Polynucleotides and polypeptides in plants

Abstract

The invention relates to plant transcription factor polypeptides, polynucleotides that encode them, homologs from a variety of plant species, and methods of using the polynucleotides and polypeptides to produce transgenic plants having advantageous properties compared to a reference plant. Sequence information related to these polynucleotides and polypeptides can also be used in bioinformatic search methods and is also disclosed.

1 . A transgenic plant comprising a recombinant polynucleotide having a polynucleotide sequence, or a complementary polynucleotide sequence thereof, selected from the group consisting of:
 (a) a nucleotide sequence encoding a polypeptide that initiates transcription, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 2N, wherein N=1-480; SEQ ID NO: 2N−1, where N=857-970; SEQ ID NO: 989, 990, 991, 1001, 1002, 1012, 1018, 1021, 1022, 1025, 1027, 1028, 1029, 1034, 1050, 1051, 1072, 1073, 1074, 1075, 1076, 1091, 1092, 1093, 1094, 1095, 1109, 1110, 1111, 1112, 1150, 1165, 1166, 1167, 1168, 1169, 1189, 1190, 1191, 1197, 1198, 1199, 1213, 1214, 1215, 1216, 1226, 1227, 1233, 1239, 1246, 1247, 1258, 1259, 1269, 1307, 1308, 1309, 1310, 1323, 1329, 1330, 1331, 1332, 1338, 1339, 1340, 1361, 1362, 1373, 1374, 1375, 1384, 1389, 1390, 1391, 1396, 1411, 1412, 1413, 1414, 1424, 1435, 1436, 1437, 1448, 1456, 1457, 1458, 1459, 1460, 1472, 1483, 1484, 1500, 1508, 1510, 1511, 1520, 1538, 1539, 1540, 1541, 1542, 1543, 1563, 1564, 1565, 1566, 1567, 1568, 1569, 1582, 1583, 1594, 1611, 1612, 1618, 1619, 1620, 1626, 1627, 1635, 1636, 1640, 1641, 1655, 1656, 1657, 1658, 1672, 1673, 1680, 1682, 1686, 1687, 1688, 1689, 1696, 1702, 1703, 1945, 1947, 1949, 1951, 1953, 1955, 1957, 1959, 1961, 1963, 1965, 1967, 1969, 1971, and 1973;   (b) a nucleotide sequence encoding a polypeptide that initiates transcription, wherein said nucleotide sequence is selected from the group consisting of SEQ ID NO: 2N−1, where N=1-480; SEQ ID NO: 2N, where N=856-969; SEQ ID NO: 961, 962, 963, 964, 965, 967, 968, 969, 970, 971, 972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983, 984, 985, 986, 987, 988, 992, 993, 994, 995, 996, 997, 998, 999, 1000, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011, 1013, 1014, 1015, 1016, 1017, 1019, 1020, 1023, 1024, 1026, 1030, 1031, 1032, 1033, 1035, 1036, 1037, 1038, 1039, 1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049, 1052, 1053, 1054, 1055, 1056, 1057, 1058, 1059, 1060, 1061, 1062, 1063, 1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1077, 1078, 1079, 1080, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1096, 1097, 1098, 1099, 1100, 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1120, 1121, 1122, 1123, 1124, 1125, 1126, 1127, 1128, 1129, 1130, 1131, 1132, 1133, 1134, 1135, 1136, 1137, 1138, 1139, 1140, 1141, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1151, 1152, 1153, 1154, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1164, 1170, 1171, 1172, 1173, 1174, 1175, 1176, 1177, 1178, 1179, 1180, 1181, 1182, 1183, 1184, 1185, 1186, 1187, 1188, 1192, 1193, 1194, 1195, 1196, 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210, 1211, 1212, 1217, 1218, 1219, 1220, 1221, 1222, 1223, 1224, 1225, 1228, 1229, 