238,860  B2  7/2007    Ratcliffe et al.     
 7,345,217  B2  3/2008    Zhang et al.     
 2003//0093837  A1  5/2003    Keddie et al.     
 2003//0121070  A1  6/2003    Adam et al.     
 2003//0217383  A1  11/2003    Reuber et al.     
 2004//0019927  A1  1/2004    Sherman et al.     
 2004//0128712  A1  7/2004    Jiang et al.     
 2005//0086718  A1  4/2005    Heard et al.     
 2005//0097638  A1  5/2005    Jiang et al.     
 2005//0155117  A1  7/2005    Century et al.     
 2005//0172364  A1  8/2005    Heard et al.     
 2006//0008874  A1  1/2006    Creelman et al.     
 2006//0015972  A1  1/2006    Heard et al.     
 2006//0162018  A1  7/2006    Gutterson et al.     
 2006//0195944  A1  8/2006    Heard et al.     
 2006//0242738  A1  10/2006    Sherman et al.     
 2006//0272060  A1  11/2006    Heard et al.     
 2007//0022495  A1  1/2007    Reuber     
 2007//0101454  A1  5/2007    Jiang et al.     
 2007//0186308  A1  8/2007    Reuber et al.     
 2007//0199107  A1  8/2007    Ratcliffe et al.     
 2007//0209086  A1  9/2007    Ratcliffe et al.     
 2007//0226839  A1  9/2007    Gutterson et al.     
 2008//0010703  A1  1/2008    Creelman et al.     
 2008//0155706  A1  6/2008    Riechmann et al.     
 2008//0163397  A1  7/2008    Ratcliffe et al.     
 2008//0229448  A1  9/2008    Libby et al.     
 2008//0301836  A1  12/2008    Century et al.     
 2008//0301840  A1  12/2008    Gutterson et al.     
 2008//0301841  A1  12/2008    Ratcliffe et al.     
 2008//0313756  A1  12/2008    Zhang et al.     
 2009//0049566  A1  2/2009    Zhang et al.     

 
 FOREIGN PATENT DOCUMENTS 
 
       WO       WO03/013227       A2                2/2003      
       WO       WO03/014327       A2                2/2003      
       WO       WO20/04076638       A2                9/2004      
       WO       WO20/05047516       A2                5/2005      
       WO       WO20/07028165       A2                3/2007      

 OTHER PUBLICATIONS
  
  Whisstock J.C. et al. Prediction of protein function from protein sequence and structure. Q Rev Biophys. Aug. 2003;36(3):307-40. Review. *
  Heim et al. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity Mol Biol Evol. May 2003;20(5):735-47. Epub Apr. 2, 2003. *
  Lloyd et al. Arabidopsis and Nicotiana anthocyanin production activated by maize regulators R and C1. Science. Dec. 11, 1992;258(5089):1773-5. *
  NCBI acc. No. ACO23064 (gi: 6939205) (Feb. 8, 2000); Lin,X., et al. “Arabidopsis thaliana chromosome I clone IGF-F12A4, *** Sequencing In Progress ***, 4 unordered pieces”; source: Arabidopsis thaliana (thale cress); Title: “Arabidopsis thaliana ‘IGF’ BAC ‘F12A4’ genomic sequence near marker ‘mi342’” (Unpublished).
  NCBI acc. No. AAG52112 (gi: 12324283) (Jan. 19, 2001): Lin,X. et al. “helix-loop-helix protein 1A, putative; 28707-26892 [Arabidopsis thaliana]”; source: Arabidopsis thaliana (thale cress); Title: “Arabidopsis thaliana chromosome 1 Bac F12A4 genomic sequence ”(Unpublished).
  NCBI acc. No. BF096555 (gi: 10902265) (Oct. 19, 2000); van der Hoeven,R.S., et al. “EST360582 tomato nutrient deficient roots Solanum lycopersicum cDNA clone cLEW12M9 5′ sequence similar to putative protein {Arabidopsis thaliana}, mRNA sequence”; source: Solanum lycopersicum (Lycopersicon esculentum); Title: “Generation of ESTs from tomato nutrient-deficient roots” (Unpublished (1999)).
  BF005956 NCBI acc. No. BF005956 (gi: 10706231) (Oct. 6, 2000); Fedorova,M., et al. “EST434454 DSLC Medicago truncatula cDNA clone pDSLC-39M21, mRNA sequence”; source: Medicago truncatula (barrel medic); Title: “ESTs from Medicago truncatula leaves and cotyledons” (Unpublished(2000)).
  BI426449 NCBI acc. No. BI426449 (gi: 15203681) (Aug. 16, 2001); Shoemaker,R., et al. “sag03d07.y1 Gm-c1080 Glycine max cDNA clone GENOME1 Systems Clone Id: Gm-c1080-157 5′ similar to TR:O48535 O48535 Unknown Protein, mRNA sequence”; source: Glycine max (soybean); Title: “Public Soybean.EST Project” (Unpublished (1999)).
  NCBI acc. No. AI099951 (gi: 3449690) (Aug. 22, 1998); Newman,T., et al. “34104 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142D15XP 3′, mRNA sequence”; source: Arabidopsis thaliana (thale cress); Title: “Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones” (Plant Physiol. 106, 1241-1255 (1994)).
  NCBI acc. No. BI320524 (gi: 14999710) (Jul. 23, 2001); Shoemaker,R., et al. “sah56f09.y1 Gm-c1049 Glycine max cDNA clone Genome Systems Clone ID: Gm-c1049-2561 5′ similar to TR:O48535 O48535 Unknown Protein, mRNA sequence”; source: Glycine max (soybean); Title: “Public Soybean EST Project” (Unpublished (1999)).
  NCBI acc. No. AAF04760 (gi: 6166283) (Nov. 1, 1999); Allona,I., et al. “helix-loop-helix protein 1A [Pinus taeda]”; source: Pinus taeda (loblolly pine); Title: “Alternative splicing gives rise to three variants of a novel basic helix loop helix protein in pine xylem” (Unpublished).
  Mandel, M. et al., A gene triggering flower formation in Arabidopsis. 1995, Nature 377, 522-524.
  Weigel, D. and Nilsson, O., A developmental switch sufficient for flower initiation in diverse plants. 1995, Nature 377, 495-500.
  Simon et al., Activation of floral meristem identity genes in Arabidopsis. 1996, Nature 384, 59-62.
  Daly et al. Plant Systematics in the Age of Genomcs. 2001 Plant Physiology 127:1328-1333.
  Littlewood et al, Transcription factors 2: helix-loop-helix (1994) Prot. Profile 1:639-709.
  Ratcliffe et al., Regulation of Flowering in Arabidopsis by an FLC Homologue 2001, Plant Physiology 126:122- 132.
  An et al., Organ-Specific and Developmental regulation of the Nopaline Synthase Promoter in transgenic Tobacco plants, (1988) Plant Physiol 88:547-552.
  U.S. Appl. No. 12/064,961, Gutterson, N. et al.
  U.S. Appl. No. 12/077,535, Repetti, P. et al.
  U.S. Appl. No. 11/632,390, Zhang, James et al.
  U.S. Appl. No. 11/986,992, Kuminoto, R. et al.
 
 
     * cited by examiner
 
     Primary Examiner —Cynthia Collins
     Art Unit — 1638
     Exemplary claim number — 17
 
(74)Attorney, Agent, or Firm — Yifan Mao; Jeffrey M. Libby

(57)

Abstract

The invention relates to plant transcription factor polypeptides, polynucleotides that encode them, homologs from a variety of plant species, and methods of using the polynucleotides and polypeptides to produce transgenic plants having advantageous properties compared to a reference plant. Sequence information related to these polynucleotides and polypeptides can also be used in bioinformatic search methods and is also disclosed.
21 Claims, 1 Drawing Sheet, and 1 Figure


[0001] This application claims the benefit of U.S. Non-provisional application Ser. No. 09/837,444, filed Apr. 18, 2001, U.S. Provisional Application No. 60/310,847, filed Aug. 9, 2001, U.S. Provisional Application No. 60/336,049, filed Dec. 5, 2001, U.S. Provisional Application No. 60/338,692, filed Dec. 11, 2001, and U.S. Non-provisional application Ser. No. 10/171,468, filed Jun. 14, 2002, the entire contents of which are hereby incorporated by reference.

JOINT RESEARCH AGREEMENT

[0002] The claimed invention, in the field of functional genomics and the characterization of plant genes for the improvement of plants, was made by or on behalf of Mendel Biotechnology, Inc. and Monsanto Company as a result of activities undertaken within the scope of a joint research agreement in effect on or before the date the claimed invention was made.

FIELD OF THE INVENTION

[0003] This invention relates to the field of plant biology. More particularly, the present invention pertains to compositions and methods for phenotypically modifying a plant.

INTRODUCTION

[0004] A plant's traits, such as its biochemical, developmental, or phenotypic characteristics, may be controlled through a number of cellular processes. One important way to manipulate that control is through transcription factors—proteins that influence the expression of a particular gene or sets of genes. Transformed and transgenic plants that comprise cells having altered levels of at least one selected transcription factor, for example, possess advantageous or desirable traits. Strategies for manipulating traits by altering a plant cell's transcription factor content can therefore result in plants and crops with commercially valuable properties. Applicants have identified polynucleotides encoding transcription factors, developed numerous transgenic plants using these polynucleotides, and have analyzed the plants for a variety of important traits. In so doing, applicants have identified important polynucleotide and polypeptide sequences for producing commercially valuable plants and crops as well as the methods for making them and using them. Other aspects and embodiments of the invention are described below and can be derived from the teachings of this disclosure as a whole.

BACKGROUND OF THE INVENTION

[0005] Transcription factors can modulate gene expression, either increasing or decreasing (inducing or repressing) the rate of transcription. This modulation results in differential levels of gene expression at various developmental stages, in different tissues and cell types, and in response to different exogenous (e.g., environmental) and endogenous stimuli throughout the life cycle of the organism.
[0006] Because transcription factors are key controlling elements of biological pathways, altering the expression levels of one or more transcription factors can change entire biological pathways in an organism. For example, manipulation of the levels of selected transcription factors may result in increased expression of economically useful proteins or metabolic chemicals in plants or to improve other agriculturally relevant characteristics. Conversely, blocked or reduced expression of a transcription factor may reduce biosynthesis of unwanted compounds or remove an undesirable trait. Therefore, manipulating transcription factor levels in a plant offers tremendous potential in agricultural biotechnology for modifying a plant's traits.
[0007] The present invention provides novel transcription factors useful for modifying a plant's phenotype in desirable ways.

SUMMARY OF THE INVENTION

[0008] In a first aspect, the invention relates to a recombinant polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a nucleotide sequence encoding a polypeptide comprising a polypeptide sequence selected from those of the Sequence Listing, SEQ ID NOs:2 to 2N, where N=2-561, or those listed in Table 5, or a complementary nucleotide sequence thereof; (b) a nucleotide sequence encoding a polypeptide comprising a variant of a polypeptide of (a) having one or more, or between 1 and about 5, or between 1 and about 10, or between 1 and about 30, conservative amino acid substitutions; (c) a nucleotide sequence comprising a sequence selected from those of SEQ ID NOs:1 to (2N−1), where N=2-561, or those included in Table 5, or a complementary nucleotide sequence thereof; (d) a nucleotide sequence comprising silent substitutions in a nucleotide sequence of (c); (e) a nucleotide sequence which hybridizes under stringent conditions over substantially the entire length of a nucleotide sequence of one or more of: (a), (b), (c), or (d); (f) a nucleotide sequence comprising at least 10 or 15, or at least about 20, or at least about 30 consecutive nucleotides of a sequence of any of (a)-(e), or at least 10 or 15, or at least about 20, or at least about 30 consecutive nucleotides outside of a region encoding a conserved domain of any of (a)-(e); (g) a nucleotide sequence comprising a subsequence or fragment of any of (a)-(f), which subsequence or fragment encodes a polypeptide having a biological activity that modifies a plant's characteristic, functions as a transcription factor, or alters the level of transcription of a gene or transgene in a cell; (h) a nucleotide sequence having at least 31% sequence identity to a nucleotide sequence of any of (a)-(g); (i) a nucleotide sequence having at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 95% sequence identity to a nucleotide sequence of any of (a)-(g) or a 10 or 15 nucleotide, or at least about 20, or at least about 30 nucleotide region of a sequence of (a)-(g) that is outside of a region encoding a conserved domain; (j) a nucleotide sequence that encodes a polypeptide having at least 31% sequence identity to a polypeptide listed in Table 5, or the Sequence Listing; (k) a nucleotide sequence which encodes a polypeptide having at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 95% sequence identity to a polypeptide listed in Table 5, or the Sequence Listing; and (l) a nucleotide sequence that encodes a conserved domain of a polypeptide having at least 85%, or at least 90%, or at least 95%, or at least 98% sequence identity to a conserved domain of a polypeptide listed in Table 4 5, or the Sequence Listing. The recombinant polynucleotide may further comprise a constitutive, inducible, or tissue-specific promoter operably linked to the nucleotide sequence. The invention also relates to compositions comprising at least two of the above-described polynucleotides.
[0009] In a second aspect, the invention comprises an isolated or recombinant polypeptide comprising a subsequence of at least about 10, or at least about 15, or at least about 20, or at least about 30 contiguous amino acids encoded by the recombinant or isolated polynucleotide described above, or comprising a subsequence of at least about 8, or at least about 12, or at least about 15, or at least about 20, or at least about 30 contiguous amino acids outside a conserved domain.
[0010] In a third aspect, the invention comprises an isolated or recombinant polynucleotide that encodes a polypeptide that is a paralog of the isolated polypeptide described above. In one aspect, the invention is an paralog which, when expressed in Arabidopsis, modifies a trait of the Arabidopsis plant.
[0011] In a fourth aspect, the invention comprises an isolated or recombinant polynucleotide that encodes a polypeptide that is an ortholog of the isolated polypeptide described above. In one aspect, the invention is an ortholog which, when expressed in Arabidopsis, modifies a trait of the Arabidopsis plant.
[0012] In a fifth aspect, the invention comprises an isolated polypeptide that is a paralog of the isolated polypeptide described above. In one aspect, the invention is an paralog which, when expressed in Arabidopsis, modifies a trait of the Arabidopsis plant.
[0013] In a sixth aspect, the invention comprises an isolated polypeptide that is an ortholog of the isolated polypeptide described above. In one aspect, the invention is an ortholog which, when expressed in Arabidopsis, modifies a trait of the Arabidopsis plant.
[0014] The present invention also encompasses transcription factor variants. A preferred transcription factor variant is one having at least 40% amino acid sequence identity, a more preferred transcription factor variant is one having at least 50% amino acid sequence identity and a most preferred transcription factor variant is one having at least 65% amino acid sequence identity to the transcription factor amino acid sequence SEQ ID NOs:2 to 2N, where N=2-561, and which contains at least one functional or structural characteristic of the transcription factor amino acid sequence. Sequences having lesser degrees of identity but comparable biological activity are considered to be equivalents.
[0015] In another aspect, the invention is a transgenic plant comprising one or more of the above-described isolated or recombinant polynucleotides. In yet another aspect, the invention is a plant with altered expression levels of a polynucleotide described above or a plant with altered expression or activity levels of an above-described polypeptide. Further, the invention is a plant lacking a nucleotide sequence encoding a polypeptide described above or substantially lacking a polypeptide described above. The plant may be any plant, including, but not limited to, Arabidopsis, mustard, soybean, wheat, corn, potato, cotton, rice, oilseed rape, sunflower, alfalfa, sugarcane, turf, banana, blackberry, blueberry, strawberry, raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, pumpkin, spinach, squash, sweet corn, tobacco, tomato, watermelon, rosaceous fruits, vegetable brassicas, and mint or other labiates. In yet another aspect, the inventions is an isolated plant material of a plant, including, but not limited to, plant tissue, fruit, seed, plant cell, embryo, protoplast, pollen, and the like. In yet another aspect, the invention is a transgenic plant tissue culture of regenerable cells, including, but not limited to, embryos, meristematic cells, microspores, protoplast, pollen, and the like.
[0016] In yet another aspect the invention is a transgenic plant comprising one or more of the above described polynucleotides wherein the encoded polypeptide is expressed and regulates transcription of a gene.
[0017] In a further aspect the invention provides a method of using the polynucleotide composition to breed a progeny plant from a transgenic plant including crossing plants, producing seeds from transgenic plants, and methods of breeding using transgenic plants, the method comprising transforming a plant with the polynucleotide composition to create a transgenic plant, crossing the transgenic plant with another plant, selecting seed, and growing the progeny plant from the seed.
[0018] In a further aspect, the invention provides a progeny plant derived from a parental plant wherein said progeny plant exhibits at least three fold greater messenger RNA levels than said parental plant, wherein the messenger RNA encodes a DNA-binding protein which is capable of binding to a DNA regulatory sequence and inducing expression of a plant trait gene, wherein the progeny plant is characterized by a change in the plant trait compared to said parental plant. In yet a further aspect, the progeny plant exhibits at least ten fold greater messenger RNA levels compared to said parental plant. In yet a further aspect, the progeny plant exhibits at least fifty fold greater messenger RNA levels compared to said parental plant.
[0019] In a further aspect, the invention relates to a cloning or expression vector comprising the isolated or recombinant polynucleotide described above or cells comprising the cloning or expression vector.
[0020] In yet a further aspect, the invention relates to a composition produced by incubating a polynucleotide of the invention with a nuclease, a restriction enzyme, a polymerase; a polymerase and a primer; a cloning vector, or with a cell.
[0021] Furthermore, the invention relates to a method for producing a plant having a modified trait. The method comprises altering the expression of an isolated or recombinant polynucleotide of the invention or altering the expression or activity of a polypeptide of the invention in a plant to produce a modified plant, and selecting the modified plant for a modified trait. In one aspect, the plant is a monocot plant. In another aspect, the plant is a dicot plant. In another aspect the recombinant polynucleotide is from a dicot plant and the plant is a monocot plant. In yet another aspect the recombinant polynucleotide is from a monocot plant and the plant is a dicot plant. In yet another aspect the recombinant polynucleotide is from a monocot plant and the plant is a monocot plant. In yet another aspect the recombinant polynucleotide is from a dicot plant and the plant is a dicot plant.
[0022] In another aspect, the invention is a transgenic plant comprising an isolated or recombinant polynucleotide encoding a polypeptide wherein the polypeptide is selected from the group consisting of SEQ ID NOs: 2-2N, where N=2-561. In yet another aspect, the invention is a plant with altered expression levels of a polypeptide described above or a plant with altered expression or activity levels of an above-described polypeptide. Further, the invention is a plant lacking a polynucleotide sequence encoding a polypeptide described above or substantially lacking a polypeptide described above. The plant may be any plant, including, but not limited to, Arabidopsis, mustard, soybean, wheat, corn, potato, cotton, rice, oilseed rape, sunflower, alfalfa, sugarcane, turf, banana, blackberry, blueberry, strawberry, raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, pumpkin, spinach, squash, sweet corn, tobacco, tomato, watermelon, rosaceous fruits, vegetable brassicas, and mint or other labiates. In yet another aspect, the inventions is an isolated plant material of a plant, including, but not limited to, plant tissue, fruit, seed, plant cell, embryo, protoplast, pollen, and the like. In yet another aspect, the invention is a transgenic plant tissue culture of regenerable cells, including, but not limited to, embryos, meristematic cells, microspores, protoplast, pollen, and the like.
[0023] In another aspect, the invention relates to a method of identifying a factor that is modulated by or interacts with a polypeptide encoded by a polynucleotide of the invention. The method comprises expressing a polypeptide encoded by the polynucleotide in a plant; and identifying at least one factor that is modulated by or interacts with the polypeptide. In one embodiment the method for identifying modulating or interacting factors is by detecting binding by the polypeptide to a promoter sequence, or by detecting interactions between an additional protein and the polypeptide in a yeast two hybrid system, or by detecting expression of a factor by hybridization to a microarray, subtractive hybridization, or differential display.
[0024] In yet another aspect, the invention is a method of identifying a molecule that modulates activity or expression of a polynucleotide or polypeptide of interest. The method comprises placing the molecule in contact with a plant comprising the polynucleotide or polypeptide encoded by the polynucleotide of the invention and monitoring one or more of the expression level of the polynucleotide in the plant, the expression level of the polypeptide in the plant, and modulation of an activity of the polypeptide in the plant.
[0025] In yet another aspect, the invention relates to an integrated system, computer or computer readable medium comprising one or more character strings corresponding to a polynucleotide of the invention, or to a polypeptide encoded by the polynucleotide. The integrated system, computer or computer readable medium may comprise a link between one or more sequence strings to a modified plant trait.
[0026] In yet another aspect, the invention is a method for identifying a sequence similar or homologous to one or more polynucleotides of the invention, or one or more polypeptides encoded by the polynucleotides. The method comprises providing a sequence database, and querying the sequence database with one or more target sequences corresponding to the one or more polynucleotides or to the one or more polypeptides to identify one or more sequence members of the database that display sequence similarity or homology to one or more of the one or more target sequences.
[0027] The method may further comprise of linking the one or more of the polynucleotides of the invention, or encoded polypeptides, to a modified plant phenotype.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING, AND FIGURE

[0028] The Sequence Listing provides exemplary polynucleotide and polypeptide sequences of the invention. The traits associated with the use of the sequences are included in the Examples.
[0029] CD-ROM1 (Copy 1) is a read-only memory computer-readable compact disc and contains a copy of the Sequence Listing in ASCII text format. The Sequence Listing is named “Seq Listing.txt” and is 923 kilobytes in size. The copies of the Sequence Listing on the CD-ROM disc are hereby incorporated by reference in their entirety.
[0030] CD-ROM2 (Copy 2) is an exact copy of CD-R1 (Copy 1).
[0031] CD-ROM3 contains a CRF copy of the Sequence Listing as a text (.txt) file and is 1846 kilobytes in size.
[0032] FIG. 1 shows a phylogenic tree of related plant families adapted from Daly et al. (2001 Plant Physiology 127:1328-1333).

DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS

[0033] In an important aspect, the present invention relates to polynucleotides and polypeptides, e.g. for modifying phenotypes of plants. Throughout this disclosure, various information sources are referred to and/or are specifically incorporated. The information sources include scientific journal articles, patent documents, textbooks, and World Wide Web browser-inactive page addresses, for example. While the reference to these information sources clearly indicates that they can be used by one of skill in the art, applicants specifically incorporate each and every one of the information sources cited herein, in their entirety, whether or not a specific mention of “incorporation by reference” is noted. The contents and teachings of each and every one of the information sources can be relied on and used to make and use embodiments of the invention.
[0034] It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a plant” includes a plurality of such plants, and a reference to “a stress” is a reference to one or more stresses and equivalents thereof known to those skilled in the art, and so forth.
[0035] The polynucleotide sequences of the invention encode polypeptides that are members of well-known transcription factor families, including plant transcription factor families, as disclosed in Table 5. Generally, the transcription factors encoded by the present sequences are involved in cell differentiation and proliferation and the regulation of growth. Accordingly, one skilled in the art would recognize that by expressing the present sequences in a plant, one may change the expression of autologous genes or induce the expression of introduced genes. By affecting the expression of similar autologous sequences in a plant that have the biological activity of the present sequences, or by introducing the present sequences into a plant, one may alter a plant's phenotype to one with improved traits. The sequences of the invention may also be used to transform a plant and introduce desirable traits not found in the wild-type cultivar or strain. Plants may then be selected for those that produce the most desirable degree of over- or underexpression of target genes of interest and coincident trait improvement.
[0036] The sequences of the present invention may be from any species, particularly plant species, in a naturally occurring form or from any source whether natural, synthetic, semi-synthetic or recombinant. The sequences of the invention may also include fragments of the present amino acid sequences. In this context, a “fragment” refers to a fragment of a polypeptide sequence which is at least 5 to about 15 amino acids in length, most preferably at least 14 amino acids, and which retain some biological activity of a transcription factor. Where “amino acid sequence” is recited to refer to an amino acid sequence of a naturally occurring protein molecule, “amino acid sequence” and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule.
[0037] As one of ordinary skill in the art recognizes, transcription factors can be identified by the presence of a region or domain of structural similarity or identity to a specific consensus sequence or the presence of a specific consensus DNA-binding site or DNA-binding site motif (see, for example, Riechmann et al., (2000) Science 290: 2105-2110). The plant transcription factors may belong to one of the following transcription factor families: the AP2 (APETALA2) domain transcription factor family (Riechmann and Meyerowitz (1998) Biol. Chem. 379:633-646); the MYB transcription factor family (Martin and Paz-Ares, (1997) Trends Genet. 13:67-73); the MADS domain transcription factor family (Riechmann and Meyerowitz (1997) Biol. Chem. 378:1079-1101); the WRKY protein family (Ishiguro and Nakamura (1994) Mol. Gen. Genet. 244:563-571); the ankyrin-repeat protein family (Zhang et al. (1992) Plant Cell 4:1575-1588); the zinc finger protein (Z) family (Klug and Schwabe (1995) FASEB J. 9: 597-604); the homeobox (HB) protein family (Buerglin in Guidebook to the Homeobox Genes, Duboule (ed.) (1994) Oxford University Press); the CAAT-element binding proteins (Forsburg and Guarente (1989) Genes Dev. 3:1166-1178); the squamosa promoter binding proteins (SPB) (Klein et al. (1996) Mol. Gen. Genet. 1996 250:7-16); the NAM protein family (Souer et al. (1996) Cell 85:159-170); the IAA/AUX proteins (Rouse et al. (1998) Science 279:1371-1373); the HLH/MYC protein family (Littlewood et al. (1994) Prot. Profile 1:639-709); the DNA-binding protein (DBP) family (Tucker et al. (1994) EMBO J. 13:2994-3002); the bZIP family of transcription factors (Foster et al. (1994) FASEB J. 8:192-200); the Box P-binding protein (the BPF-1) family (da Costa e Silva et al. (1993) Plant J 4:125-135); the high mobility group (HMG) family (Bustin and Reeves (1996) Prog. Nucl. Acids Res. Mol. Biol. 54:35-100); the scarecrow (SCR) family (Di Laurenzio et al. (1996) Cell 86:423-433); the GF14 family (Wu et al. (1997) Plant Physiol. 114:1421-1431); the polycomb (PCOMB) family (Kennison (1995) Annu. Rev. Genet. 29:289-303); the teosinte branched (TEO) family (Luo et al. (1996) Nature 383:794-799; the ABI3 family (Giraudat et al. (1992) Plant Cell 4:1251-1261); the triple helix (TH) family (Dehesh et al. (1990) Science 250:1397-1399); the EIL family (Chao et al. (1997) Cell 89:1133-44); the AT-HOOK family (Reeves and Nissen (1990) J. Biol. Chem. 265:8573-8582); the S1FA family (Zhou et al. (1995) Nucleic Acids Res. 23:1165-1169); the bZIPT2 family (Lu and Ferl (1995) Plant Physiol. 109:723); the YABBY family (Bowman et al. (1999) Development 126:2387-96); the PAZ family (Bohmert et al. (1998) EMBO J. 17:170-80); a family of miscellaneous (MISC) transcription factors including the DPBF family (Kim et al. (1997) Plant J 11:1237-1251) and the SPF1 family (Ishiguro and Nakamura (1994) Mol. Gen. Genet. 244:563-571); the golden (GLD) family (Hall et al. (1998) Plant Cell 10:925-936), the TUBBY family (Boggin et al, (1999) Science 286:2119-2125), the heat shock family (Wu C (1995) Annu Rev Cell Dev Biol 11:441-469), the ENBP family (Christiansen et al (1996) Plant Mol Biol 32:809-821), the RING-zinc family (Jensen et al. (1998) FEBS letters 436:283-287), the PDBP family (Janik et al Virology. (1989) 168:320-329), the PCF family (Cubas P, et al. Plant J. (1999) 18:215-22), the SRS(SHI-related) family (Fridborg et al Plant Cell (1999) 11:1019-1032), the CPP (cysteine-rich polycomb-like) family (Cvitanich et al Proc. Natl. Acad. Sci. USA. (2000) 97:8163-8168), the ARF (auxin response factor) family (Ulmasov, et al. (1999) Proc. Natl. Acad. Sci. USA 96: 5844-5849), the SWI/SNF family (Collingwood et al J. Mol. End. 23:255-275), the ACBF family (Seguin et al (1997) Plant Mol. Biol. 35:281-291), PCGL (CG-1 like) family (da Costa e Silva et al. (1994) Plant Mol Biol. 25:921-924) the ARID family (Vazquez et al. (1999) Development. 126: 733-42), the Jumonji family, Balciunas et al (2000, Trends Biochem Sci. 25: 274-276), the bZIP-NIN family (Schauser et al (1999) Nature 402: 191-195), the E2F family Kaelin et al (1992) Cell 70: 351-364) and the GRF-like family (Knaap et al (2000) Plant Physiol. 122: 695-704). As indicated by any part of the list above and as known in the art, transcription factors have been sometimes categorized by class, family, and sub-family according to their structural content and consensus DNA-binding site motif, for example. Many of the classes and many of the families and sub-families are listed here. However, the inclusion of one sub-family and not another, or the inclusion of one family and not another, does not mean that the invention does not encompass polynucleotides or polypeptides of a certain family or sub-family. The list provided here is merely an example of the types of transcription factors and the knowledge available concerning the consensus sequences and consensus DNA-binding site motifs that help define them as known to those of skill in the art (each of the references noted above are specifically incorporated herein by reference). A transcription factor may include, but is not limited to, any polypeptide that can activate or repress transcription of a single gene or a number of genes. This polypeptide group includes, but is not limited to, DNA-binding proteins, DNA-binding protein binding proteins, protein kinases, protein phosphatases, GTP-binding proteins, and receptors, and the like.
[0038] In addition to methods for modifying a plant phenotype by employing one or more polynucleotides and polypeptides of the invention described herein, the polynucleotides and polypeptides of the invention have a variety of additional uses. These uses include their use in the recombinant production (i.e., expression) of proteins; as regulators of plant gene expression, as diagnostic probes for the presence of complementary or partially complementary nucleic acids (including for detection of natural coding nucleic acids); as substrates for further reactions, e.g., mutation reactions, PCR reactions, or the like; as substrates for cloning e.g., including digestion or ligation reactions; and for identifying exogenous or endogenous modulators of the transcription factors. A “polynucleotide” is a nucleic acid sequence comprising a plurality of polymerized nucleotides, e.g., at least about 15 consecutive polymerized nucleotides, optionally at least about 30 consecutive nucleotides, at least about 50 consecutive nucleotides. In many instances, a polynucleotide comprises a nucleotide sequence encoding a polypeptide (or protein) or a domain or fragment thereof. Additionally, the polynucleotide may comprise a promoter, an intron, an enhancer region, a polyadenylation site, a translation initiation site, 5′ or 3′ untranslated regions, a reporter gene, a selectable marker, or the like. The polynucleotide can be single stranded or double stranded DNA or RNA. The polynucleotide optionally comprises modified bases or a modified backbone. The polynucleotide can be, e.g., genomic DNA or RNA, a transcript (such as an mRNA), a cDNA, a PCR product, a cloned DNA, a synthetic DNA or RNA, or the like. The polynucleotide can comprise a sequence in either sense or antisense orientations.
[0039] A “recombinant polynucleotide” is a polynucleotide that is not in its native state, e.g., the polynucleotide comprises a nucleotide sequence not found in nature, or the polynucleotide is in a context other than that in which it is naturally found, e.g., separated from nucleotide sequences with which it typically is in proximity in nature, or adjacent (or contiguous with) nucleotide sequences with which it typically is not in proximity. For example, the sequence at issue can be cloned into a vector, or otherwise recombined with one or more additional nucleic acid.
[0040] An “isolated polynucleotide” is a polynucleotide whether naturally occurring or recombinant, that is present outside the cell in which it is typically found in nature, whether purified or not. Optionally, an isolated polynucleotide is subject to one or more enrichment or purification procedures, e.g., cell lysis, extraction, centrifugation, precipitation, or the like.
[0041] A “polypeptide” is an amino acid sequence comprising a plurality of consecutive polymerized amino acid residues e.g., at least about 15 consecutive polymerized amino acid residues, optionally at least about 30 consecutive polymerized amino acid residues, at least about 50 consecutive polymerized amino acid residues. In many instances, a polypeptide comprises a polymerized amino acid residue sequence that is a transcription factor or a domain or portion or fragment thereof. Additionally, the polypeptide may comprise a localization domain, 2) an activation domain, 3) a repression domain, 4) an oligomerization domain or 5) a DNA-binding domain, or the like. The polypeptide optionally comprises modified amino acid residues, naturally occurring amino acid residues not encoded by a codon, non-naturally occurring amino acid residues.
[0042] A “recombinant polypeptide” is a polypeptide produced by translation of a recombinant polynucleotide. A “synthetic polypeptide” is a polypeptide created by consecutive polymerization of isolated amino acid residues using methods well known in the art. An “isolated polypeptide,” whether a naturally occurring or a recombinant polypeptide, is more enriched in (or out of) a cell than the polypeptide in its natural state in a wild type cell, e.g., more than about 5% enriched, more than about 10% enriched, or more than about 20%, or more than about 50%, or more, enriched, i.e., alternatively denoted: 105%, 110%, 120%, 150% or more, enriched relative to wild type standardized at 100%. Such an enrichment is not the result of a natural response of a wild type plant. Alternatively, or additionally, the isolated polypeptide is separated from other cellular components with which it is typically associated, e.g., by any of the various protein purification methods herein.
[0043] “Identity” or “similarity” refers to sequence similarity between two polynucleotide sequences or between two polypeptide sequences, with identity being a more strict comparison. The phrases “percent identity” and “% identity” refer to the percentage of sequence similarity found in a comparison of two or more polynucleotide sequences or two or more polypeptide sequences. Identity or similarity can be determined by comparing a position in each sequence that may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same nucleotide base or amino acid, then the molecules are identical at that position. A degree of similarity or identity between polynucleotide sequences is a function of the number of identical or matching nucleotides at positions shared by the polynucleotide sequences. A degree of identity of polypeptide sequences is a function of the number of identical amino acids at positions shared by the polypeptide sequences. A degree of homology or similarity of polypeptide sequences is a function of the number of amino acids, i.e., structurally related, at positions shared by the polypeptide sequences.
[0044] “Altered” nucleic acid sequences encoding polypeptide include those sequences with deletions, insertions, or substitutions of different nucleotides, resulting in a polynucleotide encoding a polypeptide with at least one functional characteristic of the polypeptide. Included within this definition are polymorphisms that may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding polypeptide, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding polypeptide. The encoded polypeptide protein may also be “altered”, and may contain deletions, insertions, or substitutions of amino acid residues that produce a silent change and result in a functionally equivalent polypeptide. Deliberate amino acid substitutions may be made on the basis of similarity in residue side chain chemistry, including, but not limited to, polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as the biological activity of polypeptide is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, positively charged amino acids may include lysine and arginine, and amino acids with uncharged polar head groups having similar hydrophilicity values may include leucine, isoleucine, and valine; glycine and alanine; asparagine and glutamine; serine and threonine; and phenylalanine and tyrosine. Alignments between different polypeptide sequences may be used to calculate “percentage sequence similarity”.
[0045] The term “plant” includes whole plants, shoot vegetative organs/structures (e.g., leaves, stems and tubers), roots, flowers and floral organs/structures (e.g., bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (e.g., vascular tissue, ground tissue, and the like) and cells (e.g., guard cells, egg cells, and the like), and progeny of same. The class of plants that can be used in the method of the invention is generally as broad as the class of higher and lower plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), gymnosperms, ferns, horsetails, psilophytes, lycophytes, bryophytes, and multicellular algae. (See for example, FIG. 1, adapted from Daly et al. 2001 Plant Physiology 127:1328-1333; and see also Tudge, C., The Variety of Life, Oxford University Press, New York, 2000, pp. 547-606.)
[0046] A “transgenic plant” refers to a plant that contains genetic material not found in a wild type plant of the same species, variety or cultivar. The genetic material may include a transgene, an insertional mutagenesis event (such as by transposon or T-DNA insertional mutagenesis), an activation tagging sequence, a mutated sequence, a homologous recombination event or a sequence modified by chimeraplasty. Typically, the foreign genetic material has been introduced into the plant by human manipulation, but any method can be used as one of skill in the art recognizes.
[0047] A transgenic plant may contain an expression vector or cassette. The expression cassette typically comprises a polypeptide-encoding sequence operably linked (i.e., under regulatory control of) to appropriate inducible or constitutive regulatory sequences that allow for the expression of polypeptide. The expression cassette can be introduced into a plant by transformation or by breeding after transformation of a parent plant. A plant refers to a whole plant as well as to a plant part, such as seed, fruit, leaf, or root, plant tissue, plant cells or any other plant material, e.g., a plant explant, as well as to progeny thereof, and to in vitro systems that mimic biochemical or cellular components or processes in a cell.
[0048] “Ectopic expression or altered expression” in reference to a polynucleotide indicates that the pattern of expression in, e.g., a transgenic plant or plant tissue, is different from the expression pattern in a wild type plant or a reference plant of the same species. The pattern of expression may also be compared with a reference expression pattern in a wild type plant of the same species. For example, the polynucleotide or polypeptide is expressed in a cell or tissue type other than a cell or tissue type in which the sequence is expressed in the wild type plant, or by expression at a time other than at the time the sequence is expressed in the wild type plant, or by a response to different inducible agents, such as hormones or environmental signals, or at different expression levels (either higher or lower) compared with those found in a wild type plant. The term also refers to altered expression patterns that are produced by lowering the levels of expression to below the detection level or completely abolishing expression. The resulting expression pattern can be transient or stable, constitutive or inducible. In reference to a polypeptide, the term “ectopic expression or altered expression” further may relate to altered activity levels resulting from the interactions of the polypeptides with exogenous or endogenous modulators or from interactions with factors or as a result of the chemical modification of the polypeptides.
[0049] A “fragment” or “domain,” with respect to a polypeptide, refers to a subsequence of the polypeptide. In some cases, the fragment or domain, is a subsequence of the polypeptide which performs at least one biological function of the intact polypeptide in substantially the same manner, or to a similar extent, as does the intact polypeptide. For example, a polypeptide fragment can comprise a recognizable structural motif or functional domain such as a DNA-binding site or domain that binds to a DNA promoter region, an activation domain, or a domain for protein-protein interactions. Fragments can vary in size from as few as 6 amino acids to the full length of the intact polypeptide, but are preferably at least about 30 amino acids in length and more preferably at least about 60 amino acids in length. In reference to a polynucleotide sequence, “a fragment” refers to any subsequence of a polynucleotide, typically, of at least about 15 consecutive nucleotides, preferably at least about 30 nucleotides, more preferably at least about 50 nucleotides, of any of the sequences provided herein.
[0050] The invention also encompasses production of DNA sequences that encode transcription factors and transcription factor derivatives, or fragments thereof, entirely by synthetic chemistry. After production, the synthetic sequence may be inserted into any of the many available expression vectors and cell systems using reagents well known in the art. Moreover, synthetic chemistry may be used to introduce mutations into a sequence encoding transcription factors or any fragment thereof.
[0051] A “conserved domain”, with respect to a polypeptide, refers to a domain within a transcription factor family which exhibits a higher degree of sequence homology, such as at least 65% sequence identity including conservative substitutions, and preferably at least 80% sequence identity, and more preferably at least 85%, or at least about 86%, or at least about 87%, or at least about 88%, or at least about 90%, or at least about 95%, or at least about 98% amino acid residue sequence identity of a polypeptide of consecutive amino acid residues. A fragment or domain can be referred to as outside a consensus sequence or outside a consensus DNA-binding site that is known to exist or that exists for a particular transcription factor class, family, or sub-family. In this case, the fragment or domain will not include the exact amino acids of a consensus sequence or consensus DNA-binding site of a transcription factor class, family or sub-family, or the exact amino acids of a particular transcription factor consensus sequence or consensus DNA-binding site. Furthermore, a particular fragment, region, or domain of a polypeptide, or a polynucleotide encoding a polypeptide, can be “outside a conserved domain” if all the amino acids of the fragment, region, or domain fall outside of a defined conserved domain(s) for a polypeptide or protein. The conserved domains for each of polypeptides of SEQ ID NOs:2-2N, where N=2-561, are listed in Table 5 as described in Example VII. Also, many of the polypeptides of Table 5 have conserved domains specifically indicated by start and stop sites. A comparison of the regions of the polypeptides in SEQ ID NOs:2-2N, where N=2-561, or of those in Table 5, allows one of skill in the art to identify conserved domain(s) for any of the polypeptides listed or referred to in this disclosure, including those in Table 5.
[0052] A “trait” refers to a physiological, morphological, biochemical, or physical characteristic of a plant or particular plant material or cell. In some instances, this characteristic is visible to the human eye, such as seed or plant size, or can be measured by biochemical techniques, such as detecting the protein, starch, or oil content of seed or leaves, or by observation of a metabolic or physiological process, e.g. by measuring uptake of carbon dioxide, or by the observation of the expression level of a gene or genes, e.g., by employing Northern analysis, RT-PCR, microarray gene expression assays, or reporter gene expression systems, or by agricultural observations such as stress tolerance, yield, or pathogen tolerance. Any technique can be used to measure the amount of, comparative level of, or difference in any selected chemical compound or macromolecule in the transgenic plants, however.
[0053] “Trait modification” refers to a detectable difference in a characteristic in a plant ectopically expressing a polynucleotide or polypeptide of the present invention relative to a plant not doing so, such as a wild type plant. In some cases, the trait modification can be evaluated quantitatively. For example, the trait modification can entail at least about a 2% increase or decrease in an observed trait (difference), at least a 5% difference, at least about a 10% difference, at least about a 20% difference, at least about a 30%, at least about a 50%, at least about a 70%, or at least about a 100%, or an even greater difference compared with a wild type plant. It is known that there can be a natural variation in the modified trait. Therefore, the trait modification observed entails a change of the normal distribution of the trait in the plants compared with the distribution observed in wild type plant.

I. TRAITS WHICH MAY BE MODIFIED

[0054] Trait modifications of particular interest include those to seed (such as embryo or endosperm), fruit, root, flower, leaf, stem, shoot, seedling or the like, including: enhanced tolerance to environmental conditions including freezing, chilling, heat, drought, water saturation, radiation and ozone; improved tolerance to microbial, fungal or viral diseases; improved tolerance to pest infestations, including nematodes, mollicutes, parasitic higher plants or the like; decreased herbicide sensitivity; improved tolerance of heavy metals or enhanced ability to take up heavy metals; improved growth under poor photoconditions (e.g., low light and/or short day length), or changes in expression levels of genes of interest. Other phenotype that can be modified relate to the production of plant metabolites, such as variations in the production of taxol, tocopherol, tocotrienol, sterols, phytosterols, vitamins, wax monomers, anti-oxidants, amino acids, lignins, cellulose, tannins, prenyllipids (such as chlorophylls and carotenoids), glucosinolates, and terpenoids, enhanced or compositionally altered protein or oil production (especially in seeds), or modified sugar (insoluble or soluble) and/or starch composition. Physical plant characteristics that can be modified include cell development (such as the number of trichomes), fruit and seed size and number, yields of plant parts such as stems, leaves, inflorescences, and roots, the stability of the seeds during storage, characteristics of the seed pod (e.g., susceptibility to shattering), root hair length and quantity, internode distances, or the quality of seed coat. Plant growth characteristics that can be modified include growth rate, germination rate of seeds, vigor of plants and seedlings, leaf and flower senescence, male sterility, apomixis, flowering time, flower abscission, rate of nitrogen uptake, osmotic sensitivity to soluble sugar concentrations, biomass or transpiration characteristics, as well as plant architecture characteristics such as apical dominance, branching patterns, number of organs, organ identity, organ shape or size.

Transcription Factors Modify Expression of Endogenous Genes

[0055] Expression of genes which encode transcription factors that modify expression of endogenous genes, polynucleotides, and proteins are well known in the art. In addition, transgenic plants comprising isolated polynucleotides encoding transcription factors may also modify expression of endogenous genes, polynucleotides, and proteins. Examples include Peng et al. (1997, Genes and Development 11:3194-3205) and Peng et al. (1999, Nature, 400:256-261). In addition, many others have demonstrated that an Arabidopsis transcription factor expressed in an exogenous plant species elicits the same or very similar phenotypic response. See, for example, Fu et al. (2001, Plant Cell 13:1791-1802); Nandi et al. (2000, Curr. Biol. 10:215-218); Coupland (1995, Nature 377:482-483); and Weigel and Nilsson (1995, Nature 377:482-500).
[0056] In another example, Mandel et al. (1992, Cell 71-133-143) and Suzuki et al. (2001, Plant J. 28:409-418) teach that a transcription factor expressed in another plant species elicits the same or very similar phenotypic response of the endogenous sequence, as often predicted in earlier studies of Arabidopsis transcription factors in Arabidopsis (see Mandel et al., 1992, supra; Suzuki et al., 2001, supra).
[0057] Other examples include Müller et al. (2001, Plant J. 28:169-179); Kim et al. (2001, Plant J. 25:247-259); Kyozuka and Shimamoto (2002, Plant Cell Physiol. 43:130-135); Boss and Thomas (2002, Nature, 416:847-850); He et al. (2000, Transgenic Res., 9:223-227); and Robson et al. (2001, Plant J. 28:619-631).
[0058] In yet another example, Gilmour et al. (1998, Plant J. 16:433-442) teach an Arabidopsis AP2 transcription factor, CBF1, which, when overexpressed in transgenic plants, increases plant freezing tolerance. Jaglo et al (2001, Plant Physiol. 127:910-017) further identified sequences in Brassica napus which encode CBF-like genes and that transcripts for these genes accumulated rapidly in response to low temperature. Transcripts encoding CBF-like proteins were also found to accumulate rapidly in response to low temperature in wheat, as well as in tomato. An alignment of the CBF proteins from Arabidopsis, B. napus, wheat, rye, and tomato revealed the presence of conserved amino acid sequences, PKK/RPAGRxKFxETRHP and DSAWR, that bracket the AP2/EREBP DNA binding domains of the proteins and distinguish them from other members of the AP2/EREBP protein family. (See Jaglo et al., supra.)

III. POLYPEPTIDES AND POLYNUCLEOTIDES OF THE INVENTION

[0059] The present invention provides, among other things, transcription factors (TFs), and transcription factor homologue polypeptides, and isolated or recombinant polynucleotides encoding the polypeptides, or novel variant polypeptides or polynucleotides encoding novel variants of transcription factors derived from the specific sequences provided here. These polypeptides and polynucleotides may be employed to modify a plant's characteristic. Exemplary polynucleotides encoding the polypeptides of the invention were identified in the Arabidopsis thaliana GenBank database using publicly available sequence analysis programs and parameters. Sequences initially identified were then further characterized to identify sequences comprising specified sequence strings corresponding to sequence motifs present in families of known transcription factors. In addition, further exemplary polynucleotides encoding the polypeptides of the invention were identified in the plant GenBank database using publicly available sequence analysis programs and parameters. Sequences initially identified were then further characterized to identify sequences comprising specified sequence strings corresponding to sequence motifs present in families of known transcription factors. Polynucleotide sequences meeting such criteria were confirmed as transcription factors.
[0060] Additional polynucleotides of the invention were identified by screening Arabidopsis thaliana and/or other plant cDNA libraries with probes corresponding to known transcription factors under low stringency hybridization conditions. Additional sequences, including full length coding sequences were subsequently recovered by the rapid amplification of cDNA ends (RACE) procedure, using a commercially available kit according to the manufacturer's instructions. Where necessary, multiple rounds of RACE are performed to isolate 5′ and 3′ ends. The full length cDNA was then recovered by a routine end-to-end polymerase chain reaction (PCR) using primers specific to the isolated 5′ and 3′ ends. Exemplary sequences are provided in the Sequence Listing.
[0061] The polynucleotides of the invention can be or were ectopically expressed in overexpressor or knockout plants and the changes in the characteristic(s) or trait(s) of the plants observed. Therefore, the polynucleotides and polypeptides can be employed to improve the characteristics of plants.
[0062] The polynucleotides of the invention can be or were ectopically expressed in overexpressor plant cells and the changes in the expression levels of a number of genes, polynucleotides, and/or proteins of the plant cells observed. Therefore, the polynucleotides and polypeptides can be employed to change expression levels of a genes, polynucleotides, and/or proteins of plants.

IV. PRODUCING POLYPEPTIDES

[0063] The polynucleotides of the invention include sequences that encode transcription factors and transcription factor homologue polypeptides and sequences complementary thereto, as well as unique fragments of coding sequence, or sequence complementary thereto. Such polynucleotides can be, e.g., DNA or RNA, e.g., mRNA, cRNA, synthetic RNA, genomic DNA, cDNA synthetic DNA, oligonucleotides, etc. The polynucleotides are either double-stranded or single-stranded, and include either, or both sense (i.e., coding) sequences and antisense (i.e., non-coding, complementary) sequences. The polynucleotides include the coding sequence of a transcription factor, or transcription factor homologue polypeptide, in isolation, in combination with additional coding sequences (e.g., a purification tag, a localization signal, as a fusion-protein, as a pre-protein, or the like), in combination with non-coding sequences (e.g., introns or inteins, regulatory elements such as promoters, enhancers, terminators, and the like), and/or in a vector or host environment in which the polynucleotide encoding a transcription factor or transcription factor homologue polypeptide is an endogenous or exogenous gene.
[0064] A variety of methods exist for producing the polynucleotides of the invention. Procedures for identifying and isolating DNA clones are well known to those of skill in the art, and are described in, e.g., Berger and Kimmel, Guide to Molecular Cloning Techniques Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif. (“Berger”); Sambrook et al., Molecular Cloning—A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989 (“Sambrook”) and Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (supplemented through 2000) (“Ausubel”).
[0065] Alternatively, polynucleotides of the invention, can be produced by a variety of in vitro amplification methods adapted to the present invention by appropriate selection of specific or degenerate primers. Examples of protocols sufficient to direct persons of skill through in vitro amplification methods, including the polymerase chain reaction (PCR) the ligase chain reaction (LCR), Qbeta-replicase amplification and other RNA polymerase mediated techniques (e.g., NASBA), e.g., for the production of the homologous nucleic acids of the invention are found in Berger (supra), Sambrook (supra), and Ausubel (supra), as well as Mullis et al., (1987) PCR Protocols A Guide to Methods and Applications (Innis et al. eds) Academic Press Inc. San Diego, Calif. (1990) (Innis). Improved methods for cloning in vitro amplified nucleic acids are described in Wallace et al., U.S. Pat. No. 5,426,039. Improved methods for amplifying large nucleic acids by PCR are summarized in Cheng et al. (1994) Nature 369: 684-685 and the references cited therein, in which PCR amplicons of up to 40 kb are generated. One of skill will appreciate that essentially any RNA can be converted into a double stranded DNA suitable for restriction digestion, PCR expansion and sequencing using reverse transcriptase and a polymerase. See, e.g., Ausubel, Sambrook and Berger, all supra.
[0066] Alternatively, polynucleotides and oligonucleotides of the invention can be assembled from fragments produced by solid-phase synthesis methods. Typically, fragments of up to approximately 100 bases are individually synthesized and then enzymatically or chemically ligated to produce a desired sequence, e.g., a polynucleotide encoding all or part of a transcription factor. For example, chemical synthesis using the phosphoramidite method is described, e.g., by Beaucage et al. (1981) Tetrahedron Letters 22:1859-1869; and Matthes et al. (1984) EMBO J. 3:801-805. According to such methods, oligonucleotides are synthesized, purified, annealed to their complementary strand, ligated and then optionally cloned into suitable vectors. And if so desired, the polynucleotides and polypeptides of the invention can be custom ordered from any of a number of commercial suppliers.

