US 2006O195944A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2006/0195944 A1 Heard et al. (43) Pub. Date: Aug. 31, 2006 (54) TRANSCRIPTION FACTOR SEQUENCES (60) Provisional application No. 60/713.952, filed on Aug. FOR CONFERRING ADVANTAGEOUS 31, 2005. Provisional application No. 60/336,049, PROPERTIES TO PLANTS filed on Nov. 19, 2001. Provisional application No. 60/310,847, filed on Aug. 9, 2001. Provisional appli (75) Inventors: Jacqueline E. Heard, Stonington, CT cation No. 60/338,692, filed on Dec. 11, 2001. Pro (US); Jose Luis Riechmann, Pasadena, visional application No. 60/465,809, filed on Apr. 24. CA (US); Oliver Ratcliffe, Oakland, 2003. Provisional application No. 60/434,166, filed CA (US); Omaira Pineda, Vero Beach, on Dec. 17, 2002. Provisional application No. 60/411, FL (US) 837, filed on Sep. 18, 2002. Correspondence Address: Mendel Biotechnology, Inc. Publication Classification 21375 Cabot Blvd. Hayward, CA 94545 (US) (51) Int. Cl. (73) Assignee: Mendel Biotechnology, Inc., Hayward, AOIH I/00 (2006.01) CA CI2N 5/82 (2006.01) CI2N 5/04 (2006.01) (21) Appl. No.: 11/375,241 (52) U.S. Cl. ........................... 800/287: 435/419, 435/468 (22) Filed: Mar. 13, 2006 (57) ABSTRACT Related U.S. Application Data (63) Continuation-in-part of application No. 10/225,067, The invention relates to plant transcription factor polypep filed on Aug. 9, 2002, and which is a continuation tides, polynucleotides that encode them, homologs from a in-part of application No. 09/837,944, filed on Apr. variety of plant species, and methods of using the polynucle 18, 2001, now abandoned, and which is a continua otides and polypeptides to produce transgenic plants having tion-in-part of application No. 10/171.468, filed on advantageous properties compared to a reference or control Jun. 14, 2002, now abandoned. plant, including increased plant size, seed size, increased Continuation-in-part of application No. 10/714,887, leaf size, lignification, water deprivation tolerance, cold filed on Nov. 13, 2003. tolerance, or altered flowering time. Sequence information Continuation-in-part of application No. 10/666,642, related to these polynucleotides and polypeptides can also be filed on Sep. 18, 2003. used in bioinformatic search methods and is also disclosed. Patent Application Publication Aug. 31, 2006 Sheet 1 of 9 US 2006/0195944 A1 Fagales Cucurbitales Rosales Fabales Oxalidales Malpighiales Sapindales Malvales Brassicales Myrtales GeranialesDipSacales Asterales Apiales Aquifoliales Solanales Lamiales Gentianales Garryales Ericales Cornales Saxifragales Santalales Caryophyllales Proteales Ranunculales Zingiberales Commelinales Poales Arecales Pandanales Liliales Dioscoreales Asparagales Alismatales AcoralesPiperales Magnoliales Laurales Ceratophyllales FIG. 1 Patent Application Publication Aug. 31, 2006 Sheet 2 of 9 US 2006/0195944 A1 Patent Application Publication Aug. 31, 2006 Sheet 3 of 9 US 2006/0195944 A1 64 G3652 O. Satiya 95 G3653 O. sativa 97. G3655 O. sativa 99. G3654 O. sativa G2576 A. thaliana 98. G872 A. thaliana G3657 O. sativa 100. G2115 A. thaliana 80G2294 A. thaliana G1090 A. thaliana 86 CBF4A. thaliana 100 CBF2 A. thaliana 89 CBF3A. thaliana 50 CBF1 A. thaliana 80 G3644 O. Satiya 100 G3651 O. Sativa G3650 Z. mavs G3649 O. Satiya 93 G3643 G. max G3647 Z. elegans 56 98 G2133 A. thaliana G3646 B. oleracea 99 G3645 B. rapa 98 G47 A. thaliana G3656 Z. mays 97 -G12 A. thaliana 99 G24 A. thaliana 93. -G1277 A. thaliana 99. G1379 A. thaliana G867 A. thaliana FIG. 3 Patent Application Publication Aug. 31, 2006 Sheet 5 of 9 US 2006/0195944 A1 G47 (SEO ID NO: 66) and G2133 (SEO ID NO: 152) conserved domains G47 : QSKYKGIRRRKWGKWVSEIRVPGTRDRLWLGSFSTAEGAAVAHDVA QSKYKGIRRRKWGKWVSEIRVPGTR RLWLGSFSTAEGAAVAHDVA G21.33: QSKYKGIRRRKWGKWVSEIRVPGTRORLWLGSFSTAEGAAVAHDVA G47 : FFCLHOPDSL--ESLNFPHLLNPSLV F-CLH-P SIL ES NFPHILL SIL G2133 : FYCLHRPSSLDDESFNFPHILLTTSILA G47 (SEO ID NO: 66) and G3643 (SEQ ID NO: 158) conserved domains G47 : SKYKGIRRRKWGKWVSEIRVPGTRDRLWLGSFSTAEGAAVAHDVAF --K KG-RRRKWGKWVSEIRVPGT----RLWLG------T E AAVAHDVA G3643 : NKLKGVRRRKWGKWVSEIRVPGTOERLWLGTYATPEAAAVAHDVAV G47 : FCLHOPDSLESLNFPHLLN +CL +P SL-- INFP T-- G3643 : YCLSRPSSLDKLNFPETLS G47 (SEQ ID NO 66) and G3649 (SEO ID NO: 154) conserved domains G47 : KYKGIRRRKWGKWVSEIRVPGTRDRIWGSFSTAEGAAVAHDVA --Y--G--RRR- WGKWVSEIRVPGTR-RLWLGS----TAE AAVAHD A G3649 : RYRGVRRRRWGKWVSEIRVPGTRERLWLGSYATAEAAAVAHDAA G47 (SEO ID NO: 6) and G3644 (SEO ID NO: 156) conserved domains G47 : KYKGIRRRKWGKWVSEIRVPGTRDRLWLGSFSTAEGAAVAHDVA +Y+G+RRR--WGKWVSEIRVPGTR-RLWLGS----T E AAVAHD A G3644 : RYRGVRRRRWGKWVSEIRVPGTRERLWLGSYATPEAAAVAHDTA G47: FFCL + Lu G3644 : VYFL FIG. 5 Patent Application Publication Aug. 31, 2006 Sheet 6 of 9 US 2006/0195944 A1 Patent Application