1230, 1231, 1232, 1234, 1235, 1236, 1237, 1238, 1240, 1241, 1242, 1243, 1244, 1245, 1248, 1249, 1250, 1251, 1252, 1253, 1254, 1255, 1256, 1257, 1260, 1261, 1262, 1263, 1264, 1265, 1266, 1267, 1268, 1270, 1271, 1272, 1273, 1274, 1275, 1276, 1277, 1278, 1279, 1280, 1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1289, 1290, 1291, 1292, 1293, 1294, 1295, 1296, 1297, 1298, 1299, 1300, 1301, 1302, 1303, 1304, 1305, 1306, 1311, 1312, 1313, 1314, 1315, 1316, 1317, 1318, 1319, 1320, 1321, 1322, 1324, 1325, 1326, 1327, 1328, 1333, 1334, 1335, 1336, 1337, 1341, 1342, 1343, 1344, 1345, 1346, 1347, 1348, 1349, 1350, 1351, 1352, 1353, 1354, 1355, 1356, 1357, 1358, 1359, 1360, 1363, 1364, 1365, 1366, 1367, 1368, 1369, 1370, 1371, 1372, 1376, 1377, 1378, 1379, 1380, 1381, 1382, 1383, 1385, 1386, 1387, 1388, 1392, 1393, 1394, 1395, 1397, 1398, 1399, 1400, 1401, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 1410, 1415, 1416, 1417, 1418, 1419, 1420, 1421, 1422, 1423, 1425, 1426, 1427, 1428, 1429, 1430, 1431, 1432, 1433, 1434, 1438, 1439, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1449, 1450, 1451, 1452, 1453, 1454, 1455, 1461, 1462, 1463, 1464, 1465, 1466, 1467, 1468, 1469, 1470, 1471, 1473, 1474, 1475, 1476, 1477, 1478, 1479, 1480, 1481, 1482, 1485, 1486, 1487, 1488, 1489, 1490, 1491, 1492, 1493, 1494, 1495, 1496, 1497, 1498, 1499, 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1509, 1512, 1513, 1514, 1515, 1516, 1517, 1518, 1519, 1521, 1522, 1523, 1524, 1525, 1526, 1527, 1528, 1529, 1530, 1531, 1532, 1533, 1534, 1535, 1536, 1537, 1544, 1545, 1546, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1555, 1556, 1557, 1558, 1559, 1560, 1561, 1562, 1570, 1571, 1572, 1573, 1574, 1575, 1576, 1577, 1578, 1579, 1580, 1581, 1584, 1585, 1586, 1587, 1588, 1589, 1590, 1591, 1592, 1593, 1595, 1596, 1597, 1598, 1599, 1600, 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1608, 1609, 1610, 1613, 1614, 1615, 1616, 1617, 1621, 1622, 1623, 1624, 1625, 1628, 1629, 1630, 1631, 1632, 1633, 1634, 1637, 1638, 1639, 1642, 1643, 1644, 1645, 1646, 1647, 1648, 1649, 1650, 1651, 1652, 1653, 1654, 1659, 1660, 1661, 1662, 1663, 1664, 1665, 1666, 1667, 1668, 1669, 1670, 1671, 1674, 1675, 1676, 1677, 1678, 1679, 1681, 1683, 1684, 1685, 1690, 1691, 1692, 1693, 1694, 1695, 1697, 1698, 1699, 1700, 1701, 1704, 1705, 1706, 1707, 1708, 1709, 1710, 1711, 1944, 1946, 1948, 1950, 1952, 1954, 1956, 1958, 1960, 1962, 1964, 1966, 1968, 1970, and 1972;   (c) a nucleotide sequence encoding the polypeptide sequence of (a) with conservative substitutions as defined in Table 2;   (d) a variant of the nucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b);   (e) an orthologous sequence of the nucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b);   (f) a paralogous sequence of the nucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b);   (g) a nucleotide sequence encoding a polypeptide comprising a conserved domain that exhibits at least 80% sequence homology with the conserved domain of the polypeptide of (a); and wherein said conserved domain of (a) is bounded by amino acid residue coordinates according to Tables 5a and 5b, and   (h) a nucleic acid sequence that hybridizes to the polynucleotide of (a) or (b) under stringent conditions.   
     
