Polynucleotides and polypeptides in plants

• US 20040045049A1
• Filed: 04/10/2003
• Published: 03/04/2004
• Est. Priority Date: 09/22/1998
• Status: Active Grant

• Current Assignee: Arnold N. Dubell, Bradley K. Sherman, Cai-Zhong Jiang, Guo-Liang Yu, Jacqueline E. Heard, James S. Keddie, James Zhang, Jose Luis Riechmann, Luc J. Adam, Marsha L. Pilgrim, Michael E. Fromm, Oliver Ratcliffe, Omaira Pineda, Pierre E. Broun, Raymond S. Samaha, Reuber T. Lynne, Robert A. Creelman, Roderick Kumimoto
• Original Assignee: Mendel Biotechnology, Inc. (KOCH Industries Incorporated)
• Inventors: Samaha, Raymond S., Reuber, T. Lynne, Yu, Guo-Liang, Jiang, Cai-Zhong, Zhang, James, Heard, Jacqueline E., Ratcliffe, Oliver, Sherman, Bradley K., Keddie, James S., Creelman, Robert A., Broun, Pierre E., Pineda, Omaira, Riechmann, Jose Luis, Adam, Luc J., Kumimoto, Roderick, Pilgrim, Marsha L., DuBell, Arnold N., Fromm, Michael E.
• Granted Patent: US 7,345,217 B2
• Time in Patent Office: Days
• US Class Current: 800/278
• CPC Class Codes: C07K 14/415 from plants
• CPC Class Codes: C12N 15/8214 Plastid transformation
• CPC Class Codes: C12N 15/8245 involving modified carbohydrate or sugar alcohol metabolism, e.g. starch biosynthesis
• CPC Class Codes: C12N 15/8247 involving modified lipid metabolism, e.g. seed oil composition
• CPC Class Codes: C12N 15/8249 involving ethylene biosynthesis, senescence or fruit development, e.g. modified tomato ripening, cut flower shelf-life
• CPC Class Codes: C12N 15/825 involving pigment biosynthesis
• CPC Class Codes: C12N 15/8251 Amino acid content, e.g. synthetic storage proteins, altering amino acid biosynthesis
• CPC Class Codes: C12N 15/8261 with agronomic (input) traits, e.g. crop yield
• CPC Class Codes: C12N 15/8262 involving plant development
• CPC Class Codes: C12N 15/8266 Abscission; Dehiscence; Senescence
• CPC Class Codes: C12N 15/8267 Seed dormancy, germination or sprouting
• CPC Class Codes: C12N 15/827 Flower development or morphology, e.g. flowering promoting factor [FPF]
• CPC Class Codes: C12N 15/8271 for stress resistance, e.g. heavy metal resistance
• CPC Class Codes: C12N 15/8273 for drought, cold, salt resistance
• CPC Class Codes: C12N 15/8275 Glyphosate
• CPC Class Codes: C12N 15/8279 for biotic stress resistance, pathogen resistance, disease resistance
• CPC Class Codes: C12N 15/8281 for bacterial resistance
• CPC Class Codes: C12N 15/8282 for fungal resistance
• CPC Class Codes: C12N 15/8287 for fertility modification, e.g. apomixis
• CPC Class Codes: C12N 15/8291 Hormone-influenced development
• CPC Class Codes: C12N 15/8293 : Abscisic acid [ABA]
• CPC Class Codes: Y02A 40/146 : Genetically Modified [GMO] plants, e.g. transgenic 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.

Claims

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, or 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, or 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 Sb, and

(h) a nucleic acid sequence that hybridizes to the polynucleotide of (a) or (b) under stringent conditions.

2. The transgenic plant of claim 1, wherein said stringent conditions are 6×

SSC and 65°

C.

3. The transgenic plant of claim 2, 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. The transgenic plant of claim 3, wherein said polynucleotide sequence is derived from a monocotyledonous plant.

5. The transgenic plant of claim 4, wherein said transgenic plant is dicotyledenous.

6. The transgenic plant of claim 3, wherein said polynucleotide sequence is derived from a dicotyledonous plant.

7. The transgenic plant of claim 6, wherein said transgenic plant is monocotyledonous.

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. The transgenic plant of claim 3, further comprising a constitutive, inducible, or tissue-specific promoter operably linked to said polynucleotide sequence or said complementary polynucleotide sequence.

10. The transgenic plant of claim 3, wherein the encoded polypeptide of (a)-(h) is expressed and regulates transcription of at least one gene.

11. The transgenic plant of claim 10, wherein the encoded polypeptide of (a)-(h) is SEQ ID NO:

468.

12. The transgenic plant of claim 3, wherein said altered trait is an enhanced tolerance to abiotic stress.

13. The transgenic plant of claim 12, wherein said abiotic stress is increased tolerance to chilling and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

183, 437, 805, and polynucleotide variants thereof.

