US2011061124A1PendingUtilityA1

Nucleotide sequences and corresponding polypeptides conferring improved nitrogen use efficiency characteristics in plants

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Assignee: CERES INCPriority: Feb 20, 2008Filed: Feb 20, 2009Published: Mar 10, 2011
Est. expiryFeb 20, 2028(~1.6 yrs left)· nominal 20-yr term from priority
Inventors:Gregory NadzanRichard SchneebergerHan Suk KimDavid Van-Dinh DangKenneth A. Feldmann
C07K 14/415C12Q 1/6895Y10T436/143333Y02A40/146C12N 15/8271C12N 15/8261
73
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Claims

Abstract

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

Claims

exact text as granted — not AI-modified
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 about 20, said HMM based on the amino acid sequences depicted in one of  FIGS. 1-57 , and wherein said plant has a difference in the level of low-nitrogen tolerance as compared to the corresponding level of low-nitrogen tolerance of 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 NO:3, SEQ ID NO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ ID NO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQ ID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510, SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ ID NO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQ ID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853, SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ ID NO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112, SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ ID NO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302, SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ ID NO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525, SEQ ID NO:1537, SEQ ID NO:1554, and SEQ ID NO:1577, wherein a plant produced from said plant cell has a difference in the level of low-nitrogen tolerance as compared to the corresponding level of low-nitrogen tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         3 . The method of  claim 1  or  2 , wherein the polypeptide comprises a Pfam domain having 70 percent or greater sequence identity to a Pfam domain in any one of the polypeptides in the sequence listing. 
     
     
         4 . 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 NO:1, SEQ ID NO:48, SEQ ID NO:76, SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:151, SEQ ID NO:165, SEQ ID NO:175, SEQ ID NO:185, SEQ ID NO:207, SEQ ID NO:217, SEQ ID NO:233, SEQ ID NO:245, SEQ ID NO:299, SEQ ID NO:331, SEQ ID NO:367, SEQ ID NO:509, SEQ ID NO:532, SEQ ID NO:555, SEQ ID NO:557, SEQ ID NO:592, SEQ ID NO:612, SEQ ID NO:645, SEQ ID NO:686, SEQ ID NO:729, SEQ ID NO:745, SEQ ID NO:768, SEQ ID NO:791, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:852, SEQ ID NO:854, SEQ ID NO:890, SEQ ID NO:916, SEQ ID NO:943, SEQ ID NO:975, SEQ ID NO:981, SEQ ID NO:1053, SEQ ID NO:1098, SEQ ID NO:1111, SEQ ID NO:1115, SEQ ID NO:1156, SEQ ID NO:1158, SEQ ID NO:1165, SEQ ID NO:1184, SEQ ID NO:1193, SEQ ID NO:1209, SEQ ID NO:1273, SEQ ID NO:1301, SEQ ID NO:1341, SEQ ID NO:1384, SEQ ID NO:1408, SEQ ID NO:1427, SEQ ID NO:1462, SEQ ID NO:1490, SEQ ID NO:1509, SEQ ID NO:1524, SEQ ID NO:1536, SEQ ID NO:1553, and SEQ ID NO:1576, or a fragment thereof, wherein a tissue of a plant produced from said plant cell has a difference in the level of low-nitrogen tolerance as compared to the corresponding level of low-nitrogen tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         5 . A method of producing a plant, said method comprising growing a plant cell comprising an exogenous nucleic acid, said exogenous nucleic acid effective for down-regulating an endogenous nucleic acid in the plant cell, wherein the endogenous nucleic acid encodes a polypeptide, and wherein the HMM bit score of the amino acid sequence of the polypeptide is greater than about 20, said HMM on the amino acid sequences depicted in one of  FIGS. 1-57 . 
     
     
         6 . A method of modulating the level of low-nitrogen 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 20, said HMM based on the amino acid sequences depicted in one of  FIGS. 1-57 , and wherein a tissue of a plant produced from said plant cell has a difference in the level of low-nitrogen tolerance as compared to the corresponding level of low-nitrogen tolerance of a control plant that does not comprise said exogenous nucleic acid. 
     