     
         2 . (canceled) 
     
     
         3 . The transgenic plant of  claim 1 , wherein:
 the transgenic plant possesses an altered trait as compared to a non-transformed plant; or the transgenic plant exhibits an altered phenotype as compared to said non-transformed plant;   or the transgenic plant expresses an altered level of one or more genes associated with a plant trait as compared to said non-transformed plant;   wherein said non-transformed plant does not overexpress the recombinant polynucleotide.   
     
     
         4 - 7 . (canceled) 
     
     
         8 . The transgenic plant of  claim 3 , wherein the plant is selected from the group consisting of: soybean, wheat, corn, potato, cotton, rice, oilseed rape, sunflower, alfalfa, clover, sugarcane, turf, banana, blackberry, blueberry, strawberry, raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, pumpkin, spinach, squash, sweet corn, tobacco, tomato, watermelon, mint and other labiates, rosaceous fruits, and vegetable brassicas. 
     
     
         9 - 22 . (canceled) 
     
     
         23 . The transgenic plant of  claim 3 , wherein said altered trait is altered hormone sensitivity. 
     
     
         24 . The transgenic plant of  claim 23 , wherein said altered hormone sensitivity is:
 (i) reduced sensitivity to abscisic acid and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 721, 941, and polynucleotide variants thereof; or   (ii) an altered response to ethylene and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 507, 713, 741, and polynucleotide variants thereof.   
     
     
         25 . (canceled) 
     
     
         26 . The transgenic plant of  claim 3 , wherein said altered trait is altered susceptibility to disease. 
     
     
         27 . The transgenic plant of  claim 26 , wherein said altered susceptibility to disease is:
 (i) altered susceptibility to  Botrytis  and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 37, 117, 171, 191, 575, 587, 793, and polynucleotide variants thereof;   (ii) altered susceptibility to  Fusarium  and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 97, 345, 595, and polynucleotide variants thereof;   (iii) altered susceptibility to  Erysiphe  and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 21, 37, 159, 241, 261, 345, 389, 401, 575, 581, 587, 695, 799, and polynucleotide variants thereof;   (iv) altered susceptibility to  Pseudomonas syringae  and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 267, 337, 345, and polynucleotide variants thereof; or   (v) altered susceptibility to  Sclerotinia  and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 37, 303, 539, 553, and polynucleotide variants thereof.   
     
     
         28 - 31 . (canceled) 
     
     
         32 . The transgenic plant of  claim 3 , wherein said altered trait is altered sugar sensing and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 33, 41, 49, 117, 137, 163, 179, 193, 217, 343, 369, 463, 529, 531, 579, 605, 615, 659, 719, 831, 861, 911, 939, and polynucleotide variants thereof. 
     
     
         33 . The transgenic plant of  claim 32 , wherein said altered sugar sensing:
 (i) is increased tolerance to sugars and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 137, 529, 531, 579, 605, 911, 939, and polynucleotide variants thereof;   (ii) confers improved seed germination; or   (iii) confers improved seedling vigor.   
     
     
         34 - 35 . (canceled) 
     
