(en)Polynucleotides and polypeptides incorporated into expression vectors are introduced into plants and were ectopically expressed. These polypeptides may confer at least one regulatory activity and increased photosynthetic resource use efficiency, increased yield, greater vigor, greater biomass as compared to a control plant.

1.ApplicationNumber: US-201314419264-A
1.PublishNumber: US-2015247159-A1
2.Date Publish: 20150903
3.Inventor: HYMUS GRAHAM
MARION COLLEEN
REUBER T. LYNNE
RATCLIFFE OLIVER
LIBBY JEFFREY
MAO YIFAN

4.Inventor Harmonized: HYMUS GRAHAM(US)
MARION COLLEEN(US)
REUBER T LYNNE(US)
RATCLIFFE OLIVER(US)
LIBBY JEFFREY(US)
MAO YIFAN(US)

5.Country: US
6.Claims:
(en)Polynucleotides and polypeptides incorporated into expression vectors are introduced into plants and were ectopically expressed. These polypeptides may confer at least one regulatory activity and increased photosynthetic resource use efficiency, increased yield, greater vigor, greater biomass as compared to a control plant.

7.Description:
(en)FIELD OF THE INVENTION
The present invention relates to plant genomics and plant improvement.
BACKGROUND OF THE INVENTION
A plant's phenotypic characteristics that enhance photosynthetic resource use efficiency may be controlled through a number of cellular processes. One important way to manipulate that control is by manipulating the characteristics or expression of regulatory proteins, proteins that influence the expression of a particular gene or sets of genes. For example, transformed or transgenic plants that comprise cells with altered levels of at least one selected regulatory polypeptide may possess advantageous or desirable traits, and strategies for manipulating traits by altering a plant cell's regulatory polypeptide content or expression level can result in plants and crops with commercially valuable properties. Examples of such trait manipulation include:
Increasing Canopy Photosynthesis to Increase Crop Yield.
Recent studies by crop physiologists have provided evidence that crop-canopy photosynthesis is correlated with crop yield, and that increasing canopy photosynthesis can increase crop yield (Long et al., 2006. Plant Cell Environ. 29:315-33; Murchie et al., 2009 New Phytol. 181:532-552; Zhu et al., 2010 . Ann. Rev. Plant Biol. 61:235-261). Two overlapping strategies for increasing canopy photosynthesis have been proposed. The first recognizes great potential to increase canopy photosynthesis by improving multiple discrete reactions that currently limit photosynthetic capacity (reviewed in Zhu et al., 2010. supra). The second focuses upon improving plant physiological status during environmental conditions that limit the realization of photosynthetic capacity. It is important to distinguish this second goal from recent industry and academic screening for genes to improve stress tolerance. Arguably, these efforts may have identified genes that improve plant physiological status during severe stresses not typically experienced on productive acres (Jones, 2007. J. Exp. Bot. 58:119-130; Passioura, 2007. J. Exp. Bot. 58:113-117). In contrast, improving the efficiency with which photosynthesis operates relative to the availability of key resources of water, nitrogen and light, is thought to be more appropriate for improving yield on productive acres (Long et al., 1994 . Ann. Rev. Plant Physiol. Plant Molec. Biol. 45:633-662; Morison et al., 2008. Philosophical Transactions of the Royal Society B: Biological Sciences 363:639-658; Passioura, 2007, supra).
Increasing Nitrogen Use Efficiency (NUE) to Increase Crop Yield.
There has been a large increase in food productivity over the past 50 years causing a decrease in world hunger despite a significant increase in population (Godfray et al., 2010. Science 327:812-818). A significant contribution to this increased yield was a 20-fold increase in the application of nitrogen fertilizers (Glass, 2003. Crit. Rev. Plant Sci. 22:453-470). About 85 million to 90 million metric tons of nitrogen are applied annually to soil, and this application rate is expected to increase to 240 million metric tons by 2050 (Good et al., 2004. Trends Plant Sci. 9:597-605). However, plants use only 30 to 40% of the applied nitrogen and the rest is lost through a combination of leaching, surface run-off, denitrification, volatilization, and microbial consumption (Frink et al., 1999 . Proc. Natl. Acad. Sci. USA 96:1175-1180; Glass, 2003, supra; Good et al., 2004, supra; Raun and Johnson, 1999. Agron. J. 91:357-363). The loss of more than 60% of applied nitrogen can have serious environmental effects, such as groundwater contamination, anoxic coastal zones, and conversion to greenhouse gases. In addition, while most fertilizer components are mined (such as phosphates), inorganic nitrogen is derived from the energy intensive conversion of gaseous nitrogen to ammonia. Thus, the addition of nitrogen fertilizer is typically the highest single input cost for many crops, and since its production is energy intensive, the cost is dependent on the price of energy (Rothstein, 2007. Plant Cell 19:2695-2699). With an increasing demand for food from an increasing human population, agriculture yields must be increased at the same time as dependence on applied fertilizers is decreased. Therefore, to minimize nitrogen loss, reduce environmental pollution, and decrease input cost, it is crucial to develop crop varieties with higher nitrogen use efficiency (Garnett et al., 2009. Plant Cell Environ. 32:1272-1283; Hirel et al., 2007. J. Exp. Bot. 58:2369-2387; Lea and Azevedo, 2007 . Ann. Appl. Biol. 151:269-275; Masclaux-Daubresse et al., 2010 . Ann. Bot. 105:1141-1157; Moll et al., 1982. Agron. J. 74:562-564; Sylvester-Bradley and Kindred, 2009. J. Exp. Bot. 60:1939-1951).
Improving Water Use Efficiency (WUE) to Improve Yield.
Freshwater is a limited and dwindling global resource; therefore, improving the efficiency with which food and biofuel crops use water is a prerequisite for maintaining and improving yield (Karaba et al., 2007 . Proc. Natl. Acad. Sci. USA. 104:15270-15275). WUE can be used to describe the relationship between water use and crop productivity over a range of time integrals. The basic physiological definition of WUE equates the ratio of photosynthesis (A) to transpiration (T) at a given moment in time, also referred to as transpiration efficiency. However, the WUE concept can be scaled significantly, for example, over the complete lifecycle of a crop, where biomass or yield can be expressed per cumulative total of water transpired from the canopy. Thus far, the engineering of major field crops for improved WUE with single genes has not yet been achieved (Karaba et al., 2007. supra). Regardless, increased yields of wheat cultivars bred for increased transpiration efficiency (the ratio of photosynthesis to transpiration) have provided important support for the proposition that crop yield can be increased over broad acres through improvement in crop water-use efficiency (Condon et al., 2004 . J. Exp. Bot. 55:2447-2460).
Estimates of water-use efficiency integrated over the life of plant tissues can be derived from analysis of the ratio of the 13 C carbon isotope to the 12 C carbon isotope in those tissues. The theory that underlies this means to estimating WUE is that during photosynthesis, incorporation of 13 C into the products of photosynthesis is slower than the lighter isotope 12 C. Effectively, 13 C is discriminated against relative to 12 C during photosynthesis, an effect that is integrated over the life of the plant resulting in biomass with a distinct 13 C/ 12 C signature. Of the many steps in the photosynthetic process during which this discrimination occurs, discrimination at the active site of Rubisco is of most significance, a consequence of kinetic constraints associated with the 13 CO 2 molecule being larger. Significantly, the discrimination by Rubisco is not constant, but varies depending on the CO 2 concentration within the leaf. At high CO 2 concentration discrimination by Rubisco is highest, however as CO 2 concentration decreases discrimination decreases. Because the CO 2 concentration within the leaf is overwhelmingly dependent on the balance between CO 2 influx through the stomatal pore and the rate of photosynthesis, and because the stomatal pore controls the rate of transpiration from the leaf, the 13 C/ 12 C isotopic signature of plant material provides an integrated record of the balance between transpiration and photosynthesis during the life of the plant and as such a surrogate measure of water-use efficiency (Farquhar et al. 1989. Annu. Rev. Plant Physiol. Plant Mol. Biol. 40:503-537).
With these needs in mind, new technologies for yield enhancement are required. In this disclosure, a phenotypic screening platform that directly measures photosynthetic capacity, water use efficiency, and nitrogen use efficiency of mature plants was used to discover advantageous properties conferred by ectopic expression of the described regulatory proteins in plants.
SUMMARY
The instant description is directed to a transgenic plant or plants that have greater photosynthetic resource use efficiency with respect to a control plant, or a plant part derived from such a plant, e.g., shoot vegetative organs/structures (e.g., leaves, stems and tubers), roots, flowers and floral organs/structures (e.g., bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (e.g., vascular tissue, ground tissue, and the like), pulped, pureed, ground-up, macerated or broken-up tissue, and cells (e.g., guard cells, egg cells, etc.). In this regard, the transgenic plant or plants comprise at least one recombinant nucleic acid construct (which may also be referred to as a recombinant construct or recombinant polynucleotide) that comprises a promoter of interest. The recombinant construct or constructs also encode a polypeptide that has a least one conserved domain, wherein the polypeptide expressed from the construct confers an improved trait (for example, greater yield, enhanced photosynthetic resource use efficiency, or improved water us efficiency) to the transgenic plant as compared to a control plant that does not contain the recombinant construct. The promoter and the nucleic acid sequence that encodes the polypeptide may be located in the same single construct, in which case the promoter is part of a cis-acting regulatory sequence that directly drives expression of the polypeptide. Alternatively, the promoter and the nucleic acid sequence that encodes the polypeptide may be located on separate constructs, in which case the promoter drives the expression of a trans-regulatory element and expression of the nucleic acid sequence occurs via transactivation. The choice of promoter may include a constitutive promoter or a promoter with enhanced activity in a tissue capable of photosynthesis (also referred to herein as a “photosynthetic promoter” or a “photosynthetic tissue-enhanced promoter”) such as a leaf tissue or other green tissue. Examples of photosynthetic promoters include for example, an RBCS3 promoter (SEQ ID NO: 1693), an RBCS4 promoter (SEQ ID NO: 1694) or others such as the At4g01060 promoter (SEQ ID NO: 1695), the latter regulating expression in a guard cell. The promoter regulates a polypeptide that is encoded by the recombinant polynucleotide or by a second (or target) recombinant polynucleotide (in which case expression of the polypeptide may be regulated by a trans-regulatory element). The promoter may also regulate expression of a polypeptide to an effective level of expression in a photosynthetic tissue, that is, to a level that, as a result of expression of the polypeptide to that level, improves photosynthetic resource use efficiency in a transgenic plant relative to a control plant. The recombinant polynucleotide may comprise the promoter and also encode the polypeptide or alternatively, the polynucleotide may comprise the promoter and drive expression of the polypeptide that is encoded by the second recombinant polynucleotide. In a preferred embodiment, the polypeptide comprises SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135, or a sequence that is homologous, paralogous or orthologous to SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135, being structurally-related to SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135 and having a function similar to SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135, as described herein. Expression of the polypeptide under the regulatory control of the constitutive or leaf-enhanced or photosynthetic tissue-enhanced promoter in the transgenic plant confers greater photosynthetic resource use efficiency to the transgenic plants, and may ultimately increase yield that may be obtained from the plants.
The instant description also pertains to methods for increasing photosynthetic resource use efficiency in, or increasing yield from, a plant or plants including the method conducted by growing a transgenic plant comprising and/or transformed with an expression cassette comprising the recombinant polynucleotide that comprises a constitutive promoter or a promoter expressed in photosynthetic tissue, which may be a leaf-enhanced or green tissue-enhanced promoter, such as for example, the RBCS3, RBCS4 or At4g01060 (SEQ ID NO: 1693, 1694, or 1695, respectively), or another photosynthetic tissue-enhanced promoter. Examples of photosynthetic tissue-enhanced promoters are found in the sequence listing or in Table 22. The promoter regulates expression of a polypeptide that comprises SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135, or a polypeptide sequence within the AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade (recombinant polynucleotides encoding AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptides are described in the following paragraphs (a)-(c), and exemplary polypeptides within the clade are described in the following paragraphs (d)-(f) and are shown in FIGS. 1 , 2 A- 2 I, 5 , 6 A- 6 J, 7 , 8 A- 8 I, 10 , 11 A- 11 H, 13 , 14 A- 14 L, 15 , 16 A- 16 J, 17 , 18 A- 18 L, 20 , 21 A- 21 O, 23 , 24 A- 24 O, 28 , 29 A- 29 I, 32 , 33 A- 33 H, 35 , and 36 A- 36 E).
The recombinant polynucleotide that encodes an AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptide may include:
(a) nucleic acid sequences that are at least 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identical to SEQ ID NO 1368, 1370, 1372, 1374, 1376, 1378, 1380, 1382, 1384, 1386, 1388, 1390, 1392, 1394, 1396, 1398, 1400, 1402, 1404, 1406, 1408, 1410, 1412, 1414, 1416, 1418, 1420, 1422, 1424, 1426, 1428, 1430, 1432; or 1506, 1508, 1510, 1512, 1514, 1516, 1518, 1520, 1522, 1524, 1526, 1528, 1530; or 863, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921; or 1015, 1017, 1019, 1021, 1023, 1025, 1027, 1029, 1031, 1033, 1035, 1037, 1039, 1041, 1043, 1045, 1047, 1049, 1051, 1053, 1055, 1057, 1059, 1061, 1063, 1065, 1067, 1069, 1071; or 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33; or 489, 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, 541, 543, 545, 547; or 306, 308, 310, 312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382, 384, 386, 388, 390, 392, 394; or 1155, 1157, 1159, 1161, 1163, 1165, 1167, 1169, 1171, 1173, 1175, 1177, 1179, 1181, 1183, 1185, 1187, 1189, 1191, 1193, 1195, 1197, 1199, 1201, 1203, 1205, 1207, 1209, 1211, 1213, 1215, 1217, 1219, 1221, 1223, 122; 5 or 1590, 1592, 1594, 1596, 1598, 1600, 1602, 1604, 1606, 1608, 1610, 1612, 1614, 1616; or 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782; or 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664; or 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208; and/or
(b) nucleic acid sequences that encode polypeptide sequences that are at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identical in their amino acid sequences to the entire length of any of SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209; or
(c) nucleic acid sequences that hybridize under stringent conditions (e.g., hybridization followed by one, two, or more wash steps of 6×SSC and 65° C. for ten to thirty minutes per step) to any of SEQ ID NO: SEQ ID NO 1368, 1370, 1372, 1374, 1376, 1378, 1380, 1382, 1384, 1386, 1388, 1390, 1392, 1394, 1396, 1398, 1400, 1402, 1404, 1406, 1408, 1410, 1412, 1414, 1416, 1418, 1420, 1422, 1424, 1426, 1428, 1430, 1432; or 1506, 1508, 1510, 1512, 1514, 1516, 1518, 1520, 1522, 1524, 1526, 1528, 1530; or 863, 865, 867, 869, 871, 873, 875, 877, 879, 881, 883, 885, 887, 889, 891, 893, 895, 897, 899, 901, 903, 905, 907, 909, 911, 913, 915, 917, 919, 921; or 1015, 1017, 1019, 1021, 1023, 1025, 1027, 1029, 1031, 1033, 1035, 1037, 1039, 1041, 1043, 1045, 1047, 1049, 1051, 1053, 1055, 1057, 1059, 1061, 1063, 1065, 1067, 1069, 1071; or 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33; or 489, 491, 493, 495, 497, 499, 501, 503, 505, 507, 509, 511, 513, 515, 517, 519, 521, 523, 525, 527, 529, 531, 533, 535, 537, 539, 541, 543, 545, 547; or 306, 308, 310, 312, 314, 316, 318, 320, 322, 324, 326, 328, 330, 332, 334, 336, 338, 340, 342, 344, 346, 348, 350, 352, 354, 356, 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382, 384, 386, 388, 390, 392, 394; or 1155, 1157, 1159, 1161, 1163, 1165, 1167, 1169, 1171, 1173, 1175, 1177, 1179, 1181, 1183, 1185, 1187, 1189, 1191, 1193, 1195, 1197, 1199, 1201, 1203, 1205, 1207, 1209, 1211, 1213, 1215, 1217, 1219, 1221, 1223, 122; 5 or 1590, 1592, 1594, 1596, 1598, 1600, 1602, 1604, 1606, 1608, 1610, 1612, 1614, 1616; or 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782; or 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664; or 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, or 208.
The AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptides may include:
(d) polypeptide sequences encoded by the nucleic acid sequences of (a), (b) and/or (c); and/or
(e) polypeptide sequences that have at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% amino acid identity to SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209; and/or
(f) polypeptide sequences that have at least 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% amino acid identity to the SEQ ID NO:1434 (‘NAM domain’) or SEQ ID NO: 1435, 1436, 1437, 1438, 1439, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 1450, 1451, 1452, 1453, 1454, 1455, 1456, 1457, 1458, 1459, 1460, 1461, 1462, 1463, 1464, 1465 1466, or SEQ ID NO: 1507 (‘Plant Zinc Cluster Domain’) or SEQ ID NOs: 1532, 1533, 1534, 1535, 1536, 1537, 1538, 1539, 1540, 1541, 1542, 1543 1544, or SEQ ID NO:864 (‘BTB domain’) or any of SEQ ID NOs: 923-950, or SEQ ID NO: 1016 (‘bHLH-MYC_N domain’) or SEQ ID NO: 1073, 1075, 1077, 1079, 1081, 1083, 1085, 1087, 1089, 1091, 1093, 1095, 1097, 1099, 1101, 1103, 1105, 1107, 1109, 1111, 1113, 1115, 1117, 1119, 1121, 1123, 1125, 1127 1129, or SEQ ID NO: 2 (‘Myb DNA binding domain 1’) or SEQ ID NOs: 61-77 (‘Myb Domain’), or SEQ ID NO: 1156 (‘WRKY Domain 1’) or SEQ ID NO: 1227, 1229, 1231, 1233, 1235, 1237, 1239, 1241, 1243, 1245, 1247, 1249, 1251, 1253, 1255, 1257, 1259, 1261, 1263, 1265, 1267, 1269, 1271, 1273, 1275, 1277, 1279, 1281, 1283, 1285, 1287, 1289, 1291, 1293, 1295 1297; or SEQ ID NO: 1591 (‘Z-C2H2-1’) or SEQ ID NO: 1618, 1619, 1620, 1621, 1622, 1623, 1624, 1625, 1626, 1627, 1628, 1629, 1630 1631, or (‘AP2 domain’) 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577 578, or SEQ ID NO: 307 (‘AP2 domain’) or any of SEQ ID NO: 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439 440, or SEQ ID NO: 625 (‘HLH domain’) or SEQ ID NO: 666, 667, 668, 669, 670, 671, 672, 673, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685 686; and/or, or SEQ ID NO: 735 (‘SANT domain 1’) or SEQ ID NO: 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830 832, or SEQ ID NO: 135 (‘Myb DNA binding domain 1’) or SEQ ID NOs: 210, 212, 214, 216, 218, 220, 222, 224, 226, 228, 230, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282 284; or to SEQ ID NO: 1507 (‘WRKY DNA-binding Domain’) or SEQ ID NOs: 1545, 1546, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1555, 1556 1557 or SEQ ID NO:864 (‘ANK domain’) or any of SEQ ID NOs: 951 to 980 or SEQ ID NO: 1016 (‘HLH domain 2’) or SEQ ID NO: 1074, 1076, 1078, 1080, 1082, 1084, 1086, 1088, 1090, 1092, 1094, 1096, 1098, 1100, 1102, 1104, 1106, 1108, 1110, 1112, 1114, 1116, 1118, 1120, 1122, 1124, 1126, 1128, 1130 or SEQ ID NO: 2 (′Myb DNA binding domain 2′) or SEQ ID NOs: 95-111 or SEQ ID NO: 1156 (‘WRKY Domain 2’) or SEQ ID NO: 1228, 1230, 1232, 1234, 1236, 1238, 1240, 1242, 1244, 1246, 1248, 1250, 1252, 1254, 1256, 1258, 1260, 1262, 1264, 1266, 1268, 1270, 1272, 1274, 1276, 1278, 1280, 1282, 1284, 1286, 1288, 1290, 1292, 1294, 1296 1298 or SEQ ID NO: 1591 (‘Z-C2H2-2 domain’) or SEQ ID NO: 1632, 1633, 1634, 1635, 1636, 1637, 1638, 1639, 1640, 1641, 1642, 1643, 1644 1645 or SEQ ID NO: 735 (‘SANT domain 2’) or SEQ ID NO: 785, 787, 789, 791, 793, 795, 797, 799, 801, 803, 805, 807, 809, 811, 813, 815, 817, 819, 821, 823, 825, 827, 829, 831 833 or SEQ ID NO: 135 (‘Myb DNA binding domain 2’) or SEQ ID NOs: 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285; and/or
(g) polypeptide sequences that comprise a subsequence that is at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identical to a consensus sequence of SEQ ID NO: 1467, 1468, 1469 of the AtNAC6 clade, SEQ ID NO: 1558, 1559, 1560, 1561 of the WRKY17 clade, SEQ ID NO: 981, 982, 983, 984, 985, 986 of the AtNPR3 clade, SEQ ID NO: 1153, 1154 of the AtMYC1 clade, SEQ ID NO: 129, 130, or 133 of the AtMYB19 clade, SEQ ID NO: 579, 580, 581 of the ERF058 clade, SEQ ID NO: 441, 442 of the CRF1 clade, SEQ ID NO: 1299, 1300 of the WRKY3 clade, SEQ ID NO: 1646, 1647, 1648, of the ZAT11 clade, SEQ ID NO: 834, 835, 836 of the MYB111 clade, SEQ ID NO: 687 of the SPATULA clade, or SEQ ID NO: 302, 303, 304, 305 of the AtMYB50 clade, or that comprises a consensus sequence of SEQ ID NO: 1467, 1468, 1469 of the AtNAC6 clade, SEQ ID NO: 1558, 1559, 1560, 1561 of the WRKY17 clade, SEQ ID NO: 981, 982, 983, 984, 985, 986 of the AtNPR3 clade, SEQ ID NO: 1153, 1154 of the AtMYC1 clade, SEQ ID NO: 129, 130, or 133 of the AtMYB19 clade, SEQ ID NO: 579, 580, 581 of the ERF058 clade, SEQ ID NO: 441, 442 of the CRF1 clade, SEQ ID NO: 1299, 1300 of the WRKY3 clade, SEQ ID NO: 1646, 1647, 1648, of the ZAT11 clade, SEQ ID NO: 834, 835, 836 of the MYB111 clade, SEQ ID NO: 687 of the SPATULA clade, or SEQ ID NO: 302, 303, 304, 305 of the AtMYB50 clade.



BRIEF DESCRIPTION OF THE SEQUENCE LISTING AND DRAWINGS
The Sequence Listing provides exemplary polynucleotide and polypeptide sequences of the instant description. The traits associated with the use of the sequences are included in the Examples.
Incorporation of the Sequence Listing.
The Sequence Listing provides exemplary polynucleotide and polypeptide sequences. The copy of the Sequence Listing, being submitted electronically with this patent application, provided under 37 CFR §1.821-1.825, is a read-only memory computer-readable file in ASCII text format. The Sequence Listing is named “MBI-0215PCT.txt”, the electronic file of the Sequence Listing was created on Jul. 31, 2013, and is (3,383,248 bytes in size (3.22 megabytes in size as measured in MS-WINDOWS). The Sequence Listing is herein incorporated by reference in its entirety.
In FIG. 1 , a phylogenetic tree of the AtMYB19 (also referred to as AT5G52260.1 or G1309) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. The AtMYB19 clade members appear in the large box with the solid line boundary. AtMYB19 appears in the oval. An ancestral sequence of AtMYB19 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 1 . AtMYB19 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by LOC_Os04g45020.1 and Solyc03g025870.2.1 (indicated by the box around these sequences). A related clade is represented by the node indicated by arrow “B”.
FIGS. 2A-2I show an alignment of the AtMYB19 (AT5G52260.1) clade and related proteins which appear in the boxes with the solid line boundaries. The alignment was generated with MUSCLE v3.8.31 (Edgar (2004) Nucleic Acids Res. 32:1792-1797) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second Myb DNA binding domains appear in boxes with the dashed line boundaries. The conserved residues within the clade are shown in the last rows of FIG. 2B-2D and are presented as SEQ ID NOs: 129 (underlined), 130 (double underlined) and 130. SEQ ID NOs: 129 and 130 share the triple underlined Glu residue in FIG. 2C .
FIG. 3 presents a plot of photosynthetic capacity at growth temperature, showing increased light saturated photosynthesis (A sat ) over a range of leaf, sub-stomatal CO 2 concentration (C i ), in five AtMYB19 overexpression lines, compared to a control line. Data were collected over a range of C i over which the activity of Rubisco is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least nine replicate plants for each line.
FIG. 4 presents a plot of photosynthetic capacity at growth temperature showing increased A sat over a range of leaf, sub-stomatal C i in five AtMYB19 overexpression lines, compared to a control line. Data were collected over a range of C i over which the capacity to regenerate RuBP is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least nine replicate plants for each line.
Legend for FIG. 3 and FIG. 4 :
 control ◯ AtMYB19-Line 2 ⋄ AtMYB19-Line 3 Δ AtMYB19-Line 6 □ AtMYB19-Line 7  AtMYB19-Line 8

In FIG. 5 , a phylogenetic tree of the AtMYB50 (also referred to as AT1G57560.1 or G1319) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. The AtMYB50 clade members appear in the large box with the solid line boundary. AtMYB50 (AT1G57560.1) appears in the rounded rectangle. An ancestral sequence of AtMYB50 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 5 . AtMYB50 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by LOC_Os01g18240.1 and POPTR — 0013 s00290.1 (indicated by the box around these sequences).
FIGS. 6A-6J show an alignment of AtMYB50 and representative clade-related proteins. The AtMYB50 clade sequences are identified within the bracket along the left-hand side of the sequences. The alignment was generated with MUSCLE v3.8.31 with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second Myb DNA binding domains appear in boxes with the dashed line boundaries in FIG. 6A-6C . A clade consensus sequence (SEQ ID NO: 302) comprising both of the conserved residues is shown in the last row in FIG. 6A-6C .
In FIG. 7 , a phylogenetic tree of CRF1 or AT4G11140.1 (also referred to as NP — 192852 or G1421) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. The CRF1 clade members appear in the large box. CRF1 (AT4G11140.1) appears in the rounded rectangle. An ancestral sequence of CRF1 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 7 . CRF1 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi2g07357.1 and Solyc08g081960.1.1 (indicated by the box around these sequences).
FIGS. 8A-8I show an alignment of CRF1 and representative clade-related proteins. The CRF1 clade sequences are identified within the large box in FIG. 8A-8I . The alignment was generated with MUSCLE v3.8.31 with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved AP2 domains appear above the consensus sequence (SEQ ID NO: 441) in FIG. 8C-8D . A small clade consensus sequence (SEQ ID NO: 442) comprising conserved residues is also shown in the last row in FIG. 8A-8B .
FIG. 9 shows the δ 13 C values for dried, bulked rosette tissue from five independent CRF1 transgenic events, an empty vector control line (control) and a transgenic line know to increased rosette δ 13 C (control+). Data were collected over two screening runs.
In FIG. 10 , a phylogenetic tree of ERF058 or AT1G22190.1 (also referred to as ERF58 or G974) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. The ERF058 clade members appear in the large box with the solid line boundary. ERF058 (AT1G22190.1) appears in the rounded rectangle. An ancestral sequence of ERF058 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 10 . ERF058 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi4g29010.1 and POPTR — 0005 s16690.1 (indicated by the box around these sequences).
FIGS. 11A-11H show an alignment of ERF058 and representative clade-related proteins. The alignment was generated with MUSCLE v3.8.31 with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The amino acid residues of the conserved AP2 domains appear in boldface FIG. 11D-11E . Clade consensus sequences comprising conserved residues are shown in the last row in FIG. 11D-11H , in which a small letter ‘x’ refers to any amino acid, and a capital ‘X’ refers to conserved amino acids as identified in SEQ ID NO: 579 (shown in boldface), 580 or 581.
FIG. 12 shows how ectopic expression of ERF058 expression increases water-use efficiency. In these 35S::ERF058 lines derived from independent insertion events lines 1-3 left of control bars, and in a separate and subsequent analysis lines 1-5 to the right of the control bars), the ratio of 13 C to 12 C in the plant material was generally increased relative to control lines (that is, the ratio of 13 C to 12 C was generally less negative relative to a standard control plant). This directional change was consistent with decreased discrimination against 13 C during photosynthesis, the consequence of a lower concentration of CO 2 within the leaf and indicative of an increase in water-use efficiency integrated over the life of the plant's rosette.
In FIG. 13 , a phylogenetic tree of SPATULA or AT4G36930 (also referred to as G590) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. The SPATULA clade members appear in the large box with the dashed line boundary. The SPATULA (AT4G36930) polypeptide appears in the rounded rectangle. An ancestral sequence of SPATULA and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 13 . SPATULA clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi1g48400.1_BRADI and Solyc04g078690.2.1_SOLLY (indicated by the box around these sequences with the dashed boundary). A related clade descends from a related ancestral sequence represented by the node indicated by arrow “B”.
FIGS. 14A-14L show an alignment of SPATULA and representative clade-related proteins. The SPATULA clade sequences are identified within the bracket along the left-hand side of the sequences. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved HLH domains appear in the box with the dashed line boundaries in FIG. 14H . A clade consensus sequence (SEQ ID NO: 687) comprising conserved residues is shown in the last row in FIG. 14H-14I , in which X 1 is E or Q; X 2 is R or K; X 3 is G or S; X 4 is I, V, L, or M; X 5 is E or D; X 6 is Q or H; X 7 is Q or K; X 8 is I, V, L, M, or absent; and X 9 is S, T, A, or absent. In the sequences examined thus far, clade member polypeptides possess the three unique highlighted residues (position 17 is G or S and positions 32 and 33 are N and S, respectively). The alignment was generated with MUSCLE v3.8.31 with default parameters.
In FIG. 15 , a phylogenetic tree of MYB111 (or AT5G49330 or G1640) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. The MYB111 clade members appear in the large box with the dashed line boundary. MYB111 (AT5G49330) appears in the rounded rectangle. An ancestral sequence of MYB111 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 15 . MYB111 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by LOC_Os01g19970.1 and Glyma15g15400.1 (indicated by the dashed box around these sequences). A related clade is represented by the node indicated by arrow “B”.
FIGS. 16A-16J show an alignment of MYB111 and representative clade-related proteins. The MYB111 clade sequences are identified within the bracket along the left-hand side of the sequences. The alignment was generated with MUSCLE v3.8.31 with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second SANT domains appear in boxes with the dashed line boundaries in FIG. 16A-16C . A clade consensus sequence (SEQ ID NO: 834) comprises conserved residues shown in the last row in FIG. 16A-16C .
In FIG. 17 , a phylogenetic tree of AtNPR3 or AT5G45110.1 (also referred to as G839) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. AtNPR3 clade members appear in the large box with the dashed line boundary. AtNPR3 (AT5G45110) appears in the rounded rectangle. An ancestral sequence of AtNPR3 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 17 . AtNPR3 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by GRMZM2G076450_T01 and Glyma15g13320. A related clade is represented by the node indicated by arrow “B”.
FIGS. 18A-18L show an alignment of AtNPR3 and representative clade-related proteins. The alignment was generated with MUSCLE v3.8.31 with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved BTB and ANK domains appear in boxes in FIGS. 18B-18E and FIGS. 18F-18H , respectively. The BTB domain comprises consensus sequences SEQ ID NOs: 981 and 982). The ANK domain comprises consensus sequence SEQ ID NO: 983. Distinct small conserved or consensus motifs are shown in FIG. 18E between the BTB and DUF3420 domains (SEQ ID NO: 984), at the start of the DUF3420 domain in FIG. 18F (SEQ ID NO: 985), and within the NPR1-like C domain, in FIGS. 18H-18I (SEQ ID NO: 986).
FIG. 19 : Plot showing increased rate of light saturated photosynthesis (A sat ) over a range of leaf sub-stomatal CO 2 concentration (C i ) in 5 AtNPR3 overexpression lines (line 1-5), compared to a control line. The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line.
In FIG. 20 , a phylogenetic tree of AtMYC1 or AT4G00480.1 (also referred to as G581) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. The AtMYC1 clade members appear in the large box with the solid line boundary. AtMYC1 (AT4G00480.1) appears in the rounded rectangle. An ancestral sequence of AtMYC1 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 20 . AtMYC1 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by LOC_Os01g39650.1 and POPTR — 0003 s0012810.1 (indicated by the box around these sequences). A related clade is represented by the node indicated by arrow “B”.
FIGS. 21A-21O show an alignment of AtMYC1 and representative clade-related proteins. The AtMYC1 clade sequences are identified within the bracket along the left-hand side of the sequences. The alignment was generated with MUSCLE v3.8.31 with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved bHLH-MYC_N domain and HLH domain appear in boxes with the dashed line boundaries in FIG. 21A-21E and FIG. 21J-21K , respectively. Clade consensus sequences comprising conserved residues are shown in the last row in FIG. 21A-21D (SEQ ID NO: 1153) and FIG. 21K (SEQ ID NO: 1154).
FIG. 22 shows increased rate of light saturated photosynthesis (A sat ) over a range of leaf, sub-stomatal CO 2 concentration (C i ) in five AtMYC1 overexpression lines (line 1-5), compared to a control line. Data were collected over a range of C, over which the activity of Rubisco is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least 6 replicate plants for each line. Control line is represented by the solid black circles (). Line 1 is represented by open triangles (Δ). Line 2 is represented by solid squares (▪). Line 3 is represented by open squares (□). Line 4 is represented by open circles (◯). Line 5 is represented by open diamonds (⋄).
In FIG. 23 , a phylogenetic tree of WRKY3 or AT2G03340.1 (also referred to as G878) clade members were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. WRKY3 (AT2G03340.1) appears in the rounded rectangle. An ancestral sequence of WRKY3 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 23 . WRKY3 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi1g07970.1 and Solyc03g104810.2.1.
FIGS. 24A-24O show an alignment of WRKY3 and representative clade-related proteins. The WRKY3 clade sequences are identified within the bracket along the left-hand side of the sequences. The alignment was generated with MUSCLE v3.8.31 with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second WRKY domains of WRKY3 polypeptide clade members appear in boxes with the dashed line boundaries in FIG. 24G-24H and FIG. 24K-24L , respectively. Consensus SEQ ID NO: 1299 spans FIG. 24G-24H . Consensus SEQ ID NO: 1299 spans FIG. 24K-24L .
FIG. 25 shows the photosynthetic capacity of WRKY3 overexpressors at 22° C. This plot shows the increased rate of light-saturated photosynthesis (A sat ) at a given leaf, sub-stomatal CO 2 concentration (C i ) for an empty-vector control line (e.g., plants that did not comprise a recombinant construct encoding a WRKY3-related polypeptide or overexpress a WRKY3 clade or phylogenetically-related regulatory protein and described below simply as ‘control’) and four independent WRKY3 overexpression lines. The data presented were collected during two independent experiments and after 40 minutes of acclimation to a photosynthetically-active radiation (PAR), intensity of 700 μmol PAR m −2 s −1 , known to be saturating for photosynthesis, at an air temperature of 22° C. The data presented are the means±1 standard error for data collected on at least seven replicate plants for each line. Gray circles () refer to Control (1); gray squares (▪) show results for Control (2); white triangles (Δ) show results for WRKY3-line 1 (1); white squares (□) show results for WRKY3-line 2 (1); black squares (▪) show results for WRKY3-line 2 (2); white circles (◯) show results for WRKY3-line 3 (1), black circles () show results for WRKY3-line 3 (2), and white diamonds (⋄) show results for WRKY3-line 4 (2). Lines identified with a ‘1’ in parentheses in the figure legend were screened in the first experiment, lines identified with a ‘2’ in parentheses were screened in the second experiment.
FIG. 26 Photosynthetic capacity at 35° C.: Plot showing increased rate of light-saturated photosynthesis (A sat ) at a given leaf, sub-stomatal CO 2 concentration (C i ) for a control line and four independent WRKY3 overexpression lines. Data presented were collected during two independent experiments and after 40 minutes acclimation to a photosynthetically-active radiation (PAR), intensity of 700 μmol PAR m −2 s −1 , known to be saturating for photosynthesis, at an air temperature of 35° C. All data are the means±1 standard error for data collected on at least seven replicate plants for each line. In the same identification scheme of FIG. 25 , gray circles () refer to Control (1); gray squares (▪) show results for Control (2); white triangles (Δ) show results for WRKY3-line 1 (1); white squares (□) show results for WRKY3-line 2 (1); black squares (▪) show results for line 2 (2); white circles (◯) show results for WRKY3-line 3 (1), black circles () show results for WRKY3-line 3 (2), and white diamonds (⋄) show results for WRKY3-line 4 (2). Lines identified with a ‘1’ in parentheses in the figure legend, were screened in the first experiment, lines identified with a ‘2’ in parentheses were screened in the second experiment.
FIG. 27 shows increased light saturated photosynthesis (A sat ) over a range of leaf sub-stomatal CO 2 concentration (C i ), in two WRKY3 overexpression lines (lines 2 and 3), compared to a control line. Data were collected over a range of C i over which the activity of Rubisco is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least 6 replicate plants for each line. Control line is represented by solid black circles (). Line 2 is represented by open squares (□). Line 3 is represented by open diamonds (⋄).
In FIG. 28 , a phylogenetic tree of the AtNAC6 or AT5G39610 (also referred to as G525) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. AtNAC6 (AT5G39610) appears in the rounded rectangle. An ancestral sequence of AtNAC6 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 28 . AtNAC6 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi3g46900.1 and GSVIVT01007982001.
FIGS. 29A-29I show an alignment of AtNAC6 and representative clade-related proteins. The AtNAC6 clade sequences are identified within the bracket along the left-hand side of the sequences. The alignment was generated with MUSCLE v3.8.31 with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved NAM Domains appear in boxes with the dashed line boundaries in FIG. 29A-29C . A clade consensus sequence (SEQ ID NO: 1467) comprising conserved residues of the NAM domains is shown in the last row in FIG. 29A-29C . Two small consensus sequences (SEQ ID NOs: 1468 and 1469) are also shown in the last row of in FIGS. 29D and 29E , respectively.
FIG. 30 illustrates Rubisco limited photosynthetic capacity of Arabidopsis plants in a plot showing increased light-saturated photosynthesis (A sat ) over a range of leaf, sub-stomatal CO 2 concentration (C i ), in three AtNAC6 overexpression lines, as compared to a control line. Data were collected over a range of C i over which the activity of Rubisco is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line.
FIG. 31 illustrates RuBP-regeneration limited photosynthetic capacity of Arabidopsis plants in a plot showing increased light-saturated photosynthesis (A sat ) over a range of leaf, sub-stomatal CO 2 concentration (C i ), in three AtNAC6 overexpression lines, compared to a control line. Data were collected over a range of C i over which the capacity to regenerate RuBP is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line.
Legend for FIG. 30 and FIG. 31 :
 Control: □ AtNAC6-Line 1 Δ AtNAC6-Line 3 ◯ AtNAC6-Line 4

In FIG. 32 , a phylogenetic tree of WRKY17 or AT2G24570.1 (also referred to as G866) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. The WRKY17 clade members appear in the large box with the solid line boundary. WRKY17 (AT2G24570) appears in the rounded rectangle. An ancestral sequence of WRKY17 and closely-related WRKY17 clade sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 32 . WRKY17 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by LOC_Os08g13840.1 and Solyc12g096350.1.1 (indicated by the box around these sequences). A related clade is represented by the node indicated by arrow “B”.
FIGS. 33A-33H show an alignment of WRKY17 and representative clade-related proteins. The WRKY17 clade sequences are identified within the box around the first 13 listed Sequence Identifiers. The alignment was generated with MUSCLE v3.8.31 with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved “Plant Zinc Cluster Domain” and “WRKY DNA-binding Domain” appear in boxes with the dashed line boundaries in FIGS. 33E-33F and 33 F- 33 G, respectively. Two consensus sequences comprising conserved residues are shown in the last row in FIG. 33B (single underlined SEQ ID NO: 1558 and double underlined SEQ ID NO: 1559) and FIG. 33F-33G (single underlined SEQ ID NO: 1560 and double underlined SEQ ID NO: 1561).
FIG. 34 is a plot of photosynthetic capacity at growth temperature showing increased light-saturated photosynthesis (A sat ) over a range of leaf, sub-stomatal CO2 concentration (C i ), in three independent WRKY17 overexpression lines and a control line. Data were collected over a range of C, over which the activity of Rubisco is known to limit A sat . Data labeled as ‘repeat’ was collected in an independent experiment. The solid lines shown are a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line.
Legend for FIG. 34 :
◯ Control Δ WRKY17-Line 1 ⋄ WRKY17-Line 2 □ WRKY17-Line 3 Control (repeat) WRKY17-Line 1 (repeat)

In FIG. 35 , a phylogenetic tree of ZAT11 or AT2G37430 (also referred to as G355) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008 . Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. ZAT11 (AT2G37430.1) appears in the rounded rectangle. An ancestral sequence of ZAT11 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 35 . ZAT11 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi1g03810.1 and Solyc05g054650.1.1.
FIGS. 36A-36E show an alignment of ZAT11 and representative clade-related proteins. ZAT11 clade sequences are identified within the bracket along the right-hand side of the sequences. The alignment was generated with MUSCLE v3.8.31 with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second Z-C2H2 domains appear in boxes in FIG. 36B and FIGS. 36C-36D , respectively (comprising consensus sequences SEQ ID NOs 1646 and 1647). A distinct motif and its consensus sequence (SEQ ID NO: 1648) that is found with these clade members is shown in the last lines of FIG. 36D-36E .
FIG. 37 shows increased light saturated photosynthesis (A sat ) over a range of leaf sub-stomatal CO 2 concentrations (C i ), in four out of five ZAT11 overexpression lines, compared to a control line. Data were collected over a range of C i over which the activity of Rubisco is known to limit A sat . The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line.
Legend for FIG. 37 :
Control ◯ ZAT11-Line 1  ZAT11-Line 2 Δ ZAT11-Line 3 ▪ ZAT11-Line 4 □ ZAT11-Line 5




