Nucleotide sequences and corresponding polypeptides conferring modulated growth rate and biomass in plants grown in saline and oxidative conditions

Abstract

The present invention related to isolated nucleic acid molecules and their corresponding encoded polypeptides able confer the trait of improved plant size, vegetative growth, growth rate seedling vigor and/or biomass in plants challenged with saline and/or oxidative stress conditions. 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 plant size, vegetative growth, growth rate, seedling vigor and/or biomass that are improved in saline and/or oxidative stress conditions with respect to wild-type plants grown under similar conditions.

1 . A method of producing a plant having increased tolerance to salinity or increased tolerance to oxidative stress, 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, and wherein the HMM bit score of the amino acid sequence encoded by said polypeptide is greater than about 30, said HMM based on the amino acid sequences depicted in one of  FIGS. 1-6 , and wherein said plant has a difference in the level of tolerance to salinity or oxidative stress as compared to the corresponding level in tolerance to salinity or oxidative stress of a control plant that does not comprise said nucleic acid. 
     
     
         2 . The method according to  claim 1 , wherein the HMM bit score of the amino acid sequence encoded by said polypeptide is greater than about 400, said HMM based on the amino acid sequences depicted in  FIG. 1 . 
     
     
         3 . The method according to  claim 1 , wherein the HMM bit score of the amino acid sequence encoded by said polypeptide is greater than about 30, said HMM based on the amino acid sequences depicted in  FIG. 2 . 
     
     
         4 . The method according to  claim 1 , wherein the HMM bit score of the amino acid sequence encoded by said polypeptide is greater than about 120, said HMM based on the amino acid sequences depicted in  FIG. 3 . 
     
     
         5 . The method according to  claim 1 , wherein the HMM bit score of the amino acid sequence encoded by said polypeptide is greater than about 150, said HMM based on the amino acid sequences depicted in  FIG. 4 . 
     
     
         6 . The method according to  claim 1 , wherein the HMM bit score of the amino acid sequence encoded by said polypeptide is greater than about 425, said HMM based on the amino acid sequences depicted in  FIG. 5 . 
     
     
         7 . The method according to  claim 1 , wherein the HMM bit score of the amino acid sequence encoded by said polypeptide is greater than about 550, said HMM based on the amino acid sequences depicted in  FIG. 6 . 
     
     
         8 . A method of producing a plant having increased tolerance to salinity or increased tolerance to oxidative stress, 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 85 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 9, 11, 13, 14, 15, 17, 19, 20, 22, 23, 24, 25, 27, 29, 30, 31, 33, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 47, 49, 50, 52, 54, 56, 58, 60, 62, 63, 64, 66, 68, 69, 71, 73, 74, 76, 78, 80, 81, 83, 84, 86, 88, 90, 91, 93, 94, 96, 98, 100, 101, 102, 104, 106, 107, 109, 110, 112, 114, 116, 118, 119, 121, 122, 123, 125, 126, 127, 128, 129, 130, 132, 134, 136, 138, 140, 141, 142, 143, 144, 145, 147, 149, 151, 153, 154, 156, 158, 160, 162, 163, 165, 166, 167, 168, and amino acid coordinates 1 to 135 of SEQ ID NO: 140, wherein said plant produced from said plant cell has a difference in the level of tolerance to salinity or oxidative stress as compared to the corresponding level in a control plant that does not comprise said nucleic acid. 
     
     
         9 . 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 85 percent or greater sequence identity to a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 10, 12, 16, 18, 21, 26, 28, 32, 34, 40, 46, 48, 51, 53, 55, 57, 59, 61, 65, 67, 70, 72, 75, 77, 79, 82, 85, 87, 89, 92, 95, 97, 99, 103, 105, 108, 111, 113, 115, 117, 120, 124, 131, 133, 135, 137, 139, 146, 148, 150, 152, 155, 157, 159, 161, and 164, wherein a plant produced from said plant cell has a difference in the level of tolerance to salinity or oxidative stress as compared to the corresponding level in tolerance to salinity or oxidative stress of a control plant that does not comprise said nucleic acid. 
     
     
         10 . A method of modulating the level of tolerance to salinity or oxidative stress 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 about 30, said HMM based on the amino acid sequences depicted in one of  FIGS. 1-6 , and wherein a plant produced from said plant cell has a difference in the level of tolerance to salinity or oxidative stress as compared to the corresponding level in tolerance to salinity or oxidative stress of a control plant that does not comprise said exogenous nucleic acid. 
     