     
         36 . The transgenic plant of  claim 3 , wherein said altered trait is:
 (i) early flowering and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 57, 59, 61, 69, 87, 89, 91, 119, 143, 181, 249, 301, 387, 391, 405, 539, 575, 685, 787, 819, 867, 921, 937, 941, 943, 945, 947, 951, 957, 1952, 1954, 1956, 1958, 1960, 1962, 1964, 1966, 1968, 1970, 1972, and polynucleotide variants thereof;   (ii) late flowering and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 11, 69, 101, 109, 127, 157, 173, 237, 275, 307, 361, 375, 389, 463, 487, 489, 497, 503, 567, 585, 603, 615; 639, 657, 699, 723, 745, 859, 887, 893, 901, 911, 1944, 1946, 1948, 1950, 1970, 1972, and polynucleotide variants thereof;   (iii) an extended period of flowering and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 949 and polynucleotide variants thereof;   (iv) altered flower structure and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 55, 95, 295, 357, 381, 399, 419, 483, 449, 525, 581, 647, 717, 725, 741, 799, 827, 849, 883, 891, 913, 925, 929, 949, polynucleotide variants thereof;   (v) an inflorescence architectural change and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 59, 245, 381, 575, 805, 883, 901, 913, and polynucleotide variants thereof;   (vi) a change in stem bifurcations and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 249 and polynucleotide variants thereof;   (vii) a lack of a shoot meristem and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 899 and polynucleotide variants thereof;   (viii) reduced meristem cell differentiation and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 919 and polynucleotide variants thereof;   (ix) altered phyllotaxy and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 419 and polynucleotide variants thereof;   (x) an altered branching pattern and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 283, 913, and polynucleotide variants thereof;   (xi) reduced apical dominance and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 357, 483, 793, 807, 929, and polynucleotide variants thereof;   (xii) reduced trichome density or lack of trichomes and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 31, 123, 139, 141, 457, 467, 855, 939, 959, and polynucleotide variants thereof;   (xiii) ectopic trichome development or altered trichome development and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 169 and polynucleotide variants thereof;   (xiv) an increase in trichome number and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 415 and polynucleotide variants thereof;   (xv) altered stem morphology and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 283, 497, and polynucleotide variants thereof;   (xvi) increased root growth and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 13, 905, and polynucleotide variants thereof;   (xvii) increased root hairs and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 139, 141, 467, 939, 959, and polynucleotide variants thereof;   (xviii) altered seed development and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 649 and polynucleotide variants thereof;   (xix) altered cell proliferation or cell differentiation and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 919 and polynucleotide variants thereof;   (xx) slow growth and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 285, 491, 713, 859, 901, and polynucleotide variants thereof;   (xxi) premature senescence and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 417, 737, and polynucleotide variants thereof;   (xxii) delayed senescence and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 173, 375, 585, 697, and polynucleotide variants thereof;   (xxiii) lethality when overexpressed and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 239, 379, 583, 727, 817, and polynucleotide variants thereof;   (xxiv) increased necrosis and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 29 and polynucleotide variants thereof;   (xxv) an increase in seedling or plant size and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 53, 723, 829, 887, 893, and polynucleotide variants thereof;   (xxvi) decreased plant size and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 1, 5, 25, 29, 35, 89, 103, 185, 203, 245, 285, 417, 447, 449, 489, 507, 557, 573, 581, 591, 627, 647, 655, 657, 673, 677, 701, 717, 725, 753, 775, 799, 801, 807, 809, 825, 827, 831, 837, 841, 843, 849, 855, 857, 869, 901, 921, 925, and polynucleotide variants thereof.   (xxvii) an increase in root anthocyanins and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 435 and polynucleotide variants thereof;   (xxviii) an increase in plant anthocyanins and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 435, 905, and polynucleotide variants thereof; or   (xxix) an alteration in light response or shade avoidance, and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 235, 713, 841, and polynucleotide variants thereof.   
     
     
         37 - 61 . (canceled) 
     
     
         62 . The transgenic plant of  claim 3 , wherein said altered trait is a change in leaf morphology. 
     
     
         63 . The transgenic plant of  claim 62 , wherein said change in leaf morphology is:
 (i) dark green leaves and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 245, 285, 615, 627, 647, 737, 801, 843, 851, 857, 913, and polynucleotide variants thereof;   (ii) altered leaf shape and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 39, 137, 271, 291, 407, 449, 487, 603, 605, 619, 627, 647, 687, 717, 723, 725, 803, 911, 929, and polynucleotide variants thereof;   (iii) increased altered leaf development, and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 929, and polynucleotide variants thereof;   (iv) increased leaf size and mass, and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 283, 805, 893, and polynucleotide variants thereof;   (v) glossy leaves and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 643, 801, and polynucleotide variants thereof; or   (vi) leaf cell expansion and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 331 and polynucleotide variants thereof.   
     
