WO2014093614A2 - Photosynthetic resource use efficiency in plants expressing regulatory proteins ii - Google Patents

Abstract

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.

Description

PHOTOSYNTHETIC RESOURCE USE EFFICIENCY IN PLANTS EXPRESSING

REGULATORY PROTEINS II

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. . Exp. Bot. 58:119-130; Passioura, 2007. . 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. . 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. . 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. . 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 ¹³C carbon isotope to the ¹²C carbon isotope in those tissues. The theory that underlies this means to estimating WUE is that during photosynthesis, incorporation of C into the products of photosynthesis is slower than the lighter isotope ¹²C. Effectively, ¹³C is discriminated against relative to ¹²C during photosynthesis, an effect that is integrated over the life of the plant resulting in biomass with a distinct ¹³C/¹²C 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 ¹³C0₂ molecule being larger. Significantly, the discrimination by Rubisco is not constant, but varies depending on the C0₂ concentration within the leaf. At high C0₂ concentration discrimination by Rubisco is highest, however as C0₂ concentration decreases discrimination decreases. Because the C0₂ concentration within the leaf is overwhelmingly dependent on the balance between C0₂ influx through the stomatal pore and the rate of photosynthesis, and because the stomatal pore controls the rate of transpiration from the leaf, the ¹³C/¹²C 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, AtMYCl, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade (recombinant polynucleotides encoding AtNAC6, WRKY17, AtNPR3, AtMYCl, 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 Fig. 1, 2A-2I, 5, 6A-6J, 7, 8A-8I, 10, 11A-11H, 13, 14A-14L, 15, 16A-16J, 17, 18A-18L, 20, 21A-210, 23, 24A-240, 28, 29A-29I, 32, 33A-33H, 35, and 36A- 36E).

The recombinant polynucleotide that encodes an AtNAC6, WRKY17, AtNPR3, AtMYCl, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB 111, 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 6x 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, AtMYCl, AtMYB 19, ERF058, CRF1, WRKY3, ZAT11, MYB 111, 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 ( lant 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 (ΆΡ2 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 (ΆΡ2 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 (ΆΝΚ 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 AtMYCl 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 CRFl 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 AtMYCl 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 CRFl 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 MYB 111 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 July 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 Figure 1, a phylogenetic tree of the AtMYB 19 (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. AtMYB 19 appears in the oval. An ancestral sequence of AtMYB 19 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".

Figures 2A-2I show an alignment of the AtMYB 19 (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.

Figure 3 presents a plot of photosynthetic capacity at growth temperature, showing increased light saturated photosynthesis (A_sat) over a range of leaf, sub-stomatal C0₂ concentration (Q ), in five AtMYB19 overexpression lines, 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 nine replicate plants for each line.

Figure 4 presents a plot of photosynthetic capacity at growth temperature showing increased A_sat over a range of leaf, sub-stomatal C_\ in five AtMYB19 overexpression lines, compared to a control line. Data were collected over a range of C_\ 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

o AtMYB 19-Line 2

O AtMYB 19-Line 3

Δ AtMYB 19-Line 6

□ AtMYB 19-Line 7

AtMYB 19-Line 8 In Figure 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_Os01gl 8240.1 and POPTR_0013s00290.1 (indicated by the box around these sequences).

Figures 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 Figure 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).

Figures 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.

13

Figure 9 shows the δ 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

13

δ C (control +). Data were collected over two screening runs. In Figure 10, a phylogenetic tree of ERF058 or AT 1G22190.1 (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_0005s 16690.1 (indicated by the box around these sequences).

Figures 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. 1 lD-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.

Figure 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

13 12 a separate and subsequent analysis lines 1-5 to the right of the control bars), the ratio of C to C in the

13 12

plant material was generally increased relative to control lines (that is, the ratio of C to C was generally less negative relative to a standard control plant). This directional change was consistent with

13

decreased discrimination against C during photosynthesis, the consequence of a lower concentration of C0₂ within the leaf and indicative of an increase in water-use efficiency integrated over the life of the plant's rosette.

In Figure 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 Bradilg48400.1_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". Figures 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 X¹ is E or Q; X² is R or K; X³ is G or S; X⁴ is I, V, L, or M; X⁵ is E or D; X⁶ is Q or H; X⁷ is Q or K; X⁸ is I, V, L, M, or absent; and X⁹ 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 Figure 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. MYBl l l 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_Os01gl9970.1 and Glymal5gl5400.1 (indicated by the dashed box around these sequences). A related clade is represented by the node indicated by arrow "B".

Figures 16A-16J show an alignment of MYB111 and representative clade-related proteins. The

MYBl l l 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 Figure 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 Glymal5gl3320. A related clade is represented by the node indicated by arrow "B".

Figures 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 Figs 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 NPRl-like C domain, in Figs. 18H-18I (SEQ ID NO: 986).

Figure 19: Plot showing increased rate of light saturated photosynthesis (A_sat) over a range of leaf sub-stomatal C0₂ concentration ( ) 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 Figure 20, a phylogenetic tree of AtMYCl 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 AtMYCl clade members appear in the large box with the solid line boundary. AtMYCl (AT4G00480.1) appears in the rounded rectangle. An ancestral sequence of AtMYCl and closely-related sequences is represented by the node of the tree indicated by the arrow "A" in Fig. 20. AtMYCl 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_0003s0012810.1 (indicated by the box around these sequences). A related clade is represented by the node indicated by arrow "B".

Figures 21A-210 show an alignment of AtMYCl and representative clade -related proteins. The

AtMYCl 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. 21 A-21D (SEQ ID NO: 1153) and Fig. 21K (SEQ ID NO: 1154).

Figure 22 shows increased rate of light saturated photosynthesis (A_sat) over a range of leaf, sub- stomatal C0₂ concentration ( ) in five AtMYCl overexpression lines (line 1-5), compared to a control line. Data were collected over a range of Q 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 (o). Line 5 is represented by open diamonds (0).

In Figure 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 Bradilg07970.1 and Solyc03g 104810.2.1.

Figures 24A-240 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.-

Figure 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 C0₂ concentration (CO 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 μηιοΐ 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 (o) show results for WRKY3-line 3 (1), black circles (·) show results for WRKY3-line 3 (2), and white diamonds (0) show results for WRKY3-line 4 (2). Lines identified with a Ί ' 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.

Figure 26 Photosynthetic capacity at 35 °C: Plot showing increased rate of light-saturated photosynthesis (A_sat) at a given leaf, sub-stomatal C0₂ concentration (CO 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 μηιοΐ 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 (o) show results for WRKY3-line 3 (1), black circles (·) show results for WRKY3-line 3 (2), and white diamonds (0) show results for WRKY3-line 4 (2). Lines identified with a T 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.

Figure 27 shows increased light saturated photosynthesis (A_sat) over a range of leaf sub-stomatal C0₂ concentration (Q ), in two WRKY3 overexpression lines (lines 2 and 3), compared to a control line. Data were collected over a range of Q 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 (0).

In Figure 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.

Figures 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 Fig. 29D and 29E, respectively.

Figure 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 C0₂ concentration (Q), in three AtNAC6 overexpression lines, as 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 six replicate plants for each line.

Figure 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 C0₂ concentration ( ), in three AtNAC6 overexpression lines, compared to a control line. Data were collected over a range of 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

O AtNAC6-Line 4

In Figure 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_Os08gl3840.1 and Solycl2g096350.1.1 (indicated by the box around these sequences). A related clade is represented by the node indicated by arrow "B".

Figures 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 Fig. 33E-33F and 33F-33G, 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).

Figure 34 is a plot of photosynthetic capacity at growth temperature showing increased light- saturated photosynthesis (A_sat) over a range of leaf, sub-stomatal C02 concentration (Q), in three independent WRKY 17 overexpression lines and a control line. Data were collected over a range of Q 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:

O Control

Δ WRKY 17-Line 1

O WRKY17-Line 2

□ WRKY17-Line 3

<D Control (repeat)

Δ WRKY17-Line 1 (repeat)

In Figure 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 Bradilg03810.1 and Solyc05g054650.1.1.

Figures 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. Figure 37 shows increased light saturated photosynthesis (A_sat) over a range of leaf sub-stomatal C0₂ concentrations (Ci), in four out of five ZATl 1 overexpression lines, compared to a control line. Data were collected over a range of Q 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

O ZATl l-Line l

• ZAT11-Line 2

Δ ZATl 1-Line 3

■ Z AT 11 -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 2A-2I, 6A-6J, 8A-8I, 11A- 11H, 14A-14L, 16A-16J, 18A-18L, 21A-210, 24A-240, 29A-29I, 33A-33H, and 36 A- 36E 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, CA).

"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, AtMYCl clade, AtMYB19 clade, ERF058 clade, CRF1 clade, WRKY3 clade, ZAT11 clade, MYB 111 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 Fig. 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, AtMYCl, 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, WRKY 17 clade, AtNPR3 clade, AtMYCl clade, AtMYB 19 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, AtMYCl clade, AtMYB 19 clade, ERF058 clade, CRF1 clade, WRKY3 clade, ZAT11 clade, MYB 111 clade, SPATULA clade, and AtMYB 50 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, WRKY 17 clade, AtNPR3 clade, AtMYCl clade, AtMYB19 clade, ERF058 clade, CRFl clade, WRKY3 clade, ZAT11 clade, MYB 111 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, WRKY 17, AtNPR3, AtMYCl, AtMYB19, ERF058, CRFl, WRKY3, ZATl l, MYBl l l, 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, AtMYCl 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. patent 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. patent no. 7,365,186, or U.S. patent 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

12 13

antennae, a decrease in the ratio of the carbon isotope C to 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-l,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 C0₂ 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-l,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 C0₂ 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 C0₂ diffusion into, and H₂0 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 C0₂ 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. U S A. 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. U S A. 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; Ulker 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 Miiller 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

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. patent 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. . 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, AtMYCl 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, MYB 111 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, AtMYCl, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptides or sequences in the AtNAC6, WRKY17, AtNPR3, AtMYCl, 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. . 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, New York, 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. patent 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. patents 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. patent 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, AtMYCl, AtMYB19, ERF058, CRFl, WRKY3, ZATl l, MYB l l l, SPATULA, and AtMYB50 clade polypeptide sequences, would also perform similar functions when ectopically expressed.

Background Information for the AtNAC6 clade, WRKY17 clade, AtNPR3 clade, AtMYCl clade, AtMYB19 clade, ERF058 clade, CRFl clade, WRKY3 clade, ZATl l clade, MYBl l l 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, AtMYCl, AtMYB 19, ERF058, CRFl, WRKY3, ZATl l, MYBl l l, 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, AtMYCl, AtMYB19, ERF058, CRFl, WRKY3, ZATl l, MYB 111 , 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, AtMYCl , AtMYB 19, ERF058, CRF1 , WRKY3, ZAT11 , MYB 111 , 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 of AtMYB 19 and closely related sequences

PGLKHGMFS REEEET

WSPEEDQRLKNYVLQ

HGHPCWSSVPINAGL

Cc/clementineO. 48%

14 22-82 QRNGKSCRLRWINYL 67 77% (47/61) 9_033485m (115/237)

RPGLKRGVFNMQEEE

T

WS PEEDQRLRN Y VLK

Pt/POPTR_001 50% HGHGCWS S VPINAGL

16 22-82 68 77% (47/61) 5sl3190.1 (109/217) QRNGKSCRLRWINYL

RPGLKRGTFS AQEEET

WS PEEDQKLRN Y VLK

Eg/EUCGR.KO 49% HGHGCWS SVPINTGL

18 18-78 69 76% (46/60)

0250.1 (107/217) QRNGKSCRLRWINYL

RPGLKRGMFTMEEEEI

WSPEEDQRLRNYILNH

Eg/EUCGR.KO 48% GHGYWSSVPINTGLQ

20 18-78 70 75% (45/60)

0251.1 (110/226) RNGKSCRLRWINYLR

PGLKRGMFTLEEEEI

WSPEEDQRLGSYVFQ

Pt/POPTR_001 48% HGHGCWS S VPINAGL

22 52-112 71 75% (46/61) 2s 13260.1 (109/223) QRTGKSCRLRWINYL

RPGLKRGAFSTDEEET

WS PEEDNKLRNHIIKH

Gm Glymal6g3 48% GHGCWS S VPIKAGLQ

24 18-78 72 75% (46/61)

1280.1 (116/238) RNGKSCRLRWINYLR

PGLKRGVFSKHEEDT

WS PEEDNKLRNHIIKH

Gm Glyma09g2 49% GHGCWS S VPIKAGLQ

26 18-78 73 73% (45/61)

5590.1 (103/209) RNGKSCRLRWINYLR

PGLKRGVFSKHEKDT

WS PDEDDRLKN YMIK

Sl/Solyc03g025 40% HGHGCWS S VPINAGL

28 19-79 74 73% (44/60)

870.2.1 (115/283) QRNGKSCRLRWINYL

RPGLKRGAFSLEEEDI

WS PEED ARLRNY VLK

Vv/GSVIVTOIO 42% YGLGCWSSVPVNAGL

30 20-80 75 72% (44/61) 28984001 (115/272) QRNGKSCRLRWINYL

RPGLKRGMFTIEEEET

WS PDEDQRLRN YIHK

Eg/EUCGR.AO 51 % HGYSCWSSVPINAGL

32 18-78 76 70% (44/61)

2796.1 (112/217) QRNGKSCRLRWINYL

RPGLKRGAFTVQEEET

WSPEEDEKLRSHVLK

At/AT3G48920. 51 %) YGHGCWSTIPLQAGL

34 23-83 77 69% (41-59)

1 (99/191) QRNGKSCRLRWVNYL

RPGLKKSLFTKQEETI

Table 3. Conserved second M b DNA bindin domains of AtMYB 19 and closel related se uences

in Col. 1 to amino acid Myb 5 to Myb DNA AtMYB 19 coordinates domain binding domain

2 of AtMYB 19

FSEEEEETILTLHSSL

At/AtMYB 19 100%

70-112 GNKWS RI AK YLPGRT 95 100% (43/43) AT5G52260.1 (268/268)

DNEIKNYWHSYL

ISAEEEETILTFHSSLG

At/ 60%

68-110 NKWSQIAKFLPGRTD 96 88% (37/42)

AT4G25560.1 (169/280)

NEIKNYWHSHL

FSREEEETVMNLHAT

Os/LOC_Os04g 48%

71-113 MGNKWSQIARHLPG 97 72% (31/43) 45020.1 (96/200)

RTDNEVKNYWNSYL

FSQEEEETVMSLHAT

Bd/ 53%

71-113 LGNKWS RI AQHLPGR 98 76% (33/43)

Bradi5g 16672.1 (102/192)

TDNEVKNYWNSYL

FSPEEEETVMSLHAT

Zm GRMZM2 50%

71-113 LGNKWS RI ARHLPGR 99 76% (33/43) G170049_T01 (97/191)

TDNEVKNYWNSYL

FSREEEETVMSLHAK

48%

Si/SiO 12304m 71-113 LGNKWS QI ARHLPGR 100 74% (32/43)

(98/202)

TDNEVKNYWNSYL

FNMQEEETILTVHRL

Cc/clementineO. 48%

75-117 LGNKWSQIAQHLPGR 101 76% (33/43) 9_033485m (115/237)

TDNEIKNYWHSHL

FS AQEEETIL ALHHM

Pt/POPTR_001 50%

75-117 LGNKWSQIAQHLPGR 102 79% (34/43) 5sl3190.1 (109/217)

TDNEIKNHWHSYL

FTMEEEEIIFSLHHLIG

Eg/EUCGR.KO 49%

71-113 NKWSQIAKHLPGRTD 103 74% (32/43) 0250.1 (107/217)

NEIKNHWHSYL

FTLEEEEIILSLHRLIG

Eg/EUCGR.KO 48%

71-113 NKWSQIAKHLPGRTD 104 76% (33/43) 0251.1 (110/226)

NEIKNHWHSYL

FS TDEEETILTLHRML

Pt/POPTR_001 48%

105-147 GNKWSQIAQHLPGRT 105 81 % (35/43) 2s 13260.1 (109/223)

DNEIKNHWHSYL

FS KHEEDTIM VLHHM

Gm Glymal6g3 48%

71-113 LGNKWSQIAQHLPGR 106 76% (33/43) 1280.1 (116/238)

TDNEIKNYWHSYL

FSKHEKDTIMALHH

Gm/Glyma09g2 49% MLGNKWSQIAQHLP

71-113 107 72% (31/43) 5590.1 (103/209) GRTDNEVKNYWHSY

L

FSLEEEDIILTLHAMF

Sl/Solyc03g025 40%

72-114 GNKWSQIAQQLPGRT 108 76% (33/43) 870.2.1 (115/283)

DNEIKNHWHSYL

FTIEEEETIMALHRLL

Vv/GSVIVTOl 42%

73-115 GNKWSQIAQNFPGRT 109 74% (32/43) 028984001 (115/272)

DNEIKNYWHSCL

FTVQEEETILNLHHLL

Eg/EUCGR.AO 51 %

71-113 GNKWSQIAQHLPGRT 110 76% (33/43) 2796.1 (112/217)

DNEIKNHWHSYL FTKQEETILLSLHSML

At/AT3G48920. 51 %

34 76-118 GNKWSQISKFLPGRT 111 72% (31/43)

1 (99/191)

DNEIKNYWHSNL

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; SI - 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 AtMYB 19-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants. These "functionally- related and/or closely-related" AtMYB 19 clade polypeptides generally contain the consensus sequence of the Myb DNA binding domain 1 of SEQ ID NO: 129:

WSPX'EDxxLxxxX^xxGxxxWX^ X²PxxxGLQRxGKSCRLRWX²NYLRPGLKxxxxxxxE;

where x represents any amino acid;

X¹ is D or E;

X² is I, V, L or M;

and X³ represents S or T;

as provided in Fig. 2B-2C.

Other highly conserved residues found in the Myb DNA binding domain 2 of AtMYB 19 clade members, as shown in Fig. 2C-2D and SEQ ID NO: 130:

ExxxX¹xxxHxxxGNKWSxIX²xxxPGRTDNEX¹KNxWxSxL

where x represents any amino acid;

X¹ is I, V, L or M; and

X² 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'W

where x represents any amino acid; and

X¹ 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 AtMYB 19 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 "AtMYB 19 clade polypeptides" or "AtMYB 19 clade polypeptides", or which fall within the "AtMYB 19 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 binding domain of AtMYB50 and closely related sequences

YL

KGLWSPEEDEKLLNYI

GmJ

90% TKHGHGC WS S VPKL A

147 Glyma20g22230 14-61 232 98% (47/48)

(121/135) GLQRCGKS CRLRWIN

.1

YL

KGLWSPEEDEKLLNYI

At/ 64% TRHGHGCWSSVPKLA

139 14-61 214 96% (46/48)

AT5G26660.1 (131/206) GLQRCGKS CRLRWIN

YL

KGLWSPEEDEKLLNYI

Pt/

44% TKHGLGCWS S VPKLA

153 POPTR_0013sO 14-61 218 96% (46/48)

(192/444) GLQRCGKS CRLRWIN

0290.1

YL

KGLWSPEEDEKLLNHI

GmJ

91 % TKHGHGC WS S VPKLA

141 Glymal0g28250 14-61 216 96% (46/48)

(1 19/132) GLQRCGKS CRLRWIN

.1

YL

KGLWSPEEDEKLLNYI

Pt/

45% TKHGHGCWSSVPKQA

143 POPTR_0005sO 14-61 230 94% (45/48)

(196/440) DLQRCGKS CRLRWIN

0340.1

YL

KGLWSPEEDEKLMNH

ZmJ

87% ITKHGHGC WS S VPKL

185 GRMZM2G171 14-61 260 94% (45/48)

(1 16/134) AGLQRCGKS CRLRWI

781_T01

NYL

KGLWSPEEDEKLMNH

Os/

89% ITKHGHGC WS S VPKL

191 LOC_Os05g048 14-61 266 94% (45/48)

(1 18/134) AGLQRCGKS CRLRWI

20.1

NYL

KGLWSPEEDEKLLTHI

At/ 58% TNHGHGC WS S VPKLA

137 14-61 212 92% (44/48)

AT1G09540.1 (21 1/367) GLQRCGKS CRLRWIN

YL

KGLWSPEEDEKLLNYI

Eg/ 75% TTYGHGCWSAVPKLA

149 14-61 226 92% (44/48)

Eucgr.H01337.1 (124/166) GLQRCGKS CRLRWIN

YL

KGLWSPEEDEKLLNYI

Eg/ 87% AKFGLGC WS S VPKLA

159 67-1 14 224 92% (44/48)