     
         11 . A method of modulating the level of tolerance to salinity or oxidative stress 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 85 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 9, 11, 13, 14, 15, 17, 19, 20, 22, 23, 24, 25, 27, 29, 30, 31, 33, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 47, 49, 50, 52, 54, 56, 58, 60, 62, 63, 64, 66, 68, 69, 71, 73, 74, 76, 78, 80, 81, 83, 84, 86, 88, 90, 91, 93, 94, 96, 98, 100, 101, 102, 104, 106, 107, 109, 110, 112, 114, 116, 118, 119, 121, 122, 123, 125, 126, 127, 128, 129, 130, 132, 134, 136, 138, 140, 141, 142, 143, 144, 145, 147, 149, 151, 153, 154, 156, 158, 160, 162, 163, 165, 166, 167, 168, and amino acid coordinates 1 to 135 of SEQ ID NO: 140, wherein a plant produced from said plant cell has a difference in the level of tolerance to salinity or oxidative stress as compared to the corresponding level in tolerance to salinity or oxidative stress of a control plant that does not comprise said nucleic acid. 
     
     
         12 . The method of any one of  claims 1 - 8 ,  10  or  11 , wherein said polypeptide is selected from the group consisting of SEQ ID NO: 43, 44, 45, 86, 140, 141, 142, 143, 144, and amino acid coordinates 1 to 135 of SEQ ID NO: 140, and said plant has a difference in the level of tolerance to salinity as compared to the corresponding level in tolerance to salinity of a control plant that does not comprise said nucleic acid. 
     
     
         13 . The method of any one of  claims 1 - 8 ,  10  or  11 , wherein said polypeptide is selected from the group consisting of SEQ ID NO: 136, and 141, and said plant has a difference in the level of tolerance to oxidative stress as compared to the corresponding level in tolerance to oxidative stress of a control plant that does not comprise said nucleic acid. 
     
     
         14 . A method of modulating the level of tolerance to salinity or oxidative stress 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 85 percent or greater sequence identity to a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 10, 12, 16, 18, 21, 26, 28, 32, 34, 40, 46, 48, 51, 53, 55, 57, 59, 61, 65, 67, 70, 72, 75, 77, 79, 82, 85, 87, 89, 92, 95, 97, 99, 103, 105, 108, 111, 113, 115, 117, 120, 124, 131, 133, 135, 137, 139, 146, 148, 150, 152, 155, 157, 159, 161, and 164, wherein a plant produced from said plant cell has a difference in the level of tolerance to salinity or oxidative stress as compared to the corresponding level in tolerance to salinity or oxidative stress of a control plant that does not comprise said nucleic acid. 
     
     
         15 . 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 about 30, said HMM based on the amino acid sequences depicted in one of  FIGS. 1-6 , and wherein said plant cell has a difference in the level of tolerance to salinity or oxidative stress as compared to the corresponding level in tolerance to salinity or oxidative stress of a control plant that does not comprise said nucleic acid. 
     
     
         16 . 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 85 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 2, 4, 6, 8, 9, 11, 13, 14, 15, 17, 19, 20, 22, 23, 24, 25, 27, 29, 30, 31, 33, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 47, 49, 50, 52, 54, 56, 58, 60, 62, 63, 64, 66, 68, 69, 71, 73, 74, 76, 78, 80, 81, 83, 84, 86, 88, 90, 91, 93, 94, 96, 98, 100, 101, 102, 104, 106, 107, 109, 110, 112, 114, 116, 118, 119, 121, 122, 123, 125, 126, 127, 128, 129, 130, 132, 134, 136, 138, 140, 141, 142, 143, 144, 145, 147, 149, 151, 153, 154, 156, 158, 160, 162, 163, 165, 166, 167, 168, and amino acid coordinates 1 to 135 of SEQ ID NO: 140, wherein a plant produced from said plant cell has a difference in the level of tolerance to salinity or oxidative stress as compared to the corresponding level in tolerance to salinity or oxidative stress of a control plant that does not comprise said nucleic acid. 
     
     
         17 . A plant cell comprising an exogenous nucleic acid said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence having 85 percent or greater sequence identity to a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, 3, 5, 7, 10, 12, 16, 18, 21, 26, 28, 32, 34, 40, 46, 48, 51, 53, 55, 57, 59, 61, 65, 67, 70, 72, 75, 77, 79, 82, 85, 87, 89, 92, 95, 97, 99, 103, 105, 108, 111, 113, 115, 117, 120, 124, 131, 133, 135, 137, 139, 146, 148, 150, 152, 155, 157, 159, 161, and 164, wherein a plant produced from said plant cell has a difference in the level of tolerance to salinity or oxidative stress as compared to the corresponding level in tolerance to salinity or oxidative stress of a control plant that does not comprise said nucleic acid. 
     
