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 cold tolerance levels and plant products produced from plants having increased cold tolerance levels.

1 . A method of producing a plant and/or plant tissue, 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 about 130, said HMM based on the amino acid sequences depicted in one of  FIG. 1 ,  2 ,  3 ,  4 , or  5  and wherein said plant and/or plant tissue has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         2 . The method of  claim 1 , wherein the HMM bit score of the amino acid is greater than about 180 based on the amino acid sequences depicted in  FIG. 2 . 
     
     
         3 . The method of  claim 1 , wherein the HMM bit score of the amino acid is greater than about 650 based on the amino acid sequences depicted in  FIG. 3 . 
     
     
         4 . The method of  claim 1 , wherein the HMM bit score of the amino acid is greater than about 310, the HMM is based on the amino acid sequences depicted in  FIG. 4 , and wherein the polypeptide is about 150 to 170 amino acids in length. 
     
     
         5 . A method of producing a plant and/or plant tissue, 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 NO: 2, 4, 6, 8, 10, 12, 13, 15, 17, 20, 20, 22, 24, 26, 28, 29, 30, 32, 34, 36, 38, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 58, 59, 60, 61, 62, 63, 64, 65, 68, 69, 71, 74, 76, 77, 79, 81, 82, 83, 85, 86, 88, 90, 93, 95, 96, 98, 100, 101, 102, 104, 106, 107, 108, 110, 112, 114, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 130, 131, 132, 134, 136, 137, 138, 139, 141, 143, 170, 172, 173, 175, 176, 178, 180, 181, 182, 183, 185, 186, 187, 189, 190, 192, 193, 194, 195, 196, 198, 199, 201, 203, 204, 205, 206, 207, 208, 210, 211, 212, 213, 214, 216, 218, 219, 220, 221, 223, 163, 164, 165, 167, 169, 157, 158, 159, 160, 161, 225, 226, 227, 229, 231, 233, 235, 237, 239, 241, 242, 244, 246, 247, 249, 250, 252, 254, 255, 256, 258, 259, and 260, wherein a plant and/or plant tissue produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         6 . The method of  claim 1  or  5 , wherein the polypeptide comprises a B-box zinc finger domain having 60 percent or greater sequence identity to the B-box zinc finger domain of residues 56 to 103 of SEQ ID NO: 20 and a CCT motif having 60 percent or greater sequence identity to the CCT motif of residues 285 to 329 of SEQ ID NO: 20. 
     
     
         7 . The method of  claim 1  or  5 , wherein the polypeptide comprises a short chain dehydrogenase domain having 60 percent or greater sequence identity to the short chain dehydrogenase domain of residues 38 to 173 of SEQ ID NO: 74. 
     
     
         8 . The method of  claim 1  or  5 , wherein the polypeptide comprises a B3 DNA binding domain having 60 percent or greater sequence identity to the B3 DNA binding domain of residues 163 to 268 of SEQ ID NO: 112 and a auxin response factor domain having 60 percent or greater sequence identity to the auxin response factor domain of residues 290 to 372 of SEQ ID NO: 112. 
     
     
         9 . The method of  claim 5 , wherein the HMM bit score of the amino acid sequence of said polypeptide is greater than about 130, said HMM based on the amino acid sequences depicted in one of  FIG. 1 ,  2 ,  3 ,  4 , or  5 . 
     
     
         10 . The method of  claim 1  or  5 , wherein said polypeptide is selected from the group consisting of SEQ ID NO: 2, 20, and 93. 
     
     
         11 . A method of producing a plant according to  claim 1 , wherein said method comprises growing a plant cell comprising an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence or its complement having 80 percent or greater sequence identity of a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, 3, 5, 7, 9, 11, 14, 16, 18, 19, 21, 23, 25, 27, 31, 33, 35, 37, 39, 41, 55, 57, 66, 66, 67, 67, 70, 72, 73, 75, 78, 80, 84, 87, 89, 91, 92, 94, 97, 99, 103, 105, 109, 111, 113, 115, 129, 133, 135, 140, 142, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 162, 166, 168, 171, 174, 177, 179, 184, 188, 191, 197, 200, 202, 209, 215, 217, 222, 224, 228, 230, 232, 234, 236, 238, 240, 243, 245, 248, 251, 253, and 257, or a fragment thereof, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         12 . 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 about 130, said HMM based on the amino acid sequences depicted in one of  FIG. 1 ,  2 ,  3 ,  4 , or  5 , and wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said exogenous nucleic acid. 
     
