Manipulating plant sensitivity to light

Abstract

The present disclosure identifies new genes which have the potential to increase broad acre yield in crops. This disclosure is based upon our fundamental knowledge of light signal transduction and our understanding of the roles these genes play in regulating plant growth and development in response to light. Transgenic plants with gain- or loss-of-function of one of these genes, or in combination, are expected to show significant improvements in broad acre yield and stress tolerance.

1 - 31 . (canceled) 
     
     
         32 . A method for modifying a trait in a plant, the method comprising the steps of:
 providing a target plant comprising at least one recombinant polynucleotide comprising at least one nucleotide sequence that encodes a polypeptide, wherein the nucleotide sequence is selected from the group consisting of:   (a) a nucleotide sequence set forth as SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 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, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233; 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, 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 549;   (b) a nucleotide sequence encoding SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 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, 210, 212, 214, 216, 218, 220, 222, 224, 226, 228, 230, 232, 234, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 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, 550, or any of SEQ ID NO: 235 to 427; and   (c) a nucleotide sequence encoding a polypeptide wherein the polypeptide has a percentage identity to at least one of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 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, 210, 212, 214, 216, 218, 220, 222, 224, 226, 228, 230, 232, 234, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 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, 550, or any of SEQ ID NO: 235 to 427;   wherein the nucleotide sequence is operably linked to a promoter that is expressed in a plant cell;   
       wherein the target plant overexpresses the polypeptide and said overexpression results in the target plant expressing the modified trait;
 wherein the percentage identity is selected from the group consisting of 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 61%, at least 62%, at least 63%, at least 64%, at least 65%, at least 66%, at least 67%, at least 68%, at least 69%, 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%, at least 96%, at least 97%, at least 98%, at least 99% and 100%; 
 wherein the modified trait is selected from the group consisting of decreased sensitivity to light, increased yield, greater height, greater stem diameter, greater resistance to lodging, increased branching, increased secondary rooting, greater cold tolerance, greater tolerance to water deprivation, reduced stomatal conductance, altered C/N sensing, increased tolerance to nitrogen limiting conditions, improved late season growth and vigor, greater number of primary nodes, greater late season canopy coverage, increased tolerance to abiotic stress, increased tolerance to hyperosmotic stress, altered levels of ureides, altered levels of hexose sugars, altered sucrose phosphate synthase (SPS) activity, altered levels of starch, and delayed senescence, as compared to a control plant that does not comprise the recombinant polynucleotide; and, 
 optionally, selecting a transgenic plant having at least one of the modified traits as compared to the control plant. 
 
     
     
         33 . The method of  claim 32 , wherein the target plant comprises a second recombinant polynucleotide comprising a trans-acting element that controls expression of the polypeptide. 
     
     
         34 . The method of  claim 33 , wherein the target plant expresses a protein encoded by a nucleic acid selected from the group consisting of: SEQ ID NO: 429, SEQ ID NO: 431, SEQ ID NO: 433, and SEQ ID NO: 529. 
     
     
         35 . A transgenic plant produced by the method of  claim 32 , wherein the transgenic plant comprises the at least one recombinant polynucleotide of  claim 32 . 
     
     
         36 . A seed from the transgenic plant of  claim 35 , wherein the seed comprises the at least one recombinant polynucleotide. 
     
     
         37 . A transgenic progeny plant, or a part thereof, produced by growing the seed of  claim 36 . 
     
     
         38 . The transgenic progeny plant of  claim 37 , wherein the transgenic progeny plant has a modified trait relative to a control plant,
 wherein the modified trait is selected from the group consisting of decreased sensitivity to light, increased yield, greater height, greater stem diameter, greater resistance to lodging, increased branching, increased secondary rooting, greater cold tolerance, greater tolerance to water deprivation, reduced stomatal conductance, altered C/N sensing, increased tolerance to nitrogen limiting conditions, improved late season growth and vigor, greater number of primary nodes, greater late season canopy coverage, increased tolerance to abiotic stress, increased tolerance to hyperosmotic stress, altered levels of ureides, altered levels of hexose sugars, altered SPS activity, altered levels of starch, and delayed senescence, as compared to a control plant that does not comprise the recombinant polynucleotide.   
     
     
         39 . A tissue culture produced from protoplasts or cells from the transgenic plant of  claim 35 , wherein said cells or protoplasts are produced from a plant part selected from the group consisting of leaf, pollen, ovule, embryo, cotyledon, hypocotyl, meristematic cell, root, root tip, pistil, anther, flower, seed, shoot, stem, pod and petiole. 
     
     
         40 . A regenerated plant regenerated from the tissue culture of  claim 39 . 
     
     
         41 . The method of  claim 32 , wherein the target plant is stably transformed with the at least one recombinant polynucleotide. 
     
     
         42 . The method of  claim 32 , wherein the promoter is a constitutive, inducible, tissue-specific, tissue-enhanced, cell-enhanced, or cell-specific promoter. 
     
     
         43 . The method of  claim 32 , wherein the promoter:
 regulates expression of the polypeptide in vascular, shoot apical meristem, hypocotyl or leaf primordia tissue;   or the promoter is a light-regulated promoter;   or the promoter is a stress-inducible promoter.   or the promoter is a diurnally-regulated promoter.   or the promoter is a chemically-inducible promoter.   
     