14. The transgenic plant of claim 12, wherein said abiotic stress is increased germination in cold conditions and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

137, 183, 437, 805, 841, and polynucleotide variants thereof.

15. The transgenic plant of claim 12, wherein said abiotic stress is increased freezing tolerance and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

615 and polynucleotide variants thereof.

16. The transgenic plant of claim 12, wherein said abiotic stress is increased tolerance to heat and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

291, 467, 573, 635, 819, and polynucleotide variants thereof.

17. The transgenic plant of claim 12, wherein said abiotic stress is increased tolerance to drought and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

53, 615, 941, and polynucleotide variants thereof.

18. The transgenic plant of claim 12, wherein said abiotic stress is increased tolerance to osmotic stress and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

97, 223, 309, 721, 731, 941, and polynucleotide variants thereof.

19. The transgenic plant of claim 12, wherein said abiotic stress is increased tolerance to salt and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

27, 105, 141, 549, 579, 591, and polynucleotide variants thereof.

20. The transgenic plant of claim 12, wherein said abiotic stress is decreased sensitivity to nitrogen limitation and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

139, 141, 467, 805, 939, 959, and polynucleotide variants thereof.

21. The transgenic plant of claim 12, wherein said abiotic stress is increased tolerance to phosphate limitation and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

345 and polynucleotide variants thereof.

22. The transgenic plant of claim 12, wherein said abiotic stress is increased tolerance to potassium limitation and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

269, 359, 613, and polynucleotide variants thereof.

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 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.

25. The transgenic plant of claim 23, wherein said altered hormone sensitivity is 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.

26. The transgenic plant of claim 3, wherein said altered trait is disease resistance.

27. The transgenic plant of claim 26, wherein said altered trait is 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.

28. The transgenic plant of claim 26, wherein said altered trait is 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.

29. The transgenic plant of claim 26, wherein said altered trait is 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.

30. The transgenic plant of claim 26, wherein said altered trait is 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.

31. The transgenic plant of claim 26, wherein said altered trait is 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.

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 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.

34. The transgenic plant of claim 32, wherein said altered sugar sensing confers improved seed germination.

35. The transgenic plant of claim 32, wherein said altered sugar sensing confers improved seedling vigor.

36. The transgenic plant of claim 3, wherein said altered trait is 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.

37. The transgenic plant of claim 3, wherein said altered trait is 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.

38. The transgenic plant of claim 3, wherein said altered trait is an extended period of flowering and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

949 and polynucleotide variants thereof.

39. The transgenic plant of claim 3, wherein said altered trait is 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.

40. The transgenic plant of claim 3, wherein said altered trait is 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.

41. The transgenic plant of claim 3, wherein said altered trait is a change in stem bifurcations and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

249 and polynucleotide variants thereof.

42. The transgenic plant of claim 3, wherein said altered trait is 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.

43. The transgenic plant of claim 3, wherein said altered trait is reduced meristem cell differentiation and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

919 and polynucleotide variants thereof.

44. The transgenic plant of claim 3, wherein said altered trait is altered phyllotaxy and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

419 and polynucleotide variants thereof.

45. The transgenic plant of claim 3, wherein said altered trait is an altered branching pattern and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

283, 913, and polynucleotide variants thereof.

46. The transgenic plant of claim 3, wherein said altered trait is 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.

47. The transgenic plant of claim 3, wherein said altered trait is 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.

48. The transgenic plant of claim 3, wherein said altered trait is 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.

49. The transgenic plant of claim 3, wherein said altered trait is an increase in trichome number and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

415 and polynucleotide variants thereof.

50. The transgenic plant of claim 3, wherein said altered trait is altered stem morphology and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

283, 497, and polynucleotide variants thereof.

51. The transgenic plant of claim 3, wherein said altered trait is increased root growth and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

13, 905, and polynucleotide variants thereof.

52. The transgenic plant of claim 3, wherein said altered trait is 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.

53. The transgenic plant of claim 3, wherein said altered trait is altered seed development and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

649 and polynucleotide variants thereof.

54. The transgenic plant of claim 3, wherein said altered trait is 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.

55. The transgenic plant of claim 3, wherein said altered trait is 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.

56. The transgenic plant of claim 3, wherein said altered trait is premature senescence and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

417, 737, and polynucleotide variants thereof.

57. The transgenic plant of claim 3, wherein said altered trait is delayed senescence and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

173, 375, 585, 697, and polynucleotide variants thereof.

58. The transgenic plant of claim 3, wherein said altered trait is 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.

59. The transgenic plant of claim 3, wherein said altered trait is increased necrosis and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

29 and polynucleotide variants thereof.

60. The transgenic plant of claim 3, wherein said altered trait is 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.

61. The transgenic plant of claim 3, wherein said altered trait is 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.

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 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.

64. The transgenic plant of claim 62, wherein said change in leaf morphology is 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.

65. The transgenic plant of claim 62, wherein said change in leaf morphology is increased altered leaf development, and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

929, and polynucleotide variants thereof.