Eucgr.B01827.1 (1 13/130) GLQRCGKS CRLRWIN

YL

KGLWSPEEDEKLMNH

Os/

82% ITKHGHGC WS T VPKL

165 LOC_Os01gl82 14-61 240 92% (44/48)

(124/153) AGLQRCGKS CRLRWI

40.1

NYL

KGLWSPEEDEKLLMH

Vv/

88% ITK YGHGC WS S VPKL

193 GSVIVT010313 14-61 192 92% (44/48)

(1 16/132) AGLQRCGKS CRLRWI

41001

NYL

KGLWSPEEDEKLMNH

ZmJ

67% ITKHGHGC WS T VPKL

199 GRMZM2G017 14-61 274 92% (44/48)

(128/192) AGLQRCGKS CRLRWI

520_T01

NYL

205 ZmJ 80% 14-61 KGLWSPEEDEKLMNH 280 92% (44/48) GRMZM2G127 (122/153) ITKHGHGC WS S IPKL A

490_T01 GLQRCGKS CRLRWIN

YL

KGLWSPEEDEKLIKHI

SI/

82% TKFGHGC WS S VPKL A

161 SolycOlg 10234 14-61 236 90% (43/48)

(1 18/144) GLQRCGKS CRLRWIN

0.2.1

YL

KGLWSPEEDEKLLRHI

GmJ

66% TKYGHGCWSSVPKQA

163 Glymal9g4101 14-61 238 90% (43/48)

(130/197) GLQRCGKS CRLRWIN

0.1

YL

KGLWSPEEDEKLLRHI

GmJ

89% TKYGHGCWSSVPKQA

181 Glyma02g0096 14-61 256 90% (43/48)

(1 17/132) GLQRCGKS CRLRWIN

0.1

YL

KGLWSPEEDEKLLRHI

Vv/

83% TKYGHGCWSSVPKQA

183 GSVIVT010282 14-61 258 90% (43/48)

(1 19/145) GLQRCGKS CRLRWIN

35001

YL

RGLWSPEEDEKLFRYI

Vv/

78% TEHGHGCWSSVPKQA

155 GSVIVT010177 14-61 220 88% (42/48)

(1 13/145) GLQRCGKS CRLRWIN

16001

YL

RGLWSPEEDEKLMNH

ZmJ

64% IAKYGHGCWS S VPKL

179 GRMZM2G147 14-61 254 88% (42/48)

(103/161) AGLDRCGKS CRLRWI

698_T01

NYL

KGLWCPEEDEKLINH

SI/

80% VTK YGHGC WS S VPKL

203 Solycl0g04468 13-60 278 86% (41/48)

(103/130) A ALQRCGKS CRLRWI

0.1.1

NYL

KGLWSPEEDEKLLRYI

At/ 74% TKYGHGCWSSVPKQA

197 14-73 272 74% (44/60)

AT4G01680.2 (1 19/163) GTFLFIQIHLLFGLQRC

GKSCRLRWINYL

KGLWSPEEDEKLLNYI

Cc/ TKHGHGC WS S VPKL A

42%

143 clementine0.9_0 14-89 GKIYLENNNHACSVIL 228 62% (47/76)

(192/462)

09770m MFNAFNTMFLLAGLQ

RCGKSCRLRWINYL

Table 5. Conserved second Myb DNA binding domains of AtMYB50 and closely relatec sequences

Col. 1 Col. 2 Col. 3 Col. 4 Col. 5 Col. 6 Col. 7

SEQ Species/ Percent Myb DNA Conserved Myb DNA SEQ ID Percent identity ID Identifier identity of binding binding domain 2 NO: of of second Myb NO: polypeptide domain 2 in second domain in Col.

in Col. 1 to amino acid Myb 5 to Myb DNA AtMYB50 coordinates domain binding domain

2 of AtMYB50

RG AFS SEEQNLI VELH

At/AtMYB50 or 100%

135 67-1 12 AVLGNRWSQIAARLP 21 1 100% (44/44) AT1G57560.1 (314/314)

GRTDNEIKNLWNS CI RGAFSPEEENLIVELH

At/ 58%

137 67-112 AVLGNRWSQIASRLP 213 92% (42/46)

AT1G09540.1 (211/367)

GRTDNEIKNLWNS SI

RGAFSQEEEDLIVEL

Os/

82% H A VLGNR WS QI ATRL

165 LOC_Os01gl8 67-112 241 92% (42/46)

(124/153) PGRTDNEIKNLWNSC

240.1

I

Pt/ RGAFSQQEENLIIELH

45%

143 POPTR_0005s0 67-112 AVLGNRWSQIAAQLP 231 90% (41/46)

(196/440)

0340.1 GRTDNEIKNLWNS CI

Pt/ RGAFSQQEENLIIELH

44%

153 POPTR_0013sO 67-112 AVLGNRWSQIAAQLP 219 90% (41/46)

(192/444)

0290.1 GRTDNEIKNLWNS CI

Os/ RGAFSQEEEDLIIELH

89%

191 LOC_Os05g04 67-112 AVLGNRWSQIAAQLP 277 90% (41/46)

(118/134)

820.1 GRTDNEIKNLWNS CI

Zm RGAFSEEEEDLIVELH

67%

199 GRMZM2G017 67-112 AVLGNRWSQIATRLP 275 90% (41/46)

(128/192)

520_T01 GRTDNEIKNLWNS SI

RGAFSQQEENMIVEL

Gml

91 % HA VLGNR WS QI A AQ

141 Glymal0g28250 67-112 217 87% (40/46)

(119/132) LPGRTDNEIKNLWNS

.1

CL

Cc/ RGAFSVQEESLIVELH

42%

145 clementine0.9_0 95-140 AVLGNRWSQIAAQLP 229 87% (40/46)

(192/462)

09770m GRTDNEIKNLWNS SI

RGAFSQQEENMIVEL

Gml

90% HA VLGNR WS QI A AQ

147 Glyma20g22230 67-112 233 87% (40/46)

(121/135) LPGRTDNEIKNLWNS

.1

CL

RGAFSQQEENSIVEL

Gml

86% HA VLGNR WS QI A AQ

157 Glyma03g38660 67-112 223 87% (40/46)

(118/138) LPGRTDNEIKNLWNS

.1

CL

RGAFSQQEESLIIELH

Eg/ 87%

159 120-165 AVLGNRWSQIAAHLP 225 87% (38/44)

Eucgr.B01827.1 (113/130)

GRTDNEIKNLWNSGL

Gml RGTFS QEEENLIIELH

89%

181 Glyma02g0096 67-112 AVLGNRWSQIAAQLP 257 87% (40/46)

(117/132)

0.1 GRTDNEIKNLWNS CL

Vv/ RGAFSQQEESLIIELH

88%

193 GSVIVT01031 67-112 AVLGNRWSQIAAQLP 193 87% (40/46)

(116/132)

341001 GRTDNEIKNLWNS CI

RGAFSQDEENLIIELH

At/ 74%

197 79-124 AVLGNRWSQIAAQLP 273 87% (40/46)

AT4G01680.2 (119/163)

GRTDNEIKNLWNS CL

Zm/ RGAFSQDEEDLIIELH

80%

205 GRMZM2G127 67-112 AVLGNRWSQIAAQLP 281 87% (40/46)

(122/153)

490_T01 GRTDNEIKNLWNS CI

RGAFSHQEENLIIELH

Eg/ 75%

149 67-112 AVLGNRWSQIAARLP 227 85% (39/46)

Eucgr.H01337.1 (124/166)

GRTDNEIKNFWNSSL

Gml 86% RGAFSQQEENSIIELH

151 67-112 235 85% (39/46) Glymal9g41250 (118/138) AVLGNRWSQIAAQLP .1 GRTDNEIKNLWNSCL

SI/ RGTFS QDEENLIIELH

82%

161 SolycOlg 10234 67-112 AVLGNKWSQIAARLP 237 85% (39/46)

(118/144)

0.2.1 GRTDNEIKNLWNS SI

Gml RGTFS QEEETLIIELH

66%

163 Glymal9g4101 67-112 AVLGNRWSQIAAQLP 239 85% (39/46)

(130/197)

0.1 GRTDNEIKNLWNSCL

Zm RGAFAQDEEDLIIELH

87%

185 GRMZM2G171 67-112 AVLGNRWSQIAAQLP 261 85% (39/46)

(116/134)

781_T01 GRTDNEIKNLWNS CI

Vv/ RGTFSLQEENLIIELH

83%

183 GSVIVT01028 67-112 SVLGNRWSQIAAQLP 259 83% (38/46)

(119/145)

235001 GRTDNEIKNLWNSCL

RGAFSQDEESLIIELH

At/ 64%

139 67-112 AALGNRWSQIATRLP 215 81 % (37/46)

AT5G26660.1 (131/206)

GRTDNEIKNFWNSCL

RGAFTGQEEKLIVEL

Vv/

78% HEILGNRWSQIASHL

155 GSVIVT010177 67-112 221 77% (35/46)

(113/145) PGRTDNEIKNQWNS S

16001

I

SI/ RGTFSQQEENLIIQLH

80%

203 Solycl0g04468 66-111 SLLGNKWSQIASRLP 279 77% (35/46)

(103/130)

0.1.1 GRTDNEIKNLWNS SI

Zm RGTFS QEEEDLIIHLH

64%

179 GRMZM2G147 67-112 SLLGNKWSQIAAQLP 255 72% (33/46)

(103/161)

698_T01 GRTDNEVKNFWNSYI

Species abbreviations for Tables 4 and 5: At - Arabidopsis 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:

X¹GLWX²PEEDEKLxxxX³X⁴xxGHGCWSX⁵X³PKxAxX⁸X⁹X¹⁰X⁹X¹¹X¹²X¹¹X¹³X¹⁰X¹⁰X⁹X¹⁴LxRCG KSCRLRWINYLRPDX³X¹RGX⁴FX⁶xxExxxIX³xLHxxX³GNX¹WSQIAX⁶xLPGRTDNEX³KNxWNSx X³KKX¹X³xxX¹GIDPxTHX⁷. *

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:

X¹GLWX²PEEDEKLxxxX³X⁴xxGHGCWSX⁵X³PKxAxX⁸X⁹X¹⁰X⁹X¹¹X¹²X¹¹X¹³X¹⁰X¹⁰X⁹X¹⁴LxRCG KSCRLRWINYL. *

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^X^xExxxD^xLHxxX^NxVSQIAX^LPGRTDNEX^NxWNSxX³. *

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^IDPxTHX⁷. *

*In the above consensus sequences of SEQ ID NO: 302-305, x represents any amino acid; X is K or R; X² is S or C; X³ is I, V, L, or M; X⁴ is T or A; X⁵ is S or T; X⁶ is S, A, or T; X⁷ is K or Q; X⁸ is T or absent; X⁹ is F or absent; X¹⁰ is L or absent; X¹¹ is I or absent; X¹² is Q or absent; X¹³ is H or absent; and X¹⁴ 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_Os01gl 8240.1 and POPTR_0013s00290.1 (indicated by the box around these sequences).

Table 6. Conserved AP2 domain of CRF1 and closely related sequences Col. 3 Col. 7

Col. 4 Col. 6

Col. 1 Col. 2

Percent Col. 5 Percent identity

AP2 SEQ ID

identity of of AP2 domain

SEQ Species/ domain in NO: of

polypeptide Conserved AP2 domain in Col. 5 to AP2 ID Identifier amino acid AP2

in Col. 1 to domain of NO: coordinates domain

CRF1 CRF1

FRGVRQRPWGKWAA

307 At/CRFl or 100% EIRDPSRRVRVWLGT

87-142 396 100% AT4G11140.1 (287/287) FDTAEEAAIVYDNAA (56/56)

IQLRGPNAELNF

Gm Glyma08g0 FRGVRQRPWGKWAA

333 2460.1 43% EIRDPSRRVRLWLGT

109-164 409 90% (125/295) YDTAEEAAIVYDNA (50/56)

AIQLRGADALTNF

Gm Glyma05g3 FRGVRQRPWGKWAA

331 7120.1 39% EIRDPLRRVRLWLGT

109-164 408 88% (125/328) YDTAEEAAIVYDNA (49/56)

AIQLRGADALTNF

Gm Glyma01g4 FRGVRQRPWGKWAA

335 3350.1 38% EIRDPSRRVRLWLGT

107-162 410 88% (109/294) YDTAEEAALVYDNA (49/56)

AIRLRGPHALTNF

Zm GRMZM2G FRGVRRRPWGKYAA

341 044077_T01 44% EIRDPWRRVRVWLG

118-173 413 88% (79/183) TFDT AEE A AKV YDS A (49/56)

AVQLRGRDATTNF

Cc/clementineO. FRGVRQRPWGKWAA

381 9_015380m 43% EIRDPLRRVRLWLGT

120-175 433 88% (131/310) YDTAEEAAMVYDNA (49/56)

AIQLRGPDALTNF

Pt/POPTR_0001 FRGVRQRPWGKWAA

387 S10300.1 43% EIRDPLRRVRLWLGT

130-185 436 88% (138/323) YDTAEEAAMVYDNA (49/56)

AIQLRGPDALTNF

Sl Solyc03g0074 FRGVRQRPWGKWAA

319 60.1.1 49% EIRDPARRVRLWLGT

129-184 402 86% (95/195) YDTAEEAAMVYDNA (48/56)

AIKLRGPDALTNF

Sl Solyc06g0518 FRGVRQRPWGKWAA

321 40.1.1 52% EIRDPARRVRLWLGT

125-180 403 86% (94/182) YDTAEEAAMVYDNA (48/56)

AIKLRGPDALTNF

Gm Glyma04g4 FRGVRQRPWGKWAA

323 1740.1 45% EIRDPARRVRLWLGT

103-158 404 86% (100/227) YDTAEEAAMVYDNA (48/56)

AIRLRGPDALTNF

Gm Glyma06gl FRGVRQRPWGKWAA

325 3040.1 38% EIRDPARRVRLWLGT

102-157 405 86% (114/303) YDTAEEAAMVYDNA (48/56)

AIRLRGPDALTNF

Sl Solyc08g0819 FRGVRQRPWGKWAA

337 60.1.1 40% EIRDPLRRVRLWLGT

138-193 411 86% (128/322) YDTAEEAAMVYDHA (48/56)

AIQLRGPDALTNF Si/Si002247m FRGVRRRPWGKYAA

345 40% EIRDPWRRVRVWLG %

117-172 415 86 (98/251) TFDT AEE A AKV YDS A (48/56)

AIQLRGPDATTNF

Os/LOC_Os01g FRGVRRRPWGKFAA

347 46870.1 61 % EIRDPWRGVRVWLG

103-158 416 86% (61/101) TFDT AEE AARVYDN (48/56)

A AIQLRGPS ATTNF

Cc/clementineO. FRGVRQRPWGKWAA

373 9_013577m 37% EIRDPARRVRLWLGT

126-181 429 86% (125/343) YDTAEEAARVYDNA (48/56)

AIKLRGPDALTNF

Pt/POPTR_0012 FRGVRQRPWGKWAA

377 sO 1260.1 40% EIRDPARRVRLWLGT

183-238 431 86% (109/274) YDTAEEAARVYDNA (48/56)

AIKLRGPDALTNF

Gm/Glymal IgO FRGVRQRPWGKWAA

385 2140.1 42% EIRDPARRVRLWLGT

113-168 435 86% (128/307) YDTAEEAALVYDNA (48/56)

AIKLRGPHALTNF

Pt/POPTR_0003 FRGVRQRPWGKWAA

389 S13610.1 43% EIRDPLRRVRLWLGT

127-182 437 86% (137/322) YDTAEEAAMVYDNA (48/56)

AIQLRGADALTNF

Eg/Eucgr.K0032 FRGVRQRPWGKWAA

391 1.1 43% EIRDPARRVRLWLGT 438 86%

90-145

(101/239) YDTAEEAAMVYDNA (48/56)

AIKLRGPDALTNF

At/AT4G23750. FRGVRQRPWGKWAA

313 1 51 % EIRDPLKRVRLWLGT

122-177 399 84% (177/350) YNTAEEAAMVYDNA (47/56)

AIQLRGPDALTNF

Os/LOC_Os01g FRGVRRRPWGKYAA

339 12440.1 41 % EIRDPWRRVRVWLG

150-205 412 84% (111/273) TFDT AEE AAKVYDT (47/56)

AAIQLRGRD ATTNF

Zm GRMZM2G FRGVRRRPWGKYAA

343 142179_T01 37% EIRDPWRRVRVWLG

-170 414 84%

115

(119/329) TFDT AEE A AKV YDS A (47/56)

AIQLRGAD ATTNF

Zm/ GRMZM2G FRGVRRRPWGKFAA

351 160971_T01 48% EIRDPWRGVRVWLG

89-144 418 84% (72/152) TFDT AEE AARVYDTA (47/56)

AIQLRGANATTNF

Eg/Eucgr.E0083 FRGVRQRPWGKWAA

367 4.1 42% EIRDPKKGTRVWLGT

116-171 426 84% (126/303) FGTAEEAALVYDNA (47/56)

AIQLRGPDALTNF

Eg/Eucgr.A0266 FRGVRQRPWGKWAA

375 9.1 46% EIRDPTRRVRLWLGT

128-183 430 84% (89/195) YDTAEEAAMVYDNA (47/56)

ALKLRGPDAQTNF

Pt/POPTR_0015 FRGVRQRPWGKWAA

379 41 %

S06070.1 130-185 EIRDPARRQRLWLGT 432 84%

(113/281) (47/56)

YDTAEEAARVYDNA AIKLRGPDALTNF

Eg/Eucgr.D0177 FRGVRRRPWGKWAA

383 5.1 45% EIRDPLRRVRLWLGT

122-177 434 84%

(134/302) YDTAEEAAMVYDQA (47/56)

AIQLRGPDALTNF

Bd/Bradi2g0735 FRGVRRRPWGKYAA

393 7.1 35% EIRDPWRRVRVWLG

124-179 439 84%

(115/329) TFDTAEEAARVYDSA (47/56)

AIKLRGPDATVNF

At/AT4G27950. YRGVRQRPWGKWA

315 1 43% AEIRDPEQRRRIWLG

118-173 400 83% (91/213) TFATAEEAAIVYDNA (46/56)

AIKLRGPDALTNF

At/AT5G53290. FRGVRQRPWGKWAA

317 1 50% EIRDPEQRRRIWLGTF 401 83%

125-180

(82/165) ETAEEAAVVYDNAAI (46/56)

RLRGPDALTNF

Gm/Glymal3g0 FRGVRQRPWGKWAA

327 8490.1 37% EIRDPVQRVRIWLGT

108-163 406 83%

(119/322) FETAEEAALCYDNAA (46/56)

IMLRGPDALTNF

Gm Glymal4g2 FRGVRQRPWGKWAA

329 9040.1 40% EIRDPVQRVRIWLGT

103-158 407 83%

(116/292) FKTAEEAALCYDNA (46/56)

AITLRGPDALTNF

Zm GRMZM2G FRGVRRRPWGKFAA

349 151542_T01 43% EIRDPWRGVRVWLG

93-148 417 83%

(67/156) TFDTAEEAARVYDA (46/56)

AAVQLRGANATTNF

Bd/Bradi2g4553 FRGVRRRPWGKYAA

395 0.1 39% EIRDPWRGVRVWLG

99-154 440 83%

(77/200) TFDTAEEAARVYDSA (46/56)

AIQLRGASATTNF

Cc/clementineO. YRGVRMRPWGKWA

365 9_017304m 42% AEIRDPFQRTRVWLG

106-161 425 77%

(77/185) TFETAEEAALVYDQA (43/56)

AIRLKGPHAQTNF

Pt/POPTR_0014 YRGVRQRPWGRWA

371 S09020.1 40% AEIRDPYRRTRVWLG

119-174 428 77%

(84/214) TYDTAEEAAMVYDQ (43/56)

AAIRIKGPDAQTNF

At/AT3G61630. YRGVRQRPWGKFAA

311 1 48% EIRDPS S RTRI WLGTF

105-160 398 77%

(82/174) VTAEEAAIAYDRAAI (43/56)

HLKGPKALTNF

Pt/POPTR_0002 YRGVRQRPWGRWA

369 si 6900.1 43% AEIRDPYRRTRLWLG

107-162 427 75%

(92/215) TYDTAEEAAMVYDQ (42/56)

AAIRIKGPDAQTNF

At/AT2G46310. YRGVRQRPWGKFAA

309 1 47% EIRDPS S RTRL WLGTF

99-154 397 75%

(85/181) ATAEEAAIGYDRAAI (42/56)

RIKGHNAQTNF

353 Os/LOC_Os06g 36% 121-176 FRGVRKRPWGKYGA 419 72% 06540.1 (90/253) EIRVSQQSARVWLGT (40/56)

FDTAEEAARVYDHA ALRLRGPS ATTNF

Zm GRMZM2G YRGVRRRPWGKYAA

355 328197_T01 36% EIRDPHKGERLWLGT 420 72%

103-158

(68/191) FDTAEEAAREYDSAA (40/56)

RRLRGPS ATTNF

Si/Si008428m YRGVRRRPWGKYAA

359 35% EIRDPHKNARVWLGT

94-149 422 72% (112/321) FDTAEEAARMYDSE (40/56)

ARRLRGPS ATTNF

Zm GRMZM2G FRGVRRRPWGRWAA

361 009598_T01 43% EIREPHNRRRLWLGT

80-135 423 70% (60/141) FDTAEEAANAYDAA (39/56)

NIRFRG VS ATTNF

Zm/ GRMZM2G YRGVRRRPWGRYAA

357 429378_T01 38% EIRDPHKGERLWLGT

101-156 421 67% (66/177) FDTAEEAARRYDSET (37/56)

RRLRGPS AITNF

Si/Si037209m FRGVRRRAWGRWA

363 41 % AEIRDPHGSRRIWLG

84-139 424 65% (55/137) TFNSAEEAAAAYDV (36/56)

ANIRFRG AS AHTNF

Species abbreviations for Table 6: At - Arabidopsis 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; 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 CRFl-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" CRFl clade polypeptides generally contain a consensus AP2 domain sequence of the CRFl clade, SEQ ID NO: 441 : X'RGX^XRX^GX^VAEIRXXXXXXRXSVLGTX'XX^EEAAXXYDXXXXXXX^XXAXXNF.*

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

X⁶xX⁶xxxDxxxTX⁸SSX⁹xX⁸*

*In the above consensus sequences of SEQ ID NO: 441-442, x represents any amino acid; X¹ can be F or Y; X² can be P or A; X³ can be R or K; X⁴ can be W, F or Y; X⁵ can be A or G; X⁶ can be I, V, L, or M; X⁷ can be T or S; X⁸ can be D or E; and X⁹ 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 CRFl 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=l-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 "CRFl clade polypeptides" or "G1421 clade polypeptides", or which fall within the "CRFl 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 ΆΡ2 domain' of ERF058 and closel related se uences

TAEEAALAYDKAAYKL

RGDFARLNFPNLRHQ

LYRGVRQRHWGKWVA EIRLPKNRTRLWLGTFD

Sl/Solyc04g054 45%

498 76-141 TAEEAALAYDKAAYKL 553 95% (59/62)