     
         7 . A method of modulating the level of low-nitrogen 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 NO:3, SEQ ID NO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ ID NO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQ ID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510, SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ ID NO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQ ID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853, SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ ID NO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112, SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ ID NO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302, SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ ID NO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525, SEQ ID NO:1537, SEQ ID NO:1554, and SEQ ID NO:1577, wherein a tissue of a plant produced from said plant cell has a difference in the level of low-nitrogen tolerance as compared to the corresponding level of low-nitrogen tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         8 . The method of  claim 1 , wherein said polypeptide is selected from the group consisting of SEQ ID NO:3, SEQ ID NO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ ID NO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQ ID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510, SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ ID NO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQ ID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853, SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ ID NO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112, SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ ID NO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302, SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ ID NO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525, SEQ ID NO:1537, SEQ ID NO:1554, and SEQ ID NO:1577. 
     
     
         9 . A method of modulating the level of low-nitrogen 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 NO:1, SEQ ID NO:48, SEQ ID NO:76, SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:151, SEQ ID NO:165, SEQ ID NO:175, SEQ ID NO:185, SEQ ID NO:207, SEQ ID NO:217, SEQ ID NO:233, SEQ ID NO:245, SEQ ID NO:299, SEQ ID NO:331, SEQ ID NO:367, SEQ ID NO:509, SEQ ID NO:532, SEQ ID NO:555, SEQ ID NO:557, SEQ ID NO:592, SEQ ID NO:612, SEQ ID NO:645, SEQ ID NO:686, SEQ ID NO:729, SEQ ID NO:745, SEQ ID NO:768, SEQ ID NO:791, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:852, SEQ ID NO:854, SEQ ID NO:890, SEQ ID NO:916, SEQ ID NO:943, SEQ ID NO:975, SEQ ID NO:981, SEQ ID NO:1053, SEQ ID NO:1098, SEQ ID NO:1111, SEQ ID NO:1115, SEQ ID NO:1156, SEQ ID NO:1158, SEQ ID NO:1165, SEQ ID NO:1184, SEQ ID NO:1193, SEQ ID NO:1209, SEQ ID NO:1273, SEQ ID NO:1301, SEQ ID NO:1341, SEQ ID NO:1384, SEQ ID NO:1408, SEQ ID NO:1427, SEQ ID NO:1462, SEQ ID NO:1490, SEQ ID NO:1509, SEQ ID NO:1524, SEQ ID NO:1536, SEQ ID NO:1553, and SEQ ID NO:1576, or a fragment thereof, wherein a tissue of a plant produced from said plant cell has a difference in the level of low-nitrogen tolerance as compared to the corresponding level of low-nitrogen tolerance of 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 encoding a polypeptide, wherein the HMM bit score of the amino acid sequence of said polypeptide is greater than about 20, said HMM based on the amino acid sequences depicted in one of  FIGS. 1-57 , and wherein said plant cell has a difference in the level of low-nitrogen tolerance as compared to the corresponding level of low-nitrogen tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         11 . 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:3, SEQ ID NO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ ID NO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQ ID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510, SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ ID NO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQ ID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853, SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ ID NO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112, SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ ID NO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302, SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ ID NO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525, SEQ ID NO:1537, SEQ ID NO:1554, and SEQ ID NO:1577, wherein a tissue of a plant produced from said plant cell has a difference in the level of low-nitrogen tolerance as compared to the corresponding level of low-nitrogen tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         12 . 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 NO:1, SEQ ID NO:48, SEQ ID NO:76, SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:151, SEQ ID NO:165, SEQ ID NO:175, SEQ ID NO:185, SEQ ID NO:207, SEQ ID NO:217, SEQ ID NO:233, SEQ ID NO:245, SEQ ID NO:299, SEQ ID NO:331, SEQ ID NO:367, SEQ ID NO:509, SEQ ID NO:532, SEQ ID NO:555, SEQ ID NO:557, SEQ ID NO:592, SEQ ID NO:612, SEQ ID NO:645, SEQ ID NO:686, SEQ ID NO:729, SEQ ID NO:745, SEQ ID NO:768, SEQ ID NO:791, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:852, SEQ ID NO:854, SEQ ID NO:890, SEQ ID NO:916, SEQ ID NO:943, SEQ ID NO:975, SEQ ID NO:981, SEQ ID NO:1053, SEQ ID NO:1098, SEQ ID NO:1111, SEQ ID NO:1115, SEQ ID NO:1156, SEQ ID NO:1158, SEQ ID NO:1165, SEQ ID NO:1184, SEQ ID NO:1193, SEQ ID NO:1209, SEQ ID NO:1273, SEQ ID NO:1301, SEQ ID NO:1341, SEQ ID NO:1384, SEQ ID NO:1408, SEQ ID NO:1427, SEQ ID NO:1462, SEQ ID NO:1490, SEQ ID NO:1509, SEQ ID NO:1524, SEQ ID NO:1536, SEQ ID NO:1553, and SEQ ID NO:1576, or a fragment thereof, wherein a tissue of a plant produced from said plant cell has a difference in the level of low-nitrogen tolerance as compared to the corresponding level of low-nitrogen tolerance of a control plant that does not comprise said nucleic acid. 
     