V. HOMOLOGOUS SEQUENCES

[0067] Sequences homologous, i.e., that share significant sequence identity or similarity, to those provided in the Sequence Listing, derived from Arabidopsis thaliana or from other plants of choice are also an aspect of the invention. Homologous sequences can be derived from any plant including monocots and dicots and in particular agriculturally important plant species, including but not limited to, crops such as soybean, wheat, corn, potato, cotton, rice, rape, oilseed rape (including canola), sunflower, alfalfa, sugarcane and turf; or fruits and vegetables, such as banana, blackberry, blueberry, strawberry, and raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, pumpkin, spinach, squash, sweet corn, tobacco, tomato, watermelon, rosaceous fruits (such as apple, peach, pear, cherry and plum) and vegetable brassicas (such as broccoli, cabbage, cauliflower, Brussels sprouts, and kohlrabi). Other crops, fruits and vegetables whose phenotype can be changed include barley, rye, millet, sorghum, currant, avocado, citrus fruits such as oranges, lemons, grapefruit and tangerines, artichoke, cherries, nuts such as the walnut and peanut, endive, leek, roots, such as arrowroot, beet, cassaya, turnip, radish, yam, and sweet potato, and beans. The homologous sequences may also be derived from woody species, such pine, poplar and eucalyptus, or mint or other labiates.

Orthologs And Paralogs

[0068] Several different methods are known by those of skill in the art for identifying and defining these functionally homologous sequences. Three general methods for defining paralogs and orthologs are described; a paralog or ortholog or homolog may be identified by one or more of the methods described below.
[0069] Orthologs and paralogs are evolutionarily related genes that have similar sequence and similar functions. Orthologs are structurally related genes in different species that are derived from a speciation event. Paralogs are structurally related genes within a single species that are derived by a duplication event.
[0070] Within a single plant species, gene duplication may cause two copies of a particular gene, giving rise to two or more genes with similar sequence and similar function known as paralogs. A paralog is therefore a similar gene with a similar function within the same species. Paralogs typically cluster together or in the same lade (a group of similar genes) when a gene family phylogeny is analyzed using programs such as CLUSTAL (Thompson et al. (1994) Nucleic Acids Res. 22:4673-4680; Higgins et al. (1996) Methods Enzymol. 266 383-402). Groups of similar genes can also be identified with pair-wise BLAST analysis (Feng and Doolittle (1987) J. Mol. Evol. 25:351-360). For example, a lade of very similar MADS domain transcription factors from Arabidopsis all share a common function in flowering time (Ratcliffe et al. (2001) Plant Physiol. 126:122-132), and a group of very similar AP2 domain transcription factors from Arabidopsis are involved in tolerance of plants to freezing (Gilmour et al. (1998) Plant J. 16:433-442). Analysis of groups of similar genes with similar function that fall within one clade can yield sub-sequences that are particular to the clade. These sub-sequences, known as consensus sequences, can not only be used to define the sequences within each clade, but define the functions of these genes; genes within a clade may contain paralogous or orthologous sequences that share the same function. (See also, for example, Mount, D. W. (2001) Bioinformatics: Sequence and Genome Analysis Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. page 543.)
[0071] Speciation, the production of new species from a parental species, can also give rise to two or more genes with similar sequence and similar function. These genes, termed orthologs, often have an identical function within their host plants and are often interchangeable between species without losing function. Because plants have common ancestors, many genes in any plant species will have a corresponding orthologous gene in another plant species. Once a phylogenic tree for a gene family of one species has been constructed using a program such as CLUSTAL (Thompson et al. (1994) Nucleic Acids Res. 22:4673-4680; Higgins et al. (1996) Methods Enzymol. 266:383-402), potential orthologous sequences can placed into the phylogenetic tree and its relationship to genes from the species of interest can be determined. Once the ortholog pair has been identified, the function of the test ortholog can be determined by determining the function of the reference ortholog.
[0072] Transcription factors that are homologous to the listed sequences will typically share at least about 30% amino acid sequence identity, or at least about 30% amino acid sequence identity outside of a known consensus sequence or consensus DNA-binding site. More closely related transcription factors can share at least about 50%, about 60%, about 65%, about 70%, about 75% or about 80% or about 90% or about 95% or about 98% or more sequence identity with the listed sequences, or with the listed sequences but excluding or outside a known consensus sequence or consensus DNA-binding site, or with the listed sequences excluding one or all conserved domain. Factors that are most closely related to the listed sequences share, e.g., at least about 85%, about 90% or about 95% or more % sequence identity to the listed sequences, or to the listed sequences but excluding or outside a known consensus sequence or consensus DNA-binding site or outside one or all conserved domain. At the nucleotide level, the sequences will typically share at least about 40% nucleotide sequence identity, preferably at least about 50%, about 60%, about 70% or about 80% sequence identity, and more preferably about 85%, about 90%, about 95% or about 97% or more sequence identity to one or more of the listed sequences, or to a listed sequence but excluding or outside a known consensus sequence or consensus DNA-binding site, or outside one or all conserved domain. The degeneracy of the genetic code enables major variations in the nucleotide sequence of a polynucleotide while maintaining the amino acid sequence of the encoded protein. Conserved domains within a transcription factor family may exhibit a higher degree of sequence homology, such as at least 65% sequence identity including conservative substitutions, and preferably at least 80% sequence identity, and more preferably at least 85%, or at least about 86%, or at least about 87%, or at least about 88%, or at least about 90%, or at least about 95%, or at least about 98% sequence identity. Transcription factors that are homologous to the listed sequences should share at least 30%, or at least about 60%, or at least about 75%, or at least about 80%, or at least about 90%, or at least about 95% amino acid sequence identity over the entire length of the polypeptide or the homolog. In addition, transcription factors that are homologous to the listed sequences should share at least 30%, or at least about 60%, or at least about 75%, or at least about 80%, or at least about 90%, or at least about 95% amino acid sequence similarity over the entire length of the polypeptide or the homolog.
[0073] Percent identity can be determined electronically, e.g., by using the MEGALIGN program (DNASTAR, Inc. Madison, Wis.). The MEGALIGN program can create alignments between two or more sequences according to different methods, e.g., the clustal method. (See, e.g., Higgins, D. G. and P. M. Sharp (1988) Gene 73:237-244.) The clustal algorithm groups sequences into clusters by examining the distances between all pairs. The clusters are aligned pairwise and then in groups. Other alignment algorithms or programs may be used, including FASTA, BLAST, or ENTREZ, FASTA and BLAST. These are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with or without default settings. ENTREZ is available through the National Center for Biotechnology Information. In one embodiment, the percent identity of two sequences can be determined by the GCG program with a gap weight of 1, e.g., each amino acid gap is weighted as if it were a single amino acid or nucleotide mismatch between the two sequences (see U.S. Pat. No. 6,262,333).
[0074] Other techniques for alignment are described in Methods in Enzymology, vol. 266: Computer Methods for Macromolecular Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc., San Diego, Calif., USA. Preferably, an alignment program that permits gaps in the sequence is utilized to align the sequences. The Smith-Waterman is one type of algorithm that permits gaps in sequence alignments. See Methods Mol. Biol. 70: 173-187 (1997). Also, the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. An alternative search strategy uses MPSRCH software, which runs on a MASPAR computer. MPSRCH uses a Smith-Waterman algorithm to score sequences on a massively parallel computer. This approach improves ability to pick up distantly related matches, and is especially tolerant of small gaps and nucleotide sequence errors. Nucleic acid-encoded amino acid sequences can be used to search both protein and DNA databases.
[0075] The percentage similarity between two polypeptide sequences, e.g., sequence A and sequence B, is calculated by dividing the length of sequence A, minus the number of gap residues in sequence A, minus the number of gap residues in sequence B, into the sum of the residue matches between sequence A and sequence B, times one hundred. Gaps of low or of no similarity between the two amino acid sequences are not included in determining percentage similarity. Percent identity between polynucleotide sequences can also be counted or calculated by other methods known in the art, e.g., the Jotun Hein method. (See, e.g., Hein, J. (1990) Methods Enzymol. 183:626-645.) Identity between sequences can also be determined by other methods known in the art, e.g., by varying hybridization conditions (see US Patent Application No. 20010010913).
[0076] Thus, the invention provides methods for identifying a sequence similar or paralogous or orthologous or homologous to one or more polynucleotides as noted herein, or one or more target polypeptides encoded by the polynucleotides, or otherwise noted herein and may include linking or associating a given plant phenotype or gene function with a sequence. In the methods, a sequence database is provided (locally or across an inter or intra net) and a query is made against the sequence database using the relevant sequences herein and associated plant phenotypes or gene functions.
[0077] In addition, one or more polynucleotide sequences or one or more polypeptides encoded by the polynucleotide sequences may be used to search against a BLOCKS (Bairoch et al. (1997) Nucleic Acids Res. 25:217-221), PFAM, and other databases which contain previously identified and annotated motifs, sequences and gene functions. Methods that search for primary sequence patterns with secondary structure gap penalties (Smith et al. (1992) Protein Engineering 5:35-51) as well as algorithms such as Basic Local Alignment Search Tool (BLAST; Altschul, S. F. (1993) J. Mol. Evol. 36:290-300; Altschul et al. (1990) supra), BLOCKS (Henikoff, S, and Henikoff, G. J. (1991) Nucleic Acids Research 19:6565-6572), Hidden Markov Models (HMM; Eddy, S. R. (1996) Cur. Opin. Str. Biol. 6:361-365; Sonnhammer et al. (1997) Proteins 28:405-420), and the like, can be used to manipulate and analyze polynucleotide and polypeptide sequences encoded by polynucleotides. These databases, algorithms and other methods are well known in the art and are described in Ausubel et al. (1997; Short Protocols in Molecular Biology, John Wiley & Sons, New York N.Y., unit 7.7) and in Meyers, R. A. (1995; Molecular Biology and Biotechnology, Wiley VCH, New York N.Y., p 856-853).
[0078] Furthermore, methods using manual alignment of sequences similar or homologous to one or more polynucleotide sequences or one or more polypeptides encoded by the polynucleotide sequences may be used to identify regions of similarity and conserved domains. Such manual methods are well-known of those of skill in the art and can include, for example, comparisons of tertiary structure between a polypeptide sequence encoded by a polynucleotide which comprises a known function with a polypeptide sequence encoded by a polynucleotide sequence which has a function not yet determined. Such examples of tertiary structure may comprise predicted alpha helices, beta-sheets, amphipathic helices, leucine zipper motifs, zinc finger motifs, proline-rich regions, cysteine repeat motifs, and the like.

VI. IDENTIFYING POLYNUCLEOTIDES OR NUCLEIC ACIDS BY HYBRIDIZATION

[0079] Polynucleotides homologous to the sequences illustrated in the Sequence Listing and tables can be identified, e.g., by hybridization to each other under stringent or under highly stringent conditions. Single stranded polynucleotides hybridize when they associate based on a variety of well characterized physical-chemical forces, such as hydrogen bonding, solvent exclusion, base stacking and the like. The stringency of a hybridization reflects the degree of sequence identity of the nucleic acids involved, such that the higher the stringency, the more similar are the two polynucleotide strands. Stringency is influenced by a variety of factors, including temperature, salt concentration and composition, organic and non-organic additives, solvents, etc. present in both the hybridization and wash solutions and incubations (and number thereof), as described in more detail in the references cited above. Encompassed by the invention are polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, and, in particular, to those shown in SEQ ID NOs: 860; 802; 240; 274; 558; 24; 1120; 44; 460; 286; 120; 130; 134; 698; 832; 580; 612; 48, and fragments thereof under various conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A. R. (1987) Methods Enzymol. 152:507-511.) Estimates of homology are provided by either DNA-DNA or DNA-RNA hybridization under conditions of stringency as is well understood by those skilled in the art (Hames and Higgins, Eds. (1985) Nucleic Acid Hybridisation, IRL Press, Oxford, U.K.). Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms. Post-hybridization washes determine stringency conditions.
[0080] In addition to the nucleotide sequences listed in Tables 4 and 5, full length cDNA, orthologs, paralogs and homologs of the present nucleotide sequences may be identified and isolated using well known methods. The cDNA libraries orthologs, paralogs and homologs of the present nucleotide sequences may be screened using hybridization methods to determine their utility as hybridization target or amplification probes.
[0081] An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or northern blot is about 5° C. to 20° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Nucleic acid molecules that hybridize under stringent conditions will typically hybridize to a probe based on either the entire cDNA or selected portions, e.g., to a unique subsequence, of the cDNA under wash conditions of 0.2×SSC to 2.0×SSC, 0.1% SDS at 50-65° C. For example, high stringency is about 0.2×SSC, 0.1% SDS at 65° C. Ultra-high stringency will be the same conditions except the wash temperature is raised about 3 to about 5° C., and ultra-ultra-high stringency will be the same conditions except the wash temperature is raised about 6 to about 9° C. For identification of less closely related homologues washes can be performed at a lower temperature, e.g., 50° C. In general, stringency is increased by raising the wash temperature and/or decreasing the concentration of SSC, as known in the art.
[0082] In another example, stringent salt concentration will ordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate, preferably less than about 500 mM NaCl and 50 mM trisodium citrate, and most preferably less than about 250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, while high stringency hybridization can be obtained in the presence of at least about 35% formamide, and most preferably at least about 50% formamide. Stringent temperature conditions will ordinarily include temperatures of at least about 30° C., more preferably of at least about 37° C., and most preferably of at least about 42° C. Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS), and the inclusion or exclusion of carrier DNA, are well known to those skilled in the art. Various levels of stringency are accomplished by combining these various conditions as needed. In a preferred embodiment, hybridization will occur at 30° C. in 750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. In a more preferred embodiment, hybridization will occur at 37° C. in 500 mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide, and 100 μg/ml denatured salmon sperm DNA (ssDNA). In a most preferred embodiment, hybridization will occur at 42° C. in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide, and 200 μg/ml ssDNA. Useful variations on these conditions will be readily apparent to those skilled in the art.
[0083] The washing steps that follow hybridization can also vary in stringency. Wash stringency conditions can be defined by salt concentration and by temperature. As above, wash stringency can be increased by decreasing salt concentration or by increasing temperature. For example, stringent salt concentration for the wash steps will preferably be less than about 30 mM NaCl and 3 mM trisodium citrate, and most preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate. Stringent temperature conditions for the wash steps will ordinarily include temperature of at least about 25° C., more preferably of at least about 42° C. Another preferred set of highly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDS at 65° C. The most preferred high stringency washes are of at least about 68° C. For example, in a preferred embodiment, wash steps will occur at 25° C. in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS. In a more preferred embodiment, wash steps will occur at 42° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. In a most preferred embodiment, the wash steps will occur at 68° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Additional variations on these conditions will be readily apparent to those skilled in the art (see U.S. Patent Application No. 20010010913).
[0084] As another example, stringent conditions can be selected such that an oligonucleotide that is perfectly complementary to the coding oligonucleotide hybridizes to the coding oligonucleotide with at least about a 5-10× higher signal to noise ratio than the ratio for hybridization of the perfectly complementary oligonucleotide to a nucleic acid encoding a transcription factor known as of the filing date of the application. Conditions can be selected such that a higher signal to noise ratio is observed in the particular assay which is used, e.g., about 15×, 25×, 35×, 50× or more. Accordingly, the subject nucleic acid hybridizes to the unique coding oligonucleotide with at least a 2× higher signal to noise ratio as compared to hybridization of the coding oligonucleotide to a nucleic acid encoding known polypeptide. Again, higher signal to noise ratios can be selected, e.g., about 5×, 10×, 25×, 35×, 50× or more. The particular signal will depend on the label used in the relevant assay, e.g., a fluorescent label, a colorimetric label, a radioactive label, or the like.
[0085] Alternatively, transcription factor homolog polypeptides can be obtained by screening an expression library using antibodies specific for one or more transcription factors. With the provision herein of the disclosed transcription factor, and transcription factor homologue nucleic acid sequences, the encoded polypeptide(s) can be expressed and purified in a heterologous expression system (e.g., E. coli) and used to raise antibodies (monoclonal or polyclonal) specific for the polypeptide(s) in question. Antibodies can also be raised against synthetic peptides derived from transcription factor, or transcription factor homologue, amino acid sequences. Methods of raising antibodies are well known in the art and are described in Harlow and Lane (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York. Such antibodies can then be used to screen an expression library produced from the plant from which it is desired to clone additional transcription factor homologues, using the methods described above. The selected cDNAs can be confirmed by sequencing and enzymatic activity.

VII. SEQUENCE VARIATIONS

[0086] It will readily be appreciated by those of skill in the art, that any of a variety of polynucleotide sequences are capable of encoding the transcription factors and transcription factor homologue polypeptides of the invention. Due to the degeneracy of the genetic code, many different polynucleotides can encode identical and/or substantially similar polypeptides in addition to those sequences illustrated in the Sequence Listing. Nucleic acids having a sequence that differs from the sequences shown in the Sequence Listing, or complementary sequences, that encode functionally equivalent peptides (i.e., peptides having some degree of equivalent or similar biological activity) but differ in sequence from the sequence shown in the sequence listing due to degeneracy in the genetic code, are also within the scope of the invention.
[0087] Altered polynucleotide sequences encoding polypeptides include those sequences with deletions, insertions, or substitutions of different nucleotides, resulting in a polynucleotide encoding a polypeptide with at least one functional characteristic of the instant polypeptides. Included within this definition are polymorphisms which may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding the instant polypeptides, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding the instant polypeptides.
[0088] Allelic variant refers to any of two or more alternative forms of a gene occupying the same chromosomal locus. Allelic variation arises naturally through mutation, and may result in phenotypic polymorphism within populations. Gene mutations can be silent (i.e., no change in the encoded polypeptide) or may encode polypeptides having altered amino acid sequence. The term allelic variant is also used herein to denote a protein encoded by an allelic variant of a gene. Splice variant refers to alternative forms of RNA transcribed from a gene. Splice variation arises naturally through use of alternative splicing sites within a transcribed RNA molecule, or less commonly between separately transcribed RNA molecules, and may result in several mRNAs transcribed from the same gene. Splice variants may encode polypeptides having altered amino acid sequence. The term splice variant is also used herein to denote a protein encoded by a splice variant of an mRNA transcribed from a gene.
[0089] Those skilled in the art would recognize that G681, SEQ ID NO: 580, represents a single transcription factor; allelic variation and alternative splicing may be expected to occur. Allelic variants of SEQ ID NO: 579 can be cloned by probing cDNA or genomic libraries from different individual organisms according to standard procedures. Allelic variants of the DNA sequence shown in SEQ ID NO: 579, including those containing silent mutations and those in which mutations result in amino acid sequence changes, are within the scope of the present invention, as are proteins which are allelic variants of SEQ ID NO: 580. cDNAs generated from alternatively spliced mRNAs, which retain the properties of the transcription factor are included within the scope of the present invention, as are polypeptides encoded by such cDNAs and mRNAs. Allelic variants and splice variants of these sequences can be cloned by probing cDNA or genomic libraries from different individual organisms or tissues according to standard procedures known in the art (see U.S. Pat. No. 6,388,064).
[0090] For example, Table 1 illustrates, e.g., that the codons AGC, AGT, TCA, TCC, TCG, and TCT all encode the same amino acid: serine. Accordingly, at each position in the sequence where there is a codon encoding serine, any of the above trinucleotide sequences can be used without altering the encoded polypeptide.
[0091] 
[00001] [TABLE-US-00001]
  TABLE 1
 
  Amino acid   Possible Codons
 
 
  Alanine   Ala   A   GCA   GCC   GCG   GCU    
  Cysteine   Cys   C   TGC   TGT
  Aspartic acid   Asp   D   GAC   GAT
  Glutamic acid   Glu   E   GAA   GAG
  Phenylalanine   Phe   F   TTC   TTT
  Glycine   Gly   G   GGA   GGC   GGG   GGT
  Histidine   His   H   CAC   CAT
  Isoleucine   Ile   I   ATA   ATC   ATT
  Lysine   Lys   K   AAA   AAG
  Leucine   Leu   L   TTA   TTG   CTA   CTC   CTG   CTT
  Methionine   Met   M   ATG
  Asparagine   Asn   N   AAC   AAT
  Proline   Pro   P   CCA   CCC   CCG   CCT
  Glutamine   Gln   Q   CAA   CAG
  Arginine   Arg   R   AGA   AGG   CGA   CGC   CGG   CGT
  Serine   Ser   S   AGC   AGT   TCA   TCC   TCG   TCT
  Threonine   Thr   T   ACA   ACC   ACG   ACT
  Valine   Val   V   GTA   GTC   GTG   GTT
  Tryptophan   Trp   W   TGG
  Tyrosine   Tyr   Y   TAC   TAT
 
[0092] Sequence alterations that do not change the amino acid sequence encoded by the polynucleotide are termed “silent” variations. With the exception of the codons ATG and TGG, encoding methionine and tryptophan, respectively, any of the possible codons for the same amino acid can be substituted by a variety of techniques, e.g., site-directed mutagenesis, available in the art. Accordingly, any and all such variations of a sequence selected from the above table are a feature of the invention.
[0093] In addition to silent variations, other conservative variations that alter one, or a few amino acids in the encoded polypeptide, can be made without altering the function of the polypeptide, these conservative variants are, likewise, a feature of the invention.
[0094] For example, substitutions, deletions and insertions introduced into the sequences provided in the Sequence Listing are also envisioned by the invention. Such sequence modifications can be engineered into a sequence by site-directed mutagenesis (Wu (ed.) Meth. Enzymol. (1993) vol. 217, Academic Press) or the other methods noted below. Amino acid substitutions are typically of single residues; insertions usually will be on the order of about from 1 to 10 amino acid residues; and deletions will range about from 1 to 30 residues. In preferred embodiments, deletions or insertions are made in adjacent pairs, e.g., a deletion of two residues or insertion of two residues. Substitutions, deletions, insertions or any combination thereof can be combined to arrive at a sequence. The mutations that are made in the polynucleotide encoding the transcription factor should not place the sequence out of reading frame and should not create complementary regions that could produce secondary mRNA structure. Preferably, the polypeptide encoded by the DNA performs the desired function.
[0095] Conservative substitutions are those in which at least one residue in the amino acid sequence has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the Table 2 when it is desired to maintain the activity of the protein. Table 2 shows amino acids which can be substituted for an amino acid in a protein and which are typically regarded as conservative substitutions.
[0096] 
[00002] [TABLE-US-00002]
  TABLE 2
 
    Conservative
  Residue   Substitutions
 
  Ala   Ser
  Arg   Lys
  Asn   Gln; His
  Asp   Glu
  Gln   Asn
  Cys   Ser
  Glu   Asp
  Gly   Pro
  His   Asn; Gln
  Ile   Leu, Val
  Leu   Ile; Val
  Lys   Arg; Gln
  Met   Leu; Ile
  Phe   Met; Leu; Tyr
  Ser   Thr; Gly
  Thr   Ser; Val
  Trp   Tyr
  Tyr   Trp; Phe
  Val   Ile; Leu
 
[0097] Similar substitutions are those in which at least one residue in the amino acid sequence has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the Table 3 when it is desired to maintain the activity of the protein. Table 3 shows amino acids which can be substituted for an amino acid in a protein and which are typically regarded as structural and functional substitutions. For example, a residue in column 1 of Table 3 may be substituted with residue in column 2; in addition, a residue in column 2 of Table 3 may be substituted with the residue of column 1.
[0098] 
[00003] [TABLE-US-00003]
  TABLE 3
 
  Residue   Similar Substitutions
 
 
  Ala   Ser; Thr; Gly; Val; Leu; Ile  
  Arg   Lys; His; Gly
  Asn   Gln; His; Gly; Ser; Thr
  Asp   Glu, Ser; Thr
  Gln   Asn; Ala
  Cys   Ser; Gly
  Glu   Asp
  Gly   Pro; Arg
  His   Asn; Gln; Tyr; Phe; Lys; Arg
  Ile   Ala; Leu; Val; Gly; Met
  Leu   Ala; Ile; Val; Gly; Met
  Lys   Arg; His; Gln; Gly; Pro
  Met   Leu; Ile; Phe
  Phe   Met; Leu; Tyr; Trp; His; Val; Ala
  Ser   Thr; Gly; Asp; Ala; Val; Ile; His
  Thr   Ser; Val; Ala; Gly
  Trp   Tyr; Phe; His
  Tyr   Trp; Phe; His
  Val   Ala; Ile; Leu; Gly; Thr; Ser; Glu
 
[0099] Substitutions that are less conservative than those in Table 2 can be selected by picking residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. The substitutions which in general are expected to produce the greatest changes in protein properties will be those in which (a) a hydrophilic residue, e.g., seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g., leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine.