     
         44 . The method of  claim 32 , the method steps further comprising:
 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.   
     
     
         45 . The method of  claim 32 , wherein:
 the target plant is a monocot plant, a dicot plant, or a conifer plant; and/or   the at least one nucleotide sequence is derived from the dicot plant, the monocot plant, or the conifer plant; and   optionally, the dicot plant, the monocot plant, or the conifer plant is selected from the group consisting of: the family Pinaceae, cedar, fir, hemlock, larch, pine, spruce, the family Alliaceae, onion, leek, garlic, the family Amaranthaceae, spinach, the family Anacardiaceae, mango, the family Asteraceae, sunflower, endive, lettuce, artichoke, the family Brassicaceae,  Arabidopsis thaliana , rape, oilseed rape, canola, cauliflower, turnip, radish, broccoli, cabbage, cauliflower, Brussels sprouts, kohlrabi, the family Bromeliaceae, pineapple, the family Caricaceae, papaya, the family Chenopodiaceae, beet, the family Curcurbitaceae, melon, cantaloupe, squash, watermelon, honeydew, cucumber, pumpkin, the family Dioscoreaceae, yam, the family Ericaceae, blueberry, the family Euphorbiaceae, cassava, the family Fabaceae, alfalfa, clover, peanut, the family Grossulariaceae, currant; the family Juglandaceae, walnut, the family Lamiaceae, mint, the family Lauraceae, avocado, the family Leguminosae, soybean, bean, pea, the family Malvaceae, cotton, the family Marantaceae, arrowroot, the family Myrtaceae, guava, eucalyptus, the family Rosaceae, peach, apple, cherry, plum, pear, prune, blackberry, raspberry, strawberry, the family Rubiaceae, coffee, the family Rutaceae, citrus, orange, lemon, grapefruit, tangerine, the family Salicaceae, poplar, willow, the family Solanaceae, potato, sweet potato, tomato,  Capsicum , tobacco, tomatillo, eggplant,  Atropa belladona, Datura stramonium , the family Vitaceae, grape, the family Umbelliferae, carrot, the family Musaceae, banana, the family Poaceae, wheat, maize, sweet corn, rice, wild rice, barley, rye; millet, sorghum, sugar cane, turfgrass, bamboo, oats, brome-grass,  Miscanthus , pampas grass, switchgrass ( Panicum ), and teosinte.   
     
     
         46 . A method for modifying a trait in a plant, the method comprising the steps of:
 introducing into a target plant at least one recombinant polynucleotide that suppresses the expression of at least a polypeptide, wherein the polypeptide is encoded by a polynucleotide comprising a nucleotide sequence selected from the group consisting of:   (a) a nucleotide sequence set forth as SEQ ID NO: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 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, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233; 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, 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 549;   (b) a nucleotide sequence encoding SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 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, 210, 212, 214, 216, 218, 220, 222, 224, 226, 228, 230, 232, 234, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 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, 550, or any of SEQ ID NO: 235 to 427;   (c) a nucleotide sequence encoding a polypeptide wherein the polypeptide has a percentage identity to at least one of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 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, 210, 212, 214, 216, 218, 220, 222, 224, 226, 228, 230, 232, 234, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 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, 550, or any of SEQ ID NO: 235 to 427; and   wherein the percentage identity is selected from the group consisting of 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 61%, at least 62%, at least 63%, at least 64%, at least 65%, at least 66%, at least 67%, at least 68%, at least 69%, 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%, at least 96%, at least 97%, at least 98%, at least 99% and 100%;   wherein the nucleotide sequence is operably linked to a promoter that is expressed in a plant cell;   wherein the target plant overexpresses the polypeptide and said overexpression results in the target plant expressing the modified trait wherein the modified trait is selected from the group consisting of decreased sensitivity to light, increased yield, greater height, greater stem diameter, greater resistance to lodging, increased branching, increased secondary rooting, greater cold tolerance, greater tolerance to water deprivation, reduced stomatal conductance, altered C/N sensing, increased tolerance to nitrogen limiting conditions, improved late season growth and vigor, greater number of primary nodes, greater late season canopy coverage, increased tolerance to abiotic stress, increased tolerance to hyperosmotic stress, altered levels of ureides, altered levels of hexose sugars, altered SPS activity, altered levels of starch, and delayed senescence, as compared to a control plant that does not comprise the recombinant polynucleotide; and optionally, selecting a transgenic plant having at least one of the modified traits as compared to the control plant.   
     
     
         47 . The method of  claim 46 , wherein the target plant comprises a second recombinant polynucleotide comprising a trans-acting element that controls expression of the polypeptide. 
     
     
         48 . The method of  claim 46 , wherein the target plant expresses a protein encoded by a nucleic acid selected from the group consisting of: SEQ ID NO: 429, SEQ ID NO: 431, SEQ ID NO: 433, and SEQ ID NO: 529. 
     
     
         49 . The method of  claim 46 , wherein the target plant is stably transformed with the at least one recombinant polynucleotide. 
     
     
         50 . The method of  claim 46 , wherein the promoter is a constitutive, inducible, tissue-specific, tissue-enhanced, cell-enhanced, or cell-specific promoter.