Nucleotide sequences and corresponding polypeptides conferring modulated plant characteristics

Abstract

The present invention relates to isolated nucleic acid molecules and their corresponding encoded polypeptides able confer the trait of modulated plant size, vegetative growth, organ number, plant architecture, sterility or seedling lethality in plants. The present invention further relates to the use of these nucleic acid molecules and polypeptides in making transgenic plants, plant cells, plant materials or seeds of a plant having such modulated growth or phenotype characteristics that are altered with respect to wild type plants grown under similar conditions.

1 . An isolated nucleic acid molecule comprising a nucleotide sequence that encodes a polypeptide having at least 85% sequence identity to the any of the amino acid sequences from  Populus balsamifera  set forth in the Sequence Listing. 
     
     
         2 . The isolated nucleic acid molecule of  claim 1  comprising a nucleotide sequence that encodes a polypeptide having any one of the amino acid sequences from  Populus balsamifera  set forth in the Sequence Listing. 
     
     
         3 . A vector, comprising:
 (a) a first nucleic acid molecule comprising a plant regulatory region; and   (b) a second nucleic acid molecule comprising a nucleotide sequence according to any one of the nucleotide sequences of  claim 1  or  2 , wherein said first and second nucleic acid molecules are operably linked.   
     
     
         4 . The vector of  claim 3 , wherein said regulatory region is a promoter selected from the group consisting of YP0092 (SEQ ID NO: 4146), PT0676 (SEQ ID NO: 4120), PT0708 (SEQ ID NO: 4125), PT0613 (SEQ ID NO: 4113), PT0672 (SEQ ID NO: 4119), PT0678 (SEQ ID NO: 4121), PT0688 (SEQ ID NO: 4123), PT0837 (SEQ ID NO: 4132), the napin promoter, the Arcelin-5 promoter, the phaseolin gene promoter, the soybean trypsin inhibitor promoter, the ACP promoter, the stearoyl-ACP desaturase gene, the soybean α′ subunit of β-conglycinin promoter, the oleosin promoter, the 15 kD zein promoter, the 16 kD zein promoter, the 19 kD zein promoter, the 22 kD zein promoter, the 27 kD zein promoter, the Osgt-1 promoter, the beta-amylase gene promoter, the barley hordein gene promoter, p326 (SEQ ID NO: 4184), YP0144 (SEQ ID NO: 4163), YP0190 (SEQ ID NO: 4167), p13879 (SEQ ID NO: 4183), YP0050 (SEQ ID NO: 4143), p32449 (SEQ ID NO: 4185), 21876 (SEQ ID NO: 4109), YP0158 (SEQ ID NO: 4165), YP0214 (SEQ ID NO: 4169), YP0380 (SEQ ID NO: 4178), PT0848 (SEQ ID NO: 4134), PT0633 (SEQ ID NO: 4172), the cauliflower mosaic virus (CaMV) 35S promoter, the mannopine synthase (MAS) promoter, the 1′ promoter from the T-DNA of  Agrobacterium tumefaciens , the 2′ promoter from the T-DNA of  Agrobacterium tumefaciens , the figwort mosaic virus 34S promoter, an actin promoter, the rice actin promoter, a ubiquitin promoter, the maize ubiquitin-1 promoter, a ribulose-1,5-bisphosphate carboxylase (RbcS) promoters, the RbcS promoter from eastern larch ( Larix laricina ), the pine cab6 promoter, the Cab-1 gene promoter from wheat, the CAB-1 promoter from spinach, the cab1R promoter from rice, the pyruvate orthophosphate dikinase (PPDK) promoter from corn, the tobacco Lhcb1*2 promoter, the  Arabidopsis thaliana  SUC2 sucrose-H+ symporter promoter, and thylakoid membrane protein promoters from spinach (psaD, psaF, psaE, PC, FNR, atpC, atpD, cab, rbcS, PT0535 (SEQ ID NO: 4111), PT0668 (SEQ ID NO: 4110), PT0886 (SEQ ID NO: 4137), PR0924 (SEQ ID NO: 4192), YP0144 (SEQ ID NO: 4163), YP0380 (SEQ ID NO:4178) and PT0585 (SEQ ID NO: 4112) 
     
     
         5 . A method of modulating plant growth, development and/or phenotype characteristics in a plant, said method comprising introducing into a plant cell an exogenous nucleic acid molecule, said exogenous nucleic acid molecule comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide having an amino acid sequence with at least 85 percent sequence identity to any of the amino acid sequences set forth in the Sequence Listing, wherein a tissue of a plant produced from said plant cell has a difference in the level of growth, development and/or phenotype characteristics as compared to the corresponding level in tissue of a control plant that does not comprise said nucleic acid. 
     
     
         6 . The method of  claim 5 , wherein the modulated plant growth, development and/or phenotype characteristics comprise a modulation in any one of plant size, plant height, plant strength, vegetative growth, color, plant architecture, amount of branching, branching angle, branching length, number or leaves per branch, organ number, organ size, organ shape, leaf shape, leaf structure, leaf size, leaf number, leaf angle, biomass, sterility, seedling lethality, seed weight, seed size, seed color, seed yield, seed germination, seed content, seed structure, seed carbon content, seed nitrogen content, seed fiber content, fruit composition, fruit shape, fruit size, fruit length, fruit yield, silique length, silique shape, flower length, flower shape, flower size, inflorescence length, inflorescence thickness, cotyledon size, cotyledon number, cotyledon shape, crop development or harvest time, flowering time, senescence, time to bolting, drought or stress tolerance, biotic stress tolerance, abiotic stress tolerance, tolerance to high density plant population, tolerance to high pH, tolerance to low pH, tolerance to low nitrogen conditions, tolerance to no nitrogen conditions, tolerance to high nitrogen conditions, tolerance to nutrient limiting conditions, tolerance to oxidative stress, tolerance to cold stress, tolerance to heat stress, tolerance to saltstress, chlorophyll content, photosynthetic capacity, root growth, nutrient uptake, chemical composition, anthocyanin content, starch content, nitrogen content, internode length, hypocotyls length, ability to grow in shade, and shade avoidance as compared to the corresponding characteristics of a control plant that does not comprise said exogenous nucleic acid molecule. 
     