     
         13 . A method of modulating the level of cold tolerance in a plant according to  claim 12  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 NO: 2, 4, 6, 8, 10, 12, 13, 15, 17, 20, 20, 22, 24, 26, 28, 29, 30, 32, 34, 36, 38, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 58, 59, 60, 61, 62, 63, 64, 65, 68, 69, 71, 74, 76, 77, 79, 81, 82, 83, 85, 86, 88, 90, 93, 95, 96, 98, 100, 101, 102, 104, 106, 107, 108, 110, 112, 114, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 130, 131, 132, 134, 136, 137, 138, 139, 141, 143, 170, 172, 173, 175, 176, 178, 180, 181, 182, 183, 185, 186, 187, 189, 190, 192, 193, 194, 195, 196, 198, 199, 201, 203, 204, 205, 206, 207, 208, 210, 211, 212, 213, 214, 216, 218, 219, 220, 221, 223, 163, 164, 165, 167, 169, 157, 158, 159, 160, 161, 225, 226, 227, 229, 231, 233, 235, 237, 239, 241, 242, 244, 246, 247, 249, 250, 252, 254, 255, 256, 258, 259, and 260, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         14 . A method of modulating the level of cold tolerance in a plant according to  claim 12 , 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 NO: 1, 3, 5, 7, 9, 11, 14, 16, 18, 19, 21, 23, 25, 27, 31, 33, 35, 37, 39, 41, 55, 57, 66, 66, 67, 67, 70, 72, 73, 75, 78, 80, 84, 87, 89, 91, 92, 94, 97, 99, 103, 105, 109, 111, 113, 115, 129, 133, 135, 140, 142, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 162, 166, 168, 171, 174, 177, 179, 184, 188, 191, 197, 200, 202, 209, 215, 217, 222, 224, 228, 230, 232, 234, 236, 238, 240, 243, 245, 248, 251, 253, and 257, or a fragment thereof, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance 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 130, said HMM based on the amino acid sequences depicted in one of  FIG. 1 ,  2 ,  3 ,  4 , or  5 , and wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         16 . The plant cell of  claim 15 , wherein the polypeptide has 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 13, 15, 17, 20, 20, 22, 24, 26, 28, 29, 30, 32, 34, 36, 38, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 58, 59, 60, 61, 62, 63, 64, 65, 68, 69, 71, 74, 76, 77, 79, 81, 82, 83, 85, 86, 88, 90, 93, 95, 96, 98, 100, 101, 102, 104, 106, 107, 108, 110, 112, 114, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 130, 131, 132, 134, 136, 137, 138, 139, 141, 143, 170, 172, 173, 175, 176, 178, 180, 181, 182, 183, 185, 186, 187, 189, 190, 192, 193, 194, 195, 196, 198, 199, 201, 203, 204, 205, 206, 207, 208, 210, 211, 212, 213, 214, 216, 218, 219, 220, 221, 223, 163, 164, 165, 167, 169, 157, 158, 159, 160, 161, 225, 226, 227, 229, 231, 233, 235, 237, 239, 241, 242, 244, 246, 247, 249, 250, 252, 254, 255, 256, 258, 259, and 260. 
     