Publication Aug. 31, 2006 Sheet 7 of 9 US 2006/0195944 A1 FIG. 7B Patent Application Publication Aug. 31, 2006 Sheet 8 of 9 US 2006/0195944 A1 Patent Application Publication Aug. 31, 2006 Sheet 9 of 9 US 2006/0195944 A1 FIG. 9 US 2006/0195944 A1 Aug. 31, 2006 TRANSCRIPTION FACTOR SEQUENCES FOR result in a transgenic plant having the desired phenotype CONFERRING ADVANTAGEOUS PROPERTIES TO with the enhanced agronomic trait. Therefore, methods to PLANTS select individual transgenic events from a population may be 0001) This application claims the benefit of U.S. Provi required to identify those transgenic events that are charac sional Application No. 60/713,952, filed Aug. 31, 2005 terized by the enhanced agronomic trait. (pending); and this application is a continuation-in-part of 0004) Other aspects and embodiments of the invention prior U.S. application Ser. No. 10/225,067, filed Aug. 9. are described below and can be derived from the teachings 2002 (pending) which claims the benefit of U.S. Provisional of this disclosure as a whole. Application No. 60/336,049, filed Nov. 19, 2001 (now abandoned), U.S. Provisional Application No. 60/310,847, BACKGROUND OF THE INVENTION filed Aug. 9, 2001 (now abandoned) and U.S. Provisional Application No. 60/338,692, filed Dec. 11, 2001 (now 0005 Transcription factors can modulate gene expres abandoned); and, prior U.S. application Ser. No. 10/225,067, Sion, either increasing or decreasing (inducing or repressing) filed Aug. 9, 2002 (pending) is a continuation-in-part of U.S. the rate of transcription. This modulation results in differ Non-provisional application Ser. No. 09/837,944, filed Apr. ential levels of gene expression at various developmental 18, 2001 (now abandoned), and U.S. Non-provisional appli stages, in different tissues and cell types, and in response to cation Ser. No. 10/171.468, filed Jun. 14, 2002 (now aban different exogenous (e.g., environmental) and endogenous doned); and, this application is a continuation-in-part of stimuli throughout the life cycle of the organism. prior U.S. application Ser. No. 10/714,887, filed Nov. 13, 0006 Because transcription factors are key controlling 2003 (pending); and, this application is a continuation-in elements of biological pathways, altering the expression part of prior U.S. application Ser. No. 10/666,642, filed Sep. levels of one or more transcription factors can change entire 18, 2003 (pending) which claims the benefit of U.S. Provi biological pathways in an organism. For example, manipu sional Application No. 60/465,809, filed Apr. 24, 2003 (now lation of the levels of selected transcription factors may abandoned), U.S. Provisional Application No. 60/434,166, result in increased expression of economically useful pro filed Dec. 17, 2002 (now abandoned) and U.S. Provisional teins or metabolic chemicals in plants or to improve other Application No. 60/411,837, filed Sep. 18, 2002. Each of agriculturally relevant characteristics. Conversely, blocked these applications is hereby incorporated by reference in or reduced expression of a transcription factor may reduce their entirety. biosynthesis of unwanted compounds or remove an unde sirable trait. Therefore, manipulating transcription factor FIELD OF THE INVENTION levels in a plant offers tremendous potential in agricultural 0002 This invention relates to the field of plant biology. biotechnology for modifying a plant's traits. More particularly, the present invention pertains to compo 0007. The present invention provides novel transcription sitions and methods for phenotypically modifying a plant. factors useful for modifying a plant's phenotype in desirable ways. INTRODUCTION 0003 Transgenic plants with improved traits, including SUMMARY OF THE INVENTION enhanced yield, environmental stress tolerance, pest resis 0008. The present invention pertains to transgenic plants, tance, herbicide tolerance, improved seed compositions, and and methods for producing the transgenic plant, that have the like are desired by both farmers and consumers. desirable characteristics relative to wild-type or control Although considerable efforts in plant breeding have pro plants. The desirable characteristics in the transgenic plants, vided significant gains in desired traits, the ability to intro which have been transformed with a sequence that is closely duce specific DNA into plant genomes provides further or phylogenetically related to G47, polynucleotide SEQ ID opportunities for generation of plants with improved and/or NO: 65 and polypeptide SEQ ID NO: 66, include increased unique traits. Fortunately, a plant's traits, such as its bio size and/or biomass, tolerance to osmotic stress or drought, chemical, developmental, or phenotypic characteristics, may and/or increased