(19) & (11) EP 2 270 166 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 05.01.2011 Bulletin 2011/01 C12N 15/29 (2006.01) C12N 15/82 (2006.01) A01H 5/00 (2006.01) (21) Application number: 10176922.2 (22) Date of filing: 18.09.2003 (84) Designated Contracting States: • Reuber, T. Lynne AT BE BG CH CY CZ DE DK EE ES FI FR GB GR San Mateo, CA 94402 (US) HU IE IT LI LU MC NL PT RO SE SI SK TR • Riechmann, Jose Luis Pasadena, CA 91101 (US) (30) Priority: 18.09.2002 US 411837 P • Haake, Volker 17.12.2002 US 434166 P 10715 Berlin (DE) 24.04.2003 US 465809 P • Dubell, Arnold N. San Leandro, CA 94578 (US) (62) Document number(s) of the earlier application(s) in • Keddie, James S. accordance with Art. 76 EPC: San Mateo, CA 94402 (US) 03779082.1 / 1 546 336 • Sherman, Bradley K. Berkeley, CA 94708 (US) (71) Applicant: Mendel Biotechnology, Inc. Hayward, CA 94545 (US) (74) Representative: Brasnett, Adrian Hugh et al Mewburn Ellis LLP (72) Inventors: 33 Gutter Lane • Jiang, Cai-Zhong London Fremont, CA 94555 (US) EC2V 8AS (GB) • Heard, Jacqueline E. San Mateo, CA 94402 (US) Remarks: • Ratcliffe, Oliver •Thecomplete document including Reference Tables Oakland, CA 94606 (US) and the Sequence Listing can be downloaded from • Creelman, Robert A. the EPO website Castro Valley, CA 94546 (US) •This application was filed on 15-09-2010 as a • Adam, Luc J. divisional application to the application mentioned Hayward, CA 94545 (US) under INID code 62. (54) Polynucleotides and polypeptides in plants (57) The invention relates to plant transcription factor pared to a reference plant. Sequence information related polypeptides, polynucleotides that encode them, ho- to these polynucleotides and polypeptides can also be mologs from a variety of plant species, and methods of used in bioinformatic search methods and is also dis- using the polynucleotides and polypeptides to produce closed. transgenic plants having advantageous properties com- EP 2 270 166 A2 Printed by Jouve, 75001 PARIS (FR) EP 2 270 166 A2 Description TECHNICAL FIELD 5 [0001] This invention relates to the field of plant biology, and to compositions and methods for modifying the phenotype of a plant. BACKGROUND OF THE INVENTION 10 [0002] 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 comprise cells having altered levels of at least one selected transcription factor, and may possess advantageous or desirable traits. Strategies for manipulating traits by altering a plant cell’s transcription factor content can therefore result in plants and 15 crops with new and/or improved commercially valuable properties. [0003] 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. 20 [0004] 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 biomolecules in plants or improvement in other agriculturally relevant characteristics. Conversely, blocked or reduced expression of a transcription factor may reduce biosynthesis of unwanted compounds or remove an undesirable trait. 25 Therefore, manipulating transcription factor levels in a plant offers tremendous potential in agricultural biotechnology for modifying a plant’s traits [0005] We 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, we have identified important polynucleotide and polypeptide sequences for producing commercially valuable plants and crops as well as 30 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. SUMMARY OF THE INVENTION 35 [0006] The present invention is directed to novel recombinant polynucleotides , transgenic plants comprising the polynucleotides, and methods for producing the transgenic plants. [0007] The recombinant polynucleotides may include any of the following sequences: (a) the nucleotide sequences found in the sequence listing; 40 (b) nucleotide sequences encoding polypeptides found in the sequence listing; (c) sequence variants that are at least 70% sequence identical to any of the nucleotide sequences of (a) or (b); (d) orthologous and paralogous nucleotide sequences that are at least 70% identical to any of the nucleotide se- quences of (a) or (b); (e) nucleotide sequence that hybridize to any of the nucleotide sequences of (a) or (b) under stringent conditions, 45 whichmay include, for example, hybridization with wash steps of 6x SSCand 65 Cfor tento thirty minutes per step;and (f) nucleotide sequences encoding a polypeptide having a conserved domain required for the function of regulating transcription and altering a trait in a transgenic plant, the conserved domain being at least 70% identical with a conserved domain of a polypeptide of the invention (i.e.,, a polypeptide listed in the sequence listing, or encoded by any of the above nucleotide sequences). 50 [0008] The invention also pertains to transgenic plants that may be produced by transforming plants with any recom- binant polynucleotide of the invention. Due to the function of these polynucleotides, the transgenic plant will become altered phenotypically when compared with a wild-type plant. The traits that may be altered by transforming a plant with one of the present polynucleotides are numerous and varied, and may include, for example: 55 increased tolerance to various abiotic stresses, including cold, heat, freezing, low nitrogen and phosphorus condi- tions, osmotic stresses such as drought, and high salt concentrations; increased tolerance to disease, including fungal disease, and particularlyErysiphe, Fusarium, and Botrytis ; the 2 EP 2 270 166 A2 present polynucleotides may be used to confer increased tolerance to multiple pathogens in transformed plants; altered sensitivity or resistance to treatments that include glyphosate, ABA, and ACC, altered carbon/nitrogen (C/N) sensing; advanced or delayed flowering time; 5 altered floral characteristics such as flower structure, loss of flower determinacy, or reduced fertility; altered shoot meristem development, altered stem morphology and vascular tissue structure, and altered branching patterns; reduced apical dominance; altered trichome density, development, or structure; 10 altered root development, including root mass, branching and root hairs; altered shade avoidance; altered seed characteristics such as size, oil content, protein content, development, ripening, germination, or prenyl lipid content; altered leaf characteristics, including size, mass, shape, color, glossiness, prenyl lipid content and other chemical 15 modifications; slower or faster growth than wild-type; altered cell differentiation, proliferation, and expansion; altered phase change; altered senescence, programmed cell death and necrosis, 20 increased plant size and/or biomass, including larger seedlings than controls; dwarfed plants; and altered pigment, including anthocyanin, levels, in various plant tissues. [0009] Methods for producing transgenic plants having altered traits are also encompassed by the invention. These method steps include first providing an expression vector having a recombinant polynucleotide of the invention, and at 25 least one regulatory element flanking the polynucleotide sequence Generally, the regulatory element (s) control expres- sion of the recombinant polynucleotide in a target plant. The expression vector is then introduced into plant cells. The plant cells are grown into plants, which are allowed to overexpress a polypeptide encoded by the recombinant polynu- cleotide. This overexpression results in the trait alteration, in the plant. Those plants that have altered traits are identifi ed and selected on the basis of the desirability and degree of the altered trait. 30 Brief Description of the Sequence Listing and Figures [0010] The file of this patent contains at least one drawing executed in color. Copies of this patent with color drawing (s) will be provided by the Patent and Trademark Office upon request and payment of the necessary fee. 35 [0011] 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. Figure 1 shows a conservative estimate of phylogenetic relationships among the orders of flowering plants (modified from Angiosperm Phylogeny Group (1998) Ann. Missouri Bot. Guard. 84: 1-49). Those plants with a single cotyledon 40 (monocots) are a monophyletic clade nested within at least two major lineages of dicots; the eudicots are further