VIII. FURTHER MODIFYING SEQUENCES OF THE INVENTION

Mutation/Forced Evolution

[0100] In addition to generating silent or conservative substitutions as noted, above, the present invention optionally includes methods of modifying the sequences of the Sequence Listing. In the methods, nucleic acid or protein modification methods are used to alter the given sequences to produce new sequences and/or to chemically or enzymatically modify given sequences to change the properties of the nucleic acids or proteins.
[0101] Thus, in one embodiment, given nucleic acid sequences are modified, e.g., according to standard mutagenesis or artificial evolution methods to produce modified sequences. The modified sequences may be created using purified natural polynucleotides isolated from any organism or may be synthesized from purified compositions and chemicals using chemical means well know to those of skill in the art. For example, Ausubel, supra, provides additional details on mutagenesis methods. Artificial forced evolution methods are described, for example, by Stemmer (1994) Nature 370:389-391, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751, and U.S. Pat. Nos. 5,811,238, 5,837,500, and 6,242,568. Methods for engineering synthetic transcription factors and other polypeptides are described, for example, by Zhang et al. (2000) J. Biol. Chem. 275:33850-33860, Liu et al. (2001) J. Biol. Chem. 276:11323-11334, and Isalan et al. (2001) Nature Biotechnol. 19:656-660. Many other mutation and evolution methods are also available and expected to be within the skill of the practitioner.
[0102] Similarly, chemical or enzymatic alteration of expressed nucleic acids and polypeptides can be performed by standard methods. For example, sequence can be modified by addition of lipids, sugars, peptides, organic or inorganic compounds, by the inclusion of modified nucleotides or amino acids, or the like. For example, protein modification techniques are illustrated in Ausubel, supra. Further details on chemical and enzymatic modifications can be found herein. These modification methods can be used to modify any given sequence, or to modify any sequence produced by the various mutation and artificial evolution modification methods noted herein.
[0103] Accordingly, the invention provides for modification of any given nucleic acid by mutation, evolution, chemical or enzymatic modification, or other available methods, as well as for the products produced by practicing such methods, e.g., using the sequences herein as a starting substrate for the various modification approaches.
[0104] For example, optimized coding sequence containing codons preferred by a particular prokaryotic or eukaryotic host can be used e.g., to increase the rate of translation or to produce recombinant RNA transcripts having desirable properties, such as a longer half-life, as compared with transcripts produced using a non-optimized sequence. Translation stop codons can also be modified to reflect host preference. For example, preferred stop codons for Saccharomyces cerevisiae and mammals are TAA and TGA, respectively. The preferred stop codon for monocotyledonous plants is TGA, whereas insects and E. coli prefer to use TAA as the stop codon.
[0105] The polynucleotide sequences of the present invention can also be engineered in order to alter a coding sequence for a variety of reasons, including but not limited to, alterations which modify the sequence to facilitate cloning, processing and/or expression of the gene product. For example, alterations are optionally introduced using techniques which are well known in the art, e.g., site-directed mutagenesis, to insert new restriction sites, to alter glycosylation patterns, to change codon preference, to introduce splice sites, etc.
[0106] Furthermore, a fragment or domain derived from any of the polypeptides of the invention can be combined with domains derived from other transcription factors or synthetic domains to modify the biological activity of a transcription factor. For instance, a DNA-binding domain derived from a transcription factor of the invention can be combined with the activation domain of another transcription factor or with a synthetic activation domain. A transcription activation domain assists in initiating transcription from a DNA-binding site. Examples include the transcription activation region of VP16 or GAL4 (Moore et al. (1998) Proc. Natl. Acad. Sci. USA 95: 376-381; and Aoyama et al. (1995) Plant Cell 7:1773-1785), peptides derived from bacterial sequences (Ma and Ptashne (1987) Cell 51; 113-119) and synthetic peptides (Giniger and Ptashne, (1987) Nature 330:670-672).

IX. EXPRESSION AND MODIFICATION OF POLYPEPTIDES

[0107] Typically, polynucleotide sequences of the invention are incorporated into recombinant DNA (or RNA) molecules that direct expression of polypeptides of the invention in appropriate host cells, transgenic plants, in vitro translation systems, or the like. Due to the inherent degeneracy of the genetic code, nucleic acid sequences which encode substantially the same or a functionally equivalent amino acid sequence can be substituted for any listed sequence to provide for cloning and expressing the relevant homologue.

X. VECTORS, PROMOTERS, AND EXPRESSION SYSTEMS

[0108] The present invention includes recombinant constructs comprising one or more of the nucleic acid sequences herein. The constructs typically comprise a vector, such as a plasmid, a cosmid, a phage, a virus (e.g., a plant virus), a bacterial artificial chromosome (BAC), a yeast artificial chromosome (YAC), or the like, into which a nucleic acid sequence of the invention has been inserted, in a forward or reverse orientation. In a preferred aspect of this embodiment, the construct further comprises regulatory sequences, including, for example, a promoter, operably linked to the sequence. Large numbers of suitable vectors and promoters are known to those of skill in the art, and are commercially available.
[0109] General texts that describe molecular biological techniques useful herein, including the use and production of vectors, promoters and many other relevant topics, include Berger, Sambrook and Ausubel, supra. Any of the identified sequences can be incorporated into a cassette or vector, e.g., for expression in plants. A number of expression vectors suitable for stable transformation of plant cells or for the establishment of transgenic plants have been described including those described in Weissbach and Weissbach, (1989) Methods for Plant Molecular Biology, Academic Press, and Gelvin et al., (1990) Plant Molecular Biology Manual, Kluwer Academic Publishers. Specific examples include those derived from a Ti plasmid of Agrobacterium tumefaciens, as well as those disclosed by Herrera-Estrella et al. (1983) Nature 303: 209, Bevan (1984) Nucl Acid Res. 12: 8711-8721, Klee (1985) Bio/Technology 3: 637-642, for dicotyledonous plants.
[0110] Alternatively, non-Ti vectors can be used to transfer the DNA into monocotyledonous plants and cells by using free DNA delivery techniques. Such methods can involve, for example, the use of liposomes, electroporation, microprojectile bombardment, silicon carbide whiskers, and viruses. By using these methods transgenic plants such as wheat, rice (Christou (1991) Bio/Technology 9: 957-962) and corn (Gordon-Kamm (1990) Plant Cell 2: 603-618) can be produced. An immature embryo can also be a good target tissue for monocots for direct DNA delivery techniques by using the particle gun (Weeks et al. (1993) Plant Physiol 102: 1077-1084; Vasil (1993) Bio/Technology 10: 667-674; Wan and Lemeaux (1994) Plant Physiol 104: 37-48, and for Agrobacterium-mediated DNA transfer (Ishida et al. (1996) Nature Biotech 14: 745-750).
[0111] Typically, plant transformation vectors include one or more cloned plant coding sequence (genomic or cDNA) under the transcriptional control of 5′ and 3′ regulatory sequences and a dominant selectable marker. Such plant transformation vectors typically also contain a promoter (e.g., a regulatory region controlling inducible or constitutive, environmentally- or developmentally-regulated, or cell- or tissue-specific expression), a transcription initiation start site, an RNA processing signal (such as intron splice sites), a transcription termination site, and/or a polyadenylation signal.
[0112] Examples of constitutive plant promoters which can be useful for expressing the TF sequence include: the cauliflower mosaic virus (CaMV) 35S promoter, which confers constitutive, high-level expression in most plant tissues (see, e.g., Odell et al. (1985) Nature 313:810-812); the nopaline synthase promoter (An et al. (1988) Plant Physiol 88:547-552); and the octopine synthase promoter (Fromm et al. (1989) Plant Cell 1: 977-984).
[0113] A variety of plant gene promoters that regulate gene expression in response to environmental, hormonal, chemical, developmental signals, and in a tissue-active manner can be used for expression of a TF sequence in plants. Choice of a promoter is based largely on the phenotype of interest and is determined by such factors as tissue (e.g., seed, fruit, root, pollen, vascular tissue, flower, carpel, etc.), inducibility (e.g., in response to wounding, heat, cold, drought, light, pathogens, etc.), timing, developmental stage, and the like. Numerous known promoters have been characterized and can favorably be employed to promote expression of a polynucleotide of the invention in a transgenic plant or cell of interest. For example, tissue specific promoters include: seed-specific promoters (such as the napin, phaseolin or DC3 promoter described in U.S. Pat. No. 5,773,697), fruit-specific promoters that are active during fruit ripening (such as the dru 1 promoter (U.S. Pat. No. 5,783,393), or the 2A11 promoter (U.S. Pat. No. 4,943,674) and the tomato polygalacturonase promoter (Bird et al. (1988) Plant Mol Biol 11:651), root-specific promoters, such as those disclosed in U.S. Pat. Nos. 5,618,988, 5,837,848 and 5,905,186, pollen-active promoters such as PTA29, PTA26 and PTA13 (U.S. Pat. No. 5,792,929), promoters active in vascular tissue (Ringli and Keller (1998) Plant Mol Biol 37:977-988), flower-specific (Kaiser et al, (1995) Plant Mol Biol 28:231-243), pollen (Baerson et al. (1994) Plant Mol Biol 26:1947-1959), carpels (Ohl et al. (1990) Plant Cell 2:837-848), pollen and ovules (Baerson et al. (1993) Plant Mol Biol 22:255-267), auxin-inducible promoters (such as that described in van der Kop et al. (1999) Plant Mol Biol 39:979-990 or Baumann et al. (1999) Plant Cell 11:323-334), cytokinin-inducible promoter (Guevara-Garcia (1998) Plant Mol Biol 38:743-753), promoters responsive to gibberellin (Shi et al. (1998) Plant Mol Biol 38:1053-1060, Willmott et al. (1998) 38:817-825) and the like. Additional promoters are those that elicit expression in response to heat (Ainley et al. (1993) Plant Mol Biol 22: 13-23), light (e.g., the pea rbcS-3A promoter, Kuhlemeier et al. (1989) Plant Cell 1:471, and the maize rbcS promoter, Schaffner and Sheen (1991) Plant Cell 3: 997); wounding (e.g., wunI, Siebertz et al. (1989) Plant Cell 1: 961); pathogens (such as the PR-1 promoter described in Buchel et al. (1999) Plant Mol. Biol. 40:387-396, and the PDF1.2 promoter described in Manners et al. (1998) Plant Mol. Biol. 38:1071-80), and chemicals such as methyl jasmonate or salicylic acid (Gatz et al. (1997) Plant Mol Biol 48: 89-108). In addition, the timing of the expression can be controlled by using promoters such as those acting at senescence (An and Amazon (1995) Science 270: 1986-1988); or late seed development (Odell et al. (1994) Plant Physiol 106:447-458).
[0114] Plant expression vectors can also include RNA processing signals that can be positioned within, upstream or downstream of the coding sequence. In addition, the expression vectors can include additional regulatory sequences from the 3′-untranslated region of plant genes, e.g., a 3′ terminator region to increase mRNA stability of the mRNA, such as the PI-II terminator region of potato or the octopine or nopaline synthase 3′ terminator regions.

Additional Expression Elements

[0115] Specific initiation signals can aid in efficient translation of coding sequences. These signals can include, e.g., the ATG initiation codon and adjacent sequences. In cases where a coding sequence, its initiation codon and upstream sequences are inserted into the appropriate expression vector, no additional translational control signals may be needed. However, in cases where only coding sequence (e.g., a mature protein coding sequence), or a portion thereof, is inserted, exogenous transcriptional control signals including the ATG initiation codon can be separately provided. The initiation codon is provided in the correct reading frame to facilitate transcription. Exogenous transcriptional elements and initiation codons can be of various origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of enhancers appropriate to the cell system in use.

Expression Hosts

[0116] The present invention also relates to host cells which are transduced with vectors of the invention, and the production of polypeptides of the invention (including fragments thereof) by recombinant techniques. Host cells are genetically engineered (i.e., nucleic acids are introduced, e.g., transduced, transformed or transfected) with the vectors of this invention, which may be, for example, a cloning vector or an expression vector comprising the relevant nucleic acids herein. The vector is optionally a plasmid, a viral particle, a phage, a naked nucleic acid, etc. The engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants, or amplifying the relevant gene. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to those skilled in the art and in the references cited herein, including, Sambrook and Ausubel.
[0117] The host cell can be a eukaryotic cell, such as a yeast cell, or a plant cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. Plant protoplasts are also suitable for some applications. For example, the DNA fragments are introduced into plant tissues, cultured plant cells or plant protoplasts by standard methods including electroporation (Fromm et al., (1985) Proc. Natl. Acad. Sci. USA 82, 5824, infection by viral vectors such as cauliflower mosaic virus (CaMV) (Hohn et al., (1982) Molecular Biology of Plant Tumors, (Academic Press, New York) pp. 549-560; U.S. Pat. No. 4,407,956), high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface (Klein et al., (1987) Nature 327, 70-73), use of pollen as vector (WO 85/01856), or use of Agrobacterium tumefaciens or A. rhizogenes carrying a T-DNA plasmid in which DNA fragments are cloned. The T-DNA plasmid is transmitted to plant cells upon infection by Agrobacterium tumefaciens, and a portion is stably integrated into the plant genome (Horsch et al. (1984) Science 233:496-498; Fraley et al. (1983) Proc. Natl. Acad. Sci. USA 80, 4803).
[0118] The cell can include a nucleic acid of the invention which encodes a polypeptide, wherein the cells expresses a polypeptide of the invention. The cell can also include vector sequences, or the like. Furthermore, cells and transgenic plants that include any polypeptide or nucleic acid above or throughout this specification, e.g., produced by transduction of a vector of the invention, are an additional feature of the invention.
[0119] For long-term, high-yield production of recombinant proteins, stable expression can be used. Host cells transformed with a nucleotide sequence encoding a polypeptide of the invention are optionally cultured under conditions suitable for the expression and recovery of the encoded protein from cell culture. The protein or fragment thereof produced by a recombinant cell may be secreted, membrane-bound, or contained intracellularly, depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides encoding mature proteins of the invention can be designed with signal sequences which direct secretion of the mature polypeptides through a prokaryotic or eukaryotic cell membrane.

XI. MODIFIED AMINO ACID RESIDUES

[0120] Polypeptides of the invention may contain one or more modified amino acid residues. The presence of modified amino acids may be advantageous in, for example, increasing polypeptide half-life, reducing polypeptide antigenicity or toxicity, increasing polypeptide storage stability, or the like. Amino acid residue(s) are modified, for example, co-translationally or post-translationally during recombinant production or modified by synthetic or chemical means.
[0121] Non-limiting examples of a modified amino acid residue include incorporation or other use of acetylated amino acids, glycosylated amino acids, sulfated amino acids, prenylated (e.g., farnesylated, geranylgeranylated) amino acids, PEG modified (e.g., “PEGylated”) amino acids, biotinylated amino acids, carboxylated amino acids, phosphorylated amino acids, etc. References adequate to guide one of skill in the modification of amino acid residues are replete throughout the literature.
[0122] The modified amino acid residues may prevent or increase affinity of the polypeptide for another molecule, including, but not limited to, polynucleotide, proteins, carbohydrates, lipids and lipid derivatives, and other organic or synthetic compounds.

XII. IDENTIFICATION OF ADDITIONAL FACTORS

[0123] A transcription factor provided by the present invention can also be used to identify additional endogenous or exogenous molecules that can affect a phentoype or trait of interest. On the one hand, such molecules include organic (small or large molecules) and/or inorganic compounds that affect expression of (i.e., regulate) a particular transcription factor. Alternatively, such molecules include endogenous molecules that are acted upon either at a transcriptional level by a transcription factor of the invention to modify a phenotype as desired. For example, the transcription factors can be employed to identify one or more downstream gene with which is subject to a regulatory effect of the transcription factor. In one approach, a transcription factor or transcription factor homologue of the invention is expressed in a host cell, e.g., a transgenic plant cell, tissue or explant, and expression products, either RNA or protein, of likely or random targets are monitored, e.g., by hybridization to a microarray of nucleic acid probes corresponding to genes expressed in a tissue or cell type of interest, by two-dimensional gel electrophoresis of protein products, or by any other method known in the art for assessing expression of gene products at the level of RNA or protein. Alternatively, a transcription factor of the invention can be used to identify promoter sequences (i.e., binding sites) involved in the regulation of a downstream target. After identifying a promoter sequence, interactions between the transcription factor and the promoter sequence can be modified by changing specific nucleotides in the promoter sequence or specific amino acids in the transcription factor that interact with the promoter sequence to alter a plant trait. Typically, transcription factor DNA-binding sites are identified by gel shift assays. After identifying the promoter regions, the promoter region sequences can be employed in double-stranded DNA arrays to identify molecules that affect the interactions of the transcription factors with their promoters (Bulyk et al. (1999) Nature Biotechnology 17:573-577).
[0124] The identified transcription factors are also useful to identify proteins that modify the activity of the transcription factor. Such modification can occur by covalent modification, such as by phosphorylation, or by protein-protein (homo or -heteropolymer) interactions. Any method suitable for detecting protein-protein interactions can be employed. Among the methods that can be employed are co-immunoprecipitation, cross-linking and co-purification through gradients or chromatographic columns, and the two-hybrid yeast system.
[0125] The two-hybrid system detects protein interactions in vivo and is described in Chien et al. ((1991), Proc. Natl. Acad. Sci. USA 88:9578-9582) and is commercially available from Clontech (Palo Alto, Calif.). In such a system, plasmids are constructed that encode two hybrid proteins: one consists of the DNA-binding domain of a transcription activator protein fused to the TF polypeptide and the other consists of the transcription activator protein's activation domain fused to an unknown protein that is encoded by a cDNA that has been recombined into the plasmid as part of a cDNA library. The DNA-binding domain fusion plasmid and the cDNA library are transformed into a strain of the yeast Saccharomyces cerevisiae that contains a reporter gene (e.g., lacZ) whose regulatory region contains the transcription activator's binding site. Either hybrid protein alone cannot activate transcription of the reporter gene. Interaction of the two hybrid proteins reconstitutes the functional activator protein and results in expression of the reporter gene, which is detected by an assay for the reporter gene product. Then, the library plasmids responsible for reporter gene expression are isolated and sequenced to identify the proteins encoded by the library plasmids. After identifying proteins that interact with the transcription factors, assays for compounds that interfere with the TF protein-protein interactions can be preformed.

XIII. IDENTIFICATION OF MODULATORS

[0126] In addition to the intracellular molecules described above, extracellular molecules that alter activity or expression of a transcription factor, either directly or indirectly, can be identified. For example, the methods can entail first placing a candidate molecule in contact with a plant or plant cell. The molecule can be introduced by topical administration, such as spraying or soaking of a plant, and then the molecule's effect on the expression or activity of the TF polypeptide or the expression of the polynucleotide monitored. Changes in the expression of the TF polypeptide can be monitored by use of polyclonal or monoclonal antibodies, gel electrophoresis or the like. Changes in the expression of the corresponding polynucleotide sequence can be detected by use of microarrays, Northerns, quantitative PCR, or any other technique for monitoring changes in mRNA expression. These techniques are exemplified in Ausubel et al. (eds) Current Protocols in Molecular Biology, John Wiley & Sons (1998, and supplements through 2001). Such changes in the expression levels can be correlated with modified plant traits and thus identified molecules can be useful for soaking or spraying on fruit, vegetable and grain crops to modify traits in plants.
[0127] Essentially any available composition can be tested for modulatory activity of expression or activity of any nucleic acid or polypeptide herein. Thus, available libraries of compounds such as chemicals, polypeptides, nucleic acids and the like can be tested for modulatory activity. Often, potential modulator compounds can be dissolved in aqueous or organic (e.g., DMSO-based) solutions for easy delivery to the cell or plant of interest in which the activity of the modulator is to be tested. Optionally, the assays are designed to screen large modulator composition libraries by automating the assay steps and providing compounds from any convenient source to assays, which are typically run in parallel (e.g., in microtiter formats on microtiter plates in robotic assays).
[0128] In one embodiment, high throughput screening methods involve providing a combinatorial library containing a large number of potential compounds (potential modulator compounds). Such “combinatorial chemical libraries” are then screened in one or more assays, as described herein, to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as target compounds.
[0129] A combinatorial chemical library can be, e.g., a collection of diverse chemical compounds generated by chemical synthesis or biological synthesis. For example, a combinatorial chemical library such as a polypeptide library is formed by combining a set of chemical building blocks (e.g., in one example, amino acids) in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound of a set length). Exemplary libraries include peptide libraries, nucleic acid libraries, antibody libraries (see, e.g., Vaughn et al. (1996) Nature Biotechnology, 14(3):309-314 and PCT/US96/10287), carbohydrate libraries (see, e.g., Liang et al. Science (1996) 274:1520-1522 and U.S. Pat. No. 5,593,853), peptide nucleic acid libraries (see, e.g., U.S. Pat. No. 5,539,083), and small organic molecule libraries (see, e.g., benzodiazepines, Baum C&EN January 18, page 33 (1993); isoprenoids, U.S. Pat. No. 5,569,588; thiazolidinones and metathiazanones, U.S. Pat. No. 5,549,974; pyrrolidines, U.S. Pat. Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Pat. No. 5,506,337) and the like.
[0130] Preparation and screening of combinatorial or other libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Pat. No. 5,010,175; Furka, (1991) Int. J. Pept. Prot. Res. 37:487-493; and Houghton et al. (1991) Nature 354:84-88). Other chemistries for generating chemical diversity libraries can also be used.
[0131] In addition, as noted, compound screening equipment for high-throughput screening is generally available, e.g., using any of a number of well known robotic systems that have also been developed for solution phase chemistries useful in assay systems. These systems include automated workstations including an automated synthesis apparatus and robotic systems utilizing robotic arms. Any of the above devices are suitable for use with the present invention, e.g., for high-throughput screening of potential modulators. The nature and implementation of modifications to these devices (if any) so that they can operate as discussed herein will be apparent to persons skilled in the relevant art.
[0132] Indeed, entire high throughput screening systems are commercially available. These systems typically automate entire procedures including all sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detector(s) appropriate for the assay. These configurable systems provide high throughput and rapid start up as well as a high degree of flexibility and customization. Similarly, microfluidic implementations of screening are also commercially available.
[0133] The manufacturers of such systems provide detailed protocols the various high throughput. Thus, for example, Zymark Corp. provides technical bulletins describing screening systems for detecting the modulation of gene transcription, ligand binding, and the like. The integrated systems herein, in addition to providing for sequence alignment and, optionally, synthesis of relevant nucleic acids, can include such screening apparatus to identify modulators that have an effect on one or more polynucleotides or polypeptides according to the present invention.
[0134] In some assays it is desirable to have positive controls to ensure that the components of the assays are working properly. At least two types of positive controls are appropriate. That is, known transcriptional activators or inhibitors can be incubated with cells/plants/etc. in one sample of the assay, and the resulting increase/decrease in transcription can be detected by measuring the resulting increase in RNA/protein expression, etc., according to the methods herein. It will be appreciated that modulators can also be combined with transcriptional activators or inhibitors to find modulators that inhibit transcriptional activation or transcriptional repression. Either expression of the nucleic acids and proteins herein or any additional nucleic acids or proteins activated by the nucleic acids or proteins herein, or both, can be monitored.
[0135] In an embodiment, the invention provides a method for identifying compositions that modulate the activity or expression of a polynucleotide or polypeptide of the invention. For example, a test compound, whether a small or large molecule, is placed in contact with a cell, plant (or plant tissue or explant), or composition comprising the polynucleotide or polypeptide of interest and a resulting effect on the cell, plant, (or tissue or explant) or composition is evaluated by monitoring, either directly or indirectly, one or more of: expression level of the polynucleotide or polypeptide, activity (or modulation of the activity) of the polynucleotide or polypeptide. In some cases, an alteration in a plant phenotype can be detected following contact of a plant (or plant cell, or tissue or explant) with the putative modulator, e.g., by modulation of expression or activity of a polynucleotide or polypeptide of the invention. Modulation of expression or activity of a polynucleotide or polypeptide of the invention may also be caused by molecular elements in a signal transduction second messenger pathway and such modulation can affect similar elements in the same or another signal transduction second messenger pathway.

XIV. SUBSEQUENCES

[0136] Also contemplated are uses of polynucleotides, also referred to herein as oligonucleotides, typically having at least 12 bases, preferably at least 15, more preferably at least 20, 30, or 50 bases, which hybridize under at least highly stringent (or ultra-high stringent or ultra-ultra-high stringent conditions) conditions to a polynucleotide sequence described above. The polynucleotides may be used as probes, primers, sense and antisense agents, and the like, according to methods as noted supra.
[0137] Subsequences of the polynucleotides of the invention, including polynucleotide fragments and oligonucleotides are useful as nucleic acid probes and primers. An oligonucleotide suitable for use as a probe or primer is at least about 15 nucleotides in length, more often at least about 18 nucleotides, often at least about 21 nucleotides, frequently at least about 30 nucleotides, or about 40 nucleotides, or more in length. A nucleic acid probe is useful in hybridization protocols, e.g., to identify additional polypeptide homologues of the invention, including protocols for microarray experiments. Primers can be annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, and then extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR) or other nucleic-acid amplification methods. See Sambrook and Ausubel, supra.
[0138] In addition, the invention includes an isolated or recombinant polypeptide including a subsequence of at least about 15 contiguous amino acids encoded by the recombinant or isolated polynucleotides of the invention. For example, such polypeptides, or domains or fragments thereof, can be used as immunogens, e.g., to produce antibodies specific for the polypeptide sequence, or as probes for detecting a sequence of interest. A subsequence can range in size from about 15 amino acids in length up to and including the full length of the polypeptide.
[0139] To be encompassed by the present invention, an expressed polypeptide which comprises such a polypeptide subsequence performs at least one biological function of the intact polypeptide in substantially the same manner, or to a similar extent, as does the intact polypeptide. For example, a polypeptide fragment can comprise a recognizable structural motif or functional domain such as a DNA binding domain that binds to a specific DNA promoter region, an activation domain or a domain for protein-protein interactions.

XV. PRODUCTION OF TRANSGENIC PLANTS

Modification of Traits

[0140] The polynucleotides of the invention are favorably employed to produce transgenic plants with various traits, or characteristics, that have been modified in a desirable manner, e.g., to improve the seed characteristics of a plant. For example, alteration of expression levels or patterns (e.g., spatial or temporal expression patterns) of one or more of the transcription factors (or transcription factor homologues) of the invention, as compared with the levels of the same protein found in a wild type plant, can be used to modify a plant's traits. An illustrative example of trait modification, improved characteristics, by altering expression levels of a particular transcription factor is described further in the Examples and the Sequence Listing.