     
         64 - 68 . (canceled) 
     
     
         69 . The transgenic plant of  claim 3 , wherein said altered trait is a change in seed morphology. 
     
     
         70 . The transgenic plant of  claim 69 , wherein said change in seed morphology is:
 (i) altered seed coloration and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 67, 435, 443, and polynucleotide variants thereof;   (ii) increased seed size and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 115, 385, 793, and polynucleotide variants thereof;   (iii) decreased seed size and said nucleotide sequence is SEQ ID NO: 749 and polynucleotide variants thereof; or   (iv) altered seed shape and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 713, 749, and polynucleotide variants thereof.   
     
     
         71 - 73 . (canceled) 
     
     
         74 . The transgenic plant of  claim 3 , wherein said altered trait is a change in leaf biochemistry. 
     
     
         75 . The transgenic plant of  claim 74 , wherein said change in leaf biochemistry is:
 (i) increased leaf wax and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 643, 801, and polynucleotide variants thereof;   (ii) an alteration in leaf prenyl lipid content and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 127, 203, 653, 739, 845, 853, and polynucleotide variants thereof;   (iii) increased leaf insoluble sugars and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 121, 159, 165, 199, 215, 271, 277, 337, 393, 521, 581, 825, and polynucleotide variants thereof;   (iv) decreased leaf insoluble sugars and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 215, 271, 671, and polynucleotide variants thereof;   (v) increased leaf anthocyanins and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 435, and polynucleotide variants thereof;   (vi) an alteration of leaf fatty acid content and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 127, 151, 473, 799, 861, and polynucleotide variants thereof; or   (vii) an alteration of leaf glucosinolate content and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 91, 465, 721, 763, 841, and polynucleotide variants thereof.   
     
     
         76 - 81 . (canceled) 
     
     
         82 . The transgenic plant of  claim 3 , wherein said altered trait is a change in seed biochemistry. 
     
     
         83 . The transgenic plant of  claim 82 , wherein said change in seed biochemistry is:
 (i) an increase in seed oil content and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 71, 147, 151, 209, 287, 291, 359, 387, 393, 483, 565, 633, 759, 763, and polynucleotide variants thereof;   (ii) a decrease in seed oil content and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 87, 101, 111, 135, 163, 435, 443, 473, 483, 521, 613, 843, 941, and polynucleotide variants thereof.   (iii) an increase in seed fatty acid content and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 523, 571, 581, 631, 637, 877, 881, and polynucleotide variants thereof;   (iv) a decrease in seed fatty acid content and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 519, 541, 631, 653, 881, and polynucleotide variants thereof;   (v) an increase in seed protein content and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 111, 135, 141, 163, 407, 409, 435, 443, 473, 483, 575, 613, 695, 843, 891, 941, and polynucleotide variants thereof;   (vi) a decrease in seed protein content and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 147, 151, 267, 287, 291, 483, 927, and polynucleotide variants thereof;   (vii) an alteration in seed prenyl lipid content and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 127, 473, 497, 589, 699, and polynucleotide variants thereof;   (viii) an increase in seed sterols and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 23 and polynucleotide variants thereof; or   (ix) an up-regulation of genes involved in secondary metabolism, and said nucleotide sequence is selected from the group consisting of SEQ ID NO: 147 and polynucleotide variants thereof.   
     
