Methods and compositions for herbicide tolerance in plants

Abstract

Provided herein are novel methods and compositions for conferring tolerance to auxin herbicides to plants. Also provided are herbicide tolerant plants, seeds, cells, and plant parts containing modified AUX/IAA proteins, as well as methods of producing the same.

1 . A modified plant or seed, wherein the modified plant or seed is sensitive to at least one endogenous auxin, and wherein the modified plant or seed exhibits tolerance to at least one auxin herbicide. 
     
     
         2 . The modified plant or seed of  claim 1 , wherein said endogenous auxin is selected from the group consisting of IAA and NAA, and wherein said auxin herbicide is selected from the group consisting of dicamba, 2,4-D, picloram, triclopyr, quinclorac and fluroxypyr. 
     
     
         3 . The modified plant or seed of  claim 1 , wherein said modified plant or seed comprises at least one modification in an endogenous gene encoding an AUX/IAA protein, wherein said at least one modification confers tolerance to an auxin herbicide as compared to a control plant without said at least one modification. 
     
     
         4 . The modified plant or seed of  claim 3 , wherein said modification results in:
 i) an AUX/IAA polypeptide comprising a modified degron domain that comprises the motif X 1 WPPX 2 , wherein X 1  has been modified relative to a wild type AUX/IAA polypeptide, to be asparagine (N), isoleucine (I), or leucine (L) relative to a wild type AUX/IAA polypeptide and wherein X 2  is isoleucine (I), valine (V), leucine (L), or methionine (M)   ii) an AUX/IAA polypeptide comprising an amino acid sequence at least 90% identical to SEQ ID NO: 219, wherein the modified plant or seed is not a  Kochia scoparia  plant or seed,   iii) an AUX/IAA polypeptide comprising an amino acid sequence of SEQ ID NO: 219, wherein the modified plant or seed is not a  Kochia scoparia  plant or seed, or   iv) increased tolerance to an auxin herbicide as compared to a control plant or seed lacking said modification.   
     
     
         5 - 6 . (canceled) 
     
     
         7 . The modified plant or seed of  claim 1 , wherein said modified plant or seed is a crop plant or crop seed. 
     
     
         8 . The modified plant or seed of  claim 7 , wherein said crop plant is a monocot or dicot crop plant. 
     
     
         9 . The modified plant or seed of  claim 8 , wherein said crop plant is selected from the group consisting of maize, sorghum, wheat, canola, soy, and cotton, grapes, tomato, potato, lettuce, broccoli, cucumber, peanut, melon, leeks, onion, rice, and barley. 
     
     
         10 . (canceled) 
     
     
         11 . The modified plant or seed of  claim 8 , wherein said crop plant is selected from the group consisting of soybean, alfalfa, sunflower, cotton, canola, and sugar beet. 
     
     
         12 . (canceled) 
     
     
         13 . A method of generating a modified plant comprising the steps of:
 a. introducing a modification in a AUX/IAA gene of a plant cell;   b. identifying and selecting one or more plant cells of step (a) comprising said modification in a degron domain of AUX/IAA; and   c. regenerating at least one plant from at least one or more cells selected in step (b).   
     
     
         14 . A modified DNA molecule encoding a modified auxin/indole-3-acetic acid (AUX/IAA) polypeptide, wherein said AUX/IAA polypeptide comprises a modified degron domain that comprises the motif X 1 WPPX 2 , wherein X 1  has been modified to be asparagine (N), isoleucine (I), or leucine (L) relative to a wild type AUX/IAA polypeptide and wherein X 2  is isoleucine (I), valine (V), leucine (L), or methionine (M). 
     
     
         15 . The modified DNA molecule of  claim 14 , wherein:
 i) X 1  has been modified from glycine to asparagine, or   ii) said modified AUX/IAA polypeptide comprises a polypeptide sequence selected from the group consisting of:
 a. a sequence having at least 90% sequence identity to SEQ ID NOs: 2n-1, wherein n=1-110, or wherein any of SEQ ID NOs: 247-284; and 
 b. a fragment of the sequence of a) having auxin/indole-3-acetic acid binding activity. 
   
     
     
         16 . (canceled) 
     
     
         17 . The modified DNA molecule of  claim 15 , wherein said modified AUX/IAA polypeptide comprises:
 i) a polynucleotide sequence having at least 95% sequence identity to SEQ ID NO: 220 or   ii) the polynucleotide sequence of SEQ ID NO: 220.   
     
     
         18 . (canceled) 
     
     
         19 . A DNA construct comprising the modified DNA molecule of  claim 14  operably linked to a heterologous promoter. 
     
     
         20 . The DNA construct of  claim 19 , wherein the promoter is defined as an inducible promoter or a native auxin/indole-3-acetic acid gene promoter. 
     
     
         21 . (canceled) 
     
     
         22 . A recombinant plant, plant part, cell, seed or plant genome comprising the modified DNA molecule of  claim 14 . 
     
     
         23 . (canceled) 
     
     
         24 . A method for conferring auxin herbicide tolerance to a plant comprising expressing in said plant the modified DNA molecule of  claim 14 . 
     
     
         25 . The method of  claim 24 , further defined as comprising transforming said plant or a progenitor thereof with the modified DNA molecule of  claim 14 . 
     
     
         26 . A method for producing an auxin herbicide tolerant plant comprising:
 modifying an AUX/IAA polypeptide of said plant to alter residue X 1  in a degron domain that comprises the motif X 1 WPPX 2  relative to SEQ ID NO: 217, wherein X 2  is an isoleucine, valine, leucine, or methionine.   
     
     
         27 . The method of  claim 26 , wherein X 1  is modified from glycine to asparagine, isoleucine, or leucine. 
     
     
         28 . The method of  claim 26 , wherein said modifying comprises site-specific mutagenesis. 
     
     
         29 . A plant produced by the method of  claim 26 . 
     
     
         30 . A method of detecting a plant exhibiting sensitivity at least one endogenous auxin and tolerance to at least one auxin herbicide, comprising the steps of:
 a. obtaining a genomic DNA sample from said plant;   b. amplifying said DNA sample using a first primer and a second primer to produce an amplicon;   c. detecting in said amplicon a polynucleotide sequence encoding the motif X 1 WPPX 2  within SEQ ID NO: 219.   
     
     
         31 . The method of  claim 30 , wherein:
 i) said first primer has a sequence of SEQ ID NO: 221 and said second primer has a sequence of SEQ ID NO: 222,   ii) said first primer has a sequence of SEQ ID NO: 223 and said second primer has a sequence of SEQ ID NO: 224,   iii) detecting comprises restriction fragment length polymorphism (RFLP) analysis, or   iv) detecting comprises using a probe selected from the group consisting of SEQ ID NO: 225, SEQ ID NO: 226, or combinations thereof.   
     
     
         32 - 34 . (canceled)