910.2.1 (132/294)

RGEFARLNFPHLRHQLN N

LYRGVRQRHWGKWVA

Pt/POPTR_000 47% EIRLPKNRTRLWLGTFD

502 176-237 555 95% (59/62) 7s05690.1 (132/284) TAEEAALAYDKAAYKL

RGEFARLNFPHLRH

LYRGVRQRHWGKWVA

Sl/Solycl2g056 48% EIRLPKNRTRLWLGTFD

526 124-186 567 95% (60/63)

980.1.1 (150/316) TAEEAALAYDKAAYKL

RGEFARLNFPHLRHN

LYRGVRQRHWGKWVA

Bd/Bradi4g2901 45% EIRLPRNRTRLWLGTFD

528 109-168 568 94% (56/59)

0.1 (126/282) TAEEAALAYDQAAYRL

RGDAARLNFPDN

LYRGVRQRHWGKWVA

Vv/GSVIVTOIO 50% EIRLPKNRTRLWLGTFD

504 94-155 556 93% (58/62)

02262001 (138/281) TAEEAALAYDKAAFKL

RGEFARLNFPNLRH

LYRGVRQRHWGKWVA EIRLPKNRTRLWLGTFD

Gm Glymal4g3 44%

514 150-216 TAEEAALAYDKAAYRL 561 93% (57/61)

4590.1 (140/324)

RGDF ARLNFPSLKG S CP GE

LYRGVRQRHWGKWVA

Pt/POPTR_000 62% EIRLPKNRTRLWLGTFD

520 162-224 564 93% (58/62) 2s09480.1 (125/203) TAEEAALAYDRAAYKL

RGDFARLNFPNLLHQ

LYRGVRQRHWGKWVA

Os/LOC_Os08g 52% EIRLPRNRTRLWLGTFD

530 103-162 569 93% (55/59)

31580.1 (101/197) TAEEAALTYDQAAYRL

RGDAARLNFPDN

LYRGVRQRHWGKWVA EIRLPKNRTRLWLGTFD

Gm Glymal3g0 47%

510 137-203 TAEEAALAYDKAAYRL 559 91 % (56/61)

1930.1 (147/317)

RGDLARLNFPNLKGSCP GE

LYRGVRQRHWGKWVA

Zm GRMZM2G 46% EIRLPRNRTRLWLGTFD

546 113-173 577 91 % (56/61) 113060_T01 (100/219) TAEEAALAYDGAAFRL

RGDSARLNFPELR

LYRGVRQRHWGKWVA

Pt/POPTR_000 53% EIRLPKNRTRLWLGTYD

500 172-233 554 90% (56/62) 5s07900.1 (118/226) TAEEAALAYDNAAYKL

RGEYARLNFPHLRH

LYRGVRQRHWGKWVA

Gm Glyma05g3 45% EIRLPKNRTRLWLGTFD

506 116-178 557 90% (57/63)

1370.1 (141/314) TAEEAALAYDNAAFKL

RGEFARLNFPHLRHH

Gm Glyma08gl 45% LYRGVRQRHWGKWVA

508 120-182 558 90% (57/63)

4600.1 (142/318) EIRLPKNRTRLWLGTFD TAEEAALAYDNAAFKL

RGEFARLNFPHLRHH

LYRGVRQRHWGKWVA

54% EIRLPKNRTRLWLGTFD

534 Si/SiO 17760m 161-221 571 90% (55/61)

(107/201) TAEDAALAYDKAAFRL

RGDMARLNFPALR

LYRGVRQRHWGKWVA

Os/LOC_Os02g 53% EIRLPKNRTRLWLGTFD

536 168-228 572 90% (55/61)

51670.1 (109/209) TAEDAALAYDKAAFRL

RGDLARLNFPTLR

LYRGVRQRHWGKWVA

Zm GRMZM5 G 54% EIRLPRNRTRLWLGTFD

540 173-233 574 90% (55/61) 852704_T01 (108/200) S AED A AL AYDKA AFRL

RGDAARLNFPSLR

LYRGVRQRHWGKWVA

Os/LOC_Os03g 50% EIRLPRNRTRLWLGTFD

544 111-171 576 90% (55/61)

09170.1 (104/211) T AEE A ALA YDS A AFRLR

GESARLNFPELR

LYRGVRQRHWGKWVA

43% EIRLPKNRTRLWLGTFD

548 At/ AT4G39780 92-155 578 89% (57/64)

(120/282) TAEEAAMAYDLAAYKL

RGEFARLNFPQFRHED

LYRGVRQRHWGKWVA

Gm/Glymal8g0 43% EIRLPKNRTRLWLGTFD

512 122-184 560 88% (56/63)

2170.1 (130/306) TAEEAALAYDNAAFKL

RGENARLNFPHLRHH

LYRGVRQRHWGKWVA

Zm GRMZM2G 54% EIRLPKNRTRLWLGTFD

532 147-207 570 88% (54/61) 029323_T01 (106/199) TAEGAALAYDEAAFRL

RGDT ARLNFPS LR

LYRGVRQRHWGKWVA

Bd/Bradi3g5898 52% EIRLPKNRTRLWLGTFD

538 155-215 573 88% (54/61)

0.1 (93/182) AAEDAALAYDKAAFRL

RGDQARLNFPALR

LYRGVRQRHWGKWVA

54% EIRLPRNRTRLWLGTFG

542 Si/Si008385m 173-233 575 88% (54/61)

(108/200) S AED A AL AYDKA AFRL

RGDAARLNFPSLR

LYRGVRQRQWGKWVA

At/AT5G65130. 50% EIRLPKNRTRLWLGTFE

496 110-169 552 85% (51/60)

1 (99/201) TAQEAALAYDQAAHKI

RGDNARLNFPDI

LYRGVRQRHWGKWVA

At/AT2G22200. 48% EIRLPKNRTRLWLGTFE

494 70-133 551 82% (53/64)

1 (101/214) TAEKAALAYDQAAFQL

RGDIAKLNFPNLIHED

Species abbreviations for Table 7: At - Arabidopsis thaliana; Bd - Brachypodium distachyon; Gm - Glycine max; Os - Oryza sativa; Pt- Populus trichocarpa; Si-Setaria italica; SI - 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. 1 ID- 1 IE, 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. 1 lD-1 IE).

LYRGVRQRxVGK AEIRLPX²NRTRLWLGTX³xX⁴AX AAX⁶X⁷YDxAAxX⁸X⁶RGX⁹xAX²LNF

P;

wherein x represents any amino acid; X¹ is Q or H; X² is K or R; X³ is F or Y; X⁴ is A, S or T; X⁵ is Q or E; X⁶ is M, I, L, or V; X⁷ is A or T; X⁸ is K, Q or R; and X⁹ 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:

wherein x represents any amino acid; X⁴ is A, S or T; X⁶ is M, I, L, or V; X¹⁰ is A or S; and X¹¹ is N or D.

There is also a small motif in Fig. 1 lG-11H that is present in ERF058 clade member proteins, and is identifiable as SEQ ID NO: 581 :

LxxxPSxX⁹IX¹²XⁿWxX¹⁰X⁶.

wherein x represents any amino acid; X⁶ is M, I, L, or V; X⁹ is E or D; X¹⁰ is A or S; and X¹¹ is N or D; and X¹² 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_0005s 16690.1 (indicated by the box around these sequences).

Table 8. Conserved HLH domain of SPATULA and closely related sequences

9_029807m (103/188) RSRINEKMKALQSLIP

NSNKTDKASMLDEAI EYLKHLQLQVQ

Os/LOC_Os06g RSRAAEVHNLSEKRR

06900.1 68% RSKINEKMKALQSLIP

643 101-157 675 98% (54/55)

(77/113) NSNKTDKASMLDEAI

EYLKQLQLQVQ

Zm GRMZM2G RSRAAEVHNLSEKRR

017349_T01 82% RSKINEKMKALQSLIP

645 103-159 676 98% (54/55)

(69/84) NSNKTDKASMLDEAI

EYLKQLQLQVQ

Gm Glymal IgO RSRAAEVHNLSEKRR

5810.1 41 % RGRINEKMKALQNLIP

647 138-194 677 96% (53/55)

(144/348) NSNKTDKASMLDEAI

EYLKQLQLQVQ

Cc/clementineO. RSRAAEVHNLSEKRR

9_017382m 54% RSRINEKLKALQNLIP

649 104-160 678 96% (53/55)

(93/170) NSNKTDKASMLDEAI

EYLKQLQLQVQ

Cc/clementineO. RSRAAEVHNLSEKRR

9_017468m 54% RSRINEKLKALQNLIP

651 103-159 679 96% (53/55)

(93/170) NSNKTDKASMLDEAI

EYLKQLQLQVQ

Os/LOC_Os02g RSRAAEVHNLSEKRR

56140.1 83% RSRINEKMKALQSLIP

653 52-108 680 96% (53/55)

(64/77) NSSKTDKASMLDDAIE

YLKQLQLQVQ

Sl/Solyc04g0786 RSRSAEVHNLSEKRRR

90.2.1 48% SRINEKLKALQNLIPNS

655 132-188 681 94% (52/55)

(84/175) NKTDKASMLDEAIEY

LKQLQLQVQ

Gm/Glymal 7gl RNRAAEVHNLSEKRR

9500.1 79% RSRINEKLKALQNLIP

657 19-75 682 92% (51/55)

(66/83) NSNKTDKASMLDEAI

EYLKQLHLKVQ

Pt/POPTR_0005 RTRAAEVHNLSEKRR

sl8280.1 73% RSRINEKMKALQNLIP

659 134-190 683 92% (52/56)

(72/98) NSSKTDKASMLDEAIE

YLKLLQLQVQ

Zm GRMZM2G RSRAAEVHNLSEKRR

030744_T02 79% RSRINEKMKALQTLIP

661 43-99 684 92% (51/55)

(65/82) NSSKTDKASMLDDAIE

YLKHLQLQVQ

Zm GRMZM2G RSRAAEVHNLSEKRR

030744_T03 79% RSRINEKMKALQTLIP

663 43-99 685 92% (51/55)

(65/82) NSSKTDKASMLDDAIE

YLKHLQLQVQ

At/AT5G67110. RNIDAQFHNLSEKKRR

1 79% S KINEKMK ALQKLIPN

665 91-147 686 90% (48/53)

(55/69) SNKTDKASMLDEAIE

YLKQLQLQVQ

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; SI - 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. 141, these "functionally-related and/or closely-related" SPATULA clade polypeptides generally contain a consensus sequence of the SPATULA clade, SEQ ID NO: 687: KRxxxAX^HNLSEKX^RX^^NEKX^ALQxLIPNSxKTDKASMLDX^IEYLKxLX^x QxX⁸ X⁹X⁸.*

*In the above consensus sequence of SEQ ID NO: 687, x represents any amino acid;

X¹ is E or Q; X² is R or K; X³ is G or S; X⁴ is I, V, L, or M; X⁵ is E or D; X⁶ is Q or H; X⁷ is Q or

K; X⁸ is I, V, L, M, or absent; and X⁹ 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 Bradilg48400.1_BRADI and Solyc04g078690.2.1_SOLLY (indicated by the box with the dashed border around these sequences).

Table 9. MYBl 11 clade sequences and conserved first SANT domains of MYBl 11 and closely related se uences

Gm/Glyma07g3 KGRWTAEEDKILTDYI

7140.1 56% QENGEGS WS SLPKN A 87%

759 14-63 808

(121/215) GLLRCGKSCRLRWIN (43/49)

YLRS

Si/Si039538m RGRWTAEEDEILANYI

81 % AKHGEGSWRSLPKNA 87%

783 14-63 832

(97/119) GLLRCGKSCRLRWIN (43/49)

YLRA

Gm Glyma03g3 KGRWTEEEDDILTKYI

7640.1 43% QANGEGSWRSLPTNS 85%

743 14-63 792

(143/332) GLLRCGKSCRLRWIN (42/49)

YLRA

Sl/Solycl2g0493 RGRWTIEEDERLTNYI

50.1.1 76% QANGEGSWRTLPKNA 85%

757 14-63 806

(94/123) GLLRCGKSCRLRWIN (42/49)

YLKS

Gm Glyma09g0 KGRWTAEEDKILTDYI

4370.1 43% QENGEGSWKILPKNA 85%

763 14-63 812

(150/345) GLLRCGKSCRLRWIN (42/49)

YLRA

Gm Glymal5gl KGRWTAEEDKILTDYI

5400.1 83% QENGEGSWKTLPKNA 85%

765 14-63 814

(99/119) GLLRCGKSCRLRWIN (42/49)

YLRA

At/AT3G62610. KGR WT AEEDRTLS D Y

1 55% IQSNGEGSWRSLPKNA 83%

739 14-63 788

(106/190) GLKRCGKS CRLRWIN (41/49)

YLRS

Zm GRMZM2G KGRWTREEDEILARYI

051528_T01 79% EEHGEGSWRSLPKNA 83%

771 14-63 820

(94/118) GLLRCGKSCRLRWIN (41/49)

YLRA

Si/Si002107m KGRWTKEEDEILGRYI

81 % KEHGEGSWRSLPKNA 83%

773 14-63 822

(97/119) GLLRCGKSCRLRWIN (41/49)

YLRA

Os/LOC_Os03g RGRWTTEEDEKLAGY

19120.1 64% IAKHGEGSWRSLPKN 83%

775 14-63 824

(94/146) AGLLRCGKSCRLRWI (41/49)

NYLRA

Zm GRMZM2G RGRWTKEEDQILANYI

022686_T01 61 % AEHGEGSWRSLPKNA 83%

777 14-63 826

(106/173) GLLRCGKSCRLRWIN (41/49)

YLRA

Zm GRMZM2G RGRWTAEEDQLLANY

057027_T02 80% lAEHGEGSWRSLPKNA 83%

779 14-63 828

(96/119) GLLRCGKSCRLRWIN (41/49)

YLRA

Zm GRMZM2G RGRWTAEEDQLLANY

084799_T01 61 % lAEHGEGSWRSLPKNA 83%

781 14-63 830

(105/172) GLLRCGKSCRLRWIN (41/49)

YLRA

Os/LOC_Os01g RGRWTKEEDEKLARY

52% 81 %

767 19970.1 14-63 IRENGEGAWRSMPKN 816

(124/237) (40/49)

AGLLRCGKSCRLRWI NYLRA

Zm/GRMZM2G KGRWTKEEDEVLARY

051256_T01 78% IKEHGEGSWRSLPKNA 81%

769 14-63 818

(94/119) GLLRCGKSCRLRWIN (40/49)

YLRA

Table 10. MYB 111 clade sequences and conserved second SANT domains of MYB 111 and closely related sequences

Col. 7

Col. 3

Col. 4 Col. 6

Col. 1

Col. 2 Col. 5 Percent identity

Percent

SANT SEQ ID of second

SEQ identity of

Species/ domain 2 in Conserved SANT NO: of SANT domain ID polypeptide

Identifier amino acid domain 2 SANT in Col. 5 to NO: in Col. 1 to

coordinates domain 2 SANT domain 2 MYB111

of MYBl l l

RGNITSDEEEIIVKLH

At/

100% SLLGNRWSLIATHLP

735 MYB111 67-114 785 48/48 (100%)

(342/342) GRTDNEIKNYWNSH

AT5G49330

LSR

RGNITPEEEELVVKL

At/AT2G47460. 61% HSTLGNRWSLIAGHL 87%

737 67-114 787

1 (120/194) PGRTDNEIKNYWNSH (42/48)

LSR

RGNITSQEEDIIIKLH

Sl/Solyc01g079 75% ATLGNRWSLIAEHLS 85%

753 67-114 803

620.2.1 (103/137) GRTDNEIKNYWNSH (41/48)

LSR

RGNITSDEEAIIIKLR

Sl/Solyc06g009 82% ATLGNRWSLIAEHLP 85%

755 67-114 805

710.2.1 (103/125) GRTDNEIKNYWNSH (41/48)

LRR

RGNITPQEEEIIVKLH

Gm/Glyma07g3 56% AVLGNRWSVIAGHLP 85%

759 67-114 809

7140.1 (121/215) GRTDNEIKNYWNSH (41/48)

LRR

RGNITPQEEEIIVKLH

Gm/Glymal7g0 55% AVLGNRWSVIAGHLP 85%

761 67-114 811

3480.1 (128/231) GRTDNEIKNYWNSH (41/48)

LRR

RGNITPEEEEIIVKLH

Gm Glyma09g0 43% AVLGNRWSVIAGHLP 85%

763 67-114 813

4370.1 (150/345) GRTDNEIKNYWNSH (41/48)

LRR

RGNISTEEEEIIVQLH

Pp/POPTR_000 58% ASLGNRWSLIASYLP 83%

747 67-114 797

2s 19920.1 (118/203) GRTDNEIKNYWNSH (40/48)

LSR

RGNIS AEEEEIIINLH

Pp/POPTR_001 73% ASLGNRWSLIASHLP 83%

749 67-114 799

4sl l780.1 (107/146) GRTDNEIKNYWNSH (40/48)

LSR

751 Pp/POPTR_001 42% 67-114 RGNITKEEEETIVKL 801 83% 0s 15090.1 (160/377) HTALGNRWSFIAAQL (40/48)

PGRTDNEIKNYWNSH LSR

RGNITPEEEEIIVKLH

Gm Glymal5gl 83% AVLGNRWSVIAGRLP 83%

765 67-114 815

5400.1 (99/119) GRTDNEIKNYWNSH (40/48)

LRR

RGNISEEEEEMIIKLH

81 % ATLGNRWSLIAGHLP 83%

773 Si/Si002107m 67-114 823

(97/119) GRTDNEIKNYWNSH (40/48)

LSR

RGNISKEEEDIIIKLH

Zm/ GRMZM2G 80% ATLGNRWSLIASHLP 83%

779 67-114 829

057027_T02 (96/119) GRTDNEIKNYWNSH (40/48)

LSR

RGNISKEEEDIIIKLH

Zm GRMZM2G 61 % ATLGNRWSLIASHLP 83%

781 67-114 831

084799_T01 (105/172) GRTDNEIKNYWNSH (40/48)

LSR

RGNITPEEEDVIVKL

At/AT3G62610. 55% HSTLGTRWSTIASNL 81 %

739 67-114 789

1 (106/190) PGRTDNEIKNYWNSH (39/48)

LSR

RGNIS AEEENTI VKL

Gm/Glyma02g0 57% HASFGNRWSLIANHL 81 %

741 67-114 791

1740.1 (125/219) PGRTDNEIKNYWNSH (39/48)

LSR

RGNISFEEESIILKLH

Gm/Glyma03g3 43% ASFGNRWSLIASHLP 81 %

743 67-114 793

7640.1 (143/332) GRTDNEIKNYWNSH (39/48)

LSR

RGNISPQEEDIILNLH

Os/LOC_Os01g 52% ATLGNRWSLIAGHLP 81 %

767 67-114 817

19970.1 (124/237) GRTDNEIKNYWNSH (39/48)

LSR

RGNISEEEEDMIIKLH

Zm/ GRMZM2G 78% ATLGNRWSLIAGHLP 81 %

769 67-114 819

051256_T01 (94/119) GRTDNEIKNYWNSH (39/48)

LSR

RGNITEEEEDVIVKL

Zm/ GRMZM2G 79% HATLGNRWSLIAGHL 81 %

771 67-114 821

051528_T01 (94/118) PGRTDNEIKNHWNSH (39/48)

LRR

RGNISKEEEDVIIKLH

Zm/ GRMZM2G 61 % ATLGNRWSLIASHLP 81 %

777 67-114 827

022686_T01 (106/173) GRTDNEIKNYWNSH (39/48)

LSR

RGNISKEEEDVIIKLH

81 % ATLGNRWSLIASHLP 81 %

783 Si/Si039538m 67-114 833

(97/119) GRTDNEIKNYWNSH (39/48)

LSR

RGNITSEEEAIIIKLRA

Sl/Solycl2g049 76% TLGNRWSLIAEYLPH 77%

757 67-114 807

350.1.1 (94/123) RTDNEIKNYWNSRLC (37/48)

R RGNFSVEEESTILKL

Gm Glymal9g4 81 % HASFGSSWSLIASHLP 72%

745 67-114 795

0250.1 (97/119) GRTDNEIKNYWNSH (35/48)

LSR

RGNISNQEEDVIIKLH

ATLGNRKS Y V VKRM

Os/LOC_Os03g 64% DYVCLGARDYCFQQ 52%

775 67-141 825

19120.1 (94/146) NTHVRWSLIASHLPG (39/75)

RTDNEIKNYWNSHLS

R

Species abbreviations for Tables 9 and 10: At - Arabidopsis thaliana; Gm - Glycine max; Os - Oryza sativa; Pt- Populus trichocarpa; Si-Setaria italica; SI - Solarium 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" MYB 111 clade polypeptides generally contain a consensus sequence of the MYB111 clade, SEQ ID NO: 834:

MXRX'PCCX^^X^VGRWTXEEDXXLXXX^XXX^X^SWXXX^XXX'GLXRCGKSCRLRWX³ NYLxxxX³KRGNxX¹xX⁸EExxX³X³xLxX¹xX⁹GXXXXXXXXXXXXXXXXXXXXXXXXXXXxWSxI AxxX³xxRTDNEX³KNxWNX¹xLxX⁴X¹⁰.*

As shown in Fig. 16A-16B, these "functionally-related and/or closely-related" MYB 111 clade polypeptides also generally contain a consensus first SANT domain sequence SEQ ID NO: 835 which is found within the MYB 111 clade consensus sequence:

X⁴GRWTxEEDxxLxxX⁵X³xxX⁶GX⁷GSWxxX³PxxX¹GLxRCGKSCRLRWX³NYL. *

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 MYB 111 clade consensus sequence:

RGNxX¹xX⁸EExxX³X³xLxX¹xX⁹GXXXXXXXXXXXXXXXXXXXXXXXXXXXxWSxIAxxX³xxRTD NEX³KNxWNX¹xLxX⁴. *

*In the above consensus sequences of SEQ ID NO: 834, 835, or 836, x represents any amino acid; X¹ is S, A, or T; X² is E or G; X³ is I, V, L, or M; X⁴ is K or R; X⁵ is Y or F; X⁶ is N or H; X⁷ is E or Q; X⁸ is E, D, or Q; X⁹ is L or F; and X¹⁰ 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 "MYB 111 clade" or "G1640 clade" exemplified in the phylogenetic tree in Fig. 15 as those polypeptides bounded by

LOC_Os01gl9970.1 and Glymal5gl5400.1 (indicated by the box around these sequences).