     
         84 - 100 . (canceled) 
     
     
         101 . A method for producing a modified plant having a modified trait, the method comprising:
 (a) selecting a polynucleotide that encodes a polypeptide, wherein said polynucleotide has a sequence, or a complementary sequence thereof, selected from the group consisting of:
 (i) a nucleotide sequence encoding a polypeptide that initiates transcription, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 2N, wherein N=1-480; SEQ ID NO: 2N−1, where N=857-970; SEQ ID NO: 989, 990, 991, 1001, 1002, 1012, 1018, 1021, 1022, 1025, 1027, 1028, 1029, 1034, 1050, 1051, 1072, 1073, 1074, 1075, 1076, 1091, 1092, 1093, 1094, 1095, 1109, 1110, 1111, 1112, 1150, 1165, 1166, 1167, 1168, 1169, 1189, 1190, 1191, 1197, 1198, 1199, 1213, 1214, 1215, 1216, 1226, 1227, 1233, 1239, 1246, 1247, 1258, 1259, 1269, 1307, 1308, 1309, 1310, 1323, 1329, 1330, 1331, 1332, 1338, 1339, 1340, 1361, 1362, 1373, 1424, 1435, 1436, 1437, 1510, 1511, 1520, 1538, 1569, 1582, 1583, 1594, 1374, 1375, 1384, 1389, 1448, 1456, 1457, 1458, 1539, 1540, 1541, 1542, 1611, 1612, 1618, 1619, 1390, 1391, 1396, 1411, 1412, 1459, 1460, 1472, 1483, 1484, 1543, 1563, 1564, 1565, 1566, 1620, 1626, 1627, 1635, 1636, 1413, 1500, 1567, 1640, 1414, 1508, 1568, 1641, 1655, 1656, 1657, 1658, 1672, 1673, 1680, 1682, 1686, 1687, 1688, 1689, 1696, 1702, 1703, 1945, 1947, 1949, 1951, 1953, 1955, 1957, 1959, 1961, 1963, 1965, 1967, 1969, 1971, and 1973; 
 (ii) a nucleotide sequence encoding a polypeptide that initiates transcription, wherein said nucleotide sequence is selected from the group consisting of SEQ ID NO: 2N−1, where N=1-480; SEQ ID NO: 2N, where N=856-969; SEQ ID NO: 961, 962, 963, 964, 965, 967, 968, 969, 970, 971, 972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983, 984, 985, 986, 987, 988, 992, 993, 994, 995, 996, 997, 998, 999, 1000, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011, 1013, 1014, 1015, 1016, 1017, 1019, 1020, 1023, 1024, 1026, 1030, 1031, 1032, 1033, 1035, 1036, 1037, 1038, 1039, 1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049, 1052, 1053, 1054, 1055, 1056, 1057, 1058, 1059, 1060, 1061, 1062, 1063, 1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1077, 1078, 1079, 1080, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1096, 1097, 1098, 1099, 1100, 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1120, 1121, 1122, 1123, 1124, 1125, 1126, 1127, 1128, 1129, 1130, 1131, 1132, 1133, 1134, 1135, 1136, 1137, 1138, 1139, 1140, 1141, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1151, 1152, 1153, 1154, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1164, 1170, 1171, 1172, 1173, 1174, 1175, 1176, 1177, 1178, 1179, 1180, 1181, 1182, 1183, 1184, 1185, 1186, 1187, 1188, 1192, 1193, 1194, 1195, 1196, 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210, 1211, 1212, 1217, 1218, 1219, 1220, 1221, 1222, 1223, 1224, 1225, 1228, 1229, 1230, 1231, 1232, 1234, 1235, 1236, 1237, 1238, 1240, 1241, 1242, 1243, 1244, 1245, 1248, 1249, 1250, 1251, 1252, 1253, 1254, 1255, 1256, 1257, 1260, 1261, 1262, 1263, 1264, 1265, 1266, 1267, 1268, 1270, 1271, 1272, 1273, 1274, 1275, 1276, 1277, 1278, 1279, 1280, 1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1289, 1290, 1291, 1292, 1293, 1294, 