DETAILED DESCRIPTION
The present description relates to polynucleotides and polypeptides for modifying phenotypes of plants, particularly those associated with increased photosynthetic resource use efficiency and increased yield with respect to a control plant (for example, a wild-type plant). Throughout this disclosure, various information sources are referred to and/or are specifically incorporated. The information sources include scientific journal articles, patent documents, textbooks, and internet entries. While the reference to these information sources clearly indicates that they can be used by one of skill in the art, each and every one of the information sources cited herein are specifically incorporated in their entirety, whether or not a specific mention of “incorporation by reference” is noted. The contents and teachings of each and every one of the information sources can be relied on and used to make and use embodiments of the instant description.
As used herein and in the appended claims, the singular forms “a”, “an”, and “the” include the plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a host cell” includes a plurality of such host cells, and a reference to “a plant” is a reference to one or more plants, and so forth.
A “recombinant polynucleotide” is a polynucleotide that is not in its native state, e.g., the polynucleotide comprises a nucleotide sequence not found in nature, or the polynucleotide is in a context other than that in which it is naturally found, e.g., separated from nucleotide sequences with which it typically is in proximity in nature, or adjacent (or contiguous with) nucleotide sequences with which it typically is not in proximity. For example, the sequence at issue can be cloned into a vector, or otherwise recombined with one or more additional nucleic acid.
A “polypeptide” is an amino acid sequence comprising a plurality of consecutive polymerized amino acid residues e.g., at least about 15 consecutive polymerized amino acid residues. In many instances, a polypeptide comprises a polymerized amino acid residue sequence that is a regulatory polypeptide or a domain or portion or fragment thereof. Additionally, the polypeptide may comprise: (i) a localization domain; (ii) an activation domain; (iii) a repression domain; (iv) an oligomerization domain; (v) a protein-protein interaction domain; (vi) a DNA-binding domain; or the like. The polypeptide optionally comprises modified amino acid residues, naturally occurring amino acid residues not encoded by a codon, or non-naturally occurring amino acid residues.
“Protein” refers to an amino acid sequence, oligopeptide, peptide, polypeptide or portions thereof whether naturally occurring or synthetic.
In the instant description, “exogenous” refers to a heterologous nucleic acid or polypeptide that may not be naturally expressed in a plant of interest. Exogenous nucleic acids may be introduced into a plant in a stable or transient manner via, for example, transformation or breeding, and may thus serve to produce in planta a homologous RNA molecule and an encoded and functional polypeptide. Exogenous nucleic acids and polypeptides introduced thusly may comprise sequences that are wholly or partially identical or homologous to sequences that naturally occur in (i.e., that are endogenous with respect to) the plant.
A “recombinant polypeptide” is a polypeptide produced by translation of a recombinant polynucleotide. A “synthetic polypeptide” is a polypeptide created by consecutive polymerization of isolated amino acid residues using methods well known in the art. An “isolated polypeptide,” whether a naturally occurring or a recombinant polypeptide, is more enriched in (or out of) a cell than the polypeptide in its natural state in a wild-type cell, e.g., more than about 5% enriched, more than about 10% enriched, or more than about 20%, or more than about 50%, or more, enriched, i.e., alternatively denoted: 105%, 110%, 120%, 150% or more, enriched relative to wild type standardized at 100%. Such an enrichment is not the result of a natural response of a wild-type plant. Alternatively, or additionally, the isolated polypeptide is separated from other cellular components with which it is typically associated, e.g., by any of the various protein purification methods herein.
“Identity” or “similarity” refers to sequence similarity between two polynucleotide sequences or between two polypeptide sequences, with identity being a more strict comparison. The phrases “percent identity” and “% identity” refer to the percentage of sequence similarity found in a comparison of two or more polynucleotide sequences or two or more polypeptide sequences. “Sequence similarity” refers to the percent similarity in base pair sequence (as determined by any suitable method) between two or more polynucleotide sequences. Two or more sequences can be anywhere from 0-100% similar or identical, or any integer value between 0-100%. Identity or similarity can be determined by comparing a position in each sequence that may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same nucleotide base or amino acid, then the molecules are identical at that position. A degree of similarity or identity between polyBLAST nucleotide sequences is a function of the number of identical, matching or corresponding nucleotides at positions shared by the polynucleotide sequences. A degree of identity of polypeptide sequences is a function of the number of identical amino acids at corresponding positions shared by the polypeptide sequences. A degree of homology or similarity of polypeptide sequences is a function of the number of amino acids at corresponding positions shared by the polypeptide sequences. The fraction or percentage of components in common is related to the homology or identity between the sequences. Alignments such as those of 2 A- 2 I, 6 A- 6 J, 8 A- 8 I, 11 A- 11 H, 14 A- 14 L, 16 A- 16 J, 18 A- 18 L, 21 A- 21 O, 24 A- 24 O, 29 A- 29 I, 33 A- 33 H, and 36 A- 36 E may be used to identify conserved domains and relatedness within these domains. An alignment may suitably be determined by means of computer programs known in the art, such as MACVECTOR software, (1999; Accelrys, Inc., San Diego, Calif.).
“Homologous sequences” refers to polynucleotide or polypeptide sequences that are similar due to common ancestry and sequence conservation. The terms “ortholog” and “paralog” are defined below in the section entitled “Orthologs and Paralogs”. In brief, orthologs and paralogs are evolutionarily related genes that have similar sequences and functions. Orthologs are structurally related genes in different species that are derived by a speciation event. Paralogs are structurally related genes within a single species that are derived by a duplication event.
“Functional homologs” are polynucleotide or polypeptide sequences, including orthologs and paralogs, that are similar due to common ancestry and sequence conservation and have identical or similar function at the catalytic, cellular, or organismal levels. The presently disclosed AtNAC6 clade, WRKY17 clade, AtNPR3 clade, AtMYC1 clade, AtMYB19 clade, ERF058 clade, CRF1 clade, WRKY3 clade, ZAT11 clade, MYB111 clade, SPATULA clade, and AtMYB50 clade polypeptides are “functionally-related and/or closely-related” by having descended from a common ancestral sequence (from the node shown by arrow A in FIGS. 1 , 5 , 7 , 10 , 13 , 15 , 17 , 20 , 23 , 28 , 32 , and 35 ), and/or by being sufficiently similar to the sequences and domains listed in Tables 2 through 21 that they confer the same function to plants of increased photosynthetic resource use efficiency and associated improved plant vigor, quality, yield, size, and/or biomass.
Functionally-related and/or closely-related polypeptides may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, and AtMYB50-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
“Conserved domains” are recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis. A “conserved domain” or “conserved region” as used herein refers to a region in heterologous polynucleotide or polypeptide sequences where there is a relatively high degree of sequence identity between the distinct sequences. Conserved domains contain conserved sequence patterns or motifs that allow for their detection in, and identification and characterization of, polypeptide sequences. The NAM domain, Plant Zinc Cluster domain, BTB domain, bHLH-MYC domain, Myb DNA binding domain, WRKY domain, C2H2-type zinc finger (Z-C2H2) domain, AP2 domain, HLH domain, SANT domain, ANK domain, HLH domain, or Myb DNA binding domain, are examples of conserved domains.
A transgenic plant is expected to have improved or increased photosynthetic resource use efficiency relative to a control plant when the transgenic plant is transformed with a recombinant polynucleotide encoding any of the listed sequences or another AtNAC6 clade, WRKY17 clade, AtNPR3 clade, AtMYC1 clade, AtMYB19 clade, ERF058 clade, CRF1 clade, WRKY3 clade, ZAT11 clade, MYB111 clade, SPATULA clade, and AtMYB50 clade sequence, or when the transgenic plant contains or expresses a polypeptide sequence of the AtNAC6 clade, WRKY17 clade, AtNPR3 clade, AtMYC1 clade, AtMYB19 clade, ERF058 clade, CRF1 clade, WRKY3 clade, ZAT11 clade, MYB111 clade, SPATULA clade, and AtMYB50 clades.
The terms “highly stringent” or “highly stringent condition” refer to conditions that permit hybridization of DNA strands whose sequences are highly complementary, wherein these same conditions exclude hybridization of significantly mismatched DNAs. Polynucleotide sequences capable of hybridizing under stringent conditions with the polynucleotides of the present description may be, for example, variants of the disclosed polynucleotide sequences, including allelic or splice variants, or sequences that encode orthologs or paralogs of presently disclosed polypeptides. Nucleic acid hybridization methods are disclosed in detail by Kashima et al., 1985. Nature 313: 402-404; Sambrook et al., 1989. Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., and by Haymes et al., 1985. Nucleic Acid Hybridization: A Practical Approach , IRL Press, Washington, D.C., which references are incorporated herein by reference.
In general, stringency is determined by the temperature, ionic strength, and concentration of denaturing agents (e.g., formamide) used in a hybridization and washing procedure (for a more detailed description of establishing and determining stringency, see the section “Identifying Polynucleotides or Nucleic Acids by Hybridization”, below). The degree to which two nucleic acids hybridize under various conditions of stringency is correlated with the extent of their similarity. Thus, similar nucleic acid sequences from a variety of sources, such as within a plant's genome (as in the case of paralogs) or from another plant (as in the case of orthologs) that may perform similar functions can be isolated on the basis of their ability to hybridize with known related polynucleotide sequences. Numerous variations are possible in the conditions and means by which nucleic acid hybridization can be performed to isolate related polynucleotide sequences having similarity to sequences known in the art and are not limited to those explicitly disclosed herein. Such an approach may be used to isolate polynucleotide sequences having various degrees of similarity with disclosed polynucleotide sequences, such as, for example, encoded regulatory polypeptides also having at least 28% identity to SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135, and/or at least 37% identity to a NAM domain, Plant Zinc Cluster domain, BTB domain, bHLH-MYC domain, Myb DNA binding domain, WRKY domain, C2H2-type zinc finger (Z-C2H2) domain, AP2 domain, HLH domain, ANK domain, or SANT domain of SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135, increasing by steps of 1% to about 100%, identity with the conserved domains of disclosed sequences (see, for example, Tables 2-21 showing AtNAC6 clade, WRKY17 clade, AtNPR3 clade, AtMYC1 clade, AtMYB19 clade, ERF058 clade, CRF1 clade, WRKY3 clade, ZAT11 clade, MYB111 clade, SPATULA clade, and AtMYB50 clade polypeptides having at least 37%% acid identity with said domains of SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135.
“Fragment”, with respect to a polynucleotide, refers to a clone or any part of a polynucleotide molecule that retains a usable, functional characteristic. Useful fragments include oligonucleotides and polynucleotides that may be used in hybridization or amplification technologies or in the regulation of replication, transcription or translation. A “polynucleotide fragment” refers to any subsequence of a polynucleotide, typically, of at least about nine consecutive nucleotides, preferably at least about 30 nucleotides, more preferably at least about 50 nucleotides, of any of the sequences provided herein. Exemplary polynucleotide fragments are the first sixty consecutive nucleotides of the polynucleotides listed in the Sequence Listing. Exemplary fragments also include fragments that comprise a region that encodes an conserved domain of a polypeptide. Exemplary fragments also include fragments that comprise a conserved domain of a polypeptide. Exemplary fragments include fragments that comprise an conserved domain of a polypeptide, for example, of AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 (SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135), or the amino acid residues of the domains listed in Tables 2 through 21.
Fragments may also include subsequences of polypeptides and protein molecules, or a subsequence of the polypeptide. Fragments may have uses in that they may have antigenic potential. In some cases, the fragment or domain is a subsequence of the polypeptide which performs at least one biological function of the intact polypeptide in substantially the same manner, or to a similar extent, as does the intact polypeptide. For example, a polypeptide fragment can comprise a recognizable structural motif or functional domain such as a DNA-binding site or domain that binds to a DNA promoter region, an activation domain, or a domain for protein-protein interactions, and may initiate transcription. Fragments can vary in size from as few as three amino acid residues to the full length of the intact polypeptide, but are preferably at least about 30 amino acid residues in length and more preferably at least about 60 amino acid residues in length.
Fragments may also refer to a functional fragment of a promoter region. For example, a recombinant polynucleotide capable of modulating transcription in a plant may comprise a nucleic acid sequence with similarity to, or a percentage identity to, a promoter region exemplified by a promoter sequence provided in the Sequence Listing (also see promoters listed in Example I), a fragment thereof, or a complement thereof, wherein the nucleic acid sequence, or the fragment thereof, or the complement thereof, regulates expression of a polypeptide in a plant cell.
The term “plant” includes whole plants, shoot vegetative organs/structures (for example, leaves, stems and tubers), roots, flowers and floral organs/structures (for example, bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (for example, vascular tissue, ground tissue, and the like), pulped, pureed, ground-up, macerated or broken-up tissue, and cells (for example, guard cells, egg cells, and the like), and progeny of same. The class of the plants that can be transformed using the methods provided of the instant description is generally as broad as the class of higher and lower plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), gymnosperms, ferns, horsetails, psilophytes, lycophytes, and bryophytes. These plant parts, organs, structures, cells, tissue, or progeny may contain a recombinant polynucleotide of interest, such as one that comprises a described or listed polynucleotide or one that encodes a described, listed, or an AtNAC6 clade, WRKY17 clade, AtNPR3 clade, AtMYC1 clade, AtMYB19 clade, ERF058 clade, CRF1 clade, WRKY3 clade, ZAT11 clade, MYB111 clade, SPATULA clade, and AtMYB50 clade member polypeptide.
A “control plant” as used in the present description refers to a plant cell, seed, plant component, plant tissue, plant organ or whole plant used to compare against transgenic or genetically modified plant for the purpose of identifying an enhanced phenotype in the transgenic or genetically modified plant. A control plant may in some cases be a transgenic plant line that comprises an empty vector or marker gene, but does not contain the recombinant polynucleotide of the present description that is expressed in the transgenic or genetically modified plant being evaluated. In general, a control plant is a plant of the same line or variety as the transgenic or genetically modified plant being tested. A suitable control plant would include a genetically unaltered or non-transgenic plant of the parental line used to generate a transgenic plant herein.
A “transgenic plant” refers to a plant that contains genetic material not found in a wild-type plant of the same species, variety or cultivar. The genetic material may include a transgene, an insertional mutagenesis event (such as by transposon or T-DNA insertional mutagenesis), an activation tagging sequence, a mutated sequence, a homologous recombination event or a sequence modified by chimeraplasty. Typically, the foreign genetic material has been introduced into the plant by human manipulation, but any method can be used as one of skill in the art recognizes.
A transgenic line or transgenic plant line refers to the progeny plant or plants deriving from the stable integration of heterologous genetic material into a specific location or locations within the genome of the original transformed cell.
A transgenic plant may contain an expression vector or cassette. The expression vector or cassette typically comprises a polypeptide-encoding sequence operably linked (i.e., under regulatory control of) to appropriate inducible, tissue-enhanced, tissue-specific, or constitutive regulatory sequences that allow for the controlled expression of the polypeptide. The expression vector or cassette can be introduced into a plant by transformation or by breeding after transformation of a parent plant. A plant refers to a whole plant as well as to a plant part, such as seed, fruit, leaf, or root, plant tissue, plant cells or any other plant material, e.g., a plant explant, as well as to progeny thereof, and to in vitro systems that mimic biochemical or cellular components or processes in a cell. In some other embodiments, the expression vectors or cassettes do not occur naturally. In some embodiments, the expression vectors or cassettes comprise a promoter of the present application, and a gene of interest, wherein the promoter and the gene of interest do not link to each other under natural conditions, e.g., the linkage between the promoter and the gene of interest does not exist in nature. For example, in some embodiments, the promoter and the gene of interest are derived from a same plant species, but are not linked to each other under natural conditions. In some embodiments, the promoter and the gene of interest are derived from two different species, e.g., the promoter and the gene of interest are heterologous to each other. In some embodiments, the gene of interest is derived from a different plant species, a bacteria species, a fungal species, a viral species, an algae species, or an animal species. In some embodiments, the expression vectors or cassettes comprise synthetic sequences.
“Germplasm” refers to a genetic material or a collection of genetic resources for an organism from an individual plant, a group of related individual plants (for example, a plant line, a plant variety or a plant family), or a clone derived from a plant line, plant variety, plant species, or plant culture.
A constitutive promoter is active under most environmental conditions, and in most plant parts. Regulation of protein expression in a constitutive manner refers to the control of expression of a gene and/or its encoded protein in all tissues regardless of the surrounding environment or development stage of the plant.
Alternatively, expression of the disclosed or listed polypeptides may be under the regulatory control of a promoter that is not a constitutive promoter. For example, tissue-enhanced (also referred to as tissue-preferred), tissue-specific, cell type-specific, and inducible promoters constitute non-constitutive promoters; that is, these promoters do not regulate protein expression in a constitutive manner. Tissue-enhanced or tissue-preferred promoters facilitate expression of a gene and/or its encoded protein in specific tissue(s) and generally, although perhaps not completely, do not express the gene and/or protein in all other tissues of the plant, or do so to a much lesser extent. Promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as xylem, leaves, roots, or seeds. Such promoters are examples of tissue-enhanced or tissue-preferred promoters (see U.S. Pat. No. 7,365,186). Tissue-specific promoters generally confine transgene expression to a single plant part, tissue or cell-type, although many such promoters are not perfectly restricted in their expression and their regulatory control is more properly described as being “tissue-enhanced” or “tissue-preferred”. Tissue-enhanced promoters primarily regulate transgene expression in a limited number of plant parts, tissues or cell-types and cause the expression of proteins to be overwhelming restricted to a few particular tissues, plant parts, or cell types. An example of a tissue-enhanced promoter is a “photosynthetic tissue-enhanced promoter”, for which the promoter preferentially regulates gene or protein expression in photosynthetic tissues (e.g., leaves, cotyledons, stems, etc.). Tissue-enhanced promoters can be found upstream and operatively linked to DNA sequences normally transcribed in higher levels in certain plant tissues or specifically in certain plant tissues, respectively. “Cell-enhanced”, “tissue-enhanced”, or “tissue-specific” regulation thus refer to the control of gene or protein expression, for example, by a promoter that drives expression that is not necessarily totally restricted to a single type of cell or tissue, but where expression is elevated in particular cells or tissues to a greater extent than in other cells or tissues within the organism, and in the case of tissue-specific regulation, in a manner that is primarily elevated in a specific tissue. Tissue-enhanced or preferred promoters have been described in, for example, U.S. Pat. No. 7,365,186, or U.S. Pat. No. 7,619,133.
Another example of a promoter that is not a constitutive promoter is a “condition-enhanced” promoter, the latter term referring to a promoter that activates a gene in response to a particular environmental stimulus. This may include, for example, an abiotic stress, infection caused by a pathogen, light treatment, etc., and a condition-enhanced promoter drives expression in a unique pattern which may include expression in specific cell and/or tissue types within the organism (as opposed to a constitutive expression pattern in all cell types of an organism at all times).
“Wild type” or “wild-type”, as used herein, refers to a plant cell, seed, plant component, plant tissue, plant organ or whole plant that has not been genetically modified or treated in an experimental sense. Wild-type cells, seed, components, tissue, organs or whole plants may be used as controls to compare levels of expression and the extent and nature of trait modification with cells, tissue or plants of the same species in which a polypeptide's expression is altered, e.g., in that it has been knocked out, overexpressed, or ectopically expressed.
When two or more plants have “similar morphologies”, “substantially similar morphologies”, “a morphology that is substantially similar”, or are “morphologically similar”, the plants have comparable forms or appearances, including analogous features such as overall dimensions, height, width, mass, root mass, shape, glossiness, color, stem diameter, leaf size, leaf dimension, leaf density, internode distance, branching, root branching, number and form of inflorescences, and other macroscopic characteristics at a particular stage of growth. It may be difficult to distinguish two plants that are genotypically distinct but morphologically similar based on morphological characteristics alone. If the plants are morphologically similar at all stages of growth, they are also “developmentally similar”.
With regard to gene knockouts as used herein, the term “knockout” (KO) refers to a plant or plant cell having a disruption in at least one gene in the plant or cell, where the disruption results in a reduced expression or activity of the polypeptide encoded by that gene compared to a control cell. The knockout can be the result of, for example, genomic disruptions, including transposons, tilling, and homologous recombination, antisense constructs, sense constructs, RNA silencing constructs, or RNA interference. A T-DNA insertion within a gene is an example of a genotypic alteration that may abolish expression of that gene.
“Ectopic expression” or “altered expression” in reference to a polynucleotide indicates that the pattern of expression in, e.g., a transgenic plant or plant tissue, is different from the expression pattern in a wild-type plant or a reference plant of the same species. The pattern of expression may also be compared with a reference expression pattern in a wild-type plant of the same species. For example, the polynucleotide or polypeptide is expressed in a cell or tissue type other than a cell or tissue type in which the sequence is expressed in the wild-type plant, or by expression at a time other than at the time the sequence is expressed in the wild-type plant, or by a response to different inducible agents, such as hormones or environmental signals, or at different expression levels (either higher or lower) compared with those found in a wild-type plant. The term also refers to altered expression patterns that are produced by lowering the levels of expression to below the detection level or completely abolishing expression. The resulting expression pattern can be transient or stable, constitutive or inducible. In reference to a polypeptide, the term “ectopic expression or altered expression” further may relate to altered activity levels resulting from the interactions of the polypeptides with exogenous or endogenous modulators or from interactions with factors or as a result of the chemical modification of the polypeptides.
The term “overexpression” as used herein refers to a greater expression level of a gene in a plant, plant cell or plant tissue, compared to expression of that gene in a wild-type plant, cell or tissue, at any developmental or temporal stage. Overexpression can occur when, for example, the genes encoding one or more polypeptides are under the control of a strong promoter (e.g., the cauliflower mosaic virus 35S transcription initiation region). Overexpression may also be achieved by placing a gene of interest under the control of an inducible or tissue specific promoter, or may be achieved through integration of transposons or engineered T-DNA molecules into regulatory regions of a target gene. Other means for inducing overexpression may include making targeted changes in a gene's native promoter, e.g. through elimination of negative regulatory sequences or engineering positive regulatory sequences, though the use of targeted nuclease activity (such as zinc finger nucleases or TAL effector nucleases) for genome editing. Elimination of micro-RNA binding sites in a gene's transcript may also result in overexpression of that gene. Additionally, a gene may be overexpressed by creating an artificial transcriptional activator targeted to bind specifically to its promoter sequences, comprising an engineered sequence-specific DNA binding domain such as a zinc finger protein or TAL effector protein fused to a transcriptional activation domain. Thus, overexpression may occur throughout a plant, in specific tissues of the plant, or in the presence or absence of particular environmental signals, depending on the promoter or overexpression approach used.
Overexpression may take place in plant cells normally lacking expression of polypeptides functionally equivalent or identical to the present polypeptides. Overexpression may also occur in plant cells where endogenous expression of the present polypeptides or functionally equivalent molecules normally occurs, but such normal expression is at a lower level. Overexpression thus results in a greater than normal production, or “overproduction” of the polypeptide in the plant, cell or tissue.
“Photosynthetic resource-use efficiency” is defined as the rate of photosynthesis achieved per unit use of a given resource. Consequently, increases in photosynthesis relative to the use of a given resource will improve photosynthetic resource-use efficiency. Photosynthesis is constrained by the availability of various resources, including light, water and nitrogen. Improving the efficiency with which photosynthesis makes use of light, water and nitrogen is a means for increasing plant productivity, crop growth, and yield. For the purposes of comparing a plant of interest to a reference or control plant, the ratio of photosynthesis to use of a given resource is often determined for a fixed unit of leaf area. Examples of increased photosynthetic resource-use efficiency would be an increase in the ratio of the rate of photosynthesis for a given leaf relative to, for example, the rate of transpiration from the same leaf area, nitrogen or chlorophyll invested in that leaf area, or light absorbed by that same leaf area. Increased photosynthetic resource use efficiency may result from increased photosynthetic rate, photosynthetic capacity, a decrease in leaf chlorophyll content, a decrease in percentage of nitrogen in leaf dry weight, increased transpiration efficiency, an increase in resistance to water vapor diffusion exerted by leaf stomata, an increased rate of relaxation of photoprotective reactions operating in the light harvesting antennae, a decrease in the ratio of the carbon isotope 12 C to 13 C in above-ground biomass, and/or an increase in the total dry weight of above-ground plant material.
“Photosynthetic rate” refers to the rate of photosynthesis achieved by a leaf, and is typically expressed relative to a unit of leaf area. The photosynthetic rate at any given time results from the photosynthetic capacity of the leaf (see below) and the biotic or abiotic environmental constraints prevailing at that time.
“Photosynthetic capacity” refers to the capacity for photosynthesis per unit leaf area and is set by the leafs investment in the components of the photosynthetic apparatus. Key components, among many, would be the pigments and proteins required to regulate light absorption and transduction of light energy to the photosynthetic reaction centers, and the enzymes required to operate the C3 and C4 dark reactions of photosynthesis. Increasing photosynthetic capacity is seen as an important means of increasing leaf and crop-canopy photosynthesis, and crop yield.
“Rubisco (ribulose-1,5-bisphosphate carboxylase oxygenase) activity” refers to the activation state of Rubisco, the most abundant protein in the chloroplast and a key limitation to C3 photosynthesis. Increasing Rubisco activity by: increasing the amount of Rubisco in the chloroplast; impacting any combination of specific reactions that regulate Rubisco activity; or increasing the concentration of CO 2 in the chloroplast, is seen as an important means to improving C3 leaf and crop-canopy photosynthesis and crop yield.
The “capacity for RuBP (ribulose-1,5-bisphosphate) regeneration” refers to the rate at which RuBP, a key photosynthetic substrate is regenerated in the Calvin cycle. Increasing the capacity for RuBP regeneration by increasing the activity of enzymes in the regenerative phase of the Calvin cycle is seen as an important means to improving C3 leaf and crop-canopy photosynthesis and crop yield that will become progressively more important as atmospheric CO 2 concentrations continue to rise.
“Leaf chlorophyll content” refers to the chlorophyll content of the leaf expressed either per unit leaf area or unit weight. Sun leaves in the upper part of crop canopies are thought to have higher leaf chlorophyll content than is required for photosynthesis. The consequence is that these leaves: invest more nitrogen in chlorophyll than is required for photosynthesis; are prone to photodamage associated with absorbing more light energy than can be dissipated via photosynthesis; and impair the transmission of light into the leaf and lower canopy where photosynthesis is light limited. Consequently, decreasing leaf chlorophyll content of upper canopy leaves is considered an effective means to improving photosynthetic resource-use efficiency.
“Non-photochemical quenching” is a term that covers photoprotective processes that dissipate absorbed light energy as heat from the light-harvesting antenna of photosystem II. Non-photochemical quenching is a key regulator of the efficiency with which electron transport is initiated by PSII and the efficiency of photosynthesis at low light. Decreasing the level of non-photochemical quenching, or increasing the speed with which it relaxes is expected to confer cumulative gains in photosynthesis every time the light intensity to which the canopy is exposed transitions from high to low, and is considered a means to improving canopy photosynthesis when integrated over a growing season.
“Nitrogen limitation” or “nitrogen-limiting” refers to nitrogen levels that act as net limitations on primary production in terrestrial or aquatic biomes. Much of terrestrial growth, including much of crop growth, is limited by the availability of nitrogen, which can be alleviated by nitrogen input through deposition or fertilization.
“Water use efficiency”, or WUE, measured as the biomass produced per unit transpiration, describes the relationship between water use and crop production. The basic physiological definition of WUE equates to the ratio of photosynthesis (A) to transpiration (T), also referred to as transpiration efficiency (Karaba et al. 2007, supra; Morison et al., 2008, supra).
“Stomatal conductance” refers to a measurement of the limitation that the stomatal pore imposes on CO 2 diffusion into, and H 2 O diffusion out of, the leaf. Decreasing stomatal conductance will decrease water loss from the leaf and crop canopy via transpiration. This will conserve soil water, delay the onset and reduce the severity of drought effects on canopy photosynthesis and other physiology. Decreasing stomatal conductance will also decrease photosynthesis. However, the magnitude of the decrease in photosynthesis will typically be less than the decrease in transpiration, and transpiration efficiency will increase as a result. Conversely, increasing stomatal conductance can increase the diffusion of CO 2 into the leaf and increase photosynthesis in a C3 leaf. Typically, transpiration will increase to a greater extent than photosynthesis, and transpiration efficiency will therefore decrease.
“Yield” or “plant yield” refers to increased plant growth, increased crop growth, increased biomass, and/or increased plant product production (including grain), and is dependent to some extent on temperature, plant size, organ size, planting density, light, water and nutrient availability, and how the plant copes with various stresses, such as through temperature acclimation and water or nutrient use efficiency. For grain crops, yield generally refers to an amount of grain produced or harvested per unit of land area, such as bushels or tons per acre or tonnes per hectare. Increased or improved yield may be measured as increased seed yield, increased plant product yield (plant products include, for example, plant tissue, including ground or otherwise broken-up plant tissue, and products derived from one or more types of plant tissue), or increased vegetative yield.
DESCRIPTION OF THE SPECIFIC EMBODIMENTS
Regulatory Polypeptides Modify Expression of Endogenous Genes
A regulatory polypeptide may include, but is not limited to, any polypeptide that can activate or repress transcription of a single gene or a number of genes. As one of ordinary skill in the art recognizes, regulatory polypeptides can be identified by the presence of a region or domain of structural similarity or identity to a specific consensus sequence or the presence of a specific consensus DNA-binding motif (see, for example, Riechmann et al., 2000a. supra). The plant regulatory polypeptides of the instant description belong to the MYB-(R1)R2R3 family (Shore and Sharrocks, 1995. Eur. J. Biochem. 229:1-13; Ng and Yanofsky, 2001. Nat. Rev. Genet. 2:186-195; Alvarez-Buylla et al., 2000. Proc. Natl. Acad. Sci. USA. 97:5328-5333), AP2 family (Shore and Sharrocks, 1995. Eur. J. Biochem. 229:1-13; Ng and Yanofsky, 2001. Nat. Rev. Genet. 2:186-195; Alvarez-Buylla et al., 2000. Proc. Natl. Acad. Sci. USA. 97:5328-5333), HLH/MYC family (Toledo-Ortiz et al. (2003) The Plant Cell (15) 1749-1770; Heim et al. (2003) Mol. Biol. Evol. 20(5): 735-747; Weigel and Nilsson, 1995. Nature 377: 495-500; Goff, 1992. Genes Dev. 6: 864-875; Murre, 1989. Cell 58: 537-544), MYB-(R1)R2R3 family (Myb Domain Protein 111, NCBI Reference Sequence: NP — 199744.1; Stracke et al., 2007. Plant J. 50:660-677; Dai et al. 2007. Plant Physiol. 143: 1739-1751; Gabrielsen et al. 1991. Science 253:1140-1143), AKR family (Michaely et al. (1992) Trends Cell Biol. 2:127-129; Bork (1993) Proteins 17:363-374; Cao et al. (1997) Cell 88:57-63), WRKY family (Ishiguro and Nakamura (1994) Mol. Gen. Genet. 244:563-571; Eulgem et al. (2000) Trends Plant Sci. 5:199-206; Ülker and Somssich IE (2004) Curr. Opin. Plant Biol. 7:491-498; Zhang and Wang (2005) BMC Evol. Biol. 5:1; Lai et al., (2008) BMC Plant Biol. 8:68; Pandey and Somssich (2009) Plant Physiol. 150:1648-1655), NAC family (Olsen et al. 2005. Trends Plant Sci. 10:79-87; Ooka et al. 2003. DNA Res. 10:239-47), Z-C2H2 family (Berg, 1988. Proc. Natl. Acad. Sci. USA. 85: 99-102; Meissner and Michael, 1997. Plant Mol. Biol. 33: 615-624; Thiesen and Bach, 1993. Ann. NY Acad. Sci. 684: 246-249) family and are putative regulatory polypeptides.
Generally, regulatory polypeptides control the manner in which information encoded by genes is used to produce gene products and control various pathways, and may be involved in diverse processes including, but not limited to, cell differentiation, proliferation, morphogenesis, and the regulation of growth or environmental responses. Accordingly, one skilled in the art would recognize that by expressing the present sequences in a plant, one may change the expression of autologous genes or induce the expression of introduced genes. By affecting the expression of similar autologous sequences in a plant that have the biological activity of the present sequences, or by introducing the present sequences into a plant, one may alter a plant's phenotype to one with improved traits related to photosynthetic resource use efficiency. The sequences of the instant description may also be used to transform a plant and introduce desirable traits not found in the wild-type cultivar or strain. Plants may then be selected for those that produce the most desirable degree of over- or under-expression of target genes of interest and coincident trait improvement.
The sequences of the present description may be from any species, particularly plant species, in a naturally occurring form or from any source whether natural, synthetic, semi-synthetic or recombinant. The sequences of the instant description may also include fragments of the present amino acid sequences. Where “amino acid sequence” is recited to refer to an amino acid sequence of a naturally occurring protein molecule, “amino acid sequence” and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule.
In addition to methods for modifying a plant phenotype by employing one or more polynucleotides and polypeptides of the instant description described herein, the polynucleotides and polypeptides of the instant description have a variety of additional uses. These uses include their use in the recombinant production (i.e., expression) of proteins; as regulators of plant gene expression, as diagnostic probes for the presence of complementary or partially complementary nucleic acids (including for detection of natural coding nucleic acids); as substrates for further reactions, e.g., mutation reactions, PCR reactions, or the like; as substrates for cloning e.g., including digestion or ligation reactions; and for identifying exogenous or endogenous modulators of the regulatory polypeptides. The polynucleotide can be, e.g., genomic DNA or RNA, a transcript (such as an mRNA), a cDNA, a PCR product, a cloned DNA, a synthetic DNA or RNA, or the like. The polynucleotide can comprise a sequence in either sense or antisense orientations.
Expression of genes that encode polypeptides that modify expression of endogenous genes, polynucleotides, and proteins are well known in the art. In addition, transgenic plants comprising polynucleotides encoding regulatory polypeptides may also modify expression of endogenous genes, polynucleotides, and proteins. Examples include Peng et al., 1997. Genes Development 11: 3194-3205, and Peng et al., 1999. Nature 400: 256-261. In addition, many others have demonstrated that an Arabidopsis regulatory polypeptide expressed in an exogenous plant species elicits the same or very similar phenotypic response. See, for example, Fu et al., 2001. Plant Cell 13: 1791-1802; Nandi et al., 2000. Curr. Biol. 10: 215-218; Coupland, 1995. Nature 377: 482-483; and Weigel and Nilsson, 1995. Nature 377: 482-500.
In another example, Mandel et al., 1992b. Cell 71-133-143, and Suzuki et al., 2001. Plant J. 28: 409-418, teach that a transcription factor expressed in another plant species elicits the same or very similar phenotypic response of the endogenous sequence, as often predicted in earlier studies of Arabidopsis transcription factors in Arabidopsis (see Mandel et al., 1992a. Nature 360: 273-277; Suzuki et al., 2001. supra). Other examples include Müller et al., 2001. Plant J. 28: 169-179; Kim et al., 2001. Plant J. 25: 247-259; Kyozuka and Shimamoto, 2002. Plant Cell Physiol. 43: 130-135; Boss and Thomas, 2002. Nature, 416: 847-850; He et al., 2000. Transgenic Res. 9: 223-227; and Robson et al., 2001. Plant J. 28: 619-631.
In yet another example, Gilmour et al., 1998. Plant J. 16: 433-442 teach an Arabidopsis AP2 transcription factor, CBF1, which, when overexpressed in transgenic plants, increases plant freezing tolerance. Jaglo et al., 2001. Plant Physiol. 127: 910-917, further identified sequences in Brassica napus which encode CBF-like genes and that transcripts for these genes accumulated rapidly in response to low temperature. Transcripts encoding CBF proteins were also found to accumulate rapidly in response to low temperature in wheat, as well as in tomato. An alignment of the CBF proteins from Arabidopsis, B. napus , wheat, rye, and tomato revealed the presence of conserved consecutive amino acid residues which bracket the AP2/EREBP DNA binding domains of the proteins and distinguish them from other members of the AP2/EREBP protein family (Jaglo et al., 2001. supra).
Regulatory polypeptides mediate cellular responses and control traits through altered expression of genes containing cis-acting nucleotide sequences that are targets of the introduced regulatory polypeptide. It is well appreciated in the art that the effect of a regulatory polypeptide on cellular responses or a cellular trait is determined by the particular genes whose expression is either directly or indirectly (e.g., by a cascade of regulatory polypeptide binding events and transcriptional changes) altered by regulatory polypeptide binding. In a global analysis of transcription comparing a standard condition with one in which a regulatory polypeptide is overexpressed, the resulting transcript profile associated with regulatory polypeptide overexpression is related to the trait or cellular process controlled by that regulatory polypeptide. For example, the PAP2 gene and other genes in the Myb family have been shown to control anthocyanin biosynthesis through regulation of the expression of genes known to be involved in the anthocyanin biosynthetic pathway (Bruce et al., 2000. Plant Cell 12: 65-79; and Borevitz et al., 2000. Plant Cell 12: 2383-2393). Further, global transcript profiles have been used successfully as diagnostic tools for specific cellular states (e.g., cancerous vs. non-cancerous; Bhattacharjee et al., 2001 . Proc. Natl. Acad. Sci. USA 98: 13790-13795; and Xu et al., 2001 . Proc. Natl. Acad. Sci. USA 98: 15089-15094). Consequently, it is evident to one skilled in the art that similarity of transcript profile upon overexpression of different regulatory polypeptides would indicate similarity of regulatory polypeptide function.
Polypeptides and Polynucleotides of the Present Description.
The present description includes putative regulatory polypeptides, and isolated or recombinant polynucleotides encoding the polypeptides, or novel sequence variant polypeptides or polynucleotides encoding novel variants of polypeptides derived from the specific sequences provided in the Sequence Listing; the recombinant polynucleotides of the instant description may be incorporated in expression vectors for the purpose of producing transformed plants.
Because of their relatedness at the nucleotide level, the claimed sequences will typically share at least about 30% nucleotide sequence identity, or at least 35% identity, at least 40% nucleotide sequence identity, at least 45% identity, at least 50%, at least 51%, at least 52%, at least 53%, at least 54%, at least 55%, at least 56%, at least 57%, at least 58%, at least 59%, at least 60%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95% or at least 96%, at least 97%, at least 98%, at least 99%, or about 100% sequence identity to one or more of the listed full-length sequences, or to a listed sequence but excluding or outside of the region(s) encoding a known consensus sequence or consensus DNA-binding site, or outside of the region(s) encoding one or all conserved domains. The degeneracy of the genetic code enables major variations in the nucleotide sequence of a polynucleotide while maintaining the amino acid sequence of the encoded protein.
Because of their relatedness at the protein level, the claimed nucleotide sequences will typically encode a polypeptide that is at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identical, in its amino acid sequence to the entire length of any of SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209.
Also provided are methods for modifying yield from a plant by modifying the mass, size or number of plant organs or seed of a plant by controlling a number of cellular processes, and for increasing a plant's photosynthetic resource use efficiency. These methods are based on the ability to alter the expression of critical regulatory molecules that may be conserved between diverse plant species. Related conserved regulatory molecules may be originally discovered in a model system such as Arabidopsis and homologous, functional molecules then discovered in other plant species. The latter may then be used to confer increased yield or photosynthetic resource use efficiency in diverse plant species.
Sequences in the Sequence Listing, derived from diverse plant species, may be ectopically expressed in overexpressor plants. The changes in the characteristic(s) or trait(s) of the plants may then be observed and found to confer increased yield and/or increased photosynthetic resource use efficiency. Therefore, the polynucleotides and polypeptides can be used to improve desirable characteristics of plants.
The polynucleotides of the instant description are also ectopically expressed in overexpressor plant cells and the changes in the expression levels of a number of genes, polynucleotides, and/or proteins of the plant cells observed. Therefore, the polynucleotides and polypeptides can be used to change expression levels of genes, polynucleotides, and/or proteins of plants or plant cells.
The data presented herein represent the results obtained in experiments with polynucleotides and polypeptides that may be expressed in plants for the purpose of increasing yield that arises from improved photosynthetic resource use efficiency.
Variants of the Disclosed Sequences.
Also within the scope of the instant description is a variant of a nucleic acid listed in the Sequence Listing, that is, one having a sequence that differs from the one of the polynucleotide sequences in the Sequence Listing, or a complementary sequence, that encodes a functionally equivalent polypeptide (i.e., a polypeptide having some degree of equivalent or similar biological activity) but differs in sequence from the sequence in the Sequence Listing, due to degeneracy in the genetic code. Included within this definition are polymorphisms that may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding polypeptide, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding polypeptide.
Differences between presently disclosed polypeptides and polypeptide variants are limited so that the sequences of the former and the latter are closely similar overall and, in many regions, identical. Presently disclosed polypeptide sequences and similar polypeptide variants may differ in amino acid sequence by one or more substitutions, additions, deletions, fusions and truncations, which may be present in any combination. These differences may produce silent changes and result in a functionally equivalent polypeptides. Thus, it will be readily appreciated by those of skill in the art, that any of a variety of polynucleotide sequences is capable of encoding the polypeptides and homolog polypeptides of the instant description. A polypeptide sequence variant may have “conservative” changes, wherein a substituted amino acid has similar structural or chemical properties.
Conservative substitutions include substitutions in which at least one residue in the amino acid sequence has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the Table 1 when it is desired to maintain the activity of the protein. Table 1 shows amino acids which can be substituted for an amino acid in a protein and which are typically regarded as conservative substitutions.





TABLE 1



Possible conservative amino acid substitutions






Amino Acid
Conservative


Residue
substitutions





Ala
Ser


Arg
Lys


Asn
Gln; His


Asp
Glu


Gln
Asn


Cys
Ser


Glu
Asp


Gly
Pro


His
Asn; Gln


Ile
Leu, Val


Leu
Ile; Val


Lys
Arg; Gln


Met
Leu; Ile


Phe
Met; Leu; Tyr


Pro
Gly


Ser
Thr; Gly


Thr
Ser; Val


Trp
Tyr


Tyr
Trp; Phe


Val
Ile; Leu










































The polypeptides provided in the Sequence Listing have a novel activity, such as, for example, regulatory activity. Although all conservative amino acid substitutions (for example, one basic amino acid substituted for another basic amino acid) in a polypeptide will not necessarily result in the polypeptide retaining its activity, it is expected that many of these conservative mutations would result in the polypeptide retaining its activity. Most mutations, conservative or non-conservative, made to a protein but outside of a conserved domain required for function and protein activity will not affect the activity of the protein to any great extent.
Deliberate amino acid substitutions may thus be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as a significant amount of the functional or biological activity of the polypeptide is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, positively charged amino acids may include lysine and arginine, and amino acids with uncharged polar head groups having similar hydrophilicity values may include leucine, isoleucine, and valine; glycine and alanine; asparagine and glutamine; serine and threonine; and phenylalanine and tyrosine. More rarely, a variant may have “non-conservative” changes, e.g., replacement of a glycine with a tryptophan. Similar minor variations may also include amino acid deletions or insertions, or both. Related polypeptides may comprise, for example, additions and/or deletions of one or more N-linked or O-linked glycosylation sites, or an addition and/or a deletion of one or more cysteine residues. Guidance in determining which and how many amino acid residues may be substituted, inserted or deleted without abolishing functional or biological activity may be found using computer programs well known in the art, for example, DNASTAR software (see U.S. Pat. No. 5,840,544).
Conserved Domains.
Conserved domains are recurring functional and/or structural units of a protein sequence within a protein family (for example, a family of regulatory proteins), and distinct conserved domains have been used as building blocks in molecular evolution and recombined in various arrangements to make proteins of different protein families with different functions. Conserved domains often correspond to the 3-dimensional domains of proteins and contain conserved sequence patterns or motifs, which allow for their detection in polypeptide sequences with, for example, the use of a Conserved Domain Database (for example, at www.ncbi.nlm.nih.gov/cdd). The National Center for Biotechnology Information Conserved Domain Database defines conserved domains as recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis. Conserved domains contain conserved sequence patterns or motifs, which allow for their detection in polypeptide sequences (Conserved Domain Database; www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml). A “conserved domain” or “conserved region” as used herein refers to a region in heterologous polynucleotide or polypeptide sequences where there is a relatively high degree of sequence identity between the distinct sequences. A ‘NAM domain’ is an example of a conserved domain.
Conserved domains may also be identified as regions or domains of identity to a specific consensus sequence (see, for example, Riechmann et al., 2000a. Science 290, 2105-2110; Riechmann et al., 2000b. Curr Opin Plant Biol 3: 423-434). Thus, by using alignment methods well known in the art, the conserved domains of the plant polypeptides, for example, for the NAM domain proteins may be determined. The polypeptides of Table 17 have conserved domains specifically indicated by amino acid coordinate start and stop sites. A comparison of the regions of these polypeptides allows one of skill in the art (see, for example, Reeves and Nissen, 1990. J. Biol. Chem. 265, 8573-8582; Reeves and Nissen, 1995. Prog. Cell Cycle Res. 1: 339-349) to identify domains or conserved domains for any of the polypeptides listed or referred to in this disclosure.
Conserved domain models are generally identified with multiple sequence alignments of related proteins spanning a variety of organisms (for example, exemplary conserved domains of the disclosed sequences can be found in Tables 2-21) and the Sequence Listing. These alignments reveal sequence regions containing the same, or similar, patterns of amino acids. Multiple sequence alignments, three-dimensional structure and three-dimensional structure superposition of conserved domains can be used to infer sequence, structure, and functional relationships (Conserved Domain Database, supra). Since the presence of a particular conserved domain within a polypeptide is highly correlated with an evolutionarily conserved function, a conserved domain database may be used to identify the amino acids in a protein sequence that are putatively involved in functions such as binding or catalysis, as mapped from conserved domain annotations to the query sequence. For example, the presence in a protein of a NAM domain that is structurally and phylogenetically similar to one or more domains shown in Table 17 would be a strong indicator of a related function in plants (e.g., the function of regulating and/or improving photosynthetic resource use efficiency, yield, size, biomass, and/or vigor; i.e., a polypeptide with such a domain is expected to confer altered photosynthetic resource use efficiency, yield, size, biomass, and/or vigor when its expression level is altered). Sequences herein referred to as functionally-related and/or closely-related to the sequences or domains listed in Tables 2 through 21 including polypeptides that are closely related to the polypeptides of the instant description, may have conserved domains that share at least 15 amino acid residues in length and at least 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% amino acid identity to the sequences provided in the Sequence Listing or in Tables 2 through 21, or at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% sequence identity to a listed or disclosed consensus sequence, and have similar functions in that the polypeptides of the instant description. Said polypeptides may, when their expression level is altered by suppressing their expression, knocking out their expression, or increasing their expression, confer at least one regulatory activity selected from the group consisting of increased photosynthetic resource use efficiency, greater yield, greater size, greater biomass, and/or greater vigor as compared to a control plant. Methods using manual alignment of sequences similar or homologous to one or more polynucleotide sequences or one or more polypeptides encoded by the polynucleotide sequences may be used to identify regions of similarity and the NAM domain, Plant Zinc Cluster domain, BTB domain, bHLH-MYC domain, Myb DNA binding domain, WRKY DNA-binding domain, C2H2-type zinc finger (Z-C2H2) domain, AP2 domain, HLH domain, SANT domain, ANK domain, HLH domain, or (‘Z-C2H2-2’) domain, or other motifs. Such manual methods are well-known of those of skill in the art and can include, for example, comparisons of tertiary structure between a polypeptide sequence encoded by a polynucleotide that comprises a known function and a polypeptide sequence encoded by a polynucleotide sequence that has a function not yet determined. Such examples of tertiary structure may comprise predicted alpha helices, beta-sheets, amphipathic helices, leucine zipper motifs, zinc finger motifs, proline-rich regions, cysteine repeat motifs, and the like.
With respect to polynucleotides encoding presently disclosed polypeptides, a conserved domain refers to a subsequence within a polypeptide family the presence of which is correlated with at least one function exhibited by members of the polypeptide family, and which exhibits a high degree of sequence homology, such as at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identity to a consensus sequence of a polypeptide of the Sequence Listing (e.g., any of
AtNAC6 clade sequences SEQ ID NO: 1467, 1468, 1469, WRKY17 clade sequences SEQ ID NO: 1558, 1559, 1560, 1561, AtNPR3 clade sequences SEQ ID NO: 981 to 986, AtMYC1 clade sequences SEQ ID NO: 1153, 1154, AtMYB19 clade consensus sequences SEQ ID NO: 129, 130, 131, 132, ERF058 clade consensus sequences SEQ ID NO: 579, 580, 581, CRF1 clade consensus sequences SEQ ID NO: 441, 442, WRKY3 clade consensus sequences SEQ ID NO: 1299, 1300, ZAT11 clade consensus sequences SEQ ID NO: 1646, 1647, 1648, MYB111 clade consensus sequences SEQ ID NO: 834, 835, 836, SPATULA clade consensus sequence SEQ ID NO: 687, or AtMYB50 clade consensus sequences SEQ ID NO: 302, 303, 304, 305, or presented in the present Figures. Sequences that possess or encode for conserved domains that meet these criteria of percentage identity, and that have comparable biological and regulatory activity to the present polypeptide sequences, thus being members of the AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptides or sequences in the AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade, are described. Sequences having lesser degrees of identity but comparable biological activity are considered to be equivalents.
Orthologs and Paralogs.
Homologous sequences as described above can comprise orthologous or paralogous sequences. Several different methods are known by those of skill in the art for identifying and defining these functionally homologous sequences. General methods for identifying orthologs and paralogs, including phylogenetic methods, sequence similarity and hybridization methods, are described herein; an ortholog or paralog, including equivalogs, may be identified by one or more of the methods described below.
As described by Eisen, 1998. Genome Res. 8: 163-167, evolutionary information may be used to predict gene function. It is common for groups of genes that are homologous in sequence to have diverse, although usually related, functions. However, in many cases, the identification of homologs is not sufficient to make specific predictions because not all homologs have the same function. Thus, an initial analysis of functional relatedness based on sequence similarity alone may not provide one with a means to determine where similarity ends and functional relatedness begins. Fortunately, it is well known in the art that protein function can be classified using phylogenetic analysis of gene trees combined with the corresponding species. Functional predictions can be greatly improved by focusing on how the genes became similar in sequence (i.e., by evolutionary processes) rather than on the sequence similarity itself (Eisen, supra). In fact, many specific examples exist in which gene function has been shown to correlate well with gene phylogeny (Eisen, supra). Thus, “[t]he first step in making functional predictions is the generation of a phylogenetic tree representing the evolutionary history of the gene of interest and its homologs. Such trees are distinct from clusters and other means of characterizing sequence similarity because they are inferred by techniques that help convert patterns of similarity into evolutionary relationships . . . . After the gene tree is inferred, biologically determined functions of the various homologs are overlaid onto the tree. Finally, the structure of the tree and the relative phylogenetic positions of genes of different functions are used to trace the history of functional changes, which is then used to predict functions of [as yet] uncharacterized genes” (Eisen, supra).
Within a single plant species, gene duplication may cause two copies of a particular gene, giving rise to two or more genes with similar sequence and often similar function known as paralogs. A paralog is therefore a similar gene formed by duplication within the same species. Paralogs typically cluster together or in the same clade (a group of similar genes) when a gene family phylogeny is analyzed using programs such as CLUSTAL (Thompson et al., 1994 . Nucleic Acids Res. 22: 4673-4680; Higgins et al., 1996 . Methods Enzymol. 266: 383-402). Groups of similar genes can also be identified with pair-wise BLAST analysis (Feng and Doolittle, 1987 . J. Mol. Evol. 25: 351-360). For example, a clade of very similar MADS domain transcription factors from Arabidopsis all share a common function in flowering time (Ratcliffe et al., 2001. Plant Physiol. 126: 122-132), and a group of very similar AP2 domain transcription factors from Arabidopsis are involved in tolerance of plants to freezing (Gilmour et al., 1998. supra). Analysis of groups of similar genes with similar function that fall within one clade can yield sub-sequences that are particular to the clade. These sub-sequences, known as consensus sequences, can not only be used to define the sequences within each clade, but define the functions of these genes; genes within a clade may contain paralogous sequences, or orthologous sequences that share the same function (see also, for example, Mount, 2001, in Bioinformatics: Sequence and Genome Analysis , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., p. 543).
Regulatory polypeptide gene sequences are conserved across diverse eukaryotic species lines (Goodrich et al., 1993 . Cell 75:519-530; Lin et al., 1991. Nature 353:569-571; Sadowski et al., 1988. Nature 335: 563-564). Plants are no exception to this observation; diverse plant species possess regulatory polypeptides that have similar sequences and functions. Speciation, the production of new species from a parental species, gives rise to two or more genes with similar sequence and similar function. These genes, termed orthologs, often have an identical function within their host plants and are often interchangeable between species without losing function. Because plants have common ancestors, many genes in any plant species will have a corresponding orthologous gene in another plant species. Once a phylogenic tree for a gene family of one species has been constructed using a program such as CLUSTAL (Thompson et al., 1994. supra; Higgins et al., 1996. supra) potential orthologous sequences can be placed into the phylogenetic tree and their relationship to genes from the species of interest can be determined. Orthologous sequences can also be identified by a reciprocal BLAST strategy. Once an orthologous sequence has been identified, the function of the ortholog can be deduced from the identified function of the reference sequence.
By using a phylogenetic analysis, one skilled in the art would recognize that the ability to deduce similar functions conferred by closely-related polypeptides is predictable. This predictability has been confirmed by our own many studies in which we have found that a wide variety of polypeptides have orthologous or closely-related homologous sequences that function as does the first, closely-related reference sequence. For example, distinct regulatory polypeptides, including:
(i) AP2 family Arabidopsis G47 (found in U.S. Pat. No. 7,135,616), a phylogenetically-related sequence from soybean, and two phylogenetically-related homologs from rice all can confer greater tolerance to drought, hyperosmotic stress, or delayed flowering as compared to control plants;
(ii) CAAT family Arabidopsis G481 (found in PCT patent publication no. WO2004076638), and numerous phylogenetically-related sequences from eudicots and monocots can confer greater tolerance to drought-related stress as compared to control plants;
(iii) Myb-related Arabidopsis G682 (found in U.S. Pat. Nos. 7,223,904 and 7,193,129) and numerous phylogenetically-related sequences from eudicots and monocots can confer greater tolerance to heat, drought-related stress, cold, and salt as compared to control plants;
(iv) WRKY family Arabidopsis G1274 (found in U.S. Pat. No. 7,196,245) and numerous closely-related sequences from eudicots and monocots have been shown to confer increased water deprivation tolerance, and
(v) AT-hook family soy sequence G3456 (found in U.S. patent publication no. 20040128712A1) and numerous phylogenetically-related sequences from eudicots and monocots, increased biomass compared to control plants when these sequences are overexpressed in plants.
The polypeptides sequences belong to distinct clades of polypeptides that include members from diverse species. In each case, most or all of the clade member sequences derived from both eudicots and monocots have been shown to confer increased yield or tolerance to one or more abiotic stresses when the sequences were overexpressed. These studies each demonstrate that evolutionarily conserved genes from diverse species are likely to function similarly (i.e., by regulating similar target sequences and controlling the same traits), and that polynucleotides from one species may be transformed into closely-related or distantly-related plant species to confer or improve traits.
Orthologs and paralogs of presently disclosed polypeptides may be cloned using compositions provided by the present description according to methods well known in the art. cDNAs can be cloned using mRNA from a plant cell or tissue that expresses one of the present sequences. Appropriate mRNA sources may be identified by interrogating Northern blots with probes designed from the present sequences, after which a library is prepared from the mRNA obtained from a positive cell or tissue. Polypeptide-encoding cDNA is then isolated using, for example, PCR, using primers designed from a presently disclosed gene sequence, or by probing with a partial or complete cDNA or with one or more sets of degenerate probes based on the disclosed sequences. The cDNA library may be used to transform plant cells. Expression of the cDNAs of interest is detected using, for example, microarrays, Northern blots, quantitative PCR, or any other technique for monitoring changes in expression. Genomic clones may be isolated using similar techniques to those.
Examples of orthologs of the Arabidopsis polypeptide sequences and their functionally similar orthologs are listed in Tables 2 through 21 and the Sequence Listing. In addition to the sequences in Tables 2 through 21 and the Sequence Listing, the claimed nucleotide sequences are phylogenetically and structurally similar to sequences listed in the Sequence Listing and can function in a plant by increasing photosynthetic resource use efficiency and/or and increasing yield, vigor, or biomass when ectopically expressed, or overexpressed, in a plant. Since a significant number of these sequences are phylogenetically and sequentially related to each other and may be shown to increase yield from a plant and/or photosynthetic resource use efficiency, one skilled in the art would predict that other similar, phylogenetically related sequences falling within the present clades of polypeptides, including AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, and AtMYB50 clade polypeptide sequences, would also perform similar functions when ectopically expressed.
Background Information for the AtNAC6 clade, WRKY17 clade, AtNPR3 clade, AtMYC1 clade, AtMYB19 clade, ERF058 clade, CRF1 clade, WRKY3 clade, ZAT11 clade, MYB111 clade, SPATULA clade, and AtMYB50 clades. A number of phylogenetically-related sequences have been found in other plant species. Tables 2 through 21 list a number of AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade sequences from diverse species. The tables include the SEQ ID NO: (Column 1), the species from which the sequence was derived and the Gene Identifier (“GID”; Column 2), the percent identity of the polypeptide in Column 1 to the full length AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 polypeptide, SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135, respectively, as determined by a BLASTp analysis, for example, with a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (Henikoff and Henikoff, 1989 . Proc. Natl. Acad. Sci. USA 89:10915; Henikoff and Henikoff, 1991 . Nucleic Acids Res. 19: 6565-6572) (Column 3), the amino acid residue coordinates for the listed conserved domains in amino acid coordinates beginning at the N-terminus, of each of the sequences (Column 4), the conserved domain sequences of the respective polypeptides (Column 5); the SEQ ID NO: of each of the conserved domain (Column 6), and the percentage identity of the conserved domain in Column 5 to the conserved domain of the Arabidopsis AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 sequence, SEQ ID NO: 1369, 1507, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, or 135 (as determined by a BLASTp analysis, wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix, and with the proportion of identical amino acids in parentheses; Column 7).