Table 11. Conserved BTB domains of AtNPR3 and closely related sequences

LPYGNVGYEAFLIFLSY

LYTGKLKPSPMEVSTC

VDNVCAHDSCRPAITF

AVELTYASSIFQVPELV

SLFQRRLLNFV

DADIVVEGTAIGVHRC

ILGARSKFFHELFRREK

GSSEKEGKPKYCMSDL

Pt/POPTR_00 62% LPCGKVGYEAFLIFLSY 68%

908 65-190 945

15sl5800.1 (350/564) LYTGKLKPSPMEVSTC (86/126)

VDNVCAHDACRPAINF

AVELMYASSIFQVPEL

VSLFQRRLQNFV

DADLVVEGIPVSVHRC

ILASRSKFFHELFKREK

GS SEKEGKLK YNMND

Gm Glyma09g 63% LLPYGKVGYEAFLIFLG 66%

918 65-190 948

02430.1 (333/527) YVYTGKLKPSPMEVST (84/126)

CVDNVCAHDACRPAIN

FAVELMYASSIFQIPEL

VSLFQRRLLNFI

DADIVVEGISVSVHRCI

LASRSKFFHELFKREK

GSSEKEGKLKYNMSDL

Gm Glymal5g 62% LPYGKVGYEAFLIFLG 65%

922 65-190 950

13320.1 (328/527) YVYTGKLKPSPMEVST (82/126)

CVDSVCAHDACRPAIN

FAVELMYASYIFQIPEF

VSLFQRRLLNFI

DADIVVENISVGVHRCI

LAARSDFFNNLFKREK

GS SEKEGKPKYNMDD

Eg/Eucgr.E019 59% LLPYGKVGYEAFLIFLS 65%

916 65-190 947

22.1 (314/526) YAYTGKLKRSPLEVST (82/126)

CVDDMCSHDACSPAIN

FAVELMYASYIFQIREL

VSLLQRHLVNFV

DAEIVVEGVSLGVHRC ILA ARS SFFRDLFRKRN GNCGKEGKPSYSMIDI

Sl Solyc02g06 58% LPCGKVGYEAFLTFLS 63%

910 67-192 946

9310.2.1 (307/525) YL YS GKLKHFPPE AS T (80/126)

CVNSLCSHDSCRPAINF HVELMYASFVFQVPEL VSLFLRHLFSFV

DAEIFVEGTPVGVHRC

VLAARSQFFHELFKKG

NNNSTNGDKPRYLMS

Pt/POPTR_00 57% DLVPYGGVGYEAFHVF 60%

904 65-190 943

02s05740.1 (227/397) LH YL YTGKLKPS PPE V (76/126)

SRCVDDACAHDVCRP

AINYVVELMCASATFQ

MKELVLLFQRRLLNFI

Gm Glyma02g 55% DAEILVEDIPVGIHRCIL 58%

894 64-189 938

45260.1 (294/527) ASRSLFFHELFKKGTD (74/126) GSGKEGKPRYLMSDLV

PYGTVGYEAFQVFLYY

LYTGRLKASPTEVTTC

VDETCTHDACRPAINY

ALELM Y AS ATFQMKE

LVLLFQRHLLNFV

DAEILVEDIPVGIHRCIL

ASRSLFFHELFKKGTD

GSGKEGKPRYLMSDLV

Gm Glyma02g 55% PYGTVGYEAFQVFLYY 58%

898 64-189 940

45260.2 (256/465) LYTGRLKASPTEVTTC (74/126)

VDETCTHDACRPAINY

ALELM Y AS ATFQMKE

LVLLFQRHLLNFV

DAEIVVEGIPVGVHRCI

LAARSQFFHELFKKVD

SNSTSGDKPRYLMSDL

Pt/POPTR_00 53% MPYGGVGYEAFNVFL 57%

906 65-190 944

05s22770.1 (283/526) HYLYTGKHKSSPPEVS (72/126)

QCVYDACAHDACRPAI

NYAVELMYASATFQM

KELVLLFQRRLLSFI

DAEILIEDIPVGIHRCIL

ASRSPFFHELFKKGTD

GSGKEGKPRYLMSDL

Gm Glymal4g 55% MPYGTVGYQAFQVFL 55%

896 64-189 939

03510.1 (293/529) YYLYTGRLKASPTEET (70/126)

TCVDETCIHVACRPAIN

H ALELM Y AS ATFQMK

ELVLLFQRHLLNFV

DAEIVVEGKSVALHRC

ILS ARS QFFHELFKKGN

NNDGSAVSEGKPKYL

MTELVPYGKVGYEAL

Cc/clementine 53% 55%

892 67-195 NVILYYFYTGKLKPSPS 937

0.9_005587m (285/531) (72/129)

EVSTCVDDACAHDACP

PAINYAIELMYASAAF

QMKELVLLFQRRLLNF

V

DAEIVVEGINVGVNRC

ILAARSQFFHEKFKEKN

ENSLKNEKPKYLLKDL

Sl Solyc07g04 51 % VCVS SIGYEVFM VLLN 53%

872 51-176 927

4980.2.1 (278/541) YLYTGKIKSSPSEVSSC (68/126)

VDNACAHDACRPAINY

AVELMYASSTFQIKEL

VMFVERYLDNFV

DAVIVVEGVPVGVHR

CLLAARSQFLHEFFKQ

GGGDNAREGKPRYPIS

Eg/Eucgr.A02 48% DLVKKGHVGCEAFKY 53%

900 61-186 941

033.1 (258/528) VLRYMYTGKLKLFPAE (68/126)

VSTCVDSSCAHDVCGP

AINYAVELMYASATFE

IAELVMLVQRRLLHFI DAVIVVEGVPVGVHR

CLLAARSQFLHEFFKQ

GGGDNAREGKPRYPIS

Eg/Eucgr.A02 51 % DLVKKGHVGCEAFKY 53%

902 61-186 942

033.2 (189/368) VLRYMYTGKLKLFPAE (68/126)

VSTCVDSSCAHDVCGP

AINYAVELMYASATFE

IAELVMLVQRRLLHFI

DAEVVLADGGDEATV

PVHRCILAARSNFFLDH

FSSLSSPAAGGGKPRLE

Bd/Bradilgl2 47% LAELVPGGRHVGHEAL 52%

878 57-187 930

870.1 (256/538) VAVLGYLYTGRLKPPP (69/131)

QEAAICVDDRCRHQAC

RP AIDF V VES T Y A AS GF

QISELVSLFQRRLSDFV

DAEVALAAGKGGAAV

GVHRCILAARSAFFRD

HFASLPPPAAVGEKPR

LELADLVPGGRHIGQD

47% 49%

882 Si/Si034834m 56-186 ALVPVLGYLYTGRLKS 932

(256/538) (65/131)

APQDATVCMDDACGH

GACRPAIDFVVESMYA

ASGFQISELVSLFQRRL

SDFV

DAEIVVEGKSVAVNRS

ILSERSQFFRRLFNLRN

DGSVSEGKPKYLLTDL

Cc/clementine 46% VPHGKVGYEAFNDTL 50%

890 92-217 936

0.9_005201m (246/525) HYIYTGKTKAPPPEVST (63/126)

CVDDACVHVSCPPTIN

YVIELMYASAALQMK

KLVIRLELWLLNLV

DAEIALAAARGGGAV

GVHRCILAARSAFFLD

HLASLPAPAAAGERPR

LELADLVPGGRHIGRD

Zm GRMZM2 47% 48%

888 45-175 ALVPVLGYLYTGRLKP 935

G115162_T01 (256/541) (64/131)

PAQDATVCMDDACGH

GTCRPAIDFVVESMYA

ASGFQISELASLFQRRL

SDFV

DAEIVLASGGGDPGGG

AVVGVHRCILAARSRF

F YDHFS S AP AP AP AT A

GDKPQLDLDGLVPGGR

Os/LOC_Os03 48% 48%

880 51-187 HIGRDALVAVLSYLYT 931

g46440.3 (263/545) (67/137)

GRLRSAPPEAAACLDD

GCSHDACRPAIDFVVE

STYAASGFQISELVSLF

QRRLSDFV

DAEIVLASGGGDPGGG

Os/LOC_Os03 48% AVVGVHRCILAARSRF 48%

884 51-187 933

g46440.1 (263/545) F YDHFS S AP AP AP AT A (67/137)

GDKPQLDLDGLVPGGR HIGRDALVAVLSYLYT

GRLRSAPPEAAACLDD GCSHDACRPAIDFVVE STYAASGFQISELVSLF QRRLSDFV

DAEIVLASGGGDPGGG

AVVGVHRCILAARSRF

F YDHFS S AP AP AP AT A

GDKPQLDLDGLVPGGR

Os/LOC_Os03 48% 48%

886 51-187 HIGRDALVAVLSYLYT 934

g46440.2 (263/545) (67/137)

GRLRSAPPEAAACLDD

GCSHDACRPAIDFVVE

STYAASGFQISELVSLF

QRRLSDFV

DADVDMADGGPLVPV

HRCILAARSPFFHEFFA

ARGRGNSGDGPPSASA

AGVGGGGEGTGRPRY

Bd/Bradi2g51 52% 48%

874 81-225 KMEELVPGGRVGREAF 928

030.1 (289/547) (70/145)

LGFMRYLYTGKLRPAP

PDVVSCVDPVCPHDSC

PPAIRFAVELMYAASTF

NIPELISLFQRRLLNFV

DADIEVPDGGPPVPVH

RCILAVRSPFFYDIFAA

RGRGGAARGDAAAGA

RGAGEGAASGRPRYK

52% 46%

868 Si/Si000647m 82-225 MEELVPGGRVGREAFQ 925

(298/573) (67/143)

AFLGYLYTGKLRPAPL

DVVSCADPVCPHDSCP

PAIRFAVELMYAAWTF

KIPELISLFQRRLLNFV

DADIEVPDGGPPVPVH

RCILAVRSPFFYDIFAA

RGRGGAARGDAAAGA

RGAGEGAASGRPRYK

52% 46%

870 Si/Si000671m 82-225 MEELVPGGRVGREAFQ 926

(298/563) (67/143)

AFLGYLYTGKLRPAPL

DVVSCADPVCPHDSCP

PAIRFAVELMYAAWTF

KIPELISLFQRRLLNFV

DADVDVPDGGPPVPIH

RCILAARSDFFYDLFAA

RGRAGAARGDAAAGA

GVAAEGAASGRPRYK

Zm GRMZM2 53% MEDLVPAGRVGREAF 44%

866 82-225 924

G076450_T01 (291/545) QAFLGYLYTGKLRPAP (64/143)

VDVVSCADPVCHHDS

CPPAIRS A VELM Y A AC

TFKIPELTSLFQRRLLN

FV

DADVDVADGGPPVPV

Os/LOC_Os01 51 % HRCILAARSTFFYNLFA 43%

876 98-241 929

g56200.1 (287/558) ARGRGGDGAAGGGGG (62/143)

GGGGGGERTGGRPRY KMEELVPGGRVGRDA

FLS LLG YL YTGKLRP A

PDDVVSCADPMCPHDS

CPPAIRFNVEQMYAAW

AFKITELISLFQRRLLNF

V

Table 12. Conserved ANK repeats of AtNPR3 and closely related sequences

AASYCDLKVVSEVLSL

GLADVNLRNSRGYTVL

HIAAMRKEPSVIVSML

AKG AS ALDLT

IHMALDSDDVELVKLL

LTESDISLDDANALHY

Pt/POPTR_001 61 % CASYCDLKVMSEVLSL 68%

920 272-361 979

2s 11900.1 (334/543) GLANVNLRNSRGYTVL (60/87)

HIAAMRKEPSVIVSLLA KGAS ALDLT

IHRALDSDDVELVKLL

LNESDITLDDANALHY

Zm GRMZM2 53% AASYCDPKVVSELLDL 68%

866 306-395 952

G076450_T01 (291/545) AM ANLNLKNS RG YT A (62/90)

LHLAAMRREPAIIMCL LNKGANVSQLT

IHKALDSDDVELVELL

LSESNLTLDDAYALHY

Pt/POPTR_000 57% AVAYCDPKIVKEVLSL 67%

904 272-361 971

2s05740.1 (227/397) GS ADLNLRNS RG YS VL (59/88)

HVAARRKEPSIIMALLT RGASASETT

IHKALESDDVELVQLL

LSESNFTLDDAYALHY

Pt/POPTR_000 53% AVSYCDPKVVKEVLAL 66%

906 272-361 972

5s22770.1 (283/526) GLADLNLRNSRGYTVL (60/90)

HV AARRKES SILV ALL AKGARASEIT

IHK ALD S DDIEL VTLLL

SESNINLDEAYGLHYA

Eg/Eucgr.E019 59% AAYCDPKVVSELLGLG 66%

916 272-361 977

22.1 (314/526) LANVNLRNPRGYTVLH (60/90)

VAAMRKETKIIVSLLSK GACASELT

IHRALDSDDVELVKLL

LNESEITLDDANALHY

52% AASYCDSKVVSELLEL 64%

868 Si/Si000647m 306-395 953

(298/573) GLANLNLKNSRGYTAL (58/90)

HLAAMRREPAIIMCLL

NKGATVSQLT

IHRALDSDDVELVKLL

LNESEITLDDANALHY

52% AASYCDSKVVSELLEL 64%

870 Si/Si000671m 306-395 954

(298/563) GLANLNLKNSRGYTAL (58/90)

HLAAMRREPAIIMCLL

NKGATVSQLT

IHRALDSDDVELVKLL

LNESEITLDDANALHY

Bd/Bradi2g510 52% AAAYCDSKVVSELLDL 64%

874 306-395 956

30.1 (289/547) GLANLNLKNNRGYTA (58/90)

LHLAAMRREPTIIMCLL

NKGAVASQLT

IHRALDSDDVELVKLL

Os/LOC_Os01 51 % 64%

876 322-411 LNESEITLDDANALHY 957

g56200.1 (287/558) (58/90)

AAAYCDSKVVSELLDL RLANLNLKNSRGYTAL

HLAAMRREPAIIMCLL

NKGAAVSQLT

IHK ALD S DD VELLKLL

LNESSVTLDDAHALHY

Gm Glyma02g 55% ACAYSDSKVIQEVLSL 63%

894 271-360 966

45260.1 (294/527) GMADILRRNSRGYTVL (57/90)

HVAARRKDPSILVALL

NKGACASDTT

IHK ALD S DD VELLKLL

LNESSVTLDDAYALHY

Gm Glymal4g 55% ACAYSDSKVIQEVLSL 63%

896 271-360 967

03510.1 (293/529) GMADILRRNSRGYTVL (57/90)

HVAARRKDPSILVALL

NKGARASDTT

IHK ALD S DD VELLKLL

LNESSVTLDDAHALHY

Gm Glyma02g 55% ACAYSDSKVIQEVLSL 63%

898 271-360 968

45260.2 (256/465) GMADILRRNSRGYTVL (57/90)

HVAARRKDPSILVALL

NKGACASDTT

ILKALDSDDVDLVGLL

LKESTVTLDDAFAIHY

Zm GRMZM2 47% AAAYCEPKVFAELLKL 61 %

888 252-341 963

G115162_T01 (256/541) DSANVNLKNSGGYTPL (55/90)

HI ACMRREPDIILS L VE

RGACVLERT

IHKALDSDDVALVGML

LKESAITLDDAHAIHY

Bd/Bradilgl28 47% AAAYCEPKVLAGMLN 60%

878 268-357 958

70.1 (256/538) LDSANVNLKNDSGYTP (54/90)

LHIACMRREPDIIVSLIE

KGASVLERT

IHKALDSDDVDLVGML

LKESPVTLDDAFAIHY

Os/LOC_Os03 48% AAAYCEPKVLAELLKL 60%

880 265-354 959

g46440.3 (263/545) ESANVNLKNSSGYTPL (54/90)

HMACMRREPDIIVSLIE

KGASVLERT

IHKALDSDDVDLVGML

LKESPVTLDDAFAIHY

Os/LOC_Os03 48% AAAYCEPKVLAELLKL 60%

884 265-354 961

g46440.1 (263/545) ESANVNLKNSSGYTPL (54/90)

HMACMRREPDIIVSLIE

KGASVLERT

IHKALDSDDVDLVGML

LKESPVTLDDAFAIHY

Os/LOC_Os03 48% AAAYCEPKVLAELLKL 60%

886 265-354 962

g46440.2 (263/545) ESANVNLKNSSGYTPL (54/90)

HMACMRREPDIIVSLIE

KGASVLERT

ILKALDSDDVDLVGLL

47% LKESAVTLDDAFAVHY 58%

882 Si/Si034834m 267-356 960

(256/538) AAAYCEPKVFAELLKL (53/90)

NSANVNLKNNSGYTPL HI ACMRREPDIILS L VE

RGASVMERT

ILKALESDDIELLTLLLE

ESNVTLNDACALHYA

Sl/Solyc07g044 51 % AAYCNSKVVNEVLEL 58%

872 256-346 955

980.2.1 (278/541) GLGADVNLQNSRGYN (53/91)

VLHVAARRKEPSIIMG

LLAKGASVLDTT

IHK ALD S DD VELLKLL

LDESNVTLDDAYALHY

Cc/clementineO 53% AAAYCNPKVFKEVLN 57%

892 277-366 965

.9_005587m (285/531) MGLADLNLKNARGHT (52/90)

VLHVAARRKEPAVLVT

LLSKGACASETT

IHKALDNDDVELVRRL

LNESVVTLDDAYALHY

Eg/Eucgr.A020 48% ATAYCHPKIFKEVLGL 56%

900 268-357 969

33.1 (258/528) GLADLNLKDSRGYTVL (51/90)

HVAARRKAPSILLPLLY

KGACAMEST

IHKALDNDDVELVRRL

LNESVVTLDDAYALHY

Eg/Eucgr.A020 51 % ATAYCHPKIFKEVLGL 56%

902 268-357 970

33.2 (189/368) GLADLNLKDSRGYTVL (51/90)

HVAARRKAPSILLPLLY

KGACAMEST

IHK ALD S DD VELLKLL

LDVSNVTLDDAYALH

Cc/clementineO 46% YAAAYCSPKVFKEVLN 55%

890 299-388 964

.9_005201m (246/525) MDLACLNLKDARGRT (50/90)

VLHVAARRNEPEVMV

TLLSKGACASETT

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; SI - 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: DAxX² X² X¹X¹X¹X¹X¹X¹X¹X¹xxxX² X²X³RX⁴X²LX^sxRSxFX⁶xxxX⁶ * (SEQ ID NO: 981).

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:

X⁷xxxxX²xxX²X²xxX⁸xX⁹X²xxX¹⁰xX⁶xxxX²xYxYX⁵GX⁷xX⁷xxxxXⁿxxxCxxxxCxHxxCxPX⁵IxxxX² X¹²xxxAX⁵xxX⁶xX²xxX²xxxxxxxLxxX⁶X² * (SEQ ID NO: 982).

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

IxxALXⁿxDDX²xLX²xxLLxxSxxxLX¹³xAxxX²HYxxxYX⁴xxKX²xxxX²LxX²xxX¹⁴xxX²xxX¹⁵X¹³xxGx xxLHxAxxRxxxxX²X²X²xX²X²xX⁷GAxxxX¹⁶ * (SEQ ID NO: 983).

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:

X⁵xxXⁿX¹³X²X²PX²X²xxA. *

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:

SxX¹⁷xxxxX²XⁿX¹⁵X¹⁸X² (SEQ ID NO: 985). * And, there is also a small motif that is present in AtNPR3 clade member proteins within the

NPRl-like_C domain, and is identifiable in Figs. 18H-18I:

KxxX²CX²xxLX¹²xxX²X¹⁹xX⁷ (SEQ ID NO: 986).*

*In the above consensus sequences of SEQ ID NOs: 981-986, x represents any amino acid; X¹ is any amino acid or absent; X² is I, V, L, or M; X³ is H or N; X⁴ is C or S; X⁵ is S, A, or T; X⁶ is F or L; X⁷ is K or R; X⁸ is G or S; X⁹ is H or absent; X¹⁰ is E, K or Q; X¹¹ is E or D; X¹² is E or Q; X¹³ is D or N; X¹⁴ is G or absent; X¹⁵ is K, R, or Q; X¹⁶ is E, D, or Q; X¹⁷ is I, V, L, M, or F; X¹⁸ is E or R; and X¹⁹ 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 Glymal5gl3320.1 (indicated by the box around these sequences).

Table 13. Conserved bHLH-MYC_N domain ("domain 1") of AtMYCl and closely related sequences

Col. 7

Col. 3 Col. 4 Col. 6 Percent

Col. 1 Col. 5 identity of first

Col. 2

Percent bHLH- SEQ ID bHLH-

SEQ identity of MYC_N Conserved bHLH- NO: of MYC_N

Species/

ID polypeptide domain in MYC_N domain bHLH- domain in Col.