1295, 1296, 1297, 1298, 1299, 1300, 1301, 1302, 1303, 1304, 1305, 1306, 1311, 1312, 1313, 1314, 1315, 1316, 1317, 1318, 1319, 1320, 1321, 1322, 1324, 1325, 1326, 1327, 1328, 1333, 1334, 1335, 1336, 1337, 1341, 1342, 1343, 1344, 1345, 1346, 1347, 1348, 1349, 1350, 1351, 1352, 1353, 1354, 1355, 1356, 1357, 1358, 1359, 1360, 1363, 1364, 1365, 1366, 1367, 1368, 1369, 1370, 1371, 1372, 1376, 1377, 1378, 1379, 1380, 1381, 1382, 1383, 1385, 1386, 1387, 1388, 1392, 1393, 1394, 1395, 1397, 1398, 1399, 1400, 1401, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 1410, 1415, 1416, 1417, 1418, 1419, 1420, 1421, 1422, 1423, 1425, 1426, 1427, 1428, 1429, 1430, 1431, 1432, 1433, 1434, 1438, 1439, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1449, 1450, 1451, 1452, 1453, 1454, 1455, 1461, 1462, 1463, 1464, 1465, 1466, 1467, 1468, 1469, 1470, 1471, 1473, 1474, 1475, 1476, 1477, 1478, 1479, 1480, 1481, 1482, 1485, 1486, 1487, 1488, 1489, 1490, 1491, 1492, 1493, 1494, 1495, 1496, 1497, 1498, 1499, 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1509, 1512, 1513, 1514, 1515, 1516, 1517, 1518, 1519, 1521, 1522, 1523, 1524, 1525, 1526, 1527, 1528, 1529, 1530, 1531, 1532, 1533, 1534, 1535, 1536, 1537, 1544, 1545, 1546, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1555, 1556, 1557, 1558, 1559, 1560, 1561, 1562, 1570, 1571, 1572, 1573, 1574, 1575, 1576, 1577, 1578, 1579, 1580, 1581, 1584, 1585, 1586, 1587, 1588, 1589, 1590, 1591, 1592, 1593, 1595, 1596, 1597, 1598, 1599, 1600, 1601, 1602, 1603, 1604, 1605, 1606, 1607, 1608, 1609, 1610, 1613, 1614, 1615, 1616, 1617, 1621, 1622, 1623, 1624, 1625, 1628, 1629, 1630, 1631, 1632, 1633, 1634, 1637, 1638, 1639, 1642, 1643, 1644, 1645, 1646, 1647, 1648, 1649, 1650, 1651, 1652, 1653, 1654, 1659, 1660, 1661, 1662, 1663, 1664, 1665, 1666, 1667, 1668, 1669, 1670, 1671, 1674, 1675, 1676, 1677, 1678, 1679, 1681, 1683, 1684, 1685, 1690, 1691, 1692, 1693, 1694, 1695, 1697, 1698, 1699, 1700, 1701, 1704, 1705, 1706, 1707, 1708, 1709, 1710, 1711, 1944, 1946, 1948, 1950, 1952, 1954, 1956, 1958, 1960, 1962, 1964, 1966, 1968, 1970, and 1972; 
 (iii) a nucleotide sequence encoding the polypeptide sequence of (i) with conservative substitutions as defined in Table 2; 
 (iv) a variant of the nucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (i) or (ii); 
 (v) an orthologous sequence of the nucleotide sequences of (i) or (ii), which is at least 80% identical to a sequence of (i) or (ii); 
 (vi) a paralogous sequence of the nucleotide sequences of (i) or (ii), which is at least 80% identical to a sequence of (i) or (ii); 
 (vii) a nucleotide sequence encoding a polypeptide comprising a conserved domain that exhibits at least 80% sequence homology with the conserved domain of the polypeptide of (i); and wherein said conserved domain of (i) is bounded by amino acid residue coordinates according to Tables 5a and 5b, and 
 (viii) a nucleic acid sequence that hybridizes to the polynucleotide of (i) or (ii) under stringent conditions; 
   (b) inserting the polynucleotide into an expression cassette;   (c) introducing the expression cassette into a plant or a cell of a plant to overexpress the polypeptide, thereby producing said modified plant; and   (d) selecting said modified plant having said modified trait.   
     