TABLE 2



Conserved ‘Myb DNA binding domain 1’

of AtMYB19 and closely related sequences















Col. 7






Col. 6
Percent



Col. 3
Col. 4

SEQ ID
identity of



Percent
Myb DNA

NO: of
first



identity of
binding
Col. 5
Myb
Myb domain in

Col. 1

polypeptide
domain 1
Conserved
DNA
Col. 5 to Myb

SEQ
Col. 2
in
in amino
Myb DNA
binding
DNA binding

ID
Species/
Col. 1 to
acid
binding
domain
domain 1 of

NO:
Identifier
AtMYB19
coordinates
domain 1
1
AtMYB19











2
At/AtMYB19
100%
17-77
WSPEEDQKLKSFILSR
61
100% (61/61)


AT5G52260.1
(268/268)

GHACWTTVPILAGLQ







RNGKSCRLRWINYLR







PGLKRGSFSEEEEET





4
At/
60%
15-75
WSPEEDEKLRSFILSY
62
85% (52/61)


AT4G25560.1
(169/280)

GHSCWTTVPIKAGLQ







RNGKSCRLRWINYLR







PGLKRDMISAEEEET





6
Os/LOC_Os
48%
18-78
WSPEEDQKLRDFILRY
63
80% (49/61)


04g45020.1
(96/200)

GHGCWSAVPVKAGLQ







RNGKSCRLRWINYLR







PGLKHGMFSREEEET





8
Bd/Bradi
53%
18-78
WSPEEDQKLRDYIIRY
64
78% (48/61)


5g16672.1
(102/192)

GHSCWSTVPVKAGLQ







RNGKSCRLRWINYLR







PGLKHGMFSQEEEET





10
Zm/GRMZM2G
50%
18-78
WSPEEDQKLRDYILLH
65
77% (47/61)


170049_T01
(97/191)

GHGCWSALPAKAGLQ







RNGKSCRLRWINYLR







PGLKHGMFSPEEEET





12
Si/
48%
18-78
WSPEEDEKLRDFILRY
66
77% (47/61)


Si012304m
(98/202)

GHGCWSALPAKAGLQ







RNGKSCRLRWINYLR







PGLKHGMFSREEEET





14
Cc/clementine
48%
22-82
WSPEEDQRLKNYVLQH
67
77% (47/61)


0.9_033485m
(115/237)

GHPCWSSVPINAGLQ







RNGKSCRLRWINYLR







PGLKRGVFNMQEEET





16
Pt/POPTR_
50%
22-82
WSPEEDQRLRNYVLKH
68
77% (47/61)


0015s13190.1
(109/217)

GHGCWSSVPINAGLQ







RNGKSCRLRWINYLR







PGLKRGTFSAQEEET





18
Eg/EUCGR.
49%
18-78
WSPEEDQKLRNYVLKH
69
76% (46/60)


K00250.1
(107/217)

GHGCWSSVPINTGLQ







RNGKSCRLRWINYLR







PGLKRGMFTMEEEEI





20
Eg/EUCGR.
48%
18-78
WSPEEDQRLRNYILNH
70
75% (45/60)


K00251.1
(110/226)

GHGYWSSVPINTGLQ







RNGKSCRLRWINYLR







PGLKRGMFTLEEEEI





22
Pt/POPTR_
48%
52-112
WSPEEDQRLGSYVFQH
71
75% (46/61)


0012s13260.1
(109/223)

GHGCWSSVPINAGLQ







RTGKSCRLRWINYLR







PGLKRGAFSTDEEET





24
Gm/Glyma
48%
18-78
WSPEEDNKLRNHIIKH
72
75% (46/61)


16g31280.1
(116/238)

GHGCWSSVPIKAGLQ







RNGKSCRLRWINYLR







PGLKRGVFSKHEEDT





26
Gm/Glyma
49%
18-78
WSPEEDNKLRNHIIKH
73
73% (45/61)


09g25590.1
(103/209)

GHGCWSSVPIKAGLQ







RNGKSCRLRWINYLR







PGLKRGVFSKHEKDT





28
Sl/Solyc
40%
19-79
WSPDEDDRLKNYMIKH
74
73% (44/60)


03g025870.2.1
(115/283)

GHGCWSSVPINAGLQ







RNGKSCRLRWINYLR







PGLKRGAFSLEEEDI





30
Vv/GSVIVT
42%
20-80
WSPEEDARLRNYVLKY
75
72% (44/61)


01028984001
(115/272)

GLGCWSSVPVNAGLQ







RNGKSCRLRWINYLR







PGLKRGMFTIEEEET





32
Eg/EUCGR.
51%
18-78
WSPDEDQRLRNYIHKH
76
70% (44/61)


A02796.1
(112/217)

GYSCWSSVPINAGLQ







RNGKSCRLRWINYLR







PGLKRGAFTVQEEET





34
At/
51%)
23-83
WSPEEDEKLRSHVLKY
77
69% (41-59)


AT3G48920.1
(99/191)

GHGCWSTIPLQAGLQ







RNGKSCRLRWVNYLR







PGLKKSLFTKQEETI

























































































































TABLE 3



Conserved second Myb DNA binding domains

of AtMYB19 and closely related sequences















Col. 7



Col. 3



Percent



Percent
Col. 4

Col. 6
identity



identity of
Myb DNA
Col. 5
SEQ ID
of second Myb

Col. 1

polypeptide
binding
Conserved
NO: of
domain in Col.

SEQ
Col. 2
in
domain 2 in
Myb DNA
second
5 to Myb DNA

ID
Species/
Col. 1 to
amino acid
binding
Myb
binding domain

NO:
Identifier
AtMYB19
coordinates
domain 2
domain
2 of AtMYB19



2
At/AtMYB19
100%
70-112
FSEEEEETILTLHSS
95
100%


AT5G52260.1
(268/268)

LGNKWSRIAKYLPGR

(43/43)





TDNEIKNYWHSYL





4
At/
60%
68-110
ISAEEEETILTFHSS
96
88%


AT4G25560.1
(169/280)

LGNKWSQIAKFLPGR

(37/42)





TDNEIKNYWHSHL





6
Os/LOC_
48%
71-113
FSREEEETVMNLHAT
97
72%


Os04g45020.1
(96/200)

MGNKWSQIARHLPGR

(31/43)





TDNEVKNYWNSYL





8
Bd/
53%
71-113
FSQEEEETVMSLHAT
98
76%


Bradi5g16672.1
(102/192)

LGNKWSRIAQHLPGR

(33/43)





TDNEVKNYWNSYL





10
Zm/GRMZM2
50%
71-113
FSPEEEETVMSLHAT
99
76%


G170049_T01
(97/191)

LGNKWSRIARHLPGR

(33/43)





TDNEVKNYWNSYL





12
Si/Si012304m
48%
71-113
FSREEEETVMSLHAK
100
74%



(98/202)

LGNKWSQIARHLPGR

(32/43)





TDNEVKNYWNSYL





14
Cc/clementine
48%
75-117
FNMQEEETILTVHRL
101
76%


0.9_033485m
(115/237)

LGNKWSQIAQHLPGR

(33/43)





TDNEIKNYWHSHL





16
Pt/POPTR_
50%
75-117
FSAQEEETILALHHM
102
79%


0015s13190.1
(109/217)

LGNKWSQIAQHLPGR

(34/43)





TDNEIKNHWHSYL





18
Eg/EUCGR.
49%
71-113
FTMEEEEIIFSLHHL
103
74%


K00250.1
(107/217)

IGNKWSQIAKHLPGR

(32/43)





TDNEIKNHWHSYL





20
Eg/EUCGR.
48%
71-113
FTLEEEEIILSLHRL
104
76%


K00251.1
(110/226)

IGNKWSQIAKHLPGR

(33/43)





TDNEIKNHWHSYL





22
Pt/POPTR_
48%
105-147
FSTDEEETILTLHRM
105
81%


0012s13260.1
(109/223)

LGNKWSQIAQHLPGR

(35/43)





TDNEIKNHWHSYL





24
Gm/Glyma
48%
71-113
FSKHEEDTIMVLHHM
106
76%


16g31280.1
(116/238)

LGNKWSQIAQHLPGR

(33/43)





TDNEIKNYWHSYL





26
Gm/Glyma
49%
71-113
FSKHEKDTIMALHHM
107
72%


09g25590.1
(103/209)

LGNKWSQIAQHLPGR

(31/43)





TDNEVKNYWHSYL





28
Sl/Solyc
40%
72-114
FSLEEEDIILTLHAM
108
76%


03g025870.2.1
(115/283)

FGNKWSQIAQQLPGR

(33/43)





TDNEIKNHWHSYL





30
Vv/GSVIVT
42%
73-115
FTIEEEETIMALHRL
109
74%


01028984001
(115/272)

LGNKWSQIAQNFPGR

(32/43)





TDNEIKNYWHSCL





32
Eg/EUCGR.
51%
71-113
FTVQEEETILNLHHL
110
76%


A02796.1
(112/217)

LGNKWSQIAQHLPGR

(33/43)





TDNEIKNHWHSYL





34
At/
51%
76-118
FTKQEETILLSLHSM
111
72%


AT3G489201.1
(99/191)

LGNKWSQISKFLPGR

(31/43)





DTNEIKNYWHSNL



Species abbreviations for Tables 2 and 3:

At— Arabidopsis thaliana ;

Bd— Brachypodium distachyon ;

Cc— Citrus x clementina ;

Eg— Eucalyptus grandis ;

Gm— Glycine max ;

Os— Oryza sativa ;

Pt— Populus trichocarpa ;

Si— Setaria italica ;

Sl— Solanum lycopersicum ;

Vv— Vitis vinifera ;

Zm— Zea mays









































































































Sequences that are functionally-related and/or closely-related to the polypeptides in Tables 2 and 3 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed AtMYB19-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants. These “functionally-related and/or closely-related” AtMYB19 clade polypeptides generally contain the consensus sequence of the Myb DNA binding domain 1 of SEQ ID NO: 129:
WSPX 1 EDxxLxxxX 2 xxxGxxxWX 3 xX 2 PxxxGLQRxGKSCRLRW X 2 NYLRPGLKxxxxxxxE;
where x represents any amino acid;

X 1 is D or E;
X 2 is I, V, L or M;
and X 3 represents S or T;

as provided in FIG. 2B-2C .

Other highly conserved residues found in the Myb DNA binding domain 2 of AtMYB19 clade members, as shown in FIG. 2C-2D and SEQ ID NO: 130:
ExxxX 1 xxxHxxxGNKWSxIX 2 xxxPGRTDNEX 1 KNxWxSxL

where x represents any amino acid;

X 1 is I, V, L or M; and
X 2 represents A or S.
There is also a small motif that is present in AtMYB19 clade member proteins, identifiable as SEQ ID NO: 133 and that can be located spanning FIGS. 2E-2F :
PxFxX 1 W
where x represents any amino acid; and

X 1 is D or E.
The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. An AtMYB19 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Tables 2 or 3 may also have at least 40%, 42%, 48%, 49%, 50%, 51%, 53%, 60%, or about 100% amino acid identity to SEQ ID NO: 2 or to SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, and/or at least 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% amino acid identity to the first Myb DNA binding domain of SEQ ID NO: 2, or to a listed first Myb DNA binding domain or to SEQ ID NOs: 61-77, and/or 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% amino acid identity to a listed second Myb DNA binding domain or to the second Myb DNA binding domain of SEQ ID NO: 2 or SEQ ID NOs: 95-111, or to an amino acid sequence having at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95% or at least 96%, at least 97%, at least 98%, at least 99%, or about 100% sequence identity to SEQ ID NOs: 129-132. The presence of the disclosed conserved first Myb DNA binding domains and/or second Myb DNA binding domains in the polypeptide sequence (for example, SEQ ID NO: 61-77 or 95-111), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “AtMYB19 clade polypeptides” or “AtMYB19 clade polypeptides”, or which fall within the “AtMYB19 clade” or “G1309 clade” exemplified in the tree in FIG. 1 as those polypeptides bounded by LOC_Os04g45020.1 and Solyc03g025870.2.1 (indicated by the box around these sequences).





TABLE 4



Conserved ‘Myb DNA bindingdomain 1’of

AtMYB50 and closely related sequences















Col. 7







Percent







identity




Col. 4

Col. 6
of first



Col. 3
Myb DNA

SEQ ID
Myb domain



Percent
binding
Col. 5
NO: of
in Col. 5

Col. 1

identity of
domain 1
Conserved
Myb
to Myb

SEQ
Col. 2
polypeptide
in amino
Myb DNA
DNA
DNA binding

ID
Species/
in Col. 1
acid
binding
binding
domain 1 of

NO:
Identifier
to AtMYB50
coordinates
domain 1
domain 1
AtMYB50



135
At/AtMYB50 or
100%
14-61
KGLWSPEEDEKLLNY
210
100%


AT1G57560.1
(314/314)

ITKHGHGCWSSVPKL

(48/48)





AGLERCGKSCRLRWI







NYL





151
Gm/
86%
14-61
KGLWSPEEDEKLLNY
234
98%


Glymal9g41250.1
(118/138)

ITKHGHGCWSSVPKL

(47/48)





AGLQRCGKSCRLRWI







NYL





157
Gm/
86%
14-61
KGLWSPEEDEKLLNY
222
98%


Glyma03g38660.1
(118/138)

ITKHGHGCWSSVPKL

(47/48)





AGLQRCGKSCRLRWI







NYL





147
Gm/
90%
14-61
KGLWSPEEDEKLLNY
232
98%


Glyma20g22230.1
(121/135)

ITKHGHGCWSSVPKL

(47/48)





AGLQRCGKSCRLRWI







NYL





139
At/
64%
14-61
KGLWSPEEDEKLLNY
214
96%


AT5G26660.1
(131/206)

ITRHGHGCWSSVPKL

(46/48)





AGLQRCGKSCRLRWI







NYL





153
Pt/
44%
14-61
KGLWSPEEDEKLLNY
218
96%


POPTR_0013s
(192/444)

ITKHGLGCWSSVPKL

(46/48)


00290.1


AGLQRCGKSCRLRWI







NYL





141
Gm/
91%
14-61
KGLWSPEEDEKLLNH
216
96%


Glyma10g28250.1
(119/132)

ITKHGHGCWSSVPKL

(46/48)





AGLQRCGKSCRLRWI







NYL





143
Pt/
45%
14-61
KGLWSPEEDEKLLNY
230
94%


POPTR_0005s
(196/440)

ITKHGHGCWSSVPKQ

(45/48)


00340.1


ADLQRCGKSCRLRWI







NYL





185
Zm/
87%
14-61
KGLWSPEEDEKLMNH
260
94%


GRMZM2G171781_
(116/134)

ITKHGHGCWSSVPKL

(45/48)


T01


AGLQRCGKSCRLRWI







NYL





191
Os/
89%
14-61
KGLWSPEEDEKLMNH
266
94%


LOC_Os05g
(118/134)

ITKHGHGCWSSVPKL

(45/48)


04820.1


AGLQRCGKSCRLRWI







NYL





137
At/
58%
14-61
KGLWSPEEDEKLLTH
212
92%


AT1G09540.1
(211/367)

ITNHGHGCWSSVPKL

(44/48)





AGLQRCGKSCRLRWI







NYL





149
Eg/
75%
14-61
KGLWSPEEDEKLLNY
226
92%


Eucgr.H01337.1
(124/166)

ITTYGHGCWSAVPKL

(44/48)





AGLQRCGKSCRLRWI







NYL





159
Eg/
87%
67-114
KGLWSPEEDEKLLNY
224
92%


Eucgr.B01827.1
(113/130)

IAKFGLGCWSSVPKL

(44/48)





AGLQRCGKSCRLRWI







NYL





165
Os/
82%
14-61
KGLWSPEEDEKLMNH
240
92%


LOC_Os01g18240.1
(124/153)

ITKHGHGCWSTVPKL

(44/48)





AGLQRCGKSCRLRWI







NYL





193
Vv/
88%
14-61
KGLWSPEEDEKLLMH
192
92%


GSVIVT010313
(116/132)

ITKYGHGCWSSVPKL

(44/48)


41001


AGLQRCGKSCRLRWI







NYL





199
Zm/
67%
14-61
KGLWSPEEDEKLMNH
274
92%


GRMZM2G017520_
(128/192)

ITKHGHGCWSTVPKL

(44/48)


T01


AGLQRCGKSCRLRWI







NYL





205
Zm/
80%
14-61
KGLWSPEEDEKLMNH
280
92%


GRMZM2G127490_
(122/153)

ITKHGHGCWSSIPKL

(44/48)


T01


AGLQRCGKSCRLRWI







NYL





161
Sl/
82%
14-61
KGLWSPEEDEKLIKH
236
90%


Solyc0lg
(118/144)

ITKFGHGCWSSVPKL

(43/48)


102340.2.1


AGLQRCGKSCRLRWI







NYL





163
Gm/
66%
14-61
KGLWSPEEDEKLLRH
238
90%


Glyma19g
(130/197)

ITKYGHGCWSSVPKQ

(43/48)


41010.1


AGLQRCGKSCRLRWI







NYL





181
Gm/
89%
14-61
KGLWSPEEDEKLLRH
256
90%


Glyma02g
(117/132)

ITKYGHGCWSSVPKQ

(43/48)


00960.1


AGLQRCGKSCRLRWI







NYL





183
Vv/
83%
14-61
KGLWSPEEDEKLLRH
258
90%


GSVIVT010282
(119/145)

ITKYGHGCWSSVPKQ

(43/48)


35001


AGLQRCGKSCRLRWI







NYL





155
Vv/
78%
14-61
RGLWSPEEDEKLFRY
220
88%


GSVIVT010177
(113/145)

ITEHGHGCWSSVPKQ

(42/48)


16001


AGLQRCGKSCRLRWI







NYL





179
Zm/
64%
14-61
RGLWSPEEDEKLMNH
254
88%


GRMZM2G147698_
(103/161)

IAKYGHGCWSSVPKL

(42/48)


T01


AGLDRCGKSCRLRWI







NYL





203
Sl/
80%
13-60
KGLWCPEEDEKLINH
278
86%


Solyc10g
(103/130)

VTKYGHGCWSSVPKL

(41/48)


044680.1.1


AALQRCGKSCRLRWI







NYL





197
At/
74%
14-73
KGLWSPEEDEKLLRY
272
74%


AT4G01680.2
(119/163)

ITKYGHGCWSSVPKQ

(44/60)





AGTFLFIQIHLLFGL







QRCGKSCRLRWINYL





143
Cc/
42%
14-89
KGLWSPEEDEKLLNY
228
62%


clementine0.9_
(192/462)

ITKHGHGCWSSVPKL

(47/76)


009770m


AGKIYLENNNHACSV







ILMFNAFNTMFLLAG







LQRCGKSCRLRWINY







L






































































































































































TABLE 5



Conserved second Myb DNA binding domains

of AtMYB50 and closely related sequences















Col. 7







Percent







identity







of second



Col. 3
Col. 4

Col. 6
Myb domain



Percent
Myb DNA
Col. 5
SEQ ID
in Col. 5

Col. 1

identity of
binding
Conserved
NO: of
to Myb DNA

SEQ
Col. 2
polypeptide
domain 2 in
Myb DNA
second
binding

ID
Species/
in Col. 1
amino acid
binding
Myb
domain 2 of

NO:
Identifier
to AtMYB50
coordinates
domain 2
domain
AtMYB50



135
At/AtMYB50 or
100%
67-112
RGAFSSEEQNLIVEL
211
100%


AT1G57560.1
(314/314)

HAVLGNRWSQIAARL

(44/44)





PGRTDNEIKNLWNSC







I





137
At/
58%
67-112
RGAFSPEEENLIVEL
213
92%


AT1G09540.1
(211/367)

HAVLGNRWSQIASRL

(42/46)





PGRTDNEIKNLWNSS







I





165
Os/
82%
67-112
RGAFSQEEEDLIVEL
241
92%


LOC_Os01g
(124/153)

HAVLGNRWSQIATRL

(42/46)


18240.1


PGRTDNEIKNLWNSC







I





143
Pt/
45%
67-112
RGAFSQQEENLIIEL
231
90%


POPTR_0005s
(196/440)

HAVLGNRWSQIAAQL

(41/46)


00340.1


PGRTDNEIKNLWNSC







I





153
Pt/
44%
67-112
RGAFSQQEENLIIEL
219
90%


POPTR_0013s
(192/444)

HAVLGNRWSQIAAQL

(41/46)


00290.1


PGRTDNEIKNLWNSC







I





191
Os/
89%
67-112
RGAFSQEEEDLIIEL
277
90%


LOC_Os05g
(118/134)

HAVLGNRWSQIAAQL

(41/46)


04820.1


PGRTDNEIKNLWNSC







I





199
Zm/
67%
67-112
RGAFSEEEEDLIVEL
275
90%


GRMZM2G017520_
(128/192)

HAVLGNRWSQIATRL

(41/46)


T01


PGRTDNEIKNLWNSS







I





141
Gm/
91%
67-112
RGAFSQQEENMIVEL
217
87%


Glyma10g28250.1
(119/132)

HAVLGNRWSQIAAQL

(40/46)





PGRTDNEIKNLWNSC







L





145
Cc/
42%
95-140
RGAFSVQEESLIVEL
229
87%


clementine0.9_
(192/462)

HAVLGNRWSQIAAQL

(40/46)


009770m


PGRTDNEIKNLWNSS







I





147
Gm/
90%
67-112
RGAFSQQEENMIVEL
233
87%


Glyma20g22230.1
(121/135)

HAVLGNRWSQIAAQL

(40/46)





PGRTDNEIKNLWNSC







L





157
Gm/
86%
67-112
RGAFSQQEENSIVEL
223
87%


Glyma03g38660.1
(118/138)

HAVLGNRWSQIAAQL

(40/46)





PGRTDNEIKNLWNSC







L





159
Eg/
87%
120-165
RGAFSQQEESLIIEL
225
87%


Eucgr.B01827.1
(113/130)

HAVLGNRWSQIAAHL

(38/44)





PGRTDNEIKNLWNSG







L





181
Gm/
89%
67-112
RGTFSQEEENLIIEL
257
87%


Glyma02g00960.1
(117/132)

HAVLGNRWSQIAAQL

(40/46)





PGRTDNEIKNLWNSC







L





193
Vv/
88%
67-112
RGAFSQQEESLIIEL
193
87%


GSVIVT01031
(116/132)

HAVLGNRWSQIAAQL

(40/46)


341001


PGRTDNEIKNLWNSC







I





197
At/
74%
79-124
RGAFSQDEENLIIEL
273
87%


AT4G01680.2
(119/163)

HAVLGNRWSQIAAQL

(40/46)





PGRTDNEIKNLWNSC







L





205
Zm/
80%
67-112
RGAFSQDEEDLIIEL
281
87%


GRMZM2G127490_
(122/153)

HAVLGNRWSQIAAQL

(40/46)


T01


PGRTDNEIKNLWNSC







I





149
Eg/
75%
67-112
RGAFSHQEENLIIEL
227
85%


Eucgr.H01337.1
(124/166)

HAVLGNRWSQIAARL

(39/46)





PGRTDNEIKNFWNSS







L





151
Gm/
86%
67-112
RGAFSQQEENLIIEL
235
85%


Glyma19g41250.1
(118/138)

HAVLGNRWSQIAAQL

(39/46)





PGRTDNEIKNLWNSC







L



161
Sl/
82%
67-112
RGTFSQDEENLIIEL
237
85%


Solyc01g
(118/144)

HAVLGNKWSQIAARL

(39/46)


102340.2.1


PGRTDNEIKNLWNSS







I



163
Gm/
66%
67-112
RGTFSQEEETLIIEL
239
85%


Glyma19g
(130/197)

HAVLGNRWSQIAAQL

(39/46)


41010.1


PGRTDNEIKNLWNSC







L



185
Zm/
87%
67-112
RGAFAQDEEDLIIEL
261
85%


GRMZM2G171781_
(116/134)

HAVLGNRWSQIAAQL

(39/46)


T01


PGRTDNEIKNLWNSC







I



183
Vv/
83%
67-112
RGTFSLQEENLIIEL
259
83%


GSVIVT01028
(119/145)

HSVLGNRWSQIAAQL

(38/46)


235001


PGRTDNEIKNLWNSC







L



139
At/
64%
67-112
RGAFSQDEESLIIEL
215
81%


AT5G26660.1
(131/206)

HAALGNRWSQIATRL

(37/46)





PGRTDNEIKNLWNSC







L



155
Vv/
78%
67-112
RGAFTGQEEKLIVEL
221
77%


GSVIVT010177
(113/145)

HEILGNRWSQIASHL

(35/46)


16001


PGRTDNEIKNQWNSS







I



203
Sl/
80%
66-111
RGTFSQQEENLIIQL
279
77%


Solyc10g
(103/130)

HSLLGNKWSQIASRL

(35/46)


044680.1.1


PGRTDNEIKNLWNSS







I



179
Zm/
64%
67-112
RGTFSQEEEDLIIHL
255
72%


GRMZM2G147698_
(103/161)

HSLLGNKWSQIAAQL

(33/46)


T01


PGRTDNEVKNFWNSY







I



Species abbreviations for Tables 4 and 5:

At— Aralidopsis thaliana ;

Bd— Brachypodium distachyon ;

Cc— Citrus clementina ;

Eg— Eucalyptus grandis ;

Gm— Glycine max ;

Os— Oryza sativa ;

Pt— Populus trichocarpa ;

Si— Setaria italica ;

Si— Solanum lycopersicum ;

Vv- Vitis vinifera ;

Zm— Zea mays

































































































































































As shown in FIG. 6A-6C , these “functionally-related and/or closely-related” AtMYB50 clade polypeptides generally contain a consensus sequence of the AtMYB50 clade, SEQ ID NO: 302:







X 1 GLWX 2 PEEDEKLxxxX 3 X 4 xxGHGCWSX 5 X 3 PKxAxX 8 X 9 X 10 X 9





X 11 X 12 X 11 X 13 X 10 X 10 X 9 X 14 LxRCGKSCRLRWINYLRPDX 3 X 1 RGX 4





FX 6 xxExxxIX 3 xLHxxX 3 GNX 1 WSQIAX 6 xLPGRTDNEX 3 KNxW





NSxX 3 KKX 1 X 3 xxX 1 GIDPxTHX 7 .*














As shown in FIG. 6A-6B , these “functionally-related and/or closely-related” AtMYB50 clade polypeptides also generally contain a consensus sequence Myb DNA binding domain 1, SEQ ID NO: 303:







X 1 GLWX 2 PEEDEKLxxxX 3 X 4 xxGHGCWSX 5 X 3 PKxAxX 8 X 9 X 10 X 9





X 11 X 12 X 11 X 13 X 10 X 10 X 9 X 14 LxRCGKSCRLRWINYL.*










As shown in FIG. 6B-6C , the instant “functionally-related and/or closely-related” AtMYB50 clade polypeptides also generally contain a consensus sequence Myb DNA binding domain 2, SEQ ID NO: 304 (said sequence is underlined in FIG. 6B-6C ):







RGX 4 FX 6 xxExxxIX 3 xLHxxX 3 GNX 1 WSQIAX 6 xLPGRTDNEX 3





KNxWNSxX 3 .*










There is also a small motif that is present in AtMYB50 clade member proteins, and is identifiable as SEQ ID NO: 305 (said sequence is double underlined in FIG. 6C ):







X 1 GIDPxTHX 7 .*








*In the above consensus sequences of SEQ ID NO: 302-305, x represents any amino acid; X 1 is K or R; X 2 is S or C; X 3 is I, V, L, or M; X 4 is T or A; X 5 is S or T; X 6 is S, A, or T; X 7 is K or Q; X 8 is T or absent; X 9 is F or absent; X 10 is L or absent; X 11 is I or absent; X 12 is Q or absent; X 13 is H or absent; and X 14 is G or absent.
The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. An AtMYB50 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Tables 4 or 5 may also have at least 42%, 44%, 45%, 58%, 64%, 66%, 67%, 74%, 75%, 78%, 80%, 82%, 83%, 86%, 87%, 88%, 89%, 90%, 91%, or about 100% amino acid identity to SEQ ID NO 135, and/or at least 62%, 74%, 86%, 88%, 90%, 92%, 94%, 96%, 98% or about 100% amino acid identity to the first Myb DNA binding domain of SEQ ID NO 135, and/or at least 72%, 77%, 81%, 83%, 85%, 87%, 90%, 92%, or about 100% amino acid identity to the second Myb DNA binding domain of SEQ ID NO 135 in its amino acid sequence to the entire length of a listed sequence or to a listed first Myb DNA binding domains, or to a listed second Myb DNA binding domains, or to the amino acid sequence of SEQ ID NO 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, or 210-285. The presence of the disclosed conserved first Myb DNA binding domains and/or second Myb DNA binding domains in the polypeptide sequence (for example, SEQ ID NO: 210-285), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “AtMYB50 clade polypeptides” or “AtMYB50 clade polypeptides”, or which fall within the “AtMYB50 clade” or “G1319 clade” exemplified in the phylogenetic tree in FIG. 5 as those polypeptides bounded by LOC_Os01g18240.1 and POPTR — 0013 s00290.1 (indicated by the box around these sequences).





TABLE 6



Conserved AP2 domain of CRF1 and closely related sequences















Col. 7







Percent







identity



Col. 3



of AP2



Percent
Col. 4

Col. 6
domain

Col. 1

identity of
AP2

SEQ ID
in Col. 5

SEQ
Col. 2
polypeptide
domain in
Col. 5
NO: of
to AP2

ID
Species/
in Col. 1
amino acid
Conserved
AP2
domain of

NO:
Identifier
to CRF1
coordinates
AP2 domain
domain
CRF1



307
At/CRF1 or
100%
87-142
FRGVRQRPWGKWAAE
396
100%


AT4G11140.1
(287/287)

IRDPSRRVRVWLGTF

(56/56)





DTAEEAAIVYDNAAI







QLRGPNAELNF





333
Gm/Glyma08g
43%
109-164
FRGVRQRPWGKWAAE
409
90%


02460.1
(125/295)

IRDPSRRVRLWLGTY

(50/56)





DTAEEAAIVYDNAAI







QLRGADALTNF





331
Gm/Glyma05g
39%
109-164
FRGVRQRPWGKWAAE
408
88%


37120.1
(125/328)

IRDPLRRVRLWLGTY

(49/56)





DTAEEAAIVYDNAAI







QLRGADALTNF





335
Gm/Glyma01g
38%
107-162
FRGVRQRPWGKWAAE
410
88%


43350.1
(109/294)

IRDPSRRVRLWLGTY

(49/56)





DTAEEAALVYDNAAI







RLRGPHALTNF





341
Zm/GRMZM2G
44%
118-173
FRGVRRRPWGKYAAE
413
88%


044077_T01
(79/183)

IRDPWRRVRVWLGTF

(49/56)





DTAEEAAKVYDSAAV







QLRGRDATTNF





381
Cc/clementine
43%
120-175
FRGVRQRPWGKWAAE
433
88%


0.9_015380m
(131/310)

IRDPLRRVRLWLGTY

(49/56)





DTAEEAAMVYDNAAI







QLRGPDALTNF





387
Pt/POPTR_0001
43%
130-185
FRGVRQRPWGKWAAE
436
88%


s10300.1
(138/323)

IRDPLRRVRLWLGTY

(49/56)





DTAEEAAMVYDNAAI







QLRGPDALTNF





319
Sl/Solyc03g
49%
129-184
FRGVRQRPWGKWAAE
402
86%


007460.1.1
(95/195)

IRDPARRVRLWLGTY

(48/56)





DTAEEAAMVYDNAAI







KLRGPDALTNF





321
Sl/Solyc06g
52%
125-180
FRGVRQRPWGKWAAE
403
86%


051840.1.1
(94/182)

IRDPARRVRLWLGTY

(48/56)





DTAEEAAMVYDNAAI







KLRGPDALTNF





323
Gm/Glyma04g
45%
103-158
FRGVRQRPWGKWAAE
404
86%


41740.1
(100/227)

IRDPARRVRLWLGTY

(48/56)





DTAEEAAMVYDNAAI







RLRGPDALTNF





325
Gm/Glyma06g
38%
102-157
FRGVRQRPWGKWAAE
405
86%


13040.1
(114/303)

IRDPARRVRLWLGTY

(48/56)





DTAEEAAMVYDNAAI







RLRGPDALTNF





337
Sl/Solyc08g
40%
138-193
FRGVRQRPWGKWAAE
411
86%


081960.1.1
(128/322)

IRDPLRRVRLWLGTY

(48/56)





DTAEEAAMVYDHAAI







QLRGPDALTNF





345
Si/Si002247m
40%
117-172
FRGVRRRPWGKYAAE
415
86%



(98/251)

IRDPWRRVRVWLGTF

(48/56)





DTAEEAAKVYDSAAI







QLRGPDATTNF





347
Os/LOC_Os01g
61%
103-158
FRGVRRRPWGKFAAE
416
86%


46870.1
(61/101)

IRDPWRGVRVWLGTF

(48/56)





DTAEEAARVYDNAAI







QLRGPSATTNF





373
Cc/clementine
37%
126-181
FRGVRQRPWGKWAAE
429
86%


0.9_013577m
(125/343)

IRDPARRVRLWLGTY

(48/56)





DTAEEAARVYDNAAI







KLRGPDALTNF





377
Pt/POPTR_0012
40%
183-238
FRGVRQRPWGKWAAE
431
86%


s01260.1
(109/274)

IRDPARRVRLWLGTY

(48/56)





DTAEEAARVYDNAAI







KLRGPDALTNF





385
Gm/Glyma11g
42%
113-168
FRGVRQRPWGKWAAE
435
86%


02140.1
(128/307)

IRDPARRVRLWLGTY

(48/56)





DTAEEAALVYDNAAI







KLRGPHALTNF





389
Pt/POPTR_0003
43%
127-182
FRGVRQRPWGKWAAE
437
86%


s13610.1
(137/322)

IRDPLRRVRLWLGTY

(48/56)





DTAEEAAMVYDNAAI







QLRGADALTNF





391
Eg/Eucgr.
43%
90-145
FRGVRQRPWGKWAAE
438
86%


K00321.1
(101/239)

IRDPARRVRLWLGTY

(48/56)





DTAEEAAMVYDNAAI







KLRGPDALTNF





313
At/AT4G23750.1
51%
122-177
FRGVRQRPWGKWAAE
399
84%



(177/350)

IRDPLKRVRLWLGTY

(47/56)





NTAEEAAMVYDNAAI







QLRGPDALTNF





339
Os/LOC_Os01g
41%
150-205
FRGVRRRPWGKYAAE
412
84%


12440.1
(111/273)

IRDPWRRVRVWLGTF

(47/56)





DTAEEAAKVYDTAAI







QLRGRDATTNF





343
Zm/GRMZM2G
37%
115-170
FRGVRRRPWGKYAAE
414
84%


142179_T0l
(119/329)

IRDPWRRVRVWLGTF

(47/56)





DTAEEAAKVYDSAAI







QLRGADATTNF





351
Zm/GRMZM2G
48%
89-144
FRGVRRRPWGKFAAE
418
84%


160971_T01
(72/152)

IRDPWRGVRVWLGTF

(47/56)





DTAEEAARVYDTAAI







QLRGANATTNF





367
Eg/Eucgr.
42%
116-171
FRGVRQRPWGKWAAE
426
84%


E00834.1
(126/303)

IRDPKKGTRVWLGTF

(47/56)





GTAEEAALVYDNAAI







QLRGPDALTNF





375
Eg/Eucgr.
46%
128-183
FRGVRQRPWGKWAAE
430
84%


A02669.1
(89/195)

IRDPTRRVRLWLGTY

(47/56)





DTAEEAAMVYDNAAL







KLRGPDAQTNF





379
Pt/POPTR_
41%
130-185
FRGVRQRPWGKWAAE
432
84%


0015s06070.1
(113/281)

IRDPARRQRLWLGTY

(47/56)





DTAEEAARVYDNAAI







KLRGPDALTNF





383
Eg/Eucgr.
45%
122-177
FRGVRRRPWGKWAAE
434
84%


D01775.1
(134/302)

IRDPLRRVRLWLGTY

(47/56)





DTAEEAAMVYDQAAI







QLRGPDALTNF





393
Bd/Bradi2g
35%
124-179
FRGVRRRPWGKYAAE
439
84%


07357.1
(115/329)

IRDPWRRVRVWLGTF

(47/56)





DTAEEAARVYDSAAI







KLRGPDATVNF





315
At/AT4G27950.1
43%
118-173
YRGVRQRPWGKWAAE
400
83%



(91/213)

IRDPEQRRRIWLGTF

(46/56)





ATAEEAAIVYDNAAI







KLRGPDALTNF





317
At/AT5G53290.1
50%
125-180
FRGVRQRPWGKWAAE
401
83%



(82/165)

IRDPEQRRRIWLGTF

(46/56)





ETAEEAAVVYDNAAI







RLRGPDALTNF





327
Gm/Glyma13g
37%
108-163
FRGVRQRPWGKWAAE
406
83%


08490.1
(119/322)

IRDPVQRVRIWLGTF

(46/56)





LTAFFAALCYDNAAI







MLRGPDALTNF





329
Gm/Glyma14g
40%
103-158
FRGVRQRPWGKWAAE
407
83%


29040.1
(116/292)

IRDPVQRVRIWLGTF

(46/56)





KTAEEAALCYDNAAI







TLRGPDALTNF





349
Zm/GRMZM2G
43%
93-148
FRGVRRRPWGKFAAE
417
83%


151542_T01
(67/156)

IRDPWRGVRVWLGTF

(46/56)





DTAEEAARVYDAAAV







QLRGANATTNF





395
Bd/Bradi2g
39%
99-154
FRGVRRRPWGKYAAE
440
83%


45530.1
(77/200)

IRDPWRGVRVWLGTF

(46/56)





DTAEEAARVYDSAAI







QLRGASATTNF





365
Cc/clementine
42%
106-161
YRGVRMRPWGKWAAE
425
77%


0.9_017304m
(77/185)

IRDPFQRTRVWLGTF

(43/56)





ETAEEAALVYDQAAI







RLKGPHAQTNF





371
Pt/POPTR_0014
40%
119-174
YRGVRQRPWGRWAAE
428
77%


s09020.1
(84/214)

IRDPYRRTRVWLGTY

(43/56)





DTAEEAAMVYDQAAI







RIKGPDAQTNF





311
At/AT3G61630.1
48%
105-160
YRGVRQRPWGKFAAE
398
77%



(82/174)

IRDPSSRTRIWLGTF

(43/56)





VTAEEAAIAYDRAAI







HLKGPKALTNF





369
Pt/POPTR_0002
43%
107-162
YRGVRQRPWGRWAAE
427
75%


s16900.1
(92/215)

IRDPYRRTRLWLGTY

(42/56)





DTAEEAAMVYDQAAI







RIKGPDAQTNF





309
At/AT2G46310.1
47%
99-154
YRGVRQRPWGKFAAE
397
75%



(85/181)

IRDPSSRTRLWLGTF

(42/56)





ATAEEAAIGYDRAAI







RIKGHNAQTNF





353
Os/LOC_Os06g
36%
121-176
FRGVRKRPWGKYGAE
419
72%


06540.1
(90/253)

IRVSQQSARVWLGTF

(40/56)





DTAEEAARVYDHAAL







RLRGPSATTNF





355
Zm/GRMZM2G
36%
103-158
YRGVRRRPWGKYAAE
420
72%


328197_T01
(68/191)

IRDPHKGERLWLGTF

(40/56)





DTAEEAAREYDSAAR







RLRGPSATTNF





359
Si/Si008428m
35%
94-149
YRGVRRRPWGKYAAE
422
72%



(112/321)

IRDPHKNARVWLGTF

(40/56)





DTAEEAARMYDSEAR







RLRGPSATTNF





361
Zm/GRMZM2G
43%
80-135
FRGVRRRPWGRWAAE
423
70%


009598_T01
(60/141)

IREPHNRRRLWLGTF

(39/56)





DTAEEAANAYDAANI







RFRGVSATTNF





357
Zm/GRMZM2G
38%
101-156
YRGVRRRPWGRYAAE
421
67%


429378_T0l
(66/177)

IRDPHKGERLWLGTF

(37/56)





DTAEEAARRYDSETR







RERGPSAITNE





363
Si/Si037209m
41%
84-139
FRGVRRRAWGRWAAE
424
65%



(55/137)

IRDPHGSRRIWLGTF

(36/56)





NSAEEAAAAYDVANI







RFRGASAHTNF



Species abbreviations for Table 6:

At— Arabidopsis haliana ;

Bd— Brachypodium distachyon ;

Cc— Citrus clementina ;

Eg— Eucalyptus grandis ;

Gm— Glycine max ;

Os— Oryza sativa ;

Pt— Populus trichocarpa ;

Si— Setaria italica ;

Sl— Solanum lycopersicum ;

Zm— Zea mays





































































































































































































































































Sequences that are functionally-related and/or closely-related to the polypeptides in Table 6 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed CRF1-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
As shown in FIG. 8C-8D , these “functionally-related and/or closely-related” CRF1 clade polypeptides generally contain a consensus AP2 domain sequence of the CRF1 clade, SEQ ID NO: 441:







X 1 RGX 6 RxRX 2 WGX 3 X 4 X 5 AEIRxxxxxxRX 6 WLGTX 1 xX 7 AEEAAxx





YDxxxxxxX 3 GxxAxxNF.*










As shown in FIG. 8A-8B , these “functionally-related and/or closely-related” CRF1 clade polypeptides also generally contain a consensus sequence of SEQ ID NO: 442:







X 6 xX 6 xxxDxxxTV 8 SSX 9 xX 8 *








*In the above consensus sequences of SEQ ID NO: 441-442, x represents any amino acid; X 1 can be F or Y; X 2 can be P or A; X 3 can be R or K; X 4 can be W, F or Y; X 5 can be A or G; X 6 can be I, V, L, or M; X 7 can be T or S; X 8 can be D or E; and X 9 can be G or S.
The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. A CRF1 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Table 6 may also have at least 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 61%, or about 100% amino acid identity to SEQ ID NO: 307 or to the amino acid sequence of SEQ ID NO: 307, where n=1-45, and/or at least 65%, 67%, 70%, 72%, 75%, 77%, 83%, 84%, 86%, 88%, 90% or about 100% amino acid identity to the AP2 domain of SEQ ID NO: 307 or SEQ ID NO: 396-440. The presence of the disclosed conserved AP2 domains in the polypeptide sequence (for example, SEQ ID NO: 396-440), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “CRF1 clade polypeptides” or “G1421 clade polypeptides”, or which fall within the “CRF1 clade” or “G1421 clade” exemplified in the phylogenetic tree in FIG. 7 as those polypeptides bounded by Bradi2g07357.1 and Solyc08g081960.1.1 (indicated by the box around these sequences).





TABLE 7



Conserved ‘AP2 domain’ of ERF058

and closely related sequences















Col. 7







Percent







identity



Col. 3
Col. 4


of AP2



Percent
Amino

Col. 6
domain

Col. 1

identity of
acids

SEQ ID
in Col. 5

SEQ
Col. 2
polypeptide
spanning
Col. 5
NO: of
to AP2

ID
Species/
in Col. 1
AP2
Conserved
AP2
domain

NO:
Identifier
to ERF058
domain
AP2 domain
domain
of ERF058



490
At/ERF058 or
100%
82-145
LYRGVRQRHWGKWVA
549
100%


AT1G22190.1
(261/261)

EIRLPRNRTRLWLGT

(64/64)





FDTAEEAALAYDKAA







YKLRGDFARLNFPDL







RHND





492
At/AT1G78080.1
53%
151-213
LYRGVRQRHWGKWVA
550
98%



(177/338)

EIRLPRNRTRLWLGT

(62/63)





FDTAEEAALAYDKAA







YKLRGDFARLNFPNL







RHN





516
Gm/Glyma04g
48%
138-199
LYRGVRQRHWGKWVA
562
96%


11290.1
(154/323)

EIRLPKNRTRLWLGT

(60/62)





FDTAEEAALAYDKAA







YKLRGDFARLNFPNL







RH





518
Gm/Glyma06g
49%
127-188
LYRGVRQRHWGKWVA
563
96%


11010.1
(149/308)

EIRLPKNRTRLWLGT

(60/62)





FDTAEEAALAYDKAA







YKLRGDFARLNFPNL







RH





522
Pt/POPTR_0005
63%
171-233
LYRGVRQRHWGKWVA
565
96%


s16690.1
(126/201)

EIRLPKNRTRLWLGT

(60/62)





FDTAEEAALAYDKAA







YKLRGDFARLNFPNL







RHQ





524
Vv/GSVIVT010
60%
112-174
LYRGVRQRHWGKWVA
566
96%


09007001
(121/204)

EIRLPKNRTRLWLGT

(60/62)





FDTAEEAALAYDKAA







YKLRGDFARLNFPNL







RHQ





498
Sl/Solyc04g
45%
76-141
LYRGVRQRHWGKWVA
553
95%


054910.2.1
(132/294)

EIRLPKNRTRLWLGT

(59/62)





FDTAEEAALAYDKAA







YKLRGEFARLNFPHL







RHQLNN





502
Pt/POPTR_0007
47%
176-237
LYRGVRQRHWGKWVA
555
95%


s05690.1
(132/284)

EIRLPKNRTRLWLGT

(59/62)





FDTAEEAALAYDKAA







YKLRGEFARLNFPHL







RH





526
Sl/Solyc12g
48%
124-186
LYRGVRQRHWGKWVA
567
95%


056980.1.1
(150/316)

EIRLPKNRTRLWLGT

(60/63)





FDTAEEAALAYDKAA







YKLRGEFARLNFPHL







RHN





528
Bd/Bradi4g
45%
109-168
LYRGVRQRHWGKWVA
568
94%


29010.1
(126/282)

EIRLPRNRTRLWLGT

(56/59)





FDTAEEAALAYDQAA







YRLRGDAARLNFPDN





504
Vv/GSVIVT010
50%
94-155
LYRGVRQRHWGKWVA
556
93%


02262001
(138/281)

EIRLPKNRTRLWLGT

(58/62)





FDTAEEAALAYDKAA







FKLRGEFARLNFPNL







RH





514
Gm/Glyma14g
44%
150-216
LYRGVRQRHWGKWVA
561
93%


34590.1
(140/324)

EIRLPKNRTRLWLGT

(57/61)





FDTAEEAALAYDKAA







YRLRGDFARLNFPSL







KGSCPGE





520
Pt/POPTR_0002
62%
162-224
LYRGVRQRHWGKWVA
564
93%


s09480.1
(125/203)

EIRLPKNRTRLWLGT

(58/62)





FDTAEEAALAYDRAA







YKLRGDFARLNFPNL







LHQ





530
Os/LOC_Os08g
52%
103-162
LYRGVRQRHWGKWVA
569
93%


31580.1
(101/197)

EIRLPRNRTRLWLGT

(55/59)





FDTAEEAALTYDQAA







YRLRGDAARLNFPDN





510
Gm/Glyma13g
47%
137-203
LYRGVRQRHWGKWVA
559
91%


01930.1
(147/317)

EIRLPKNRTRLWLGT

(56/61)





FDTAEEAALAYDKAA







YRLRGDLARLNFPNL







KGSCPGE





546
Zm/GRMZM2G
46%
113-173
LYRGVRQRHWGKWVA
577
91%


113060_T01
(100/219)

EIRLPRNRTRLWLGT

(56/61)





FDTAEEAALAYDGAA







FRLRGDSARLNFPEL







R





500
Pt/POPTR_0005
53%
172-233
LYRGVRQRHWGKWVA
554
90%


s07900.1
(118/226)

EIRLPKNRTRLWLGT

(56/62)





YDTAEEAALAYDNAA







YKLRGEYARLNFPHL







RH





506
Gm/Glyma05g
45%
116-178
LYRGVRQRHWGKWVA
557
90%


31370.1
(141/314)

EIRLPKNRTRLWLGT

(57/63)





FDTAEEAALAYDNAA







FKLRGEFARLNFPHL







RHH





508
Gm/Glyma08g
45%
120-182
LYRGVRQRHWGKWVA
558
90%


14600.1
(142/318)

EIRLPKNRTRLWLGT

(57/63)





FDTAEEAALAYDNAA







FKLRGEFARLNFPHL







RHH





534
Si/Si017760m
54%
161-221
LYRGVRQRHWGKWVA
571
90%



(107/201)

EIRLPKNRTRLWLGT

(55/61)





FDTAEDAALAYDKAA







FRLRGDMARLNFPAL







R





536
Os/LOC_Os02g
53%
168-228
LYRGVRQRHWGKWVA
572
90%


51670.1
(109/209)

EIRLPKNRTRLWLGT

(55/61)





FDTAEDAALAYDKAA







FRLRGDLARLNFPTL







R





540
Zm/GRMZM5G
54%
173-233
LYRGVRQRHWGKWVA
574
90%


852704_T01
(108/200)

EIRLPRNRTRLWLGT

(55/61)





FDSAEDAALAYDKAA







FRLRGDAARLNFPSL







R





544
Os/LOC_Os03g
50%
111-171
LYRGVRQRHWGKWVA
576
90%


09170.1
(104/211)

EIRLPRNRTRLWLGT

(55/61)





FDTAEEAALAYDSAA







FRLRGESARLNFPEL







R





548
At/AT4G39780
43%
92-155
LYRGVRQRHWGKWVA
578
89%



(120/282)

EIRLPKNRTRLWLGT

(57/64)





FDTAEEAAMAYDLAA







YKLRGEFARLNFPQF







RHED





512
Gm/Glyma18g
43%
122-184
LYRGVRQRHWGKWVA
560
88%


02170.1
(130/306)

EIRLPKNRTRLWLGT

(56/63)





FDTAEEAALAYDNAA







FKLRGENARLNFPHL







RHH





532
Zm/GRMZM2G
54%
147-207
LYRGVRQRHWGKWVA
570
88%


029323_T01
(106/199)

EIRLPKNRTRLWLGT

(54/61)





FDTAEGAALAYDEAA







FRLRGDTARLNFPSL







R





538
Bd/Bradi3g
52%
155-215
LYRGVRQRHWGKWVA
573
88%


58980.1
(93/182)

EIRLPKNRTRLWLGT

(54/61)





FDAAEDAALAYDKAA







FRLRGDQARLNFPAL







R





542
Si/Si008385m
54%
173-233
LYRGVRQRHWGKWVA
575
88%



(108/200)

EIRLPRNRTRLWLGT

(54/61)





FGSAEDAALAYDKAA







FRLRGDAARLNFPSL







R





496
At/AT5G65130.1
50%
110-169
LYRGVRQRQWGKWVA
552
85%



(99/201)

EIRLPKNRTRLWLGT

(51/60)





FETAQEAALAYDQAA







HKIRGDNARLNFPDI





494
At/AT2G22200.1
48%
70-133
LYRGVRQRHWGKWVA
551
82%



(101/214)

EIRLPKNRTRLWLGT

(53/64)





FETAEKAALAYDQAA







FQLRGDIAKLNFPNL







IHED



Species abbreviations for Table 7:

At— Arabidopsis thaliana ;

Bd— Brachypodium distachyon ;

Gm— Glycine max ;

Os— Oryza sativa ;

Pt— Populus trichocarpa ;

Si— Setaria italica ;

Sl— Solanum lycopersicum ;

Vv— Vitis vinifera ;

Zm— Zea mays





















































































































































































































Sequences that are functionally-related and/or closely-related to the polypeptides in Table 7 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed ERF058-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
Several consensus sequences may be used to identify members of the ERF058 clade of polypeptide, which are sequences that are expected to function as indicated in the embodiments of this specification provided below. As shown in FIG. 11D-11E , these functionally-related and/or closely-related ERF058 clade polypeptides generally contain a consensus sequence of the ERF058 clade, SEQ ID NO: 579 (which is found in boldface in FIG. 11D-11E ).







