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.

What is claimed is: 
     
         1 . An isolated nucleic acid molecule comprising:
 (a) a nucleotide sequence encoding an amino acid sequence that is at least 85% identical to any one of the polypeptides in the Sequence Listing;   (b) a nucleotide sequence encoding an amino acid sequence that is at least 85% identical to any one of the polypeptides from  Sorghum  in the Sequence Listing;   (c) a nucleotide sequence according to any one of the nucleotide sequences from  Sorghum  in the Sequence Listing;   (d) a nucleotide sequence that is an interfering RNA to a nucleotide sequence according to paragraph (a) or paragraph (b);   (e) a nucleotide sequence able to form a hybridized nucleic acid duplex with the nucleic acid according to any one of paragraphs (a)-(d) at a temperature from about 10° C. to about 8° C. below a melting temperature of the hybridized nucleic acid duplex; or   (f) a nucleotide sequence encoding any one of the polypeptide sequences from  Sorghum  in the Sequence Listing.   
     
     
         2 . An isolated nucleic acid molecule comprising:
 (a) a nucleotide sequence encoding an amino acid sequence that is at least 85% identical to any one of the polypeptides from  Sorghum  in the Sequence Listing;   (b) a nucleotide sequence according to any one of the nucleotide sequences from  Sorghum  in the Sequence Listing;   (c) a nucleotide sequence that is an interfering RNA to a nucleotide sequence according to paragraph (a) or paragraph (b);   (d) a nucleotide sequence able to form a hybridized nucleic acid duplex with the nucleic acid according to any one of paragraphs (a)-(d) at a temperature from about 10° C. to about 8° C. below a melting temperature of the hybridized nucleic acid duplex; or   (e) a nucleotide sequence encoding any one of the polypeptide sequences from  Sorghum  in the Sequence Listing.   
     
     
         3 . A vector, comprising:
 (a) a first nucleic acid having a plant regulatory region; and   (b) a second nucleic acid having a nucleotide sequence according to any one the nucleotide sequences of  claim 1  or  2 , wherein said first and second nucleic acids are operably linked.   
     
     
         4 . A method of modulating plant growth, development or phenotype characteristics, said method comprising introducing into a plant cell a nucleic acid molecule according to  claim 1  or  2 , wherein a plant produced from said plant cell has modulated plant growth, development or phenotype characteristics as compared to the corresponding level of said characteristic in tissue of a control plant that does not comprise said nucleic acid molecule. 
     
     
         5 . The method of  claim 4 , wherein the modulated plant growth, development 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 nucleic acid. 
     
     
         6 . The method of  claim 4 , wherein said isolated nucleic acid is operably linked to a regulatory region. 
     
     
         7 . The method of  claim 6 , wherein said regulatory region is a promoter selected from the group consisting of YP0092, PT0676, PT0708, PT0613, PT0678, PT0688, PT0837, 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, YP0144, YP0190, p13879, YP0050, p32449, 21876, YP0158, YP0214, YP0380, PT0848, and PT0633, the cauliflower mosaic virus (CaMV) 35S promoter, the mannopine synthase (MAS) promoter, the 1′ or 2′ promoters derived from T-DNA of  Agrobacterium tumefaciens , the figwort mosaic virus 34S promoter, actin promoters such as the rice actin promoter, ubiquitin promoters such as the maize ubiquitin-1 promoter, ribulose-1,5-bisphosphate carboxylase (RbcS) promoters such as 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, PT0668, PT0886, PR0924, and PT0585. 
     
     
         8 . A plant cell comprising a nucleotide sequence according to  claim 1 , wherein a plant produced from said plant cell has modulated plant growth, development or phenotype characteristics as compared to a control plant that does not comprise said nucleic acid. 
     
     
         9 . A plant cell which comprises a first nucleic acid molecule according to  claim 1  operably linked to a second nucleic acid molecule that is heterologous with respect to said first nucleic acid molecule. 
     
     
         10 . A transgenic plant comprising the plant cell of  claim 8  or  9 . 
     
     
         11 . Progeny of the plant of  claim 9 , wherein said progeny has modulated plant growth, development or phenotype characteristics as compared to a control plant that does not comprise said nucleic acid. 
     
     
         11 . Seed from a transgenic plant according to  claim 9 . 
     
     
         12 . Vegetative tissue from a transgenic plant according to  claim 9 . 
     
     
         13 . A food product comprising vegetative tissue from a transgenic plant according to  claim 9 . 
     
     
         14 . A feed product comprising vegetative tissue from a transgenic plant according to  claim 9 . 
     
     
         15 . A method for detecting a nucleic acid in a sample, comprising:
 (a) providing an isolated nucleic acid according to  claim 1  or  2 ;   (b) contacting said isolated nucleic acid with a sample under conditions that permit a comparison of the nucleotide sequence of the isolated nucleic acid with a nucleotide sequence of nucleic acid in the sample; and   (c) analyzing the comparison.   
     
     
         16 . A method for modulating plant growth, development or phenotype characteristics in a plant, comprising:
 (a) transforming a plant with a nucleic acid molecule according to  claim 1  or  2 ; and   (b) expressing said nucleotide sequence in said transformed plant, whereby said transformed plant has modulated plant growth, development or phenotype characteristics as compared to a plant that has not been transformed with said nucleotide sequence.   
     
     
         17 . A method for modulating the growth, development or phenotype characteristics of a plant, said method comprising altering the level of expression in said plant of a nucleic acid molecule according to  claim 1  or  2 . 
     
     
         18 . A transgenic plant having modified growth, development or phenotype characteristics as compared to a wild-type plant of the same species, wherein the transgenic plant comprises a recombinant polynucleotide having a nucleotide sequence according to  claim 1  or  2 , and wherein the polypeptide encoded by said nucleotide sequence confers to the transgenic plant modified growth, development or phenotype characteristics as compared to a wild-type plant of the same species. 
     
     
         19 . A method for producing a transgenic plant having modified growth, development or phenotype characteristics as compared to a wild-type plant of the same species, the method steps comprising: (a) inserting a nucleotide sequence according to  claim 1  or  2  into an expression vector; (b) introducing the vector into a plant or a cell of a plant to overexpress the encoded polypeptide of the nucleotide sequence; and (c) selecting the transgenic plant for modified growth, development or phenotype characteristics as compared to the wild-type plant of the same species. 
     
     
         20 . A method of identifying whether a polymorphism is associated with variation in a plant trait, said method comprising:
 a) determining whether one or more polymorphisms in a population of  Sorghum  plants exists within the locus for a first polypeptide selected from the group consisting of the polypeptides in the Sequence Listing; and   b) measuring the correlation between variation in the trait in said plants of said population and the presence of said one or more polymorphisms in said plants of said population, thereby identifying whether or not said one or more polymorphisms are associated with variation is said trait.   
     
     
         21 . A method of identifying whether a polymorphism is associated with variation in a plant trait, said method comprising:
 a) preparing DNA libraries from individuals in a population of  Sorghum  plants;   b) sequencing the DNA from said libraries;   c) identifying a first polypeptide selected from the group consisting of the polypeptides in the Sequence Listing being associated with a plant trait of interest;   d) determining whether one or more polymorphisms in said population of plants are genetically linked to the locus for said first polypeptide; and   e) measuring the correlation between variation in said trait of interest in said plants of said population and the presence of said one or more polymorphisms in said plants of said population, thereby identifying whether or not said one or more polymorphisms are associated with variation is said trait of interest.   
     
     
         22 . The method according to  claim 21 , wherein said trait is the plant trait identified in the miscellaneous feature section of the Sequence Listing for said first polypeptide.