     
         102 - 107 . (canceled) 
     
     
         108 . The method of  claim 101 , wherein said altered trait is a trait selected from the group consisting of enhanced tolerance to abiotic stress, enhanced tolerance to glyphosate, altered hormone sensitivity, altered disease resistance, altered sugar sensing, earlier flowering, later flowering, altered flower structure, altered inflorescence architecture, altered shoot meristem development, altered branching pattern, reduced apical dominance, altered trichome density, altered stem morphology, increased root growth, increased root hairs, altered seed development, altered seed germination, altered cell differentiation, altered cell proliferation, rapid plant development, premature senescence, lethality when overexpressed, increased necrosis, increased plant size, larger seedlings, more compact plants, dark green leaves, leaf shape, light green leaves, variegation, glossy leaves, seed coloration, increased seed size, decreased seed size, altered seed shape, increased leaf wax, altered leaf prenyl lipid content, increased leaf insoluble sugars, increased leaf anthocyanins, altered leaf fatty acid content, increased seed oil, decreased seed oil, altered seed fatty acid content, increased seed protein, decreased seed protein, altered seed prenyl lipid content, increased seed anthocyanins, increased root anthocyanins, altered light response, altered shade avoidance, or increased plant anthocyanin level. 
     
     
         109 - 111 . (canceled) 
     
     
         112 . A method of generating a transgenic plant expressing SEQ ID NO: 66 comprising:
 (a) providing a recombinant construct encoding a polypeptide that comprises a conserved domain that is at least 85% identical to amino acids 1-57 of SEQ ID NO: 66, wherein the polypeptide is at least 60% identical over the entire length of SEQ ID NO: 66; and   (b) introducing the recombinant construct into a target plant to produce the transgenic plant;   wherein when the polypeptide is over-expressed in the transgenic plant, the polypeptide confers an altered trait that is selected from the group consisting of greater tolerance to low nitrogen conditions, altered sensing of its carbon nitrogen balance, flowering earlier, and producing greater yield relative to a control plant.   
     
     
         113 . The method of  claim 112 , wherein said introducing comprises transforming said target plant. 
     
     
         114 . The method of  claim 112 , wherein said introducing comprises crossing a plant expressing SEQ ID NO: 66 with a plant lacking SEQ ID NO: 66. 
     
     
         115 . The method of  claim 112 , wherein:
 said progeny plant expresses SEQ ID NO: 66 mRNA that encodes a DNA-binding protein that binds to a DNA regulatory sequence and induces expression of a plant trait gene;   said mRNA is expressed at a level greater than a non-transformed plant; and   said progeny plant is characterized by a change in a plant trait compared to said non-transformed plant;   wherein said non-transformed plant does not comprise the recombinant polynucleotide.   
     
     
         116 . The method of  claim 112 , wherein the method further comprises the step of:
 (c) identifying the transgenic plant by selecting a transgenic plant that over-expresses the polypeptide or selecting a transgenic plant that has the altered trait relative to the control plant.   
     
     
         117 . The method of  claim 112 , wherein the polypeptide comprises a conserved domain that is at least 90% identical to amino acids 1-57 of SEQ ID NO: 66. 
     
     
         118 . The method of  claim 112 , wherein the polypeptide comprises a conserved domain that is at least 95% identical to amino acids 1-57 of SEQ ID NO: 66. 
     
     
         119 . The method of  claim 112 , wherein the recombinant polynucleotide further comprises a constitutive, inducible, or tissue-specific promoter that regulates expression of the polypeptide. 
     
     
         120 . The method of  claim 112 , wherein the transgenic plant is a corn (maize) plant.