Arabidopsis as a Model System

[0141] Arabidopsis thaliana is the object of rapidly growing attention as a model for genetics and metabolism in plants. Arabidopsis has a small genome, and well documented studies are available. It is easy to grow in large numbers and mutants defining important genetically controlled mechanisms are either available, or can readily be obtained. Various methods to introduce and express isolated homologous genes are available (see Koncz, et al., eds. Methods in Arabidopsis Research. et al. (1992), World Scientific, New Jersey, New Jersey, in “Preface”). Because of its small size, short life cycle, obligate autogamy and high fertility, Arabidopsis is also a choice organism for the isolation of mutants and studies in morphogenetic and development pathways, and control of these pathways by transcription factors (Koncz, supra, p. 72). A number of studies introducing transcription factors into A. thaliana have demonstrated the utility of this plant for understanding the mechanisms of gene regulation and trait alteration in plants. See, for example, Koncz, supra, and U.S. Pat. No. 6,417,428).

Arabidopsis Genes in Transgenic Plants.

[0142] Expression of genes which encode transcription factors modify expression of endogenous genes, polynucleotides, and proteins are well known in the art. In addition, transgenic plants comprising isolated polynucleotides encoding transcription factors may also modify expression of endogenous genes, polynucleotides, and proteins. Examples include Peng et al. (1997, Genes and Development 11:3194-3205) and Peng et al. (1999, Nature, 400:256-261). In addition, many others have demonstrated that an Arabidopsis transcription factor expressed in an exogenous plant species elicits the same or very similar phenotypic response. See, for example, Fu et al. (2001, Plant Cell 13:1791-1802); Nandi et al. (2000, Curr. Biol. 10:215-218); Coupland (1995, Nature 377:482-483); and Weigel and Nilsson (1995, Nature 377:482-500).

Homologous Genes Introduced into Transgenic Plants.

[0143] Homologous genes that may be derived from any plant, or from any source whether natural, synthetic, semi-synthetic or recombinant, and that share significant sequence identity or similarity to those provided by the present invention, may be introduced into plants, for example, crop plants, to confer desirable or improved traits. Examples of non-arabidopsis sequences homologous to arabidopsis are listed in Table 4. Consequently, transgenic plants may be produced that comprise a recombinant expression vector or cassette with a promoter operably linked to one or more sequences homologous to presently disclosed sequences. The promoter may be, for example, a plant or viral promoter.
[0144] 
[00004] [TABLE-US-00004]
  TABLE 4
 
  Orthologs of arabidopsis sequences
        Smallest     Test Sequence
  SEQ ID     Test   Sum   Test Sequence   GenBank
  NO   GID   Sequence ID   Probability   Species   Annotation
 
  859   G192   AW596933   7.70E-40   [Glycine max]   sj84f07.yl Gm-c1034 Glycine max cDNA clone GENO
  859   G192   AV423663   2.40E-39   [Lotus japonicus]   AV423663 Lotus japonicus young plants (two-
  859   G192   B1422074   4.50E-34   [Lycopersicon esculentum]   EST532740 tomato callus, TAMU Lycop
  859   G192   AW447931   1.40E-27   [Triticum aestivum]   BRY_1082 BRY Triticum aestivum cDNA clone
  859   G192   BE998060   2.60E-24   [Medicago truncatula]   EST429783 GVSN Medicago truncatula cDNA
  859   G192   AC018727   1.70E-23   [Oryza sativa]   chromosome 10 clone OSJNBa0056G17,*** SEQUENC
  859   G192   BG600477   1.00E-20   [Solanum tuberosum]   EST505372 cSTS Solanum tuberosum cDNA clo
  859   G192   BG356878   2.80E-16   [Sorghum bicolor]   OV2_11_B04.g1_A002 Ovary 2 (OV2) Sorghum bi
  859   G192   gi12039364   1.10E-31   [Oryza sativa]   putative DNA-binding protein.
  859   G192   gi4894963   3.30E-14   [Avena sativa]   DNA-binding protein WRKY3.
  859   G192   gi1432056   5.80E-14   [Petroselinum crispum]   WRKY3.
  859   G192   gi4760596   2.60E-13   [Nicotiana tabacum]   DNA-binding protein NtWRKY3.
  859   G192   gi11993901   1.40E-12   [Dactylis glomerata]   somatic embryogenesis related protein.
  859   G192   gi927025   7.60E-09   [Cucumis sativus]   SPF 1-like DNA-binding protein.
  859   G192   gi13620227   8.40E-09   [Lycopersicon esculentum]   hypothetical protein.
  859   G192   gi3420906   2.80E-08   [Pimpinella brachycarpa]   zinc finger protein; WRKY1.
  859   G192   gi1159877   4.70E-08   [Avena fatua]   DNA-binding protein.
  859   G192   gi484261   1.60E-07   [Ipomoea batatas]   SPF1 protein.
  801   G1946   LPHSF8   1.10E-119   [Lycopersicon peruvianum]   L.peruvianum Lp-hsf8 mRNA for heat
  801   G1946   AC087771   4.10E-112   [Medicago truncatula]   clone 8D15,*** SEQUENCING IN PROGRESS
  801   G1946   LEHSF8   5.90E-103   [Lycopersicon esculentum]   L.esculentum Le-hsf8 gene for heat
  801   G1946   AW569138   3.10E-75   [Glycine max]   si63g09.yl Gm-r1030 Glycine max cDNA clone GENO
  801   G1946   BG890899   1.30E-70   [Solanum tuberosum]   EST516750 cSTD Solanum tuberosum cDNA clo
  801   G1946   AC027658   4.60E-53   [Oryza sativa]   subsp. japonica BAC nbxb0006I13, chromosome 10
  801   G1946   AV833112   4.90E-52   [Hordeum vulgare subsp.vulgare]   AV833112 K. Sato unpublished
  801   G1946   gi19492   2.80E-121   [Lycopersicon peruvianum]   heat shock transcription factor 8
  801   G1946   gi19260   5.10E-106   [Lycopersicon esculentum]   heat stress transcription factor
  801   G1946   gi662924   2.00E-47   [Glycine max]   heat shock transcription factor 21.
  801   G1946   gi5821138   9.70E-46   [Nicotiana tabacum]   heat shock factor.
  801   G1946   gi11761077   2.90E-40   [Oryza sativa]   putative heat shock factor protein 1 (HSF 1)
  801   G1946   gi886742   3.20E-40   [Zea mays]   heat shock factor.
  801   G1946   gi7158882   2.70E-38   [Medicago sativa]   heat shock transcription factor.
  801   G1946   gi3550588   1.90E-30   [Pisum sativum]   heat shock transcription factor (HSFA).
  801   G1946   gi100546   0.46   [Avena sativa]   avenin precursor - oat.
  801   G1946   gi14190783   1   [Apium graveolens]   putative phloem transcription factor M1.
  239   G375   AW696439   3.40E-33   [Medicago truncatula]   NF106B07ST1F1060 Developing stem Medica
  239   G375   BG595870   1.90E-31   [Solanum tuberosum]   EST494548 cSTS Solanum tuberosum cDNA clo
  239   G375   A1899263   3.70E-31   [Lycopersicon esculentum]   EST268706 tomato ovary, TAMU Lycope
  239   G375   NTBBF3   4.00E-31   [Nicotiana tabacum]   N.tabacum mRNA for zinc finger protein, B
  239   G375   BG405482   2.70E-30   [Glycine max]   sac44a11.y1 Gm-c1062 Glycine max cDNA clone GEN
  239   G375   AB028130   3.30E-30   [Oryza sativa]   mRNA for Dof zinc finger protein, complete cds
  239   G375   AB026297   7.30E-28   [Pisum sativum]   mRNA for elicitor-responsive Dof protein ERDP
  239   G375   HVBPBF   1.10E-27   [Hordeum vulgare]   mRNA for DNA binding protein BPBF.
  239   G375   BG263089   1.70E-27   [Triticum aestivum]   WHE2337_A02 A03ZS Wheat pre-anthesis spik
  239   G375   ZMU82230   4.20E-27   [Zea mays]   endosperm-specific prolamin box binding factor (PB
  239   G375   gi4996640   1.90E-37   [Oryza sativa]   Dof zinc finger protein.
  239   G375   gi3777436   8.10E-35   [Hordeum vulgare]   DNA binding protein.
  239   G375   gi2393775   1.10E-33   [Zea mays]   prolamin box binding factor.
  239   G375   gi1360088   2.00E-33   [Nicotiana tabacum]   Zn finger protein.
  239   G375   gi3790264   4.30E-32   [Triticum aestivum]   PBF protein.
  239   G375   gi6092016   1.30E-29   [Pisum sativum]   elicitor-responsive Dof protein ERDP.
  239   G375   gi7688355   5.60E-29   [Solanum tuberosum]   Dof zinc finger protein.
  239   G375   gi1669341   4.60E-20   [Cucurbita maxima]   AOBP (ascorbate oxidase promoter-binding
  239   G375   gi3929325   5.50E-18   [Dendrobium grex Madame Thong-In]   putative DNA-binding prot
  239   G375   gi19547   5.50E-06   [Medicago sativa subsp. falcata]   environmental stress and a
  273   G1255   AC087181   1.60E-46   [Oryza sativa]   chromosome 3 clone OSJNBa0018H01, *** SEQUENCI
  273   G1255   BG239774   4.50E-33   [Glycine max]   clone GEN
  273   G1255   BG321336   1.70E-32   [Descurainia sophia]   Ds01_06h10_A DsO1_AAFC ECORC_cold_stress
  273   G1255   A1772841   2.90E-30   [Lycopersicon esculentum]   E5T253941 tomato resistant, Cornell
  273   G1255   BF480245   4.60E-29   [Mesembryanthem um crystallinum]   L0-2152T3 Ice plant Lambda Un
  273   G1255   AW688119   2.10E-28   [Medicago truncatula]   NF002E075T1F1000 Developing stem Medica
  273   G1255   BF266327   1.80E-26   [Hordeum vulgare]   HV_CEa00l4N02fHordeum vulgare seedling gre
  273   G1255   AW671538   5.80E-25   [Sorghum bicolor]   LG1_348_B08.bl_A002_Light Grown 1 (LG1)Sor
  273   G1255   B1072021   5.30E-20   [Populus tremula x   C067P76U Populus stra
          Populus tremuloides]
  273   G1255   BG273908   4.90E-19   [Vitis vinifera]   EST 110 Green Grape berries Lambda Zap II Li
  273   G1255   gi13702811   3.70E-52   [Oryza sativa]   putative zinc finger protein.
  273   G1255   gi11037311   4.00E-21   [Brassica nigra]   constans-like protein.
  273   G1255   gi2303683   1.10E-19   [Brassica napus]   unnamed protein product.
  273   G1255   gi4091804   2.30E-18   [Malus x domestica]   CONSTANS-like protein 1.
  273   G1255   gi3341723   4.30E-18   [Raphanus sativus]   CONSTANS-like 1 protein.
  273   G1255   gi10946337   5.20E-17   [Ipomoea nil]   CONSTANS-like protein.
  273   G1255   gi4557093   3.30E-15   [Pinus radiata]   zinc finger protein.
  273   G1255   gi8132543   0.97   [Chloroplast Zamia furfuracea]   cytochrome b559 alpha subuni
  273   G1255   gi11795   0.99   [Nicotiana tabacum]   put. psbE protein (aa 1-83).
  273   G1255   gi65646   0.99   [Chloroplast Nicotiana tabacum]   cytochrome b559 component p
  557   G865   BE419451   3.70E-32   [Triticum aestivum]   WWS012.C2R000101 ITEC WWS Wheat Scutellum
  557   G865   AW560968   1.10E-28   [Medicago truncatula]   EST316016 DSIR Medicago truncatula cDNA
  557   G865   AW782252   1.20E-26   [Glycine max]   sm03d11.y1 Gm-c1027 Glycine max cDNA clone GENO
  557   G865   B1421895   3.60E-25   [Lycopersicon esculentum]   E5T532561 tomato callus, TAMU Lycop
  557   G865   BE642320   1.60E-24   [Ceratopteris richardii]   Cri2_5_L17_SP6 Ceratopteris Spore Li
  557   G865   BE494041   1.60E-24   [Secale cereale]   WHE1277_B09_D17ZS Secale cereale anther cDNA
  557   G865   D39914   2.60E-24   [Oryza sativa]   RJCS1576A Rice shoot Oryza sativa cDNA, mRNA s
  557   G865   AV428124   9.00E-23   [Lotus japonicus]   AV428124 Lotus japonicus young plants (two-
  557   G865   TOBBY4D   1.80E-21   [Nicotiana tabacum]   Tobacco mRNA for EREBP-2, complete cds.
  557   G865   gi1208495   2.40E-23   [Nicotiana tabacum]   ERF1.
  557   G865   gi8809571   5.10E-23   [Nicotiana sylvestris]   ethylene-responsive element binding
  557   G865   gi3342211   1.40E-22   [Lycopersicon esculentum]   Pti4.
  557   G865   gi7528276   1.70E-22   [Mesembryanthem um crystallinum]   AP2-related transcription f
  557   G865   gi15217291   7.80E-22   [Oryza sativa]   Putative AP2 domain containing protein.
  557   G865   gi3264767   2.70E-21   [Prunus armeniaca]   AP2 domain containing protein.
  557   G865   gi8980313   2.10E-20   [Catharanthus roseus]   AP2-domain DNA-binding protein.
  557   G865   gi8571476   9.30E-20   [Atriplex hortensis]   apetala2 domain-containing protein.
  557   G865   gi1688233   1.40E-19   [Solanum tuberosum]   DNA binding protein homolog.
  557   G865   gi6478845   1.80E-19   [Matricaria chamomilla]   ethylene-responsive element binding
  23   G2509   BH577856   2.50E-29   [Brassica oleracea]   BOHOJ67TR BOHO Brassica oleracea genomic
  23   G2509   BM269574   5.90E-28   [Glycine max]   sak01eO8.yl Gm-c1074 Glycine max cDNA clone SOY
  23   G2509   BE419451   2.20E-27   [Triticum aestivum]   WWS012.C2R000101 ITEC WWS Wheat Scutellum
  23   G2509   A1483636   7.80E-27   [Lycopersicon esculentum]   E5T249507 tomato ovary, TAMU Lycope
  23   G2509   AW560968   8.90E-27   [Medicago truncatula]   EST316016 DSIR Medicago truncatula cDNA
  23   G2509   BE642320   4.30E-26   [Ceratopteris richardii]   Cri2_S_L17_SP6 Ceratopteris Spore Li
  23   G2509   AP003286   1.00E-25   [Oryza sativa]   chromosome 1 clone P0677H08, *** SEQUENCING IN
  23   G2509   BE494041   3.20E-25   [Secale cereale]   WHE1277_B09_D17ZS Secale cereale anther cDNA
  23   G2509   BE602106   1.10E-24   [Hordeum vulgare]   HVSMEh0102I06f Hordeum vulgare 5-45 DAP spi
  23   G2509   AV428124   1.00E-23   [Lotus japonicus]   AV428124 Lotus japonicus young plants (two-
  23   G2509   gi3264767   4.00E-27   [Prunus armeniaca]   AP2 domain containing protein.
  23   G2509   gi12003376   1.40E-23   [Nicotiana tabacum]   Avr9/Cf-9 rapidly elicited protein 1.
  23   G2509   gi14140141   2.30E-23   [Oryza sativa]   putative AP2-related transcription factor.
  23   G2509   gi1688233   5.40E-23   [Solanum tuberosum]   DNA binding protein homolog.
  23   G2509   gi4099921   2.60E-22   [Stylosanthes hamata]   EREBP-3 homolog.
  23   G2509   gi8809571   7.80E-22   [Nicotiana sylvestris]   ethylene-responsive element binding
  23   G2509   gi3342211   1.00E-21   [Lycopersicon esculentum]   Pti4.
  23   G2509   gi7528276   2.70E-21   [Mesembryanthemum crystallinum]   AP2-related transcription f
  23   G2509   gi17385636   1.90E-20   [Matricaria chamomilla]   ethylene-responsive element binding
  23   G2509   gi1849606   3.30E-20   [Fagus sylvatica]   ethylene responsive element binding prote
  1119   G2347   B1931517   5.30E-31   [Lycopersicon esculentum]   E5T551406 tomato flower, 8 mm to pr
  1119   G2347   BE058432   4.20E-29   [Glycine max]   sn16a06.yl Gm-c1016 Glycine max eDNA clone GENO
  1119   G2347   AMSPB1   1.80E-28   [Antirrhinum majus]   A.majus mRNA for squamosa-promoter bindin
  1119   G2347   BG525285   5.70E-28   [Stevia rebaudiana]   48-3 Stevia field grown leaf cDNA Stevia
  1119   G2347   L38193   4.60E-27   [Brassica rapa]   BNAF1025E Mustard flower buds Brassica rapa c
  1119   G2347   BG455868   6.40E-27   [Medicago truncatula]   NF068F05PL1F1045 Phosphate starved leaf
  1119   G2347   BG097153   1.70E-24   [Solanum tuberosum]   E5T461672 potato leaves and petioles Sola
  1119   G2347   BF482644   1.60E-23   [Triticum aestivum]   WHE2301-2304_A21_A21ZS Wheat pre-anthesis
  1119   G2347   AW747167   2.30E-23   [Sorghum bicolor]   WS1_66_F11.b1_A002 Water-stressed 1 (WS1) S
  1119   G2347   BG442540   2.50E-23   [Gossypium arboreum]   GA_Ea0017G06f Gossypium arboreum 7-10 d
  1119   G2347   gi1183864   1.50E-31   [Antirrhinum majus]   squamosa-promoter binding protein 2.
  1119   G2347   gi5931786   3.40E-25   [Zea mays]   SBP-domain protein 5.
  1119   G2347   gi8468036   1.40E-21   [Oryza sativa]   Similar to Arabidopsis thaliana chromosome 2
  1119   G2347   gi9087308   6.60E-09   [Mitochondrion Beta vulgaris   orf102a.
          var. altissima]
  1119   G2347   gi7209500   0.83   [Brassica rapa]   S-locus pollen protein.
  43   G988   CRU303349   3.10E-208   [Capsella rubella]   ORF1, ORF2, ORF3, ORF4, ORF5 and ORF6(pa
  43   G988   A84072   4.50E-86   [Lycopersicon esculentum]   Sequence 1 from Patent WO9846759.
  43   G988   A84080   3.30E-85   [Solanum tuberosum]   Sequence 9 from Patent WO9846759.
  43   G988   AP003944   1.30E-57   [Oryza sativa]   chromosome 6 clone OJ1126_F05, *** SEQUENCING
  43   G988   AX081276   2.80E-43   [Brassica napus]   Sequence 1 from Patent WO0109356.
  43   G988   ZMA242530   1.50E-40   [Zea mays]   partial d8 gene for gibberellin response modulato
  43   G988   AX005804   2.50E-37   [Triticum aestivum]   Sequence 13 from Patent WO9909174.
  43   G988   AB048713   9.10E-33   [Pisum sativum]   PsSCR mRNA for SCARECROW, complete cds.
  43   G988   AW774515   2.00E-29   [Medicago truncatula]   E5T333666 KV3 Medicago truncatula cDNA
  43   G988   BE822458   1.20E-27   [Glycine max]   GM700017A20H12 Gm-r1070 Glycine max cDNA clone
  43   G988   gi13620166   8.00E-211   [Capsella rubella]   hypothetical protein.
  43   G988   gi4160441   1.40E-87   [Lycopersicon esculentum]   lateral suppressor protein.
  43   G988   gi10178637   2.20E-48   [Zea mays]   SCARECROW.
  43   G988   gi6970472   1.20E-47   [Oryza sativa]   OsGAI.
  43   G988   gi5640157   2.80E-45   [Triticum aestivum]   gibberellin response modulator.
  43   G988   gi13170126   7.10E-45   [Brassica napus]   unnamed protein product.
  43   G988   gi13365610   1.10E-40   [Pisum sativum]   SCARECROW.
  43   G988   gi14318115   1.10E-14   [Zea mays subsp. mays]   gibberellin response modulator.
  43   G988   gi14318165   7.30E-14   [Tripsacum dactyloides]   gibberellin response modulator.