Identifier

NO: in Col. 1 to amino acid sequence MYC_N 5 to the bHLH- AtMYCl coordinates domain MYC_N domain of

AtMYCl

LRKQLALAVRSVQWS

Y AIFWS S SLTQPG VLE

WGEGCYNGDMKKRK

KSYESHYKYGLQKSK

ELRKLYLSMLEGDSG

526/526 TTVSTTHDNLNDDDD 195/195

At/ AtMYCl or

1016 (100%) 23-217 NCHSTSMMLSPDDLS 1073 (100%) AT4G00480.1

DEEWYYLVSMSYVFS

PSQCLPGRASATGETI

WLCN AQ Y AENKLFS R

SLLARSASIQTVVCFP

YLGGVIELGVTELISE

DHNLLRNIKSCL

FRKQLAAAVRSISWT

Y AIFWS I S TTRPG VLT

88/184

LOC_Os01g395 WNDGFYNGEIKTRKIE 87/184 (47%)

1018 (47%) 19-196 1075

60.1 NNLVTELTAEQLLLQR

SEQLRELYNSLLSGES

ADQQRRRPVTALSPE DLGNVEWYYVVCMT

YAFRPGQCVPGKSFAS

NGCAWLCNAQSADSK

AFPRKLLAKNASIQTI

VCVPFMTGVLELGTT

DPAAVARG

FRSLLAAAVRSISWSY

AIFWSISTSCPGVLTW

NDGFYNGVVKTRKIS

NS ADLT AGQLV VQRS

EQLRELYYSLLSGECD

92/201

LOC_Os04g470 HR ARRPI A ALS PEDL A 91/194 (46%)

1020 (45%) 19-202 1077

40.1 DTEWYYVVCMTYSFQ

PGQGLPGKSYASNAS

VWLRNAQSADSKTFL

RSLLAKSASIQTIICIPF

TSGVLELGTTDPVLED

PKLVNRIVAYF

FRSQLAAAARSINWT

YAIFWSISTSRPGVLT

WKDGFYNGEIKTRKIT

NSMNLMADELVLQRS

EQLRELYDSLLSGECG

90/201

LOC_Os04g470 HRARRPVAALLPEDL 90/197 (45%)

1022 (44%) 12-196 1079

80.1 GDTEWYYVVCMTYA

FGPRQGLPGKSFASNE

FVWLTNAQSADRKLF

HRALIAKSASIKTIVCV

PFIMHGVLELGTTDPIS

EDPALVDRIAASF

LRKQLAAAARSINWS

YSLFWSISSTQRPRVL

TWTDGFYNGEVKTRK

ISHSVELTADQLLMQR

158/564 SEQLRELYEALQSGEC

GRMZM2G172 71/160 (44%)

1024 (28%) 20-180 DRRAARPVGSLSPEDL 1081

795_T01

GDTEWYYVICMTYAF

LPGQGLPGRS S ASNEH

V WLCN AHL AG S KDFP

RALLAKVPEDPDLINR

ATAAF

LEKKLS R VLT WTDGF

YNGEVKTRKISNSVEL

TSDHLVMQRSDQLRE

LYE ALLS GEGDRR A A

67/172 P ARP AGS LS PEDLGDT

GRMZM5G822 66/163 (40%)

1026 (38%) 20-179 EWYYVVSMTYAFRPG 1083

829_T01

QGLPGRSFASDEHVW

LCNAHLAGSKAFPRA

LL AKS ILCIP VMGG VL

ELGTTDTVPEAPDLVS

RATAAF

87/204 MRSQLAAAARSINWS

GRMZM5G822 85/191 (44%)

1028 (42%) 24-204 YALFWSISDTQPGVLT 1085

829_T03

WTDGFYNGEVKTRKI SNSVELTSDHLVMQR

SDQLRELYEALLSGEG

DRR A AP ARP AGS LS PE

DLGDTEWYYVVSMT

YAFRPGQGLPGRSFAS

DEHVWLCNAHLAGSK

AFPR ALL AKS ILCIP V

MGGVLELGTTDTVPE

APDLVSRATAAF

LRNHLAAAVRSINWT

YALFWSISSTQPGFLT

WTDGFYNGEVKTRKI

VNS AELT ADQLVMQR

SEQLRELYEALLSGEC

166/573

DRRAARPVASLSPEDL 79/191 (41 %)

1030 Si000845m (28%) 18-196 1087

GDTELYYVVCMTYAF

RPGQGLPGRSFASNER

VWMWNSHLADSKAF

PRALLAKTIVCIPLMS

GVLELGTTDAVV

EDPSLVS RAT ASF

FLTWTDGFYNGEVKT

RKIANSAELTADQLV

MQRSEQLRELYEALLS

145/520 GECDRRTARPVASLSP

58/153 (37%)

1032 SiO 12401m (28%) 1-138 EDLGDTEWYYVVCM 1089

TYAFRPGQGLPGRSFA

SNERVWMRNSHLADS

KAFPRALLAKTIVCIPF

MS G VLELGTTD AEP

LKKQLAVSVRNIQWS

YGIFWSVSASQPGVLE

WGDGYYNGDIKTRKT

IQAAEVKIDQLGLERS

EQLRELYESLSLAESS

105/217 ASGSSQVTRRASAAA

102/198 (51 %)

1034 AT1G63650.1 (48%) 13-202 LSPEDLTDTEWYYLV 1091

CMSFVFNIGEGIPGGA

LSNGEPIWLCNAETAD

SKVFTRSLLAKSASLQ

TVVCFPFLGGVLEIGT

TEHIKEDMNVIQSVKT

LF

LKKHLAVSVRNIQWS

YGIFWSVSASQSGVLE

WGDGYYNGDIKTRKT

IQASEIKADQLGLRRS

EQLSELYESLSVAESSS

101/202

SGVAAGSQVTRRASA 100/198 (50%)

1036 AT5G41315.1 (50%) 14-206 1093

AALSPEDLADTEWYY

LVCMSFVFNIGEGMP

GRTFANGEPIWLCNA

HTADSKVFSRSLLAKS

AAVKTVVCFPFLGGV

VEIGTTEHITEDMNVI QCVKTSF

LRKQLAVAVRSIQWS

YAIFWSLSAAQQGVL

EWGDGYYNGDIKTRK

TMQAMELTPDKIGLQ

RSKQLRELYESLLKGE

129/243

clementine0.9_0 SELAYKRPSAALSPED 120/198 (60%)

1038 (53%) 15-198 1095

04500m LTDAEWYYLVCMSFV

FSSGQGLPGRALANSE

TIWLCNAQCADSKVF

SRSLLAKSASIQTVICF

PHLDGVIELGVTELVP

EDPSLLQHIKASL

MQFSGHYQLHNKGLQ

RSKQLRELYESLLKGE

SELAYKRPSAALSPED

123/313 LTDAEWYYLVCMSFV

clementine0.9_0 86/151 (56%)

1040 (39%) 1-139 FSSGQGLPGRALANSE 1097

05551m

TIWLCNAQCADSKVF

SRSLLAKSASIQTVICF

PHLDGVIELGVTELVP

EDPSLLQHIKASL

MQAMELTPDKIGLQR

SKQLRELYESLLKGES

EL A YKRPS A ALS PEDL

123/313 TDAEWYYLVCMSFVF

clementine0.9_0 85/143 (59%)

1042 (39%) 1-138 SSGQGLPGRALANSET 1099

05579m

IWLCNAQCADSKVFS

RSLLAKSASIQTVICFP

HLDGVIELGVTELVPE

DPSLLQHIKASL

LRKQLAVAVRSIQWS

Y AIFWTLS ATKQG VL

QWGDGYYNGDIKTRK

TVQAVELKPDKIGLQR

SEQLRDLYESLLEGET

128/220

DAQNKRPSAALSPEDL 121/198 (61 %)

1044 Eucgr.D02287.1 (58%) 15-198 1101

TDEEWYYLVCMSFVF

NPGEGLPGRALADGQ

TIWLCNAQYADSKVF

SRSLLAKSASIQTVVC

FPYLGGVIELGVTELV

PEDPSLLQHIKVSL

LCTQLAVAVRSIQWS

YGIFWSPSTTEERVLE

WREGYYNGDIKTRKT

VQATELEIKADKIGLQ

RSEQLKELYKFLLAGE

111/224

Glyma03g01180 ADHPQTKRPSVALAPE 105/200 (52%)

1046 (49%) 16-202 1103

.1 DLSDLEWYYLVCMSF

VFNHNQSLPGRALEIG

DTVWLCNAQHADSK

VFS RS LL AKS ATIQT V

VCFPYQKGVIEIGTTE

LVAEDPSLIQHVKACF LCTQLAVAVRSTQWS

YGIFWAPSTTEERVLE

WREGYYNGDIKTRKT

VQAMELEMKADKIGL

QRSEQLKELYKFLLAG

104/215

Glyma07g07740 EADPQTKRPSAALAPE 100/200 (50%)

1048 (48%) 16-196 1105

.1 DLSDLEWYYLVCMSF

VFNHNQSLPGRALEIG

DTVWLCNAQHADSKI

FSRSLLAKTVVCFPYQ

KGVIEIGTTELVTEDPS

LIQHVKACF

LRKQLAIAVRSVQWS

Y AIFWS LS TRQKG VLE

WGGGYYNGDIKTRKV

QATELKADKIGLQRSE

QLRELYKSLLGGDAG

133/230

POPTR_0002sl QQAKRSSPALSPEDLS 123/197 (62%)

1050 (57%) 15-197 1107

6080.1 DEEWYYLVCMSFVFN

PGEGLPGRALANKQTI

WLCNAQYADSKVFSR

SLLAKSASIQTVVCFP

YLEGVMELGVTELVT

EDPSLIQHIKASL

LRKQLAVAVRSVQWS

YAVFWSQSTRQQGVL

EWGDGYYNGDIKTRK

VEAMELKADKIGLQR

SEQLRELYESLLEGET

131/230

POPTR_0014sO GLQATRSSPALSPEDL 122/197 (61 %)

1052 (56%) 15-197 1109

7960.1 SDEEWYYLVCMSFVF

NPGEGLPGRALANKQ

PIWLCNAQYADSKVF

SRSLLAKSASIQTVVC

FPYLEGVIELGVTELV

TEDPGLIQHIKASL

LSKQLAVAVRSIQWS

YAIFWSLSTRQQGVLE

WSGGYYNGDIKTRKT

VQEMELKADKMGLQ

RSEQLRELYESLLEGE

126/220

GSVIVTO 10269 TDQQSKRPSAALSPED 119/198 (60%)

1054 (57%) 15-198 1111

27001 LSDAEWYYLVCMSFV

FNPGEGLPGRALANG

QSIWLCDAQYADSKV

FSRSLLAKSASIQTVV

CFPHMGGVIELGVTEL

VPEDPSLIQHIKACL

LRKQLALAVRGIQWS

YAIFWSTAVTQPGVL

112/201 KWIDGYYNGDIKTRK

Solyc08g081140 111/196 (56%)

1056 (55%) 15-202 TVQAGEVNEDQLGLH 1113

.2.1

RTEQLKELYSSLLTSE

SEEDLQPQAKRPSASL

S PEDLTDTEW YFL VC MSFVFNVGQGLPGKT

LATNETVWLCNAHQA

ESKVFSRSLLAKSASIQ

TVVCFPYLGGVIELGV

TELVTEDPNLIQQIKNS

F

LRNQLALAVRNIQWS

YAIFWSISTRQPGVLE

WGDGYYNGDIKTRKT

VQAVEFNADQMGLQ

RSEQLRELYESLSIGES

212/546

GSVIVT010197 NPQPRRHSAALSPEDL 115/196 (58%)

1058 (38%) 14-197 1115

50001 TDAEWYYLVCMSFVF

DIGQGLPGRTLASGQP

IWLCNAPYAESKVFSR

SLLAKSASIQTVVCFP

YLGGVIELGATEMVL

EDPSLIQHIKTSF

LKKQLALAVRKIQWS

YGIFWSISTRQPGVLE

WGDGYYNGDIKTRKT

IQAVELNTDQIGMQRS

EQLRELYESLSAGESS

109/201

PQVRRPSAALSPEDLT 107/198 (54%)

1060 Eucgr.D01841.1 (54%) 15-198 1117

DAEWYYLVCMSFIYD

IGQGLPGRTLTTGQPT

WLCNAHYADSKVFTR

SLLAKSASIQTVVCFPF

RGGVIELGVTDQVSED

PGVIHQVKGTL

MTQAIELNGGDHMDL

HRSEQLRELYESLSGS

EPNPQTSRRPSVALSP

74/144 EDLADAEWYYLVCM

72/140 (51 %)

1062 Eucgr.E00624.1 (51 %) 1-141 SFIFNIGQCLPGQSLAT 1119

GKLIWLCNAHCADSK

VFSRSLLAKSASIQTV

VCFPFLDGVIELGTTD

PVLEDPNLIQHVKTYL

LKKQLALAVRSIHWS

YAIFWTDSTTQPGVLS

WGEGYYNGDIKTRKT

SQGVELNSDQIGLQRS

EQLRELFKSLKTVEVS

105/206

Glyma05g37770 PQTKRPS A ALS PEDLT 102/196 (52%)

1064 (50%) 6-184 1121

.1 DAEWYYLVCMSFIFNI

GQGLPGRTLAKGQSI

WLNNAHSADCKIFSRS

LLAKTVVCFPFREGVI

ELGTTEQVSEDLSVIE

RIKTSF

LKKQLALAVRSIHWS

104/199

Glyma08g01810 YAIFWTDSTTQPGVLS 104/196 (53%)

1066 (52%) 6-190 1123

.1 WGEGYYNGDIKTRKT

SQGVELNSDQIGLQRS EQLRELFKSLKTVEVT

PQTKRPS A A ALS PEDL TDAEWYYLVCMSFIF NIGQGLPGRTLAKGQP IWLNNAHSSDCKIFSR SLL AKS AS IET V VCFPF REGVIELGTTEQVPED LSVIELIKTSF

LKKQLALAVRSIQWS

YAIFWTISDTQPGVLE

WGDGYYNGDIKTRKT

IQSVELSSNQLGLQRS

EQLREL YES LS AGES H

124/272

clementine0.9_0 PQ A AS KRPS A ALS PED 108/196 (55%)

1068 (45%) 16-196 1125

05250m LTDTEWYYLVCMSFN

FNIGEGLPGRALANNQ

PIWLCNAQYADSKVF

SRSLLAKTVVCFPHLH

GVVELGVTELVLEEPD

FIQHIKTSF

LKKQLAIAVRSIQWSY

AIFWSMSARQPGVLE

WGDGYYNGDIKTRKT

IQSIELDEDELGLQRSE

QLRELYESLSVGEASP

110/201

POPTR_0001s0 Q ARRPS A ALS PEDLTD 108/196 (55%)

1070 (54%) 15-198 1127

9450.1 TEWYYLVCMSFIFDIG

QGLPGTTLANGHPTW

LCNAHSADSKVFSRSL

LAKSASIQTVVCFPFM

RGVIELGVTEQVLEDP

SLINHIKTSF

LKKQLALAVRSIQWS

YAIFWSNPTGQPGVLE

WADGYYNGDIKTRKT

VQSIELNADELGLQRS

EQLREL YESLSAGEAN

103/201

POPTR_0003sl PQ ARRPS AALSPEDLT 101/196 (51 %)

1072 (51 %) 15-193 1129

2810.1 DTEWYYLVCMSFVFD

NGQGLPGTTLANGHP

T WLCN APS ADS KIFS R

SLLAKTVVCFPFMRG

VVELGVSEQVLEDPSL

IQHIKTSF

Table 14. Conserved HLH domain ("domain 2") of AtMYCl and closel related se uences

coordinates

SQNSGLNQDDPSDRR

526/526

At/AtMYCl or KENEKFS VLRTM VPT

1016 (100%) 1074 100% (44/44) AT4G00480.1 VNEVDKESILNNTIK

YLQELEARVEE

RGSRAALTQESGIKN

92/201 HVISERRRREKLNEM

Os/LOC_Os04 28/63 (44%)

1020 (45%) 370-435 FLILKSIVPSIHKVDK 1078

g47040.1

ASILEETIAYLKVLEK

RVKE

GDSSAAAMTTQGSSI

90/201 KNHVMSERRRREKL

Os/LOC_Os04 28/59 (47%)

1022 (44%) 383-450 NEMFLILKSVVPSIHR 1080

g47080.1

VDKASILAETIAYLKE

LEKRVEE

NCGGGGTTVTAQEN

158/564 GAKNHVMLERKRRE

Zm GRMZM2 24/43 (55%)

1024 (28%) 363-431 KLNEMFLVLKSLVPS 1082

G172795_T01

IHKVDKASILAETIAY LKELQRRVQE

GGATGAAQEMSGTG

67/172 TKNHVMSERKRREK

Zm GRMZM5 22/43 (51 %)

1026 (38%) 375-442 LNEMFLVLKSLLPSIH 1084

G822829_T01

RVNKASILAETIAYL

KELQRRVQE

GGATGAAQEMSGTG

87/204 TKNHVMSERKRREK

Zm GRMZM5 22/43 (51 %)

1028 (42%) 400-467 LNEMFLVLKSLLPSIH 1086

G822829_T03

RVNKASILAETIAYL

KELQRRVQE

GGGGTTRMAQESGV

166/573 KNHVMSERKRREKL

30/65 (46%)

1030 Si/Si000845m (28%) 395-425 NEMFL VLKS L VPS IH 1088

KVDKASILAETIAYL KELQRRVQE

GGGGTTRMAQESGV

145/520 KNHVMSERKRREKL

30/65 (46%)

1032 Si/SiO 12401m (28%) 289-355 NEMFL VLKSLVPSIH 1090

KVDKASILAETIAYL KELQRRVQE

EELLPDTPEETGNHA

105/217 LSEKKRREKLNERFM

At/ATI G6365 22/43 (51 %)

1034 (48%) 393-456 TLRSIIPSISKIDKVSIL 1092

0.1

DDTIEYLQDLQKRVQ

E

EKLMLDSPEARDETG

101/202 NHAVLEKKRREKLN

At/AT5G4131 25/43 (58%)

1036 (50%) 426-492 ERFMTLRKIIPSINKID 1094

5.1

KVSILDDTIEYLQELE

RRVQE

1038 Cc/clementine 129/243 440-509 SQKEICRKYCPVTME 1096 33/45 (73%) 0.9_004500m (53%) S DNFCEEHIS S DKRTE

NEKFMVLRSMVPYIS E VDK AS ILS DTIK YLK KLEARVEE

SQKEICRKYCPVTME

123/313 S DNFCEEHIS S DKRTE

Cc/clementine 33/45 (73%)

1040 (39%) 381-450 NEKFMVLRSMVPYIS 1098

0.9_005551m

E VDK AS ILS DTIK YLK KLEARVEE

SQKEICRKYCPVTME

123/313 S DNFCEEHIS S DKRTE

Cc/clementine 33/45 (73%)

1042 (39%) 380-449 NEKFMVLRSMVPYIS 1100

0.9_005579m

E VDK AS ILS DTIK YLK KLEARVEE

SELQNGVESLLGDVD

128/220 FCAGHILSTKKKEHE

Eg/Eucgr.D02 29/45 (64%)

1044 (58%) 437-503 KFL VLRS MIPS IEEID 1102

287.1

KASILDDTIMYLRELE ARVEE

SQKGNDRMEWTSKL

111/224 ENDDHGLIGK AFS DK

Gm Glyma03g 25/46 (54%)

1046 (49%) 405-476 KREIKNFQVVKSMVP 1104

01180.1

SSISEVEKISILGDTIK YLKKLETRVEE

SQKENGRMKWTSKL

104/215 EN ANDGFMEKTFS D

Gm Glyma07g 28/55 (50%)

1048 (48%) 405-476 KKRENKNFHVVKPM 1106

07740.1

VPSSISEVEKISILGDT IKYLKKLETRVEE

FDKENGGTDCLKKLE

133/230 GCETCKEH YKS DKQ

Pt/POPTR_00 27/45 (60%)

1050 (57%) 437-506 RVNDKFIVLRSMVPSI 1108

02s 16080.1

SEIDKESILSDTINYLK QLESRVAE

SDKENAGKDCLKNL

131/230 EGCETCKLHFESEKQ

Pt/POPTR_00 23/45 (51 %)

1052 (56%) 438-507 KENEKYLALESIVASI 1110

14s07960.1

NEIDKASILSDTINYP

RQLESRVAE

SQKENAGRDGLWKS

126/220 GSDGICKQHALSDKK

Vv/GSVIVTO 31/60 (51 %)

1054 (57%) 420-489 REKEKFLVLRSMVPS 1112

1026927001

INKIDEVSILGDTIEYL KKLE ARVEE

FSRENGKKNSLWRPE

112/201 VDDIDRNRVISERRR

Sl Solyc08g08 23/43 (53%)

1056 (55%) 415-487 REKINERFMHLASML 1114

1140.2.1

PTSSKVDKISLLDETI

EYMKELERRVQE

SRDNNGDNDEIWRPE

212/546 ADEITLNHVLSERKR

Vv/GSVIVTO 26/43 (60%)

1058 (38%) 323-395 REKINERFSVLRSLVP 1116

1019750001

SINQVNKVSVLDDTI

EYLKELKRRVEE

1060 Eg/Eucgr.DOl 109/201 411-483 SPLEDGGENGVWRPE 1118 27/54 (50%) 841.1 (54%) ADEIGLNHAILERKQ

KEKINDRLGVLKSMV PSVSKVDKLSILDDTI AYLRELQRKVEE

ISKVSCKRDGLWMA

74/144 LTDELSPDHTLSESRQ

Eg/Eucgr.EOO 26/43 (60%)

1062 (51 %) 343-415 REKINEQFSVLNSILP 1120

624.1

LVNKVDKISILDNTIE

YVKELQRRAEE

SQEENDYKEGMRVE

105/206 ADENGMNHVMSERR

Gm Glyma05g 21/43 (48%)

1064 (50%) 406-477 RRAKLNQRFLTLRSM 1122

37770.1

VPSISKDDKVSILDDA

IEYLKKLERRINE

SQEENDYKEGMRVE

104/199 ADENGMNHVMSERR

Gm Glyma08g 23/43 (53%)

1066 (52%) 412-483 RRAKLNERFLTLRSM 1124

01810.1

VPSISKDDKVSILDDA

IDYLKKLERRVKE

SSEDNHIKDDVSRLE

124/272 AEETATNHVKSERRQ

Cc/clementine 24/43 (55%)

1068 (45%) 419-491 RGKLNERFVILKSMV 1126

0.9_005250m

PSVSKFDKVSILDDTI

EYVQELERKVKE

SPEYNSNKVVVGRPE

110/201 ADENGASHALSERK

Pt/POPTR_00 24/44 (54%)

1070 (54%) 410-487 QREKLNKRFMILKS I 1128

01s09450.1

VPSISKVVDKVSILDE TIEYLQELERKVEE

SPEYSSDKVVGGRPE

103/201 ADEIGASHVLSERRR

Pt/POPTR_00 24/43 (55%)

1072 (51 %) 407-479 REKLNKRFMILKS I VP 1130

03sl2810.1

SISKVDKVSILDDTIQ YLQELERKVEE

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; SI - 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 AtMYCl -related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.