LYRGVRQRX 1 WGKWVAEIRLPX 2 NRTRLWLGTX 3 xX 4 AX 5 xAAX 6 X 7





YDxAAxX 8 X 6 RGX 9 xAX 2 LNFP;










wherein x represents any amino acid; X 1 is Q or H; X 2 is K or R; X 3 is F or Y; X 4 is A, S or T; X 5 is Q or E; X 6 is M, I, L, or V; X 7 is A or T; X 8 is K, Q or R; and X 9 is E or D.
As shown in FIG. 11E-11F , these functionally-related and/or closely-related ERF058 clade polypeptides also generally contain a ERF058 clade consensus sequence SEQ ID NO: 580:







X 6 xxX 10 X 6 X 11 X 4 KX 6 xxX 6 C;








wherein x represents any amino acid; X 4 is A, S or T; X 6 is M, I, L, or V; X 10 is A or S; and X 11 is N or D.
There is also a small motif in FIG. 11G-11H that is present in ERF058 clade member proteins, and is identifiable as SEQ ID NO: 581:
LxxxPSxX 9 IX 12 x 11 WxX 10 X 6 .
wherein x represents any amino acid; X 6 is M, I, L, or V; X 9 is E or D; X 10 is A or S; and X 11 is N or D; and X 12 is F or absent.

The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. An ERF058 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Table 7 may also have at least 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 52%, 53%, 54%, 60%, 62%, 63%, or about 100% amino acid identity to SEQ ID NO: 490 or to the entire length of a listed sequence, or to the amino acid sequence of SEQ ID NO: 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, and/or at least 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% amino acid identity to the AP2 domain of SEQ ID NO: 490 or to SEQ ID NO: 549-581. The presence of the disclosed conserved AP2 domain in the polypeptide sequence (for example, SEQ ID NO: 549-578), or a clade consensus sequence of SEQ ID NO: 579, 580, or 581, is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “ERF058 clade polypeptides” or “ERF058 clade polypeptides”, or which fall within the “ERF058 clade” or “G974 clade” exemplified in the phylogenetic tree in FIG. 10 as those polypeptides bounded by Bradi4g29010.1 and POPTR — 0005 s16690.1 (indicated by the box around these sequences).





TABLE 8



Conserved HLH domain of SPATULA

and closely related sequences















Col. 7







Percent







identity



Col. 3



of the



Percent
Col. 4

Col. 6
HLH domain

Col. 1

identity of
HLH

SEQ ID
in Col. 5

SEQ
Col. 2
polypeptide
domain in
Col. 5
NO: of
to the

ID
Species/
in Col. 1
amino acid
Conserved
HLH
HLH domain

NO:
Identifier
to SPATULA
coordinates
HLH domain
domain
of SPATULA



625
At/SPATULA or
100%
195-251
RCRAAEVHNLSEKRR
666
100%


AT4G36930
(373/373)

RSRINEKMKALQSLI

(57/57)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





627
Bd/Bradi1g
83%
104-160
RTRAAEVHNLSEKRR
667
98%


48400.1
(70/84)

RSRINEKMKALQSLI

(56/57)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





629
Gm/Glyma01g
51%
139-195
RSRAAEVHNLSEKRR
668
98%


39450.1
(127/245)

RSRINEKMKALQNLI

(54/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





631
Pt/POPTR_0014
50%
121-177
RSRAAEVHNLSEKRR
669
98%


s02590.1
(103/203)

RSRINEKMKALQNLI

(54/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





633
Sl/Solyc02g
50%
140-196
RSRAAEVHNLSEKRR
670
98%


093280.2.1
(104/204)

RSRINEKMKALQKLI

(54/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





635
Eg/Eucgr.
60%
22-78
RSRTAEVHNLSEKRR
671
98%


I00906.1
(91/151)

RSRINEKMKALQSLI

(54/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





637
Vv/GSVIVT010
54%
137-193
RSRAAEVHNLSEKRR
672
98%


22111001
(119/217)

RSRINEKMKALQNLI

(54/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





639
Vv/GSVIVT010
52%
185-241
RSRAAEVHNLSEKRR
673
98%


09467001
(113/214)

RSRINEKMKALQNLI

(54/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





641
Cc/clementine
54%
157-213
RSRAAEVHNLSEKRR
674
98%


0.9_029807m
(103/188)

RSRINEKMKALQSLI

(54/55)





PNSNKTDKASMLDEA







IEYLKHLQLQVQ





643
Os/LOC_Os06g
68%
101-157
RSRAAEVHNLSEKRR
675
98%


06900.1
(77/113)

RSKINEKMKALQSLI

(54/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





645
Zm/GRMZM2G
82%
103-159
RSRAAEVHNLSEKRR
676
98%


017349_T01
(69/84)

RSKINEKMKALQSLI

(54/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





647
Gm/Glyma11g
41%
138-194
RSRAAEVHNLSEKRR
677
96%


05810.1
(144/348)

RGRINEKMKALQNLI

(53/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





649
Cc/clementine
54%
104-160
RSRAAEVHNLSEKRR
678
96%


0.9_017382m
(93/170)

RSRINEKLKALQNLI

(53/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





651
Cc/clementine
54%
103-159
RSRAAEVHNLSEKRR
679
96%


0.9_017468m
(93/170)

RSRINEKLKALQNLI

(53/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





653
Os/LOC_Os02g
83%
52-108
RSRAAEVHNLSEKRR
680
96%


56140.1
(64/77)

RSRINEKMKALQSLI

(53/55)





PNSSKTDKASMLDDA







IEYLKQLQLQVQ





655
Sl/Solyc04g
48%
132-188
RSRSAEVHNLSEKRR
681
94%


078690.2.1
(84/175)

RSRINEKLKALQNLI

(52/55)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ





657
Gm/Glyma17g
79%
19-75
RNRAAEVHNLSEKRR
682
92%


19500.1
(66/83)

RSRINEKLKALQNLI

(51/55)





PNSNKTDKASMLDEA







IEYLKQLHLKVQ





659
Pt/POPTR_0005
73%
134-190
RTRAAEVHNLSEKRR
683
92%


s18280.1
(72/98)

RSRINEKMKALQNLI

(52/56)





PNSSKTDKASMLDEA







IEYLKLLQLQVQ





661
Zm/GRMZM2G
79%
43-99
RSRAAEVHNLSEKRR
684
92%


030744_T02
(65/82)

RSRINEKMKALQTLI

(51/55)





PNSSKTDKASMLDDA







IEYLKHLQLQVQ





663
Zm/GRMZM2G
79%
43-99
RSRAAEVHNLSEKRR
685
92%


030744_T03
(65/82)

RSRINEKMKALQTLI

(51/55)





PNSSKTDKASMLDDA







IEYLKHLQLQVQ





665
At/AT5G67110.1
79%
91-147
RNIDAQFHNLSEKKR
686
90%



(55/69)

RSKINEKMKALQKLI

(48/53)





PNSNKTDKASMLDEA







IEYLKQLQLQVQ



Species abbreviations for Table 8:

At— Arabidopsis thaliana ;

Bd— Brachypodium distachyon ;

Cc— Citrus clementina ;

Eg— Eucalyptus grandis ;

Gm— Glycine max ;

Os— Oryza sativa ;

Pt— Populus trichocarpa ;

Si— Setaria italica ;

Sl— Solanum lycopersicum ;

Vv— Vitis vinifera ;

Zm— Zea mays















































































































































Sequences that are functionally-related and/or closely-related to the polypeptides in Table 8 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed SPATULA-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
As shown in FIG. 14H-FIG . 14 I, these “functionally-related and/or closely-related” SPATULA clade polypeptides generally contain a consensus sequence of the SPATULA clade, SEQ ID NO: 687:







KRxxxAX 1 xHNLSEKX 2 RRX 3 X 2 INEKX 4 KALQxLIPNSxKTDKASM





LDX 5 AIEYLKxLX 6 LX 7 VQxX 8 X 9 X 8 .*










*In the above consensus sequence of SEQ ID NO: 687, x represents any amino acid;
X 1 is E or Q; X 2 is R or K; X 3 is G or S; X 4 is I, V, L, or M; X 5 is E or D; X 6 is Q or H; X 7 is Q or K; X 8 is I, V, L, M, or absent; and X 9 is S, T, A, or absent. Alternative consensus sequences comprising the above with conservative substitutions found in Table 1 are also envisaged and may be expected to provide equivalent function(s).
The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. A SPATULA clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Table 8 may also have at least 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% amino acid identity to SEQ ID NO: 625, and/or at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% amino acid identity to the HLH domain of SEQ ID NO: 625, in its amino acid sequence to the entire length of a listed sequence or to a listed domain, or to the amino acid sequence of SEQ ID NO: 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 666, 667, 668, 669, 670, 671, 672, 673, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685, or 686. The presence of the disclosed conserved HLH domain and/or other domains in the polypeptide sequence (for example, in any of SEQ ID NO: 666-686), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “SPATULA clade polypeptides” or “SPATULA clade polypeptides”, or which fall within the “SPATULA clade” or “G590 clade” exemplified in the phylogenetic tree in FIG. 13 as those polypeptides bounded by Bradi1g48400.1_BRADI and Solyc04g078690.2.1_SOLLY (indicated by the box with the dashed border around these sequences).





TABLE 9



MYB111 Glade sequences and conserved first SANT

domains of MYB111 and closely related sequences















Col. 7







Percent







identity







of first



Col. 3
Col. 4


SANT



Percent
SANT

Col. 6
domain

Col. 1

identity of
domain 1
Col. 5
SEQ ID
in Col. 5

SEQ
Col. 2
polypeptide
in amino
Conserved
NO: of
to SANT

ID
Species/
in Col. 1
acid
SANT
SANT
domain 1

NO:
Identifier
to MYB111
coordinates
domain 1
domain 1
of MYB111



735
At/
100%
14-63
RGRWTAEEDEILTKY
784
50/50


MYB111
(342/342)

IQTNGEGSWRSLPKK

(100%)


AT5G49330


AGLLRCGKSCRLRWI







NYLRR





741
Gm/Glyma02g
57%
14-63
KGRWTAEEDEILAKY
790
91%


01740.1
(125/219)

IQANGEGSWRSLPKN

(45/49)





AGLLRCGKSCRLRWI







NYLRA





749
Pp/POPTR_
73%
14-63
KGRWTAEEDEKLTKY
798
91%


0014s11780.1
(107/146)

IQANGEGSWRSLPKN

(44/48)





AGLLRCGKSCRLRWI







NYLAA





745
Gm/Glyma19g
81%
14-63
KGRWTTEEDEILTKY
794
89%


40250.1
(97/119)

IMANGEGSWRSLPKN

(44/49)





AGLLRCGKSCRLRWI







NYLRA





753
Sl/Solyc01g
75%
14-63
RGRWTAEEDQILTNY
802
89%


079620.2.1
(103/137)

IISNGEGSWRSLPKN

(44/49)





AGLLRCGKSCRLRWI







NYLRS





755
Sl/Solyc06g
82%
14-63
RGRWTSEEDEILTNY
804
89%


009710.2.1
(103/125)

IQANGEGSWRSLPKN

(44/49)





AGLLRCGKSCRLRWI







NYLKS





761
Gm/Glyma17g
55%
14-63
KGRWTAEEDKILTDY
810
89%


03480.1
(128/231)

QIENGEGSWRSLPKN

(44/49)





AGLLRCGKSCRLRWI







NYLRS





737
At/AT2G47460.1
61%
14-63
RGRWTAEEDQILSNY
786
87%



(120/194)

IQANGEGSWRSLPKN

(43/49)





AGLKRCGKSCRLRWI







NYLRS





747
Pp/POPTR_
58%
14-63
KGRWTAEEDEKLAKY
796
87%


0002s19920.1
(118/203)

IQANGEGSWRSMPKN

(43/49)





AGLLRCGKSCRLRWI







NYLRA





751
Pp/POPTR_
42%
14-63
KGRWTAEEDEVLTKY
800
87%


0010s15090.1
(160/377)

ILANGEGSWKSLPKN

(43/49)





AGLLRCGKSCRLRWI







NYLRA





759
Gm/Glyma07g
56%
14-63
KGRWTAEEDKILTDY
808
87%


37140.1
(121/215)

IQENGEGSWSSLPKN

(43/49)





AGLLRCGKSCRLRWI







NYLRS





783
Si/Si039538m
81%
14-63
RGRWTAEEDEILANY
832
87%



(97/119)

IAKHGEGSWRSLPKN

(43/49)





AGLLRCGKSCRLRWI







NYLRA





743
Gm/Glyma03g
43%
14-63
KGRWTEEEDDILTKY
792
85%


37640.1
(143/332)

IQANGEGSWRSLPTN

(42/49)





SGLLRCGKSCRLRWI







NYLRA





757
Sl/Solyc12g
76%
14-63
RGRWTIEEDERLTNY
806
85%


049350.1.1
(94/123)

IQANGEGSWRTLPKN

(42/49)





AGLLRCGKSCRLRWI







NYLKS





763
Gm/Glyma09g
43%
14-63
KGRWTAEEDKILTDY
812
85%


04370.1
(150/345)

IQENGEGSWKILPKN

(42/49)





AGLLRCGKSCRLRWI







NYLRA





765
Gm/Glyma15g
83%
14-63
KGRWTAEEDKILTDY
814
85%


15400.1
(99/119)

IQENGEGSWKTLPKN

(42/49)





AGLLRCGKSCRLRWI







NYLRA





739
At/AT3G62610.1
55%
14-63
KGRWTAEEDRTLSDY
788
83%



(106/190)

IQSNGEGSWRSLPKN

(41/49)





AGLKRCGKSCRLRWI







NYLRS





771
Zm/GRMZM2G
79%
14-63
KGRWTREEDEILARY
820
83%


051528_T01
(94/118)

IEEHGEGSWRSLPKN

(41/49)





AGLLRCGKSCRLRWI







NYLRA





773
Si/Si002107m
81%
14-63
KGRWTKEEDEILGRY
822
83%



(97/119)

IKEHGEGSWRSLPKN

(41/49)





AGLLRCGKSCRLRWI







NYLRA





775
Os/LOC_Os03g
64%
14-63
RGRWTTEEDEKLAGY
824
83%


19120.1
(94/146)

IAKHGEGSWRSLPKN

(41/49)





AGLLRCGKSCRLRWI







NYLRA





777
Zm/GRMZM2G
61%
14-63
RGRWTKEEDQHANYI
826
83%


022686_T01
(106/173)

AEHGEGSWRSLPKNA

(41/49)





GLLRCGKSCRLRWIN







YLRA





779
Zm/GRMZM2G
80%
14-63
RGRWTAEEDQLLANY
828
83%


057027_T02
(96/119)

IAEHGEGSWRSLPKN

(41/49)





AGLLRCGKSCRLRWI







NYLRA





781
Zm/GRMZM2G
61%
14-63
RGRWTAEEDQLLANY
830
83%


084799_T01
(105/172)

IAEHGEGSWRSLPKN

(41/49)





AGLLRCGKSCRLRWI







NYLRA





767
Os/LOC_Os01g
52%
14-63
RGRWTKEEDEKLARY
816
81%


19970.1
(124/237)

IRENGEGAWRSMPKN

(40/49)





AGLLRCGKSCRLRWI







NYLRA





769
Zm/GRMZM2G
78%
14-63
KGRWTKEEDEVLARY
818
81%


051256_T01
(94/119)

IKEHGEGSWRSLPKN

(40/49)





AGLLRCGKSCRLRWI







NYLRA































































































































































TABLE 10



MYB111 Glade sequences and conserved second SANT

domains of MYB111 and closely related sequences















Col. 7







Percent







identity







of second



Col. 3
Col. 4


SANT



Percent
SANT

Col. 6
domain

Col. 1

identity of
domain 2
Col. 5
SEQ ID
in Col. 5

SEQ
Col. 2
polypeptide
in amino
Conserved
NO: of
to SANT

ID
Species/
in Col. 1
acid
SANT
SANT
domain 2

NO:
Identifier
to MYB111
coordinates
domain 2
domain 2
of MYB111



735
At/
100%
67-114
RGNITSDEEEIIVKL
785
48/48


MYB111
(342/342)

HSLLGNRWSLIATHL

(100%)


AT5G49330


PGRTDNEIKNYWNSH







LSR





737
At/AT2G47460.1
61%
67-114
RGNITPEEEELVVKL
787
87%



(120/194)

HSTLGNRWSLIAGHL

(42/48)





PGRTDNEIKNYWNSH







LSR





753
Sl/Solyc01g
75%
67-114
RGNITSQEEDIIIKL
803
85%


079620.2.1
(103/137)

HATLGNRWSLIAEHL

(41/48)





SGRTDNEIKNYWNSH







LSR





755
Sl/Solyc06g
82%
67-114
RGNITSDEEAIIIKL
805
85%


009710.2.1
(103/125)

RATLGNRWSLIAEHL

(41/48)





PGRTDNEIKNYWNSH







LRR





759
Gm/Glyma07g
56%
67-114
RGNITPQEEEIIVKL
809
85%


37140.1
(121/215)

HAVLGNRWSVIAGHL

(41/48)





PGRTDNEIKNYWNSH







LRR





761
Gm/Glyma17g
55%
67-114
RGNITPQEEEIIVKL
811
85%


03480.1
(128/231)

HAVLGNRWSVIAGHL

(41/48)





PGRTDNEIKNYWNSH







LRR





763
Gm/Glyma09g
43%
67-114
RGNITPEEEEIIVKL
813
85%


04370.1
(150/345)

HAVLGNRWSVIAGHL

(41/48)





PGRTDNEIKNYWNSH







LRR





747
Pp/POPTR_
58%
67-114
RGNISTEEEEIIVQL
797
83%


0002s19920.1
(118/203)

HASLGNRWSLIASYL

(40/48)





PGRTDNEIKNYWNSH







LSR





749
Pp/POPTR_
73%
67-114
RGNISAEEEEIIINL
799
83%


0014s11780.1
(107/146)

HASLGNRWSLIASHL

(40/48)





PGRTDNEIKNYWNSH







LSR





751
Pp/POPTR_
42%
67-114
RGNITKEEEETIVKL
801
83%


0010s15090.1
(160/377)

HTALGNRWSFIAAQL

(40/48)





PGRTDNEIKNYWNSH







LSR





765
Gm/Glyma15g
83%
67-114
RGNITPEEEEIIVKL
815
83%


15400.1
(99/119)

HAVLGNRWSVIAGRL

(40/48)





PGRTDNEIKNYWNSH







LRR





773
Si/Si002107m
81%
67-114
RGNISEEEEEMIIKL
823
83%



(97/119)

HATLGNRWSLIAGHL

(40/48)





PGRTDNEIKNYWNSH







LSR





779
Zm/GRMZM2G
80%
67-114
RGNISKEEEDIIIKL
829
83%


057027_T02
(96/119)

HATLGNRWSLIASHL

(40/48)





PGRTDNEIKNYWNSH







LSR





781
Zm/GRMZM2G
61%
67-114
RGNISKEEEDIIIKL
831
83%


084799_T01
(105/172)

HATLGNRWSLIASHL

(40/48)





PGRTDNEIKNYWNSH







LSR





739
At/AT3G62610.1
55%
67-114
RGNITPEEEDVIVKL
789
81%



(106/190)

HSTLGTRWSTIASNL

(39/48)





PGRTDNEIKNYWNSH







LSR





741
Gm/Glyma02g
57%
67-114
RGNISAEEENTIVKL
791
81%


01740.1
(125/219)

HASFGNRWSLIANHL

(39/48)





PGRTDNEIKNYWNSH







LSR





743
Gm/Glyma03g
43%
67-114
RGNISFLEESIILKL
793
81%


37640.1
(143/332)

HASFGNRWSLIASHL

(39/48)





PGRTDNEIKNYWNSH







LSR





767
Os/LOC_Os01g
52%
67-114
RGNISPQEEDIILNL
817
81%


19970.1
(124/237)

HATLGNRWSLIAGHL

(39/48)





PGRTDNEIKNYWNSH







LSR





769
Zm/GRMZM2G
78%
67-114
RGNISEEEEDMIIKL
819
81%


051256_T01
(94/119)

HATLGNRWSLIAGHL

(39/48)





PGRTDNEIKNYWNSH







LSR





771
Zm/GRMZM2G
79%
67-114
RGNITEEEEDVIVKL
821
81%


051528_T01
(94/118)

HATLGNRWSLIAGHL

(39/48)





PGRTDNEIKNHWNSH







LRR





777
Zm/GRMZM2G
61%
67-114
RGNISKEEEDVIIKL
827
81%


022686_T01
(106/173)

HATLGNRWSLIASHL

(39/48)





PGRTDNEIKNYWNSH







LSR





783
Si/Si039538m
81%
67-114
RGNISKEEEDVIIKL
833
81%



(97/119)

HATLGNRWSLIASHL

(39/48)





PGRTDNEIKNYWNSH







LSR





757
Sl/Solyc12g
76%
67-114
RGNITSEEEAIIIKL
807
77%


049350.1.1
(94/123)

RATLGNRWSLIAEYL

(37/48)





PHRTDNEIKNYWNSR







LCR





745
Gm/Glyma19g
81%
67-114
RGNFSVEEESTILKL
795
72%


40250.1
(97/119)

HASFGSSWSLIASHL

(35/48)





PGRTDNEIKNYWNSH







LSR





775
Os/LOC_Os03g
64%
67-141
RGNISNQEEDVIIKL
825
52%


19120.1
(94/146)

HATLGNRKSYVVKRM

(39/75)





DYVCLGARDYCFQQN







THVRWSLIASHLPGR







TDNEIKNYWNSHLSR



Species abbreviations for Tables 9 and 10:

At— Arabidopsis thaliana ;

Gm— Glycine max ;

Os— Oryza sativa ;

Pt— Populus trichocarpa ;

Si— Setaria italica ;

Sl— Solanum lycopersicum ;

Zm— Zea mays

































































































































































Sequences that are functionally-related and/or closely-related to the polypeptides in Tables 9 and 10 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed MYB111-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
As shown in FIG. 16A-16C , these “functionally-related and/or closely-related” MYB111 clade polypeptides generally contain a consensus sequence of the MYB111 clade, SEQ ID NO: 834:







MxRX 1 PCCX 2 KX 3 GX 3 X 4 X 4 GRWTxEEDxxLxxX 5 X 3 xxX 6 GX 7 GSWxx





X 3 PxxX 1 GLxRCGKSCRLRWX 3 NYLxxxX 3 KRGNxX 1 xX 8 EExxX 3 X 3





xLxX 1 xX 9 GXXXXXXXXXXXXXXXXXXXXXXXXXXXxWSxIAxxX 3





xxRTDNEX 3 KNxWNX 1 xLxX 4 X 10 .*














As shown in FIG. 16A-16B , these “functionally-related and/or closely-related” MYB111 clade polypeptides also generally contain a consensus first SANT domain sequence SEQ ID NO: 835 which is found within the MYB111 clade consensus sequence:







X 4 GRWTxEEDxxLxxX 5 X 3 xxX 6 GX 7 GSWxxX 3 PxxX 1 GLxRCGKSC





RLRWX 3 NYL.*










As shown in FIG. 16B-16C , the instant “functionally-related and/or closely-related” MYB111 clade polypeptides also generally contain a consensus second SANT domain sequence, SEQ ID NO: 836 which is also found within the MYB111 clade consensus sequence:







RGNxX 1 xX 8 EExxX 3 X 3 xLxX 1 xX 9 GXXXXXXXXXXXXXXXXXXXXX





XXXXXXxWSxIAxxX 3 xxRTDNEX 3 KNxWNX 1 xLxX 4 .*










*In the above consensus sequences of SEQ ID NO: 834, 835, or 836, x represents any amino acid; X 1 is S, A, or T; X 2 is E or G; X 3 is I, V, L, or M; X 4 is K or R; X 5 is Y or F; X 6 is N or H; X 7 is E or Q; X 8 is E, D, or Q; X 9 is L or F; and X 10 is R, K, or Q. Alternative consensus sequences comprising the above with conservative substitutions found in Table 1 and Tables 9 and 10 are also envisaged and may be expected to provide equivalent function(s) in MYB-(R1)R2R3 regulatory proteins.
The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. A MYB111 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Tables 9 or 10 may also have at least 42%, 43%, 52%, 55%, 56%, 57%, 58%, 61%, 64%, 73%, 75%, 76%, 78%, 79%, 80%, 81%, 82%, 83%, or about 100% amino acid identity to SEQ ID NO: 735, and/or at least 81%, 83%, 85%, 87%, 89%, 91%, or about 100% amino acid identity to the first SANT domain of SEQ ID NO: 735, and/or at least 52%, 72%, 77%, 81%, 83%, 85%, 87%, or about 100% amino acid identity to the second SANT domain of SEQ ID NO: 735 in its amino acid sequence to the entire length of a listed sequence or to a listed first SANT domains, or to a listed second SANT domains, or to the amino acid sequence of SEQ ID NO: 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, or 783, or 784-833. The presence of the disclosed conserved first SANT domains and/or second SANT domains in the polypeptide sequence (for example, SEQ ID NO: 784-833), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “MYB111 clade polypeptides” or “MYB111 clade polypeptides”, or which fall within the “MYB111 clade” or “G1640 clade” exemplified in the phylogenetic tree in FIG. 15 as those polypeptides bounded by LOC_Os01g19970.1 and Glyma15g15400.1 (indicated by the box around these sequences).





TABLE 11



Conserved BTB domains of AtNPR3

and closely related sequences















Col. 7







Percent







identity



Col. 3



of the BTB



Percent
Col. 4

Col. 6
domains

Col. 1

identity of
BTB

SEQ ID
in Col. 5

SEQ
Col. 2
polypeptide
domains in
Col. 5
NO: of
to the BTB

ID
Species/
in Col. 1
amino acid
Conserved
BTB
domain of

NO:
Identifier
to AtNPR3
coordinates
BTB domains
domains
AtNPR3



864
At/AtNPR3 or
100%
61-185
DAEIIVDGVPVGVHRCI
923
100%


AT5G45110.1
(586/586)

LAARSKFFQDLFKKEKK

(143/143)





ISKTEKPKYQLREMLPY







GAVAHEAFLYFLSYIYT







GRLKPFPLEVSTCVDPV







CSHDCCRPAIDFVVQLM







YASSVLQVPELVSSFQR







RLCNFV





920
Pt/POPTR_
61%
65-190
DADIVVEGIAVGVHRCI
949
69%


0012s11900.1
(334/543)

LASRSKFFHELFRREKG

(87/126)





SLEKDGKPKYCMSELLP







YGNVGYEAFLIFLSYLY







TGKLKPSPMEVSTCVDN







VCAHDSCRPAITFAVEL







TYASSIFQVPELVSLFQ







RRLLNFV





908
Pt/POPTR_
62%
65-190
DADIVVEGTAIGVHRCI
945
68%


0015s15800.1
(350/564)

LGARSKFFHELFRREKG

(86/126)





SSEKEGKPKYCMSDLLP







CGKVGYEAFLIFLSYLY







TGKLKPSPMEVSTCVDN







VCAHDACRPAINFAVEL







MYASSIFQVPELVSLFQ







RRLQNFV





918
Gm/Glyma09g
63%
65-190
DADLVVEGIPVSVHRCI
948
66%


02430.1
(333/527)

LASRSKFFHELFKREKG

(84/126)





SSEKEGKLKYNMNDLLP







YGKVGYEAFLIFLGYVY







TGKLKPSPMEVSTCVDN







VCAHDACRPAINFAVEL







MYASSIFQIPELVSLFQ







RRLLNFI





922
Gm/Glyma15g
62%
65-190
DADIVVEGISVSVHRCI
950
65%


13320.1
(328/527)

LASRSKFFHELFKREKG

(82/126)





SSEKEGKLKYNMSDLLP







YGKVGYEAFLIFLGYVY







TGKLKPSPMEVSTCVDS







VCAHDACRPAINFAVEL







MYASYIFQIPEFVSLFQ







RRLLNFI





916
Eg/Eucgr.
59%
65-190
DADIVVENISVGVHRCI
947
65%


E01922.1
(314/526)

LAARSDFFNNLFKREKG

(82/126)





SSEKEGKPKYNMDDLLP







YGKVGYEAFLIFLSYAY







TGKLKRSPLEVSTCVDD







MCSHDACSPAINFAVEL







MYASYIFQIRELVSLLQ







RHLVNFV





910
Sl/Solyc02g
58%
67-192
DAEIVVEGVSLGVHRCI
946
63%


069310.2.1
(307/525)

LAARSSFFRDLFRKRNG

(80/126)





NCGKEGKPSYSMIDILP







CGKVGYEAFLTFLSYLY







SGKLKHFPPEASTCVNS







LCSHDSCRPAINFHVEL







MYASFVFQVPELVSLFL







RHLFSFV





904
Pt/POPTR_
57%
65-190
DAEIFVEGTPVGVHRCV
943
60%


0002s05740.1
(227/397)

LAARSQFFHELFKKGNN

(76/126)





NSTNGDKPRYLMSDLVP







YGGVGYEAFHVFLHYLY







TGKLKPSPPEVSRCVDD







ACAHDVCRPAINYVVEL







MCASATFQMKELVLLFQ







RRLLNFI





894
Gm/Glyma02g
55%
64-189
DAEILVEDIPVGIHRCI
938
58%


45260.1
(294/527)

LASRSLFFHELFKKGTD

(74/126)





GSGKEGKPRYLMSDLVP







YGTVGYEAFQVFLYYLY







TGRLKASPTEVTTCVDE







TCTHDACRPAINYALEL







MYASATFQMKELVLLFQ







RHLLNFV





898
Gm/Glyma02g
55%
64-189
DAEILVEDIPVGIHRCI
940
58%


45260.2
(256/465)

LASRSLFFHELFKKGTD

(74/126)





GSGKEGKPRYLMSDLVP







YGTVGYEAFQVFLYYLY







TGRLKASPTEVTTCVDE







TCTHDACRPAINYALEL







MYASATFQMKELVLLFQ







RHLLNFV





906
Pt/POPTR_
53%
65-190
DAEIVVEGIPVGVHRCI
944
57%


0005s22770.1
(283/526)

LAARSQFFHELFKKVDS

(72/126)





NSTSGDKPRYLMSDLMP







YGGVGYEAFNVFLHYLY







TGKHKSSPPEVSQCVYD







ACAHDACRPAINYAVEL







MYASATFQMKELVLLFQ







RRLLSFI





896
Gm/Glyma14g
55%
64-189
DAEILIEDIPVGIHRCI
939
55%


03510.1
(293/529)

LASRSPFFHELFKKGTD

(70/126)





GSGKEGKPRYLMSDLMP







YGTVGYQAFQVFLYYLY







TGRLKASPTEETTCVDE







TCIHVACRPAINHALEL







MYASATFQMKELVLLFQ







RHLLNFV





892
Cc/clementine
53%
67-195
DAEIVVEGKSVALHRCI
937
55%


0.9_005587m
(285/531)

LSARSQFFHELFKKGNN

(72/129)





NDGSAVSEGKPKYLMTE







LVPYGKVGYEALNVILY







YFYTGKLKPSPSEVSTC







VDDACAHDACPPAINYA







IELMYASAAFQMKELVL







LFQRRLLNFV





872
Sl/Solyc07g
51%
51-176
DAEIVVEGINVGVNRCI
927
53%


044980.2.1
(278/541)

LAARSQFFHEKFKEKNE

(68/126)





NSLKNEKPKYLLKDLVC







VSSIGYEVFMVLLNYLY







TGKIKSSPSEVSSCVDN







ACAHDACRPAINYAVEL







MYASSTFQIKELVMFVE







RYLDNFV





900
Eg/Eucgr.
48%
61-186
DAVIVVEGVPVGVHRCL
941
53%


A02033.1
(258/528)

LAARSQFLHEFFKQGGG

(68/126)





DNAREGKPRYPISDLVK







KGHVGCEAFKYVLRYMY







TGKLKLFPAEVSTCVDS







SCAHDVCGPAINYAVEL







MYASATFLIAELVMLVQ







RRLLHFI





902
Eg/Eucgr.
51%
61-186
DAVIVVEGVPVGVHRCL
942
53%


A02033.2
(189/368)

LAARSQFLHEFFKQGGG

(68/126)





DNAREGKPRYPISDLVK







KGHVGCEAFKYVLRYMY







TGKLKLFPAEVSTCVDS







SCAHDVCGPAINYAVEL







MYASATFEIAELVMLVQ







RRLLHFI





878
Bd/Bradi1g
47%
57-187
DAEVVLADGGDEATVPV
930
52%


12870.1
(256/538)

HRCILAARSNFFLDHFS

(69/131)





SLSSPAAGGGKPRLELA







ELVPGGRHVGHEALVAV







LGYLYTGRLKPPPQEAA







ICVDDRCRHQACRPAID







EVVESTYAASGFQISEL







VSLFQRRLSDFV





882
Si/Si034834m
47%
56-186
DAEVALAAGKGGAAVGV
932
49%



(256/538)

HRCILAARSALFRDHFA

(65/131)





SLPPPAAVGEKPRLELA







DLVPGGRHIGQDALVPV







LGYLYTGRLKSAPQDAT







VCMDDACGHGACRPAID







FVVESMYAASGFQISEL







VSLFQRRLSDFV





890
Cc/clementine
46%
92-217
DAEIVVEGKSVAVNRSI
936
50%


0.9_005201m
(246/525)

LSERSQFFRRLFNLRND

(63/126)





GSVSEGKPKYLLTDLVP







HGKVGYEAFNDTLHYIY







TGKTKAPPPEVSTCVDD







ACVHVSCPPTINYVIEL







MYASAALQMKKLVIRLE







LWLLNLV





888
Zm/GRMZM2
47%
45-175
DAEIALAAARGGGAVGV
935
48%


G115162_T01
(256/541)

HRCILAARSAFFLDHLA

(64/131)





SLPAPAAAGERPRLELA







DLVPGGRHIGRDALVPV







LGYLYTGRLKPPAQDAT







VCMDDACGHGTCRPAID







FVVESMYAASGFQISEL







ASLFQRRLSDFV





880
Os/LOC_Os03g
48%
51-187
DAEIVLASGGGDPGGGA
931
48%


46440.3
(263/545)

VVGVHRCILAARSRFFY

(67/137)





DHFSSAPAPAPATAGDK







PQLDLDGLVPGGRHIGR







DALVAVLSYLYTGRLRS







APPEAAACLDDGCSHDA







CRPAIDFVVESTYAASG







FQISELVSLFQRRLSDF







V





884
Os/LOC_Os03g
48%
51-187
DAEIVLASGGGDPGGGA
933
48%


46440.1
(263/545)

VVGVHRCILAARSRFFY

(67/137)





DHFSSAPAPAPATAGDK







PQLDLDGLVPGGRHIGR







DALVAVLSYLYTGRLRS







APPEAAACLDDGCSHDA







CRPAIDFVVESTYAASG







FQISELVSLFQRRLSDF







V





886
Os/LOC_0s03g
48%
51-187
DAEIVLASGGGDPGGGA
934
48%


46440.2
(263/545)

VVGVHRCILAARSRFFY

(67/137)





DHFSSAPAPAPATAGDK







PQLDLDGLVPGGRHIGR







DALVAVLSYLYTGRLRS







APPEAAACLDDGCSHDA







CRPAIDFVVESTYAASG







FQISELVSLFQRRLSDF







V





874
Bd/Bradi2g
52%
81-225
DADVDMADGGPLVPVHR
928
48%


51030.1
(289/547)

CILAARSPFFHEFFAAR

(70/145)





GRGNSGDGPPSASAAGV







GGGGEGTGRPRYKMEEL







VPGGRVGREAFLGFMRY







LYTGKLRPAPPDVVSCV







DPVCPHDSCPPAIRFAV







ELMYAASTFNIPELISL







FQRRLLNFV





868
Si/Si000647m
52%
82-225
DADIEVPDGGPPVPVHR
925
46%



(298/573)

CILAVRSPFFYDIFAAR

(67/143)





GRGGAARGDAAAGARGA







GEGAASGRPRYKMEELV







PGGRVGREAFQAFLGYL







YTGKLRPAPLDVVSCAD







PVCPHDSCPPAIRFAVE







LMYAAWTFKIPELISLF







QRRLLNFV





870
Si/Si000671m
52%
82-225
DADIEVPDGGPPVPVHR
926
46%



(298/563)

CILAVRSPFFYDIFAAR

(67/143)





GRGGAARGDAAAGARGA







GEGAASGRPRYKMEELV







PGGRVGREAFQAFLGYL







YTGKLRPAPLDVVSCAD







PVCPHDSCPPAIRFAVE







LMYAAWTFKIPELISLF







QRRLLNFV





866
Zm/GRMZM2
53%
82-225
DADVDVPDGGPPVPIHR
924
44%


G076450_T01
(291/545)

CILAARSDFFYDLFAAR

(64/143)





GRAGAARGDAAAGAGVA







AEGAASGRPRYKMEDLV







PAGRVGREAFQAFLGYL







YTGKLRPAPVDVVSCAD







PVCHHDSCPPAIRSAVE







LMYAACTFKIPELTSLF







QRRLLNFV





876
Os/LOC_Os01g
51%
98-241
DADVDVADGGPPVPVHR
929
43%


56200.1
(287/558)

CILAARSTFFYNLFAAR

(62/143)





GRGGDGAAGGGGGGGGG







GGERTGGRPRYKMEELV







PGGRVGRDAFLSLLGYL







YTGKLRPAPDDVVSCAD







PMCPHDSCPPAIRFNVE







QMYAAWAFKITELISLF







QRRLLNFV





































































































































































































































































































TABLE 12



Conserved ANK repeats of AtNPR3

and closely related sequences















Col. 7







Percent







identity



Col. 3



of the ANK



Percent
Col. 4

Col. 6
repeats in

Col. 1

identity of
ANK
Col. 5
SEQ ID
Col. 5 to

SEQ
Col. 2
Polypeptide
repeats in
Conserved
NO: of
the ANK

ID
Species/
in Col. 1
amino acid
ANK
ANK
repeats

NO:
Identifier
to AtNPR3
coordinates
repeats
repeats
of AtNPR3



864
At/AtNPR3 or
100%
266-355
ILKALDSDDVELVKLL
951
100%


AT5G45110.1
(586/586)

LTESDITLDQANGLHY

(90/90)





SVVYSDPKVVAEILAL







DMGDVNYRNSRGYTVL







HFAAMRREPSIIISLI







DKGANASEFT





910
Sl/Solyc02g
58%
273-362
IYKALDSDDVELVKLL
974
73%


069310.2.1
(307/525)

LNESDISLDGAYALHY

(66/90)





AVAYCDPKVVAEVLGL







GVANVNLRNARGYTVL







HIAAMRKEPSIIVSLL







TKGAHASEIT





912
Gm/Glyma15g
60%
90-179
IHKALDSDDVELVKLL
975
73%


13320.2
(233/382)

LNESDITLDEANALHY

(66/90)





AAAYCDPKVVSEVLGL







GLANVNLRNSRGYTVL







HIAAMRKEPSIIVSLL







TKGACASDLT





918
Gm/Glyma09g
63%
272-361
IHKALDSDDVELVKLL
978
73%


02430.1
(333/527)

LNESDITLDEANALHY

(66/90)





AAAYCDPKVVSEVLGL







GLANVNLRNSRGYTVL







HIAAMRKEPSIIVSLL







TKGACASDLT





922
Gm/Glyma15g
62%
272-361
IHKALDSDDVELVKLL
980
73%


13320.1
(328/527)

LNESDITLDEANALHY

(66/90)





AAAYCDPKVVSEVLGL







GLANVNLRNSRGYTVL







HIAAMRKEPSIIVSLL







TKGACASDLT





914
Vv/GSVIVT01
60%
106-195
ILKALDSDDVELVKLL
976
72%


026274001
(241/398)

LSESGITLDEAYALHY

(65/90)





AAAYCDPKVVSEVLSL







GLADVNRHNPRGYTVL







HVAAMRKEPSIIVSLL







TKGAHASERT





908
Pt/POPTR_
62%
272-361
IHMALDSDDVELVKLL
973
71%


0015s15800.1
(350/564)

LTESDITLDDANALHY

(62/87)





AASYCDLKVVSEVLSL







GLADVNLRNSRGYTVL







HIAAMRKEPSVIVSML







AKGASALDLT





920
Pt/POPTR_
61%
272-361
IHMALDSDDVELVKLL
979
68%


0012s11900.1
(334/543)

LTESDISLDDANALHY

(60/87)





CASYCDLKVMSEVLSL







GLANVNLRNSRGYTVL







HIAAMRKEPSVIVSLL







AKGASALDLT





866
Zm/GRMZM2
53%
306-395
IHRALDSDDVELVKLL
952
68%


G076450_T01
(291/545)

LNESDITLDDANALHY

(62/90)





AASYCDPKVVSELLDL







AMANLNLKNSRGYTAL







HLAAMRREPAIIMCLL







NKGANVSQLT





904
Pt/POPTR_
57%
272-361
IHKALDSDDVELVELL
971
67%


0002s05740.1
(227/397)

LSESNLTLDDAYALHY

(59/88)





AVAYCDPKIVKEVLSL







GSADLNLRNSRGYSVL







HVAARRKEPSIIMALL







TRGASASETT





906
Pt/POPTR_
53%
272-361
IHKALESDDVELVQLL
972
66%


0005s22770.1
(283/526)

LSESNFTLDDAYALHY

(60/90)





AVSYCDPKVVKEVLAL







GLADLNLRNSRGYTVL







HVAARRKESSILVALL







AKGARASEIT





916
Eg/Eucgr.
59%
272-361
IHKALDSDDIELVTLL
977
66%


E01922.1
(314/526)

LSESNINLDEAYGLHY

(60/90)





AAAYCDPKVVSELLGL







GLANVNLRNPRGYTVL







HVAAMRKETKIIVSLL







SKGACASELT





868
Si/Si000647m
52%
306-395
IHRALDSDDVELVKLL
953
64%



(298/573)

LNESEITLDDANALHY

(58/90)





AASYCDSKVVSELLEL







GLANLNLKNSRGYTAL







HLAAMRREPAIIMCLL







NKGATVSQLT





870
Si/Si000671m
52%
306-395
IHRALDSDDVELVKLL
954
64%



(298/563)

LNESEITLDDANALHY

(58/90)





AASYCDSKVVSELLEL







GLANLNLKNSRGYTAL







HLAAMRREPAIIMCLL







NKGATVSQLT





874
Bd/Bradi2g
52%
306-395
IHRALDSDDVELVKLL
956
64%


51030.1
(289/547)

LNESEITLDDANALHY

(58/90)





AAAYCDSKVVSELLDL







GLANLNLKNNRGYTAL







HLAAMRREPTIIMCLL







NKGAVASQLT





876
Os/LOC_Os01g
51%
322-411
IHRALDSDDVELVKLL
957
64%


56200.1
(287/558)

LNESEITLDDANALHY

(58/90)





AAAYCDSKVVSELLDL







RLANLNLKNSRGYTAL







HLAAMRREPAIIMCLL







NKGAAVSQLT





894
Gm/Glyma02g
55%
271-360
IHKALDSDDVELLKLL
966
63%


45260.1
(294/527)

LNESSVTLDDAHALHY

(57/90)





ACAYSDSKVIQEVLSL







GMADILRRNSRGYTVL







HVAARRKDPSILVALL







NKGACASDTT





896
Gm/Glyma14g
55%
271-360
IHKALDSDDVELLKLL
967
63%


03510.1
(293/529)

LNESSVTLDDAYALHY

(57/90)





ACAYSDSKVIQEVLSL







GMADILRRNSRGYTVL







HVAARRKDPSILVALL







NKGARASDTT





898
Gm/Glyma02g
55%
271-360
IHKALDSDDVELLKLL
968
63%


45260.2
(256/465)

LNESSVTLDDAHALHY

(57/90)





ACAYSDSKVIQEVLSL







GMADILRRNSRGYTVL







HVAARRKDPSILVALL







NKGACASDTT





888
Zm/GRMZM2
47%
252-341
ILKALDSDDVDLVGLL
963
61%


G115162_T01
(256/541)

LKESTVTLDDAFAIHY

(55/90)





AAAYCEPKVFAELLKL







DSANVNLKNSGGYTPL







HIACMRREPDIILSLV







ERGACVLERT





878
Bd/Bradi1g
47%
268-357
IHKALDSDDVALVGML
958
60%


12870.1
(256/538)

LKESAITLDDAHAIHY

(54/90)





AAAYCEPKVLAGMLNL







DSANVNLKNDSGYTPL







HIACMRREPDIIVSLI







EKGASVLERT





880
Os/LOC_Os03g
48%
265-354
IHKALDSDDVDLVGML
959
60%


46440.3
(263/545)

LKESPVTLDDAFAIHY

(54/90)





AAAYCEPKVLAELLKL







ESANVNLKNSSGYTPL







HMACMRREPDIIVSLI







EKGASVLERT





884
Os/LOC_Os03g
48%
265-354
IHKALDSDDVDLVGML
961
60%


46440.1
(263/545)

LKESPVTLDDAFAIHY

(54/90)





AAAYCEPKVLAELLKL







ESANVNLKNSSGYTPL







HMACMRREPDIIVSLI







EKGASVLERT





886
Os/LOC_Os03g
48%
265-354
IHKALDSDDVDLVGML
962
60%


46440.2
(263/545)

LKESPVTLDDAFAIHY

(54/90)





AAAYCEPKVLAELLKL







ESANVNLKNSSGYTPL







HMACMRREPDIIVSLI







EKGASVLERT





882
Si/Si034834m
47%
267-356
ILKALDSDDVDLVGLL
960
58%



(256/538)

LKESAVTLDDAFAVHY

(53/90)





AAAYCEPKVFAELLKL







NSANVNLKNNSGYTPL







HIACMRREPDIILSLV







ERGASVMERT





872
Sl/Solyc07g
51%
256-346
ILKALESDDIELLTLL
955
58%


044980.2.1
(278/541)

LEESNVTLNDACALHY

(53/91)





AAAYCNSKVVNEVLEL







GLGADVNLQNSRGYNV







LHVAARRKEPSIIMGL







LAKGASVLDTT





892
Cc/clementine
53%
277-366
IHKALDSDDVELLKLL
965
57%


0.9_005587m
(285/531)

LDESNVTLDDAYALHY

(52/90)





AAAYCNPKVFKEVLNM







GLADLNLKNARGHTVL







HVAARRKEPAVLVTLL







SKGACASETT





900
Eg/Eucgr.
48%
268-357
IHKALDNDDVELVRRL
969
56%


A02033.1
(258/528)

LNESVVTLDDAYALHY

(51/90)





ATAYCHPKIFKEVLGL







GLADLNLKDSRGYTVL







HVAARRKAPSILLPLL







YKGACAMEST





902
Eg/Eucgr.
51%
268-357
IHKALDNDDVELVRRL
970
56%


A02033.2
(189/368)

LNESVVTLDDAYALHY

(51/90)





ATAYCHPKIFKEVLGL







GLADLNLKDSRGYTVL







HVAARRKAPSILLPLL







YKGACAMEST





890
Cc/clementine
46%
299-388
IHKALDSDDVELLKLL
964
55%


0.9_005201m
(246/525)

LDVSNVTLDDAYALHY

(50/90)





AAAYCSPKVFKEVLNM







DLACLNLKDARGRTVL







HVAARRNEPEVMVTLL







SKGACASETT



Species abbreviations for Tables 11 and 12:

At— Arabidopsis thaliana ;

Bd— Brachypodium distachyon ;

Cc— Citrus clementina ;

Eg— Eucalyptus grandis ;

Gm— Glycine max ;

Os— Oryza sativa ;

Pt— Populus trichocarpa ;

Si— Setaria italica ;

Sl— Solanum lycopersicum ;

Vv— Vitis vinifera ;

Zm— Zea mays
























































































































































































































































Sequences that are functionally-related and/or closely-related to the polypeptides in Tables 11 and 12 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed AtNPR3-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
As shown in FIGS. 18B-18C , these “functionally-related and/or closely-related” AtNPR3 clade polypeptides generally contain a consensus sequence within the BTB domain of the AtNPR3 clade:







(SEQ ID NO: 981)


DAxX 2 xX 2 xX 1 X 1 X 1 X 1 X 1 X 1 X 1 X 1 xxxX 2 xX 2 X 3 RX 4 X 2 LX 5 xRSx





FX 6 xxxX 6 *.











As shown in FIGS. 18D-18E , these “functionally-related and/or closely-related” AtNPR3 clade polypeptides generally also contain another consensus sequence within the BTB domain of the AtNPR3 clade:







(SEQ ID NO: 982)


X 7 xxxxX 2 xxX 2 X 2 xxX 8 xX 9 X 2 xxX 10 xX 6 xxxX 2 xYxYX 5 GX 7 xX 7





xxxxX 11 xxxCxxxxCxHxxCxPX 5 IxxxX 2 X 12 xxxAX 5 xxX 6 x





X 2 xxX 2 xxxxxxxLxxX 6 X 2 *.













As shown in FIGS. 18F-18H , these “functionally-related and/or closely-related” AtNPR3 clade polypeptides also generally contain a consensus ANK domain sequence:







(SEQ ID NO: 983)


IxxALX 11 xDDX 2 xLX 2 xxLLxxSxxxLX 13 xAxxX 2 HYxxxYX 4





xxKX 2 xxxX 2 LxX 2 xxX 14 xxX 2 xxX 15 X 13 xxGxxxLHxAxxRx





xxxX 2 X 2 X 2 xX 2 X 2 xX 7 GAxxxX 16 *.