  43   G988   gi347457   2.40E-05   [Glycine max]   hydroxyproline-rich glycoprotein.
  459   G2346   AMA011622   3.10E-35   [Antirrhinum majus]   mRNA for squamosa promoter binding
  459   G2346   AW691786   1.80E-26   [Medicago truncatula]   NF044B06ST1F1000 Developing stem Medica
  459   G2346   AQ273505   7.00E-25   [Oryza sativa]   nbxb0030O03f CUGI Rice BAC Library Oryza sativ
  459   G2346   AW932595   7.90E-24   [Lycopersicon esculentum]   EST358438 tomato fruit mature green
  459   G2346   BG593787   9.50E-24   [Solanum tuberosum]   EST492465 cSTS Solanum tuberosum cDNA clo
  459   G2346   BG442540   1.00E-23   [Gossypium arboreum]   GA__Ea00l7G06fGossypium arboreum 7-10 d
  459   G2346   A7919034   1.90E-23   [Zea mays]   1006013G02.x3 1006 - RescueMu GridGZea mays geno
  459   G2346   B596165   2.70E-23   [Sorghum bicolor]PI1_50_D04.b1
            A002 Pathogen induced 1 (PI1)
  459   G2346   A1443033   2.30E-22   [Glycine max]   sa31a08.yl Gm-c1004 Glycine max cDNA clone GENO
  459   G2346   BF482644   4.30E-22   [Triticum aestivum]   WHE2301-2304_A21_A21ZS Wheat pre-anthesis
  459   G2346   gi5931643   6.20E-45   [Antirrhinum majus]   squamosa promoter binding protein-homol
  459   G2346   gi5931786   4.20E-26   [Zea mays]   SBP-domain protein 5.
  459   G2346   gi8468036   3.30E-14   [Oryza sativa]   Similar to Arabidopsis thaliana chromosome 2
  459   G2346   gi9087308   8.30E-08   [Mitochondrion Beta vilgaris var. altissima]   orf102a.
  285   G1354   BG128374   2.90E-58   [Lycopersicon esculentum]   E5T474020 tomato shoot/meristem Lyc
  285   G1354   BE202831   1.90E-56   [Medicago truncatula]   E5T402853 KV1 Medicago truncatula cDNA
  285   G1354   A1161918   6.60E-55   [Populus tremula x Populus tremuloides]   A009P50U Hybrid aspen
  285   G1354   AB028186   1.20E-53   [Oryza sativa]   mRNA for OsNAC7 protein, complete cds.
  285   G1354   BE060921   8.00E-50   [Hordeum vulgare]   HVSMEg0013N15f Hordeum vulgare pre-anthesis
  285   G1354   AF402603   1.50E-42   [Phaseolus vulgaris]   NAC domain protein NAC2 mRNA, complete c
  285   G1354   BE357920   1.60E-42   [Sorghum bicolor]   DG1_23_F03.b1_A002 Dark Grown 1 (DG1) Sorgh
  285   G1354   PHRNANAM   3.60E-42   [Petunia x hybrida]   P.hybrida mRNA encoding NAM protein.
  285   G1354   AW185617   5.30E-40   [Glycine max]   se80b05.y1 Gm-c 1023Glycine max cDNA clone GENO
  285   G1354   gi6006373   4.50E-63   [Oryza sativa]   Similar to NAM like protein (AC005310).
  285   G1354   gi5148914   2.30E-44   [Phaseolus vulgaris]   NAC domain protein NAC2.
  285   G1354   gi14485513   3.50E-44   [Solanum tuberosum]   putative NAC domain protein.
  285   G1354   gi1279640   5.90E-44   [Petunia x hybrida]   NAM.
  285   G1354   gi6175246   5.20E-41   [Lycopersicon esculentum]   jasmonic acid 2.
  285   G1354   gi4218535   5.10E-39   [Triticum sp.]   GRAB1 protein.
  285   G1354   gi6732158   5.10E-39   [Triticum monococcum]   unnamed protein product.
  285   G1354   gi7716952   3.30E-35   [Medicago truncatula]   NACi.
  285   G1354   gi4996349   2.50E-26   [Nicotiana tabacum]   NAC-domain protein.
  285   G1354   gi2982275   3.10E-14   [Picea mariana]   ATAF1-like protein.
  119   G1063   BH700922   4.50E-90   [Brassica oleracea]   BOMMZ07TR BO_2_3_KB Brassica oleraceagen
  119   G1063   BE451174   2.40E-41   [Lycopersicon esculentum]   E5T402062 tomato root, plants pre-a
  119   G1063   AW832545   2.00E-40   [Glycine max]   sm12e10.y1 Gm-c1027 Glycine max cDNA clone GENO
  119   G1063   AP004693   5.90E-37   [Oryza sativa]   chromosome 8 clone P0461F06 *** SEQUENCING IN
  119   G1063   AP004462   4.40E-32   [Oryza sativa (japonica   ( ) chromosome 8 clo
          cultivar-group)]
  119   G1063   AT002234   8.90E-32   [Brassica rapa subsp.pekinensis]   AT002234 Flower bud cDNA Br
  119   G1063   BF263465   5.40E-25   [Hordeum vulgare]   HV_CEa0006N02f Hordeum vulgare seedling gre
  119   G1063   BG557011   4.20E-22   [Sorghum bicolor]   EM1_41_E02.gl_A002 Embryo 1 (EM1) Sorghum b
  119   G1063   BG842856   3.10E-21   [Zea mays]   MEST40-H05.T3 ISUM4-TN Zea mays cDNA clone MEST40-
  119   G1063   BG559930   1.40E-18   [Sorghum propinquum]   RHIZ2_75_D09.gl_A003 Rhizome2 (RHIZ2) So
  119   G1063   gi15528743   4.20E-26   [Oryza sativa]   contains EST C74560(E31855)~unknown protein.
  119   G1063   gi6166283   8.10E-10   [Pinus taeda]   helix-loop-helix protein lA.
  119   G1063   gi11045087   8.80E-09   [Brassica napus]   putative protein.
  119   G1063   gi10998404   7.10E-08   [Petunia x hybrida]   anthocyanin 1.
  119   G1063   gi99441   2.60E-07   [Volvox carteri]   sulfated surface glycoprotein 185 - Volvox
  119   G1063   gi1142621   5.00E-07   [Phaseolus vulgaris]   phaseolin G-box binding protein PG2.
  119   G1063   gi166428   8.10E-07   [Antirrhinum majus]   DEL.
  119   G1063   gi1247386   9.50E-07   [Nicotiana alata]   PRP2.
  119   G1063   gi82091   1.00E-06   [Lycopersicon esculentum]   hydroxyproline-rich glycoprotein
  119   G1063   gi1486263   1.40E-06   [Catharanthus roseus]   extensin.
  129   G2143   BH650724   3.00E-88   [Brassica oleracea]   BOMIW43TR BO_2_3_KB Brassica oleracea gen
  129   G2143   AW832545   1.50E-40   [Glycine max]   sm12e10.y1 Gm-c1027 Glycine max cDNA clone GENO
  129   G2143   BE451174   3.50E-40   [Lycopersicon esculentum]   E5T402062 tomato root, plants pre-a
  129   G2143   AP004693   4.00E-38   [Oryza sativa]   chromosome 8 clone P0461F06, *** SEQUENCING IN
  129   G2143   AP004584   6.30E-33   [Oryza sativa(japonica cultivar-group)]   ( )chromosome 8 clo
  129   G2143   AT002234   3.00E-31   [Brassica rapa subsp. pekinensis]   AT002234 Flower bud cDNA Br
  129   G2143   BF263465   2.90E-26   [Hordeum vulgare]   HV_CEa0006N02fHordeum vulgare seedling gre
  129   G2143   BG557011   2.60E-22   [Sorghum bicolor]   EM1_41_E02.g1_A002 Embryo 1 (EM1) Sorghum b
  129   G2143   BG842856   3.50E-20   [Zea mays]   MEST4O-H05.T3 ISUM4-TN Zea mays cDNA clone MEST4O-
  129   G2143   BG559930   6.10E-18   [Sorghum propinquum]   RHIZ2_75_D09.g1_A003 Rhizome2 (RHIZ2) So
  129   G2143   gi15528743   5.50E-26   [Oryza sativa]   contains EST C74560(E31855)~unknown protein.
  129   G2143   gi1086538   7.60E-09   [Oryza rufipogon]   transcriptional activator Rb homolog.
  129   G2143   gi6166283   1.10E-08   [Pinus taeda]   helix-loop-helix protein 1A.
  129   G2143   gi1142621   4.60E-07   [Phaseolus vulgaris]   phaseolin G-box binding protein PG2.
  129   G2143   gi3399777   5.20E-07   [Glycine max]   symbiotic ammonium transporter; nodulin.
  129   G2143   gi5923912   6.10E-07   [Tulipa gesneriana]   bHLH transcription factor GBOF-1.
  129   G2143   gi10998404   9.20E-07   [Petunia x hybrida]   anthocyanin 1.
  129   G2143   gi4321762   5.20E-06   [Zea mays]   transcription factor MYC7E.
  129   G2143   gi166428   6.00E-06   [Antirrhinum majus]   DEL.
  129   G2143   gi527665   7.40E-06   [Sorghum bicolor]   myc-like regulatory R gene product.
  133   G2557   BH511840   6.70E-62   [Brassica oleracea]   BOGRJ19TR BOGR Brassica oleracea genomic
  133   G2557   BE347811   3.70E-46   [Glycine max]   sp05h10.y1 Gm-c1041 Glycine max cDNA clone GENO
  133   G2557   AP003141   2.40E-33   [Oryza sativa]   genomic DNA, chromosome 1, PAC clone:P0002B05,
  133   G2557   BF263465   3.00E-31   [Hordeum vulgare]   HV_CEa0006N02fHordeum vulgare seedling gre
  133   G2557   AT002234   6.60E-27   [Brassica rapa subsp. pekinensis]   AT002234 Flowerbud cDNA Br
  133   G2557   BG557011   6.40E-26   [Sorghum bicolor]   EM1_41_E02.g1_A002 Embryo 1 (EM1) Sorghum b
  133   G2557   AP004462   7.90E-26   [Oryza sativa   ( )chromosome 8 clo
          (japonica cultivar-group)]
  133   G2557   BE451174   3.90E-25   [Lycopersicon esculentum]   E5T402062 tomato root, plants pre-a
  133   G2557   BG842856   5.60E-22   [Zea mays]   MEST40-H05.T3 ISUM4-TN Zea mays cDNA clone MEST4O-
  133   G2557   BG559930   7.00E-14   [Sorghum propinquum]   RH1Z2_75_D09.g1 A003 Rhizome2 (RHIZ2) So
  133   G2557   gi15289790   2.40E-36   [Oryza sativa]   contains EST C74560(E31855)~unknown protein.
  133   G2557   gi3399777   2.60E-06   [Glycine max]   symbiotic ammonium transporter; nodulin.
  133   G2557   gi4206118   1.10E-05   [Mesembryanthemum crystallinum]   transporter homolog.
  133   G2557   gi6166283   1.30E-05   [Pinus taeda]   helix-loop-helix protein 1A.
  133   G2557   gi527655   3.70E-05   [Pennisetum glaucum]   myc-like regulatory R gene product.
  133   G2557   gi5923912   3.70E-05   [Tulipa gesneriana]   bHLH transcription factor GBOF-1.
  133   G2557   gi527661   7.80E-05   [Phyllostachys acuta]   myc-like regulatory R gene product.
  133   G2557   gi527665   9.50E-05   [Sorghum bicolor]   myc-like regulatory R gene product.
  133   G2557   gi1086538   0.0001   [Oryza rufipogon]   transcriptional activator Rb homolog.
  133   G2557   gi5669656   0.00013   [Lycopersicon esculentum]   ER33 protein.
  697   G2430   BF632520   1.90E-14   [Medicago truncatula]   NF039A08DT1F10541054 Drought Medicago trunc
  697   G2430   AW396912   1.20E-13   [Glycine max]   sg64g09.y1 Gm-c1007 Glycine max cDNA clone GENO
  697   G2430   D41804   4.50E-13   [Oryza sativa]   RICS4626A Rice shoot Oryza sativa cDNA, mRNA s
  697   G2430   BE214029   2.60E-10   [Hordeum vulgare]   HV_CEb0001P06fHordeum vulgare seedling gre
  697   G2430   AW564570   2.70E-10   [Sorghum bicolor]   LG1_296_E01.b1_A002 Light Grown 1 (LG1) Sor
  697   G2430   BG129795   5.40E-10   [Lycopersicon esculentum]   EST475441 tomato shoot/meristem Lyc
  697   G2430   AB060130   5.40E-09   [Zea mays]   ZmRR8 mRNA for response regulator 8, complete cds.
  697   G2430   BF587105   2.50E-05   [Sorghum propinquum]   FM1_32_C0Sbi_A003 Floral-Induced Merist
  697   G2430   AI163121   0.3   [Populus tremula x Populus tremuloides]   A033P70U Hybrid aspen
  697   G2430   BG595628   0.46   [Solanum tuberosum]   EST494306 cSTS Solanum tuberosum cDNA clo
  697   G2430   gi13661174   5.40E-18   [Zea mays]   response regulator 8.
  697   G2430   gi15289981   0.028   [Oryza sativa]   hypothetical protein.
  697   G2430   gi6942190   0.12   [Mesembryanthemum crystallinum]   CDPK substrate protein 1; C
  697   G2430   gi4519671   0.2   [Nicotiana tabacum]   transfactor.
  831   G1478   BF275913   1.50E-20   [Gossypium arboreum]   GA__Eb0025C07fGossypium arboreum 7-10 d
  831   G1478   BG157399   6.50E-19   [Glycine max]   sab36g12.y1 Gm-c1026 Glycine max cDNA clone GEN
  831   G1478   C95300   2.20E-10   [Citrus unshiu]   C95300 Citrus unshiu Miyagawa-wase maturation
  831   G1478   AW034552   2.70E-10   [Lycopersicon esculentum]   EST278168 tomato callus, TAMU Lycop
  831   G1478   B1070429   3.40E-10   [Populus tremula x Populus tremuloides]   C037P68U Populus stra
  831   G1478   AF016011   5.10E-09   [Brassica napus]   CONSTANS homolog (Bn9C0N10) gene, complete c
  831   G1478   BE598912   6.20E-09   [Sorghum bicolor]   P11_84_H11.bi_A002 Pathogen induced 1 (PI1)
  831   G1478   BG605313   6.80E-09   [Triticum aestivum]   WHE2331_C04_F07ZS Wheat pre-anthesis spik
  831   G1478   BE558327   8.90E-09   [Hordeum vulgare]   HV_CEb0017Dl9fHordeum vulgare seedling gre
  831   G1478   BG647091   1.20E-08   [Medicago truncatula]   EST508710 HOGA Medicago truncatula cDNA
  831   G1478   gi2895188   4.70E-11   [Brassica napus]   CONSTANS homolog.
  831   G1478   gi3618308   1.50E-09   [Oryza sativa]   zinc finger protein.
  831   G1478   gi11037308   4.70E-09   [Brassica nigra]   constans-like protein
  831   G1478   gi3341723   1.30E-08   [Raphanus sativus]   CONSTANS-like 1 protein.
  831   G1478   gi4091806   1.50E-07   [Malus x domestica]   CONSTANS-like protein 2.
  831   G1478   gi10946337   3.10E-07   [Ipomoea nil]   CONSTANS-like protein.
  831   G1478   gi4557093   1.40E-05   [Pinus radiata]   zinc finger protein.
  831   G1478   gi619312   0.9   [Capparis masaikai]   mabinlin III B-chain = sweet protein mabi
  831   G1478   gi4732091   1   [Zea mays]   bundle sheath defective protein 2.
  831   G1478   gi4699629   1   [Nicotiana alata]   Chain A, Putative Ancestral Protein Encod
  579   G681   BG128147   6.80E-41   [Lycopersicon esculentum]   E5T473793 tomato shoot/meristem Lyc
  579   G681   BF054497   1.50E-39   [Solanum tuberosum]   E5T439727 potato leaves and petioles Sola
  579   G681   BE054276   8.40E-39   [Gossypium arboreum]   GA__Ea0002018f
            Gossypium arboreum 7-10 d
  579   G681   BG269414   4.00E-38   [Mesembryanthemum   L0-3478T3 Ice plant Lambda Un
          crystallinum]
  579   G681   BF620286   7.40E-38   [Hordeum vulgare]   HVSMEc0019F08f Hordeum vulgare seedling sho
  579   G681   BE490032   1.00E-37   [Triticum aestivum]   WHE0364_C04_E08ZS Wheat cold-stressed see
  579   G681   B1542536   1.40E-36   [Zea mays]   949021A03.y1 949 - Juvenile leaf and shoot cDNA fr
  579   G681   BF425254   7.20E-36   [Glycine max]   su42c10.y1 Gm-c1068 Glycine max cDNA clone GENO
  579   G681   AW672062   3.20E-34   [Sorghum bicolor]   LG1_354_G05b1_A002 Light Grown 1 (LG1) Sor
  579   G681   BG448527   1.00E-33   [Medicago truncatula]   NF036F04RT1F1032 Developing root Medica
  579   G681   gi13346188   9.10E-37   [Gossypium hirsutum]   GHMYB25.
  579   G681   gi20563   6.30E-36   [Petunia x hybrida]   protein 1.
  579   G681   gi485867   1.20E-34   [Antirrhinum majus]   mixta.
  579   G681   gi2605617   1.70E-32   [Oryza sativa]   OSMYB1.
  579   G681   gi1430846   2.00E-31   [Lycopersicon esculentum]   myb-related transcription factor.
  579   G681   gi6651292   2.20E-30   [Pimpinella brachycarpa]   myb-related transcription factor.
  579   G681   gi15042116   4.90E-30   [Zea mays subsp. parviglumis]   CI protein.
  579   G681   gi82730   6.10E-30   [Zea mays]   transforming protein (myb) homolog (clone Zm38)
  579   G681   gi5139806   8.30E-30   [Glycine max]   GmMYB29A2.
  579   G681   gi19055   1.10E-29   [Hordeum vulgare]   MybHv5.
  611   G878   AF096299   6.20E-90   [Nicotiana tabacum]   DNA-binding protein 2 (WRKY2) mRNA, compl
  611   G878   CUSSLDB   1.80E-83   [Cucumis sativus]   SPF 1-like DNA-binding protein mRNA, complet
  611   G878   AF193802   3.50E-63   [Oryza sativa]   zinc finger transcription factor WRKY1 mRNA, c
  611   G878   AX192162   2.20E-62   [Glycine max]   Sequence 9 from Patent WO0149840.
  611   G878   IPBSPF1P   3.80E-58   [Ipomoea batatas]   Sweet potato mRNA for SPF1 protein, complet
  611   G878   AFABF1   2.00E-56   [Avena fatua]   A.fatua mRNA for DNA-binding protein(clone ABF
  611   G878   LE5303343   7.20E-55   [Lycopersicon esculentum]   mRNA for hypothetical protein (ORF
  611   G878   AX192164   4.00E-54   [Triticum aestivum]   Sequence 11 from Patent WO0149840.
  611   G878   AF080595   2.10E-53   [Pimpinella brachycarpa]   zinc finger protein (ZFP1) mRNA, com
  611   G878   PCU48831   2.30E-53   [Petroselinum crispum]   DNA-binding protein WRKY1 mRNA, comple
  611   G878   gi4322940   3.30E-128   [Nicotiana tabacum]   DNA-binding protein 2.
  611   G878   gi927025   1.10E-109   [Cucumis sativus]   SPF1-like DNA-binding protein.
  611   G878   gi6689916   1.50E-74   [Oryza sativa]   zinc finger transcription factor WRKY1
  611   G878   gi484261   1.10E-66   [Ipomoea batatas]   SPF1 protein.
  611   G878   gi1159877   2.30E-63   [Avena fatua]   DNA-binding protein.
  611   G878   gi13620227   4.60E-63   [Lycopersicon esculentum]   hypothetical protein.
  611   G878   gi5917653   1.70E-56   [Petroselinum crispum]   zinc-finger type transcription facto
  611   G878   gi4894965   5.00E-56   [Avena sativa]   DNA-binding protein WRKY1.
  611   G878   gi3420906   8.70E-56   [Pimpinella brachycarpa]   zinc finger protein; WRKY1.
  611   G878   gi13620168   4.20E-22   [Capsella rubella]   hypothetical protein.
  47   G374   AP004457   1.20E-73   [Oryza sativa (japonica cultivar group)]   ( )chromosome 8 clo
  47   G374   AP004693   1.90E-73   [Oryza sativa]   chromosome 8 clone P0461F06 *** SEQUENCING IN
  47   G374   BH552835   1.30E-62   [Brassica oleracea]   BOHGT56TR BOHG Brassica oleracea genomic
  47   G374   BG128229   6.50E-55   [Lycopersicon esculentum]   EST473875 tomato shoot/meristem Lyc
  47   G374   BG646959   3.20E-46   [Medicago truncatula]   E5T508578 HOGA Medicago truncatula cDNA
  47   G374   BG890162   8.70E-41   [Solanum tuberosum]   EST516013 cSTD Solanum tuberosum cDNA clo
  47   G374   AW179366   6.00E-38   [Zea mays]   618046G06.y1 618 - Inbred Tassel cDNA Library Zea
  47   G374   BF473206   1.50E-32   [Triticum aestivum]   WHE0922_G12_M24ZS Wheat 5-15 DAPspike cD
  47   G374   AW761011   2.90E-29   [Glycine max]   s161g11.y1 Gm-c1027 Glycine max cDNA clone GENO
  47   G374   AJ436050   1.50E-27   [Hordeum vulgare]   AJ436050 S00007 Hordeum vulgare cDNA clone
  47   G374   gi422012   0.8   [Sorghum bicolor]   lipid transfer protein - sorghum (fragmen
  47   G374   gi1827893   1   [Zea mays]   Maize Nonspecific Lipid Transfer Protein Complex
 