As shown in Fig. 21A-210, these "functionally-related and/or closely-related" AtMYCl clade polypeptides generally contain a consensus sequence of the AtMYCl clade, SEQ ID NO: 1153:

X^X^x-x-x-L-A-x-X^x-R-x-x-x-W-X^Y-X^X^F-W-X^x-x-x-x-x-x-x-x-L-x-W-x-x-G-x-Y-N-

G-x-X⁸-K-X⁹-R-K-X¹⁰-x-x-x-Xⁿ-X¹²-X¹³-X¹⁴-X¹⁵-x-x-x-x-x-x-X¹⁶-x-x-X¹⁷-x-X¹⁸-L-x-x-L-X¹⁹-x- x-X²⁰-x-x-x-X²¹-x-x-X²²-X²³-X²⁴-X²⁵-x-x^^

X³⁷-X³^X-X-X-X-X-X-X³⁹-X-X-L-X-P-X^ x-x-X⁴⁹-x-X⁵⁰-P-G-x-X⁵¹-x-x-x-x-x-x-X⁵²-W-X⁵³-x-X⁵⁴-X⁵⁵-x-x-X⁵⁶-x-x-K-x-F-x-R-X⁵⁷-L-X⁵⁸-A- X⁵⁹-X⁶⁰-X⁶¹-X⁶²-X⁶³-x-X⁶⁴-X⁶⁵-X⁶⁶-C-x-P-x-X⁶⁷-x-x-G-V-X⁶⁸-E-X⁶⁹-G-x-X⁷⁰-X⁷¹-x-X⁷²-x-E In the above consensus sequences of SEQ ID NO: 1153, x represents any amino acid; X¹ represents Phe or Leu; X² represents any amino acid or absent; X³ represents Ala or Serine; X⁴ represents Thr or Ser; X⁵ represents Gly, Ala, or Ser; X⁶ represents He, Val, Leu, or Met; X⁷ represents Ser, Ala, or Thr; X⁸ represents He, Val, Leu or Met; X⁹ represents Thr or Lys; X¹⁰, X¹¹, X¹², and X¹³ represents any amino acid or absent; X¹⁴ represents Glu or absent; X¹⁵ represents He, Met, or absent; X¹⁶ represents He, Val, Leu or

Met; X 17 represents Ser or Thr; X 18 represents Gin or Glu; X 19 represents Tyr or Phe; X 20 represents He,

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; X⁴⁰ represents Glu or Asp; X⁴¹ represents Gly, Ala, Ser or Thr; X⁴² represents Tyr or Phe; X⁴³ and X⁴⁴ represent He, Val, Leu or Met; X⁴⁵ represents Cys or Ser; X⁴⁶ represents Ser or Thr; X⁴⁷ and X⁴⁸ represent Tyr or Phe; X⁴⁹ represents Gin or Glu; X⁵⁰ represents He, Val, Leu or Met; X⁵¹ represents Thr, Ala, or Ser; X⁵² represents He, Val, Leu, Met, or Thr; X⁵³ represents He, Val, Leu, or Met; X⁵⁴ represents Asp or Asn; X⁵⁵ represents Ala or Ser; X⁵⁶ and X⁵⁷ represent Ala or Ser; X⁵⁸ represents He, Val, Leu, or Met; X⁵⁹ represents Lys or Arg; X⁶⁰ represents Ser or absent; X⁶¹ represent Ala or absent; X⁶² represents Ser, Ala, Thr, or absent; X⁶³ represents He, Val, Leu, Met, or absent; X⁶⁴ represents Ser or Thr; X⁶⁵ and X⁶⁶ represent He, Val, Leu, or Met; X⁶⁷ represents any amino acid or absent; X⁶⁸ represents He, Val, Leu, or Met; X⁶⁹ represents He, Val, Leu, Met, or Phe; X⁷⁰ represents Ser or Thr; X⁷¹ represents Glu or Asp; X⁷² represents He, Val, Leu, or Met.

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

S-X¹-L-x-X²-X³-I-x-Y-x- x-L-X'-x-x-X⁴- X'-E-L

In the above consensus sequences of SEQ ID NO: 1154, x represents any amino acid; X¹ is He, Val, Leu, or Met; X² is Glu, Asp, or Asn; X³ is Thr or Ala; and X⁴ 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 AtMYCl 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 "AtMYCl clade polypeptides" or "AtMYCl clade polypeptides", or which fall within the "AtMYCl clade" or "G581 clade" exemplified in the phylogenetic tree in Fig. 20 as those polypeptides bounded by

LOC_Os01g39560.1 and POPTR_0003sl2810.1 (indicated by the box around these sequences).

Table 15. Conserved first WRKY domain of WRKY3 and closely related sequences

ADDGYNWRKYGQKQ

Vv/GSVIVT

59% VKGSEYPRSYYKCTH

1172 0100133200 225-281 1243 94% (54/57)

(277/467) PSCPVKKKVERSLDG

1

QVTEIIYKGQHNH

ADDGYNWRKYGQKQ

Eg/Eucgr.GO 52% VKGSEFPRSYYKCTHP

1182 248-304 1253 94% (54/57) 2469.1 (255/495) TCPVKKKVERSLDGQI

TEIIYKGQHNH

ADDGYNWRKYGQKQ

Sl/Solyc05g 53% VKGSEYPRSYYKCTN

1174 215-271 1245 92% (53/57) 012770.2.1 (291/552) PNCPVKKKVERSLDG

QVTEIIYKGQHNH

ANDGYNWRKYGQKQ

Pt/POPTR_0 57% VKGSEYPRSYYKCTH

1192 222-278 1263 92% (53/57) 010s 17040.1 (302/532) PNCPVKKKVERSLDG

QVTEIIYKGQHNH

ADDPYNWRKYGQKH

Cc/clementin

61 % VKGSEFPRSYYKCTHP

1196 e0.9_007348 249-305 1267 92% (53/57)

(326/538) NCPVKKKVERSLDGQ

m

VTEIIYKGQHNH

ADDGYNWRKYGQKQ

Eg/Eucgr.BO 53% VKGSEFPRSYYKCTHP

1180 246-302 1251 91 % (52/57) 3189.1 (291/544) DCPVRKKVERSLDGHI

TEIIYKGQHNH

ADDGYNWRKYGQKQ

Gm GlymaO 51 % VKGSEFPRSYYKCTHP

1160 174-230 1231 87% (50/57) lg06550.1 (265/519) NCSVKKKVERSLEGH

VTAIIYKGEHNH

ADDGYNWRKYGQKQ

Gm GlymaO 51 % VKGSEFPRSYYKCTNP

1162 174-230 1233 87% (50/57) 2g 12490.1 (268/521) NCPVKKKVERSLEGH

VTAIIYKGEHNH

THDGYNWRKYGQKPI

Pt/POPTR_0 50% KGSEYPRSYYKCTHL

1188 237-294 1259 85% (47/55) 017sl2430.1 (281/561) NCPVKKKVERSSDGQI

TEIIYKGQHNH

ADDGYNWRKYGQKQ

Gm GlymaO 52% VKGSEYPRSYYKCTH

1168 228-284 1239 84% (48/57) 8g26230.1 (278/533) LNCVVKKKVERAPDG

HITEIIYKGQHNH

ADDGYNWRKYGQKQ

Gm Glymal 53% VKGSEYPRSYYKCTH

1170 226-282 1241 84% (48/57) 8g49830.1 (281/529) LNCVVKKKVERAPDG

HITEIIYKGQHNH

ADDGYNWRKYGQKV

Os/LOC_Os 41 % VKGSDCPRSYYKCTH

1202 269-325 1273 84% (48/57) 12g32250.1 (227/551) PNCPVKKKVEHAEDG

QISEIIYKGKHNH

ADDGYNWRKYGQKV

Zm GRMZ

43% VKGSDCPRSYYKCTH

1208 M2G076657 227-283 1279 84% (48/57)

(225/522) PNCPVKKKVEHAEDG

_T01

QISEIIYKGKHNH

Zm GRMZ ADDGYNWRKYGQKV

45%

1210 M2G076657 227-283 VKGSDCPRSYYKCTH 1281 84% (48/57)

(215/475)

_T02 PNCPVKKKVEHAEDG QISEIIYKGKHNH

ADDGYNWRKYGQKV

Zm GRMZ

49% VKGSDCPRSYYKCTH

1212 M2G143765 229-285 1283 84% (48/57)

(195/402) PNCPVKKKVEHAEDG

_T01

QISEIIYKGKHNH

ADDGYNWRKYGQKV

Si/Si021859 44% VKGSDCPRSYYKCTH

1216 228-284 1287 84% (48/57) m (230/521) PNCPVKKKVEHAEDG

QISEIIYKGKHNH

ADDGYNWRKYGQKV

Bd/Bradi4g0 43% VKGSDCPRSYYKCTH

1224 229-285 1295 84% (48/57) 6690.1 (225/529) PSCPVKKKVEHAEDG

QISEIIYKGKHNH

NDDGYNWRKYGQKH

Gm GlymaO 56% VKGRDFSRSYYKCTH

1164 74-130 1235 83% (47/56) 7g35380.1 (209/373) PNCPVKKKLERSLEGH

VTAIIYKGEHNH

TDDGYNWRKYGQKPI

Pt/POPTR_0 47% KGSEYPRSYYKCTHL

1186 208-264 1257 83% (47/56) 004s 12000.1 (258/550) NCLVKKKVERSSDGQI

TEIIYKGQHNH

NNDGYNWRKYGQKH

Gm Glyma2 48% VKGSDFSRSYYKCTRP

1166 173-229 1237 82% (46/56) 0g03410.1 (248/518) NCPVKKKLERSLEGH

VTAIIYKGEHNH

ADDGYNWRKYGQKA

Os/LOC_Os 46% VKGGEYPRSYYKCTH

1200 199-255 1271 80% (46/57) 03g33012.1 (196/425) LSCPVKKKVERSSDG

QITQILYRGQHNH

ADDGYNWRKYGQKA

Zm GRMZ

41 % VKGGEYPRSYYKCTH

1206 M2G171428 211-267 1277 78% (45/57)

(223/540) TSCPVKKK VERS AEG

_T01

HITQIIYRGQHNH

ADDGYNWRKYGQKA

Si/Si035317 44% VKGGEYPRSYYKCTH

1214 217-273 1285 78% (45/57) m (223/508) ASCPVKKKVERSGEG

HITQIIYRGQHNH

ASDGYNWRKYGQKM

Sl/Solyc03g 45% VKASECPRSYYKCTH

1178 213-269 1249 77% (44/57) 104810.2.1 (219/484) LKCL VKKK VERS IDG

HITEITYKGHHNH

ADDGYNWRKYGQKA

Bd/Bradilgl 43% VKGGEYPRSYYKCTQ

1222 205-261 1293 77% (44/57) 6120.1 (222/514) AGCPVKKKVERSACG

EITQIIYRGQHNH

TEDGYNWRKYGQKQ

Eg/Eucgr.I01 43% VKGCGFPRSYYKCSH

1184 295-351 1255 76% (43/56) 998.1 (226/527) LNCSVKKKVEHSLDG

RITEITYRGQHQH

ADDGYNWRKYGQKPI

Cc/clementin

51 % KGNEYPRSYYKCTHV

1194 e0.9_006505 275-331 1265 75% (43/57)

(265/524) NCPVKKKVERSSSAQI

m

TQIIYKNEHNH

1176 Sl/Solyc02g 44% 216-272 ACDGYNWRKYGQKK 1247 73% (42/57) 088340.2.1 (214/486) VKASECPRSYYKCTY

LKCL VKKK VERS VDG HITEITYNGRHNH

GKDGYNWRKYGQKQ

Bd/BradilgO 41% LKDAESPRSYYKCTRE

1218 190-246 1289 72% (40/55) 7970.1 (120/294) ACPVKKIVERSFDGCI

KEITYKGRHTH

AKDGYTWRKYGQKQ

Zm/GRMZ

48% LKDAESPRSYYKCTR

1204 M2G008029 219-275 1275 70% (40/57)

(112/232) DGCPVKKVVERSFDG

_T01

LIKEITYKGRHNH

ADDGYNWRKYGQKA

Bd/Bradilg2 41% VKGGR YPRS Y YKCTL

1220 176-231 1291 70% (40/57) 2680.1 (156/377) NCPVRKNVEHSEDGKI

IKIIYRGQHSH

TDDGYNWRKYGQKA

Os/LOC_Os 42% VKGGE YPKS Y YKCTH

1198 169-225 1269 67% (38/56) 07g40570.1 (149/353) LNCLVRKN VEHS ADG

RIVQIIYRGQHTH

ADDGYNWRKYGQKA

Ta ACD803

44% VKGGKYPRS Y YKCTL

1226 62.1 198-253 1297 66% (38/57)

(121/275) NCPARKNVEHSADRRI

(WRKY 19)

IKIIYRGQHCH

Table 16. Conserved second WRKY Domain of WRKY3 and closely related sequences

Col. 1 Col. 2 Col. 3 Col. 4 Col. 5 Col. 6 Col. 7

SEQ ID Species/ Percent WRKY Conserved WRKY SEQ ID Percent identity NO: Identifier identity of domain 2 in domain 2 NO: of of second polypeptide amino acid second WRKY domain in Col. 1 to coordinates WRKY in Col. 5 to WRKY3 domain WRKY domain

2 of WRKY3

LDDGYRWRKYGQK

At/WRKY3

V VKGNP YPRS Y YKC

or 100%

1156 414-471 TTPDCGVRKHVERA 1228 100% (58/58)

AT2G03340. (513/513)

ATDPKAVVTTYEGK

1

HNH

LDDGYRWRKYGQK V VKGNP YPRS Y YKC

At/AT1G139 68%

1158 408-465 TTPGCGVRKHVERA 1230 98% (57/58) 60.1 (370/541)

ATDPKAVVTTYEGK HNH

LLDDGYRWRKYGQ

Vv/GSVIVT KV VKGNP YPRS Y YK

59%

1172 0100133200 358-416 CTNPGCNVRKHVER 1244 93% (55/59)

(277/467)

1 AATDPKAVITTYEGK

HNH

LDDGYRWRKYGQK V VKGNP YPRS Y YKC

Eg/Eucgr.BO 53%

1180 418-475 TTPGCNVRKHVERAS 1252 93% (54/58) 3189.1 (291/544)

TDPKAVITTYEGKHN

H LDDGYRWRKYGQK

V VKGNP YPRS Y YKC

Gm GlymaO 51 %

1160 342-399 TTQGCNVRKHVERA 1232 91 % (53/58) lg06550.1 (265/519)

S TDPK A VITT YEGKH NH

LDDGYRWRKYGQK V VKGNP YPRS Y YKC

Gm GlymaO 51 %

1162 342-399 TTQGCNVRKHVERA 1234 91 % (53/58) 2g 12490.1 (268/521)

STDPKA VITT YEGKH NH

LDDGYRWRKYGQK V VKGNP YPRS Y YKC

Pt/POPTR_0 57%

1192 393-450 TTAGCKVRKHVERA 1264 91 % (53/58) 010s 17040.1 (302/532)

AADPKAVITTYEGKH NH

LDDGYRWRKYGQK

Cc/clementin V VKGNPHPRS Y YKC

51 %

1194 e0.9_006505 444-501 TNPGCNVRKHVERA 1266 91 % (53/58)

(265/524)

m PTDPKAVVTTYEGKH

NH

LDDGYRWRKYGQK

Cc/clementin V VKGNP YPRS Y YKC

61 %

1196 e0.9_007348 420-477 TTTGCNVRKHVERAS 1268 91 % (53/58)

(326/538)

m TDPKAVITTYEGKHN

H

LDDGYRWRKYGQK V VKGNP YPRS Y YKC

Gm Glyma2 48%

1166 324-381 TTQGCKVRKHVERA 1238 89% (52/58) 0g03410.1 (248/518)

SMDPKAVITTYEGKH NH

LDDGYRWRKYGQK V VKGNP YPRS Y YKC

Sl Solyc05gO 53%

1174 394-451 TSQGCNVRKHVERA 1246 89% (52/58)

12770.2.1 (291/552)

ASDPKAVITTYEGKH NH

LDDGYRWRKYGQK V VKGNPHPRS Y YKC

Pt/POPTR_0 50%

1188 421-478 TSAGCNVRKHVERA 1260 89% (52/58) 017s 12430.1 (281/561)

AADPKAVVTTYEGK HNH

LDDGYRWRKYGQK V VKGNP YPRS Y YKC

Pt/POPTR_0 55%

1190 390-447 TTPGCKVRKHVERA 1262 89% (52/58) 008s09140.1 (297/540)

AADPRAVITAYEGKH NH

LDDGYRWRKYGQK V VKGNP YPRS Y YKC

Gm GlymaO 56%

1164 225-282 ATQGCNVRKHVERA 1236 87% (51/58) 7g35380.1 (209/373)

SMDPKAVLTTYEGK HNH

LDDGYRWRKYGQK V VKGNPHPRS Y YKC

Gm Glymal 53%

1170 406-463 TSAGCNVRKHVERA 1242 87% (51/58) 8g49830.1 (281/529)

STDPKA VITT YEGKH NH LDDGYRWRKYGQK

Eg/Eucgr.GO 52% LVKGNPYPRSYYKCT

1182 411-468 1254 87% (51/58) 2469.1 (255/495) TTGCN VRKH VER AS S

DPKAVITTYEGKHNH

LDDGYRWRKYGQK V VKGNPHPRS Y YKC

Pt/POPTR_0 47%

1186 368-425 TSAGCNVRKHVERA 1258 87% (51/58) 004s 12000.1 (258/550)

AADPKAVITTYEGKH NH

LDDGYRWRKYGQK V VKGNPHPRS Y YKC

Gm GlymaO 52%

1168 409-466 TSAGCNVRKHVERA 1240 86% (50/58) 8g26230.1 (278/533)

SMDPKAVITTYEGKH NH

LDDGYRWRKYGQK V VKGNPHPRS Y YKC

Os/LOC_Os 41 %

1202 426-483 TYAGCNVRKHIERAS 1274 84% (49/58)

12g32250.1 (227/551)

S DPK A VITT YEGKHN H

LDDGYRWRKYGQK V VKGNPHPRS Y YKC

Si/Si021859 44%

1216 385-442 TFAGCNVRKHIERAS 1288 84% (49/58) m (230/521)

S DPK A VITT YEGKHN H

LDDGYRWRKYGQK V VKGNPHPRS Y YKC

Bd/Bradi4g0 43%

1224 386-443 TFAGCNVRKHIERAS 1296 84% (49/58) 6690.1 (225/529)

S DPK A VITT YEGKHN H

LDDGYRWRKYGQK

Zm GRMZM V VKGNPHPRS Y YKC

49%

1212 2G143765_T 386-443 TF AGCN VRKHIERC S 1284 82% (48/58)

(195/402)

01 S DPK A VITT YEGKHN

H

LDDGYKWRKYGQK VVKGTQHPRSYYRC

Sl Solyc02g0 44%

1176 386-443 TYPGCNVRKQVERA 1248 81 % (47/58) 88340.2.1 (214/486)

S TDPK A VITT YEGKH NH

LDDGFKWRKYGQK MVKGNHHPRSYYRC

Sl Solyc03gl 45%

1178 384-441 TYPGCNVRKHVERA 1250 79% (46/58) 04810.2.1 (219/484)

S ADPK A VITT YEGKH NH

LDDGFKWRKYGQK

Eg/Eucgr.I01 43% VVKGSSYPRSYYKCT

1184 473-530 1256 79% (46/58) 998.1 (226/527) YAGCNVRKHIERAAL

DPKS VITT YEGKHNH

LDDGYRWRKYGQK V VKGNPHPRS Y YKC

Os/LOC_Os 46%

1200 366-423 T YQGCD VKKHIERS S 1272 79% (46/58) 03g33012.1 (196/425)

QDPKAVITTYEGKHS H

Zm GRMZM 41 % LDDGYRWRKYGQK

1206 380-437 1278 79% (46/58) 2G171428_T (223/540) VVKGNPYPRSYYRCT 01 YQGCDVKKHIERSSQ

DPKAVITTYEGKHSH

LDDGYRWRKYGQK

Zm GRMZM VVKGNSHPRSYYKC

43%

1208 2G076657_T 384-441 TFAGCNVRKHIERAS 1280 79% (46/58)

(225/522)

01 S DPR A VITT YEGKHD

H

LDDGYRWRKYGQK

Zm GRMZM VVKGNSHPRSYYKC

45%

1210 2G076657_T 384-441 TFAGCNVRKHIERAS 1282 79% (46/58)

(215/475)

02 SDPRA VITT YEGKHD

H

LDDGYRWRKYGQK V VKGNPHPRS Y YKC

Si/Si035317 44%

1214 386-443 T YQGCD VKKHIERS S 1286 79% (46/58) m (223/508)

QDPKAVITTYEGKHS H

LDDGYRWRKYGQK V VKGNP YPRS Y YKC

Os/LOC_Os 42%

1198 338-395 TYLGCDVKKQVERS 1270 77% (45/58) 07g40570.1 (149/353)

VEEPNAVITTYEGKHI H

LDDGYRWRKYGQK

Zm/GRMZM

48% VVKGNPRPRSYYKCT

1204 2G008029_T 349-406 1276 77% (45/58)

(112/232) ADNCNVRKQIERATT

01

DPRCVLTTYTGRHNH

LDDGYRWRKYGQK

Bd/Bradilg2 41 % VVRGNPHPRSYYKCT

1220 341-398 1292 74% (43/58) 2680.1 (156/377) YQGCDVKKHIERSSQ

EPHAVITTYEGKHVH

LDDGYRWRKYGQK V VKGNPHPRS Y YKC

Bd/Bradilgl 43%

1222 374-431 TFQGCDVKKHIERCS 1294 74% (43/58) 6120.1 (222/514)

QDSTDVITTYEGKHS H

LDDGYRWRKYGQK

Ta/ACD8036

44% VVRGNPHPRSYYKCT

1226 2.1 362-419 1298 74% (43/58)

(121/275) YQGCD VKKHIERSSE

(WRKY19)

EPHAVITTYEGKHTH

LDDGYRWRKYGQK

Bd/BradilgO 41 % VVKGNPRPRSYYKCT

1218 323-380 1290 72% (42/58) 7970.1 (120/294) AENCN VRKQIER AS S

NPSCVLTTYTGRHSH

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; SI - 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:

X¹X²PxxDGYxWX³KYGQKxX⁴KxX⁵xxxX³SYX⁶KCTxxxCxVX³KxX⁴EX⁷X⁸xxGxX⁴xxIxYX³GxHx H *

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:

X⁹X³X¹⁰X¹⁰X¹⁰X¹⁰X¹⁰X¹⁰X⁴xX⁴xTxSX¹¹X⁴X¹²X⁴LLLGX⁶X³WRKYGQKX⁴VX³GNxxPRSYYX³CTx xxCxVX³KX¹³X⁴ERX⁸xxX¹X¹⁴xxVX⁴TX¹⁵YxGX³HxHxxX¹⁰PxxX³.*

*In the above consensus sequences of SEQ ID NO: 1299-1300, x represents any amino acid; X is D, N, or E; X² is K, R, or Q; X³ is R or K; X⁴ is I, L, V, or M; X⁵ is G, S, or A; X⁶ is Y or F; X⁷ is R or

8 9 10 11 12 13

H; X is S, A, or C; X is Q, H or R; X is any amino acid or absent; X is E or D; X is D or N; X is H or Q; X¹⁴ is P or S; and X¹⁵ 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 Bradilg07970.1 and Solyc03gl04810.2.1.