There is also a small motif that is present in AtNPR3 clade member proteins between the BTB and DUF3420 domains, and is identifiable in FIG. 18E as SEQ ID NO: 984:







X 5 xxX 11 X 13 X 2 X 2 PX 2 X 2 xxA.*








There is also a small motif that is present in AtNPR3 clade member proteins at the start of the DUF3420 domain, and is identifiable in FIG. 18F :







(SEQ ID NO: 985)


SxX 17 xxxxX 2 X 11 X 15 X 18 X 2 .*









And, there is also a small motif that is present in AtNPR3 clade member proteins within the NPR1-like_C domain, and is identifiable in FIGS. 18H-18I :







(SEQ ID NO: 986)


KxxX 2 CX 2 xxLX 12 xxX 2 X 19 xX 7 .*









*In the above consensus sequences of SEQ ID NOs: 981-986, x represents any amino acid; X 1 is any amino acid or absent; X 2 is I, V, L, or M; X 3 is H or N; X 4 is C or S; X 5 is S, A, or T; X 6 is F or L; X 7 is K or R; X 8 is G or S; X 9 is H or absent; X 10 is E, K or Q; X 11 is E or D; X 12 is E or Q; X 13 is D or N; X 14 is G or absent; X 15 is K, R, or Q; X 16 is E, D, or Q; X 17 is I, V, L, M, or F; X 18 is E or R; and X 19 is R, Q or absent. Alternative consensus sequences comprising the above with conservative substitutions found in Table 1 are also envisaged and may be expected to provide equivalent function(s).
The presence of one or more of these consensus sequences and/or these amino acid residues is indicative of the AtNPR3 clade polypeptides and the presence of one or more of these consensus sequences is correlated with conferring improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. An AtNPR3 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Tables 11 or 12 may also have at least 46%, 47%, 48%, 51%, 52%, 53%, 55%, 57%, 58%, 59%, 61%, 62%, 63%, or about 100% amino acid identity to SEQ ID NO: 864, and/or at least 43%, 44%, 46%, 48%, 49%, 50%, 52%, 53%, 55%, 57%, 58%, 60%, 63%, 65%, 66%, 68%, 69%, or about 100% amino acid identity to the BTB domain of SEQ ID NO: 864, and/or at least 55%, 56%, 57%, 58%, 60%, 61%, 63%, 64%, 66%, 67%, 68%, 71%, 72%, 73%, or about 100% amino acid identity to the ANK domain of SEQ ID NO: 864 in its amino acid sequence to the entire length of a listed sequence or to a listed BTB domains, or to a listed ANK domains, or to the amino acid sequence of SEQ ID NOs: 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, or 922, 923-980, or 951-980. The presence of the disclosed conserved BTB domains and/or ANK domains in the polypeptide sequence (for example, SEQ ID NOs: 923-980), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “AtNPR3 clade polypeptides” or “AtNPR3 clade polypeptides”, or which fall within the “AtNPR3 clade” or “G839 clade” exemplified in the phylogenetic tree in FIG. 17 as those polypeptides bounded by GRMZM2G076450_T01 and Glyma15g13320.1 (indicated by the box around these sequences).





TABLE 13



Conserved bHLH-MYC_N domain (“domain 1”)

of AtMYC1 and closely related sequences















Col. 7







Percent







identity







of first







bHLH-







MYC_N



Col. 3
Col. 4

Col. 6
domain in



Percent
bHLH-
Col. 5
SEQ ID
Col. 5 to

Col. 1

identity of
MYC_N
Conserved
NO: of
the bHLH-

SEQ
Col. 2
polypeptide
domain in
bHLH-MYC_N
bHLH-
MYC_N

ID
Species/
in Col. 1
amino acid
domain
MYC_N
domain of

NO:
Identifier
to AtMYC1
coordinates
sequence
domain
AtMYC1



1016
At/AtMYC1 or
526/526
23-217
LRKQLALAVRSVQWS
1073
195/195


AT4G00480. 1
(100%)

YAIFWSSSLTQPGVL

(100%)





EWGEGCYNGDMKKRK







KSYESHYKYGLQKSK







ELRKLYLSMLEGDSG







TTVSTTHDNLNDDDD







NCHSTSMMLSPDDLS







DEEWYYLVSMSYVFS







PSQCLPGRASATGET







IWLCNAQYAENKLFS







RSLLARSASIQTVVC







FPYLGGVIELGVTEL







ISEDHNLLRNIKSCL





1018
LOC_Os01g
88/184
19-196
FRKQLAAAVRSISWT
1075
87/184


39560.1
(47%)

YAIFWSISTTRPGVL

(47%)





TWNDGFYNGEIKTRK







IENNLVTELTAEQLL







LQRSEQLRELYNSLL







SGESADQQRRRPVTA







LSPEDLGNVEWYYVV







CMTYAFRPGQCVPGK







SFASNGCAWLCNAQS







ADSKAFPRKLLAKNA







SIQTIVCVPFMTGVL







ELGTTDPAAVARG





1020
LOC_Os04g
92/201
19-202
FRSLLAAAVRSISWS
1077
91/194


47040.1
(45%)

YAIFWSISTSCPGVL

(46%)





TWNDGFYNGVVKTRK







ISNSADLTAGQLVVQ







RSEQLRELYYSLLSG







ECDHRARRPIAALSP







EDLADTEWYYVVCMT







YSFQPGQGLPGKSYA







SNASVWLRNAQSADS







KTFLRSLLAKSASIQ







TIICIPFTSGVLELG







TTDPVLEDPKLVNRI







VAYF





1022
LOC_Os04g
90/201
12-196
FRSQLAAAARSINWT
1079
90/197


47080.1
(44%)

YAIFWSISTSRPGVL

(45%)





TWKDGFYNGEIKTRK







ITNSMNLMADELVLQ







RSEQLRELYDSLLSG







ECGHRARRPVAALLP







EDLGDTEWYYVVCMT







YAFGPRQGLPGKSFA







SNEFVWLTNAQSADR







KLFHRALIAKSASIK







TIVCVPFIMHGVLEL







GTTDPISEDPALVDR







IAASF





1024
GRMZM2G172
158/564
20-180
LRKQLAAAARSINWS
1081
71/160


795_T01
(28%)

YSLFWSISSTQRPRV

(44%)





LTWTDGFYNGEVKTR







KISHSVELTADQLLM







QRSEQLRELYEALQS







GECDRRAARPVGSLS







PEDLGDTEWYYVICM







TYAFLPGQGLPGRSS







ASNEHVWLCNAHLAG







SKDFPRALLAKVPED







PDLINRATAAF





1026
GRMZM5G822
67/172
20-179
LEKKLSRVLTWTDGF
1083
66/163


829_T01
(38%)

YNGEVKTRKISNSVE

(40%)





LTSDHLVMQRSDQLR







ELYEALLSGEGDRRA







APARPAGSLSPEDLG







DTEWYYVVSMTYAFR







PGQGLPGRSFASDEH







VWLCNAHLAGSKAFP







RALLAKSILCIPVMG







GVLELGTTDTVPEAP







DLVSRATAAF





1028
GRMZM5G822
87/204
24-204
MRSQLAAAARSINWS
1085
85/191


829_T03
(42%)

YALFWSISDTQPGVL

(44%)





TWTDGFYNGEVKTRK







ISNSVELTSDHLVMQ







RSDQLRELYEALLSG







EGDRRAAPARPAGSL







SPEDLGDTEWYYVVS







MTYAFRPGQGLPGRS







FASDEHVWLCNAHLA







GSKAFPRALLAKSIL







CIPVMGGVLELGTTD







TVPEAPDLVSRATAA







F





1030
Si000845m
166/573
18-196
LRNHLAAAVRSINWT
1087
79/191



(28%)

YALFWSISSTQPGFL

(41%)





TWTDGFYNGEVKTRK







IVNSAELTADQLVMQ







RSEQLRELYEALLSG







ECDRRAARPVASLSP







EDLGDTELYYVVCMT







YAFRPGQGLPGRSFA







SNERVWMWNSHLADS







KAFPRALLAKTIVCI







PLMSGVLELGTTDAV







VEDPSLVSRATASF





1032
Si012401m
145/520
1-138
FLTWTDGFYNGEVKT
1089
58/153



(28%)

RKIANSAELTADQLV

(37%)





MQRSEQLRELYEALL







SGECDRRTARPVASL







SPEDLGDTEWYYVVC







MTYAFRPGQGLPGRS







FASNERVWMRNSHLA







DSKAFPRALLAKTIV







CIPFMSGVLELGTTD







AEP





1034
AT1G63650.1
105/217
13-202
LKKQLAVSVRNIQWS
1091
102/198



(48%)

YGIFWSVSASQPGVL

(51%)





EWGDGYYNGDIKTRK







TIQAAEVKIDQLGLE







RSEQLRELYESLSLA







ESSASGSSQVTRRAS







AAALSPEDLTDTEWY







YLVCMSFVFNIGEGI







PGGALSNGEPIWLCN







AETADSKVFTRSLLA







KSASLQTVVCFPFLG







GVLEIGTTEHIKEDM







NVIQSVKTLF





1036
AT5G41315.1
101/202
14-206
LKKHLAVSVRNIQWS
1093
100/198



(50%)

YGIFWSVSASQSGVL

(50%)





EWGDGYYNGDIKTRK







TIQASEIKADQLGLR







RSEQLSELYESLSVA







ESSSSGVAAGSQVTR







RASAAALSPEDLADT







EWYYLVCMSFVFNIG







EGMPGRTFANGEPIW







LCNAHTADSKVFSRS







LLAKSAAVKTVVCFP







FLGGVVEIGTTEHIT







EDMNVIQCVKTSF





1038
clementine
129/243
15-198
LRKQLAVAVRSIQWS
1095
120/198


0.9_0 04500m
(53%)

YAIFWSLSAAQQGVL

(60%)





EWGDGYYNGDIKTRK







TMQAMELTPDKIGLQ







RSKQLRELYESLLKG







ESELAYKRPSAALSP







EDLTDAEWYYLVCMS







FVFSSGQGLPGRALA







NSETIWLCNAQCADS







KVFSRSLLAKSASIQ







TVICFPHLDGVIELG







VTELVPEDPSLLQHI







KASL





1040
clementine
123/313
1-139
MQFSGHYQLHNKGLQ
1097
86/151


0.9_005551m
(39%)

RSKQLRELYESLLKG

(56%)





ESELAYKRPSAALSP







EDLTDAEWYYLVCMS







FVFSSGQGLPGRALA







NSETIWLCNAQCADS







KVFSRSLLAKSASIQ







TVICFPHLDGVIELG







VTELVPEDPSLLQHI







KASL





1042
clementine
123/313
1-138
MQAMELTPDKIGLQR
1099
85/143


0.9_005579m
(39%)

SKQLRELYESLLKGE

(59%)





SELAYKRPSAALSPE







DLTDAEWYYLVCMSF







VFSSGQGLPGRALAN







SETIWLCNAQCADSK







VFSRSLLAKSASIQT







VICFPHLDGVIELGV







TELVPEDPSLLQHIK







ASL





1044
Eucgr.
128/220
15-198
LRKQLAVAVRSIQWS
1101
121/198


D02287.1
(58%)

YAIFWTLSATKQGVL

(61%)





QWGDGYYNGDIKTRK







TVQAVELKPDKIGLQ







RSEQLRDLYESLLEG







ETDAQNKRPSAALSP







EDLTDEEWYYLVCMS







FVFNPGEGLPGRALA







DGQTIWLCNAQYADS







KVFSRSLLAKSASIQ







TVVCFPYLGGVIELG







VTELVPEDPSLLQHI







KVSL





1046
Glyma03g
111/224
16-202
LCTQLAVAVRSIQWS
1103
105/200


01180.1
(49%)

YGIFWSPSTTEERVL

(52%)





EWREGYYNGDIKTRK







TVQATELEIKADKIG







LQRSEQLKELYKFLL







AGEADHPQTKRPSVA







LAPEDLSDLEWYYLV







CMSFVFNHNQSLPGR







ALEIGDTVWLCNAQH







ADSKVFSRSLLAKSA







TIQTVVCFPYQKGVI







EIGTTELVAEDPSLI







QHVKACF





1048
Glyma07g
104/215
16-196
LCTQLAVAVRSTQWS
1105
100/200


07740.1
(48%)

YGIFWAPSTTEERVL

(50%)





EWREGYYNGDIKTRK







TVQAMELEMKADKIG







LQRSEQLKELYKFLL







AGEADPQTKRPSAAL







APEDLSDLEWYYLVC







MSFVFNHNQSLPGRA







LEIGDTVWLCNAQHA







DSKIFSRSLLAKTVV







CFPYQKGVIEIGTTE







LVTEDPSLIQHVKAC







F





1050
POPTR_0002s
133/230
15-197
LRKQLAIAVRSVQWS
1107
123/197


16080.1
(57%)

YAIFWSLSTRQKGVL

(62%)





EWGGGYYNGDIKTRK







VQATELKADKIGLQR







SEQLRELYKSLLGGD







AGQQAKRSSPALSPE







DLSDEEWYYLVCMSF







VFNPGEGLPGRALAN







KQTIWLCNAQYADSK







VFSRSLLAKSASIQT







VVCFPYLEGVMELGV







TELVTEDPSLIQHIK







ASL





1052
POPTR_0014s
131/230
15-197
LRKQLAVAVRSVQWS
1109
122/197


07960.1
(56%)

YAVFWSQSTRQQGVL

(61%)





EWGDGYYNGDIKTRK







VEAMELKADKIGLQR







SEQLRELYESLLEGE







TGLQATRSSPALSPE







DLSDEEWYYLVCMSF







VFNPGEGLPGRALAN







KQPIWLCNAQYADSK







VFSRSLLAKSASIQT







VVCFPYLEGVIELGV







TELVTEDPGLIQHIK







ASL





1054
GSVIVT010
126/220
15-198
LSKQLAVAVRSIQWS
1111
119/198


26927001
(57%)

YAIFWSLSTRQQGVL

(60%)





EWSGGYYNGDIKTRK







TVQEMELKADKMGLQ







RSEQLRELYESLLEG







ETDQQSKRPSAALSP







EDLSDAEWYYLVCMS







FVFNPGEGLPGRALA







NGQSIWLCDAQYADS







KVFSRSLLAKSASIQ







TVVCFPHMGGVIELG







VTELVPEDPSLIQHI







KACL





1056
Solyc08g
112/201
15-202
LRKQLALAVRGIQWS
1113
111/196


0811402.1
(55%)

YAIFWSTAVTQPGVL

(56%)





KWIDGYYNGDIKTRK







TVQAGEVNEDQLGLH







RTEQLKELYSSLLTS







ESEEDLQPQAKRPSA







SLSPEDLTDTEWYFL







VCMSFVFNVGQGLPG







KTLATNETVWLCNAH







QAESKVFSRSLLAKS







ASIQTVVCFPYLGGV







IELGVILLVTEDPNL







IQQIKNSF





1058
GSVIVT010
212/546
14-197
LRNQLALAVRNIQWS
1115
115/196


19750001
(38%)

YAIFWSISTRQPGVL

(58%)





EWGDGYYNGDIKTRK







TVQAVEFNADQMGLQ







RSEQLRELYESLSIG







ESNPQPRRHSAALSP







EDLTDAEWYYLVCMS







FVFDIGQGLPGRTLA







SGQPIWLCNAPYAES







KVFSRSLLAKSASIQ







TVVCFPYLGGVIELG







ATEMVLEDPSLIQHI







KTSF





1060
Eucgr.
109/201
15-198
LKKQLALAVRKIQWS
1117
107/198


D01841.1
(54%)

YGIFWSISTRQPGVL

(54%)





EWGDGYYNGDIKTRK







TIQAVELNTDQIGMQ







RSEQLRELYESLSAG







ESSPQVRRPSAALSP







EDLTDAEWYYLVCMS







FIYDIGQGLPGRTLT







TGQPTWLCNAHYADS







KVFTRSLLAKSASIQ







TVVCFPFRGGVIELG







VTDQVSEDPGVIHQV







KGTL





1062
Eucgr.
74/144
1-141
MTQAIELNGGDHMDL
1119
72/140


E00624.1
(51%)

HRSEQLRELYESLSG

(51%)





SEPNPQTSRRPSVAL







SPEDLADAEWYYLVC







MSFIFNIGQCLPGQS







LATGKLIWLCNAHCA







DSKVFSRSLLAKSAS







IQTVVCFPFLDGVIE







LGTTDPVLEDPNLIQ







HVKTYL





1064
Glyma05g
105/206
6-184
LKKQLALAVRSIHWS
1121
102/196


37770.1
(50%)

YAIFWTDSTTQPGVL

(52%)





SWGEGYYNGDIKTRK







TSQGVELNSDQIGLQ







RSEQLRELFKSLKTV







EVSPQTKRPSAALSP







EDLTDAEWYYLVCMS







FIFNIGQGLPGRTLA







KGQSIWLNNAHSADC







KIFSRSLLAKTVVCF







PFREGVIELGTTEQV







SEDLSVIERIKTSF





1066
Glyma08g
104/199
6-190
LKKQLALAVRSIHWS
1123
104/196


01810.1
(52%)

YAIFWTDSTTQPGVL

(53%)





SWGEGYYNGDIKTRK







TSQGVELNSDQIGLQ







RSEQLRELFKSLKTV







EVTPQTKRPSAAALS







PEDLTDAEWYYLVCM







SFIFNIGQGLPGRTL







AKGQPIWLNNAHSSD







CKIFSRSLLAKSASI







ETVVCFPFREGVIEL







GTTEQVPEDLSVIEL







IKTSF





1068
clementine
124/272
16-196
LKKQLALAVRSIQWS
1125
108/196


0.9_005250m
(45%)

YAIFWTISDTQPGVL

(55%)





EWGDGYYNGDIKTRK







TIQSVELSSNQLGLQ







RSEQLRELYESLSAG







ESHPQAASKRPSAAL







SPEDLTDTEWYYLVC







MSFNFNIGEGLPGRA







LANNQPIWLCNAQYA







DSKVFSRSLLAKTVV







CFPHLHGVVELGVTE







LVLEEPDFIQHIKTS







F





1070
POPTR_0001s
110/201
15-198
LKKQLAIAVRSIQWS
1127
108/196


09450.1
(54%)

YAIFWSMSARQPGVL

(55%)





EWGDGYYNGDIKTRK







TIQSIELDEDELGLQ







RSEQLRELYESLSVG







EASPQARRPSAALSP







EDLTDTEWYYLVCMS







FIFDIGQGLPGTTLA







NGHPTWLCNAHSADS







KVFSRSLLAKSASIQ







TVVCFPFMRGVIELG







VTEQVLEDPSLINHI







KTSF





1072
POPTR_0003s
103/201
15-193
LKKQLALAVRSIQWS
1129
101/196


12810.1
(51%)

YAIFWSNPTGQPGVL

(51%)





EWADGYYNGDIKTRK







TVQSIELNADELGLQ







RSEQLRELYESLSAG







EANPQARRPSAALSP







EDLTDTEWYYLVCMS







FVFDNGQGLPGTTLA







NGHPTWLCNAPSADS







KIFSRSLLAKTVVCF







PFMRGVVELGVSEQV







LEDPSLIQHIKTSF






































































































































































































































































































































































































































TABLE 14



Conserved HLH domain (“domain 2”) of

AtMYC1 and closely related sequences















Col. 7




Col. 4


Percent



Col. 3
HLH

Col. 6
identity



Percent
domain

SEQ ID
of the HLH



identity of
(conserved

NO: of
domains

Col. 1

polypeptide
domain 2)
Col. 5
the
in Col. 5

SEQ
Col. 2
in
in amino
Conserved
conserved
to the HLH

ID
Species/
Col. 1 to
acid
HLH domain
HLH
domain of

NO:
Identifier
AtMYC1
coordinates
(domain 2)
domain
AtMYC1



1016
At/AtMYC1 or
526/526

SQNSGLNQDDPSDRR
1074
100%


AT4G00480.1
(100%)

KENEKFSVLRTMVPT

(44/44)





VNEVDKESILNNTIK







YLQELEARVEE





1020
Os/LOC_Os04
92/201
370-435
RGSRAALTQESGIKN
1078
28/63


g47040.1
(45%)

HVISERRRREKLNEM

(44%)





FLILKSIVPSIHKVD







KASILEETIAYLKVL







EKRVKE





1022
Os/LOC_Os04
90/201
383-450
GDSSAAAMTTQGSSI
1080
28/59


g47080.1
(44%)

KNHVMSERRRREKLN

(47%)





EMFLILKSVVPSIHR







VDKASILAETIAYLK







ELEKRVEE





1024
Zm/GRMZM2
158/564
363-431
NCGGGGTTVTAQENG
1082
24/43


G172795_T01
(28%)

AKNHVMLERKRREKL

(55%)





NEMFLVLKSLVPSIH







KVDKASILAETIAYL







KELQRRVQE





1026
Zm/GRMZM5
67/172
375-442
GGATGAAQEMSGTGT
1084
22/43


G822829_T01
(38%)

KNHVMSERKRREKLN

(51%)





EMFLVLKSLLPSIHR







VNKASILAETIAYLK







ELQRRVQE





1028
Zm/GRMZM5
87/204
400-467
GGATGAAQEMSGTGT
1086
22/43


G822829_T03
(42%)

KNHVMSERKRREKLN

(51%)





EMFLVLKSLLPSIHR







VNKASILAETIAYLK







ELQRRVQE





1030
Si/Si000845m
166/573
395-425
GGGGTTRMAQESGVK
1088
30/65



(28%)

NHVMSERKRREKLNE

(46%)





MFLVLKSLVPSIHKV







DKASILAETIAYLKE







LQRRVQE





1032
Si/Si012401m
145/520
289-355
GGGGTTRMAQESGVK
1090
30/65



(28%)

NHVMSERKRREKLNE

(46%)





MFLVLKSLVPSIHKV







DKASILAETIAYLKE







LQRRVQE





1034
At/AT1G6365
105/217
393-456
EELLPDTPEETGNHA
1092
22/43


0.1
(48%)

LSEKKRREKLNERFM

(51%)





TLRSIIPSISKIDKV







SILDDTIEYLQDLQK







RVQE





1036
At/AT5G4131
101/202
426-492
EKLMLDSPEARDETG
1094
25/43


5.1
(50%)

NHAVLEKKRREKLNE

(58%)





RFMTLRKIIPSINKI







DKVSILDDTIEYLQE







LERRVQE





1038
Cc/clementine
129/243
440-509
SQKEICRKYCPVTME
1096
33/45


0.9_004500m
(53%)

SDNFCEEHISSDKRT

(73%)





ENEKFMVLRSMVPYI







SEVDKASILSDTIKY







LKKLEARVEE





1040
Cc/clementine
123/313
381-450
SQKEICRKYCPVTME
1098
33/45


0.9_005551m
(39%)

SDNFCEEHISSDKRT

(73%)





ENEKFMVLRSMVPYI







SEVDKASILSDTIKY







LKKLEARVEE





1042
Cc/clementine
123/313
380-449
SQKEICRKYCPVTME
1100
33/45


0.9_005579m
(39%)

SDNFCEEHISSDKRT

(73%)





ENEKFMVLRSMVPYI







SEVDKASILSDTIKY







LKKLEARVEE





1044
Eg/Eucgr.
128/220
437-503
SELQNGVESLLGDVD
1102
29/45


D02287.1
(58%)

FCAGHILSTKKKEHE

(64%)





KFLVLRSMIPSIEEI







DKASILDDTIMYLRE







LEARVEE





1046
Gm/Glyma03g
111/224
405-476
SQKGNDRMEWTSKLE
1104
25/46


01180.1
(49%)

NDDHGLIGKAFSDKK

(54%)





REIKNFQVVKSMVPS







SISEVEKISILGDTI







KYLKKLETRVEE





1048
Gm/Glyma07g
104/215
405-476
SQKENGRMKWTSKLE
1106
28/55


07740.1
(48%)

NANDGFMEKTFSDKK

(50%)





RENKNFHVVKPMVPS







SISEVEKISILGDTI







KYLKKLETRVEE





1050
Pt/POPTR_00
133/230
437-506
FDKENGGTDCLKKLE
1108
27/45


02s16080.1
(57%)

GCETCKEHYKSDKQR

(60%)





VNDKFIVLRSMVPSI







SEIDKESILSDTINY







LKQLESRVAE





1052
Pt/POPTR 00
131/230
438-507
SDKENAGKDCLKNLE
1110
23/45


14s07960.1
(56%)

GCETCKLHFLSEKQK

(51%)





ENEKYLALESIVASI







NEIDKASILSDTINY







PRQLESRVAE





1054
Vv/GSVIVT0
126/220
420-489
SQKENAGRDGLWKSG
1112
31/60


1026927001
(57%)

SDGICKQHALSDKKR

(51%)





EKEKFLVLRSMVPSI







NKIDEVSILGDTIEY







LKKLEARVEE





1056
Sl/Solyc08g08
112/201
415-487
FSRENGKKNSLWRPE
1114
23/43


1140.2.1
(55%)

VDDIDRNRVISERRR

(53%)





REKERFMHLASMLPT







SSKVDKISLLDETIE







YMKELERRVQE





1058
Vv/GSVIVT0
212/546
323-395
SRDNNGDNDEIWRPE
1116
26/43


1019750001
(38%)

ADEITLNHVLSERKR

(60%)





REKINERFSVLRSLV







PSINQVNKVSVLDDT







IEYLKELKRRVEE





1060
Eg/Eucgr.D01
109/201
411-483
SPLEDGGENGVWRPE
1118
27/54


841.1
(54%)

ADEIGLNHAILERKQ

(50%)





KEKINDRLGVLKSMV







PSVSKVDKLSILDDT







IAYLRELQRKVEE





1062
Eg/Eucgr.E00
74/144
343-415
ISKVSCKRDGLWMAL
1120
26/43


624.1
(51%)

TDELSPDHTLSESRQ

(60%)





REKINEQFSVLNSIL







PLVNKVDKISILDNT







IEYVKELQRRAEE





1064
Gm/Glyma05g
105/206
406-477
SQEENDYKEGMRVEA
1122
21/43


37770.1
(50%)

DENGMNHVMSERRRR

(48%)





AKLNQRFLTLRSMVP







SISKDDKVSILDDAI







EYLKKLERRINE





1066
Gm/Glyma08g
104/199
412-483
SQEENDYKEGMRVEA
1124
23/43


01810.1
(52%)

DENGMNHVMSERRRR

(53%)





AKLNERFLTLRSMVP







SISKDDKVSILDDAI







DYLKKLERRVKE





1068
Cc/clementine
124/272
419-491
SSEDNHIKDDVSRLE
1126
24/43


0.9_005250m
(45%)

AEETATNHVKSERRQ

(55%)





RGKLNERFVILKSMV







PSVSKFDKVSILDDT







IEYVQELERKVKE





1070
Pt/POPTR 00
110/201
410-487
SPEYNSNKVVVGRPE
1128
24/44


01s09450.1
(54%)

ADENGASHALSERKQ

(54%)





REKLNKRFMILKSIV







PSISKVVDKVSILDE







TIEYLQELERKVEE





1072
Pt/POPTR_00
103/201
407-479
SPEYSSDKVVGGRPE
1130
24/43


03s12810.1
(51%)

ADEIGASHVLSERRR

(55%)





REKLNKRFMILKSIV







PSISKVDKVSILDDT







IQYLQELERKVEE



Species abbreviations for Tables 13 and 14:

At— Arabidopsis thaliana ;

Cc— Citrus clementina ;

Eg— Eucalyptus grandis ;

Gm— Glycine max ;

Os— Oryza sativa ;

Pt— Populus trichocarpa ;

Si— Setaria italica ;

Sl— Solanum lycopersicum ;

Vv— Vitis vinifera ;

Zm— Zea mays












































































































































































































Sequences that are functionally-related and/or closely-related to the polypeptides in Tables 13 and 14 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed AtMYC1-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
As shown in FIG. 21A-21O , these “functionally-related and/or closely-related” AtMYC1 clade polypeptides generally contain a consensus sequence of the AtMYC1 clade, SEQ ID NO: 1153:
X 1 -X 2 -x-x-x-L-A-x-X 3 - x -R-x-x-x-W-X 4 -Y-X 5 -X 6 - F -W- X 7 -x-x-x-x-x-x-x- x -L-x-W-x-x-G-x-Y-N- G -x-X 8 -K- X 9 -R-K-X 10 -x-x-x-X 11 -X 12 -X 13 -X 14 -X 15 -x-x-x-x-x-x-X 16 - x-x-X 17 -x-X 18 -L-x-x-L-X 19 -x-x-X 20 -x-x-x-X 21 -x-x-X 22 - X 23 -X 24 -X 25 -x-x-x-x-x-X 26 -X 27 -X 28 -X 29 -X 30 -X 31 -X 32 -X 33 - X 34 -X 35 -X 36 -X 37 -X 38 -x-x-x-x-x-x-X 39 -x-x-L-x-P-X 40 -D- L-X 41 -D-x-E-x-Y-X 42 -X 43 -X 44 -X 45 -M-X 46 -X 47 -x-X 48 -x-x- x-X 49 -x-X 50 -P-G-x-X 51 -x-x-x-x-x-x-X 52 -W-X 53 -x-X 54 - X 55 -x-x-X 56 -x-x-K-x-F-x-R-X 57 -L-X 58 -A-X 59 -X 60 -X 61 - X 62 -X 63 -x-X 64 -X 65 -X 66 -C-x-P-x-X 67 -x-x-G-V-X 68 -E-X 69 - G-x-X 70 -X 71 -x-X 72 -x-E
In the above consensus sequences of SEQ ID NO: 1153, x represents any amino acid; X 1 represents Phe or Leu; X 2 represents any amino acid or absent; X 3 represents Ala or Serine; X 4 represents Thr or Ser; X 5 represents Gly, Ala, or Ser; X 6 represents Ile, Val, Leu, or Met; X 7 represents Ser, Ala, or Thr; represents Ile, Val, Leu or Met; X 9 represents Thr or Lys; X 10 , X 11 , X 12 , and X 13 represents any amino acid or absent; X 14 represents Glu or absent; X 15 represents Ile, Met, or absent; X 16 represents Ile, Val, Leu or Met; X 17 represents Ser or Thr; X 18 represents Gln or Glu; X 19 represents Tyr or Phe; X 20 represents Ile, Val, Leu or Met; X 21 represents Glu or Asp; X 22 -X 25 and X 26 -X 38 represent any amino acid or absent; X 39 represents Ala, Ser, or absent; X 40 represents Glu or Asp; X 41 represents Gly, Ala, Ser or Thr; X 42 represents Tyr or Phe; X 43 and X 44 represent Ile, Val, Leu or Met; X 45 represents Cys or Ser; X 46 represents Ser or Thr; X 47 and X 48 represent Tyr or Phe; X 49 represents Gln or Glu; X 50 represents Ile, Val, Leu or Met; X 51 represents Thr, Ala, or Ser; X 52 represents Ile, Val, Leu, Met, or Thr; X 53 represents Ile, Val, Leu, or Met; X 54 represents Asp or Asn; X 55 represents Ala or Ser; X 56 and X 57 represent Ala or Ser; X 58 represents Ile, Val, Leu, or Met; X 59 represents Lys or Arg; X 60 represents Ser or absent; X 61 represent Ala or absent; X 62 represents Ser, Ala, Thr, or absent; X 63 represents Ile, Val, Leu, Met, or absent; X 64 represents Ser or Thr; X 65 and X 66 represent Ile, Val, Leu, or Met; X 67 represents any amino acid or absent; X 68 represents Ile, Val, Leu, or Met; X 69 represents Ile, Val, Leu, Met, or Phe; X 70 represents Ser or Thr; X 71 represents Glu or Asp; X 72 represents Ile, Val, Leu, or Met.

As shown in FIG. 21K , these “functionally-related and/or closely-related” AtMYC1 clade polypeptides also generally contain a consensus sequence SEQ ID NO: 1154:







S-X 1 -L-x-X 2 -X 3 -I-x-Y-x-x-L-X 1 -x-x-X 4 -X 1 -E-L








In the above consensus sequences of SEQ ID NO: 1154, x represents any amino acid; X 1 is Ile, Val, Leu, or Met; X 2 is Glu, Asp, or Asn; X 3 is Thr or Ala; and X 4 is Arg or Lys.
Alternative consensus sequences comprising the above with conservative substitutions found in Table 1 are also envisaged and may be expected to provide equivalent function(s).
The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. An AtMYC1 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Tables 13 or 14 may also have at least 28%, 38%, 39%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 58%, 57%, 58%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% amino acid identity to SEQ ID NO: 1016 or to the entire length of a listed full length sequence of SEQ ID NO: 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072,
and/or at least 37%, 40%, 41%, 44%, 45%, 46%, 47%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 58%, 59%, 60%, 61%, 62%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% amino acid identity to the listed bHLH-MYC_N domains, i.e., SEQ ID NO: 1073, 1075, 1077, 1079, 1081, 1083, 1085, 1087, 1089, 1091, 1093, 1095, 1097, 1099, 1101, 1103, 1105, 1107, 1109, 1111, 1113, 1115, 1117, 1119, 1121, 1123, 1125, 1127, or 1129, and/or at least 44%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%. 56%, 58%, 60%, 64%, 73%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% amino acid identity to the listed HLH domains, i.e., 1074, 1076, 1078, 1080, 1082, 1084, 1086, 1088, 1090, 1092, 1094, 1096, 1098, 1100, 1102, 1104, 1106, 1108, 1110, 1112, 1114, 1116, 1118, 1120, 1122, 1124, 1126, 1128, or 1130. The presence of the disclosed conserved bHLH-MYC_N domain and/or conserved HLH domain in the polypeptide sequence (for example, SEQ ID NO: 1073-1130), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “AtMYC1 clade polypeptides” or “AtMYC1 clade polypeptides”, or which fall within the “AtMYC1 clade” or “G581 clade” exemplified in the phylogenetic tree in FIG. 20 as those polypeptides bounded by LOC_Os01g39560.1 and POPTR — 0003s12810.1 (indicated by the box around these sequences).





TABLE 15



Conserved first WRKY domain of

WRKY3 and closely related sequences















Col. 7



Col. 3



Percent



Percent
Col. 4


identity



identity of
WRKY

Col. 6
of first



polypeptide
domain 1
Col. 5
SEQ ID
WRKY in Col.

Col. 1
Col. 2
in
in amino
Conserved
NO: of
5 to WRKY

SEQ ID
Species/
Col. 1 to
acid
WRKY
WRKY
domain 1 of

NO:
Identifier
WRKY3
coordinates
domain 1
domain 1
WRKY3



1156
At/WRKY3
100%
249-305
ADDGYNWRKYGQKQV
1227
100%


or
(513/513)

KGSDFPRSYYKCTHP

(57/57)


AT2G03340.1


ACPVKKKVERSLDGQ







VTEIIYKGQHNH





1190
Pt/POPTR_0
55%
221-277
TDDGYNWRKYGQKQV
1261
96%


008s09140.1
(297/540)

KGSEFPRSYYKCTHP

(54/56)





NCPVKKKVERSLDGQ







VTEIIYKGQHNH





1158
At/AT1G139
68%
228-284
ADDGYNWRKYGQKQV
1229
94%


60.1
(370/541)

KGSEFPRSYYKCTNP

(54/57)





GCPVKKKVERSLDGQ







VTEIIYKGQHNH





1172
Vv/GSVIVT
59%
225-281
ADDGYNWRKYGQKQV
1243
94%


01001332001
(277/467)

KGSEYPRSYYKCTHP

(54/57)





SCPVKKKVERSLDGQ







VTEIIYKGQHNH





1182
Eg/Eucgr.G0
52%
248-304
ADDGYNWRKYGQKQV
1253
94%


2469.1
(255/495)

KGSEFPRSYYKCTHP

(54/57)





TCPVKKKVERSLDGQ







ITEIIYKGQHNH





1174
Sl/SolycO5g
53%
215-271
ADDGYNWRKYGQKQV
1245
92%


012770.2.1
(291/552)

KGSEYPRSYYKCTNP

(53/57)





NCPVKKKVERSLDGQ







VTEIIYKGQHNH





1192
Pt/POPTR_0
57%
222-278
ANDGYNWRKYGQKQV
1263
92%


010s17040.1
(302/532)

KGSEYPRSYYKCTHP

(53/57)





NCPVKKKVERSLDGQ







VTEIIYKGQHNH





1196
Cc/clementine
61%
249-305
ADDPYNWRKYGQKHV
1267
92%


0.9_007348m
(326/538)

KGSEFPRSYYKCTHP

(53/57)





NCPVKKKVERSLDGQ







VTEIIYKGQHNH





1180
Eg/Eucgr.B0
53%
246-302
ADDGYNWRKYGQKQV
1251
91%


3189.1
(291/544)

KGSEFPRSYYKCTHP

(52/57)





DCPVRKKVERSLDGH







ITEIIYKGQHNH





1160
Gm/Glyma0
51%
174-230
ADDGYNWRKYGQKQV
1231
87%


1g06550.1
(265/519)

KGSEFPRSYYKCTHP

(50/57)





NCSVKKKVERSLEGH







VTAIIYKGEHNH





1162
Gm/Glyma0
51%
174-230
ADDGYNWRKYGQKQV
1233
87%


2g12490.1
(268/521)

KGSEFPRSYYKCTNP

(50/57)





NCPVKKKVERSLEGH







VTAIIYKGEHNH





1188
Pt/POPTR_0
50%
237-294
THDGYNWRKYGQKPI
1259
85%


017s12430.1
(281/561)

KGSEYPRSYYKCTHL

(47/55)





NCPVKKKVERSSDGQ







ITEIIYKGQHNH





1168
Gm/Glyma0
52%
228-284
ADDGYNWRKYGQKQV
1239
84%


8g26230.1
(278/533)

KGSEYPRSYYKCTHL

(48/57)





NCVVKKKVERAPDGH







ITEIIYKGQHNH





1170
Gm/Glyma1
53%
226-282
ADDGYNWRKYGQKQV
1241
84%


8g49830.1
(281/529)

KGSEYPRSYYKCTHL

(48/57)





NCVVKKKVERAPDGH







ITEIIYKGQHNH





1202
Os/LOC_Os
41%
269-325
ADDGYNWRKYGQKVV
1273
84%


12g32250.1
(227/551)

KGSDCPRSYYKCTHP

(48/57)





NCPVKKKVEHAEDGQ







ISEIIYKGKHNH





1208
Zm/GRMZ
43%
227-283
ADDGYNWRKYGQKVV
1279
84%


M2G076657_
(225/522)

KGSDCPRSYYKCTHP

(48/57)


T01


NCPVKKKVEHAEDGQ







ISEIIYKGKHNH





1210
Zm/GRMZ
45%
227-283
ADDGYNWRKYGQKVV
1281
84%


M2G076657_
(215/475)

KGSDCPRSYYKCTHP

(48/57)


T02


NCPVKKKVEHAEDGQ







ISEIIYKGKHNH





1212
Zm/GRMZ
49%
229-285
ADDGYNWRKYGQKVV
1283
84%


M2G143765_
(195/402)

KGSDCPRSYYKCTHP

(48/57)


TO1


NCPVKKKVEHAEDGQ







ISEIIYKGKHNH





1216
Si/Si021859m
44%
228-284
ADDGYNWRKYGQKVV
1287
84%



(230/521)

KGSDCPRSYYKCTHP

(48/57)





NCPVKKKVEHAEDGQ







ISEIIYKGKHNH





1224
Bd/Bradi4g0
43%
229-285
ADDGYNWRKYGQKVV
1295
84%


6690.1
(225/529)

KGSDCPRSYYKCTHP

(48/57)





SCPVKKKVEHAEDGQ







ISEIIYKGKHNH





1164
Gm/Glyma0
56%
74-130
NDDGYNWRKYGQKHV
1235
83%


7g35380.1
(209/373)

KGRDFSRSYYKCTHP

(47/56)





NCPVKKKLERSLEGH







VTAIIYKGEHNH





1186
Pt/POPTR_0
47%
208-264
TDDGYNWRKYGQKPI
1257
83%


004s12000.1
(258/550)

KGSEYPRSYYKCTHL

(47/56)





NCLVKKKVERSSDGQ







ITEIIYKGQHNH





1166
Gm/Glyma2
48%
173-229
NNDGYNWRKYGQKHV
1237
82%


0g03410.1
(248/518)

KGSDFSRSYYKCTRP

(46/56)





NCPVKKKLERSLEGH







VTAIIYKGEHNH





1200
Os/LOC_Os
46%
199-255
ADDGYNWRKYGQKAV
1271
80%


03g33012.1
(196/425)

KGGEYPRSYYKCTHL

(46/57)





SCPVKKKVERSSDGQ







ITQILYRGQHNH





1206
Zm/GRMZ
41%
211-267
ADDGYNWRKYGQKAV
1277
78%


M2G171428_
(223/540)

KGGEYPRSYYKCTHT

(45/57)


T01


SCPVKKKVERSAEGH







ITQIIYRGQHNH





1214
Si/Si035317m
44%
217-273
ADDGYNWRKYGQKAV
1285
78%



(223/508)

KGGEYPRSYYKCTHA

(45/57)





SCPVKKKVERSGEGH







ITQIIYRGQHNH





1178
Sl/Solyc03g
45%
213-269
ASDGYNWRKYGQKMV
1249
77%


104810.2.1
(219/484)

KASECPRSYYKCTHL

(44/57)





KCLVKKKVERSIDGH







ITEITYKGHHNH





1222
Bd/Bradi1g1
43%
205-261
ADDGYNWRKYGQKAV
1293
77%


6120.1
(222/514)

KGGEYPRSYYKCTQA

(44/57)





GCPVKKKVERSACGE







ITQIIYRGQHNH





1184
Eg/Eucgr.
43%
295-351
TEDGYNWRKYGQKQV
1255
76%


I01998.1
(226/527)

KGCGFPRSYYKCSHL

(43/56)





NCSVKKKVEHSLDGR







ITEITYRGQHQH





1194
Cc/clementine
51%
275-331
ADDGYNWRKYGQKPI
1265
75%


0.9_006505m
(265/524)

KGNEYPRSYYKCTHV

(43/57)





NCPVKKKVERSSSAQ







ITQIIYKNEHNH





1176
Sl/Solyc02g
44%
216-272
ACDGYNWRKYGQKKV
1247
73%


088340.2.1
(214/486)

KASECPRSYYKCTYL

(42/57)





KCLVKKKVERSVDGH







ITEITYNGRHNH





1218
Bd/Bradi
41%
190-246
GKDGYNWRKYGQKQL
1289
72%


1g07970.1
(120/294)

KDAESPRSYYKCTRE

(40/55)





ACPVKKIVERSFDGC







IKEITYKGRHTH





1204
Zm/GRMZ
48%
219-275
AKDGYTWRKYGQKQL
1275
70%


M2G008029_
(112/232)

KDAESPRSYYKCTRD

(40/57)


T01


GCPVKKVVERSFDGL







IKEITYKGRHNH





1220
Bd/Bradi1g
241%
176-231
ADDGYNWRKYGQKAV
1291
70%


2680.1
(156/377)

KGGRYPRSYYKCTLN

(40/57)





CPVRKNVEHSEDGKI







IKIIYRGQHSH





1198
Os/LOC_Os
42%
169-225
TDDGYNWRKYGQKAV
1269
67%


07g40570.1
(149/353)

KGGEYPKSYYKCTHL

(38/56)





NCLVRKNVEHSADGR







IVQIIYRGQHTH





1226
Ta/ACD803
44%
198-253
ADDGYNWRKYGQKAV
1297
66%


62.1
(121/275)

KGGKYPRSYYKCTLN

(38/57)


(WRKY19)


CPARKNVEHSADRRI







IKIIYRGQHCH




















































































































































































































TABLE 16



Conserved second WRKY Domain of

WRKY3 and closely related sequences















Col. 7







Percent



Col. 3



identity



Percent
Col. 4

Col. 6
of second



identity
WRKY

SEQ ID
WRKY domain



of
domain
Col. 5
NO: of
in Col. 5

Col. 1
Col. 2
polypeptide
2 in
Conserved
second
to WRKY

SEQ ID
Species/
in Col. 1
amino acid
WRKY
WRKY
domain 2

NO:
Identifier
to WRKY3
coordinates
domain 2
domain
of WRKY3



1156
At/WRKY3
100%
414-471
LDDGYRWRKYGQK
1228
100%


or
(513/513)

VVKGNPYPRSYYK

(58/58)


AT2G03340.1


CTTPDCGVRKHVE







RAATDPKAVVTTY







EGKHNH





1158
At/AT1G139
68%
408-465
LDDGYRWRKYGQK
1230
98%


60.1
(370/541)

VVKGNPYPRSYYK

(57/58)





CTTPGCGVRKHVE







RAATDPKAVVTTY







EGKHNH





1172
Vv/GSVIVT
59%
358-416
LLDDGYRWRKYGQ
1244
93%


01001332001
(277/467)

KVVKGNPYPRSYY

(55/59)





KCTNPGCNVRKHV







ERAATDPKAVITT







YEGKHNH





1180
Eg/Eucgr.B0
53%
418-475
LDDGYRWRKYGQK
1252
93%


3189.1
(291/544)

VVKGNPYPRSYYK

(54/58)





CTTPGCNVRKHVE







RASTDPKAVITTY







EGKHNH





1160
Gm/Glyma0
51%
342-399
LDDGYRWRKYGQK
1232
91%


1g06550.1
(265/519)

VVKGNPYPRSYYK

(53/58)





CTTQGCNVRKHVE







RASTDPKAVITTY







EGKHNH





1162
Gm/Glyma0
51%
342-399
LDDGYRWRKYGQK
1234
91%


2g12490.1
(268/521)

VVKGNPYPRSYYK

(53/58)





CTTQGCNVRKHVE







RASTDPKAVITTY







EGKHNH





1192
Pt/POPTR_0
57%
393-450
LDDGYRWRKYGQK
1264
91%


010s17040.1
(302/532)

VVKGNPYPRSYYK

(53/58)





CTTAGCKVRKHVE







RAAADPKAVITTY







EGKHNH





1194
Cc/clementine
51%
444-501
LDDGYRWRKYGQK
1266
91%


0.9_006505m
(265/524)

VVKGNPHPRSYYK

(53/58)





CTNPGCNVRKHVE







RAPTDPKAVVTTY







EGKHNH





1196
Cc/clementine
61%
420-477
LDDGYRWRKYGQK
1268
91%


0.9_007348m
(326/538)

VVKGNPYPRSYYK

(53/58)





CTTTGCNVRKHVE







RASTDPKAVITTY







EGKHNH





1166
Gm/Glyma2
48%
324-381
LDDGYRWRKYGQK
1238
89%


0g03410.1
(248/518)

VVKGNPYPRSYYK

(52/58)





CTTQGCKVRKHVE







RASMDPKAVITTY







EGKHNH





1174
Sl/Solyc05g0
53%
394-451
LDDGYRWRKYGQK
1246
89%


12770.2.1
(291/552)

VVKGNPYPRSYYK

(52/58)





CTSQGCNVRKHVE







RAASDPKAVITTY







EGKHNH





1188
Pt/POPTR_0
50%
421-478
LDDGYRWRKYGQK
1260
89%


017s12430.1
(281/561)

VVKGNPHPRSYYK

(52/58)





CTSAGCNVRKHVE







RAAADPKAVVTTY







EGKHNH





1190
Pt/POPTR_0
55%
390-447
LDDGYRWRKYGQK
1262
89%


008s09140.1
(297/540)

VVKGNPYPRSYYK

(52/58)





CTTPGCKVRKHVE







RAAADPRAVITAY







EGKHNH





1164
Gm/Glyma0
56%
225-282
LDDGYRWRKYGQK
1236
87%


7g35380.1
(209/373)

VVKGNPYPRSYYK

(51/58)





CATQGCNVRKHVE







RASMDPKAVLTTY







EGKHNH





1170
Gm/Glyma1
53%
406-463
LDDGYRWRKYGQK
1242
87%


8g49830.1
(281/529)

VVKGNPHPRSYYK

(51/58)





CTSAGCNVRKHVE







RASTDPKAVITTY







EGKHNH





1182
Eg/Eucgr.G0
52%
411-468
LDDGYRWRKYGQK
1254
87%


2469.1
(255/495)

LVKGNPYPRSYYK

(51/58)





CTTTGCNVRKHVE







RASSDPKAVITTY







EGKHNH





1186
Pt/POPTR_0
47%
368-425
LDDGYRWRKYGQK
1258
87%


004s12000.1
(258/550)

VVKGNPHPRSYYK

(51/58)





CTSAGCNVRKHVE







RAAADPKAVITTY







EGKHNH





1168
Gm/Glyma0
52%
409-466
LDDGYRWRKYGQK
1240
86%


8g26230.1
(278/533)

VVKGNPHPRSYYK

(50/58)





CTSAGCNVRKHVE







RASMDPKAVITTY







EGKHNH





1202
Os/LOC_Os
41%
426-483
LDDGYRWRKYGQK
1274
84%


12g32250.1
(227/551)

VVKGNPHPRSYYK

(49/58)





CTYAGCNVRKHIE







RASSDPKAVITTY







EGKHNH





1216
Si/Si021859m
44%
385-442
LDDGYRWRKYGQK
1288
84%



(230/521)

VVKGNPHPRSYYK

(49/58)





CTFAGCNVRKHIE







RASSDPKAVITTY







EGKHNH





1224
Bd/Bradi4g0
43%
386-443
LDDGYRWRKYGQK
1296
84%


6690.1
(225/529)

VVKGNPHPRSYYK

(49/58)





CTFAGCNVRKHIE







RASSDPKAVITTY







EGKHNH





1212
Zm/GRMZM
49%
386-443
LDDGYRWRKYGQK
1284
82%


2G143765_
(195/402)

VVKGNPHPRSYYK

(48/58)


T01


CTFAGCNVRKHIE







RCSSDPKAVITTY







EGKHNH





1176
Sl/Solyc02g0
44%
386-443
LDDGYKWRKYGQK
1248
81%


88340.2.1
(214/486)

VVKGTQHPRSYYR

(47/58)





CTYPGCNVRKQVE







RASTDPKAVITTY







EGKHNH





1178
Sl/Solyc03g1
45%
384-441
LDDGFKWRKYGQK
1250
79%


04810.2.1
(219/484)

MVKGNHHPRSYYR

(46/58)





CTYPGCNVRKHVE







RASADPKAVITTY







EGKHNH





1184
Eg/Eucgr.I01
43%
473-530
LDDGFKWRKYGQK
1256
79%


998.1
(226/527)

VVKGSSYPRSYYK

(46/58)





CTYAGCNVRKHIE







RAALDPKSVITTY







EGKHNH





1200
Os/LOC_Os
46%
366-423
LDDGYRWRKYGQK
1272
79%


03g33012.1
(196/425)

VVKGNPHPRSYYK

(46/58)





CTYQGCDVKKHIE







RSSQDPKAVITTY







EGKHSH





1206
Zm/GRMZM
41%
380-437
LDDGYRWRKYGQK
1278
79%


2G171428_
(223/540)

VVKGNPYPRSYYR

(46/58)


T01


CTYQGCDVKKHIE







RSSQDPKAVITTY







EGKHSH





1208
Zm/GRMZM
43%
384-441
LDDGYRWRKYGQK
1280
79%


2G076657_
(225/522)

VVKGNSHPRSYYK

(46/58)


T01


CTFAGCNVRKHIE







RASSDPRAVITTY







EGKHDH





1210
Zm/GRMZM
45%
384-441
LDDGYRWRKYGQK
1282
79%


2G076657_
(215/475)

VVKGNSHPRSYYK

(46/58)


T02


CTFAGCNVRKHIE







RASSDPRAVITTY







EGKHDH





1214
Si/Si035317m
44%
386-443
LDDGYRWRKYGQK
1286
79%



(223/508)

VVKGNPHPRSYYK

(46/58)





CTYQGCDVKKHIE







RSSQDPKAVITTY







EGKHSH





1198
Os/LOC_Os
42%
338-395
LDDGYRWRKYGQK
1270
77%


07g40570.1
(149/353)

VVKGNPYPRSYYK

(45/58)





CTYLGCDVKKQVE







RSVEEPNAVITTY







EGKHIH





1204
Zm/GRMZM
48%
349-406
LDDGYRWRKYGQK
1276
77%


2G008029_
(112/232)

VVKGNPRPRSYYK

(45/58)


T01


CTADNCNVRKQIE







RATTDPRCVLTTY







TGRHNH





1220
Bd/Bradi1g2
41%
341-398
LDDGYRWRKYGQK
1292
74%


2680.1
(156/377)

VVRGNPHPRSYYK

(43/58)





CTYQGCDVKKHIE







RSSQEPHAVITTY







EGKHVH





1222
Bd/Bradi1g1
43%
374-431
LDDGYRWRKYGQK
1294
74%


6120.1
(222/514)

VVKGNPHPRSYYK

(43/58)





CTFQGCDVKKHIE







RCSQDSTDVITTY







EGKHSH





1226
Ta/ACD8036
44%
362-419
LDDGYRWRKYGQK
1298
74%


2.1
(121/275)

VVRGNPHPRSYYK

(43/58)


(WRKY19)


CTYQGCDVKKHIE







RSSEEPHAVITTY







EGKHTH





1218
Bd/Bradilg0
41%
323-380
LDDGYRWRKYGQK
1290
72%


7970.1
(120/294)

VVKGNPRPRSYYK

(42/58)





CTAENCNVRKQIE







RASSNPSCVLTTY







TGRHSH



Species abbreviations for Tables 15 and 16:

At— Arabidopsis thaliana ;

Bd— Brachypodium distachyon ;

Cc— Citrus clementina ;

Eg— Eucalyptus grandis ;

Gm— Glycine max ;

Os— Oryza sativa ;

Pt— Populus trichocarpa ;

Si— Setaria italica ;

Sl— Solanum lycopersicum ;

Ta— Triticum aestivum ;

Vv— Vitis vinifera ;

Zm— Zea mays































































































































































































































































Sequences that are functionally-related and/or closely-related to the polypeptides in Tables 15 and 16 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed WRKY3-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
As shown in FIG. 24G-24H , these “functionally-related and/or closely-related” WRKY3 clade polypeptides generally contain a consensus sequence of the WRKY3 clade (SEQ ID NO: 1299), which contains the first WRKY domain found in WRKY3 clade members:







X 1 X 2 PxxDGYxWX 3 KYGQKxX 4 KxX 5 xxxX 3 SYX 6 KCTxxxCxVX 3 K





xX 4 EX 7 X 8 xxGxX 4 xxIxYX 3 GxHxH.*










As shown in FIG. 24K-24L , these “functionally-related and/or closely-related” WRKY3 clade polypeptides also generally contain a consensus sequence of the WRKY3 clade (SEQ ID NO: 1300), which contains the second WRKY domain found in WRKY3 clade members:







X 9 X 3 X 10 X 10 X 10 X 10 X 10 X 10 X 4 xX 4 xTxSX 11 X 4 X 12 X 4 LLLGX 6 X 3 WRKY





GQKX 4 VX 3 GNxxPRSYYX 3 CTxxxCxVX 3 KX 13 X 4 ERX 8 xxX 1 X 14 xx





VX 4 TX 15 YxGX 3 HxHxxX 10 PxxX 3 .*












*In the above consensus sequences of SEQ ID NO: 1299-1300, x represents any amino acid; X 1 is D, N, or E; X 2 is K, R, or Q; X 3 is R or K; X 4 is I, L, V, or M; X 5 is G, S, or A; X 6 is Y or F; X 7 is R or H; X 8 is S, A, or C; X 9 is Q, H or R; X 10 is any amino acid or absent; X 11 is E or D; X 12 is D or N; X 13 is H or Q; X 14 is P or S; and X 15 is T or A. Alternative consensus sequences comprising the above with conservative substitutions found in Table 1 are also envisaged and may be expected to provide equivalent function(s).
The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. A WRKY3 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Tables 15 or 16 may also have at least 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 55%, 56%, 57%, 59%, 61%, 68%, or about 100% amino acid identity to SEQ ID NO: 1156, and/or at least 66%, 67%, 70%, 72%, 73%, 75%, 76%, 77%, 78%, 80%, 82%, 83%, 84%, 85%, 87%, 91%, 92%, 94%, 96%, or about 100% amino acid identity to the first WRKY domain of SEQ ID NO: 1156, and/or at least 72%, 74, 77%, 79%, 81%, 82%, 84%, 86%, 87%, 89%, 91%, 93%, 98%, or about 100% amino acid identity to the second WRKY domain of SEQ ID NO: 1156 in its amino acid sequence to the entire length of a listed sequence or to a listed first WRKY domains, or to a listed second WRKY domains, or to the amino acid sequence of SEQ ID NO: 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, or 1226, or 1227-1298. The presence of the disclosed conserved first WRKY domains and/or second WRKY domains in the polypeptide sequence (for example, SEQ ID NO: 1227-1298), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “WRKY3 clade polypeptides” or “WRKY3 clade polypeptides”, or which fall within the “WRKY3 clade” or “G878 clade” exemplified in the phylogenetic tree in FIG. 23 as those polypeptides bounded by Bradi1g07970.1 and Solyc03g104810.2.1.