     
         17 . A plant cell according to  claim 15 , 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 NO: 2, 4, 6, 8, 10, 12, 13, 15, 17, 20, 20, 22, 24, 26, 28, 29, 30, 32, 34, 36, 38, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 58, 59, 60, 61, 62, 63, 64, 65, 68, 69, 71, 74, 76, 77, 79, 81, 82, 83, 85, 86, 88, 90, 93, 95, 96, 98, 100, 101, 102, 104, 106, 107, 108, 110, 112, 114, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 130, 131, 132, 134, 136, 137, 138, 139, 141, 143, 170, 172, 173, 175, 176, 178, 180, 181, 182, 183, 185, 186, 187, 189, 190, 192, 193, 194, 195, 196, 198, 199, 201, 203, 204, 205, 206, 207, 208, 210, 211, 212, 213, 214, 216, 218, 219, 220, 221, 223, 163, 164, 165, 167, 169, 157, 158, 159, 160, 161, 225, 226, 227, 229, 231, 233, 235, 237, 239, 241, 242, 244, 246, 247, 249, 250, 252, 254, 255, 256, 258, 259, and 260, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         18 . A plant cell according to  claim 15 , comprising an exogenous nucleic acid said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence or its complement having 80 percent or greater sequence identity of a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, 3, 5, 7, 9, 11, 14, 16, 18, 19, 21, 23, 25, 27, 31, 33, 35, 37, 39, 41, 55, 57, 66, 66, 67, 67, 70, 72, 73, 75, 78, 80, 84, 87, 89, 91, 92, 94, 97, 99, 103, 105, 109, 111, 113, 115, 129, 133, 135, 140, 142, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 162, 166, 168, 171, 174, 177, 179, 184, 188, 191, 197, 200, 202, 209, 215, 217, 222, 224, 228, 230, 232, 234, 236, 238, 240, 243, 245, 248, 251, 253, and 257, or a fragment thereof, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         19 . A transgenic plant comprising the plant cell of any one of  claims 15 - 18 . 
     
     
         20 . The transgenic plant of  claim 19 , wherein said polypeptide is selected from the group consisting of SEQ ID NO: 2, 20, and 93. 
     
     
         21 . The transgenic plant of  claim 19 , 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 aeslivum  (wheat),  Gossypium hirsutum  (cotton),  Oryza sativa  (rice),  Helianthus annuus  (sunflower),  Medicago sativa  (alfalfa),  Beta vulgaris  (sugarbeet), or  Pennisetum glaucum  (pearl millet). 
     
     
         22 . A seed product comprising embryonic tissue from a transgenic plant according to  claim 19 . 
     
     
         23 . An isolated nucleic acid comprising a nucleotide sequence having 95% or greater sequence identity to the nucleotide sequence set forth in SEQ ID NO: 3, 5, 7, 9, 11, 14, 16, 21, 23, 25, 27, 33, 37, 39, 41, 55, 57, 70, 75, 80, 84, 87, 91, 92, 97, 105, 113, 115, 129, 133, or 140. 
     
     
         24 . 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 NO: 4, 6, 8, 10, 12, 22, 24, 26, 28, 36, 38, 40, 42, 71, 74, 85, 88, 93, 105, 114, 116, 130, 134, 136, 141, or 143. 
     
     
         25 . 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 ,  2 ,  3 ,  4 , or  5  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.   
     
     
         26 . 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 ,  2 ,  3 ,  4 , or  5  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.   
     
     
         27 . The method of  claim 25  or  26 , wherein said trait is the level of cold tolerance. 
     
     
         28 . The method of  claim 25 , wherein said population is a population of switchgrass, sorghum, sugar cane, or miscanthus plants. 
     
     
         29 . A plant cell comprising an exogenous nucleic acid said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence comprising at least a fragment having 80 percent or greater sequence identity to a nucleic acid sequence selected from the group consisting of residues 305 to about 346 of SEQ ID NO: 111, residues 21 to about 62 of SEQ ID NO: 66, residues 20 to about 61 of SEQ ID NO: 67, residues 21 to about 62 of SEQ ID NO: 72, residues 21 to about 62 of SEQ ID NO: 73, residues 77 to about 118 of SEQ ID NO: 144, residues 292 to about 313 of SEQ ID NO: 145, residues 37 to about 78 of SEQ ID NO: 146, residues 56 to about 97 of SEQ ID NO: 147, residues 37 to about 78 of SEQ ID NO: 148, residues 45 to about 86 of SEQ ID NO: 149, residues 46 to about 98 of SEQ ID NO: 150, residues 476 to about 497 of SEQ ID NO: 151, residues 21 to about 62 of SEQ ID NO: 152, residues 21 to about 62 of SEQ ID NO: 153, residues 21 to about 62 of SEQ ID NO: 154, residues 21 to about 62 of SEQ ID NO: 155, and residues 21 to about 62 of SEQ ID NO: 156, or their complement, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         30 . A transgenic plant comprising the plant cell of  claim 29 . 
     
     
         31 . The transgenic plant of  claim 30 , wherein said exogenous nucleic acid comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 66, 67, 72, 73, 111, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, and 156. 
     
