Nucleotide sequences and polypeptides encoded thereby useful for modifying plant characteristics in response to cold

Abstract

Methods and materials for modulating cold tolerance levels in plants are disclosed. For example, nucleic acids encoding cold tolerance-modulating polypeptides are disclosed as well as methods for using such nucleic acids to transform plant cells. Also disclosed are plants having increased levels of cold tolerance and plant products produced from plants having increased cold tolerance levels.

1 . A method of producing a plant, said method comprising growing a plant cell comprising an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide, wherein the HMM bit score of the amino acid sequence of said polypeptide is greater than 20, said HMM based on the amino acid sequences depicted in one of  FIGS. 1-7 , and wherein said plant has a difference in the level of cold tolerance as compared to the corresponding level in a control plant that does not comprise said nucleic acid. 
     
     
         2 . A method of producing a plant, said method comprising growing a plant cell comprising an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 2, 7, 9, 20, 34, 40 and 42, and wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level in a control plant that does not comprise said nucleic acid. 
     
     
         3 . A method of producing a plant, said method comprising growing a plant cell comprising an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence having 80 percent or greater sequence identity to a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 6, 8, 19, 33, 39 and 41, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level in a control plant that does not comprise said nucleic acid. 
     
     
         4 . A method of modulating the level of cold tolerance in a plant, said method comprising introducing into a plant cell an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide, wherein the HMM bit score of the amino acid sequence of said polypeptide is greater than 20, said HMM based on the amino acid sequences depicted in one of  FIGS. 1-7 , and wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level in a control plant that does not comprise said exogenous nucleic acid. 
     
     
         5 . A method of modulating the level of cold tolerance in a plant, said method comprising introducing into a plant cell an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 2, 7, 9, 20, 34, 40 and 42, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level in a control plant that does not comprise said nucleic acid. 
     
     
         6 . The method of any one of  claims 1  to  5 , wherein said polypeptide is selected from the group consisting of SEQ ID NOs: 2-5,7,9-18, 20-32, 34-38, 40, 42-46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82-89, 109 and 204-229. 
     
     
         7 . A method of modulating the level of cold tolerance in a plant, said method comprising introducing into a plant cell an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence having 80 percent or greater sequence identity to a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 6, 8, 19, 33, 39 and 41, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level in a control plant that does not comprise said nucleic acid 
     
     
         8 . A plant cell comprising an exogenous nucleic acid said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide, wherein the HMM bit score of the amino acid sequence of said polypeptide is greater than 20, said HMM based on the amino acid sequences depicted in one of  FIGS. 1-7 , and wherein said plant has a difference in the level of cold tolerance as compared to the corresponding level in a control plant that does not comprise said nucleic acid. 
     
     
         9 . A plant cell comprising an exogenous nucleic acid said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 2, 7, 9, 20, 34, 40 and 42, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level in a control plant that does not comprise said nucleic acid. 
     
     
         10 . A plant cell comprising an exogenous nucleic acid said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence having 80 percent or greater sequence identity to a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 6, 8, 19, 33, 39 and 41, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level in a control plant that does not comprise said nucleic acid. 
     
     
         11 . A transgenic plant comprising the plant cell of any one of  claims 8 - 10 . 
     
     
         12 . The transgenic plant of  claim 11 , wherein said plant is a member of 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 sativa  (alfalfa),  Beta vulgaris  (sugarbeet), or  Pennisetum glaucum  (pearl millet). 
     
     
         13 . A transgenic plant comprising the plant cell of  claim 11 , wherein said polypeptide is selected from the group consisting of SEQ ID NOs: 2, 7, 9, 20, 34, 40 and 42. 
     
     
         14 . A vegetative product comprising plant tissue from a transgenic plant according to  claim 11 . 
     
     
         15 . An isolated nucleic acid comprising a nucleotide sequence having 95% or greater sequence identity to a nucleotide sequence set forth in the Sequence Listing. 
     
     
         16 . An isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80% or greater sequence identity to an amino acid sequence set forth in the Sequence Listing. 
     
     
         17 . A method of identifying whether a genetic polymorphism is associated with variation in a trait, said method comprising:
 a) determining whether one or more genetic polymorphisms in a population of plants is associated with the locus for a polypeptide selected from the group consisting of the polypeptides depicted in  FIGS. 1-7  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 genetic polymorphisms in plants of said population, thereby identifying whether or not said one or more genetic polymorphisms are associated with variation in said trait.   
     
     
         18 . 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 a polypeptide selected from the group consisting of the polypeptides depicted in  FIGS. 1-7  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 genetic polymorphisms is associated with variation in a trait;   c) crossing each 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   e) 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.   
     
     
         19 . The method of  claim 17  or  18 , wherein said trait is the level of cold tolerance. 
     
     
         20 . The method of  claim 17  or  18 , wherein said population is a population of switchgrass plants.