Table 17. Conserved NAM domain of AtNAC6 and closely related sequences

HEYRL

LPPGFRFHPTDEELISH

YLYRKVTDTNFSARAI

GEVDLNRSEPWDLPW

KAKMGEKEWYFFCV

Gm/Glyma06g2 68% 89%

1379 18-143 RDRKYPTGLRTNRAT 1439

1020.1 (149/217) (113/126)

ESGYWKATGKDKEIF

RGKSLVGMKKTLVFY

KGRAPKGEKTDWVM

HEYRL

LPPGFRFHPTDEELISH

YLYKKVIDTKFCARAI

GEVDLNKSEPWDLPW

KAKMGEKEWYFFCV

Gm Glymal7gl 69% 89%

1381 16-141 RDRKYPTGLRTNRAT 1440

0970.1 (149/214) (113/126)

EAGYWKATGKDKEIF

RGKSLVGMKKTLVFY

RGRAPKGEKSNWVM

HEYRL

LPPGFRFHPTDEELITH

YLS QKVLNS GFC A V AI

GEVDLNKCEPWDLPW

KAKMGEKEWYFFCV

Vv/GSVIVTOIO 56% 89%

1405 16-141 RDRKYPTGLRTNRAT 1452

11445001 (166/293) (113/126)

DAGYWKATGKDKEIY

KMKTLVGMKKTLVF

YKGRAPKGEKTNWV

MHEYRL

LPPGFRFHPTDEELITH

YLQKK VGDTGFS AK A

IGEVDLNKSEPWDLP

WKAKMGEKEWYFFC

Eg/Eucgr.B0052 64% 89%

1417 16-141 LRDRKYPTGLRTNRA 1458

9.1 (155/242) (113/126)

TESGYWKATGKDKEI

YRGKSLVGMKKTLVF

YRGRAPKGEKTNWV

MHEYRL

LPPGFRFHPTDEELITH

YLHKKVLDLGFSAKAI

GEVDLNKAEPWELPY

KAKIGEKEWYFFCVR

At/AT5G07680. 67% 88%

1371 17-142 DRKYPTGLRTNRATQ 1435

1 (159/236) (111/126)

AGYWKATGKDKEIFR

GKSLVGMKKTLVFYR

GRAPKGQKTNWVMH

EYRL

LPPGFRFHPTDEELISH

YLYRKVTHTNFSARAI

GEVDLNRSEPWDLPW

KAKMGEKEWYFFCV

Gm Glyma04g3 69% 88%

1377 3-128 RDRKYPTGLRTNRAT 1438

3270.1 (147/211) (112/126)

QSGYWKATGKDKEIF

RGKSLVGMKKTLVFY

KGRAPKGEKTDWVM

HEYRL LPPGFRFHPTDEELITH

YL APKVLDS GFC AI AI

GEVDLNKVEPWDLPW

KAKMGEKEWYFFCM

Sl/Solyc02g0881 56% 88%

1393 16-141 RDKKYPTGQRTNRAT 1446

80.2.1 (174/310) (111/126)

EAGYWKATGKDKEIF

KS KTL VGMKKTL VF Y

KGRAPRGEKTNWVM

HEYRL

LPPGFRFHPTDEELISH

YLYKKVLDINFSARAI

GDVDLNKSEPWELPW

KAKMGEKEWYFFCV

Pt/POPTR_0012 66% 88%

1399 17-142 RDRKYPTGLRTNRAT 1449

S01610.1 (156/234) (112/126)

EAGYWKATGKDKEIY

RGKSLVGMKKTLVFY

KGRAPKGEKTNWVM

HEYRL

LPPGFRFHPTDEELISH

YL YKK VLDITFS AK AI

GDVDLNKSEPWELPW

KAKMGEKEWYFFCV

Pt/POPTR_0015 61 % 88%

1401 17-142 RDRKYPTGLRTNRAT 1450

s02170.1 (161/262) (111/126)

EAGYWKATGKDKEIY

RGKFLVGMKKTLVFY

KGRAPKGGKTNWVM

HEYRL

LPPGFRFHPTDEELISH

YLYKKVIDTKFCARAI

GEVDLNKSEPWDLPS

KMGEKEWYFFCVRDR

Gm Glyma05g0 68% 87%

1391 16-139 KYPTGLRTNRATEAG 1445

0930.1 (148/217) (110/126)

YWKATGKDKEIFRGK

SLVGMKKTLVFYRGR

APKGEKSNWVMHEY

RL

LPPGFRFHPTDEELITH

YLS NK V VDTNF V AI AI

GDVDLNKVEPWDLP

WKAKMGEKEWYFFC

Sl/Solyc06g0697 70% 87%

1397 16-141 VRDKKYPTGLRTNRA 1448

10.2.1 (149/211) (110/126)

TAAGYWKATGKDREI

FRGKS L VGMKKTL VF

YKGRAPKGEKTNWVI

HEFRL

LPPGFRFHPTDEELITH

YLS KKVIDSNFS AR AI

GQVNLNNSEPWELPG

KAKMGEKEWYFFCV

Vv/GSVIVTOIO 72% 87%

1407 3-128 RDRKYPTGLRTNRAT 1453

07982001 (150/207) (110/126)

EAGYWKATGKDKEIF

RGKSLVGMKKTLVFY

AGRAPKGEKTNWVM

HEYRL

1403 Pt/POPTR_0017 59% 16-141 LPPGFRFHPTDEELITH 1451 86% S12210.1 (148/250) YLS QKVLDN YFC AR AI (109/126)

GEVDLNKCEPWDLPW

RAKMGEKEWYFFCVI

DRKYPTGLRTNRATD

AGYWKATGKDKEIYR

AKTLVGMKKTLVFYK

GRAPKGEKTNWVMH

EYRL

LPPGFRFHPTDEELITH

YLS KKV VDMNFS AI AI

GDVDMNKIEPWELPW

KAKIGEKEWYFFCVR

Sl/Solyc03gl l58 63% 84%

1395 18-143 DKKYPTGLRTNRATA 1447

50.2.1 (145/228) (107/126)

AGYWKATGKDKEIFR

GRSLVGMKKTLVFYR

GRAPRGEKTNWVTHE

YRL

LPPGFRFHPTDEELITH

YLYKKVLD VCFS CR AI

GDVDLNKNEPWELPW

KAKMGEKEWYFFCM

Cc/clementineO. 66% 84%

1409 16-141 RDRKYPTGLRTNRAT 1454

9_013688m (142/215) (106/126)

VSGYWKATGKDKEIY

RGKSLVGMKKTLVFY

RGRAPKGEKSSWVMH

EYRL

LPPGFRFHPTDEELITH

YLYKKVLD VCFS CR AI

GDVDLNKNEPWELPW

KAKMGEKEWYFFCM

Cc/clementineO. 57% 84%

1413 16-141 RDRKYPTGLRTNRAT 1456

9_012151m (142/248) (106/126)

VSGYWKATGKDKEIY

RGKSLVGMKKTLVFY

RGRAPKGEKSSWVMH

EYRL

LPPGFRFHPTDEELITH

YLTPKVLDGSFRARA

MGEVDLNKCEPWDLP

GQAKMGEKEWYFFC

Eg/Eucgr.I01958 72% 83%

1415 16-141 VRDRKYPTGMRTNRA 1457

.1 (121/167) (105/126)

TEAGYWKATGKDKEI

RRMKKVVGMKKTLV

FYRGRAPNGQKTNWV

MHEFRL

LPPGFRFHPTDEELITH

YLS QKVLDS CFC AR AI

GEADLNKCEPWDLPW

MAKMGEKEWYFFCV

Gm Glymal3g0 63% 82%

1383 20-145 RDRKYPTGQRTNRAT 1441

5540.1 (138/217) (104/126)

GVGYWKATGKDREIY

KAKALIGMKKTLVFY

KGRAPSGEKTSWVMH

EYRL

Gm/Glymal9g0 62% LPPGFRFHPTDEELITH 82%

1385 8-133 1442

2850.1 (141/225) YLS QKVLDS CFC AR AI (104/126) GEADLNKCEPWDLPC

MAKMGEKEWYFFCV

RDRKYPTGQRTNRAT

GAGYWKATGKDREIY

KAKTLIGMKKTLVFY

KGRAPSGEKSNWVM

HEYRL

LPAGFRFHPRDEELIN

HYLTKKVVDNCFCAV

AIAEVDLNKCEPWDL

PGLAKMGETEWYFFC

Gm/Glyma09g3 60% 80%

1387 19-144 VRDRKYPTGLRTNRA 1443

7050.1 (139/229) (101/126)

TDAGYWKATGKDREI

IMENALIGMKKTLVFY

KGRAPKGEKTNWVM

HEYRL

LPPGFRFHPTDEELITH

YLAKKVADARFAALA

VAEADLNKCEPWDLP

SLAKMGEKEWYFFCL

Os/LOC_Os04g 56% 80%

1431 12-137 KDRKYPTGLRTNRAT 1465

38720.1 (133/236) (101/126)

ESGYWKATGKDKDIF

RRKALVGMKKTLVFY

TGR APKGEKS G W VM

HEYRL

LPPGFRFHPTDEELITH

YLARKVADARFAAFA

VSEADLNKCEPWDLP

SLAKMGEKEWYFFCL

61 % 80%

1433 Si/Si010553m 11-136 KDRKYPTGLRTNRAT 1466

(134/217) (102/126)

EAGYWKATGKDKDIF

RGKALVGSKKTLVFY

TGR APKGEKS G W VM

HEYRL

LPAGFRFHPTDEELIN

QYLTKKVVDNCFCAI

AIGEVDLNKCEPWDL

PGLAKMGETEWYFFC

Gm Glymal8g4 62% 79%

1389 19-144 VRDRKFPTGIRTNRAT 1444

9620.1 (142/228) (100/126)

DIGYWKATGKDKEII

MENALIGMKKTLVFY

KGRAPKGEKTNWVM

HEYRL

LPPGFRFHPTDEELITH

YLAKKVADARFTAFA

VSEADLNKCEPWDLP

SLARMGEKEWYFFCL

Bd/Bradi5gl240 59% 79%

1421 3-129 KDRKYPTGLRTNRAT 1460

7.1 (133/222) (101/127)

ESGYWKATGKDKDIF

RGKGTLVGMKKTLVF

YTGR APKGEKS G W V

MHEYRL

LPPGFRFHPTDEELITH

Os/LOC_Os02g 54% 79%

1423 37-163 YLLRKAADPAGFAAR 1461

36880.1 (137/250) (101/127)

AVGEADLNKCEPWDL PS R ATMGEKE W YFFC

VKDRKYPTGLRTNRA

TESGYWKATGKDREI

FRGKALVGMKKTLVF

YTGRAPRGGKTGWV

MHEYRI

LPPGFRFHPTDEELITH

YLLRKAADPAGFAAR

AVGEADLNKCEPWDL

PSRATMGEKEWYFFC

Os/LOC_Os02g 54% 79%

1425 37-163 VKDRKYPTGLRTNRA 1462

36880.3 (137/250) (101/127)

TESGYWKATGKDREI

FRGKALVGMKKTLVF

YTGRAPRGGKTGWV

MHEYRI

LPPGFRFHPTDEELITH

YLLRKAADPAGFAAR

AVGEADLNKCEPWDL

PSRATMGEKEWYFFC

Os/LOC_Os02g 54% 79%

1427 37-163 VKDRKYPTGLRTNRA 1463

36880.2 (137/250) (101/127)

TESGYWKATGKDREI

FRGKALVGMKKTLVF

YTGRAPRGGKTGWV

MHEYRI

LPPGFRFHPTDEELITH

YLLRKAADPAGFAAR

AVGEADLNKCEPWDL

PSRATMGEKEWYFFC

Os/LOC_Os02g 54% 79%

1429 37-163 VKDRKYPTGLRTNRA 1464

36880.4 (136/250) (101/127)

TESGYWKATGKDREI

FRGKALVGMKKTLVF

YTGRAPRGGKTGWV

MHEYRI

LPPGFRFHPTDEELVT

HYLARKTADPTGFAA

RAVGEADLNKCEPWD

LPSRATMGEKEWYFF

Bd/Bradi3g4690 57% 78%

1419 16-142 VVKDRKYPTGTRTNR 1459

0.1 (136/237) (100/127)

ATES G Y WK ATGKDRE

ILRGKALVGMKKTLV

FYTGRAPKGGKTGWV

MHEYRL

Species abbreviations for Table 17: 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; SI - 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'GFRFHPXDEEX^WYLXXX^XXX^XFXXXAX XXX^NKXEPWX^PX X^XX^EXXV X¹¹FFxX²xDX⁴KX¹¹PTGxRTNRATxxGYWKATGKDX⁴X⁸IxxxxxX²X²GxKKTLVFYxGRAPxGxKX¹² xWVxHEXⁿRX². *

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:

X⁸xxX²X¹³X⁴X²F. *

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:

X²PxLxX⁸xX¹⁰. *

*In the above consensus sequences of SEQ ID NO: 1467, 1468 or 1469, x represents any amino acid; X¹ is P or A; X² is I, V, L, or M; X³ is H or Q; X⁴ is K or R; X⁵ is P or absent; X⁶ is G, A, or S; X⁷ is D or N; X⁸ is D or E; X⁹ is any amino acid or absent; X¹⁰ is A or S; X¹¹ is Y or F; X¹² is T or S; and X¹³ 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

071907_T01 (159/316) SRCHCSKRRKNRVKR

TIRVPAISSKVAD

RCREHEQSDAISGSKS

Sl/Solycl2g0963 47%

1517 211-256 TGSGKCHCKKRKAKD 1537 50% 50.1.1 (160/340)

RKVIRIPAISTRVAD

HPPCAAAGDGHGHGA

Os/LOC_Os08g 46% GHAHAHGGCHCSKKR

1525 191-239 1541 43% 13840.1 (153/327) KQR VRRT VR V A A AS A

RVAD

HPPCAAAGDGHGHGA

Os/LOC_Os08g 46% GHAHAHGGCHCSKKR

1527 191-239 1542 43% 13840.2 (153/327) KQR VRRT VRV A A AS A

RVAD

Table 19. Conserved WRKY DNA -binding Domain of WRKY17 and closely related sequences

DPAMLVVTYEGEHR

H

PADEFSWRKYGQKPI

Eg/Eucgr.C0401 62% KGSPFPRGYYKCSTM

1521 264-322 1552 89%

1.1 (214/343) RGCPARKHVERAPD

DPTMLIVTYEGEHRH

PADEFSWRKYGQKPI

Eg/Eucgr.C0401 63% KGSPFPRGYYKCSTM

1523 264-322 1553 89%

1.2 (210/332) RGCPARKHVERAPD

DPTMLIVTYEGEHRH

PSDEYSWRKYGQKPI

KGSPYPRGYYKCSTV

Zm GRMZM2G 50%

1529 211-269 RGCPARKHVERATD 1556 88%

071907_T01 (159/316)

DPAMLVVTYEGEHR

H

PGDEFSWRKYGQKPI

Sl Solycl2g096 47% KGSKYPRGYYKCSSL

1517 258-316 1550 83%

350.1.1 (160/340) RGCPARKHVERAMD

DPTMLIVTYEDEHCH

PADEYSWRKYGQKPI

KGSPYPRGYYRCSTV

Os/LOC_Os08g 46%

1525 241-299 KGCPARKHVERAAD 1554 81 %

13840.1 (153/327)

DPATLVVTYEGDHR

H

PADEYSWRKYGQKPI

KGSPYPRGYYRCSTV

Os/LOC_Os08g 46%

1527 241-299 KGCPARKHVERAAD 1555 81 %

13840.2 (153/327)

DPATLVVTYEGDHR

H

Species abbreviations for Tables 18 and 19: At - Arabidopsis thaliana; Cc- Citrus x Clementina; Eg- Eucalyptus grandis; Gm - Glycine max; Os - Oryza sativa; SI - 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'xFXWlX^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":

RX⁴GH ARFRRX⁵P. * 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:

CX⁶CxKxRKX⁷X²xX²xxxRX³X⁸X⁹X¹⁰SxX²X¹⁰AXⁿI. *

The consensus WRKY DNA -binding domain present in WRKY 17 clade member proteins is identifiable as SEQ ID NO: 1561 in Fig. 33F to Fig. 33G:

PxDXⁿX¹²SWRKYGQKPIKGSX¹³X¹⁴PRGYYX²CSX⁴X¹⁵X²GCPARKHVERAxDX¹⁶X¹⁷X¹⁸xLX³VTY ExXⁿHxH. *

*In the above consensus sequences of SEQ ID NO: 1558-1561, x represents any amino acid; X¹ is S or A; X² is K or R; X³ is I, V, L, or M; X⁴ is S or T; X⁵ is G, A or S; X⁶ is H or Q; X⁷ is N,

Q, or A; X⁸ is P or A; X⁹ is V or A; X¹⁰ is I, V, L, M, or A; X¹¹ is D or E; X¹² is Y or F; X¹³ is P or K; X¹⁴ is Y, F, or H; X¹⁵ is I, V, L, M, or F; X¹⁶ is D, N or E; X¹⁷ is P or S; and X¹⁸ 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 "WRKY 17 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_Os08gl3840.1 and Solycl2g096350.1.1 (indicated by the box around these sequences).