     
         7 . The method of  claim 5 , wherein said nucleotide sequence encodes any of the amino acid sequences set forth in the Sequence Listing. 
     
     
         8 . A plant cell comprising an exogenous nucleic acid molecule which comprises a regulatory region and a coding region, wherein said regulatory region and said coding region are operably linked, and wherein said coding region encodes a polypeptide having at least 85 percent sequence identity with any one of the amino acid sequences set forth in the Sequence Listing, and wherein said regulatory and coding regions are operably linked, and wherein a tissue of a plant produced from said plant cell has a difference in the level of growth, development and/or phenotype characteristics as compared to the corresponding level in tissue of a control plant that does not comprise said nucleic acid. 
     
     
         9 . The plant cell of  claim 8 , wherein said coding region encodes a polypeptide having at having any one of the amino acid sequences from  Populus balsamifera  set forth in the Sequence Listing. 
     
     
         10 . A transgenic plant comprising the plant cell of  claim 8  or  9 . 
     
     
         11 . The transgenic plant of  claim 10 , wherein said plant is a species selected from the group consisting of  Panicum virgatum  (switchgrass),  Sorghum bicolor  (sorghum, sudangrass),  Miscanthus giganteus  (miscanthus),  Saccharum  sp. (energycane),  Populus balsamifera  (poplar),  Zea mays  (corn),  Glycine max  (soybean),  Brassica napus  (canola),  Triticum aestivum  (wheat),  Gossypium hirsutum  (cotton),  Oryza sativa  (rice),  Helianthus annuus  (sunflower),  Medicago saliva  (alfalfa),  Beta vulgaris  (sugarbeet), or  Pennisetum glaucum  (pearl millet). 
     
     
         12 . Seed of a transgenic plant according to  claim 10 . 
     
     
         13 . A food or feed product comprising vegetative tissue from a transgenic plant according to  claim 10 . 
     
     
         14 . A method of identifying whether a polymorphism is associated with variation in a plant trait, said method comprising:
 (a) determining whether one or more genetic polymorphisms in a population of plants is associated with the locus for any one of the polypeptides set forth in the Sequence Listing and functional homologs thereof; and   (b) measuring the correlation between variation in said trait in plants of said population and the presence of said one or more polymorphisms in plants of said population, thereby identifying whether or not said one or more polymorphisms are associated with variation in said trait.   
     
     
         15 . A method of making a plant line, said method comprising:
 (a) determining whether one or more genetic polymorphisms in a population of plants is associated with the locus for any one of the polypeptides set forth in the Sequence Listing and functional homologs thereof;   (b) identifying one or more plants in said population in which the presence of at least one allele at said one or more polymorphisms is associated with variation in at least one member selected from the group of traits consisting of growth, development and phenotype;   (c) crossing each of said one or more identified plants with itself or a different plant to produce seed;   (d) crossing at least one progeny plant grown from said seed with itself or a different plant; and   repeating steps (c) and (d) for an additional 0-5 generations to make said plant line, wherein said at least one allele is present in said plant line.   
     
     
         16 . The method of  claim 15 , wherein said trait is the level of growth. 
     
     
         17 . The method of  claim 15 , wherein said population is a population of  Populus balsamifera  plants. 
     
     
         18 . A method of producing a transgenic plant having modified growth, development and/or phenotypic characteristics, said method comprising growing a plant cell comprising an exogenous nucleic acid molecule which comprises a regulatory region and a coding region, wherein said regulatory and coding regions are operably linked, and wherein said coding regions encodes a polypeptide having at least 85 percent sequence identity to any one of the amino acid sequences set forth in the Sequence Listing, wherein a tissue of a plant produced from said plant cell has a difference in the level of growth, development and/or phenotypic characteristics as compared to the corresponding level in tissues of a control plant that does not comprise said nucleic acid. 
     
     
         19 . The method of producing a transgenic plant having modified phenotypic characteristics of  claim 18 , wherein said coding region encodes a polypeptide having any one of the amino acid sequences set forth in the Sequence Listing. 
     
     
         20 . A method of modulating plant growth, development and/or phenotype characteristics in a plant, said method comprising introducing into a plant cell an exogenous nucleic acid molecule, said exogenous nucleic acid molecule comprising a regulatory region and a coding region, wherein said regulatory and coding regions are operably linked, and wherein said coding region encodes a polypeptide with an amino acid sequence that has at least 85 percent sequence identity with any of the amino acid sequences set forth in the SEQ ID NOs of the Sequence Listing, and wherein a tissue of a plant produced from said plant cell has a difference in the level of growth, development and/or phenotype characteristics indicated in Table 1 for the SEQ ID NO encoded by said regulatory region as compared to the corresponding level in the tissue of a control plant that does not comprise said nucleic acid. 
     
     
         21 . The method of modulating plant growth, development and/or phenotype characteristics in a plant of  claim 20 , wherein said coding region encodes a polypeptide with an amino acid sequence of any one of the amino acid sequences set forth in the Sequence Listing