     
         18 . A transgenic plant comprising the plant cell of any one of  claims 15 - 17 . 
     
     
         19 . The transgenic plant of  claim 18 , 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). 
     
     
         20 . A product comprising seed or vegetative tissue from a transgenic plant according to  claim 15 - 17 . 
     
     
         21 . The product of  claim 20 , wherein said product is a food or feed product. 
     
     
         22 . An isolated nucleic acid comprising a nucleotide sequence encoding a polypeptide having 80% or greater sequence identity to the amino acid sequence set forth in SEQ ID NOs: 2, 4, 6, 22, 27, 29, 49, 52, 54, 56, 60, 62, 68, 76, 83, 88, 90, 96, 98, 104, 106, 112, 114, 132, 134, 149, 151, or 160. 
     
     
         23 . A method of identifying whether a 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. 1-6  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.   
     
     
         24 . The method of  claim 23 , wherein said trait is an increased tolerance to salinity, an increased tolerance to oxidative stress, or increased biomass. 
     
     
         25 . 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. 1-6  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 salt tolerance or oxidative stress tolerance;   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.   
     
     
         26 . The method of  claim 24  or  25 , wherein said population is a population of switchgrass plants. 
     
     
         27 . The method of any one of  claims 1 ,  8 ,  10  or  11  with the proviso that said nucleotide sequence encoding a polypeptide does not encode a polypeptide specifically described in the Sequence Listing of PCT/US2007/06544. 
     
     
         28 . The method of any one of  claims 1 ,  8 ,  10  or  11  with the proviso that said nucleotide sequence encoding a polypeptide does not encode one of the following polypeptide sequences of PCT/US2007/06544: SEQ ID NO:99, SEQ ID NO:100, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:180, SEQ ID NO:252, SEQ ID NO:298, SEQ ID NO:300, SEQ ID NO:301, SEQ ID NO:306 and SEQ ID NO:312. 
     
     
         29 . The method of  claim 9  or  14  with the proviso that said nucleotide sequence is not specifically described in the Sequence Listing of PCT/US2007/06544. 
     
     
         30 . The method of  claims 9  or  14  with the proviso that said nucleotide sequence is not one of the following nucleotide sequences of PCT/US2007/06544: SEQ ID NO:98, SEQ ID NO:101, SEQ ID NO:225 and SEQ ID NO:299. 
     
     
         31 . The plant cell of  claim 15  or  16  with the proviso that said nucleotide sequence encoding a polypeptide does not encode a polypeptide specifically described in the Sequence Listing of PCT/US2007/06544. 
     
     
         32 . The plant cell of  claim 15  or  16  with the proviso that said nucleotide sequence encoding a polypeptide does not encode one of the following polypeptide sequences of PCT/US2007/06544: SEQ ID NO:99, SEQ ID NO: 100, SEQ ID NO: 102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:180, SEQ ID NO:252, SEQ ID NO:298, SEQ ID NO:300, SEQ ID NO:301, SEQ ID NO:306 and SEQ ID NO:312. 
     
     
         33 . The plant cell of  claim 17  with the proviso that said nucleotide sequence is not specifically described in the Sequence Listing of PCT/US2007/06544. 
     
     
         34 . The plant cell of  claim 17  with the proviso that said nucleotide sequence is not one of the following nucleotide sequences of PCT/US2007/06544: SEQ ID NO:98, SEQ ID NO: 101, SEQ ID NO:225 and SEQ ID NO:299. 
     
     
         35 . The nucleic acid of  claim 22  with the proviso that said nucleotide sequence not specifically described in the Sequence Listing of PCT/US2007/06544. 
     
     
         36 . The nucleic acid of  claim 22  with the proviso that said nucleotide sequence is not one of the following nucleotide sequences of PCT/US2007/06544: SEQ ID NO:98, SEQ ID NO: 101, SEQ ID NO:225 and SEQ ID NO:299. 
     
     
         37 . The method of  claim 23  or  25  with the proviso that said polypeptide is not specifically described in the Sequence Listing of PCT/US2007/06544. 
     
     
         38 . The method of  claim 23  or  25  with the proviso that said polypeptide is not one of the following polypeptide sequences of PCT/US2007/06544: SEQ ID NO:99, SEQ ID NO:100, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:104, SEQ ID NO:180, SEQ ID NO:252, SEQ ID NO:298, SEQ ID NO:300, SEQ ID NO:301, SEQ ID NO:306 and SEQ ID NO:312.