66. The transgenic plant of claim 62, wherein said change in leaf morphology is 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.

67. The transgenic plant of claim 62, wherein said change in leaf morphology is glossy leaves and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

643, 801, and polynucleotide variants thereof.

68. The transgenic plant of claim 60, wherein said change in leaf morphology is leaf cell expansion and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

331 and polynucleotide variants thereof.

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 altered seed coloration and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

67, 435, 443, and polynucleotide variants thereof.

71. The transgenic plant of claim 69, wherein said change in seed morphology is increased seed size and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

115, 385, 793, and polynucleotide variants thereof.

72. The transgenic plant of claim 69, wherein said change in seed morphology is decreased seed size and said nucleotide sequence is SEQ ID NO:

749 and polynucleotide variants thereof.

73. The transgenic plant of claim 69, wherein said change in seed morphology is altered seed shape and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

713, 749, and polynucleotide variants thereof.

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 increased leaf wax and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

643, 801, and polynucleotide variants thereof.

76. The transgenic plant of claim 74, wherein said change in leaf biochemistry is 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.

77. The transgenic plant of claim 74, wherein said change in leaf biochemistry is 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.

78. The transgenic plant of claim 74, wherein said change in leaf biochemistry is 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.

79. The transgenic plant of claim 74, wherein said change in leaf biochemistry is increased leaf anthocyanins and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

435, and polynucleotide variants thereof.

80. The transgenic plant of claim 74, wherein said change in leaf biochemistry is 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.

81. The transgenic plant of claim 74, wherein said change in leaf biochemistry is 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.

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 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.

84. The transgenic plant of claim 82, wherein said change in seed biochemistry is an 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.

85. The transgenic plant of claim 82, wherein said change in seed biochemistry is 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.

86. The transgenic plant of claim 82, wherein said change in seed biochemistry is an 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.

87. The transgenic plant of claim 82, wherein said change in seed biochemistry is 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.

88. The transgenic plant of claim 82, wherein said change in seed biochemistry is 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.

89. The transgenic plant of claim 82, wherein said change in seed biochemistry is 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.

90. The transgenic plant of claim 82, wherein said change in seed biochemistry is an increase in seed sterols and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

23 and polynucleotide variants thereof.

91. The transgenic plant of claim 82, wherein said change in seed biochemistry is an upregulation 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.

92. The transgenic plant of claim 3, wherein said altered trait is an increase in root anthocyanins and said nucleotide sequence is selected from the group consisting of SEQ ID NO:

435 and polynucleotide variants thereof.

93. The transgenic plant of claim 3, wherein said altered trait is 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.

94. The transgenic plant of claim 3, wherein said altered trait is 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.

95. A method of using a transgenic plant of claim 1 to grow a progeny plant, the method comprising:

(a) crossing the transgenic plant with itself or another plant;

(b) selecting seed that develops as a result of said crossing; and

(c) growing the progeny plant from the seed.

96. The method of claim 95, wherein:

said progeny plant expresses 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.

109. A method of identifying a factor that is modulated by or interacts with a polypeptide encoded by the polynucleotide sequence of claim 1, said method comprising:

expressing a polypeptide encoded by said polynucleotide sequence of claim 1 in a plant; and

identifying at least one factor that is modulated by or interacts with said polypeptide.

110. A method for identifying at least one downstream polynucleotide sequence that is subject to a regulatory effect of any of the polypeptides of claim 1, said method comprising:

expressing any of the polypeptides of claim 1 in a plant cell; and

identifying RNA or protein produced as a result of said expression.

111. The method of claim 110, wherein said identifying is by Northern analysis, RT-PCR, microarray gene expression assays, reporter gene expression systems subtractive hybridization, differential display, representational differential analysis, or by two-dimensional gel electrophoresis of one or more protein products.

97. An expression cassette comprising:

(1) a constitutive, inducible, or tissue-specific promoter; and

(2) 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, or 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, or 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;

wherein said recombinant polynucleotide is operably linked to said promoter.

98. The expression cassette of claim 97, wherein said stringent conditions are of 6×

SSC and 650 C.

99. The expression cassette of claim 98, wherein the encoded polypeptide of (a)-(h) is SEQ ID NO:

468.

100. A host cell comprising the expression cassette of claim 97.

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, or 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;

(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, or 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 according to claim 97;

(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. The method of claim 101, wherein said stringent conditions are of 6×

SSC and 65°

C.

103. The method of claim 102, wherein the encoded polypeptide of (i)-(viii) is SEQ ID NO:

468.

104. The method of claim 101, 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 comprise the recombinant polynucleotide.

105. The method of claim 101, 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.

106. The method of claim 101, wherein the encoded polypeptide is expressed and regulates transcription of a gene.

107. The method of claim 101, further comprising a constitutive, inducible, or tissue-specific promoter operably linked to said polynucleotide sequence or said complementary polynucleotide sequence.

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.