[0145] The invention thus provides for methods for preparing transgenic plants, and for modifying plant traits. These methods include introducing into a plant a recombinant expression vector or cassette comprising a functional promoter operably linked to one or more sequences homologous to presently disclosed sequences. Plants and kits for producing these plants that result from the application of these methods are also encompassed by the present invention.

Traits of Interest

[0146] Examples of some of the traits that may be desirable in plants, and that may be provided by transforming the plants with the presently disclosed sequences, are listed in Table 5 and 6.
[0147] 
[00005] [TABLE-US-00005]
  TABLE 5
 
  Genes, traits, transcription factor families and conserved domains
  Poly-             Poly-  
  nucleotide             peptide
  SEQ   GID           SEQ ID   Conserved
  ID NO:   No.   Trait   Category   Family   Comment   NO:   domains
 
  1   G1275   Architecture;   Dev and   WRKY   Reduced apical   2   (113-169)
      size   morph     dominance; small
            plant
  3   G1411   Architecture   Dev and morph   AP2   Loss of apical dominance   4   (87-154)
  5   G1488   Architecture;   Dev and   GATA/Zn   Reduced apical   6   (221-246)
      light   morph; seed     dominance, shorter
      response;   biochemistry     stems; constitutive
      size; seed       photomorphogenesis;
      protein       reduced size; altered
      content       seed protein content
  7   G1499   Architecture;   Dev and   HLH/MYC   Altered plant   8   (118-181)
      flower;   morph     architecture; altered
      morphology:       floral organ identity
      other       and development; dark
            green color
  9   G1543   Architecture;   Dev and   HB   Altered plant   10   (135-195)
      flower;   morph; seed     architecture; altered
      morphology:   biochemistry     carpel shape; dark
      other; seed oil       green color; decreased
            seed oil
  11   G1635   Architecture;   Dev and   MYB-   Reduced apical   12   (44-104)
      morphology:   morph   related   dominance; pale
      other; fertility       green, smaller plants;
            reduced fertility
  13   G1794   Architecture;   Dev and   AP2   Altered plant   14   (182-248)
      light   morph; seed     architecture;
      response;   biochemistry     constitutive
      seed oil and       photomorphogenesis;
      protein content       altered seed oil and
            protein content
  15   G1839   Architecture;   Dev and   AP2   Altered plant   16   (118-184)
      size   morph     architecture; reduced
            size
  17   G2108   Architecture   Dev and morph   AP2   Altered inflorescence   18   (18-85)
            structure
  19   G2291   Architecture;   Dev and   AP2   Altered plant   20   (TBD)
      flowering   morph;     architecture; late
      time   flowering     flowering
        time
  21   G2452   Architecture;   Dev and   MYB-   Reduced apical   22   (27-213)
      leaf   morph   related   dominance; pale green
            color
  23   G2509   Architecture;   Dev and morph;   AP2   Reduced apical   24   (89-156)
      seed oil and   seed biochemistry     dominance; altered
      protein content       seed oil and protein
            content
  25   G390   Architecture   Dev and   HB   Altered shoot   26   (18-81)
        morph     development
  27   G391   Architecture   Dev and   HB   Altered shoot   28   (25-85)
        morph     development
  29   G438   Architecture;   Dev and   HB   Reduced branching,   30   (22-85)
      stem   morph     reduced lignin
  31   G47   Architecture;   Dev and morph;   AP2   Altered architecture   32   (11-80)
      stem;   flowering     and inflorescence
      flowering   time; seed     development, structure
      time; altered   biochemistry     of vascular tissues;
      seed oil       late flowering; altered
      content       seed oil content
  33   G559   Architecture;   Dev and   bZIP   Loss of apical   34   (203-264)
      fertility   morph     dominance; reduced
            fertility
  35   G568   Architecture;   Dev and   bZIP   Altered branching; late   36   (215-265)
      flowering   morph;     flowering
      time   flowering
        time
  37   G580   Architecture;   Dev and   bZIP   Altered inflorescences;   38   (162-218)
      flower   morph     altered flower
            development
  39   G615   Architecture;   Dev and   TEO   Altered plant   40   (88-147)
      fertility   morph     architecture; little or
            no pollen production,
            poor filament
            elongation
  41   G732   Architecture;   Dev and   bZIP   Reduced apical   42   (31-91)
      flower; seed   morph; seed     dominance; abnormal
      oil and   biochemistry     flowers; altered seed
      protein       oil and protein content
      content
  43   G988   Architecture;   Dev and   SCR   Reduced lateral   44   (178-195)
      fertility;   morph; seed     branching; reduced
      flower; stem;   biochemistry     fertility; enlarged
      seed oil and       floral organs, short
      protein       pedicels; thicker stem,
      content       altered distribution of
            vacular bundles;
            altered seed oil and
            protein content
  45   G1519   Embryo lethal   Dev and morph   RING/C3HC4   Embryo lethal   46   (327-364)
  47   G374   Embryo lethal   Dev and morph   Z-ZPF   Embryo lethal   48   (35-67,
                245-277)
  49   G877   Embryo lethal   Dev and morph   WRKY   Embryo lethal   50   (272-328,
                487-603)
  51   G1000   Fertility; size;   Dev and   MYB-   Reduced fertility;   52   (14-117)
      flower; stem   morph   (R1)R2R3   small plant; reduced or
            absent petals and
            sepals; reduced
            inflorescence, stem
            elongation
  53   G1067   Fertility; leaf   Dev and   AT-hook   Reduced fertility,   54   (86-93)
      size   morph     altered leaf shape;
            small plant
  55   G1075   Fertility; flower;   Dev and   AT-hook   Reduced fertility,   56   (78-85)
      leaf; size   morph     reduced or absent
            petals, sepals and
            stamens; altered leaf
            shape; small plant
  57   G1266   Fertility; size   Dev and   AP2   Reduced fertility;   58   (79-147)
        morph     small plant
  59   G1311   Fertility; size   Dev and   MYB-   Reduced fertility;   60   (11-112)
        morph   (R1)R2R3   small plant
  61   G1321   Fertility; flower   Dev and   MYB-   Poor fertility; altered   62   (4-106)
        morph   (R1)R2R3   flower morphology
  63   G1326   Fertility; flower;   Dev and   MYB-   Reduced fertility;   64   (18-121)
      size   morph   (R1)R2R3   petals and sepals are
            smaller; small plant
  65   G1367   Fertility; size   Dev and   AT-hook   Reduced fertility;   66   (179-201,
        morph     reduced size     262-285,
                298-319,
                335-357)
  67   G1386   Fertility; size;   Dev and   AP2   Reduced fertility;   68   (TBD)
      seed oil and   morph; seed     and reduced size; altered
      protein   biochemistry     seed oil and protein
      content       content
  69   G1421   Fertility; size;   Dev and   AP2   Reduced fertility;   70   (74-151)
      seed oil   morph; seed     small plant; altered
      content   biochemistry     seed oil content
  71   G1453   Fertility;   Dev and   NAC   Reduced fertility;   72   (13-160)
      morphology:   morph     altered inflorescence
      other       development
  73   G1560   Fertility;   Dev and   HS   Reduced fertility;   74   (62-151)
      flower; size   morph     altered flower
            development; reduced
            size
  75   G1594   Fertility; leaf;   Dev and   HB   Reduced fertility;   76   (343-308)
      seed   morph     altered leaf shape and
            and development; large
            pale seed
  77   G1750   Fertility; size   Dev and   AP2   Reduced fertility;   78   (107-173)
      seed oil   morph; seed     reduced size;
      content   biochemistry     increased seed oil
            content
  79   G1947   Fertility; flower;   Dev and   HS   Reduced fertility;   80   (37-120)
      seed protein   morph; seed     and extended period of
      content   biochemistry     flowering; altered seed
            protein content
  81   G2011   Fertility; size   Dev and   HS   Reduced fertility;   82   (56-147)
      seed oil and   morph; seed     and reduced size; altered
      protein content   biochemistry     seed oil and protein
            content
  83   G2094   Fertility; leaf;   Dev and   GATA/Zn   Reduced fertility;   84   (43-68)
      size   morph     altered leaf
            and development; reduced
            size
  85   G2113   Fertility; leaf;   Dev and   AP2   Reduced fertility; long   86   (TBD)
      seed protein   morph; seed     petioles, altered
      content   biochemistry     orientation; altered
            seed protein content
  87   G2115   Fertility; size   Dev and morph   AP2   Reduced fertility;   88   (46-115)
            reduced size
  89   G2130   Fertility; size;   Dev and morph   AP2   Reduced fertility;   90   (93-160)
      senescence       reduced size; early
            senescence
  91   G2147   Fertility; size   Dev and morph   HLM/MYC   Reduced fertility;   92   (160-234)
            reduced size
  93   G2156   Fertility; size;   Dev and morph;   AT-hook   Reduced fertility;   94   (66-86)
      seed protein   seed biochemistry     reduced size; altered
      content       seed protein content
  95   G2294   Fertility; size   Dev and morph   AP2   Reduced fertility;   96   (32-102)
            reduced size
  97   G2510   Fertility; size   Dev and morph   AP2   Reduced fertility;   98   (41-108)
            reduced size
  99   G2893   Fertility; flower;   Dev and morph   MYB-(R1)   Reduced fertility;   100   (19-120)
      size     R2R3   altered flower
            development; reduced
            size
  101   G340   Fertility; size   Dev and morph   Z-C3H   Reduced fertility, size   102   (37-154)
  103   G39   Fertility; size   Dev and morph   AP2   Reduced fertility,   104   (24-90)
            small plant
  105   G439   Fertility; size   Dev and morph   AP2   Reduced fertility;   106   (110-177)
            small plant
  107   G470   Fertility   Dev and morph   ARF   Short stamen filaments   108   (61-393)
  109   G652   Fertility; seed;   Dev and morph;   Z-CLDSH   Reduced fertility;   110   (28-49,
      flower; size;   seed biochemistry     irregular shaped seed     137-151,
      seed oil content       altered flower     182-196)
            development; reduced
            size, slow growth;
            altered seed oil content
  111   G671   Fertility; flower;   Dev and morph   MYB-(R1)   Reduced fertility;   112   (15-115)
      leaf size; stem     R2R3   abscission; altered leaf
            shape; small plant;
            altered inflorescence
            stem structure
  113   G779   Fertility; flower   Dev and morph   HLH/MYC   Reduced fertility,   114   (126-182)
            homoerotic
            transformations
  115   G962   Fertility; size   Dev and morph   NAC   Reduced fertility;   116   (53-175)
            small plant
  117   G977   Fertility; leaf;   Dev and morph   AP2   Reduced fertility;   118   (5-72)
      morphology; other       altered leaf shape;
      size       dark green; small plant
  119   G1063   Flower; leaf;   Dev and morph;   HLM/MYC   Altered flower   120   (131-182)
      inflorescence;   seed biochemistry     development, ectopic
      seed oil and       carpel tissue; altered
      protein content       leaf shape, dark altered
            color; altered
            inflorescence
            development; altered
            seed oil and protein
            content
  121   G1140   Flower   Dev and morph   MADS   Altered flower development   122   (2-57)
  123   G1425   Flower   Dev and morph   NAC   Altered flower and   124   (20-173)
            inflorescence
  125   G1449   Flower   Dev and morph   IAA   Altered flower structure   126   (48-53,
                74-107,
                122-152)
  127   G1897   Flower; leaf;   Dev and morph   Z-Dof   Altered flower   128   (34-62)
      seed protein   seed biochemistry     development;
      content       altered leaf
            development altered
            seed protein content
  129   G2143   Flower; leaf;   Dev and morph   HLM/MYC   Altered flower   130   (128-179)
      inflorescence       development, ectopic
            carpel tissue; altered
            leaf shape, dark green
            color; altered
            inflorescence
            development
  131   G2535   Flower; seed   Dev and morph;   NAC   Altered flower   132   (11-114)
      protein content   seed biochemistry     development; altered
            seed protein
            content
  133   G2557   Flower; leaf   Dev and morph   HLM/MYC   Altered flower   134   (278-328)
            development
            ectopic carpel
            tissue; altered leaf
            shape, dark green
            color
  135   G259   Flower; leaf   Dev and morph   HS   Altered flower   136   (27-131)
            development;
            altered leaf
            development
  137   G353   Flower; leaf; size;   Dev and morph;   Z-C2H2   Short pedicels,   138   (41-61,
      seed protein   seed biochemistry     downward pointing     84-104)
      content       siliques; altered leaf
            development;
            reduced size;
            altered seed
            protein content
  139   G354   Flower; light   dev and morph   Z-C2H2   Short pedicels,   140   (42-62
      respond; size       downward pointing     88-109)
            siliques; morphogenesis;
            reduced size
  141   G638   Flower; morphology:   Dev and morph   TH   Altered flower   142   (119-206)
      other       development; multiple
            developmental defects
  143   G869   Flower; morphology:   Dev and morph;   AP2   Abnormal anther   144   (109-177)
      other; seed oil   seed biochemistry     development; small
            and spindly plant;
            altered seed fatty acids
  145   G1645   Inflorescence; leaf   Dev and morph   MYB-(R1)   Altered inflorescence   146   (90-210)
          R2R3   structure; altered leaf
            development
  147   G1038   Leaf   Dev and morph   GARP   Altered leaf shape   148   (198-247)
  149   G1073   Leaf; size;   Dev and morph;   AT-hook   Serrated leaves;   150   (33-42,
      flowering time   flowering time     increased plant size;     18-175)
            flowering appears
            to be slightly delayed
  151   G1146   Leaf   Dev and morph   PAZ   Altered leaf   152   (886-896)
            development
  153   G1267   Leaf; size   Dev and morph   WRKY   Dark green shiny   154   (70-127)
            leaves; small plant
  155   G1269   Leaf   Dev and morph   MYB-related   Long petioles,   156   (27-83)
            upturned leaves
  157   G1452   Leaf; trichome;   Dev and morph;   NAC   Altered leaf shaped,   158   (30-177)
      flowering time   flowering time     dark green color;
            reduced trichome
            density; late flowering
  159   G14949   Leaf; size; light   Dev and morph   HLH/MYC   Pale green leaves,   160   (261-311)
      response; seed       altered leaf shape;
            reduced size; long
            hypocotyls; large,
            pale seeds
  161   G1548   Leaf   Dev and morph   HB   Altered leaf development   162   (17-77)
  163   G1574   Leaf   Dev and morph   SWI/SNF   Altered leaf development   164   (28-350)
  165   G1586   Leaf; size   Dev and morph   HB   Narrow leaves; small   166   (21-81)
            plants
  167   G1786   Leaf; light   Dev and morph   MYB-(R1)   Dark green, small   168   (TBD)
      response; size     R2R3   leaves with short
            petioles; photo-
            photomorphogensis in
            the dark; small plant
  169   G1792   Leaf; seed oil   Dev and morph;   AP2   Dark green, shiny   170   (17-85)
      and protein content   seed biochemistry     leaves; altered seed
            oil and protein content
  171   G1865   Leaf; seed oil   Dev and morph;   GRF-like   Altered leaf   172   (124-149)
      and protein content   seed biochemistry     development; altered
            seed oil and protein content
  173   G1886   Leaf; size   Dev and morph   Z-Dof   Chlorotic patches in   174   (17-59)
            leaves; reduced size
  175   G1933   Leaf; size; seed   Dev and morph;   WRKY   Altered leaf   176   (205-263,
      protein content   seed biochemistry     development; reduced size     344-404)
            altered seed protein
            content
  177   G2059   Leaf; seed oil   Dev and morph;   AP2   Smaller, curled leaves;   178   (184-254)
      and protein content   seed     altered seed oil,
        biochemistry     protein content
  179   G2105   Leaf; seed   Dev and morph   TH   Alteration in leaf   180   (100-153)
            surface; large,
            pale seeds
  181   G2117   Leaf; seed oil   Dev and morph;   bZIP   Small, dark green   182   (46-106)
      and protein content   seed biochemistry     leaves; altered seed oil
            and protein content
  183   G2124   Leaf; seed protein   Dev and morph;   TEO   Altered leaf   184   (75-132)
      content   seed     development; altered
        biochemistry     seed protein content
  185   G2140   Leaf; root   Dev and morph   HLH/MYC   Altered leaf   186   (167-242)
            development; short roots
  187   G2144   Leaf; light response;   Dev and morph   HLH/MYC   Pale green leaves,   188   (203-283)
      size; seed oil content   seed     altered leaf shape;
        biochemistry     long hypocotyls; reduced
            size; altered seed oil
            content
  189   G2431   Leaf   Dev and morph   GARP   Dark green leaves;   190   (38-88)
            reduced size
  191   G2465   Morphology; other;   Dev and morph   GARP   Slowed development;   192   (219-269)
      leaf       altered leaf color
            and shape
  193   G2583   Leaf; seed oil   Dev and morph   AP2   Glossy, shiny leaves;   194   (4-71)
      and protein content   seed biochemistry     altered seed oil
            and protein content
  195   G2724   Leaf   Dev and morph   MYB-(R1)R2R3   Dark green leaves   196   (7-113)
  197   G377   Leaf; morphology:   Dev and morph   RING/C3H2C3   Altered leaf   198   (85-128)
      other       development; slow
            growth
  199   G428   Leaf   Dev and morph   HB   Altered leaf shape   200   (229-292)
  201   G447   Leaf; morphology:   Dev and morph   ARF   Dark green leaves;   202   (22-356)
      other; size       altered cotyledon
            shape; reduced size
  203   G464   Leaf   Dev and morph   IAA   Altered leaf shape   204   (20-28,
                71-82,
                126-142,
                187-224)
  205   G557   Leaf; size   Dev and morph   bZIP   Dark green color;   206   (90-150)
            small plant
  207   G577   Leaf   Dev and morph   BZIPT2   Reduced size,   208   (TBD)
            increased
            anthocyanins
  209   G674   Leaf; size   Dev and morph   MYB-(R1)   Dark green leaves,   210   (20-120)
          R2R3   upwardly oriented;
            reduced size
  211   G736   Leaf; flowering time   Dev and morph;   Z-Dof   Altered leaf shape;   212   (54-111)
        flowering time     later flowering
  213   G903   Leaf   Dev and morph   Z-C2H2   Altered leaf   214   (68-92)
            morphology
  215   G917   Leaf; seed oil   Dev and morph   MADS   Altered leaf development;   216   (2-57)
      and protein content   seed biochemistry     altered seed oil and protein
            content
  217   G921   Leaf   Dev and morph   WRKY   Serrated leaves   218   (146-203)
  219   G922   Leaf; size   Dev and morph   SCR   Altered development,   220   (225-242)
            dark green color;
            reduced size
  221   G932   Leaf; size   Dev and morph   MYB-(R1)R2R3   Altered development,   220   (225-242)
            dark green color;
            reduced size
  223   G599   Leaf; size   Dev and morph   DBP   Altered leaf shape;   224   (187-219,
            small plant     264-300)
  225   G804   Leaf; size   Dev and morph   PCF   Altered leaf shape,   226   (54-117)
            small plant
  227   G1062   Light response;   Dev and morph   HLH/MYC   Constitutive   228   (308-359)
      morphology;       photomorphogenesis;
      other; seed       slow growth; altered
            seed shape
  229   G1322   Light response; size   Dev and morph   MYB-(R1)R2R3   Photomorphogenesis   230   (26-130)
            in the dark; reduced
            size
  231   G1331   Light response;   Dev and morph;   MYB-(R1)   Constitutive   232   (8-109)
      morphology; other;   seed biochemistry   R2R3   photomorphogenesis;
      seed oil and       multiple developmental
      protein content       alterations; altered
            seed oil and protein
            content
  233   G1521   Light response   Dev and morph   RING/C3HC4   Constitutive   234   (39-80)
            photomorphogenesis
  235   G183   Light response;   Dev and morph;   WRKY   Constitutive   236   (307-363)
      seed protein content   seed biochemistry     photomorphogenesis;
            altered seed
            protein content
  237   G2555   Light response   Dev and morph   HLH/MYC   Constitutive   238   (175-245)
            photomorphogenesis
  239   G375   Light response   Dev and morph   Z-Dof   Upward pointing leaves   240   (75-103)
  241   G1007   Morphology; other   Dev and morph   AP2   Multiple   242   (TBD)
            developmental alterations
  243   G1010   Morphology; other   Dev and morph   ABI3/VP-1   Multiple   244   (33-122)
            developmental alterations
  245   G1014   Morphology; other   Dev and morph   ABI3/VP-1   Multiple   246   (90-172)
      trichome       developmental defects;
            reduced trichomes
  247   G1035   Morphology; other   Dev and morph   bZIP   Multiple   248   (39-91)
            developmental
            alterations
  249   G1046   Morphology; other   Dev and morph   bZIP   Multiple   250   (79-138)
            developmental
            alterations
  251   G1049   Morphology;   Dev and morph;   bZIP   Multiple   252   (77-132)
      other; seed   seed biochemistry     developmental
      protein content       alterations; altered
            seed protein content
  253   G1069   Morphology: other   Dev and morph;   AT-hook   Multiple   254   (67-74)
      seed oil content   seed biochemistry     developmental
            alterations; altered
            seed oil content
  255   G1070   Morphology: other   Dev and morph   AT-hook   Several developmental   256   (98-120)
            defects
  257   G1076   Morphology; other   Dev and morph   AT-hook   Lethal when   258   (82-89)
            overexpressed
  259   G1089   Morphology; other   Dev and morph   BZIPT2   Developmental defects   260   (425-500)
            at seeding stage
  261   G1093   Morphology: other   Dev and morph   RING/C3H2C3   Multiple morphological   262   (105-148)
            alterations
  263   G1127   Morphology: other   Dev and morph   AT-hook   Multiple developmental   264   (103-110,
            alterations     155-162)
  265   G1131   Morphology: other;   Dev and morph;   HLH/MYC   Multiple developmental   266   (173-220)
      seed protein content       alterations; altered
            seed protein content
  267   G1145   Morphology; other;   Dev and morph;   bZIP   Multiple developmental   268   (227-270)
      seed oil and   seed biochemistry     alterations; reduced
      protein content       seed size, altered seed
            shape; altered seed oil
            and protein content
  269   G1229   Morphology: other;   Dev and morph;   HLH/MYC   Several developmental   270   (102-160)
      seed oil and   seed biochemistry     defects; altered seed
      protein content   content     oil and protein
  271   G1246   Morphology; other   Dev and morph;   MYB-(R1)   Multiple developmental   272   (27-139)
      seed protein   seed biochemistry   R2R3   alterations; altered
      content       seed protein content
  273   G1255   Morphology; other   Dev and morph   Z-CO-like   Reduced apical   274   (18-56)
      seed       dominance; increased
            seed size
  275   G1304   Morphology: other   Dev and morph   MYB-(R1)   Lethal when   276   (13-118)
          R2R3   overexpressed
  277   G1318   Morphology: other   Dev and morph   MYB-(R1)   Multiple developmental   378   (20-123)
          R2R3   alterations
  279   G1320   Morphology: other   Dev and morph   MYB-(R1)   Multiple developmental   280   (5-108)
          R2R3   alterations
  281   G1330   Morphology: other   Dev and morph   MYB-(R1)   Multiple developmental   282   (28-134)
          R2R3   alterations
  283   G1352   Morphology: other   Dev and morph   Z-C2H2   Multiple developmental   284   (108-129,
            alterations     167-188)
  285   G1354   Morphology: other   Dev and morph   NAC   Multiple developmental   286   (TBD)
            alterations
  287   G1360   Morphology: other   Dev and morph   NAC   Lethal when overexpressed   288   (18-174)
  289   G1364   Morphology: other   Dev and morph   CAAT   Lethal when overexpressed   290   (29-120)
  291   G1379   Morphology: other   Dev and morph   AP2   Multiple developmental   292   (18-85)
            alterations
  293   G1384   Morphology: other   Dev and morph   AP2   Abnormal inflorescence   294   (TBD)
            and flower development
  295   G1399   Morphology: other   Dev and morph   AT-hook   Multiple developmental   296   (86-93)
            alterations
  297   G1415   Morphology: other   Dev and morph   AP2   Multiple developmental   298   (TBD)
            alterations
  299   G1417   Morphology: other;   Dev and morph;   WRKY   Reduced seeding   300   (239-296)
      seed oil   seed biochemistry     germination and vigor;
            increases in 18:2,
            decrease in 18:3
  301   G1442   Morphology: other   Dev and morph   GRF-like   Multiple developmental   302   (172-223)
            alterations
  303   G1454   Morphology: other;   Dev and morph;   NAC   Multiple developmental   304   (9-178)
      seed oil and   seed biochemistry     alteration; altered
      protein content       seed oil and protein
            content
  305   G1459   Morphology; other   Dev and morph   NAC   Multiple developmental   306   (10-152)
            alterations
  307   G1460   Morphology: other;   Dev and morph   NAC   Multiple developmental   308   (TBD)
      seed protein content   seed biochemistry     alterations; altered
            seed protein content
  309   G147   Morphology: other   Dev and morph   MADS   Multiple developmental   310   (2-57)
            defects
  311   G1471   Morphology: other;   Dev and morph;   Z-C2H2   Multiple developmental   312   (49-70)
      seed oil   seed biochemistry   alterations;   defects
          increased   seed oil content
  313   G1475   Morphology: other   Dev and morph   Z-C2H2   Multiple developmental   314   (51-73)
            alterations
  315   G1477   Morphology: other   Dev and morph   Z-C2H2   Multiple developmental   316   (29-48)
            alterations
  317   G1487   Morphology: other;   Dev and morph:   GATA/Zn   Multiple developmental   318   (251-276)
      seed oil and   seed biochemistry     alterations; altered
      protein content       seed oil and
            protein content
  319   G1492   Morphology: other   Dev and morph   GARP   Multiple developmental   320   (34-83)
            alterations
  321   G1531   Morphology: other;   Dev and morph;   RING/C3HC4   Multiple developmental   322   (41-77)
      seed; seed protein   seed biochemistry     alterations; pale seed;
      content       altered seed protein
            content
  323   G1540   Morphology: other   Dev and morph   HB   Reduced cell   324   (35-98)
            differentiation
            in meristem
  325   G1544   Morphology: other   Dev and morph   HB   Multiple developmental   326   (64-124)
            alterations
  327   G156   Morphology: other;   Dev and morph   MADS   Multiple developmental   328   (2-57)
      seed       defects; seed color
            alteration
  329   G1584   Morphology: other   Dev and morph   HB   Multiple developmental   330   (TBD)
            alteration
  331   G1587   Morphology: other   Dev and morph   HB   Multiple developmental   332   (61-121)
            alteration
  333   G1588   Morphology: other   Dev and morph   HB   Multiple developmental   334   (66-124)
            alteration
  335   G1589   Morphology: other   Dev and morph   HB   Multiple developmental   336   (384-448)
      seed protein content   seed biochemistry     alterations; altered
            seed protein content
  337   G160   Morphology: other   Dev and morph   MADS   Multiple developmental   338   (7-62)
            defects
  339   G1636   Morphology: other   Dev and morph   MYB-   Pale green, smaller   340   (100-165)
          related   plants
  341   G1642   Morphology: other   Dev and morph   MYB-   Multiple developmental   342   (TBD)
          (R1)R2R3   alterations
  343   G1747   Morphology: other;   Dev and morph;   MYB-(R1)   Multiple developmental   344   (11-114)
      seed protein contcent   seed biochemistry   R2R3   alterations; altered
            seed protein content
  345   G1749   Morphology: other   Dev and morph   AP2   Multiple developmental   346   (84-155)
            alterations; formation
            of necrotic lesions
  347   G1751   Morphology: other   Dev and morph   AP2   Multiple developmental   348   (TBD)
            alterations
  349   G1752   Morphology: other   Dev and morph   AP2   Multiple developmental   350   (83-151)
            alterations
  351   G1763   Morphology: other   Dev and morph   AP2   Lethal when overexpressed   352   (140-209)
  353   G1766   Morphology: other   Dev and morph   NAC   Multiple developmental   354   (10-153)
            alterations
  355   G1767   Morphology: other   Dev and morph;   SCR   Multiple developmental   356   (255-272)
      seed oil content   seed biochemistry     alterations; altered
            seed oil content
  357   G1778   Morphology: other   Dev and morph   GATA/Zn   Lethal when overexpressed   358   (94-119)
  359   G1789   Morphology: other;   Dev and morph;   MYB-related   Delayed development;   360   (1-50)
      seed protein content   seed biochemistry     altered seed protein
            content
  361   G1790   Morphology: other   Dev and morph   MYB(R1)R2R3   Lethal when overexpressed   362   (217-316)
  363   G1791   Morphology: other   Dev and morph   AP2   Multiple developmental   364   (TBD)
            alterations
  365   G1793   Morphology: other;   Dev and morph;   AP2   Multiple developmental   366   (179-255,
      seed oil   seed biochemistry     alterations; increased     281-349)
            seed oil content
  367   G1795   Morphology: other;   Dev and morph   AP2   Multiple developmental   368   (12-80)
      triichome       alterations; reduced
            trichomes
  369   G1800   Morphology: other   Dev and morph   AP2   Multiple developmental   370   (TBD)
            alterations
  371   G1806   Morphology: other   Dev and morph   bZIP   Multiple developmental   372   (165-225)
            alterations
  373   G1811   Morphology: other   Dev and morph   ABI3/VP-1   Multiple developmental   374   (TBD)
            alterations
  375   G182   Morphology: other   Dev and morph   WRKY   Multiple developmental   376   (217-276)
            alterations
  377   G1835   Morphology: other   Dev and morph   GATA/Zn   Small, spindly plant   378   (224-296)
  379   G1836   Morphology: other   Dev and morph   CAAT   Pale green   380   (30-164)
  381   G1838   Morphology: other;   Dev and morph;   AP2   Multiple developmental   382   (229-305,
      seed oil content   seed biochemistry     alterations; increaed     330-400)
            seed oil content
  383   G1843   Morphology: other   Dev and morph   MADS   Multiple developmental   384   (2-57)
            alterations
  385   G1853   Morphology: other   Dev and morph   AKR   Lethal when overexpressed   386   (entire