TABLE 17



Conserved NAM domain of AtNAC6

and closely related sequences















Col. 7



Col. 3



Percent



Percent



identity



identity of
Col. 4

Col. 6
of NAM

Col. 1

polypeptide
NAM

SEQ ID
in Col. 5

SEQ
Col. 2
in
domain in
Col. 5
NO: of
to NAM

ID
Species/
Col. 1 to
amino acid
Conserved
the NAM
domain of

NO:
Identifier
AtNAC6
coordinates
NAM domain
domain
AtNAC6



1369
At/AtNAC6 or
100%
20-145
LPPGFRFHPTDEELI
1434
100%


AT5G39610
(285/285)

THYLKPKVFNTENSA

(126/126)





TAIGEVDLNKIEPWD







LPWKAKMGEKEWYNN







CVRDRKYPTGLRTNR







ATEAGYWKATGKDKE







IFKGKSLVGMKKTLV







FYKGRAPKGVKTNWV







MHEYRL





1373
At/AT3G29035.1
62%
24-149
LPPGFRFHPTDEELI
1436
94%



(206/329)

THYLRPKVVNSNNSA

(119/126)





IAIGEVDLNKVEPWD







LPWKAKLGEKEWYFF







CVRDRKYPTGLRTNR







ATKAGYWKATGKDKE







IFKGKSLVGMKKTLV







FYKGRAPKGVKTNWV







MHEYRL





1411
Cc/clementine
51%
12-137
LPPGFRFHPTDEELI
1455
90%


0.9_014567m
(181/349)

THYLTPKVFDGCFSA

(114/126)





RAIGEVDLNKCEPWD







LPRRAKMGEKEWYFF







CVRDRKYPTGLRTNR







ATEAGYWKATGKDKE







IYKAKALVGMKKTLV







FYKGRAPKGQKTNWV







MHEYRL





1375
At/AT5G61430.1
71%
16-141
LPPGFRFHPTDEELI
1437
89%



(156/217)

THYLHKKVLDTSFSA

(113/126)





KAIGEVDLNKSEPWE







LPWMAKMGEKEWYNN







CVRDRKYPTGLRTNR







ATEAGYWKATGKDKE







IYRGKSLVGMKKTLV







FYRGRAPKGQKTNWV







MHEYRL





1379
Gm/Glyma06g2
68%
18-143
LPPGFRFHPTDEELI
1439
89%


1020.1
(149/217)

SHYLYRKVTDTNFSA

(113/126)





RAIGEVDLNRSEPWD







LPWKAKMGEKEWYFF







CVRDRKYPTGLRTNR







ATESGYWKATGKDKE







IFRGKSLVGMKKTLV







FYKGRAPKGEKTDWV







MHEYRL





1381
Gm/Glyma17g1
69%
16-141
LPPGFRFHPTDEELI
1440
89%


0970.1
(149/214)

SHYLYKKVIDTKFCA

(113/126)





RAIGEVDLNKSEPWD







LPWKAKMGEKEWYFF







CVRDRKYPTGLRTNR







ATEAGYWKATGKDKE







IFRGKSLVGMKKTLV







FYRGRAPKGEKSNWV







MHEYRL





1405
Vv/GSVIVT010
56%
16-141
LPPGFRFHPTDEELI
1452
89%


11445001
(166/293)

THYLSQKVLNSGFCA

(113/126)





VAIGEVDLNKCEPWD







LPWKAKMGEKEWYFF







CVRDRKYPTGLRTNR







ATDAGYWKATGKDKE







IYKMKTLVGMKKTLV







FYKGRAPKGEKTNWV







MHEYRL





1417
Eg/Eucgr.
64%
16-141
LPPGFRFHPTDEELI
1458
89%


B00529.1
(155/242)

THYLQKKVGDTGFSA

(113/126)





KAIGEVDLNKSEPWD







LPWKAKMGEKEWYFF







CLRDRKYPTGLRTNR







ATESGYWKATGKDKE







IYRGKSLVGMKKTLV







FYRGRAPKGEKTNWV







MHEYRL





1371
At/AT5G07680.1
67%
17-142
LPPGFRFHPTDEELI
1435
88%



(159/236)

THYLHKKVLDLGFSA

(111/126)





KAIGEVDLNKAEPWE







LPYKAKIGEKEWYFF







CVRDRKYPTGLRTNR







ATQAGYWKATGKDKE







IFRGKSLVGMKKTLV







FYRGRAPKGQKTNWV







MHEYRL





1377
Gm/Glyma04g3
69%
3-128
LPPGFRFHPTDEELI
1438
88%


3270.1
(147/211)

SHYLYRKVTHTNFSA

(112/126)





RAIGEVDLNRSEPWD







LPWKAKMGEKEWYFF







CVRDRKYPTGLRTNR







ATQSGYWKATGKDKE







IFRGKSLVGMKKTLV







FYKGRAPKGEKTDWV







MHEYRL





1393
Sl/Solyc02g0
56%
16-141
LPPGFRFHPTDEELI
1446
88%


88180.2.1
(174/310)

THYLAPKVLDSGFCA

(111/126)





IAIGEVDLNKVEPWD







LPWKAKMGEKEWYFF







CMRDKKYPTGQRTNR







ATEAGYWKATGKDKE







IFKSKTLVGMKKTLV







FYKGRAPRGEKTNWV







MHEYRL





1399
Pt/POPTR_0012
66%
17-142
LPPGFRFHPTDEELI
1449
88%


s01610.1
(156/234)

SHYLYKKVLDINFSA

(112/126)





RAIGDVDLNKSEPWE







LPWKAKMGEKEWYFL







CVRDRKYPTGLRTNR







ATEAGYWKATGKDKE







IYRGKSLVGMKKTLV







FYKGRAPKGEKTNWV







MHEYRL





1401
Pt/POPTR_0015
61%
17-142
LPPGFRFHPTDEELI
1450
88%


s02170.1
(161/262)

SHYLYKKVLDITFSA

(111/126)





KAIGDVDLNKSEPWE







LPWKAKMGEKEWYFF







CVRDRKYPTGLRTNR







ATEAGYWKATGKDKE







IYRGKFLVGMKKTLV







FYKGRAPKGGKTNWV







MHEYRL





1391
Gm/Glyma05g0
68%
16-139
LPPGFRFHPTDEELI
1445
87%


0930.1
(148/217)

SHYLYKKVIDTKFCA

(110/126)





RAIGEVDLNKSEPWD







LPSKMGEKEWYFFCV







RDRKYPTGLRTNRAT







EAGYWKATGKDKEIF







RGKSLVGMKKTLVFY







RGRAPKGEKSNWVMH







EYRL





1397
Sl/Solyc06g0697
70%
16-141
LPPGFRFHPTDEELI
1448
87%


10.2.1
(149/211)

THYLSNKVVDTNFVA

(110/126)





IAIGDVDLNKVEPWD







LPWKAKMGEKEWYFF







CVRDKKYPTGLRTNR







ATAAGYWKATGKDRE







IFRGKSLVGMKKTLV







FYKGRAPKGEKTNWV







IHEFRL





1407
Vv/GSVIVT010
72%
3-128
LPPGFRFHPTDEELI
1453
87%


07982001
(150/207)

THYLSKKVIDSNFSA

(110/126)





RAIGQVNLNNSEPWE







LPGKAKMGEKEWYFF







CVRDRKYPTGLRTNR







ATEAGYWKATGKDKE







IFRGKSLVGMKKTLV







FYAGRAPKGEKTNWV







MHEYRL





1403
Pt/POPTR_0017
59%
16-141
LPPGFRFHPTDEELI
1451
86%


s12210.1
(148/250)

THYLSQKVLDNYFCA

(109/126)





RAIGEVDLNKCEPWD







LPWRAKMGEKEWYFF







CVIDRKYPTGLRTNR







ATDAGYWKATGKDKE







IYRAKTLVGMKKTLV







FYKGRAPKGEKTNWV







MHEYRL





1395
Sl/Solyc03g1158
63%
18-143
LPPGFRFHPTDEELI
1447
84%


50.2.1
(145/228)

THYLSKKVVDMNFSA

(107/126)





IAIGDVDMNKIEPWE







LPWKAKIGEKEWYFF







CVRDKKYPTGLRTNR







ATAAGYWKATGKDKE







IFRGRSLVGMKKTLV







FYRGRAPRGEKTNWV







THEYRL





1409
Cc/clementine
66%
16-141
LPPGFRFHPTDEELI
1454
84%


0.9_013688m
(142/215)

THYLYKKVLDVCFSC

(106/126)





RAIGDVDLNKNEPWE







LPWKAKMGEKEWYFF







CMRDRKYPTGLRTNR







ATVSGYWKATGKDKE







IYRGKSLVGMKKTLV







FYRGRAPKGEKSSWV







MHEYRL





1413
Cc/clementine
57%
16-141
LPPGFRFHPTDEELI
1456
84%


0.9_012151m
(142/248)

THYLYKKVLDVCFSC

(106/126)





RAIGDVDLNKNEPWE







LPWKAKMGEKEWYFF







CMRDRKYPTGLRTNR







ATVSGYWKATGKDKE







IYRGKSLVGMKKTLV







FYRGRAPKGEKSSWV







MHEYRL





1415
Eg/Eucgr.
72%
16-141
LPPGFRFHPTDEELI
1457
83%


I01958.1
(121/167)

THYLTPKVLDGSFRA

(105/126)





RAMGEVDLNKCEPWD







LPGQAKMGEKEWYFF







CVRDRKYPTGMRTNR







ATEAGYWKATGKDKE







IRRMKKVVGMKKTLV







FYRGRAPNGQKTNWV







MHEFRL





1383
Gm/Glyma13g0
63%
20-145
LPPGFRFHPTDEELI
1441
82%


5540.1
(138/217)

THYLSQKVLDSCFCA

(104/126)





RAIGEADLNKCEPWD







LPWMAKMGEKEWYFF







CVRDRKYPTGQRTNR







ATGVGYWKATGKDRE







IYKAKALIGMKKTLV







FYKGRAPSGEKTSWV







MHEYRL





1385
Gm/Glyma19g0
62%
8-133
LPPGFRFHPTDEELI
1442
82%


2850.1
(141/225)

THYLSQKVLDSCFCA

(104/126)





RAIGEADLNKCEPWD







LPCMAKMGEKEWYFF







CVRDRKYPTGQRTNR







ATGAGYWKATGKDRE







IYKAKTLIGMKKTLV







FYKGRAPSGEKSNWV







MHEYRL





1387
Gm/Glyma09g3
60%
19-144
LPAGFRFHPRDEELI
1443
80%


7050.1
(139/229)

NHYLTKKVVDNCFCA

(101/126)





VAIAEVDLNKCEPWD







LPGLAKMGETEWYFF







CVRDRKYPTGLRTNR







ATDAGYWKATGKDRE







IIMENALIGMKKTLV







FYKGRAPKGEKTNWV







MHEYRL





1431
Os/LOC_Os04g
56%
12-137
LPPGFRFHPTDEELI
1465
80%


38720.1
(133/236)

THYLAKKVADARFAA

(101/126)





LAVAEADLNKCEPWD







LPSLAKMGEKEWYFF







CLKDRKYPTGLRTNR







ATESGYWKATGKDKD







IFRRKALVGMKKTLV







FYTGRAPKGEKSGWV







MHEYRL





1433
Si/Si010553m
61%
11-136
LPPGFRFHPTDEELI
1466
80%



(134/217)

THYLARKVADARFAA

(102/126)





FAVSEADLNKCEPWD







LPSLAKMGEKEWYFF







CLKDRKYPTGLRTNR







ATEAGYWKATGKDKD







IFRGKALVGSKKTLV







FYTGRAPKGEKSGWV







MHEYRL





1389
Gm/Glyma18g4
62%
19-144
LPAGFRFHPTDEELI
1444
79%


9620.1
(142/228)

NQYLTKKVVDNCFCA

(100/126)





IAIGEVDLNKCEPWD







LPGLAKMGETEWYFF







CVRDRKFPTGIRTNR







ATDIGYWKATGKDKE







IIMENALIGMKKTLV







FYKGRAPKGEKTNWV







MHEYRL





1421
Bd/Bradi5g1240
59%
3-129
LPPGFRFHPTDEELI
1460
79%


7.1
(133/222)

THYLAKKVADARFTA

(101/127)





FAVSEADLNKCEPWD







LPSLARMGEKEWYFF







CLKDRKYPTGLRTNR







ATESGYWKATGKDKD







IFRGKGTLVGMKKTL







VFYTGRAPKGEKSGW







VMHEYRL





1423
Os/LOC_Os02g
54%
37-163
LPPGFRFHPTDEELI
1461
79%


36880.1
(137/250)

THYLLRKAADPAGFA

(101/127)





ARAVGEADLNKCEPW







DLPSRATMGEKEWYF







FCVKDRKYPTGLRTN







RATESGYWKATGKDR







EIFRGKALVGMKKTL







VFYTGRAPRGGKTGW







VMHEYRI





1425
Os/LOC_Os02g
54%
37-163
LPPGFRFHPTDEELI
1462
79%


36880.3
(137/250)

THYLLRKAADPAGFA

(101/127)





ARAVGEADLNKCEPW







DLPSRATMGEKEWYF







FCVKDRKYPTGLRTN







RATESGYWKATGKDR







EIFRGKALVGMKKTL







VFYTGRAPRGGKTGW







VMHEYRI





1427
Os/LOC_Os02g
54%
37-163
LPPGFRFHPTDEELI
1463
79%


36880.2
(137/250)

THYLLRKAADPAGFA

(101/127)





ARAVGEADLNKCEPW







DLPSRATMGEKEWYF







FCVKDRKYPTGLRTN







RATESGYWKATGKDR







EIFRGKALVGMKKTL







VFYTGRAPRGGKTGW







VMHEYRI





1429
Os/LOC_Os02g
54%
37-163
LPPGFRFHPTDEELI
1464
79%


36880.4
(136/250)

THYLLRKAADPAGFA

(101/127)





ARAVGEADLNKCEPW







DLPSRATMGEKEWYF







FCVKDRKYPTGLRTN







RATESGYWKATGKDR







EIFRGKALVGMKKTL







VFYTGRAPRGGKTGW







VMHEYRI





1419
Bd/Bradi3g4690
57%
16-142
LPPGFRFHPTDEELV
1459
78%


0.1
(136/237)

THYLARKTADPTGFA

(100/127)





ARAVGEADLNKCEPW







DLPSRATMGEKEWYF







FVVKDRKYPTGTRTN







RATESGYWKATGKDR







EILRGKALVGMKKTL







VFYTGRAPKGGKTGW







VMHEYRL



Species abbreviations for Table 17:

At— Arabidops's thaliana ;

Bd— Brachypodium distachyon ;

Cc— Citrus x clementina ;

Eg— Eucalyptus grandis ;

Gm— Glycine max ;

Os— Oryza sativa ;

Pt— Populus trichocarpa ;

Si— Setaria italica ;

Sl— Solanum lycopersicum ;

Vv— Vitis vinifera














































































































































































































































































































































































Sequences that are functionally-related and/or closely-related to the polypeptides in Table 17 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed AtNAC6-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
As shown in FIG. 29A-29C , these “functionally-related and/or closely-related” AtNAC6 clade polypeptides generally contain a consensus sequence of the AtNAC6 clade, SEQ ID NO: 1467:





LPX 1 GFRFHPxDEEX 2 X 2 xX 3 YLxxX 4 xxxX 5 xxFxxxAX 2 X 6 xxX 7 X 2 NKx



EPWX 8 LPX 9 X 9 X 10 xX 2 GExX 8 WX 11 FFxX 2 xDX 4 XX 11 PTGxRTNRATxxGY



WKATGKDX 4 X 8 IxxxxxX 2 X 2 GxKKTLVFYxGRAPxGxKX 12 xWVxHEX 11



RX 2 . *














As shown in FIG. 29D , these “functionally-related and/or closely-related” AtNAC6 clade polypeptides also generally contain a small consensus sequence SEQ ID NO: 1468:







X 8 xxX 2 X 13 X 4 X 2 F.*








There is also a small motif that is present in AtNAC6 clade member proteins, and is identifiable in FIG. 29E and as SEQ ID NO: 1469:







X 2 PxLxX 8 xX 10 .*








*In the above consensus sequences of SEQ ID NO: 1467, 1468 or 1469, x represents any amino acid; X 1 is P or A; X 2 is I, V, L, or M; X 3 is H or Q; X 4 is K or R; X 5 is P or absent; X 6 is G, A, or S; X 7 is D or N; X 8 is D or E; X 9 is any amino acid or absent; X 10 is A or S; X 11 is Y or F; X 12 is T or S; and X 13 is C or S. Alternative consensus sequences comprising the above with conservative substitutions found in Table 1 are also envisaged and may be expected to provide equivalent function(s).
The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. A AtNAC6 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Table 17 may also have at least at least 51%, at least 54%, at least 56%, at least 57%, at least 59%, at least 60%, at least 61%, at least 62%, at least 63%, at least 64%, at least 66%, at least 67%, at least 68%, at least 69%, at least 70%, at least 71%, at least 72%, or about 100% amino acid identity to SEQ ID NO: 1369, and/or at least at least 78%, at least 79%, at least 80%, at least 82%, at least 83%, at least 84%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 94%, or about 100% amino acid identity to the NAM domain of SEQ ID NO: 1369 in its amino acid sequence to the entire length of a listed sequence or to a listed NAM domain (for example, any of SEQ ID NOs: 1434-1466), or to the amino acid sequence of SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, or 1433 and/or comprise SEQ ID NO: 1467, SEQ ID NO: 1468 and/or SEQ ID NO: 1469. The presence of the disclosed conserved NAM domains in the polypeptide sequence (for example, SEQ ID NO: 1434-1466), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “AtNAC6 clade polypeptides” or “AtNAC6 clade polypeptides”, or which fall within the “AtNAC6 clade” or G525 clade” exemplified in the phylogenetic tree in FIG. 28 as those polypeptides bounded by Bradi3g46900.1 and GSVIVT01007982001.





TABLE 18



Conserved Plant Zinc Cluster Domains' of

WRKY17 and closely related sequences















Col. 7







Percent







identity







of Plant







Zinc Cluster



Col. 3
Col. 4

Col. 6
Domain



Percent
Plant Zinc

SEQ ID
in Col.

Col. 1

identity of
Cluster

NO: of
5 to Plant

SEQ
Col. 2
polypeptide
Domain in
Col. 5
Plant Zinc
zinc cluster

ID
Species/
in Col. 1
amino acid
Plant Zinc
Cluster
domain

NO:
Identifier
to WRKY17
coordinates
Cluster Domain
Domain
of WRKY17



1507
At/WRKY17 or
100%
191-240
RKRCLEHDHSEGFSGK
1532
100%


AT2G24570
(314/314)

ISGSGNGKCHCKKSRK







NRMKRTVRVPAVSAKI







AD





1509
At/AT4G31550.1
74%
194-243
RKRCLEHEHSESFSGK
1533
86%



(244/328)

VSGSAYGKCHCKKSRK







NRMKRTVRVPAISAKI







AD





1519
Cc/clementine
64%
209-261
KKRCQDHKDHSDDLSG
1538
70%


0.9_014855m
(223/345)

KFSGSTSGNNKCHCSK







RRKNRVKKTIRVPAIS







SKIAD





1511
Gm/Glyma14g1
59%
191-235
KKRCHEHREHSGDVSG
1534
70%


7730.1
(202/337)

NSKCHCVKRRKNRVKN







TVRVPAISSKIAD





1521
Eg/Eucgr.C0401
62%
213-262
KKRCHEHDPSDNISGK
1539
68%


1.1
(214/343)

HSGSGSGKCHCSKRRK







NRVKKVTRVPAISNKI







AD





1523
Eg/Eucgr.C0401
63%
213-262
KKRCHEHDPSDNISGK
1540
68%


1.2
(210/332)

HSGSGSGKCHCSKRRK







NRVKKVTRVPAISNKI







AD





1513
Gm/Glyma17g2
59%
191-235
KKRCHEHREHSDDVSG
1535
68%


9190.1
(201/338)

NSKCHCVKRRKNRVKS







TVRVPAISSKVAD





1515
Gm/Glyma06g0
61%
175-223
KKRCHDHREHSDEISG
1536
64%


8120.1
(201/326)

KLSGSSKCHCTKRRKN







RVKKTVRVPVISSKIA







D





1531
Zm/GRMZM2G
49%
180-222
RKPCAGAHSEATTNGS
1544
62%


091331_T01
(162/327)

RCHCSKRRKNRVKRTI







RVPAISAKIAD





1529
Zm/GRMZM2G
50%
167-209
RKPCAGAHSEATTNGS
1543
58%


071907_T01
(159/316)

RCHCSKRRKNRVKRTI







RVPAISSKVAD





1517
Sl/Solyc12g0963
47%
211-256
RCREHEQSDAISGSKS
1537
50%


50.1.1
(160/340)

TGSGKCHCKKRKAKDR







KVIRIPAISTRVAD





1525
Os/LOC_Os08g
46%
191-239
HPPCAAAGDGHGHGAG
1541
43%


13840.1
(153/327)

HAHAHGGCHCSKKRKQ







RVRRTVRVAAASARVA







D





1527
Os/LOC_Os08g
46%
191-239
HPPCAAAGDGHGHGAG
1542
43%


13840.2
(153/327)

HAHAHGGCHCSKKRKQ







RVRRTVRVAAASARVA







D































































































TABLE 19



Conserved WRKY DNA-binding Domain of

WRKY17 and closely related sequences















Col. 7







Percent







identity




Col. 4

Col. 6
of WRKY



Col. 3
WRKY

SEQ ID
DNA-binding



Percent
DNA-

NO: of
Domain in Col.

Col. 1

identity of
binding
Col. 5
WRKY
5 to WRKY

SEQ
Col. 2
polypeptide
Domain in
WRKY
DNA-
DNA-binding

ID
Species/
in Col. 1
amino acid
DNA-binding
binding
Domain of

NO:
Identifier
to WRKY17
coordinates
Domain
Domain
WRKY17



1507
At/WRKY17 or
100%
242-300
PPDEYSWRKYGQKPI
1545
100%


AT2G24570.1
(314/314)

KGSPHPRGYYKCSTF







RGCPARKHVERALDD







STMLIVTYEGEHRH





1509
At/AT4G31550.1
74%
245-303
PPDEYSWRKYGQKPI
1546
96%



(244/328)

KGSPHPRGYYKCSTF







RGCPARKHVERALDD







PAMLIVTYEGEHRH





1519
Cc/clementine
64%
263-321
PPDEYSWRKYGQKPI
1551
93%


0.9_014855m
(223/345)

KGSPYPRGYYKCSTM







RGCPARKHVERAPDD







PTMLIVTYEGEHRH





1511
Gm/Glyma14g1
59%
237-295
PPDEYSWRKYGQKPI
1547
91%


7730.1
(202/337)

KGSPYPRGYYKCSTV







RGCPARKHVERAPDD







PAMLIVTYEGEHRH





1513
Gm/Glyma17g2
59%
237-295
PPDEYSWRKYGQKPI
1548
91%


9190.1
(201/338)

KGSPYPRGYYKCSTI







RGCPARKHVERAPDD







PAMLIVTYEGEHRH





1515
Gm/Glyma06g0
61%
225-283
PPDEYSWRKYGQKPI
1549
91%


8120.1
(201/326)

KGSPYPRGYYKCSSV







RGCPARKHVERAPDD







PTMLIVTYEGEHRH





1531
Zm/GRMZM2G
49%
224-282
PPDEYSWRKYGQKPI
1557
89%


091331_TO1
(162/327)

KGSPYPRGYYKCSTV







RGCPARKHVERATDD







PAMLVVTYEGEHRH





1521
Eg/Eucgr.
62%
264-322
PADEFSWRKYGQKPI
1552
89%


004011.1
(214/343)

KGSPFPRGYYKCSTM







RGCPARKHVERAPDD







PTMLIVTYEGEHRH





1523
Eg/Eucgr.
63%
264-322
PADEFSWRKYGQKPI
1553
89%


004011.2
(210/332)

KGSPFPRGYYKCSTM







RGCPARKHVERAPDD







PTMLIVTYEGEHRH





1529
Zm/GRMZM2G
50%
211-269
PSDEYSWRKYGQKPI
1556
88%


071907_T01
(159/316)

KGSPYPRGYYKCSTV







RGCPARKHVERATDD







PAMLVVTYEGEHRH





1517
SI/Solyc12g096
47%
258-316
PGDEFSWRKYGQKPI
1550
83%


350.1.1
(160/340)

KGSKYPRGYYKCSSL







RGCPARKHVERAMDD







PTMLIVTYEDEHCH





1525
Os/LOC_Os08g
46%
241-299
PADEYSWRKYGQKPI
1554
81%


13840.1
(153/327)

KGSPYPRGYYRCSTV







KGCPARKHVERAADD







PATLVVTYEGDHRH





1527
Os/LOC_Os08g
46%
241-299
PADEYSWRKYGQKPI
1555
81%


13840.2
(153/327)

KGSPYPRGYYRCSTV







KGCPARKHVERAADD







PATLVVTYEGDHRH



Species abbreviations for Tables 18 and 19:

At— Arabidopsis thaliana ;

Cc— Citrus x clementina ;

Eg— Eucalyptus grandis ;

Gm— Glycine max ;

Os— Ouzel sativa ;

Sl— Solanum lycopersicum ;

Zm— Zea mays




































































































Sequences that are functionally-related and/or closely-related to the polypeptides in Tables 18 and 19 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed WRKY17-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
As shown in FIG. 33B , these “functionally-related and/or closely-related” WRKY17 clade polypeptides generally contain a consensus sequence of the WRKY17 clade, SEQ ID NO: 1558 which comprises the conserved primary “C-region” motif (calmodulin-binding domain):







VX 1 xFX 2 xX 3 IX 3 X 3 L.*








Also provided in FIG. 33B , these “functionally-related and/or closely-related” WRKY17 clade polypeptides also generally contain a consensus sequence of SEQ ID NO: 1559, which comprises the “HARF domain’ within which is the “GHARFRR domain”:







RX 4 GHARFRRX 5 P.*








As shown in FIG. 33F , the instant “functionally-related and/or closely-related” WRKY17 clade polypeptides also generally contain a consensus sequence which comprises the “Plant Zinc Cluster Domain” SEQ ID NO: 1560:







CX 6 CxKxRKX 7 X 2 xX 2 xxxRX 3 X 8 X 9 X 10 SxX 2 X 10 AX 11 I.*








The consensus WRKY DNA-binding domain present in WRKY17 clade member proteins is identifiable as SEQ ID NO: 1561 in FIG. 33F to FIG. 33G :







PxDX 11 X 12 SWRKYGQKPIKGSX 13 X 14 PRGYYX 2 CSX 4 X 15 X 2 GCPAR


KHVERAxDX 16 X 17 X 18 xLX 3 VTYExX 11 HxH.*









*In the above consensus sequences of SEQ ID NO: 1558-1561, x represents any amino acid;
X 1 is S or A; X 2 is K or R; X 3 is I, V, L, or M; X 4 is S or T; X 5 is G, A or S; X 6 is H or Q; X 7 is N, Q, or A; X 8 is P or A; X 9 is V or A; X 10 is I, V, L, M, or A; X 11 is D or E; X 12 is Y or F; X 13 is P or K; X 14 is Y, F, or H; X 15 is I, V, L, M, or F; X 16 is D, N or E; X 17 is P or S; and X 18 is S, A, or T. Alternative consensus sequences comprising the above with conservative substitutions found in Table 1 are also envisaged and may be expected to provide equivalent function(s).
The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. A WRKY17 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Tables 18 or 19 may also have at least 46%, 47%, 49%, 50%, 59%, 61%, 62%, 63%, 64%, 74%, or about 100% amino acid identity to SEQ ID NO: 1507, and/or at least 43%, 50%, 58%, 62%, 64%, 68%, 70%, 86%, or about 100% amino acid identity to the “Plant Zinc Cluster Domain” of SEQ ID NO: 1507, and/or at least 81%, 83%, 88%, 89%, 91%, 93%, 96%, or about 100% amino acid identity to the “WRKY DNA-binding Domain” of SEQ ID NO: 1507 in its amino acid sequence to the entire length of a listed sequence or to a listed “Plant Zinc Cluster Domain”, or to a listed ““WRKY DNA-binding Domain”, or to the amino acid sequence of SEQ ID NO: 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, or 1531, or 1532-1557. The presence of the disclosed conserved “Plant Zinc Cluster” and “WRKY DNA-binding” domains in the polypeptide sequence (for example, SEQ ID NO: 1507-1557 or 1558-1561), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “WRKY17 clade polypeptides” or “WRKY17 clade polypeptides”, or which fall within the “WRKY17 clade” or “G866 clade” exemplified in the phylogenetic tree in FIG. 32 as those polypeptides bounded by LOC_Os08g13840.1 and Solyc12g096350.1.1 (indicated by the box around these sequences).





TABLE 20



Conserved ‘Z-C2H2 domain 1’ of

ZAT11 and closely related sequences















Col. 7







Percent







identity



Col. 3
Col. 4


of first



Percent
Z-C2H2

Col. 6
Z-C2H2 in

Col. 1

identity of
domain 1
Col. 5
SEQ ID
Col. 5 to

SEQ
Col. 2
polypeptide
in amino
Conserved
NO: of
Z-C2H2

ID
Species/
in Col. 1
acid
Z-C2H2
Z-C2H2
domain

NO:
Identifier
to ZAT11
coordinates
domain 1
domain 1
1 of ZAT11



1591
At/ZAT11 or
100%
47-72
FECKTCNKRFSSF
1618
100%


AT2G37430.1
(178/178)

QALGGHRASHKKP

(26/26)



1615
Eucgr.
48%
28-53
FECKTCNRRFSSF
1630
96%


A01231.1
(83/172)

QALGGHRASHKKP

(25/26)



1603
Glyma10g0521
46%
47-72
FECKTCNRKFSSF
1624
92%


0.1
(85/183)

QALGGHRASHKKP

(24/26)



1593
AT3G53600.1
63%
49-74
FECKTCNRKFDSF
1619
88%



(113/179)

QALGGHRASHKKP

(23/26)



1601
G1yma13g1955
51%
34-59
FECMTCNLKFSSF
1623
88%


0.1
(83/160)

QALGGHRASHKKP

(23/26)



1605
G1yma13g1957
45%
46-71
FECKTCNRKFPSF
1625
88%


0.1
(83/184)

QALGGHRASHKKP

(23/26)



1611
Clementine0.9_
50%
44-69
FECKTCNRQFPSF
1628
88%


035547m
(83/166)

QALGGHRASHKKP

(23/26)



1613
Eucgr.
46%
42-67
YECKTCNRQFSSF
1629
88%


A01230.1
(84/179)

QALGGHRASHKKP

(23/26)



1595
G1yma03g3305
51%
41-66
FECKTCNRKFSSF
1620
88%


0.1
(86/168)

QALGGHRASHKRS

(22/25)



1597
G1yma19g3574
50%
41-66
FECKTCNRKFSSF
1621
88%


0.1
(87/171)

QALGGHRASHKRS

(22/25)



1599
Glyma10g0518
47%
37-62
FECMTCNRKFTSF
1622
84%


0.1
(81/169)

QALGGHRASHKKP

(22/26)



1617
Eucgr.
48%
43-68
FKCKTCNRQFPSF
1631
84%


A01232.1
(92/188)

QALGGHRASHKKP

(22/26)



1607
Glyma10g0519
41%
42-67
FECKTCNRKFNSF
1626
84%


0.1
(77/185)

QALGGHRASHNKR

(21/25)



1609
G1yma13g1956
42%
41-66
FECKTCNRKFNSF
1627
80%


0.1
(77/180)

QALGGHRACHNKR

(20/25)











































































TABLE 21



Conserved ‘Z-C2H2 domain 2’ of

ZAT11 and closely related sequences















Col. 7



Col. 3
Col. 4

Col. 6
Percent identity



Percent
Z-C2H2

SEQ ID
of second Z-

Col. 1

identity of
domain 2
Col. 5
NO: of
C2H2 domain

SEQ
Col. 2
polypeptide
in amino
Conserved
second
in Col. 5 to

ID
Species/
in Col. 1
acid
Z-C2H2
Z-C2H2
Z-C2H2 domain

NO:
Identifier
to ZAT11
coordinates
domain 2
domain
2 of ZAT11



1591
At/ZAT11 or
100%
93-118
FHKCSICSQSFGT
1632
100% (26/26)


AT2G37430.1
(178/178)

GQALGGHMRRHRS





1593
AT3G53600.1
63%
92-117
MHKCTICDQMFGT
1633
76% (20/26)



(113/179)

GQALGGHMRKHRT





1609
Glyma13g1956
42%
93-118
MHNCSICGQGFSL
1641
76% (19/25)


0.1
(77/180)

GQALGGHMRRHRA





1611
Clementine0.9_
50%
89-114
LHECSICGQEFAM
1642
76% (19/25)


035547m
(83/166)

GQALGGHMRRHRI





1607
Glymal0g0519
41%
96-121
IHNCFICGQGFSL
1640
75% (18/24)


0.1
(77/185)

GQALGGHMRRHRD





1595
Glyma03g3305
51%
88-113
MHECSICGQEFSL
1634
73% (19/26)


0.1
(86/168)

GQALGGHMRRHRT





1597
G1yma19g3574
50%
89-114
MHECSICGQEFSL
1635
73% (19/26)


0.1
(87/171)

GQALGGHMRRHRT





1617
Eucgr.A01232.1
48%
91-116
MHECSICGLKFSL
1645
72% (18/25)



(92/188)

GQALGGHMRRHRV





1601
G1yma13g1955
51%
78-103
KHECSICGREFTL
1637
66% (16/24)


0.1
(83/160)

GQALGGHMKKHRI





1603
Glyma10g0521
46%
90-115
MHECSICGMEFSL
1638
65% (17/26)


0.1
(85/183)

GQALGGHMRKHRG





1605
G1yma13g1957
45%
94-119
MHECSICGMEFSL
1639
65% (17/26)


0.1
(83/184)

GQALGGHMRKHRG





1615
Eucgr.A01231.1
48%
77-102
MHECSMCGLKFAS
1644
65% (17/26)



(83/172)

GQALGGHMRRHRA





1613
Eucgr.A01230.1
46%
90-115
MHECSVCGLKFAL
1643
64% (16/25)



(84/179)

GQALGGHMRKHRA





1599
Glyma10g0518
47%
81-106
KHECTICGREFTL
1636
62% (15/24)


0.1
(81/169)

GQALGGHMKKHRI



Species abbreviations for Tables 20 and 21:

At— Arabidopsis thaliana ;

Cc— Citrus clementina ;

Eg— Eucalyptus grandis ;

Gm— Glycine max







































































Sequences that are functionally-related and/or closely-related to the polypeptides in Tables 20 and 21 may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed ZAT11-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.
As shown in FIG. 36B , these “functionally-related and/or closely-related” ZAT11 clade polypeptides also generally contain a consensus Z-C2H2-1 sequence, SEQ ID NO: 1646:







X 1 xCxTCNxX 2 FxSFQALGGHRAX 3 HX 4 X 5 X 5 .*








As shown in FIG. 36C-FIG . 36 D, the instant “functionally-related and/or closely-related” ZAT11 clade polypeptides also generally contain a consensus Z-C2H2-2 sequence, SEQ ID NO: 1647:







HxCxX 6 CxxxFxxGQALGGHMX 5 X 5 HR.*








There is also a motif near the c-terminus of ZAT11 clade member proteins that is identifiable as SEQ ID NO: 1648 ( FIG. 36D-FIG . 36 E):







LX 7 X 8 X 9 LNLX 10 PX 11 X 12 NDLxX 13 xX 6 FG.*








*In the above consensus sequences of SEQ ID NO: 1646-1648, x represents any amino acid; X 1 is F or Y; X 2 is K, R, or Q; X 3 is S or C; X 4 is N or absent; X 5 is K or R; X 6 is I, L, V, or M; X 7 is E, D, or absent; X 8 is L, M or absent; X 9 is D or N; X 10 is T or S; X 11 is L or F; X 12 is E or Q; and X 13 is L or absent. Alternative consensus sequences comprising the above with conservative substitutions found in Table 1 are also envisaged and may be expected to provide equivalent function(s).
The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. A ZAT11 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in Tables 20 or 21 may also have at least 41%, 42%, 45%, 46%, 47%, 48%, 50%, 51%, 63%, or about 100% amino acid identity to SEQ ID NO: 1591, and/or at least 80%, 84%, 88%, 92%, 96%, or about 100% amino acid identity to the first Z-C2H2 domain of SEQ ID NO: 1591, and/or at least 62%, 64%, 65%, 66%, 72%, 73%, 75%, 76%, or about 100% amino acid identity to the second Z-C2H2 domain of SEQ ID NO: 1591 in its amino acid sequence to the entire length of a listed sequence or to a listed first Z-C2H2 domain, or to a listed second Z-C2H2 domain, or to the amino acid sequence of SEQ ID NO: 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, or 1617, or 1618-1645. The presence of the disclosed conserved first Z-C2H2 domains and/or second Z-C2H2 domains in the polypeptide sequence (for example, SEQ ID NO: 1618-1647), is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as “ZAT11 clade polypeptides” or “ZAT11 clade polypeptides”, or which fall within the “ZAT11 clade” or “G355 clade” exemplified in the phylogenetic tree in FIG. 35 as those polypeptides bounded by Bradi1g03810.1 and Solyc05g054650.1.1.
Identifying Polynucleotides or Nucleic Acids by Hybridization.
Polynucleotides homologous to the sequences illustrated in the Sequence Listing and tables can be identified, e.g., by hybridization to each other under stringent or under highly stringent conditions. Stringency is influenced by a variety of factors, including temperature, salt concentration and composition, organic and non-organic additives, solvents, etc. present in both the hybridization and wash solutions and incubations, and the number of washes, as described in more detail in the references cited below (e.g., Sambrook et al., 1989. supra; Berger and Kimmel, eds., 1987 . Methods Enzymol. 152: 507-511; Anderson and Young, 1985. “Quantitative Filter Hybridisation”, In: Hames and Higgins, ed., Nucleic Acid Hybridisation, A Practical Approach . Oxford, IRL Press, 73-111), each of which are incorporated herein by reference. Conditions that are highly stringent, and means for achieving them, are also well known in the art and described in, for example, Sambrook et al., 1989. supra; Berger and Kimmel, eds., 1987 . Meth. Enzymol. 152:467-469; and Anderson and Young, 1985. supra.
Also provided in the instant description are polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, including any of the polynucleotides within the Sequence Listing, and fragments thereof under various conditions of stringency (see, for example, Wahl and Berger, 1987 . Methods Enzymol. 152: 399-407; Berger and Kimmel, ed., 1987 . Methods Enzymol. 152:507-511). In addition to the nucleotide sequences listed in the Sequence Listing, full length cDNA, orthologs, and paralogs of the present nucleotide sequences may be identified and isolated using well-known methods. The cDNA libraries, orthologs, and paralogs of the present nucleotide sequences may be screened using hybridization methods to determine their utility as hybridization target or amplification probes.
Stability of DNA duplexes is affected by such factors as base composition, length, and degree of base pair mismatch. Hybridization conditions may be adjusted to allow DNAs of different sequence relatedness to hybridize. The melting temperature (T m ) is defined as the temperature when 50% of the duplex molecules have dissociated into their constituent single strands. The melting temperature of a perfectly matched duplex, where the hybridization buffer contains formamide as a denaturing agent, may be estimated by the following equations:
T m (° C.)=81.5+16.6(log [Na+])+0.41(% G+C)−0.62(% formamide)−500/L (I) DNA-DNA:

T m (° C.)=79.8+18.5(log [Na+])+0.58(% G+C)+0.12(% G+C) 2 −0.5(% formamide)−820/L (II) DNA-RNA:

T m (° C.)=79.8+18.5(log [Na+])+0.58(% G+C)+0.12(% G+C) 2 −0.35(% formamide)−820/L (III) RNA-RNA:

where L is the length of the duplex formed, [Na+] is the molar concentration of the sodium ion in the hybridization or washing solution, and % G+C is the percentage of (guanine+cytosine) bases in the hybrid. For imperfectly matched hybrids, approximately 1° C. is required to reduce the melting temperature for each 1% mismatch.
Hybridization experiments are generally conducted in a buffer of pH between 6.8 to 7.4, although the rate of hybridization is nearly independent of pH at ionic strengths likely to be used in the hybridization buffer (Anderson and Young, 1985. supra). In addition, one or more of the following may be used to reduce non-specific hybridization: sonicated salmon sperm DNA or another non-complementary DNA, bovine serum albumin, sodium pyrophosphate, sodium dodecylsulfate (SDS), polyvinyl-pyrrolidone, ficoll and Denhardt's solution. Dextran sulfate and polyethylene glycol 6000 act to exclude DNA from solution, thus raising the effective probe DNA concentration and the hybridization signal within a given unit of time. In some instances, conditions of even greater stringency may be desirable or required to reduce non-specific and/or background hybridization. These conditions may be created with the use of higher temperature, lower ionic strength and higher concentration of a denaturing agent such as formamide.
Stringency conditions can be adjusted to screen for moderately similar fragments such as homologous sequences from distantly related organisms, or to highly similar fragments such as genes that duplicate functional enzymes from closely related organisms. The stringency can be adjusted either during the hybridization step or in the post-hybridization washes. Salt concentration, formamide concentration, hybridization temperature and probe lengths are variables that can be used to alter stringency (as described by the formula above). As a general guideline, high stringency is typically performed at T m −5° C. to T m −20° C., moderate stringency at T m −20° C. to T−35° C. and low stringency at T m −35° C. to T m −50° C. for duplex >150 base pairs. Hybridization may be performed at low to moderate stringency (25-50° C. below T m ), followed by post-hybridization washes at increasing stringencies. Maximum rates of hybridization in solution are determined empirically to occur at T m −25° C. for DNA-DNA duplex and T m −15° C. for RNA-DNA duplex. Optionally, the degree of dissociation may be assessed after each wash step to determine the need for subsequent, higher stringency wash steps.
High stringency conditions may be used to select for nucleic acid sequences with high degrees of identity to the disclosed sequences. An example of stringent hybridization conditions obtained in a filter-based method such as a Southern or Northern blot for hybridization of complementary nucleic acids that have more than 100 complementary residues is about 5° C. to 20° C. lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH. Conditions used for hybridization may include about 0.02 M to about 0.15 M sodium chloride, about 0.5% to about 5% casein, about 0.02% SDS or about 0.1% N-laurylsarcosine, about 0.001 M to about 0.03 M sodium citrate, at hybridization temperatures between about 50° C. and about 70° C. More preferably, high stringency conditions are about 0.02 M sodium chloride, about 0.5% casein, about 0.02% SDS, about 0.001 M sodium citrate, at a temperature of about 50° C. Nucleic acid molecules that hybridize under stringent conditions will typically hybridize to a probe based on either the entire DNA molecule or selected portions, e.g., to a unique subsequence, of the DNA.
Stringent salt concentration will ordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate. Increasingly stringent conditions may be obtained with less than about 500 mM NaCl and 50 mM trisodium citrate, to even greater stringency with less than about 250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, whereas high stringency hybridization may be obtained in the presence of at least about 35% formamide, and more preferably at least about 50% formamide. Stringent temperature conditions will ordinarily include temperatures of at least about 30° C., more preferably of at least about 37° C., and most preferably of at least about 42° C. with formamide present. Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS) and ionic strength, are well known to those skilled in the art. Various levels of stringency are accomplished by combining these various conditions as needed.
The washing steps that follow hybridization may also vary in stringency; the post-hybridization wash steps primarily determine hybridization specificity, with the most critical factors being temperature and the ionic strength of the final wash solution. Wash stringency can be increased by decreasing salt concentration or by increasing temperature. Stringent salt concentration for the wash steps will preferably be less than about 30 mM NaCl and 3 mM trisodium citrate, and most preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate.
Thus, high stringency hybridization and wash conditions that may be used to bind and remove polynucleotides with less than the desired homology to the nucleic acid sequences or their complements that encode the present polypeptides include, for example:
6×SSC at 65° C.;
50% formamide, 4×SSC at 42° C.; or
0.5×SSC, 0.1% SDS at 65° C.;
with, for example, two wash steps of 10-30 minutes each. Useful variations on these conditions will be readily apparent to those skilled in the art.
A person of skill in the art would not expect substantial variation among polynucleotide species provided with the present description because the highly stringent conditions set forth in the above formulae yield structurally similar polynucleotides.
If desired, one may employ wash steps of even greater stringency, including about 0.2×SSC, 0.1% SDS at 65° C. and washing twice, each wash step being about 30 minutes, or about 0.1×SSC, 0.1% SDS at 65° C. and washing twice for 30 minutes. The temperature for the wash solutions will ordinarily be at least about 25° C., and for greater stringency at least about 42° C. Hybridization stringency may be increased further by using the same conditions as in the hybridization steps, with the wash temperature raised about 3° C. to about 5° C., and stringency may be increased even further by using the same conditions except the wash temperature is raised about 6° C. to about 9° C. For identification of less closely related homologs, wash steps may be performed at a lower temperature, e.g., 50° C.
An example of a low stringency wash step employs a solution and conditions of at least 25° C. in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS over 30 minutes. Greater stringency may be obtained at 42° C. in 15 mM NaCl, with 1.5 mM trisodium citrate, and 0.1% SDS over 30 minutes. Even higher stringency wash conditions are obtained at 65° C.-68° C. in a solution of 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Wash procedures will generally employ at least two final wash steps. Additional variations on these conditions will be readily apparent to those skilled in the art (see, for example, U.S. patent publication no. 20010010913).
Stringency conditions can be selected such that an oligonucleotide that is perfectly complementary to the coding oligonucleotide hybridizes to the coding oligonucleotide with at least about a 5-10× higher signal to noise ratio than the ratio for hybridization of the perfectly complementary oligonucleotide to a nucleic acid encoding a polypeptide known as of the filing date of the application. It may be desirable to select conditions for a particular assay such that a higher signal to noise ratio, that is, about 15× or more, is obtained. Accordingly, a subject nucleic acid will hybridize to a unique coding oligonucleotide with at least a 2× or greater signal to noise ratio as compared to hybridization of the coding oligonucleotide to a nucleic acid encoding known polypeptide. The particular signal will depend on the label used in the relevant assay, e.g., a fluorescent label, a colorimetric label, a radioactive label, or the like. Labeled hybridization or PCR probes for detecting related polynucleotide sequences may be produced by oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide.
The present description also provides polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, including any of the polynucleotides within the Sequence Listing, and fragments thereof under various conditions of stringency (see, for example, Wahl and Berger, 1987, supra, pages 399-407; and Kimmel, 1987. Meth. Enzymol. 152, 507-511). In addition to the nucleotide sequences in the Sequence Listing, full length cDNA, orthologs, and paralogs of the present nucleotide sequences may be identified and isolated using well-known methods. The cDNA libraries, orthologs, and paralogs of the present nucleotide sequences may be screened using hybridization methods to determine their utility as hybridization target or amplification probes.
EXAMPLES
It is to be understood that this description is not limited to the particular devices, machines, materials and methods described. Although particular embodiments are described, equivalent embodiments may be used to practice the claims.
The specification, now being generally described, will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present description and are not intended to limit the claims or description. It will be recognized by one of skill in the art that a polypeptide that is associated with a particular first trait may also be associated with at least one other, unrelated and inherent second trait which was not predicted by the first trait.
Example I
Plant Genotypes and Vector and Cloning Information
A variety of constructs may be used to modulate the activity of regulatory polypeptides (RPs), and to test the activity of orthologs and paralogs in transgenic plant material. This platform provides the material for all subsequent analysis.
An individual plant “genotype” refers to a set of plant lines containing a particular construct or knockout (for example, this might be 35S lines for a given gene sequence (GID, Gene Identifier) being tested, 35S lines for a paralog or ortholog of that gene sequence, lines for an RNAi construct, lines for a GAL4 fusion construct, or lines in which expression of the gene sequence is driven from a particular promoter that enhances expression in particular cell, tissue or condition). For a given genotype arising from a particular transformed construct, multiple independent transgenic lines may be examined for morphological and physiological phenotypes. Each individual “line” (also sometimes known as an “event”) refers to the progeny plant or plants deriving from the stable integration of the transgene(s), carried within the T-DNA borders contained within a transformation construct, into a specific location or locations within the genome of the original transformed cell. It is well known in the art that different lines deriving from transformation with a given transgene may exhibit different levels of expression of that transgene due to so called “position effects” of the surrounding chromatin at the locus of integration in the genome, and therefore it is necessary to examine multiple lines containing each construct of interest.
(1) Overexpression/Tissue-Enhanced/Conditional Expression.
Expression of a given regulatory protein from a particular promoter, for example a photosynthetic tissue-enhanced promoter (e.g., a green tissue- or leaf-enhanced promoter), is achieved either by a direct-promoter fusion construct in which that regulatory protein is cloned directly behind the promoter of interest or by a two component system.
The Two-Component Expression System.
For the two-component system, two separate constructs are used: Promoter::LexA-GAL4TA and opLexA::RP. The first of these (Promoter::LexA-GAL4TA) comprises a desired promoter cloned in front of a LexA DNA binding domain fused to a GAL4 activation domain. The construct vector backbone (pMEN48, also known as P5375) also carries a kanamycin resistance marker, along with an opLexA::GFP (green fluorescent protein) reporter. Transgenic lines are obtained containing this first component, and a line is selected that shows reproducible expression of the reporter gene in the desired pattern through a number of generations. A homozygous population is established for that line, and the population is supertransformed with the second construct (opLexA::RP) carrying the regulatory protein of interest cloned behind a LexA operator site. This second construct vector backbone (pMEN53, also known as P5381) also contains a sulfonamide resistance marker.
Conditional Expression.
Various promoters can be used to overexpress disclosed polypeptides in plants to confer improved photosynthetic resource use efficiency. However, in some cases, there may be limitations in the use of various proteins that confer increased photosynthetic resource use efficiency when the proteins are overexpressed. Negative side effects associated with constitutive overexpression such as small size, delayed growth, increased disease sensitivity, and development and alteration in flowering time are not uncommon. A number of stress-inducible promoters can be used promote protein expression during the periods of stress, and therefore may be used to induce overexpression of polypeptides that can confer improved stress tolerance when they are needed without the adverse developmental or morphological effects that may be associated with their constitutive overexpression.
Promoters that drive protein expression in response to stress can be used to regulate the expression of the disclosed polypeptides to confer photosynthetic resource use efficiency to plants. The promoter may regulate expression of a disclosed polypeptide to an effective level in a photosynthetic tissue. Effective level in this regard refers to an expression level that confers greater photosynthetic resource use efficiency in the transgenic plant relative to the control plant that, for example, does not comprise a recombinant polynucleotide that encodes the disclosed polypeptide. Optionally, the promoter does not regulate protein expression in a constitutive manner.
Such promoters include, but are not limited to, the sequences located in the promoter regions of At5g52310 (RD29A), At5g52300, AT1G16850, At3g46230, AT1G52690, At2g37870, AT5G43840, At5g66780, At3g17520, and At4g09600.
In addition, promoters with expression specific to or enhanced in particular cells or tissue types may be used to express a given regulatory protein only in these cells or tissues. Examples of such promoter types include but are not limited to promoters expressed in green tissue, guard cell, epidermis, whole root, root hairs, vasculature, apical meristems, and developing leaves.
Table 22 lists a number of photosynthetic tissue-enhanced promoters, specifically, mesophyll tissue-enhanced promoters from rice, that may be used to regulate expression of polynucleotides and polypeptides found in the Sequence Listing and structurally and functionally-related sequences. Promoters that may be used to drive expression of polynucleotides and polypeptides found in the Sequence Listing and structurally and functionally-related sequences included, but are not limited to, promoter sequences listed in Table 22, as well as promoters that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identical to SEQ ID NO: 1693-1719, or comprise a functional fragment of promoters that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identical to SEQ ID NO: 1693-1719.