     
         13 . A transgenic plant comprising the plant cell of  claim 10  or  11 . 
     
     
         14 . The transgenic plant of  claim 13 , 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),  Poplus balsamifera  (poplar),  Zea mays  (corn),  Glycine max  (soybean),  Brassica  napes (canola),  Triticum aestivum  (wheat),  Gossypium hirsutum  (cotton),  Oryza sativa  (rice),  Helianthus annuus  (sunflower),  Medicago saliva  (alfalfa),  Beta vulgaris  (sugarbeet), or  Pennisetum glaucum  (pearl millet). 
     
     
         15 . A transgenic plant of  claim 13 , wherein said polypeptide is any one of the polypeptides in the sequence listing. 
     
     
         16 . A product comprising plant tissue from a transgenic plant according to  claims 14 . 
     
     
         17 . An isolated nucleic acid comprising a nucleotide sequence having 95% or greater sequence identity to the nucleotide sequence set forth in SEQ ID NOs: 5, 7, 37, 50, 52, 54, 66, 79, 86, 91, 103, 105, 107, 109, 112, 114, 124, 127, 136, 140, 143, 153, 155, 157, 159, 161, 163, 167, 169, 171, 175, 176, 178, 187, 189, 202, 215, 219, 221, 226, 228, 235, 237, 240, 247, 250, 252, 258, 261, 269, 273, 280, 301, 303, 305, 307, 311, 313, 315, 317, 330, 331, 333, 379, 387, 389, 397, 429, 431, 442, 457, 462, 466, 470, 472, 480, 486, 512, 514, 516, 518, 520, 522, 524, 526, 528, 534, 537, 540, 551, 557, 568, 570, 574, 582, 587, 594, 596, 598, 600, 602, 604, 606, 608, 614, 616, 621, 623, 625, 627, 629, 631, 633, 635, 637, 639, 641, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 667, 669, 673, 677, 688, 690, 692, 698, 700, 702, 704, 709, 711, 713, 715, 717, 719, 731, 734, 736, 739, 743, 747, 749, 756, 759, 780, 795, 797, 811, 829, 831, 835, 841, 843, 852, 854, 857, 859, 861, 863, 867, 869, 871, 875, 879, 881, 883, 890, 892, 897, 899, 918, 922, 924, 930, 934, 936, 938, 941, 945, 949, 951, 955, 959, 961, 963, 965, 975, 979, 981, 983, 994, 1002, 1006, 1010, 1014, 1017, 1020, 1022, 1024, 1038, 1042, 1056, 1060, 1062, 1064, 1066, 1073, 1079, 1100, 1107, 1117, 1119, 1121, 1127, 1130, 1137, 1160, 1165, 1168, 1170, 1172, 1176, 1178, 1181, 1186, 1195, 1197, 1199, 1201, 1212, 1214, 1217, 1227, 1231, 1250, 1252, 1254, 1256, 1258, 1260, 1262, 1275, 1277, 1279, 1283, 1286, 1288, 1290, 1292, 1304, 1306, 1308, 1310, 1332, 1343, 1353, 1386, 1388, 1408, 1410, 1412, 1414, 1416, 1420, 1422, 1427, 1429, 1431, 1433, 1435, 1438, 1441, 1443, 1449, 1451, 1462, 1464, 1466, 1468, 1470, 1472, 1478, 1489, 1490, 1492, 1494, 1498, 1500, 1509, 1511, 1513, 1519, 1524, 1526, 1528, 1536, 1538, 1542, 1544, 1546, 1549, 1553, 1556, 1558, 1560, 1562, 1564, 1568, 1570, 1576, 1579, 1581, 1583, 1585, 1587, 1593, 1600, 1606, 1610, 1614, 1620, 1630, 1632, 1640, 1642, 1644, 1646, 1654. 
     