     
         32 . A method of producing 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 at least a fragment having 80 percent or greater sequence identity to a nucleic acid sequence selected from the group consisting of residues 305 to about 346 of SEQ ID NO: 111, residues 21 to about 62 of SEQ ID NO: 66, residues 20 to about 61 of SEQ ID NO: 67, residues 21 to about 62 of SEQ ID NO: 72, residues 21 to about 62 of SEQ ID NO: 73, residues 77 to about 118 of SEQ ID NO: 144, residues 292 to about 313 of SEQ ID NO: 145, residues 37 to about 78 of SEQ ID NO: 146, residues 56 to about 97 of SEQ ID NO: 147, residues 37 to about 78 of SEQ ID NO: 148, residues 45 to about 86 of SEQ ID NO: 149, residues 46 to about 98 of SEQ ID NO: 150, residues 476 to about 497 of SEQ ID NO: 151, residues 21 to about 62 of SEQ ID NO: 152, residues 21 to about 62 of SEQ ID NO: 153, residues 21 to about 62 of SEQ ID NO: 154, residues 21 to about 62 of SEQ ID NO: 155, and residues 21 to about 62 of SEQ ID NO: 156, or their complement, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         33 . The method of  claim 32 , wherein expression of a target polypeptide is suppressed, said target polypeptide having 80 percent or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 112, 114, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 130, 131, 132, 134, 136, 137, 138, 139, 141, and 143. 
     
     
         34 . The method of  claim 33 , wherein the HMM bit score of the amino acid sequence of said polypeptide is greater than about 790, said HMM based on the amino acid sequences depicted in  FIG. 5 . 
     
     
         35 . The method of  claim 32 , wherein the nucleotide sequence or its complement is complementary to RNA transcribed from a gene encoding said target polypeptide. 
     
     
         36 . The method of  claim 32 , wherein the nucleotide sequence comprises a microRNA recognition site having 80 percent or greater sequence identity to a nucleic acid sequence selected from the group consisting of residues 109 to about 129 of SEQ ID NO: 66, residues 114 to about 135 of SEQ ID NO: 67, residues 119 to about 139 of SEQ ID NO: 72, residues 108 to about 128 of SEQ ID NO: 73, residues 234 to about 254 of SEQ ID NO: 144, residues 135 to about 176 of SEQ ID NO: 145, residues 173 to about 189 of SEQ ID NO: 147, residues 154 to about 170 of SEQ ID NO: 148, residues 134 to about 157 of SEQ ID NO: 149, residues 154 to about 198 of SEQ ID NO: 150, residues 319 to about 360 of SEQ ID NO: 151, residues 121 to about 141 of SEQ ID NO: 152, residues 120 to about 140 of SEQ ID NO: 153, residues 121 to about 141 of SEQ ID NO: 154, residues 121 to about 141 of SEQ ID NO: 155, residues 121 to about 141 of SEQ ID NO: 156, and residues 462 to about 483 of SEQ ID NO: 111. 
     
     
         37 . 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 or its complement having 80 percent or greater sequence identity to a nucleic acid sequence selected from the group consisting of residues 305 to about 346 of SEQ ID NO: 111, residues 21 to about 62 of SEQ ID NO: 66, residues 20 to about 61 of SEQ ID NO: 67, residues 21 to about 62 of SEQ ID NO: 72, residues 21 to about 62 of SEQ ID NO: 73, residues 77 to about 118 of SEQ ID NO: 144, residues 292 to about 313 of SEQ ID NO: 145, residues 37 to about 78 of SEQ ID NO: 146, residues 56 to about 97 of SEQ ID NO: 147, residues 37 to about 78 of SEQ ID NO: 148, residues 45 to about 86 of SEQ ID NO: 149, residues 46 to about 98 of SEQ ID NO: 150, residues 476 to about 497 of SEQ ID NO: 151, residues 21 to about 62 of SEQ ID NO: 152, residues 21 to about 62 of SEQ ID NO: 153, residues 21 to about 62 of SEQ ID NO: 154, residues 21 to about 62 of SEQ ID NO: 155, and residues 21 to about 62 of SEQ ID NO: 156, or a fragment thereof, wherein a plant produced from said plant cell has a difference in the level of cold tolerance as compared to the corresponding level of cold tolerance of a control plant that does not comprise said nucleic acid.