Table 20. Conserved 'Z-C2H2 domain 1 ' of ZATl 1 and closely related sequences

AT2G37430.1 (178/178) ALGGHMRRHRS

63% MHKCTICDQMFGTG

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

(113/179) QALGGHMRKHRT

Glymal3gl956 42% MHNCSICGQGFSLGQ

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

0.1 (77/180) ALGGHMRRHRA

Clementine0.9_ 50% LHECSICGQEFAMGQ

1611 89-114 1642 76% (19/25)

035547m (83/166) ALGGHMRRHRI

Glymal0g0519 41 % IHNCFICGQGFSLGQA

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

0.1 (77/185) LGGHMRRHRD

Glyma03g3305 51 % MHECSICGQEFSLGQ

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

0.1 (86/168) ALGGHMRRHRT

Glymal9g3574 50% MHECSICGQEFSLGQ

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

0.1 (87/171) ALGGHMRRHRT

Eucgr.A01232. 48% MHECSICGLKFSLGQ

1617 91-116 1645 72% (18/25)

1 (92/188) ALGGHMRRHRV

Glymal3gl955 51 % KHECSICGREFTLGQ

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

0.1 (83/160) ALGGHMKKHRI

Glymal0g0521 46% MHECSICGMEFSLGQ

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

0.1 (85/183) ALGGHMRKHRG

Glymal3gl957 45% MHECSICGMEFSLGQ

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

0.1 (83/184) ALGGHMRKHRG

Eucgr.A01231. 48% MHECSMCGLKFASG

1615 77-102 1644 65% (17/26)

1 (83/172) QALGGHMRRHRA

Eucgr.A01230. 46% MHECSVCGLKFALG

1613 90-115 1643 64% (16/25)

1 (84/179) QALGGHMRKHRA

Glymal0g0518 47% KHECTICGREFTLGQ

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

0.1 (81/169) ALGGHMKKHRI

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 ZAT 11 -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'xCxTCNxX^xSFQALGGHRAX^x x⁵.*

As shown in Fig. 36C - Fig. 36D, the instant "functionally-related and/or closely-related" ZAT 11 clade polypeptides also generally contain a consensus Z-C2H2-2 sequence, SEQ ID NO: 1647:

HxCxX⁶CxxxFxxGQALGGHMX⁵X⁵HR. *

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. 36E): LX⁷X⁸X⁹LNLX¹⁰PXⁿX¹²NDLxX¹³xX⁶FG. *

*In the above consensus sequences of SEQ ID NO: 1646-1648, x represents any amino acid; X¹ is F or Y; X² is K, R, or Q; X³ is S or C; X⁴ is N or absent; X⁵ is K or R; X⁶ is I, L, V, or M; X⁷ is E, D, or absent; X⁸ is L, M or absent; X⁹ is D or N; X¹⁰ is T or S; X¹¹ is L or F; X¹² is E or Q; and X¹³ 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 "ZATl 1 clade" or "G355 clade" exemplified in the phylogenetic tree in Fig. 35 as those polypeptides bounded by Bradilg03810.1 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:

(I) DNA-DNA:

T_m(°C)=81.5+16.6(log [Na+])+0.41(% G+C)- 0.62(% formamide)-500/L

(II) DNA-RNA:

T_m(°C)=79.8+18.5(log [Na+])+0.58(% G+C)+ 0.12(%G+C)² - 0.5(% formamide) - 820/L

(III) RNA-RNA:

T_m(°C)=79.8+18.5(log [Na+])+0.58(% G+C)+ 0.12(%G+C)² - 0.35(% formamide) - 820/L 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_m-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 (Tm) 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:

6X SSC at 65°C;

50% formamide, 4X SSC at 42°C; or

0.5X 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 0.2x SSC, 0.1% SDS at 65° C and washing twice, each wash step being about 30 minutes, or about 0.1 x 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 5-1 Ox 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 15x or more, is obtained. Accordingly, a subject nucleic acid will hybridize to a unique coding oligonucleotide with at least a 2x 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) Qverexpression/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:: Lex A-GAL4T A) 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 Lex A 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, At3gl7520, 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

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, ATI G31310, 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 Nptll coding region with the BAR gene of Streptomyces hygroscopicus that confers resistance to phosphinothricin. The Kpnl and Bglll 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. patent 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 3x10 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 5Prime-3Prime Inc. (Boulder, CO).

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/T echnol. 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. patent 8,273,954 (Rogers et al.) issued September 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. patent 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. patent 5,015,580 (Christou et al), issued May 14, 1991 ; and U.S. patent 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 CaCl₂ 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 Vllth 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. patent 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 μΜ α-naphthalene acetic acid and 4.4 μΜ 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 OD₆oo of 0.8.

Following cocultivation, the cotyledon explants are transferred to Petri dishes with selective medium comprising MS medium with 4.56 μΜ zeatin, 67.3 μΜ vancomycin, 418.9 μΜ cefotaxime and 171.6 μΜ 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. patent 5,563,055 (Townsend et al., issued October 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 Al.

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. patent 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 (0.5X MS, IX Gamborg's Vitamins, 5% sucrose, 200 μΙ/L Silwet® L77) until an A₆oo 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 To seed, since it is obtained from the To generation, and is later plated on selection plates (either kanamycin or sulfonamide). Resistant plants that are identified on such selection plates comprise the Tl 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, UT) 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

-2 -1

at a photosynthetic photon flux of approximately 200 μηιοΐ m s 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 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

-2 -1

plants have been acclimated to high light (700 μηιοΐ photons m s ) under LED light banks emitting visible light (400-700nm, 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

-2 -1

photon flux of 700 μηιοΐ photons m s and operate at an air temperature of 22°C. Forty minutes

-2 -1

acclimation to a photosynthetic photon flux of 700 μηιοΐ photons m s 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 C0₂ and H₂0 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

_2 _

used to calculate:_rates of C0₂ assimilation by photosynthesis (A, μηιοΐ C0₂ m s ); rates of H₂0 loss

_2 _

through transpiration (Tr, mmol H₂0 m s ); the conductance to C0₂ and H₂0 movement between the

_2 _

leaf and air through the stomatal pore (g_s, mol. ]¾0 m s ); the sub-stomatal CO2 concentration (Q, μηιοΐ CC^ mor¹); transpiration efficiency, the instantaneous ratio of photosynthesis to transpiration, (TE

_2 _

= A / Tr (μηιοΐ CO2 mmol H2O m s )); the rate of electron flow through photosystem two (ETR μηιοΐ e-

_2 _

m s ). Derivation of the parameters described above followed established published protocols (Long &

Bernacchi, 2003. . 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 CO2 concentration of 400 μηιοΐ

CO2 mol^"1, but also after stepwise changes in CO2 concentration to 350, 300, 450 and 500 μηιοΐ CO2 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 CO2 concentration to the sites of carboxylation (Farquhar et al., 1980. Planta\ \ 9, 78-90). Plotting the rate of photosynthesis against an estimate of the sub-stomatal CO2 concentration (Q) 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 CO2 of the leaf.

Consequently, for lines being screened, rates of photosynthesis are plotted against a regression plot of A vs. Ci generated for the control lines over a range of atmospheric C0₂ 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 C0₂ 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 μηιοΐ of electrons from PSII to photosystem one PSI will supply the NADPH and ATP required to fix one μηιοΐ of C0₂ 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 C0₂ at the active site of Rubisco, a regression of the ratio of electron flow to photosynthesis, generated over the range of C0₂ 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 Q as the control line, could indicate changes in the specificity of the Rubisco active site for 0₂ relative to C0₂ 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, UT, 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, AtMYCl, AtMYB19, ERF058, CRFl, WRKY3, ZATl l, MYB l l l, 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 C0₂ into the chloroplast, of which stomatal conductance, which regulates the transfer of C0₂ 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 AtMYB 19 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 C0₂ into the leaf, however this will increase photosynthesis to a greater extent in a C3 plant than a C4 plant, where chloroplast C0₂ 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 AtMYB 19 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

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

AtMYB 19/ 35S::m35S::oEnh:LexA: Increased z opLexA::G1309 No effect No effect

Line 8 GAL4_opLexA::GFP (17%)

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 C0₂ into the chloroplast, of which stomatal conductance, which regulates the transfer of C0₂ 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 C0₂ into the leaf, however this will increase photosynthesis to a greater extent in a C3 plant than a C4 plant, where chloroplast C0₂ 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

** 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::CRFl construct. Table 26 and Fig. 9 provide data detailing how discrimination against C relative to 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 (%o) when expressed using standard notation described

13 13 12

in Farquhar et. al., 1989, supra (δ C is a measure of the ratio of isotopes C: C, relative to the same ratio in a reference and reported herein in parts per thousand (per mil or %o)). 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 CRFl-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

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.

13 12

Table 27 and Fig. 12 provide data detailing how discrimination against C relative to 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 ¹³C is that the 6¹³C signature of the rosette increased by between 1.8 and 3.6 per mill (%o) when expressed using standard notation described

13 13 12

in Farquhar et. al. 1989, supra (δ C is a measure of the ratio of isotopes C: C, relative to the same ratio in a reference and reported herein in parts per thousand (per mil or %o)). 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 C0₂ 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

The results presented in Table 27 were determined after screening five independent transgenic events. For lines 1 , 2 and 3, the rosette 6¹³C 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 4?ased 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::5Pr 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

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 MYB 111 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::MYBl l l construct. The data in Table 29 detail a 26% decrease in stomatal conductance, a 20% decrease in H₂0 loss from the leaf through transpiration and a 12% increase in transpiration efficiency, the ratio of photosynthesis to transpiration, averaged across six independent MYB 111 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 MYB 111 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 C0₂ 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 MYB 111 -related polypeptide or overexpress a MYB 111 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 MYB 111 clade polypeptides Polypeptide SEQ ID Stomatal Transpiration

Transpiration rate

Sequence/Line NO: Conductance efficiency

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

Mybl l l/Line 2 735 Decreased (25%) Decreased (18%) Increased (2%)

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

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

Mybl l l/Line 5 735 Decreased (35%) Decreased (25%) Decreased (3%)

Mybl l l/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 C0₂ 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

* 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.

AtMYCl

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 C0₂ 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 [C0₂] 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 AtMYCl clade polypeptides

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 AtMYCl -related polypeptide or overexpress an AtMYCl 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 C0₂ 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 C0₂ concentration (CO (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 Q 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 C0₂ into the leaf, by increasing stomatal conductance to C0₂ 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 lants with altered ex ression of WRKY3 clade ol e tides

WRKY3

1156 35 Increased Increased (39%) Increased (121 %) -

/Line 3

WRKY3

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

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 Poly¬

SEQ

peptide Photosynthetic

ID Driver Target Photosynthesis Rosette [N] Sequence/ Capacity

NO:

Line

Increased

AtNAC6 35S::m35S::oEnh:LexA: opLexA:: Increased Increased

1369 Rubisco and

/Line 1 GAL4_opLexA::GFP AtNAC6 (27%) (0.3%)

RuBP

AtNAC6 35S::m35S::oEnh:LexA: opLexA:: Increased Decreased

1369 No effect

/Line 2 GAL4_opLexA::GFP AtNAC6 (16%) (0.3%)

Increased

AtNAC6 35S::m35S::oEnh:LexA: opLexA:: Increased Decreased

1369 Rubisco and

/Line 3 GAL4_opLexA::GFP AtNAC6 (25%) (0.9%)

RuBP

Increased

AtNAC6 35S::m35S::oEnh:LexA: opLexA:: Increased

1369 Rubisco and No data /Line 4 GAL4_opLexA::GFP AtNAC6 (19%)

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.

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.

ZAT11

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.

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, AtMYCl, AIMYB19, ERF058, CRF1, WRKY3, ZAT11, M YB 111, 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, AtMYCl, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111 , SPATULA, or AtMYB50 is driven by a constitutive promoter. In another embodiment, expression of AtNAC6, WRKY17, AtNPR3, AtMYCl, 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, AtMYCl, 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, AtMYCl, 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, AtMYCl, 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, AtMYCl, AtMYB 19, ERF058, CRF1, WRKY3, ZAT 11 , MYB 111, 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 AtMYCl clade, SEQ ID NO: 129, 130, or 133 of the AtMYB 19 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, AtMYCl, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB 111, 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, AtMYCl, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50-related sequences, the AtNAC6, WRKY17, AtNPR3, AtMYCl, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYB 111, 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 n n-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, AtMYCl, 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, AtMYCl, AtMYB 19, ERF058, CRF1, WRKY3, ZAT11, M YB 111, 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, AtMYCl, AtMYB 19, 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- Arabidopsis (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, AtMYCl, 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-l 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, WRKY 17 clade sequences SEQ ID NO: 1558, 1559, 1560, 1561, AtNPR3 clade sequences SEQ ID NO: 981 to 986, AtMYCl 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, MYB 111 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 Osl lg08230 promoter, an Os01g64390 promoter, an Os06gl5760 promoter, an Osl2g37560 promoter, an Os03gl7420 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 Os09gl l220 promoter, an Os04g21800 promoter, an Osl0g23840 promoter, an Os08gl3850 promoter, an Osl2g42980 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 Osl lg08230 promoter, an Os01g64390 promoter, an Os06gl5760 promoter, an

Osl2g37560 promoter, an Os03gl7420 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

Os09gl 1220 promoter, an Os04g21800 promoter, an Osl0g23840 promoter, an Os08gl3850 promoter, an Osl2g42980 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. 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, AtMYCl, AtMYB19,

ERF058, CRF1, WRKY3, ZAT11, MYB111, SPATULA, or AtMYB50 clade polypeptide, wherein the AtNAC6, WRKY17, AtNPR3, AtMYCl, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, M YB 111, 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, AtMYCl, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYBl l l, 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 AtMYCl clade, SEQ ID NO: 129, 130, or 133 of the AtMYB 19 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 MYB 111 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 Osl lg08230 promoter, an Os01g64390 promoter, an Os06gl5760 promoter, an Osl2g37560 promoter, an Os03gl7420 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 Os09gl l220 promoter, an Os04g21800 promoter, an Osl0g23840 promoter, an Os08gl3850 promoter, an Osl2g42980 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, AtMYCl, AtMYB19, ERF058, CRF1, WRKY3, ZAT11, MYBl l l, 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-l 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:

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 C0₂ concentration. Optionally, measurements are made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; and/or

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

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 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

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

-2 -1

acclimation to a light intensity of 700 μηιοΐ PAR m s ; 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 H₂0 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 μηιοΐ 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 μηιοΐ 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

-2 -1 made after 40 minutes of acclimation to a light intensity of 700 μηιοΐ PAR m s ; and/or

12 13

(i) a decrease in the ratio of the carbon isotope C to 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%o (0.5 per mille), or at least 1.0%o, 1.5%o, Woo,

12 13

2.5%o, 3 Woo, 3.5%o, or 4.0%o measured as a decrease in the ratio of C to 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.

Claims

What is claimed is:

1. A transgenic plant having greater photosynthetic resource use efficiency than a control plant;

wherein the transgenic plant comprises one or more exogenous recombinant polynucleotides comprising a photosynthetic tissue-enhanced promoter and a nucleic acid sequence that encodes a polypeptide comprising any of SEQ ID NO: 1507, 1369, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, 135, 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, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531, 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, 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, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 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, 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, 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, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 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 promoter regulates expression of the polypeptide 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 control plant does not comprise the recombinant polynucleotide; and

wherein expression of the polypeptide under the regulatory control of the promoter confers greater photosynthetic resource use efficiency in the transgenic plant relative to the control plant.

2. The transgenic plant of claim 1 , wherein the promoter is a photosynthetic tissue-enhanced promoter and the promoter does not regulate protein expression in a constitutive manner.

3. The transgenic plant of claim 2, wherein the photosynthetic tissue -enhanced promoter is an RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an Os02g09720 promoter, an Os05g34510 promoter, an Osl lg08230 promoter, an Os01g64390 promoter, an Os06gl5760 promoter, an Osl2g37560 promoter, an Os03gl7420 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

Os09gl 1220 promoter, an Os04g21800 promoter, an Osl0g23840 promoter, an Os08gl3850 promoter, an Osl2g42980 promoter, an Os03g29280 promoter, an Os03g20650 promoter, or an Os06g43920 promoter (SEQ ID NO: 1693-1719, respectively).

4. The transgenic plant of claim 1 , wherein the promoter is a trans-regulatory element that regulates expression of the polypeptide.

5. The transgenic plant of claim 1, wherein the transgenic plant has an altered trait that confers the greater photosynthetic resource use efficiency, wherein the altered trait is selected from the group consisting of:

(a) increased photosynthetic capacity, measured as an increase in the rate of light-saturated photosynthesis of at least 10% when compared to the rate of light-saturated photosynthesis of a control leaf at the same leaf -internal C0₂ concentration, with measurements 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 10%, with measurements made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; and/or

(c) a decrease in the chlorophyll content of the leaf of at least 10%, 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%, 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 10%, with measurements

_2 _

made after 40 minutes of acclimation to a light intensity of 700 μηιοΐ PAR m s ; 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 H₂0 loss from the leaf of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μηιοΐ 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 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μηιοΐ PAR m-2 s-1 ; and/or (h) a decrease in the relative limitation that non-photochemical quenching exerts on the operation of PSII measured as a decrease in leaf non-photochemical quenching of at least 2% after 40 minutes of

-2 -1

acclimation to a light intensity of 700 μηιοΐ PAR m s ; and/or

12 13

(i) a decrease in the ratio of the carbon isotope C to 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

12 13

least 0.5%o (0.5 per mille), measured as a decrease in the ratio of C to 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%.

6. The transgenic plant of claim 1, wherein a plurality of the transgenic plants have greater yield or greater cumulative canopy photosynthesis than the yield or canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density.

7. The transgenic plant of claim 1, wherein the transgenic plant is selected from the group consisting of a dicot plant, monocot plant, 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.

8. A method for increasing photosynthetic resource use efficiency in a plant, the method comprising:

(a) providing at least one transgenic plant that comprises one or more exogenous recombinant polynucleotides comprising a non-constitutive promoter and a nucleic acid sequence that encodes a polypeptide comprising any of SEQ ID NO: 1507, 1369, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, 135, 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, 1509, 1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531, 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, 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, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 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, 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, 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, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 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 at least one transgenic plants; and

(c) optionally, crossing one of the at least one transgenic plants 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;

wherein expression of the polypeptide in the at least one transgenic plants confers increased photosynthetic resource use efficiency relative to a control plant that does not comprise the recombinant polynucleotide.

9. The method of claim 8, wherein the photosynthetic tissue-enhanced promoter is an RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an Os02g09720 promoter, an Os05g34510 promoter, an Osl lg08230 promoter, an Os01g64390 promoter, an Os06gl5760 promoter, an Osl2g37560 promoter, an Os03gl7420 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 Os09gl l220 promoter, an Os04g21800 promoter, an Osl0g23840 promoter, an Os08gl3850 promoter, an Osl2g42980 promoter, an Os03g29280 promoter, an Os03g20650 promoter, or an Os06g43920 promoter (SEQ ID NO: 1693-1719, respectively).

10. The method of claim 8, wherein an expression cassette comprising the recombinant polynucleotide is introduced into a target plant to produce the transgenic plant.

11. The method of claim 8, wherein the transgenic plant has an altered trait that confers the greater photosynthetic resource use efficiency, wherein the altered trait is selected from the group consisting of:

(a) increased photosynthetic capacity, measured as an increase in the rate of light-saturated photosynthesis of at least 10% when compared to the rate of light-saturated photosynthesis of a control leaf at the same leaf -internal C0₂ concentration, with measurements 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 10%, with measurements made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; and/or (c) a decrease in the chlorophyll content of the leaf of at least 10%, 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%, 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 10%, with measurements

-2 -1

made after 40 minutes of acclimation to a light intensity of 700 μηιοΐ PAR m s ; 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 of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μηιοΐ 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 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μηιοΐ PAR m-2 s-1 ; and/or

(h) a decrease in the relative limitation that non-photochemical quenching exerts on the operation of PSII measured as a decrease in leaf non-photochemical quenching of at least 2% after 40 minutes of

-2 -1

acclimation to a light intensity of 700 μηιοΐ PAR m s ; and/or

12 13

(i) a decrease in the ratio of the carbon isotope C to 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

12 13

least 0.5%o (0.5 per mille), measured as a decrease in the ratio of C to 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%.

12. The method of claim 8, wherein the transgenic plant is selected for having the increased

photosynthetic resource use efficiency relative to the control plant.

13. The method of claim 8, wherein the non-constitutive promoter is a photosynthetic tissue -enhanced promoter.

14. The method of claim 8, wherein a plurality of the transgenic plants have yield or greater cumulative canopy photosynthesis than the yield or canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density.

15. The method of claim 8, wherein the transgenic plant is selected from the group consisting of a dicot plant, monocot plant, 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.

16. A method for producing and selecting a crop plant with greater yield or photosynthetic resource use efficiency than a control plant, the method comprising:

(a) providing one or more transgenic plants that each comprise one or more exogenous recombinant polynucleotides that comprise a photosynthetic tissue -enhanced promoter that regulates a polypeptide encoded by the recombinant polynucleotide, wherein the polypeptide comprises any of SEQ ID NO: 1507, 1369, 864, 1016, 2, 490, 307, 1156, 1591, 735, 625, 135, 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, 1509,

1511, 1513, 1515, 1517, 1519, 1521, 1523, 1525, 1527, 1529, 1531, 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, 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, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 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, 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, 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, 1593, 1595, 1597, 1599, 1601, 1603, 1605, 1607, 1609, 1611, 1613, 1615, 1617, 737, 739, 741, 743, 745, 747, 749, 751, 753, 755, 757, 759, 761, 763, 765, 767, 769, 771, 773, 775, 777, 779, 781, 783, 627, 629, 631, 633, 635, 637, 639, 641, 643, 645, 647, 649, 651, 653, 655, 657, 659, 661, 663, 665, 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 wherein the photosynthetic tissue -enhanced promoter does not regulate protein expression in a constitutive manner;

(b) growing a plurality of the transgenic plants;

(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; and (d) optionally, 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;

wherein expression of the polypeptide in the selected transgenic plant confers the greater yield of the selected transgenic plant relative to the control plant.

17. The method of claim 16, 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.

18. The method of claim 16, wherein the selected transgenic plant has an altered trait that confers the greater photosynthetic resource use efficiency, wherein the altered trait is selected from the group consisting of:

(a) increased photosynthetic capacity, measured as an increase in the rate of light-saturated photosynthesis of at least 10% when compared to the rate of light-saturated photosynthesis of a control leaf at the same leaf -internal C0₂ concentration, with measurements 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 10%, with measurements made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; and/or

(c) a decrease in the chlorophyll content of the leaf of at least 10%, 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%, 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 10%, with measurements

_2 _

made after 40 minutes of acclimation to a light intensity of 700 μηιοΐ PAR m s ; 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 of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μηιοΐ 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 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μηιοΐ PAR m-2 s-1 ; and/or (h) a decrease in the relative limitation that non-photochemical quenching exerts on the operation of PSII measured as a decrease in leaf non-photochemical quenching of at least 2% after 40 minutes of

-2 -1

acclimation to a light intensity of 700 μηιοΐ PAR m s ; and/or

12 13

(i) a decrease in the ratio of the carbon isotope C to 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

12 13

least 0.5%o (0.5 per mille), measured as a decrease in the ratio of C to 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%.