Polynucleotide and polypeptide sequences associated with herbicide tolerance

Abstract

This invention relates generally to the detection of genetic differences among soybeans. More particularly, soybean quantitative trait loci (QTL) associated with herbicide tolerance, including tolerance to one or more of an HPPD-inhibitor herbicide, such as mesotrione and isoxazole herbicides, and/or a PPO inhibitor herbicide; soybean plants possessing these QTLs; and genetic markers that are indicative of phenotypes associated with such herbicide tolerance are provided. Methods and compositions for use of these markers in genotyping of soybean and selection are also disclosed, as are methods and compositions for use of herbicides for weed control. Also disclosed are isolated polynucleotides and polypeptides relating to such tolerance or sensitivity and methods of introgressing such tolerance into a plant by breeding or transgenically, or by a combination thereof. Plant cells, plants, and seeds produced are also provided.

1 .- 6 . (canceled) 
     
     
         7 . An isolated polynucleotide comprising a nucleic acid sequence encoding an ABC transporter polypeptide;
 wherein the ABC transporter polypeptide comprises an amino acid sequence at least 80% identical over its full length to SEQ ID NO: 128;   wherein the ABC transporter polypeptide confers tolerance or improved tolerance to one or more herbicides; and   wherein the ABC transporter polypeptide comprises one or more amino acid substitutions, said amino acid substitutions selected from the group consisting of E478X, V520X, L584X, S611X, K961X, L1038X, and G1120X based on the amino acid positions of SEQ ID NO:128.   
     
     
         8 . The isolated polynucleotide of  claim 7 , wherein the one or more herbicides are selected from the group consisting of a mesotrione herbicide, an isoxazole herbicide, and a PPO inhibitor herbicide. 
     
     
         9 . The isolated polynucleotide of  claim 7 , wherein the ABC transporter polypeptide comprises an amino acid sequence at least about 95% identical over its full length to SEQ ID NO:128. 
     
     
         10 . (canceled) 
     
     
         11 . The isolated polynucleotide of  claim 7 , wherein the one or more amino acid substitutions are selected from the group consisting of E478G, V520A, L584I, S611I, K961R, L1038M, and G1120R based on the amino acid positions of SEQ ID NO:128. 
     
     
         12 . The isolated polynucleotide of  claim 7 , wherein the one or more amino acid substitutions comprise all of the amino acid substitutions E478G, V520A, L584I, S611I, K961R, L1038M, and G1120R based on the amino acid positions of SEQ ID NO:128. 
     
     
         13 . An isolated polynucleotide comprising a nucleic acid sequence at least about 95% identical to the full length of SEQ ID NO: 124. 
     
     
         14 . (canceled) 
     
     
         15 . The isolated polynucleotide of  claim 7 , further comprising an operably linked promoter functional in a host cell. 
     
     
         16 . The isolated polynucleotide of  claim 15 , wherein the host cell is a plant cell. 
     
     
         17 . The isolated polynucleotide of  claim 16 , wherein the plant cell is from corn, rice, sorghum, barley, oats, sugarcane, wheat, canola, soybean, alfalfa, sunflower, or safflower. 
     
     
         18 .- 23 . (canceled) 
     
     
         24 . A plant comprising an isolated polynucleotide, wherein the isolated polynucleotide is selected from the group consisting of the isolated polynucleotide of  claim 7  and a polynucleotide having a sequence at least 95% identical to one of SEQ ID NOS: 122-125. 
     
     
         25 . A plant comprising an isolated polynucleotide encoding an ABC transporter polypeptide,
 wherein said ABC transporter polypeptide comprises an amino acid sequence at least 80% identical over its full length to SEQ ID NO: 128 or SEQ ID NO: 129;   wherein said polynucleotide comprises a G at position 1455, a C at position 1581, an A at position 1772, a T at position 1854, a G at position 1954, a C at position 2773, a G at position 2904, a Tat position 3073, an A at position 3134, a G at position 3136, an A at position 3380, and a T at position 3882 based on the nucleotide positions of the sequence set forth in SEQ ID NO:124; and   wherein the plant shows tolerance to one or more herbicides selected from the group consisting of a mesotrione herbicide, an isoxazole herbicide, and a PPO inhibitor herbicide.   
     
     
         26 . A cell of the plant of  claim 25 . 
     
     
         27 . A seed of the plant of  claim 25 . 
     
     
         28 .- 33 . (canceled) 
     
     
         34 . A method to confer tolerance or improved tolerance to one or more herbicides, the method comprising:
 a. introducing into a plant cell a polynucleotide of  claim 7  operably linked to a promoter functional in the plant cell to produce a transformed plant cell; and   b. selecting a transformed plant cell having the polynucleotide stably incorporated into its genome.   
     
     
         35 . The method of  claim 34 , wherein the one or more herbicides are selected from the group consisting of a mesotrione herbicide, an isoxazole herbicide, and a PPO inhibitor herbicide. 
     
     
         36 . The method of  claim 34 , wherein the selecting comprises exposing the transformed plant cell to the one or more herbicides, wherein the one or more herbicides are at a concentration that inhibits the growth of an untransformed plant cell, and identifying the transformed plant cell by its ability to grow in the presence of the herbicide. 
     
     
         37 . (canceled) 
     
     
         38 . A method for selectively controlling weeds in a field containing a crop comprising:
 (a) planting a field with crop seeds or plants comprising the isolated polynucleotide of  claim 7 , wherein the seeds or plants have tolerance to one or more herbicides; and   (b) applying to the crop and weeds in the field a sufficient amount of the one or more herbicides to control the weeds without significantly affecting the crop.   
     
     
         39 . The method of  claim 38 , wherein the one or more herbicides are selected from the group consisting of a mesotrione herbicide, an isoxazole herbicide, and a PPO inhibitor herbicide 
     
     
         40 . The method of  claim 39 , wherein the one or more herbicides are applied as a pre-emergent herbicide. 
     
     
         41 . The method of  claim 40 , further comprising applying to the crop and weeds in the field a simultaneous or a chronologically staggered application of the one or more herbicide and an additional herbicide formulation. 
     
     
         42 . The method of  claim 41 , wherein the additional herbicide formulation comprises an active ingredient selected from the group consisting of a hydroxyphenylpyruvatedioxygenase inhibitor, a glyphosate, a sulfonylurea, a sulfonamide, an imidazolinone, a bialaphos, a phosphinothricin, an azafenidin, a butafenacil, a sulfosate, a glufosinate, a dicamba, and a protox inhibitor. 
     
     
         43 . The method of  claim 41 , wherein the crop seeds or plants further comprise tolerance to the active ingredient of the additional herbicide formulation. 
     
     
         44 . The method of  claim 43 , wherein the tolerance to the active ingredient of the additional herbicide formulation is provided by insertion of a transgene which confers the tolerance.