TABLE 22



Rice Genes with Photosynthetic Tissue-Enhanced Promoters







Rice Gene Identifier


SEQ
of Photosynthetic Tissue-


ID NO:
Enhanced Promoter





1696
Os02g09720


1697
Os05g34510


1698
Os11g08230


1699
Os01g64390


1700
Os06g15760


1701
Os12g37560


1702
Os03g17420


1703
Os04g51000


1704
Os01g01960


1705
Os05g04990


1706
Os02g44970


1707
Os01g25530


1708
Os03g30650


1709
Os01g64910


1710
Os07g26810


1711
Os07g26820


1712
Os09g11220


1713
Os04g21800


1714
Os10g23840


1715
Os08g13850


1716
Os12g42980


1717
Os03g29280


1718
Os03g20650


1719
Os06g43920















































Tissue-enhanced promoters that may be used to drive expression of polynucleotides and polypeptides found in the Sequence Listing and structurally and functionally-related sequences have also been described in U.S. patent publication no. 20110179520A1, incorporated herein by reference. Such promoters include, but are not limited to, Arabidopsis sequences located in the promoter regions of AT1G08465, AT1G10155, AT1G14190, AT1G24130, AT1G24735, AT1G29270, AT1G30950, AT1G31310, AT1G37140, AT1G49320, AT1G49475, AT1G52100, AT1G60540, AT1G60630, AT1G64625, AT1G65150, AT1G68480, AT1G68780, AT1G69180, AT1G77145, AT1G80580, AT2G03500, AT2G17950, AT2G19910, AT2G27250, AT2G33880, AT2G39850, AT3G02500, AT3G12750, AT3G15170, AT3G16340, AT3G27920, AT3G30340, AT3G42670, AT3G44970, AT3G49950, AT3G50870, AT3G54990, AT3G59270, AT4G00180, AT4G00480, AT4G12450, AT4G14819, AT4G31610, AT4G31615, AT4G31620, AT4G31805, AT4G31877, AT4G36060, AT4G36470, AT4G36850, AT4G37970, AT5G03840, AT5G12330, AT5G14070, AT5G16410, AT5G20740, AT5G27690, AT5G35770, AT5G39330, AT5G42655, AT5G53210, AT5G56530, AT5G58780, AT5G61070, and AT5G6491.
In addition to the sequences provided in the Sequence Listing or in this Example, a promoter region may include a fragment of the promoter sequences provided in the Sequence Listing or in this Example, or a complement thereof, wherein the promoter sequence, or the fragment thereof, or the complement thereof, regulates expression of a polypeptide in a plant cell, for example, in response to a biotic or abiotic stress, or in a manner that is enhanced or preferred in certain plant tissues.
(2) Knock-Out/Knock-Down
In some cases, lines mutated in a given regulatory protein may be analyzed. Where available, T-DNA insertion lines in a given gene are isolated and characterized. In cases where a T-DNA insertion line is unavailable, an RNA interference (RNAi) strategy is sometimes used.
Example II
Transformation Methods
Crop species that overexpress polypeptides of the instant description may produce plants with increased photosynthetic resource use efficiency and/or yield. Thus, polynucleotide sequences listed in the Sequence Listing recombined into, for example, one of the expression vectors of the instant description, or another suitable expression vector, may be transformed into a plant for the purpose of modifying plant traits for the purpose of improving yield, quality, and/or photosynthetic resource use efficiency. The expression vector may contain a constitutive, tissue-enhanced or inducible promoter operably linked to the polynucleotide. The cloning vector may be introduced into a variety of plants by means well known in the art such as, for example, direct DNA transfer or Agrobacterium tumefaciens -mediated transformation.
Transformation of Monocots.
Cereal plants including corn, wheat, rice, sorghum, barley, or other monocots may be transformed with the present polynucleotide sequences, including monocot or eudicot-derived sequences such as those presented in the present Tables, cloned into a vector such as pGA643 and containing a kanamycin-resistance marker, and expressed constitutively under, for example, the CaMV35S or COR15 promoters, or with tissue-enhanced or inducible promoters. The expression vectors may be one found in the Sequence Listing, or any other suitable expression vector may be similarly used. For example, pMEN020 may be modified to replace the NptII coding region with the BAR gene of Streptomyces hygroscopicus that confers resistance to phosphinothricin. The KpnI and BglII sites of the Bar gene are removed by site-directed mutagenesis with silent codon changes.
The cloning vector may be introduced into a variety of cereal plants by means well known in the art including direct DNA transfer or Agrobacterium tumefaciens -mediated transformation. The latter approach may be accomplished by a variety of means, including, for example, that of U.S. Pat. No. 5,591,616, in which monocotyledon callus is transformed by contacting dedifferentiating tissue with the Agrobacterium containing the cloning vector.
The sample tissues are immersed in a suspension of 3×10 −9 cells of Agrobacterium containing the cloning vector for 3-10 minutes. The callus material is cultured on solid medium at 25° C. in the dark for several days. The calli grown on this medium are transferred to a Regeneration Medium. Transfers are continued every two to three weeks (two or three times) until shoots develop. Shoots are then transferred to Shoot-Elongation Medium every 2-3 weeks. Healthy looking shoots are transferred to Rooting Medium and after roots have developed, the plants are placed into moist potting soil.
The transformed plants are then analyzed for the presence of the NPTII gene/kanamycin resistance by ELISA, using the ELISA NPTII kit from SPrime-3Prime Inc. (Boulder, Colo.).
It is also routine to use other methods to produce transgenic plants of most cereal crops (Vasil, 1994. Plant Mol. Biol. 25: 925-937) such as corn, wheat, rice, sorghum (Cassas et al., 1993 . Proc. Natl. Acad. Sci. USA 90: 11212-11216), and barley (Wan and Lemeaux, 1994. Plant Physiol. 104: 37-48). DNA transfer methods such as the microprojectile method can be used for corn (Fromm et al., 1990 . Bio/Technol. 8: 833-839; Gordon-Kamm et al., 1990. Plant Cell 2: 603-618; Ishida, 1990. Nature Biotechnol. 14:745-750), wheat (Vasil et al., 1992. Bio/Technol. 10:667-674; Vasil et al., 1993. Bio/Technol. 11:1553-1558; Weeks et al., 1993. Plant Physiol. 102:1077-1084), and rice (Christou, 1991. Bio/Technol. 9:957-962; Hiei et al., 1994. Plant J. 6:271-282; Aldemita and Hodges, 1996. Planta 199: 612-617; and Hiei et al., 1997. Plant Mol. Biol. 35:205-218). For most cereal plants, embryogenic cells derived from immature scutellum tissues are the preferred cellular targets for transformation (Hiei et al., 1997. supra; Vasil, 1994. supra). For transforming corn embryogenic cells derived from immature scutellar tissue using microprojectile bombardment, the A188XB73 genotype is the preferred genotype (Fromm et al., 1990. Bio/Technol. 8: 833-839; Gordon-Kamm et al., 1990. supra). After microprojectile bombardment the tissues are selected on phosphinothricin to identify the transgenic embryogenic cells (Gordon-Kamm et al., 1990. supra). Transgenic plants from transformed host plant cells may be regenerated by standard corn regeneration techniques (Fromm et al., 1990. Bio/Technol. 8: 833-839; Gordon-Kamm et al., 1990. supra).
Transformation of Dicots.
It is now routine to produce transgenic plants using most eudicot plants (see U.S. Pat. No. 8,273,954 (Rogers et al.) issued Sep. 25, 2012; Weissbach and Weissbach, 1989 . Methods for Plant Molecular Biology , Academic Press; Gelvin et al., 1990. Plant Molecular Biology Manual , Kluwer Academic Publishers; Herrera-Estrella et al., 1983. Nature 303: 209; Bevan, 1984 . Nucleic Acids Res. 12: 8711-8721; and Klee, 1985. Bio/Technology 3: 637-642). Methods for analysis of traits are routine in the art and examples are disclosed above.
Numerous protocols for the transformation of tomato and soy plants have been previously described, and are well known in the art. Gruber et al., in Glick and Thompson, 1993. Methods in Plant Molecular Biology and Biotechnology . eds., CRC Press, Inc., Boca Raton, describe several expression vectors and culture methods that may be used for cell or tissue transformation and subsequent regeneration. For soybean transformation, methods are described by Miki et al., 1993. in Methods in Plant Molecular Biology and Biotechnology , p. 67-88, Glick and Thompson, eds., CRC Press, Inc., Boca Raton; and U.S. Pat. No. 5,563,055, (Townsend and Thomas), issued Oct. 8, 1996.
There are a substantial number of alternatives to Agrobacterium -mediated transformation protocols, other methods for the purpose of transferring exogenous genes into soybeans or tomatoes. One such method is microprojectile-mediated transformation, in which DNA on the surface of microprojectile particles is driven into plant tissues with a biolistic device (see, for example, Sanford et al., 1987. Part. Sci. Technol. 5:27-37; Sanford, 1993 . Methods Enzymol. 217: 483-509; Christou et al., 1992. Plant. J. 2: 275-281; Klein et al., 1987. Nature 327: 70-73; U.S. Pat. No. 5,015,580 (Christou et al), issued May 14, 1991; and U.S. Pat. No. 5,322,783 (Tomes et al.), issued Jun. 21, 1994).
Alternatively, sonication methods (see, for example, Zhang et al., 1991. Bio/Technology 9: 996-997); direct uptake of DNA into protoplasts using CaCl 2 precipitation, polyvinyl alcohol or poly-L-ornithine (see, for example, Hain et al., 1985 . Mol. Gen. Genet. 199: 161-168; Draper et al., 1982. Plant Cell Physiol. 23: 451-458); liposome or spheroplast fusion (see, for example, Deshayes et al., 1985. EMBO J., 4: 2731-2737; Christou et al., 1987 . Proc. Natl. Acad. Sci. USA 84: 3962-3966); and electroporation of protoplasts and whole cells and tissues (see, for example, Donn et al. 1990. in Abstracts of VIIth International Congress on Plant Cell and Tissue Culture IAPTC , A2-38: 53; D'Halluin et al., 1992. Plant Cell 4: 1495-1505; and Spencer et al., 1994. Plant Mol. Biol. 24: 51-61) have been used to introduce foreign DNA and expression vectors into plants.
After a plant or plant cell is transformed (and the transformed host plant cell then regenerated into a plant), the transformed plant may propagated vegetatively or it may be crossed with itself or a plant from the same line, a non-transformed or wild-type plant, or another transformed plant from a different transgenic line of plants. Crossing provides the advantages of producing new and often stable transgenic varieties. Genes and the traits they confer that have been introduced into a tomato or soybean line may be moved into distinct line of plants using traditional backcrossing techniques well known in the art. Transformation of tomato plants may be conducted using the protocols of Koornneef et al, 1986. In Tomato Biotechnology : Alan R. Liss, Inc., 169-178, and in U.S. Pat. No. 6,613,962, the latter method described in brief here. Eight day old cotyledon explants are precultured for 24 hours in Petri dishes containing a feeder layer of Petunia hybrida suspension cells plated on MS medium with 2% (w/v) sucrose and 0.8% agar supplemented with 10 μM α-naphthalene acetic acid and 4.4 μM 6-benzylaminopurine. The explants are then infected with a diluted overnight culture of Agrobacterium tumefaciens containing an expression vector comprising a polynucleotide of the instant description for 5-10 minutes, blotted dry on sterile filter paper and cocultured for 48 hours on the original feeder layer plates. Culture conditions are as described above. Overnight cultures of Agrobacterium tumefaciens are diluted in liquid MS medium with 2% (w/v/) sucrose, pH 5.7, to an OD 600 of 0.8.
Following cocultivation, the cotyledon explants are transferred to Petri dishes with selective medium comprising MS medium with 4.56 μM zeatin, 67.3 μM vancomycin, 418.9 μM cefotaxime and 171.6 μM kanamycin sulfate, and cultured under the culture conditions described above. The explants are subcultured every three weeks onto fresh medium. Emerging shoots are dissected from the underlying callus and transferred to glass jars with selective medium without zeatin to form roots. The formation of roots in a kanamycin sulfate-containing medium is a positive indication of a successful transformation.
Transformation of soybean plants may be conducted using the methods found in, for example, U.S. Pat. No. 5,563,055 (Townsend et al., issued Oct. 8, 1996), described in brief here. In this method soybean seed is surface sterilized by exposure to chlorine gas evolved in a glass bell jar. Seeds are germinated by plating on 1/10 strength agar solidified medium without plant growth regulators and culturing at 28° C. with a 16 hour day length. After three or four days, seed may be prepared for cocultivation. The seedcoat is removed and the elongating radicle removed 3-4 mm below the cotyledons.
Eucalyptus is now considered an important crop that is grown for example to provide feedstocks for the pulp and paper and biofuel markets. This species is also amenable to transformation as described in PCT patent publication WO/2005/032241.
Crambe has been recognized as a high potential oilseed crop that may be grown for the production of high value oils. An efficient method for transformation of this species has been described in PCT patent publication WO 2009/067398 A1.
Overnight cultures of Agrobacterium tumefaciens harboring the expression vector comprising a polynucleotide of the instant description are grown to log phase, pooled, and concentrated by centrifugation. Inoculations are conducted in batches such that each plate of seed was treated with a newly resuspended pellet of Agrobacterium . The pellets are resuspended in 20 ml inoculation medium. The inoculum is poured into a Petri dish containing prepared seed and the cotyledonary nodes are macerated with a surgical blade. After 30 minutes the explants are transferred to plates of the same medium that has been solidified. Explants are embedded with the adaxial side up and level with the surface of the medium and cultured at 22° C. for three days under white fluorescent light. These plants may then be regenerated according to methods well established in the art, such as by moving the explants after three days to a liquid counter-selection medium (see U.S. Pat. No. 5,563,055).
The explants may then be picked, embedded and cultured in solidified selection medium. After one month on selective media transformed tissue becomes visible as green sectors of regenerating tissue against a background of bleached, less healthy tissue. Explants with green sectors are transferred to an elongation medium. Culture is continued on this medium with transfers to fresh plates every two weeks. When shoots are 0.5 cm in length they may be excised at the base and placed in a rooting medium.
Experimental Methods; Transformation of Arabidopsis.
Transformation of Arabidopsis is performed by an Agrobacterium -mediated protocol based on the method of Bechtold and Pelletier, 1998. Unless otherwise specified, all experimental work is performed using the Columbia ecotype.
Plant Preparation.
Arabidopsis seeds are gas sterilized and sown on plates with media containing 80% MS with vitamins, 0.3% sucrose and 1% Bacto™ agar. The plates are placed at 4° in the dark for the days then transferred to 24 hour light at 22° for 7 days. After 7 days the seedlings are transplanted to soil, placing individual seedlings in each pot. The primary bolts are cut off a week before transformation to break apical dominance and encourage auxiliary shoots to form. Transformation is typically performed at 4-5 weeks after sowing.
Bacterial Culture Preparation.
Agrobacterium stocks are inoculated from single colony plates or from glycerol stocks and grown with the appropriate antibiotics until saturation. On the morning of transformation, the saturated cultures are centrifuged and bacterial pellets are re-suspended in Infiltration Media (0.5×MS, 1× Gamborg's Vitamins, 5% sucrose, 200 μl/L Silwet® L77) until an A 600 reading of 0.8 is reached.
Transformation and Harvest of Transgenic Seeds.
The Agrobacterium solution is poured into dipping containers. All flower buds and rosette leaves of the plants are immersed in this solution for 30 seconds. The plants are laid on their side and wrapped to keep the humidity high. The plants are kept this way overnight at 22° C. and then the pots are turned upright, unwrapped, and moved to the growth racks. In most cases, the transformation process is repeated one week later to increase transformation efficiency.
The plants are maintained on the growth rack under 24-hour light until seeds are ready to be harvested. Seeds are harvested when 80% of the siliques of the transformed plants are ripe (approximately five weeks after the initial transformation). This seed is deemed T 0 seed, since it is obtained from the T 0 generation, and is later plated on selection plates (either kanamycin or sulfonamide). Resistant plants that are identified on such selection plates comprise the T1 generation, from which transgenic seed comprising an expression vector of interest may be derived.
Example III
Primary Screening Materials and Methods
Plant Growth Conditions.
Seeds from Arabidopsis lines are chlorine gas sterilized using a standard protocol and spread onto plates containing a sucrose-based media augmented with vitamins (80% MS+Vit, 1% sucrose, 0.65% PhytoBlend™ Agar; Caisson Laboratories, Inc., North Logan, Utah) and appropriate kanamycin or sulfonamide concentrations where selection is required. Seeds are stratified in the dark on plates, at 4° C. for 3 days then moved to a walk-in growth chamber (Conviron MTW120, Conviron Controlled Environments Ltd, Winnipeg, Manitoba, Canada) running at a 10 hour photoperiod at a photosynthetic photon flux of approximately 200 μmol m −2 s −1 at plant height and a photoperiod/night temperature regime of 22° C./19° C. After seven days of light exposure seedlings are transplanted into 164 ml volume pots containing autoclaved ProMix® soil. All pots are returned to the same growth-chamber where they are stood in water and covered with a lid for the first seven days. This protocol keeps the soil moist during this period. Seven days after transplanting lids are removed and a watering and nutrition regime begun. All plants receive water three times a week, and a weekly a fertilizer treatment (80% Peter's NPK fertilizer).
Primary Screening.
Between 35 and 38 days after being transferred to lighted conditions on plates, and after between 28 and 31 days growth in soil, a suite of leaf-physiological parameters are measured using an infrared gas analyzer (LI-6400XT, LI-COR® Biosciences, Lincoln, NB, USA) integrated with a fluorimeter that measures fluorescence from Chlorophyll A (LI-6400-40, LI-COR Biosciences). This technique involves clamping a leaf between two gaskets, effectively sealing it inside a chamber, then measuring the exchange of carbon dioxide and water vapor between the leaf and the air flowing through the chamber. This gas exchange is monitored simultaneously with the fluorescence levels from the chlorophyll a molecules in the leaf. The growth conditions used, and plant age and leaf selection criteria for measurement are designed to maximize the chance that the leaves sampled fill the 2 cm 2 leaf chamber of the gas-exchange system and that plants show no visible signs of having transitioned to reproductive growth.
Screening High-Light Leaf Physiology at Two Air Temperatures.
Leaf physiology is screened after plants have been acclimated to high light (700 μmol photons m −2 s −1 ) under LED light banks emitting visible light (400-700 nm, Photon Systems Instruments, Brno, Czech Republic), for 40 minutes. Other than the change in light level, the atmospheric environment is the same as that in which the plants have been grown, and the LI-6400 leaf chamber is set to reflect this, being set to deliver a photosynthetic photon flux of 700 μmol photons m −2 s −1 and operate at an air temperature of 22° C. Forty minutes acclimation to a photosynthetic photon flux of 700 μmol photons m −2 s −1 has repeatedly been shown to be sufficient to achieve a steady-state rate of light-saturated photosynthesis and stomatal conductance in control plants. Gas exchange and fluorescence data are logged simultaneously two minutes after the leaf has been closed in the chamber. Two minutes is found to be long enough for the leaf chamber CO 2 and H 2 O concentrations to stabilize after closing a new leaf inside, and thereby minimizing leaf physiological adjustment to small differences between the growth environment and the LI-6400 chamber. Screening at the growth air temperature of 22° C. is begun one hour into the photoperiod and is typically completed in two hours. After being screened at 22° C., plants are returned to growth-light levels prior to being screened again at 35° C. later in the photoperiod. The higher-temperature screening begins six hours into the photoperiod and measurements are made after the rosettes have been acclimated to the same high light dose as described above, but this time in a controlled environment with an air temperature set to 35° C. Measurements are again made in a leaf chamber set to match the warmer air temperature and logged using the protocol described above for the 22° C. measurements. Data generated at both 22° C. and 35° C. are used to calculate: rates of CO 2 assimilation by photosynthesis (A, μmol CO 2 m −2 s −1 ); rates of H 2 O loss through transpiration (Tr, mmol H 2 O m −2 s −1 ); the conductance to CO 2 and H 2 O movement between the leaf and air through the stomatal pore (g s , mol. H 2 O m −2 s −1 ); the sub-stomatal CO 2 concentration (C i , μmol CO 2 mol −1 ); transpiration efficiency, the instantaneous ratio of photosynthesis to transpiration, (TE=A/Tr (μmol CO 2 mmol H 2 O m −2 s −1 )); the rate of electron flow through photosystem two (ETR μmol e-m −2 s −1 ). Derivation of the parameters described above followed established published protocols (Long & Bernacchi, 2003. J. Exp. Botany; 54:2393-24)
Leaves from up to 10 replicate plants are screened for a given line of interest. Data generated from these lines are compared with that from an empty vector control line planted at the same time, grown within the same flats, and screened at the same time.
For control lines, data are collected not only at an atmospheric CO 2 concentration of 400 μmol CO 2 mol 1 , but also after stepwise changes in CO 2 concentration to 350, 300, 450 and 500 μmol CO 2 mol −1 . These measurements underlay screening for more complex physiological traits of: (1) photosynthetic capacity; (2) Non-photochemical quenching; and (3) non-photosynthetic metabolism.
Screening Photosynthetic Capacity.
Under most conditions, the rate of light-saturated photosynthesis in a C3 leaf is a product of the biochemical capacity of the Calvin cycle and the transfer conductance of CO 2 concentration to the sites of carboxylation (Farquhar et al., 1980. Planta: 149, 78-90). Plotting the rate of photosynthesis against an estimate of the sub-stomatal CO 2 concentration (C i ) provides a means to identify changes in photosynthetic capacity of the Calvin cycle independent of changes in stomatal conductance, a key component of the total transfer conductance to CO 2 of the leaf. Consequently, for lines being screened, rates of photosynthesis are plotted against a regression plot of A vs. C i generated for the control lines over a range of atmospheric CO 2 concentration, as described above. This technique enables visual confirmation of changes in photosynthetic capacity in lines of interest.
Screening Non-Photochemical Quenching.
During acclimation to high light, the efficiency with which photosystem PSII operates will reach a steady state regulated largely by the feedback between non-photochemical quenching (NPQ) in the antenna and the metabolic demand for energy produced in the chloroplast (Genty et al., 1989. Biochim. Biophys. Acta 990:87-92; Baker et al., 2007. Plant Cell Environ. 30:1107-1125). This understanding is used in this screen to identify lines in which the limitation that non-photochemical quenching exerts on the efficiency with which photosystem II operates is decreased or increased. A decrease in non-photochemical quenching may be the consequence of a decrease in the capacity for NPQ. This would result in lower levels of non-photochemical quenching and a higher efficiency of photosynthesis over a range of light levels, but importantly, higher rates of photosynthesis at low light where light-use efficiency is important. However, changes in rate at which NPQ responds to light could also underlie any increases or decreases in NPQ. Of these, an increase in the rate at which NPQ relaxes has the potential to increase rates of photosynthesis as leaves in crop canopies transition from high to low light, and is therefore relevant to increasing crop-canopy photosynthesis (Zhu et al., 2010. Plant Biol. 61:235-261). In keeping with the A/Ci analysis described above, a regression of the operating efficiency of PSII against non-photochemical quenching is generated for the control line from data collected over a range of atmospheric CO 2 concentration. This technique enables visual confirmation of changes in the regulation of PSII operation that are driven by changes in non-photochemical quenching in lines of interest.
Screening for Non-Photosynthetic Metabolism.
Measurement of the ratio of the rate of electron flow through PSII (ETR) to the rate of photosynthesis (A) is used to screen for changes in non-photosynthetic metabolism. This screen is based upon the understanding that the transport of four μmol of electrons from PSII to photosystem one PSI will supply the NADPH and ATP required to fix one μmol of CO 2 in the Calvin cycle. For a C3 leaf operating in an atmosphere with 21% oxygen, the ratio of electron flow to photosynthesis should be higher than four, reflecting photorespiratory and other metabolism. However, because the rate of photorespiration in a C3 leaf is dependent upon the concentration of CO 2 at the active site of Rubisco, a regression of the ratio of electron flow to photosynthesis, generated over the range of CO 2 concentrations described above, provides the reference regression against which lines being screened can be compared to controls. Changes in the ratio of ETR to A, when observed at the same C i as the control line, could indicate changes in the specificity of the Rubisco active site for O 2 relative to CO 2 and or other metabolic sinks which would be expected to have important implications for crop productivity and/or stress tolerance.
Surrogate Screening for Growth-Light Physiology.
Rosette biomass: the dry weight of whole Arabidopsis rosettes (i.e., above-ground biomass) is measured after being dried down at 80° C. for 24 hours, a time found to be sufficient to reach constant weight. Samples are taken after 35-38 days growth, and used as an assay of above-ground productivity at growth light. Typically, five replicate rosettes are sampled per Arabidopsis line being screened.
Rosette chemical and isotopic C and N analysis: after weighing, the five rosettes sampled for each line screened are pooled together and ground to a fine powder. The pooled sample generated is sub-sampled and approximately 4 μg samples are prepared for analysis.
Chlorophyll content index (CCI): measurements of light transmission through the leaf are made for plants being screened using a chlorophyll content meter (CCM-200, Apogee Instruments, Logan, Utah, USA). The first is made within the first hour of the photoperiod prior to any acclimation to high light on leaves of plants samples for rosette analysis. The second is made later in the photoperiod on leaves of plants that had undergone the high-temperature screening.
Light absorption: measurements of CCI are used as a surrogate for leaf light absorption, based upon a known relationship between the two. The estimates of light absorption by the leaf, required to construct this relationship, were made by placing the leaf on top of a quantum sensor (LI-190, LI-COR Biosciences) with both the leaf and quantum sensor then pressed firmly up to the foam gasket underneath the LI-6400 light source. This procedure provides an estimate of the transmission of a known light flux through the leaf and is used to estimate the fraction of light absorbed by the leaf.
Example IV
Experimental Results
This Example provides experimental observations for transgenic plants overexpressing AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 related polypeptides in plate-based assays and results observed for improved photosynthetic resource use efficiency.
AtMYB19
Photosynthetic rate was increased in six of nine independent lines screened at growth temperature (22° C.) and seven of nine lines for measurements made after acclimation to high temperature. For measurements made at air temperatures of 22° C. and 35° C.; photosynthesis was increased by 16% at 22° C. and 17% at 35° C., when averaged across the lines that displayed increased photosynthesis. This provided evidence that the increase in photosynthesis is conferred over a wide range of air temperatures observed in Arabidopsis plants overexpressing AtMYB19. Leaf and crop-canopy photosynthesis is known to be related to final crop yield and improving photosynthesis is widely considered to be a relevant pathway to increasing crop yield. In a C3 plant, photosynthesis at high-light can be limited by the biochemical capacity for photosynthesis, indicated as photosynthetic capacity in Tables 23 and 24, or the supply of CO 2 into the chloroplast, of which stomatal conductance, which regulates the transfer of CO 2 into the leaf through stoma, is a principle component. Both the capacity for photosynthesis and stomatal conductance were increased in Arabidopsis plants overexpressing AtMYB19 assayed at both temperatures. Photosynthetic capacity was increased in five lines at 22° C. and in three at 35° C. Focused secondary assays on select lines, enabled the biochemical limitations to photosynthesis that underlay photosynthetic capacity, to be investigated. For measurements made at 22° C., the biochemical basis for the increase in photosynthetic capacity was an increase in both the activity of Rubisco ( FIG. 3 ) and the capacity to regenerate RuBP, a key substrate for photosynthesis ( FIG. 4 ). Increases in both these parameters were observed in four lines. For measurements made at 35° C., three lines displayed an increase in the capacity to regenerate RuBP. Stomatal conductance was increased by 32% at 22° C. and 37% at 35° C., when averaged across the AtMYB19 overexpression lines that displayed increased photosynthesis. The extent to which photosynthesis is increased as a consequence of improvements in photosynthetic capacity and stomatal conductance has important implications. For example, increasing stomatal conductance will increase the supply of CO 2 into the leaf, however this will increase photosynthesis to a greater extent in a C3 plant than a C4 plant, where chloroplast CO 2 concentrations are typically maintained at close to saturating levels for photosynthesis. Increasing stomatal conductance will increase transpiration from the leaf, typically to a greater extent than photosynthesis is stimulated. This combination of traits may be more appropriate for crops growing on acreages where soil-water availability is seldom limiting yield. Conversely, an increase in photosynthetic capacity could increase photosynthetic rate without increasing stomatal conductance and water loss, and would be expected to increase crop yield over broad acres. For transgenic plants overexpressing AtMYB19 related polypeptides, the increase in photosynthetic rate was the result of increases in both photosynthetic capacity and stomatal conductance. Consequently transpiration efficiency, often used synonymously with WUE and expressed as unit carbon uptake via photosynthesis per unit water lost via transpiration, was typically not decreased across lines and temperatures.
All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding an AtMYB19-related polypeptide or overexpress an AtMYB19 clade or phylogenetically-related regulatory protein).
Tables 23 and 24 present the indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing AtMYB19 in experiments conducted to date. The data presented in Table 23 were collected on plants at their normal growth temperature of 22° C. For lines with increased photosynthetic capacity, RuBP indicates that the capacity to increase RuBP was increased and Rubisco indicates that Rubisco activity was increased.





TABLE 23



Photosynthetic resource use efficiency measurements in plants with altered

expression of AtMYB19 clade polypeptides at a growth temperature of 22° C.














Stomatal


Polypeptide
SEQ ID


Photosynthetic
Conductance
Photosynthetic

sequence/Line
NO
Driver
Target
Rate 22° C.
22° C.
Capacity



AtMYB19/Line 1
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (20%)
Increased (32%)
No effect



GAL4_opLexA::GFP

AtMYB19/Line 2
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (15%)
Increased (28%)
Increased



GAL4_opLexA::GFP



(Rubisco







and RuBP)

AtMYB19/Line 3
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (10%)
Increased (35%)
Increased



GAL4_opLexA::GFP



(Rubisco







and RuBP)

AtMYB19/Line 4
2
35S::m35S::oEnh:LexA:
opLexA::G1309
No effect
No effect
No effect



GAL4_opLexA::GFP

AtMYB19/Line 5
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (26%)
Increased (27%)
Increased



GAL4_opLexA::GFP

AtMYB19/Line 6
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (13%)
Increased (30%)
Increased



GAL4_opLexA::GFP



RuBP

AtMYB19/Line 7
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (10%)
Increased (41%)
Increased



GAL4_opLexA::GFP



RuBP

AtMYB19/Line 8
2
35S::m35S::oEnh:LexA:
opLexA::G1309
No effect
No effect
No effect



GAL4_opLexA::GFP









































The data presented in Table 24 were collected on plants acclimated to an air temperature of 35° C. For lines with increased photosynthetic capacity, RuBP indicates that the capacity to increase RuBP was increased and Rubisco indicates that Rubisco activity was increased.





TABLE 24



Photosynthetic resource use efficiency measurements in plants with altered

expression of AtMYB19 clade polypeptides at a growth temperature of 35° C.














Stomatal


Polypeptide
SEQ ID


Photosynthetic
Conductance
Photosynthetic

sequence/Line
NO
Driver
Target
Rate 22° C.
22° C.
Capacity



AtMYB19/Line 1
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (22%)
Increased (49%)
No effect



GAL4_opLexA::GFP

AtMYB19/Line 2
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (14%)
Increased (43%)
Increased



GAL4_opLexA::GFP



(RuBP)

AtMYB19/Line 3
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (15%)
Increased (23%)
Increased



GAL4_opLexA::GFP



(RuBP)

AtMYB19/Line 4
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (26%)
Increased (39%)
No effect



GAL4_opLexA::GFP

AtMYB19/Line 5
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (22%)
Increased (37%)
No effect



GAL4_opLexA::GFP

AtMYB19/Line 6
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (19%)
Increased (61%)
No effect



GAL4_opLexA::GFP

AtMYB19/Line 7
2
35S::m35S::oEnh:LexA:
opLexA::G1309
Increased (13%)
Increased (28%)
Increased



GAL4_opLexA::GFP



(RuBP)

AtMYB19/Line 8
2
35S::m35S::oEnh:LexA:
opLexA::G1309
No effect
Increased (17%)
No effect



GAL4_opLexA::GFP







































The results presented in Tables 23 and 24 were determined after screening nine independent transgenic events. Multiple lines were screened in replicate independent experiments.
AtMYB50
Table 25 lists the indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing AtMYB50 in experiments conducted to date. Each of the lines overexpressing AtMYB50 (G1319) were generated by supertransforming a 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP driver line with an opLexA::G1319 construct. Photosynthetic rate was increased by 24% for measurements made at an air temperature of 22° C. and averaged across six independent lines. Leaf and crop-canopy photosynthesis is known to be related to final crop yield, and improving photosynthesis is widely considered to be a relevant pathway to increasing crop yield. In a C3 plant, photosynthesis at high light can be limited by the biochemical capacity for photosynthesis, defined as photosynthetic capacity in Table 25, or the supply of CO 2 into the chloroplast, of which stomatal conductance, which regulates the transfer of CO 2 into the leaf through stoma, is a principal component. The extent to which photosynthesis is increased as a consequence of improvements in photosynthetic capacity and stomatal conductance has important implications. For example, increasing stomatal conductance will increase the supply of CO 2 into the leaf, however this will increase photosynthesis to a greater extent in a C3 plant than a C4 plant, where chloroplast CO 2 concentrations are typically maintained at close to saturating levels for photosynthesis. Increasing stomatal conductance will increase transpiration from the leaf, typically to a greater extent than photosynthesis is stimulated. This combination of traits may be more appropriate for crops growing on acreages where soil-water availability seldom limits yield. Conversely, an increase in photosynthetic capacity could increase photosynthetic rate without increasing stomatal conductance and water loss, and would be expected to increase crop yield over broad acres. For transgenic plants overexpressing AtMYB50 related polypeptides, the increase in photosynthetic rate was the result of increases in both photosynthetic capacity and stomatal conductance. Consequently transpiration efficiency, often used synonymously with WUE and expressed as unit carbon uptake via photosynthesis per unit water lost via transpiration, was not decreased across lines.
The dry weight of the rosette (that is, the above-ground biomass) was also increased in plants overexpressing AtMYB50. This measurement provides an estimate of productivity or net cumulative photosynthesis for these plants attained under growth conditions, not after acclimation to high light as described above. Increased rosette biomass could be the cumulative consequence of earlier seed germination, increases in the relative growth rate of the plant or improvements in underlying leaf physiology. Because increased rosette dry weight was achieved with the same availability of key resources of nitrogen and water as control plants, photosynthetic resource-use efficiency was increased under growth conditions. Regardless of the cause of the increase in productivity, this trait would be highly desirable in crops where the aboveground part of the plant is harvested. Crops farmed for seed yield could also benefit from faster canopy development that could result from earlier germination or increased relative growth rates.
All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding an AtMYB50-related polypeptide or overexpress an AtMYB50 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.





TABLE 25



Photosynthetic resource use efficiency measurements in plants

with altered expression of AtMYB50 clade polypeptides








Polypeptide
SEQ ID
Photosynthetic
Photosynthetic
Stomatal
Above-ground

Sequence/Line
NO:
Rate
Capacity
Conductance
Biomass



AtMYB50/Line 1
135
Increased (+32%)
Increased
Increased (+68%)
** (0%)

AtMYB50/Line 2
135
Increased (+23%)

** (+27%)
Increased (+32%)

AtMYB50/Line 3
135
Increased (+22%)
Increased
** (0)
Increased (+50%)

AtMYB50/Line 4
135
Increased (+19%)
Increased
Increased (+25%)
Increased (+70%)

AtMYB50/Line 5
135
** (+15%)

** (+13%)
Increased (+23%)

AtMYB50/Line 6
135
Increased (+32%)
Increased
Increased (+35%)
Increased (+23%)



** measurement was not statistically significant relative to controls



























The results presented in Table 25 were determined after screening six independent transgenic events and the observed increase in photosynthesis in five lines. These data were confirmed in two lines that received two passes through the screen.
CRF1
Table 26 lists the indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing CRF1 in experiments conducted to date. Each of the lines overexpressing CRF1 (AT4G11140.1) were generated by supertransforming a 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP driver line with an opLexA::CRF1 construct.
Table 26 and FIG. 9 provide data detailing how discrimination against 13 C relative to 12 C during photosynthesis, and integrated over the life of the rosette, was decreased in lines overexpressing CRF1 relative to control lines. The result of decreased discrimination against 13 C is that the δ 13 C signature of the rosette increased by between 1.3 and 2.2 per mill (‰) when expressed using standard notation described in Farquhar et. al., 1989, supra (δ 13 C is a measure of the ratio of isotopes 13 C: 12 C, relative to the same ratio in a reference and reported herein in parts per thousand (per mil or ‰)). These data are consistent with an increase in WUE, integrated over the life of the rosette in the CRF1 overexpression lines. All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding an CRF1-related polypeptide or overexpress an CRF1 clade or phylogenetically-related regulatory protein).





TABLE 26



Photosynthetic resource use efficiency measurements in plants

with altered expression of CRF1 clade polypeptides







Polypeptide
SEQ ID
Rosette δ 13 C


Sequence/Line
NO:
(per mil)





CRF1/Line 1
307
Increased (1.4‰)


CRF1/Line 2
307
Increased (1.6‰)


CRF1/Line 3
307
Increased (1.5‰)


CRF1/Line 4
307
Increased (2.2‰)


CRF1/Line 5
307
Increased (1.7‰)




























The results presented in Table 26 were determined after screening five independent transgenic events. These data were confirmed for the three lines that received two passes through the screen.
ERF058
Table 27 lists the indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing ERF058 in experiments conducted to date. Each of the lines overexpressing ERF058 (G974) was generated by supertransforming a 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP driver line with an opLexA::ERF058 construct.
Table 27 and FIG. 12 provide data detailing how discrimination against 13 C relative to 12 C during photosynthesis, and integrated over the life of the rosette, was decreased in lines overexpressing ERF058 relative to control lines. The result of decreased discrimination against 13 C is that the δ 13 C signature of the rosette increased by between 1.8 and 3.6 per mill (‰) when expressed using standard notation described in Farquhar et. al. 1989, supra (δ 13 C is a measure of the ratio of isotopes 13 C: 12 C, relative to the same ratio in a reference and reported herein in parts per thousand (per mil or ‰)). These data are consistent with an increase in WUE integrated over the life of the rosette in the ERF058 overexpression lines. Transpiration efficiency, the ratio of photosynthesis to transpiration, of leaves of ERF058 overexpression lines was increased by between 32% and 101% under growth light conditions (Table 27). These data provide a link between improved WUE measured at a point in time at the leaf level and an integrated assessment at the whole rosette level. Further, WUE was likely increased because stomata conductance was lower in the ERF058 overexpression lines, by between 40% and 68% (Table 27). For measurements made at growth light, decreasing stomatal conductance will decrease transpiration but have little impact on photosynthesis as light, will limit the rate of photosynthesis more than CO 2 diffusion into the leaf. All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding an ERF058-related polypeptide or overexpress an ERF058 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.





TABLE 27



Photosynthetic resource use efficiency measurements in plants

with altered expression of ERF058 clade polypeptides







Polypeptide
SEQ ID
Rosette δ 13 C
Transpiration
Stomatal

Sequence/Line
NO:
(per mil)
efficiency
Conductance



ERF058/Line 1
490
Increased (2.6‰)
Increased (101%)
Decreased (68%)

ERF058/Line 2
490
Increased (2.3‰)
Not assayed
Not assayed

ERF058/Line 3
490
Increased (3.6‰)
Increased (38%)
Decreased (47%)

ERF058/Line 4
490
Increased (1.8‰)
Increased (32%)
Decreased (40%)

ERF058/Line 5
490
No effect
No effect
No effect



























The results presented in Table 27 were determined after screening five independent transgenic events. For lines 1, 2 and 3, the rosette δ 13 C data were confirmed in a repeat experiment and data presented are the mean of these two data sets.
SPATULA
This Example provides experimental observations for transgenic plants overexpressing SPATULA-related polypeptides in plate-based assays and results observed for improved photosynthetic resource use efficiency.
Arabidopsis plants constitutively overexpressing the SPATULA protein were early flowering and exhibited a number of leaf and rosette morphological changes. Under continuous light conditions, SPATULA overexpressor typically produced visible flower buds approximately one week earlier than wild type controls. At the time of bolting, these plants had 4-8 rosette leaves compared with 8-11 in wild type. Additionally, SPATULA overexpressors had pointed leaves at early stages of development, appeared slightly small, yellow, and at a later stage had elongated leaf petioles. Other than these effects, no obvious physiological or biochemical phenotypes were recorded. Gene expression profiling revealed that SPATULA was expressed at relatively higher levels in flowers, siliques and roots. However, SPATULA expression levels appeared unaffected by multiple assay conditions. The published literature describes SPATULA as a key control on flower development (Foreman et al. (2011) Plant Signal. Behav. 6:471-476, and regulator of both seed dormancy and cotyledon expansion based upon light quality signals and interaction with DELLA proteins (Josse et al. 2011. Plant Cell 23: 1337-1351). However, there appears nothing in the peer-reviewed literature that specifically addresses crop-relevant physiological consequences of changes in SPATULA expression in plants.
Leaf chlorophyll content was decreased by 32%, for measurements made on six independent SPATULA overexpression lines at an air temperature of 22° C., and also by 32% averaged across the same six lines after plant acclimation to 35° C. (Table 28). Set against this 32% decrease in leaf chlorophyll content, light-saturated photosynthesis was decreased by only 3% at 22° C., and increased by 4% at 35° C. (Table 28). Qualitative assessments of photosynthetic capacity made during the same screening runs revealed no systematic decreases in photosynthetic capacity across the six lines tested at either temperature (Table 28). While absorption of light energy is essential for photosynthesis, crop plants are thought to overinvest resources in chlorophyll and the light harvesting apparatus, and absorb more light energy than is required to meet the energetic demands of photosynthesis. This is thought to be an evolutionary consequence of improvements in fitness acquired from shading out rival plants. Physiological consequences of absorbing light in excess under stress conditions that constrain photosynthesis are well documented and can include; damage to the photosynthetic apparatus; decreased photosynthesis and in extreme plant death. However, even under optimal conditions for photosynthesis excess leaf chlorophyll can constrain leaf and canopy photosynthesis by decreasing transmission of light energy deeper into the canopy or leaf profile where photosynthesis is light-limited. The data provided in Table 28 provide evidence that the efficiency with which photosynthesis operates at high light in SPATULA overexpression lines can be increased with respect to the amount of light absorbed, an increase in photosynthetic light-use efficiency. This increase in photosynthetic light-use efficiency would be expected to increase leaf and canopy photosynthesis and crop yield: by decreasing the potential for photodamage of the photosynthetic apparatus; increasing light-limited photosynthesis by allowing transmission of more light into the light-limited layers of the leaf and crop canopy; and, making available nitrogen that had been overinvested in light harvesting.
Table 28 lists the indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing SPATULA in experiments conducted to date. Each of the lines overexpressing SPATULA (G590 or AT4G36930) were generated by supertransforming a 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP driver line with an opLexA::SPT construct.
All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a SPATULA-related polypeptide or overexpress a SPATULA clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.