                protein)
  387   G1855   Morphology: other   Dev and morph   AKR   Slow growth   388   (entire
                protein)
  389   G187   Morphology: other   Dev and morph   WRKY   Variety of   390   (172-228)
            morphological
            alterations
  391   G1881   Morphology: other   Dev and morph   Z-CO-like   Multiple developmental   392   (5-28,
            alterations     56-79)
  393   G1882   Morphology: other   Dev and morph   Z-Dof   Lethal when overexpressed   394   (97-125)
  395   G1883   Morphology: other   Dev and morph   Z-Dof   Multiple developmental   396   (82-124)
            alterations
  397   G1884   Morphology: other   Dev and morph   Z-Dof   Multiple developmental   398   (43-71)
            alterations
  399   G1891   Morphology: other   Dev and morph   Z-Dof   Multiple developmental   400   (27-69)
            alterations
  401   G1896   Morphology: other   Dev and morph   Z-Dof   Multiple developmental   402   (43-85)
            alterations
  403   G1898   Morphology: other   Dev and morph   Z-Dof   Lethal when overexpressed   404   (31-59)
  405   G1902   Morphology: other;   Dev and morph;   Z-Dof   Multiple developmental   406   (31-59)
      seed oil content   seed biochemistry     alterations; increased
            seed oil content
  407   G1904   Morphology: other   Dev and morph   Z-Dof   Multiple developmental   408   (53-95)
            alterations
  409   G1906   Morphology: other   Dev and morph   Z-Dof   Multiple developmental   410   (19-47)
            alterations
  411   G1913   Morphology: other   Dev and morph   Z-Dof   Lethal when overexpressed   412   (27-55)
  413   G1914   Morphology: other   Dev and morph   Z-C2H2   Multiple developmental   414   (195-216,
            alterations     245-266)
  415   G1925   Morphology: other   Dev and morph   NAC   Multiple developmental   416   (6-150)
            alterations
  417   G1929   Morphology: other   Dev and morph   Z-CO-like   Slow growth, delayed   418   (31-53)
            development
  419   G1930   Morphology: other   Dev and morph   AP2   Multiple developmental   420   (59-124)
            alterations
  421   G195   Morphology: other   Dev and morph   WRKY   Multiple developmental   422   (183-239)
            defects
  423   G1954   Morphology: other   Dev and morph   HLH/MYC   Lethal when overexpressed   424   (187-259)
  425   G1958   Morphology: other;   Dev and morph;   GARP   Reduced size and root   426   (230-278)
      seed protein content   seed biochemistry     mass in plates; altered
            seed protein content
  427   G196   Morphology: other;   Dev and morph;   WRKY   Multiple developmental   428   (223-283)
      seed protein content   seed biochemistry     alterations; altered
            seed protein content
  429   G1965   Morphology: other   Dev and morph   Z-Dof   Lethal when overexpressed   430   (27-55)
  431   G1976   Morphology: other   Dev and morph   Z-C2H2   Multiple developmental   432   (219-323)
            alterations
  433   G2057   Morphology: other   Dev and morph   TEO   Multiple developmental   434   (TBD)
            alterations
  435   G2107   Morphology: other   Dev and morph   AP2   Multiple developmental   436   (TBD)
            alterations
  437   G211   Morphology: other   Dev and morph   MYB-(R1)   Multiple developmental   438   (24-137)
          R2R3   alterations
  439   G2133   Morphology: other;   Dev and morph;   AP2   Multiple developmental   440   (11-83)
      flowering time;   flowering time     alterations; late
      seed protein       flowering; altered seed
      content       protein content
  441   G2134   Morphology: other   Dev and morph   AP2   Multiple developmental   442   (TBD)
            alterations
  443   G2151   Morphology: other;   Dev and morph;   AT-hook   Multiple developmental   444   (93-113,
      seed oil and   seed biochemistry     alterations; altered     124-144)
      protein content       seed oil and protein
            content
  445   G2154   Morphology: other   Dev and morph   AT-hook   Multiple developmental   446   (97-119)
            alterations
  447   G2157   Morphology: other   Dev and morph   AT-hook   Multiple developmental   448   (82-120,
            alteration     164-107)
  449   G2181   Morphology: other   Dev and morph   NAC   Multiple developmental   450   (22-169)
            alterations
  451   G221   Morphology: other   Dev and morph   MYB-(R1)   Multiple developmental   452   (21-125)
          R2R3   alteration
  453   G2290   Morphology: other   Dev and morph   WRKY   Multiple developmental   454   (147-205)
            alterations
  455   G2299   Morphology: other   Dev and morph   AP2   Multiple developmental   456   (48-115)
            alterations
  457   G2340   Morphology: other;   Dev and morph;   MYB-(R1)   Tissue necrosis; multiple   458   (14-120)
      seed oil and   seed biochemistry   R2R3   developmental alterations;
      protein content       altered seed oil
            and protein content
  459   G2346   Morphology: other   Dev and morph   SBP   Enlarged seedlings   460   (59-135)
  461   G237   Morphology; other   Dev and morph   MYB-(R1)   Multiple developmental   462   (11-113)
          R2R3   alterations
  463   G2373   Morphology: other;   Dev and morph;   TH   Multiple developmental   464   (290-350)
      seed protein content   seed biochemistry     alterations; altered
            seed protein content
  465   G2276   Morphology: other;   Dev and morph;   TH   Seeding lethality;   466   (79-178,
      seed oil   seed biochemistry     altered seed protein     336-408)
      protein       content
  467   G24   Morphology: other   Dev and morph   AP2   Reduced size and   468   (25-93)
            necrotic patches
  469   G2424   Morphology: other   Dev and morph   MYB-(R1)   Multiple developmental   470   (107-219)
          R2R3   alterations
  471   G2505   Morphology: other   Dev and morph   NAC   Lethal when overexpressed   472   (10-159)
  473   G2512   Morphology: other   Dev and morph   AP2   Multiple developmental   474   (79-139)
            alterations
  475   G2513   Morphology: other   Dev and morph   AP2   Multiple developmental   476   (TBD)
            alterations
  477   G2519   Morphology: other   Dev and morph   HLH/MYC   Multiple developmental   478   (1-65)
            alterations
  479   G2520   Morphology: other;   Dev and morph;   HLH/MYC   Multiple developmental   480   (135-206)
      seed oil and   seed biochemistry     alterations; altered
      protein content       seed oil and
            protein content
  481   G2533   Morphology: other;   Dev and morph;   NAC   Multiple developmental   482   (11-186)
      seed protein content   seed biochemistry     alterations; altered
            seed protein content
  483   G2534   Morphology: other   Dev and morph   NAC   Lethal when overexpressed   484   (10-157)
  485   G2573   Morphology: other;   Dev and morph;   AP2   Multiple developmental   486   (31-98)
      seed oil and   seed biochemistry     alterations; altered
      protein content       seed oil and
            protein content
  487   G2589   Morphology: other   Dev and morph   MADS   Multiple developmental   488   (2-57)
            alterations
  489   G2687   Morphology: other   Dev and morph   AP2   Multiple developmental   490   (51-120)
            alterations
  491   G27   Morphology: other   Dev and morph   AP2   Abnormal development,   492   (37-104)
            small
  493   G2720   Morphology: other;   Dev and morph;   MYB-(R1)   Multiple development   494   (10-114)
      seed oil and   seed biochemistry   R2R3   alteration; altered
      protein content       seed oil and
            protein content
  495   G2787   Morphology: other;   Dev and morph;   AT-hook   Multiple developmental   496   (172-192,
      seed oil content   seed biochemistry     alterations; altered     226-247,
            seed oil content     256-276,
                290-311,
                245-366)
  497   G2789   Morphology: other   Dev and morph   AT-hook   Multiple developmental   498   (53-73,
            alterations     121-165)
  449   G31   Morphology: other   Dev and morph   AP2   Multiple developmental   500   (TBD)
            alterations
  501   G33   Morphology: other   Dev and morph   AP2   Multiple developmental   502   (50-117)
            defects
  503   G342   Morphology: other;   Dev and morph;   GATA/Zn   Multiple developmental   504   (155-190)
      seed oil and   seed biochemistry     alterations; altered
      protein content       seed oil and
            protein content
  505   G352   Morphology: other   Dev and morph   Z-C2H2   Multiple developmental   506   (99-119,
            alterations     166-186)
  507   G357   Morphology: other   Dev and morph   Z-C2H2   Developmental defect   508   (7-29)
  509   G358   Morphology: other   Dev and morph   Z-C2H2   Lethal when overexpressed   510   (124-135,
                188-210)
  511   G360   Morphology: other   Dev and morph   Z-C2H2   Multiple development   512   (42-62)
            alterations
  513   G362   Size; Morphology:   Dev and morph;   Z-C2H2   Reduced size; increased   514   (62-82)
      other; trichome;   flowering time;     pigmentation in seed
      flowering time;   seed biochemistry     embryos and other
      seed protein       organs; ectopic
      content       trichome formation;
            increased trichome
            number; late
            flowering; altered
            protein content
  515   G364   Morphology: other   Dev and morph   Z-C2H2   Developmental defect   516   (54-76)
  517   G365   Morphology: other   Dev and morph   Z-C2H2   Multiple developmental   518   (70-90)
            alterations
  519   G367   Morphology: other   Dev and morph   Z-C2H2   Lethal when overexpressed   520   (63-84)
  521   G373   Morphology: other   Dev and morph   RING/   Multiple developmental   522   (129-168)
          C3HC4   alterations
  523   G396   Morphology: other;   Dev and morph   HB   Altered leaf coloration   524   (159-220)
      size       and shape reduced
            fertility; small plant
  525   G431   Morphology: other   Dev and morph   HB   Developmental defect,   526   (286-335)
            sterile
  527   G479   Morphology: other   Dev and morph   SBP   Multiple developmental   528   (70-149)
            alterations
  529   G546   Morphology: other   Dev and morph   RING/C3H2C3   Slow growth and   530   (114-155)
            development; increased
            anthocyanin
            pigmentation
  531   G551   Morphology: other   Dev and morph   HB   Multiple developmental   532   (73-133)
            alterations
  533   G578   Morphology: other   Dev and morph   bZIP   Lethal when overexpressed   534   (36-96)
  535   G596   Morphology: other   Dev and morph   AT-hook   Multiple developmental   536   (89-96)
            alterations
  537   G617   Morphology: other   Dev and morph   TEO   Multiple developmental   538   (64-118)
            alterations
  539   G620   Morphology: other;   Dev and morph;   CAAT   Multiple developmental   540   (20-118)
      seed protein content   seed biochemistry     alterations; altered
            seed protein content
  541   G625   Morphology: other   Dev and morph   AP2   Lethal when   542   (52-119)
            overexpressed
  543   G658   Morphology: other   Dev and morph   MYB-(R1)   Developmental defect   544   (2-105)
          R2R3
  545   G716   Morphology: other   Dev and morph   ARF   Multiple developmental defects   546   (24-355)
  547   G725   Morphology: other   Dev and morph   GARP   Developmental defect   548   (39-87)
  549   G727   Morphology: other   Dev and morph   GARP   Multiple morphological   550   (226-269)
            alterations
  551   G740   Morphology: other   Dev and morph   Z-CLDSH   Slow growth   552   (24-42,
                232-268)
  553   G770   Morphology: other   Dev and morph   NAC   Multiple developmental   554   (19-162)
            alterations
  555   G858   Morphology: other   Dev and morph   MADS   Multiple developmental   556   (2-57)
            alterations
  557   G865   Morphology: other;   Dev and morph;   AP2   Altered morphology   558   (36-103)
      seed protein content   seed biochemistry     increased see protein
  559   G872   Morphology: other   Dev and morph   AP2   Multiple developmental   560   (18-85)
            alterations
  561   G904   Morphology: other   Dev and morph   RING/C3H2C3   Multiple developmental   562   (117-158)
            alterations
  563   G910   Morphology: other;   Dev and morph;   Z-CO-like   Multiple developmental   564   (14-37,
      flowering time   flowering time     alterations; late     77-103)
            flowering
  565   G912   Morphology: other;   Dev and morph;   AP2   Dark green color;   566   (51-118)
      size; sugar   sugar sensing;     small plant; reduced
      sensing;   flowering     cotyledon expansion
      flowering   time     in glucose; late
      time       flowering
  567   G290   Morphology: other   Dev and morph   WRKY   Multiple developmental   568   (152-211)
            alterations
  569   G939   Morphology: other;   Dev and morph   EIL   Pale seedlings on agar;   570   (97-106)
      size       reduced size
  571   G963   Morphology: other;   Dev and morph;   NAC   Slowed growth rate;   572   (TBD)
      seed protein   seed biochemistry     altered seed protein
      content       content
  573   G979   Morphology: other;   Dev and morph   AP2   Several development   574   (63-139,
      seed       defects; altered seed     165-233)
            development, ripening
            and germination
  575   G987   Morphology: other   Dev and morph   SCR   Developmental defects   576   (428-432,
                704-708)
  577   G993   Morphology: other   Dev and morph;   AP2   Multiple developmental   578   (69-134)
      seed protein content   seed biochemistry     alterations; altered
            seed protein content
  579   G681   Morphology: other;   Dev and morph;   MYB-(R1)   Multiple developmental   580   (14-120)
      leaf glucosinolates   leaf biochemistry   R2R3   alterations;
            overexpression results
            in an increased in M39480
  581   G1482   Root   Dev and morph   Z-CO-like   Increased root growth   582   (5-63)
  583   G225   Root; trichome   Dev and morph   MYB-related   Increased root hairs;   584   (39-76)
            glabrous, lack
            of trichomes
  585   G226   Root; trichome;   Dev and morph;   MYB-related   Increased root hair;   586   (28-78)
      seed protein content   seed biochemistry     glabrous, lack of
            trichomes; increased
            seed protein
  587   G9   Root   Dev and morph   AP2   Increased root mass   588   (62-127)
  589   G1040   Seed   Dev and morph   GARP   Smaller and more   590   (109-158)
            rounded seeds
  591   G2114   Seed   Dev and morph   AP2   Increased seed size   592   (221-297,
                323-393)
  593   G450   Seed; size;   Dev and morph;   IAA   Increased seed size;   594   (TBD)
      seed protein   seed biochemistry     reduced plant size;
      content       altered seed protein
            content
  595   G584   Seed   Dev and morph   HLH/MYC   Large seeds   596   (401-494)
  597   G668   Seed   Dev and morph   MYB-(R1)   Reduced seed color   598   (13-113)
          R2R3
  599   G1050   Senescence   Dev and morph   bZIP   Delayed senescence   600   (372-425)
  601   G1463   Senescence   Dev and morph   NAC   Premature senescence   602   (9-156)
  603   G1944   Senescence; size;   Dev and morph;   AT-hook   Early senescence;   604   (87-100)
      seed protein content   seed biochemistry     reduced size; altered
            seed protein content
  605   G2383   Senescence; seed   Dev and morph;   TEO   Early senescence;   606   (89-149)
      protein content   seed biochemistry     altered seed protein
            content
  607   G571   Senescence;   Dev and morph;   bZIP   Delayed senescence;   608   (160-220)
      flowering time   flowering time     late flowering
  609   G636   Senescence; size   Dev and morph   TH   Premature senescence;   610   (55-145,
            reduced size     405-498)
  611   G878   Senescence;   Dev and morph;   WRKY   Delayed senescence;   612   (250-305,
      flowering time   flowering time     late flowering     415-475)
  613   G1134   Silique   Dev and morph   HLH/MYC   Siliques with altered   614   (198-247)
            shape
  615   G1008   Size   Dev and morph   AP2   Small plant   616   (96-163)
  617   G1020   Size   Dev and morph   AP2   Very small T1 plants   618   (28-95)
  619   G1023   Size   Dev and morph   AP2   Reduced size   620   (128-195)
  621   G1053   Size   Dev and morph   bZIP   Small plant   622   (74-120)
  623   G1137   Size   Dev and morph   HLH/MYC   Small T1 plants   624   (264-314)
  625   G1181   Size   Dev and morph   HS   Small T1 plants   626   (24-114)
  627   G1228   Size   Dev and morph   HLH/MYC   Reduced size   628   (179-233)
  629   G1277   Size   Dev and morph   AP2   Small plant   630   (18-85)
  631   G1309   Size   Dev and morph   MYB-(R1)   Small plant   632   (9-114)
          R2R3
  633   G1314   Size; sugar   Dev and morph;   MYB-(R1)   Reduced size; reduced   634   (14-116)
      sensing; seed   sugar sensing;   R2R3   seedling vigor on high
      protein content   seed biochemistry     glucose; altered seed
            protein content
  635   G1317   Size   Dev and morph   MYB-(R1)   Reduced size   636   (13-118)
          R2R3
  637   G1323   Size; seed oil   Dev and morph;   MYB-(R1)   Small T1 plants, dark   638   (15-116)
      and protein content   seed biochemistry   R2R3   green; decreased seed
            oil, increased seed
            protein
  639   G1332   Size; trichome; seed   Dev and morph;   MYB-(R1)   Reduced size; reduced   640   (13-116)
      oil and protein   seed biochemistry   R2R3   trichome densitry;
      content       altered seed oil
            and protein content
  641   G1334   Size   Dev and morph   CAAT   Small, dark green   642   (18-190)
  643   G1381   Size   Dev and morph   AP2   Reduced size   644   (68-135)
  645   G1382   Size   Dev and morph   WRKY   Small plant   646   (210-266.
                385-437)
  647   G1435   Size; flowering   Dev and morph;   GARP   Increased plant size;   648   (146-194)
      time   flowering time     late flowering
  649   G1537   Size   Dev and morph   HB   Small T1 plants with   650   (14-74)
            altered development
  651   G1545   Size   Dev and morph   HB   Reduced size   652   (54-117)
  653   G1641   Size; seed oil   Dev and morph;   MYB- related   Small plant; altered   654   (139-200)
      and protein content   seed biochemistry     seed oil and protein
            content
  655   G165   Size; seed   Dev and morph;   MADS   Reduced size; altered   656   (7-62)
      content   seed biochemistry     seed protein content
  657   G1652   Size; seed oil   Dev and morph;   HLH/MYC   Reduced size; altered   658   (143-215)
      and protein content   seed biochemistry     seed oil and protein content
  659   G1655   Size   Dev and morph   HLH/MYC   Small plant   660   (134-192)
  661   G1671   Size   Dev and morph   NAC   Reduced size   662   (TBD)
  663   G1756   Size; seed   Dev and morph   WRKY   Reduced size; altered   664   (TBD)
      protein content   seed biochemistry     seed protein content
  665   G1757   Size; seed   Dev and morph;   WRKY   Small plant; altered   666   (158-218)
      protein content   seed biochemistry     seed protein content
  667   G1782   Size   Dev and morph   CAAT   Small, spindly plant   668   (166-238)
  669   G184   Size   Dev and morph   WRKY   Small plant   670   (295-352)
  671   G1845   Size   Dev and morph   AP2   Small plant   672   (140-207)
  673   G1879   Size; seed oil   Dev and morph;   HLH/MYC   Reduced size; altered   674   (107-176)
      and protein content   seed biochemistry     seed oil and protein
            content
  675   G1888   Size   Dev and morph   Z-CO-like   Reduced size, dark   676   (5-50)
            green leaves
  677   G189   Size; seed protein   Dev and morph;   WRKY   Increased leaf size;   678   (240-297)
      content   seed biochemistry     altered seed protein
            content
  679   G1939   Size   Dev and morph   PCF   Reduced size   680   (40-102)
  681   G194   Size   Dev and morph   WRKY   Small plant   682   (174-230)
  683   G1973   Size   Dev and morph   HLH/MYC   Reduced size   684   (335-406)
  685   G21   Size; seed oil   Dev and morph;   AP2   Reduced size; altered   686   (97-164)
      and protein content   seed biochemistry     seed oil and protein
            content
  687   G2132   Size; seed oil   Dev and morph;   AP2   Reduced size; altered   688   (TBD)
      and protein content   seed biochemistry     seed oil and protein
            content
  689   G2145   Size   Dev and morph   HLJH/MYC   Reduced size   690   (166-243)
  691   G23   Size   Dev and morph   AP2   Small T1 plants   692   (61-117)
  693   G2313   Size   Dev and morph   MYB-related   Reduced size   694   (TBD)
  695   G2344   Size   Dev and morph   CAAT   Reduced size, slow growth   696   (TBD)
  697   G2430   Size   Dev and morph   GARP   Increased leaf size,   698   (425-478)
            faster development
  699   G2517   Size   Dev and morph   WRKY   Reduced size   700   (118-234)
  701   G2521   Size   Dev and morph   HLH/MYC   Reduced size   702   (145-213)
  703   G258   Size; seed oil   Dev and morph;   MYB-(R1)   Reduced size; altered   704   (24-124)
      and protein content   seed biochemistry   R2R3   seed oil and protein
            content
  705   G280   Size; seed   Dev and morph;   AT-hook   Reduced size; altered   706   (97-104,
      protein content   seed biochemistry     seed protein content     130-137-
                155-162,
                185-192)
  707   G3   Size   Dev and morph   AP2   Small plant   708   (28-95)
  709   G343   Size   Dev and morph   GATA/Zn   Small plant   710   (178-214)
  711   G363   Size   Dev and morph   Z-C2H2   Small plant   712   (87-108)
  713   G370   Size   Dev and morph   Z-C2H2   Reduced size, shiny   714   (97-117)
            leaves
  715   G385   Size   Dev and morph   HB   Small plant, short   716   (60-123)
            inflorescence stems,
            dark green
  717   G439   Size   Dev and morph   AP2   Small plant   718   (110-177)
  719   G440   Size   Dev and morph   AP2   Small plant   720   (122-189)
  721   G5   Size   Dev and morph   AP2   Small plant   722   (149-216)
  723   G550   Size   Dev and morph   Z-Dof   Small plant   724   (134-180)
  725   G670   Size   Dev and morph   MYB-(R1)   Small plant   726   (14-122)
          R2R3
  727   G760   Size   Dev and morph   NAC   Reduced size   728   (12-156)
  729   G831   Size   Dev and morph   AKR   Reduced size   730   (470-591)
  731   G864   Size   Dev and morph   AP2   Small plant   732   (119-186)
  733   G884   Size   Dev and morph   WRKY   Reduced size   734   (227-285,
                407-465)
  735   G898   Size; seed oil   Dev and morph;   RING/C3HC4   Reduced size; altered   736   (148-185)
      and protein content   seed biochemistry     seed oil and protein
      content
  737   G900   Size   Dev and morph   Z-CO-like   Reduced size   738   (6-28,
                48-74)
  739   G913   Size; flowering   Dev and morph;   AP2   Small plant; late   740   (62-128)
      time   flowering time     flowering
  741   G937   Size   Dev and morph   GARP   Slightly reduced size   742   (197-246)
  743   G960   Size   Dev and morph   NAC   Small plant   744   (13-156)
  745   G991   Size; seed oil   Dev and morph;   IAA   Slightly reduced size;   746   (7-14,48-
      and protein content   seed biochemistry     altered seed oil and     59,82-115,
            protein content     128-164)
  747   G748   Stem; flowering   Dev and morph;   Z-Dof   More vascular bundles   748   (112-140)
      time   flowering time     in stem; late flowering
  749   G247   Trichome; seed   Dev and morph;   MYB-(R1)   Altered trichome   750   (15-116)
      seed protein   seed biochemistry   R2R3   distribution; altered
      content       seed protein content
  751   G585   Trichome   Dev and morph   HLH/MYC   Reduced trichome denisty   752   (436-501)
  753   G634   Trichome; seed   Dev and morph;   TH   Increased trichome   754   (62-147,
      protein content   seed biochemistry     density and size;     189-245)
            altered seed protein
            content
  755   G676   Trichome   Dev and morph   MYB-(R1)   reduced trichomes   756   (17-119)
          R2R3
  757   G682   Trichome   Dev and morph   MYB-related   Glabrous, lack of   758   (27-63)
            trichomes
  759   G635   Variegation   Dev and morph   TH     760   (239-323)
  761   G1068   Sugar sensing   Sugar sensing   AT-hook   Reduced cotyledon   762   (143-150)
            expansion in glucose
  763   G1225   Sugar sensing; seed   Sugar sensing;   HLH/MYC   Better germination on   764   (78-147)
      oil and protein   biochemistry     sucrose and glucose
      content       media; altered seed oil
            and protein content
  765   G1337   Sugar sensing   Sugar sensing   Z-CO-like   Decreased germination   766   (9-75)
            on sucrose medium
  767   G1759   Sugar sensing   Sugar sensing   MADS   Reduced germination   768   (2-57)
            on high glucose
  769   G1804   Sugar sensing;   Sugar sensing;   bZIP   Altered sugar sensing;   770   (357-407)
      flowering time   flowering time     late flowering
  771   G207   Sugar sensing   Sugar sensing   MYB-(R1)   Decreased germination   772   (6-106)
          R2R3   on glucose medium
  773   G218   Sugar sensing;   Sugar sensing;   MYB-(R1)   Reduced cotyledon   774   (TBD)
      seed oil content   seed biochemistry   R2R3   expansion in glucose;
            altered seed oil content
  775   G241   Sugar sensing; seed   Sugar sensing;   MYB-(R1)   Decreased germination   776   (14-114)
      oil and protein   seed biochemistry   R2R3   and growth on glucose
      content       medium; decreased
            seed oil, altered
            protein content
  777   G254   Sugar sensing   Sugar sensing   MYB-related   Decreased germination   778   (62-106)
            and growth on glucose medium
  779   G26   Sugar sensing   Sugar sensing   AP2   Decreased germination   780   (67-134)
            and growth on glucose
            medium
  781   G263   Sugar sensing   Sugar sensing   HS   Decreased root growth   728   (TBD)
            on sucrose medium,
            root specific
            expression
  783   G308   Sugar sensing   Sugar sensing   SCR   No germination on   784   (270-247)
            glucose medium
  785   G38   Sugar sensing   Sugar sensing   AP2   Reduced germination on   786   (76-143)
            glucose medium
  787   G43   Sugar sensing   Sugar sensing   AP2   Decreased germination   788   (104-172)
            and growth on glucose
            medium
  789   G536   Sugar sensing   Sugar sensing   GF14   Decreased germination   790   (226-233)
            and growth on glucose medium
  791   G567   Sugar sensing; seed   Sugar sensing; seed   b-ZIP   Decreased seedling   792   (210-270)
      oil and   biochemistry     vigor on high glucose;
      protein content       altered seed oil and
            protein content
  793   G680   Sugar sensing;   Sugar sensing;   MYB-related   Reduced germination   794   (24-70)
      flowering time   flowering time     on glucose medium;
            late flowering
  795   G867   Sugar sensing   Sugar sensing   AP2   Better seedling vigor   796   (59-124)
            on sucrose medium
  797   G956   Sugar sensing   Sugar sensing   NAC   Reduced germination   798   (TBD)
            on glucose medium
  799   G996   Sugar sensing   Sugar sensing   MYB-(R1)   Reduced germination   800   (14-114)
          R2R3   on glucose medium
  801   G1946   Seed glucosinolates   Seed biochemistry   HS   Increased in M3950;   802   (32-130)
      oil protein       increased oil content;
      content       decreased protein content
  803   G217   Seed oil composition   Seed biochemistry   MYB-related   Increased in 20:2   804   (8-67)
  805   G2192   Seed oil composition   Seed biochemistry   bZIP-NIN   Altered composition   806   (600-700)
  807   G504   Seed oil   Seed biochemistry   NAC   Altered seed oil   808   (TBD)
      composition; seed       composition and content;
      protein content       altered seed protein
            content
  809   G622   Seed oil composition   Seed biochemistry   ABI3/VP-1   Decreased 18:2 fatty acid   810   (TBD)
  811   G778   Seed oil composition   Seed biochemistry   HLH/MYC   Increased seed 18:1 fatty acid   812   (220-267)
  813   G791   Seed oil composition   Seed biochemistry   HLH/MYC   Altered seed fatty acid   814   (75-143)
            composition
  815   G861   Seed oil composition;   Seed biochemistry   MADS   Increase in 16:1;   816   (2-57)
      seed oil content       altered seed oil content
  817   G938   Seed oil composition   Seed biochemistry   EIL   Altered seed fatty acid   818   (96-104)
            composition
  819   G965   Seed oil composition   Seed biochemistry   HB   Increased in 18:1   820   (423-486)
  821   G1143   Seed oil and   Seed biochemistry   HLH/MYC   Altered seed oil and   822   (33-82)
      protein content       protein content
  823   G1190   Seed oil content   Seed biochemistry   AKR   Increased content   824   (entire protein)
  825   G1198   Seed oil and   Seed biochemistry   bZIP   Altered seed oil and   826   (173-223)
      protein content       protein content
  827   G1226   Seed oil and protein   Seed biochemistry   HLH/MYC   Altered seed oil and   828   (115-174)
      content       protein content
  829   G1451   Seed oil content   Seed biochemistry   ARF   Altered seed oil content   830   (22-357)
  831   G1478   Seed oil and   Seed biochemistry;   Z-CO-like   Altered seed oil,   832   (32-76)
      protein content;   flowering time     protein content; late
      flowering time       flowering
  833   G1496   Seed oil content   Seed biochemistry   HLH/MYC   Altered seed oil   834   (184-248)
            content
  835   G1526   Seed oil content   Seed biochemistry   SWI/SNF   Increased seed oil   836   (493-620,
            content     864-1006)
  837   G1543   Seed oil content   Seed biochemistry   HB   Decreased seed oil   838   (135-195)
  839   G162   Seed oil and   Seed biochemistry   MADS   Altered seed oil   840   (2-57)
      protein content       content; altered seed
            oil and protein content
  841   G1640   Seed oil content   Seed biochemistry   MYB-(R1)   Increased seed oil   842   (14-115)
          R2R3
  843   G1644   Seed oil and   Seed biochemistry   MYB-(R1)   Altered seed oil,   844   (39-102)
      protein content     R2R3   protein content
  845   G1646   Seed oil content   Seed biochemistry   CAAT   Altered seed oil content   846   (72-162)
  847   G1672   Seed oil content   Seed biochemistry   NAC   Altered seed oil content   848   (41-194)
  849   G1677   Seed oil and   Seed biochemistry   NAC   Altered seed oil,   850   (17-181)
      protein content       protein content
  851   G1765   Seed oil and   Seed biochemistry   NAC   Altered seed oil and   852   (20-140)
      protein content       protein content
  853   G1777   Seed oil and   Seed biochemistry   RING/C3HC4   Increased oil,   854   (124-247)
      protein content       decreased protein
            content
  855   G1793   Seed oil content   Seed biochemistry   AP2   Increased seed oil   856   (179-255,
            content     281-349)
  857   G180   Seed oil content   Seed biochemistry   WRKY   Decreased seed oil   858   (118-174)
            content
  859   G192   Seed oil and   Seed biochemistry;   WRKY   Altered seed oil and   860   (128-185)
      protein content;   flowering time     protein content; late
      flowering time       flowering
  861   G1948   Seed oil and   Seed biochemistry   AKR   Altered seed oil and   862   (entire protein)
      protein content       protein content
  863   G2123   Seed oil and