Transgenic Plants With Enhanced Traits

Abstract

This disclosure provides transgenic plants having enhanced traits such as increased yield, increased nitrogen use efficiency and enhanced drought tolerance; propagules, progeny and field crops of such transgenic plants; and methods of making and using such transgenic plants. This disclosure also provides methods of producing hybrid seed from such transgenic plants, growing such seed and selecting progeny plants with enhanced traits. Also disclosed are transgenic plants with altered phenotypes which are useful for screening and selecting transgenic events for the desired enhanced trait.

We claim: 
     
         1 . A plant comprising a recombinant DNA molecule comprising a polynucleotide encoding a polypeptide, wherein the nucleotide sequence of the polynucleotide is selected from the group consisting of:
 a) a nucleotide sequence as set forth in 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 or 115;   b) a nucleotide sequence encoding a protein, said protein having an amino acid sequence as set forth in 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, 59-92 or 116;   c) a nucleotide sequence with 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% or at least 99% identity to 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 or 115; and   d) a nucleotide sequence encoding a protein with 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% or at least 99% identity to 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, 59-92 or 116;   wherein said plant has an enhanced trait as compared to a control plant.   
     
     
         2 . The plant of  claim 1 , wherein said enhanced trait is selected from the group consisting of increased yield, increased nitrogen use efficiency, and increased water use efficiency. 
     
     
         3 . The plant of  claim 1 , wherein said plant has at least one phenotype selected from the group consisting of anthocyanin, biomass, canopy area, chlorophyll score, plant height, water applied, water content and water use efficiency that is altered for said plant as compared to a control plant. 
     
     
         4 . The plant of  claim 1 , wherein the recombinant DNA molecule further comprises a heterologous promoter that is operably linked to the polynucleotide encoding a polypeptide, wherein said promoter is selected from the group consisting of a constitutive, inducible, tissue specific, diurnally regulated, tissue enhanced, and cell specific promoter. 
     
     
         5 . The plant of  claim 1 , wherein said plant is a progeny, a propagule, or a field crop. 
     
     
         6 . The plant of  claim 5 , wherein said field crop is selected from the group consisting of corn, soybean, cotton, canola, rice, barley, oat, wheat, turf grass, alfalfa, sugar beet, sunflower, quinoa and sugar cane. 
     
     
         7 . The plant of  claim 5 , wherein said propagule is selected from the group consisting of a cell, pollen, ovule, flower, embryo, leaf, root, stem, shoot, meristem, grain and seed. 
     
     
         8 . The plant of  claim 1 , wherein said plant is a monocot plant or is a member of the family Poaceae, wheat plant, maize plant, sweet corn plant, rice plant, wild rice plant, barley plant, rye, millet plant, sorghum plant, sugar cane plant, turfgrass plant, bamboo plant, oat plant, brome-grass plant,  Miscanthus  plant, pampas grass plant, switchgrass (Panicum) plant, and/or teosinte plant, or is a member of the family Alliaceae, onion plant, leek plant, garlic plant; or wherein the plant is a dicot plant or is a member of the family Amaranthaceae, spinach plant, quinoa plant, a member of the family Anacardiaceae, mango plant, a member of the family Asteraceae, sunflower plant, endive plant, lettuce plant, artichoke plant, a member of the family Brassicaceae,  Arabidopsis thaliana  plant, rape plant, oilseed rape plant, broccoli plant, Brussels sprouts plant, cabbage plant, canola plant, cauliflower plant, kohlrabi plant, turnip plant, radish plant, a member of the family Bromeliaceae, pineapple plant, a member of the family Caricaceae, papaya plant, a member of the family Chenopodiaceae, beet plant, a member of the family Curcurbitaceae, melon plant, cantaloupe plant, squash plant, watermelon plant, honeydew plant, cucumber plant, pumpkin plant, a member of the family Dioscoreaceae, yam plant, a member of the family Ericaceae, blueberry plant, a member of the family Euphorbiaceae, cassava plant, a member of the family Fabaceae, alfalfa plant, clover plant, peanut plant, a member of the family Grossulariaceae, currant plant, a member of the family Juglandaceae, walnut plant, a member of the family Lamiaceae, mint plant, a member of the family Lauraceae, avocado plant, a member of the family Leguminosae, soybean plant, bean plant, pea plant, a member of the family Malvaceae, cotton plant, a member of the family Marantaceae, arrowroot plant, a member of the family Myrtaceae, guava plant, eucalyptus plant, a member of the family Rosaceae, peach plant, apple plant, cherry plant, plum plant, pear plant, prune plant, blackberry plant, raspberry plant, strawberry plant, a member of the family Rubiaceae, coffee plant, a member of the family Rutaceae, citrus plant, orange plant, lemon plant, grapefruit plant, tangerine plant, a member of the family Salicaceae, poplar plant, willow plant, a member of the family Solanaceae, potato plant, sweet potato plant, tomato plant,  Capsicum  plant, tobacco plant, tomatillo plant, eggplant plant,  Atropa belladona  plant,  Datura stramonium  plant, a member of the family Vitaceae, grape plant, a member of the family Umbelliferae, carrot plant, or a member of the family Musaceae, banana plant; or wherein the plant is a member of the family Pinaceae, cedar plant, fir plant, hemlock plant, larch plant, pine plant, or spruce plant. 
     
     
         9 . A method for producing a plant comprising:
 introducing into a plant cell a recombinant DNA molecule comprising a polynucleotide encoding a polypeptide, wherein the polynucleotide comprises a polynucleotide sequence selected from the group consisting of:   a) a nucleotide sequence as 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 or 115;   b) a nucleotide sequence encoding a protein comprising an amino acid sequence as set forth in 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, 59-92 or 116;   c) a nucleotide sequence with 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% or at least 99% identity to 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 or 115; and   d) a nucleotide sequence encoding a protein with 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% or at least 99% identity to 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, 59-92 or 116;   and growing a plant from said plant cell.   
     