     
         18 . 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: 6, 8, 38, 51, 53, 55, 67, 80, 87, 92, 100, 104, 106, 108, 110, 113, 115, 125, 128, 137, 141, 144, 154, 156, 158, 160, 162, 164, 168, 170, 172, 177, 179, 188, 190, 203, 216, 220, 222, 227, 229, 236, 238, 241, 248, 251, 253, 259, 262, 270, 274, 279, 281, 302, 304, 306, 308, 312, 314, 316, 318, 332, 334, 338, 368, 380, 384, 388, 390, 398, 430, 432, 443, 458, 463, 467, 471, 473, 481, 487, 513, 515, 517, 521, 523, 525, 527, 529, 535, 538, 541, 552, 558, 569, 571, 575, 583, 588, 595, 597, 599, 601, 603, 605, 607, 609, 615, 617, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 648, 650, 652, 654, 656, 658, 660, 662, 664, 666, 668, 670, 674, 678, 687, 689, 691, 693, 699, 701, 703, 705, 710, 712, 714, 716, 718, 720, 732, 735, 737, 740, 744, 748, 750, 760, 769, 781, 796, 798, 812, 830, 832, 836, 842, 844, 853, 855, 858, 860, 862, 864, 868, 870, 876, 880, 882, 884, 891, 893, 898, 900, 919, 923, 925, 931, 935, 937, 939, 942, 946, 950, 952, 956, 960, 962, 964, 966, 976, 980, 982, 984, 995, 1003, 1007, 1011, 1015, 1018, 1021, 1023, 1025, 1039, 1043, 1057, 1061, 1063, 1065, 1067, 1074, 1080, 1099, 1101, 1108, 1116, 1118, 1120, 1122, 1128, 1131, 1138, 1161, 1166, 1169, 1171, 1173, 1175, 1177, 1179, 1182, 1187, 1196, 1198, 1200, 1202, 1203, 1213, 1215, 1218, 1228, 1232, 1251, 1253, 1255, 1257, 1259, 1261, 1263, 1276, 1278, 1280, 1287, 1289, 1291, 1293, 1305, 1307, 1309, 1311, 1333, 1344, 1354, 1366, 1387, 1389, 1409, 1411, 1413, 1415, 1417, 1421, 1428, 1430, 1432, 1434, 1436, 1437, 1439, 1442, 1450, 1452, 1463, 1465, 1467, 1469, 1471, 1473, 1479, 1480, 1486, 1491, 1493, 1495, 1499, 1501, 1510, 1512, 1514, 1520, 1525, 1527, 1529, 1537, 1539, 1543, 1545, 1547, 1550, 1554, 1557, 1559, 1561, 1563, 1565, 1569, 1571, 1577, 1580, 1582, 1584, 1586, 1588, 1594, 1601, 1607, 1611, 1615, 1621, 1627, 1631, 1633, 1635, 1643, 1645. 
     
     
         19 . 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. 1-57 , SEQ ID NO:556, SEQ ID NO:853, and SEQ ID NO:1157 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.   
     
     
         20 . A method of identifying whether a polymorphism is associated with variation in a trait, said method comprising:
 a) screening a population of plants to determine whether one or more genetic polymorphisms in said population of plants is associated with the locus for a polypeptide selected from the group consisting of the polypeptides depicted in  FIGS. 1-57 ; SEQ ID NO: 556, SEQ ID NO: 853, and SEQ ID NO: 1157 and functional homologs thereof;   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;   c) selecting from said population of plants a sub-population of plants that possess said one or more genetic polymorphisms associated with said trait; and   d) crossing one or more plants from said sub-population of plants.   
     
     
         21 . The method according to  claim 20 , further comprising breeding said sub-population of plants to produce a plant line which comprises said polymorphism. 
     
     
         22 . 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. 1-57 , SEQ ID NO:556, SEQ ID NO:853, and SEQ ID NO:1157 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.   
     
     
         23 . The method of  claim 19  or  20 , wherein said trait is the level of low-nitrogen tolerance. 
     
     
         24 . The method of  claim 19  or  20 , wherein said population is a population of switchgrass, sorghum, sugar cane, or miscanthus plants.

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