TABLE 28



Photosynthetic resource use efficiency measurements in plants

with altered expression of SPATULA clade polypeptides









SEQ
Air




Polypeptide
ID
Temper-


Photosynthetic

Sequence/Line
NO:
ature
Leaf Chlorophyll
Photosynthesis
Capacity



SPATULA/Line 1
625
22
Decreased (15%)
Increased (15%)
No effect

SPATULA/Line 2
625
22
Decreased (40%)
Decreased 13%
Decreased

SPATULA/Line 3
625
22
Decreased (31%)
Decreased (5%)
Variable effect

SPATULA/Line 4
625
22
Decreased (38%)
Increased (17%)
No effect

SPATULA/Line 5
625
22
Decreased (33%)
Decreased (16%)
Variable effect

SPATULA/Line 6
625
22
Decreased (37%)
Decreased (15%)
Decreased

SPATULA/Line 1
625
35
Decreased (35%)
Increased (33%)
No effect

SPATULA/Line 2
625
35
Decreased (39%)
Increased (19%)
No effect

SPATULA/Line 3
625
35
Decreased (30%)
Decreased (17%)
No effect

SPATULA/Line 4
625
35
Decreased (32%)
Increased (14%)
No effect

SPATULA/Line 5
625
35
Decreased (30%)
Decreased (17%)
Variable

SPATULA/Line 6
625
35
Decreased (26%)
Decreased (9%)
No effect



































The results presented in Table 28 were determined after screening six independent transgenic events at two air temperatures 22 and 35° C. Lines 3 and 5 were assayed twice in two independent experiments, in which the effects on chlorophyll content and photosynthesis were repeated. Data shown for these two lines is the mean of the effect size observed in those two experiments.
MYB111
Table 29 lists the indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing MYB111 in experiments conducted to date. Each of the lines overexpressing MYB111 (AT5G49330 or G1640) were generated by supertransforming a 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP driver line with an opLexA::MYB111 construct. The data in Table 29 detail a 26% decrease in stomatal conductance, a 20% decrease in H 2 O loss from the leaf through transpiration and a 12% increase in transpiration efficiency, the ratio of photosynthesis to transpiration, averaged across six independent MYB111 overexpression lines for measurements made at 35° C. Increases in instantaneous transpiration efficiency, the ratio of photosynthesis to transpiration, improve photosynthetic resource use efficiency and are expected to be relevant to increasing crop yield. For MYB111 overexpression lines, the magnitude of the decrease in stomatal conductance and transpiration rate were larger than the increase in transpiration efficiency. This was because the decrease in stomatal conductance also decreased photosynthetic rate. This would be expected for Arabidopsis , a plant with the C3 photosynthetic pathway. However, for crops operating a C4 photosynthetic pathway, stomatal conductance can be decreased without significant decreases in photosynthetic rate, a consequence of the chloroplast CO 2 concentrating mechanism that distinguishes C3 from C4 photosynthesis. Consequently, the same magnitude of decrease in stomatal conductance in both C3 and C4 crops would be expected to increase transpiration efficiency much more in the C4 crop. However, for both C3 and C4 crops decreasing stomatal conductance is considered a yield relevant trait, even if it compromises photosynthesis. This is because the long-term benefits of decreasing leaf transpiration could more than compensate for short-term decreases in photosynthesis in crops growing in a field setting. In a field setting, soil water will be conserved under canopies with decreased stomatal conductance during early development, thereby sustaining plant-water status and canopy photosynthesis during crucial periods later in the crops development when canopy photosynthesis would typically become limited by soil water availability, such as grain filling, and protect against the deleterious effects of absorbing light energy when photosynthesis is constrained. Consequently there is good reason to assume that decreasing stomatal conductance is a means to improve photosynthetic resource efficiency when integrated over the entire life of the crop.
All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a MYB111-related polypeptide or overexpress a MYB111 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.





TABLE 29



Photosynthetic resource use efficiency measurements in plants

with altered expression of MYB111 clade polypeptides







Polypeptide
SEQ ID
Stomatal
Transpiration
Transpiration

Sequence/Line
NO:
Conductance
rate
efficiency



Myb111/Line 1
735
Decreased (21%)
Decreased (15%)
Increased (17%)

Myb111/Line 2
735
Decreased (25%)
Decreased (18%)
Increased (2%)

Myb111/Line 3
735
Decreased (10%)
Decreased (8%)
Increased (4%)

Myb111/Line 4
735
Decreased (41%)
Decreased (33%)
Increased (31%)

Myb111/Line 5
735
Decreased (35%)
Decreased (25%)
Decreased (3%)

Myb111/Line 6
735
Decreased (26%)
Decreased (20%)d
Increased (18%)




























The results presented in Table 29 were determined after screening six independent transgenic lines. Lines 1, 4 and 6 were assayed in two independent experiments, the direction of effect on all parameters in table 5 was repeated in both assays, and the data shown is the mean of the two data sets.
AtNPR3
FIG. 19 and Table 30 display and list, respectively, the indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing AtNPR3 in experiments conducted to date. Each of the lines overexpressing AtNPR3 (AT5G45110.1 or G839) were generated by supertransforming a 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP driver line with an opLexA::AtNPR3 construct.
This biochemical capacity for photosynthesis is a product of plant resource investment in numerous pigments and protein required to absorb light and couple it to the enzymatic reduction of carbon in the air to sugars, in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Of the numerous enzymes that limit photosynthesis, the activity of Rubisco is a key constraint in both C3 and C4 leaves. FIG. 19 displays data showing an increase in photosynthetic capacity in five independent AtNPR3 overexpression lines. The data were collected under low atmospheric CO 2 conditions, at which increased rates of light-saturated photosynthesis are routinely interpreted as evidence of increased Rubisco activity (Long & Bernacchi, 2003 supra). Data presented in Table 30 details up to a 15% increase in photosynthesis when averaged across five AtNPR3 overexpression lines and two independent experiments, for the lines in which Rubisco activity was increased. Averaged across all lines this increase in photosynthetic capacity and rate were achieved with a not statistically significant 3% decrease in leaf chlorophyll content, and a not statistically significant 0.03% increase in rosette nitrogen content, evidence of improved photosynthetic resource use efficiency.
All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding an AtNPR3-related polypeptide or overexpress an AtNPR3 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.





TABLE 30



Photosynthesis and photosynthetic resource use efficiency related parameters

measured in plants with altered expression of AtNPR3 clade polypeptides








Polypeptide
SEQ ID
Photosynthetic
Photosynthetic
Leaf Chlorophyll


Sequence/Line
NO:
Capacity
Rate
content
Rosette N content



AtNPR3/Line 1
864
Increased
Increased (13%)
Increased (1%*)
No data

AtNPR3/Line 2
864
Increased
Increased (15%)
Decreased (4%)
No data

AtNPR3/Line 3
864
Increased
Increased (11%)
No effect
Increased (0.03%*)

AtNPR3/Line 4
864
Increased
Increased (11%)
Decreased (8%)
Increased (0.09%*)

AtNPR3/Line 5
864
Increased
Increased (15%)
Decreased (6%)
Decreased(0.03%*)



*Denotes an effect that was not statistically significant at p < 0.1.


























The results presented in Table 30 were determined after screening five independent transgenic lines. Lines 3, 4 and 5 were assayed in two independent experiments; the direction of effect on photosynthetic capacity and photosynthesis was repeated in both assays, and the data shown is the mean of the two data sets.
AtMYC1
This biochemical capacity for photosynthesis is a product of plant resource investment in numerous pigments and protein required to absorb light and couple it to the enzymatic reduction of carbon in the air to sugars, in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Of the numerous enzymes that limit photosynthesis, the activity of Rubisco is a key constraint in both C3 and C4 leaves. FIG. 22 displays data showing an increase in photosynthetic capacity in four out of five independent overexpression lines. The data were collected under low atmospheric CO 2 conditions, at which increased rates of light-saturated photosynthesis are routinely interpreted as evidence of increased Rubisco activity (Long & Bernacchi 2003 already cited above). Data presented in table 5 records rates of photosynthesis measured at current atmospheric [CO 2 ] for the same five lines, and details an 18% increase in photosynthesis when averaged across all five overexpression lines and two independent experiments. This increase can be attributed to the increase in Rubisco activity shown in figure three. Averaged across all lines this increase in photosynthetic capacity and rate were achieved with a smaller 3.5% increase in leaf chlorophyll content, and only 0.13% increase in rosette nitrogen content, evidence of improved photosynthetic resource use efficiency.





TABLE 31



Photosynthesis and photosynthetic resource use efficiency related parameters

measured in plants with altered expression of AtMYC1 clade polypeptides








Polypeptide
SEQ ID
Photosynthetic
Photosynthetic
Leaf Chlorophyll


Sequence/Line
NO:
Capacity
Rate
Content
Rosette N Content



AtMYC1/Line 1
1016
Increased
Increased (13%)
Increased (9%)
No data

AtMYC1/Line 2
1016
No effect
Increased (14%)
Decreased (4%)
Decreased (0.01%*)

AtMYC1/Line 3
1016
Increased
Increased (28%)
Increased (1%)
Decreased (0.06%*)

AtMYC1/Line 4
1016
Increased
Increased (20%)
Increased (7%)
No data

AtMYC1/Line 5
1016
Increased
Increased (17%)
Increased (4%)
Decreased (0.32%*)



























The results presented in Table 31 were determined after screening five independent transgenic lines. Lines 2, 3 and 5 were assayed in two independent experiments. For these lines the direction of effect on photosynthetic capacity and photosynthesis parameters was repeated in both assays for two of the three lines. For all three lines the data shown is the mean of two data sets.
All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding an AtMYC1-related polypeptide or overexpress an AtMYC1 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.
WRKY
Light-saturated photosynthesis was increased in WRKY3 overexpression lines, by 23% and 27% for measurements made at 22° C. and 35° C. respectively, and averaged over four independent lines (Table 32). The rate of photosynthesis is the product of the capacity for photosynthesis, and the supply of CO 2 into the leaf. The capacity for photosynthesis depends upon plant resource investment into the numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air to sugars, in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. FIG. 25 provides repeated evidence of an increase in photosynthetic capacity in two out of four independent WRKY3 overexpression lines for measurements made at the plants growth temperature, of 22° C. This evidence is displayed by increased rates of light-saturated photosynthesis when compared to the rate of photosynthesis predicted for control lines at the same leaf internal CO 2 concentration (C i ) (Long & Bernacchi 2003 already cited above). FIG. 27 provides evidence that the biochemical basis of this increase in photosynthetic capacity is an increase in the activity of Rubisco in the WRKY3 overexpression lines relative to the control lines, as evidenced by increased rates of light-saturated photosynthesis at low C, where Rubisco activity is the principle constraint on photosynthesis (also described in Long and Bernacchi 2003). This increase in Rubisco activity would be expected to underlie some component of the, over 30% increase in photosynthetic rate in these same lines, detailed in Table 32. FIG. 26 provides evidence that photosynthetic capacity has also been increased in the same two lines after acclimation to, and at, 35° C. Increasing the supply of CO 2 into the leaf, by increasing stomatal conductance to CO 2 transfer through the stomatal pore, will also increase photosynthesis. Stomatal conductance was significantly increased in each of the four WRKY3 overexpression lines at both temperatures, repeatedly in the two lines screened twice (Table 32). When averaged across all four lines, stomatal conductance was increased by 73% and 80% for measurements made at 22° C. and 35° C. respectively. This increase in stomatal conductance underlies the increase in photosynthesis in the two lines for which photosynthetic capacity was not increased and contributes to some component of the increase in photosynthetic rate in the two lines with increased photosynthetic capacity. While leaf nitrogen content was measured for three WRKY3 overexpression line only, the large significant increases in photosynthesis were achieved with no significant effects on leaf nitrogen content, evidence of improved photosynthetic resource use efficiency.
All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a WRKY3-related polypeptide or overexpress a WRKY3 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.





TABLE 32



Photosynthesis and photosynthetic resource use efficiency related parameters

measured in plants with altered expression of WRKY3 clade polypeptides









Polypeptide
SEQ ID
Temperature
Photosynthetic
Photosynthetic
Stomatal
Rosette N

Sequence/Line
NO:
(° C.)
Capacity
Rate
Conductance
content



WRKY3/Line 1
1156
22
No effect
Increased (10%)
Increased (47%)
Decreased (0.2%)

WRKY3/Line 2
1156
22
Increased
Increased (32%)
Increased (94%)
Increased (0.5%)

WRKY3/Line 3
1156
22
Increased
Increased (35%)
Increased (120%)
Increased (0.6%)

WRKY3/Line 4
1156
22
No effect
Increased (14%)
Increased (32%)
No data

WRKY3/Line 1
1156
35
No effect
Increased (17%)
Increased (57%)
—

WRKY3/Line 2
1156
35
Increased
Increased (37%)
Increased (99%)
—

WRKY3/Line 3
1156
35
Increased
Increased (39%)
Increased (121%)
—

WRKY3/Line 4
1156
35
No effect
Increased (14%)
Increased (44%)
—






























The results presented in Table 32 were determined after screening four independent transgenic lines. Lines 2 and 3 were assayed in two independent experiments. For both these lines the direction of effect on all parameters measured was repeated in both experiments. For both repeated lines the data shown is the mean of two data sets. All increases in photosynthetic rate and stomatal conductance were statistically significant (p<0.05).
AtNAC6
The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air to sugars, in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Table 33 describes an increased capacity for photosynthesis in three of four independent lines overexpressing AtNAC6. This increase was confirmed in secondary screening designed to provide insight into the biochemistry that underlies increased photosynthetic capacity. Of the numerous steps that can limit photosynthesis, the activity of Rubisco and the capacity to regenerate RuBP in the Calvin cycle are key constraints. For all three lines with increased photosynthetic capacity in the primary screen, secondary analysis identified increases in both the activity of Rubisco ( FIG. 30 ) and the capacity to regenerate RuBP ( FIG. 31 ) in AtNAC6 overexpression lines (Table 33; Long & Bernacchi 2003, supra, describe the basis for assaying Rubisco activity and RuBP regeneration capacity). When averaged across these four lines, the increase in photosynthesis averaged 21% (Table 33). These increases in photosynthetic capacity and photosynthesis were achieved on average with a small decrease in the nitrogen content of the rosette tissue, providing evidence of improved photosynthetic resource use efficiency.
All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding an-related polypeptide or overexpress an AtNAC6 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.





TABLE 33



Increased capacity for photosynthesis in plant lines overexpressing AtNAC6









Polypeptide
SEQ ID



Photosynthetic


Sequence/Line
NO:
Driver
Target
Photosynthesis
Capacity
Rosette [N]



AtNAC6/Line 1
1369
35S::m35S::oEnh:LexA:
opLexA::
Increased (27%)
Increased
Increased (0.3%)



GAL4_opLexA::GFP
AtNAC6

Rubisco and






RuBP

AtNAC6/Line 2
1369
35S::m35S::oEnh:LexA:
opLexA::
Increased (16%)
No effect
Decreased (0.3%)



GAL4_opLexA::GFP
AtNAC6

AtNAC6/Line 3
1369
35S::m35S::oEnh:LexA:
opLexA::
Increased (25%)
Increased
Decreased (0.9%)



GAL4_opLexA::GFP
AtNAC6

Rubisco and






RuBP

AtNAC6/Line 4
1369
35S::m35S::oEnh:LexA:
opLexA::
Increased (19%)
Increased
No data



GAL4_opLexA::GFP
AtNAC6

Rubisco and






RuBP
































The results presented in Table 33 were determined after screening four independent transgenic events. Lines 1 and 3 were screened twice. For both lines the direction of the effect on AtNAC6 overexpression was the same in both screening runs, and any effect size reported for a given parameter is the mean of the two screening runs.
WRKY 17
The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air to sugars, in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthetic capacity is considered a pathway to improving crop yield across broad acres.
Table 34 describes an increased capacity for photosynthesis in three of five independent lines overexpressing WRKY17; for lines with increased photosynthetic capacity, the underlying process that has been increased is identified as Rubisco activity (Rubisco), the capacity to regenerate RuBP (RuBP), or both. Increased capacity for photosynthesis was confirmed in secondary screening designed to provide insight into the biochemistry that underlay increased photosynthetic capacity. Of the numerous steps that can limit photosynthesis, the activity of Rubisco and the capacity to regenerate RuBP in the Calvin cycle are key constraints. For all three WRKY17 overexpression lines with increased photosynthetic capacity in the primary screen, secondary analysis identified increases in the activity of Rubisco ( FIG. 34 ). For one of these lines, there was evidence that the capacity to regenerate RuBP was also higher (Table 34; Long & Bernacchi 2003, supra, who describe the basis for assaying Rubisco activity and RuBP regeneration capacity). When averaged across these five lines, the increase in photosynthesis averaged 17%, when average for the three lines with increased photosynthetic capacity, the increase in photosynthesis was 27%. These increases in photosynthetic capacity and photosynthesis were achieved on average with a small decrease in the nitrogen content of the rosette tissue (Table 34), providing evidence of improved photosynthetic resource-use efficiency.
All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a WRKY17-related polypeptide or overexpress a WRKY17 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.





TABLE 34



Increased photosynthetic capacity drives increases in photosynthetic

resource-use efficiency in plant lines overexpressing WRKY17.









Polypeptide
SEQ ID


Photosynthetic



Sequence/Line
NO:
Driver
Target
Capacity
Photosynthesis
Rosette [N]



WRKY17/Line 1
1507
35S::m35S::oEnh:LexA:
opLexA::
Increased
Increased (27%)
Decreased (2%)



GAL4_opLexA::GFP
WRKY17
Rubisco and





RuBP

WRKY17/Line 2
1507
35S::m35S::oEnh:LexA:
opLexA::
Increased
Increased (24%)
Decreased (5%)



GAL4_opLexA::GFP
WRKY17
Rubisco

WRKY17/Line 3
1507
35S::m35S::oEnh:LexA:
opLexA::
Increased
Increased (29%)
Decreased (6%)



GAL4_opLexA::GFP
WRKY17
Rubisco

WRKY17/Line 4*
1507
35S::m35S::oEnh:LexA:
opLexA::
No effect
Increased (3%)
Decreased (3%)



GAL4_opLexA::GFP
WRKY17

WRKY17/Line 5
1507
35S::m35S::oEnh:LexA:
opLexA::
No effect
Increased (2%)
Decreased (2%)



GAL4_opLexA::GFP
WRKY17

































The results presented in Table 34 were determined after screening five independent transgenic events. Line 1 was screened three times, and lines 2, 3 and 5 were screened twice. For all lines the direction of the effects on WRKY17 overexpression on photosynthetic rates and photosynthetic capacity was repeated in each screening run. Line 4 was only screened once.
ZAT 11
The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air to sugars, in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthetic capacity is considered a pathway to improving crop yield across broad acres.
Table 35 describes an increased capacity for photosynthesis and increased photosynthetic rate in five independent lines overexpressing ZAT11. An increased capacity for photosynthesis was initially identified in three lines run through a primary screen (line 1, 2 and 3). This increase was confirmed in two of these three lines and two new lines (line 4 and 5), in a secondary screening that identified an increase in the activity of Rubisco as the biochemical basis for the increase in photosynthetic capacity by the method of Long and Bernacchi, 2003, supra ( FIG. 37 ). When averaged across these five lines, the increase in photosynthetic rate averaged 16%. These increases in photosynthetic capacity and photosynthesis were achieved with a decrease in the nitrogen content of the rosette tissue in three of the four lines for which data were collected (Table 35), providing evidence of improved photosynthetic resource-use efficiency.
All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a ZAT11-related polypeptide or overexpress a ZAT11 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.





TABLE 35



Increased photosynthetic capacity drives increases in photosynthetic

resource-use efficiency in plant lines overexpressing ZAT11.









Polypeptide
SEQ ID


Photosynthetic



Sequence/Line
NO:
Driver
Target
Capacity
Photosynthesis
Rosette [N]



ZAT11/Line 1
1591
35S::m35S::oEnh:LexA:
opLexA::
Increased
Increased (21%)
Decreased (7%)



GAL4_opLexA: :GFP
ZAT11
Rubisco

ZAT11/Line 2
1591
35S::m35S::oEnh:LexA:
opLexA::
Increased
Increased (12%)
Decreased (13%)



GAL4_opLexA::GFP
ZAT11

ZAT11/Line 3
1591
35S::m35S::oEnh:LexA:
opLexA::
Increased
Increased (24%)
Decreased (9%)



GAL4_opLexA::GFP
ZAT11
Rubisco

ZAT11/Line 4*
1591
35S::m35S::oEnh:LexA:
opLexA::
Increased
Increased (5%)
Not measured



GAL4_opLexA::GFP
ZAT11
Rubisco

ZAT11/Line 5
1591
35S::m35S::oEnh:LexA:
opLexA::
Increased
Increased (18%)
No effect



GAL4_opLexA::GFP
ZAT11
Rubisco
































The results presented in Table 35 were determined after screening five independent transgenic events. Line 1, 2 and 3 were screened twice with the percent difference values in Table 35 being the mean of the effect observed in both screening runs. Increased photosynthetic capacity was repeatedly observed for Line 1 and 3, but only once for line 2. Lines 4 and 5 were screened once.
The present disclosure thus describes how the transformation of plants, which may include monocots and/or dicots, with an AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptide can confer to the transformed plants greater photosynthetic resource use efficiency than the level of photosynthetic resource use efficiency exhibited by control plants. In one embodiment, expression of AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 is driven by a constitutive promoter. In another embodiment, expression of AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 is driven by a promoter with enhanced activity in a tissue capable of photosynthesis (also referred to herein as a “photosynthetic promoter” or a “photosynthetic tissue-enhanced promoter”) such as a leaf tissue or other green tissue. Examples of photosynthetic tissue-enhanced promoters include for example, an RBCS3 promoter (SEQ ID NO: 1693), an RBCS4 promoter (SEQ ID NO: 1694) or others such as the At4g01060 (also referred to as “G682”) promoter (SEQ ID NO: 1695), the latter regulating expression in guard cells, or promoters listed in Table 22. Other photosynthetic tissue-enhanced promoters have been taught by Bassett et al., 2007. BMC Biotechnol. 7: 47, specifically incorporated herein by reference in its entirety. Other photosynthetic tissue-enhanced promoters of interest include those from the maize aldolase gene FDA (U.S. patent publication no. 20040216189, specifically incorporated herein by reference in its entirety), and the aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al., 2000. Plant Cell Physiol. 41:42-48, specifically incorporated herein by reference in its entirety). Other tissue enhanced promoters or inducible promoters are also envisioned that may be used to regulate expression of AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade member polypeptides and improve photosynthetic resource use efficiency in a variety of plants.
Example V
Utilities of AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 Clade Sequences for Improving Photosynthetic Resource Use Efficiency, Yield or Biomass
By expressing the present polynucleotide sequences in a commercially valuable plant, the plant's phenotype may be altered to one with improved traits related to photosynthetic resource use efficiency or yield. The sequences may be introduced into the commercially valuable plant, by, for example, introducing the polynucleotide in an expression vector or cassette to produce a transgenic plant, or by crossing a target plant with a second plant that comprises said polynucleotide. The transgenic or target plant may be any valuable species of interest, including but not limited to a crop or model plant such as a wheat, Setaria , corn (maize), rice, barley, rye, millet, sorghum, sugarcane, miscane, turfgrass, Miscanthus , switchgrass, soybean, cotton, rape, oilseed rape including canola, Eucalyptus , or poplar plant. The present polynucleotide sequences encode an AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptide sequence and the ectopic expression or overexpression in the transgenic or target plant of any of said polypeptides, for example, any of SEQ ID NOs: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209, or a polypeptide comprising the consensus sequence AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptide comprises a consensus sequence of SEQ ID NO: 1467, 1468, 1469 of the AtNAC6 clade, SEQ ID NO: 1558, 1559, 1560, 1561 of the WRKY17 clade, SEQ ID NO: 981, 982, 983, 984, 985, 986 of the AtNPR3 clade, SEQ ID NO: 1153, 1154 of the AtMYC1 clade, SEQ ID NO: 129, 130, or 133 of the AtMYB19 clade, SEQ ID NO: 579, 580, 581 of the ERF058 clade, SEQ ID NO: 441, 442 of the CRF1 clade, SEQ ID NO: 1299, 1300 of the WRKY3 clade, SEQ ID NO: 1646, 1647, 1648, of the ZAT11 clade, SEQ ID NO: 834, 835, 836 of the MYB111 clade, SEQ ID NO: 687 of the SPATULA clade, or SEQ ID NO: 302, 303, 304, 305 of the AtMYB50 clade, can confer improved photosynthetic resource use efficiency or yield in the plant. For plants for which biomass is the product of interest, increasing the expression level of AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade of polypeptide sequences may increase yield, photosynthetic resource use efficiency, vigor, growth rate, and/or biomass of the plants. Thus, it is thus expected that these sequences will improve yield and/or photosynthetic resource use efficiency in non- Arabidopsis plants relative to control plants. This yield improvement may result in yield increases of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30% or greater yield relative to the yield that may be obtained with control plants.
It is expected that the same methods may be applied to identify other useful and valuable sequences that are functionally-related and/or closely-related to the listed sequences or domains provided in Tables 2 through 21, and the sequences may be derived from diverse species. Because of morphological, physiological and photosynthetic resource use efficiency similarities that may occur among AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50-related sequences, the AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade sequences are expected to increase yield, plant growth, vigor, size, biomass, and/or increase photosynthetic resource use efficiency to a variety of crop plants, ornamental plants, and woody plants used in the food, ornamental, paper, pulp, lumber or other industries.
Example VI
Expression and Analysis of Increased Yield or Photosynthetic Resource Use Efficiency in Non- Arabidopsis or Crop Species
Northern blot analysis, RT-PCR or microarray analysis of the regenerated, transformed plants may be used to show expression of a polypeptide or the instant description and related genes that are capable of inducing improved photosynthetic resource use efficiency, and/or larger size.
After a eudicot plant, monocot plant or plant cell has been transformed (and the latter plant host cell regenerated into a plant) and shown to have greater photosynthetic resource use efficiency, and/or greater size, vigor, biomass, and/or produce greater yield relative to a control plant, the transformed monocot plant may be crossed with itself or a plant from the same line, a non-transformed or wild-type monocot plant, or another transformed monocot plant from a different transgenic line of plants.
The function of one or more specific polypeptides of the instant description has been analyzed and may be further characterized and incorporated into crop plants. The ectopic overexpression of one or more of AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptide sequences may be regulated using constitutive, inducible, or tissue-enhanced regulatory elements. Genes that have been examined have been shown to modify plant traits including increasing yield and/or photosynthetic resource use efficiency. It is expected that newly discovered polynucleotide and polypeptide sequences closely related, as determined by the disclosed hybridization or identity analyses, to polynucleotide and polypeptide sequences found in the Sequence Listing can also confer alteration of traits in a similar manner to the sequences found in the Sequence Listing, when transformed into any of a considerable variety of plants of different species, and including dicots and monocots. The polynucleotide and polypeptide sequences derived from monocots (e.g., the rice sequences) may be used to transform both monocot and dicot plants, and those derived from dicots (e.g., the Arabidopsis and soy genes) may be used to transform either group, although it is expected that some of these sequences will function best if the gene is transformed into a plant from the same group as that from which the sequence is derived.
As an example of a first step to determine photosynthetic resource use efficiency, seeds of these transgenic plants may be grown as described above or methods known in the art.
Closely-related homologs of AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 derived from various diverse plant species may be overexpressed in plants and have the same functions of conferring increased photosynthetic resource use efficiency. It is thus expected that structurally similar orthologs of the AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 polypeptide clade, including SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209 can confer increased yield, and/or increased vigor, biomass, or size, relative to control plants. As at least one sequence of the instant description has increased photosynthetic resource use efficiency in Arabidopsis , it is expected that the sequences provided in the Sequence Listing, or polypeptide sequences comprising one of or any of the conserved domains provided in Tables 2 21, will increase the photosynthetic resource use efficiency and/or yield of transgenic plants including transgenic non-A rabidopsis (plant species other than Arabidopsis species) crop or other commercially important plant species, including, but not limited to, non- Arabidopsis plants and plant species such as monocots and dicots, wheat, Setaria , corn (maize), teosinte ( Zea species which is related to maize), rice, barley, rye, millet, sorghum, sugarcane, miscane, turfgrass, Miscanthus , switchgrass, soybean, cotton, rape, oilseed rape including canola, tobacco, tomato, tomatillo, potato, sunflower, alfalfa, clover, 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, watermelon, rosaceous fruits including apple, peach, pear, cherry and plum, and brassicas including broccoli, cabbage, cauliflower, Brussels sprouts, and kohlrabi, currant, avocado, citrus fruits including oranges, lemons, grapefruit and tangerines, artichoke, cherries, endive, leek, roots such as arrowroot, beet, cassava, turnip, radish, yam, and sweet potato, beans, woody species including pine, poplar, Eucalyptus , mint or other labiates, nuts such as walnut and peanut. Within each of these species the Closely-related homologs of AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 may be overexpressed or ectopically expressed in different varieties, cultivars, or germplasm.
The instantly disclosed transgenic plants comprising the disclosed recombinant polynucleotides can be enhanced with other polynucleotides, resulting in a plant or plants with “stacked” or jointly introduced traits, for example, the traits of increased photosynthetic resource use efficiency and improved yield combined with an enhanced trait resulting from expression of a polynucleotide that confers herbicide, insect or and/or pest resistance in a single plant or in two or more parental lines. The disclosed polynucleotides may thus be stacked with a nucleic acid sequence providing other useful or valuable traits such as a nucleic acid sequence from Bacillus thuringensis that confers resistance to hemiopteran, homopteran, lepidopteran, coliopteran or other insects or pests.
Thus, the disclosed sequences and closely related, functionally related sequences may be identified that, when ectopically expressed or overexpressed in plants, confer one or more characteristics that lead to greater photosynthetic resource use efficiency. These characteristics include, but are not limited to, the embodiments listed below.
1. A dicot or monocot transgenic plant that has greater or increased photosynthetic resource use efficiency relative to a control plant;
wherein the transgenic plant comprises an exogenous recombinant polynucleotide comprising a constitutive promoter, a non-constitutive promoter, an inducible promoter, a tissue-enhanced promoter, or a photosynthetic tissue-enhanced promoter that regulates expression of a polypeptide having a percentage identity to an amino acid sequence comprising SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209 in a photosynthetic tissue to a level that is effective in conferring greater photosynthetic resource use efficiency in the transgenic plant relative to the control plant;
wherein the percentage identity is at least:
28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identity to the entire length of any of SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209; and/or 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identity to any of: a NAM domain of SEQ ID NO:1434, 1435, 1436, 1437, 1438, 1439, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 1450, 1451, 1452, 1453, 1454, 1455, 1456, 1457, 1458, 1459, 1460, 1461, 1462, 1463, 1464, 1465, 1466; or a Plant Zinc Cluster Domain of SEQ ID NO: 1507, 1532, 1533, 1534, 1535, 1536, 1537, 1538, 1539, 1540, 1541, 1542, 1543 1544; or a BTB domain of SEQ ID NO:864 or 923-950; or an ANK domain of SEQ ID NO 864, 951-980; or a Myb or Myb-like DNA binding domain of SEQ ID NO: 2; 61-77, 95-111, 135, 210-285; or a SANT domain of SEQ ID NO: 735-833; or a WRKY Domain of SEQ ID NO: 1156, 1227-1298; 1507, 1545-1557; or a Z-C2H2-1 domain of SEQ ID NO: 1591, 1618-1645; or an AP2 domain of SEQ ID NO: 307, 396-440; 489, 549-578; or a bHLH-MYC_N domain of SEQ ID NO: 1016 or 1073, 1075, 1077, 1079, 1081, 1083, 1085, 1087, 1089, 1091, 1093, 1095, 1097, 1099, 1101, 1103, 1105, 1107, 1109, 1111, 1113, 1115, 1117, 1119, 1121, 1123, 1125, 1127, 1129; and/or

an HLH domain of 625, 666-686, 1016, 1074, 1076, 1078, 1080, 1082, 1084, 1086, 1088, 1090, 1092, 1094, 1096, 1098, 1100, 1102, 1104, 1106, 1108, 1110, 1112, 1114, 1116, 1118, 1120, 1122, 1124, 1126, 1128, 1130; and/or
at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identical to a consensus sequence of
AtNAC6 clade sequences SEQ ID NO: 1467, 1468, 1469, WRKY17 clade sequences SEQ ID NO: 1558, 1559, 1560, 1561, AtNPR3 clade sequences SEQ ID NO: 981 to 986, AtMYC1 clade sequences SEQ ID NO: 1153, 1154, AtMYB19 clade consensus sequences SEQ ID NO: 129, 130, 131, 132, ERF058 clade consensus sequences SEQ ID NO: 579, 580, 581, CRF1 clade consensus sequences SEQ ID NO: 441, 442, WRKY3 clade consensus sequences SEQ ID NO: 1299, 1300, ZAT11 clade consensus sequences SEQ ID NO: 1646, 1647, 1648, MYB111 clade consensus sequences SEQ ID NO: 834, 835, 836, SPATULA clade consensus sequence SEQ ID NO: 687, or AtMYB50 clade consensus sequences SEQ ID NO: 302, 303, 304, 305;
wherein the control plant does not comprise the recombinant polynucleotide; and
wherein expression of the polypeptide under the regulatory control of the promoter confers greater or increased photosynthetic resource use efficiency in the transgenic plant relative to the control plant; and/or
2. The transgenic plant of embodiment 1, wherein the photosynthetic tissue-enhanced promoter is an RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an Os02g09720 promoter, an Os05g34510 promoter, an Os11g08230 promoter, an Os01g64390 promoter, an Os06g15760 promoter, an Os12g37560 promoter, an Os03g17420 promoter, an Os04g51000 promoter, an Os01g01960 promoter, an Os05g04990 promoter, an Os02g44970 promoter, an Os01g25530 promoter, an Os03g30650 promoter, an Os01g64910 promoter, an Os07g26810 promoter, an Os07g26820 promoter, an Os09g11220 promoter, an Os04g21800 promoter, an Os10g23840 promoter, an Os08g13850 promoter, an Os12g42980 promoter, an Os03g29280 promoter, an Os03g20650 promoter, or an Os06g43920 promoter (SEQ ID NO: 1693-1719, respectively), or a functional variant thereof, or a functional fragment thereof, or a promoter sequence that is at least 80% identical to SEQ ID NO: 1693-1719; and/or

3. The transgenic plant of embodiments 1 or 2, wherein:

the recombinant polynucleotide encodes the polypeptide comprising SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209, or the polypeptide is encoded by a second polynucleotide and expression of the polypeptide is regulated by a trans-regulatory element; and/or
4. The transgenic plant of any of embodiments 1 to 3, wherein, relative to the control plant, the transgenic plant has an altered trait that confers the greater photosynthetic resource use efficiency † ; and/or

5. The transgenic plant of any of embodiments 1 to 4, wherein a plurality of the transgenic plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density; and/or

6. The transgenic plant of any of embodiments 1 to 5, wherein the transgenic plant produces a greater yield than the control plant, including, but not limited to a greater yield of vegetative biomass, plant parts, whole plants, shoot vegetative organs/structures (for example, leaves, stems and tubers), roots, flowers and floral organs/structures (for example, bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (for example, vascular tissue, ground tissue, pulped, pureed, ground-up, macerated or broken-up tissue, and the like) and cells (for example, guard cells, egg cells, and the like); and/or

7. The transgenic plant of any of embodiments 1 to 6, wherein the transgenic plant is selected from the group consisting of a corn, wheat, rice, Setaria, Miscanthus , switchgrass, ryegrass, sugarcane, miscane, barley, sorghum, soy, cotton, canola, rapeseed, Crambe, Camelina , sugar beet, alfalfa, tomato, Eucalyptus , poplar, willow, pine, birch and a woody plant; and/or

8. The transgenic plant of any of embodiments 1 to 7, wherein the transgenic plant is morphologically similar at one or more stages of growth, and/or developmentally similar, to the control plant.

9. A method for increasing photosynthetic resource use efficiency in a dicot or monocot plant, the method comprising:
(a) providing one or more transgenic plants that comprise an exogenous recombinant polynucleotide that comprises a constitutive promoter, a non-constitutive promoter, an inducible promoter, a tissue-enhanced promoter, or a photosynthetic tissue-enhanced promoter that regulates a polypeptide comprising SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209; and (b) growing the one or more transgenic plants; and

wherein expression of the polypeptide in the one or more transgenic plants confers increased photosynthetic resource use efficiency relative to a control plant that does not comprise the recombinant polynucleotide; and/or
10. The method of embodiment 9, wherein the photosynthetic tissue-enhanced promoter is an RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an Os02g09720 promoter, an Os05g34510 promoter, an Os11g08230 promoter, an Os01g64390 promoter, an Os06g15760 promoter, an Os12g37560 promoter, an Os03g17420 promoter, an Os04g51000 promoter, an Os01g01960 promoter, an Os05g04990 promoter, an Os02g44970 promoter, an Os01g25530 promoter, an Os03g30650 promoter, an Os01g64910 promoter, an Os07g26810 promoter, an Os07g26820 promoter, an Os09g11220 promoter, an Os04g21800 promoter, an Os10g23840 promoter, an Os08g13850 promoter, an Os12g42980 promoter, an Os03g29280 promoter, an Os03g20650 promoter, or an Os06g43920 promoter (SEQ ID NO: 1693-1719, respectively), or a functional variant thereof, or a functional fragment thereof, or a promoter sequence that is at least 80% identical to SEQ ID NO: 1693-1719; and/or

11. The method of embodiments 9 or 10, wherein an expression cassette comprising the recombinant polynucleotide is introduced into a target plant to produce the transgenic plant; and/or

12. The method of any of embodiments 9 to 11, wherein the transgenic plant has an altered trait that confers the greater photosynthetic resource use efficiency † ; and/or

13. The method of any of embodiments 9 to 12, wherein the transgenic plant is selected for having the increased photosynthetic resource use efficiency relative to the control plant; and/or

14. The method of any of embodiments 9 to 13, wherein the transgenic plant produces a greater yield relative to the control plant; and/or

15. The method of any of embodiments 9 to 14, wherein the plant is selected for having the greater yield relative to the control plant; and/or

16. The method of any of embodiments 9 to 15, wherein a plurality of the transgenic plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density; and/or

17. The method of any of embodiments 9 to 16, wherein the transgenic plant is selected from the group consisting of a corn, wheat, rice, Setaria, Miscanthus , switchgrass, ryegrass, sugarcane, miscane, barley, sorghum, soy, cotton, canola, rapeseed, Crambe, Camelina , sugar beet, alfalfa, tomato, Eucalyptus , poplar, willow, pine, birch and a woody plant; and/or

18. The method of any of embodiments 9 to 17, the method steps further including:

crossing the target plant with itself, a second plant from the same line as the target plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed.
19. A method for producing and selecting a dicot or monocot crop plant with greater yield or greater photosynthetic resource use efficiency than a control plant, the method comprising:
(a) providing one or more dicot or monocot transgenic plants that comprise an exogenous recombinant polynucleotide that comprises photosynthetic tissue-enhanced promoter that regulates a polypeptide comprising SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209, wherein the photosynthetic tissue-enhanced promoter does not regulate protein expression in a constitutive manner; (b) growing a plurality of the transgenic plants; and (c) selecting a transgenic plant that:
has greater photosynthetic resource use efficiency than the control plant, wherein the control plant does not comprise the recombinant polynucleotide; and/or comprises the recombinant polynucleotide; wherein expression of the polypeptide in the selected transgenic plant confers the greater yield of the selected transgenic plant relative to the control plant; and/or

20. The method of embodiment 19, the method steps further including:

(d) crossing the selected transgenic plant with itself, a second plant from the same line as the selected transgenic plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed; and/or

21. The method of embodiment 19 or 20, wherein the transgenic plant is selected for having the increased photosynthetic resource use efficiency relative to the control plant; and/or

22. The method of any of embodiments 19 to 21, wherein a plurality of the selected transgenic plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density; and/or

23. The method of any of embodiments 19 to 22, wherein the selected transgenic plant has an altered trait that confers the greater photosynthetic resource use efficiency † .

24. A method for producing a dicot or monocot crop plant with greater photosynthetic resource use efficiency than a control plant, the method comprising:
(a) providing a dicot or monocot transgenic plant that comprises an exogenous recombinant polynucleotide that comprises a constitutive promoter, a non-constitutive promoter, an inducible promoter, a tissue-enhanced promoter, or a photosynthetic tissue-enhanced promoter that regulates expression of a polypeptide comprising SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209 in a photosynthetic tissue of the transgenic plant to a level that is effective in conferring greater photosynthetic resource use efficiency in the transgenic plant relative to the control plant; and (b) measuring † an altered trait that confers the greater photosynthetic resource use efficiency,
wherein expression of the polypeptide in the selected transgenic plant confers the greater photosynthetic resource use efficiency of the transgenic plant relative to the control plant, thereby producing the crop plant with greater photosynthetic resource use efficiency than the control plant; and/or

25. The method of embodiment 24, wherein the transgenic plant is selected for having the increased photosynthetic resource use efficiency relative to the control plant.

26. A method for producing a monocot plant with increased grain yield, said method including:

(a) providing a monocot plant cell or plant tissue with stably integrated, exogenous, recombinant polynucleotide comprising a promoter (for example, a constitutive, a non-constitutive, an inducible, a tissue-enhanced, or a photosynthetic tissue-enhanced promoter) that is functional in plant cells and that is operably linked to an exogenous or an endogenous nucleic acid sequence that encodes SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209 or an AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptide, wherein the AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptide is expressed in a photosynthetic tissue of the transgenic plant to a level that is effective in conferring greater photosynthetic resource use efficiency in the transgenic plant relative to a control plant that does not contain the recombinant polynucleotide; (b) generating a plant from the plant cell or the plant tissue, wherein the plant comprises the recombinant polynucleotide; (c) growing the plant; and (d) measuring † an increase in photosynthetic resource use efficiency of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 2%, 28%, 29%, or 30% relative to the control plant, or an increase in grain yield of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 2%, 28%, 29%, or 30% or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 bushels per acre; thereby producing the monocot plant with increased grain yield relative to the control plant; and/or

27. The method of embodiment 26, wherein the AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptide comprises a consensus sequence of SEQ ID NO: 1467, 1468, 1469 of the AtNAC6 clade, SEQ ID NO: 1558, 1559, 1560, 1561 of the WRKY17 clade, SEQ ID NO: 981, 982, 983, 984, 985, 986 of the AtNPR3 clade, SEQ ID NO: 1153, 1154 of the AtMYC1 clade, SEQ ID NO: 129, 130, or 133 of the AtMYB19 clade, SEQ ID NO: 579, 580, 581 of the ERF058 clade, SEQ ID NO: 441, 442 of the CRF1 clade, SEQ ID NO: 1299, 1300 of the WRKY3 clade, SEQ ID NO: 1646, 1647, 1648, of the ZAT11 clade, SEQ ID NO: 834, 835, 836 of the MYB111 clade, SEQ ID NO: 687 of the SPATULA clade, or SEQ ID NO: 302, 303, 304, 305 of the AtMYB50 clade.

28. A transgenic monocot plant produced by the method of embodiment 26; and/or

29. The transgenic monocot plant of embodiment 28, wherein transgenic monocot plant is a corn, wheat, rice, Miscanthus, Setaria , switchgrass, ryegrass, sugarcane, miscane, barley, or sorghum plant; and/or

30. The method of embodiment 26, wherein the promoter is a Cauliflower Mosaic 35S promoter, an


RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an Os02g09720 promoter, an Os05g34510 promoter, an Os11g08230 promoter, an Os01g64390 promoter, an Os06g15760 promoter, an Os12g37560 promoter, an Os03g17420 promoter, an Os04g51000 promoter, an Os01g01960 promoter, an Os05g04990 promoter, an Os02g44970 promoter, an Os01g25530 promoter, an Os03g30650 promoter, an Os01g64910 promoter, an Os07g26810 promoter, an Os07g26820 promoter, an Os09g11220 promoter, an Os04g21800 promoter, an Os10g23840 promoter, an Os08g13850 promoter, an Os12g42980 promoter, an Os03g29280 promoter, an Os03g20650 promoter, or an Os06g43920 promoter (SEQ ID NO: 1693-1719, respectively), or a functional variant thereof, or a functional fragment thereof, or a promoter sequence that is at least 80% identical to SEQ ID NO: 1693-1719; and/or
31. The method of embodiment 28, wherein the AtNAC6, WRKY17, AtNPR3, AtMYC1, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptide has at least:
28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% in its amino acid sequence to the entire length of any of SEQ ID NO: 1369, 1371, 1373, 1375, 1377, 1379, 1381, 1383, 1385, 1387, 1389, 1391, 1393, 1395, 1397, 1399, 1401, 1403, 1405, 1407, 1409, 1411, 1413, 1415, 1417, 1419, 1421, 1423, 1425, 1427, 1429, 1431, 1433; or 1507, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531; or 864, 866, 868, 870, 872, 874, 876, 878, 880, 882, 884, 886, 888, 890, 892, 894, 896, 898, 900, 902, 904, 906, 908, 910, 912, 914, 916, 918, 920, 922; or 1016, 1018, 1020, 1022, 1024, 1026, 1028, 1030, 1032, 1034, 1036, 1038, 1040, 1042, 1044, 1046, 1048, 1050, 1052, 1054, 1056, 1058, 1060, 1062, 1064, 1066, 1068, 1070, 1072; or: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34; or 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548; or 307, 309, 311, 313, 315, 317, 319, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 351, 353, 355, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 385, 387, 389, 391, 393, 395; or 1156, 1158, 1160, 1162, 1164, 1166, 1168, 1170, 1172, 1174, 1176, 1178, 1180, 1182, 1184, 1186, 1188, 1190, 1192, 1194, 1196, 1198, 1200, 1202, 1204, 1206, 1208, 1210, 1212, 1214, 1216, 1218, 1220, 1222, 1224, 1226; or 1591, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617; or 735, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783; or 625, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665; or 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, or 209; or
37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identity in its amino acid sequence to any of
a NAM domain of SEQ ID NO:1434, 1435, 1436, 1437, 1438, 1439, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 1450, 1451, 1452, 1453, 1454, 1455, 1456, 1457, 1458, 1459, 1460, 1461, 1462, 1463, 1464, 1465, 1466; or
a Plant Zinc Cluster Domain of SEQ ID NO: 1507, 1532, 1533, 1534, 1535, 1536, 1537, 1538, 1539, 1540, 1541, 1542, 1543 1544; or
a BTB domain of SEQ ID NO:864 or 923-950; or
an ANK domain of SEQ ID NO 864, 951-980; or
a Myb or Myb-like DNA binding domain of SEQ ID NO: 2; 61-77, 95-111, 135, 210-285; or
a SANT domain of SEQ ID NO: 735-833; or
a WRKY Domain of SEQ ID NO: 1156, 1227-1298; 1507, 1545-1557; or
a Z-C2H2-1 domain of SEQ ID NO: 1591, 1618-1645; or
an AP2 domain of SEQ ID NO: 307, 396-440; 489, 549-578; or
a bHLH-MYC_N domain of SEQ ID NO: 1016 or 1073, 1075, 1077, 1079, 1081, 1083, 1085, 1087, 1089, 1091, 1093, 1095, 1097, 1099, 1101, 1103, 1105, 1107, 1109, 1111, 1113, 1115, 1117, 1119, 1121, 1123, 1125, 1127, 1129; and/or
an HLH domain of 625, 666-686, 1016, 1074, 1076, 1078, 1080, 1082, 1084, 1086, 1088, 1090, 1092, 1094, 1096, 1098, 1100, 1102, 1104, 1106, 1108, 1110, 1112, 1114, 1116, 1118, 1120, 1122, 1124, 1126, 1128, 1130.
† In the above embodiments 4, 12, 23, and 24, greater photosynthetic resource use efficiency may be characterized by or measured as, but is not limited to, any one or more of following measurements or characteristics relative to a control plant. The measured or altered trait may be selected from the group consisting of:
(a) increased photosynthetic capacity, measured as an increase in the rate of light-saturated photosynthesis of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, or 40% when compared to the rate of light-saturated photosynthesis of a control leaf at the same leaf-internal CO 2 concentration. Optionally, measurements are made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; and/or (b) increased photosynthetic rate, measured as an increase in the rate of light-saturated photosynthesis of at least 5%, 10%, 15%, 19%, 20%, 22%, 23%, 25%, 30%, 32%, 35%, or 40%. Optionally, measurements are made after 40 minutes of acclimation to a light intensity known to be saturating for photosynthesis; and/or (c) a decrease in the chlorophyll content of the leaf of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, or 40%, observed in the absence of a decrease in photosynthetic capacity; and/or (d) a decrease in the percentage of the leaf dry weight that is nitrogen of at least 0.5%, 1.0%, 1.5%, 2.0%, 2.5%, 3.0%, 3.5%, or 4.0% observed in the absence of a decrease in photosynthetic capacity or increase in dry weight; and/or (e) increased transpiration efficiency, measured as an increase in the rate of light-saturated photosynthesis relative to water loss via transpiration from the leaf, of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, or 40%; optionally, measurements are made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m −2 s −1 ; and/or (f) an increase in the resistance to water vapor diffusion out of the leaf that is exerted by the stomata, measured as a decrease in stomatal conductance to H 2 O loss from the leaf of at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, or 40%; optionally, measurements were are after 40 minutes of acclimation to a light intensity of 700 μmol PAR m-2 s-1; and/or (g) a decrease in the resistance to carbon dioxide diffusion into the leaf that is exerted by the stomata, measured as an increase in stomatal conductance of at least 5%, 10%, 13%, 15%, 20%, 25%, 27%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, or 68%; optionally, measurements were are after 40 minutes of acclimation to a light intensity of 700 μmol PAR m-2 s-1; and/or (h) a decrease in non-photochemical quenching of at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, or at least 10%, for leaf measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m −2 s −1 ; and/or (i) a decrease in the ratio of the carbon isotope 12 C to 13 C found in either all the dried above-ground biomass, or specific components of the above-ground biomass, e.g., leaves or reproductive structures, of at least 0.5‰ (0.5 per mille), or at least 1.0‰, 1.5‰, 2.0‰, 2.5‰, 3.0‰, 3.5‰, or 4.0‰ measured as a decrease in the ratio of 12 C to 13 C relative to the controls with both ratio being expressed relative to the same standard; and/or (j) an increase in the total dry weight of above-ground plant material of at least 5%, 10%, 15%, 20%, 23%, 25%, 30%, 32%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, or 75%.

All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
The present invention is not limited by the specific embodiments described herein. The invention now being fully described, it will be apparent to one of ordinary skill in the art that many changes and modifications can be made thereto without departing from the spirit or scope of the appended claims. Modifications that become apparent from the foregoing description and accompanying figures fall within the scope of the claims.