     
         10 . The method of  claim 9 , further comprising selecting a plant with an enhanced trait as compared to a control plant, wherein said enhanced trait is selected from increased yield, increased nitrogen use efficiency, and increased water use efficiency as compared to a control plant. 
     
     
         11 . The plant of  claim 9 , further comprising selecting a plant with a phenotype selected from the group consisting of anthocyanin, biomass, canopy area, chlorophyll score, plant height, water applied, water content and water use efficiency, wherein said phenotype for said plant is altered as compared to a control plant. 
     
     
         12 . A method for increasing yield, increasing nitrogen use efficiency, or increasing water use efficiency in a plant comprising:
 crossing the plant of  claim 1  with itself, a second plant from the same plant line, a wild type plant, or a second plant from a different line of plants to produce a seed;   growing said seed to produce a plurality of progeny plants; and   selecting a progeny plant with increased yield, increased nitrogen use efficiency, or increased water use efficiency.   
     
     
         13 . A recombinant DNA molecule, said molecule comprising a promoter operably linked to a polynucleotide that is transcribed into a non-coding miRNA molecule, wherein:
 a) said non-coding miRNA molecule is selected from the group consisting of:
 i) a non-coding miRNA molecule which, when present in a plant, provides an altered level of a protein as compared to a control plant, wherein said protein is selected from the group consisting of: a phosphate transporter protein, an APETALA2-like transcription factor, an ANR1 MADS-box protein, an E3 ligase SCF complex F-box protein, a HOS1 protein, a bHLH transcription factor, a diphenol oxidase proteinligase; 
 ii) a non-coding miRNA molecule which, when present in a plant, provides an altered level of a protein as compared to a control plant, wherein said protein is selected from the group consisting of: the polypeptide sequences set forth in SEQ ID NO: 108, 110, 112 and 114; 
 iii) a non-coding miRNA molecule which, when present in a plant, interferes with the functioning of one or more species of an endogenous miRNA selected from the group consisting of: miR399, miR172, miR166, miR166, miR444, miR393 and miR397; 
 iv) a non-coding miRNA molecule comprising a miRNA binding site sequence as set forth in SEQ ID NOs: 100-106; 
 v) a non-coding miRNA molecule comprising a miRNA polynucleotide sequence as set forth in SEQ ID NOs: 93-99; and 
   b) said promoter is selected from the group consisting of a constitutive promoter, a developmental promoter, a tissue enhanced promoter, a tissue preferred promoter, a tissue specific promoter, a cell type-specific promoter, an inducible promoter and a diurnal promoter;   wherein, when said recombinant DNA molecule is present in a plant, said plant exhibits an altered phenotype or an enhanced trait as compared to a control plant.   
     
     
         14 . A plant comprising a recombinant DNA molecule, said molecule comprising a heterologous promoter functional in plant cells operably linked to a polynucleotide that is transcribed into a non-coding miRNA molecule, wherein
 a) said non-coding miRNA molecule is selected from the group consisting of:
 i) a non-coding miRNA molecule which, when present in a plant, provides an altered level of a protein as compared to a control plant, wherein said protein is selected from the group consisting of: a phosphate transporter protein, an APETALA2-like transcription factor, an ANR1 MADS-box protein, an E3 ligase SCF complex F-box protein, a HOS1 protein, a bHLH transcription factor, a diphenol oxidase proteinligase; 
 ii) a non-coding miRNA molecule which, when present in a plant, provides an altered level of a protein as compared to a control plant, wherein said protein is selected from the group consisting of: the polypeptide sequences set forth in SEQ ID NO: 108, 110, 112 and 114; 
 iii) a non-coding miRNA molecule which, when present in a plant, interferes with the functioning of one or more species of an endogenous miRNA selected from the group consisting of: miR399, miR172, miR166, miR166, miR444, miR393 and miR397; 
 iv) a non-coding miRNA molecule comprising a miRNA binding site sequence as set forth in SEQ ID NOs: 100-106; 
 v) a non-coding miRNA molecule comprising a miRNA polynucleotide sequence as set forth in SEQ ID NOs: 93-99; and 
   b) said promoter is selected from the group consisting of a constitutive promoter, a developmental promoter, a tissue enhanced promoter, a tissue preferred promoter, a tissue specific promoter, a cell type-specific promoter, an inducible promoter and a diurnal promoter;   wherein said plant has an enhanced trait as compared to a control plant.   
     
     
         15 . A method for producing a plant comprising:
 introducing into a plant cell a recombinant DNA molecule comprising a heterologous promoter functional in plant cells operably linked to a polynucleotide that is transcribed into a non-coding miRNA molecule, wherein   a) said plants exhibit an altered level of a protein selected from the group consisting of: a phosphate transporter protein, an APETALA2-like transcription factor, an ANR1 MADS-box protein, an E3 ligase SCF complex F-box protein, a HOS1 protein, a bHLH transcription factor, a diphenol oxidase proteinligase; or   b) said plants exhibit an altered level of a protein selected from the group consisting of: the polypeptides set forth in SEQ ID NO: 108, 110, 112 and 114; or   c) said non-coding miRNA molecule interferes with the functioning of one or more species of an endogenous miRNA selected from the group consisting of: miR399, miR172, miR166, miR166, miR444, miR393 and miR397; or   d) said non-coding miRNA molecule comprises a miRNA binding site polynucleotide sequence as set forth in SEQ ID NOs: 100-106; or   e) said non-coding miRNA molecule comprises a miRNA polynucleotide sequence as set forth in SEQ ID NOs: 93-99; and   growing a plant from said plant cell.