Plants With Altered Root Architecture, Related Constructs and Methods Involving Genes Encoding Leucine Rich Repeat Kinase (LLRK) Polypeptides and Homologs Thereof

Abstract

Isolated polynucleotides and polypeptides and recombinant DNA constructs particularly useful for altering root structure of plants, compositions (such as plants or seeds) comprising these recombinant DNA constructs, and methods utilizing these recombinant DNA constructs. The recombinant DNA construct comprises a polynucleotide operably linked to a promoter functional in a plant, wherein said polynucleotide encodes a polypeptide useful for altering plant root architecture.

1 . A plant comprising in its genome a recombinant DNA construct comprising a polynucleotide operably linked to at least one regulatory element, wherein said polynucleotide encodes a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36 and wherein said plant exhibits altered root architecture when compared to a control plant not comprising said recombinant DNA construct. 
     
     
         2 . The plant of  claim 1 , wherein the plant is a maize plant or a soybean plant. 
     
     
         3 . A plant comprising in its genome:
 a recombinant DNA construct comprising:
 (a) a polynucleotide operably linked to at least one regulatory element, wherein said polynucleotide encodes a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36, or 
 (b) a suppression DNA construct comprising at least one regulatory element operably linked to:
 (i) all or part of: (A) a nucleic acid sequence encoding a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36, or (B) a full complement of the nucleic acid sequence of (b)(i)(A); or 
 (ii) a region derived from all or part of a sense strand or antisense strand of a target gene of interest, said region having a nucleic acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to said all or part of a sense strand or antisense strand from which said region is derived, and wherein said target gene of interest encodes a LLRK or LLRK-like polypeptide, 
 
   and wherein said plant exhibits an alteration of at least one agronomic characteristic when compared to a control plant not comprising said recombinant DNA construct.   
     
     
         4 . The plant of  claim 3 , wherein the plant is a maize plant or a soybean plant. 
     
     
         5 . The plant of  claim 3 , wherein said plant exhibits said alteration of said at least one agronomic characteristic when compared, under varying environmental conditions, to said control plant not comprising said recombinant DNA construct. 
     
     
         6 . The plant of  claim 5 , wherein said varying environmental condition is at least one selected from drought, nitrogen, or disease. 
     
     
         7 . The plant of  claim 5 , wherein the plant is a maize plant or a soybean plant. 
     
     
         8 . The plant of  claim 7 , wherein the plant is a maize plant or a soybean plant. 
     
     
         9 . The plant of  claim 3 , wherein said at least one agronomic characteristic is selected from the group consisting of greenness, yield, growth rate, biomass, fresh weight at maturation, dry weight at maturation, fruit yield, seed yield, total plant nitrogen content, fruit nitrogen content, seed nitrogen content, nitrogen content in a vegetative tissue, total plant free amino acid content, fruit free amino acid content, seed free amino acid content, free amino acid content in a vegetative tissue, total plant protein content, fruit protein content, seed protein content, protein content in a vegetative tissue, drought tolerance, nitrogen uptake, root lodging, stalk lodging, plant height, ear length and harvest index. 
     
     
         10 . The plant of  claim 9 , wherein the plant is a maize plant or a soybean plant. 
     
     
         11 . The plant of  claim 3 , wherein said plant exhibits an increase of said at least one agronomic characteristic when compared to said control plant. 
     
     
         12 . The plant of  claim 11 , wherein the plant is a maize plant or a soybean plant. 
     
     
         13 . A method of altering root architecture in a plant, comprising:
 (a) introducing into a regenerable plant cell a recombinant DNA construct comprising a polynucleotide operably linked to at least one regulatory sequence, wherein the polynucleotide encodes a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36; and   (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct and exhibits altered root architecture when compared to a control plant not comprising the recombinant DNA construct.   
     
     
         14 . The method of  claim 13 , further comprising:
 (c) obtaining a progeny plant derived from the transgenic plant, wherein said progeny plant comprises in its genome the recombinant DNA construct and exhibits altered root architecture when compared to a control plant not comprising the recombinant DNA construct.   
     
     
         15 . A method of evaluating root architecture in a plant, comprising:
 (a) introducing into a regenerable plant cell a recombinant DNA construct comprising a polynucleotide operably linked to at least one regulatory sequence, wherein the polynucleotide encodes a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36;   (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct; and   (c) evaluating root architecture of the transgenic plant compared to a control plant not comprising the recombinant DNA construct.   
     
     
         16 . The method of  claim 15 , further comprising:
 (d) obtaining a progeny plant derived from the transgenic plant, wherein the progeny plant comprises in its genome the recombinant DNA construct; and   (e) evaluating root architecture of the progeny plant compared to a control plant not comprising the recombinant DNA construct.   
     
     
         17 . A method of evaluating root architecture in a plant, comprising:
 (a) introducing into a regenerable plant cell a recombinant DNA construct comprising a polynucleotide operably linked to at least one regulatory sequence, wherein the polynucleotide encodes a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36;   (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct;   (c) obtaining a progeny plant derived from the transgenic plant, wherein the progeny plant comprises in its genome the recombinant DNA construct; and   (d) evaluating root architecture of the progeny plant compared to a control plant not comprising the recombinant DNA construct.   
     
     
         18 . A method of determining an alteration of an agronomic characteristic in a plant, comprising:
 (a) introducing into a regenerable plant cell a recombinant DNA construct comprising a polynucleotide operably linked to at least one regulatory sequence, wherein the polynucleotide encodes a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36;   (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct; and   (c) determining whether the transgenic plant exhibits an alteration of at least one agronomic characteristic when compared to a control plant not comprising the recombinant DNA construct.   
     
     
         19 . The method of  claim 18 , further comprising:
 (d) obtaining a progeny plant derived from the transgenic plant, wherein the progeny plant comprises in its genome the recombinant DNA construct; and   (e) determining whether the progeny plant exhibits an alteration of at least one agronomic characteristic when compared to a control plant not comprising the recombinant DNA construct.   
     
     
         20 . The method of  claim 19 , wherein said determining step comprises determining whether the transgenic plant exhibits an alteration of at least one agronomic characteristic when compared, under varying environmental conditions, to a control plant not comprising the recombinant DNA construct. 
     
     
         21 . The method of  claim 20 , wherein said determining step (e) comprises determining whether the progeny plant exhibits an alteration of at least one agronomic characteristic when compared, under varying environmental conditions, to a control plant not comprising the recombinant DNA construct. 
     
     
         22 . A method of determining an alteration of an agronomic characteristic in a plant, comprising:
 (a) introducing into a regenerable plant cell a recombinant DNA construct comprising a polynucleotide operably linked to at least one regulatory sequence, wherein the polynucleotide encodes a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36;   (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the recombinant DNA construct;   (c) obtaining a progeny plant derived from the transgenic plant, wherein the progeny plant comprises in its genome the recombinant DNA construct; and   (d) determining whether the progeny plant exhibits an alteration of at least one agronomic characteristic when compared to a control plant not comprising the recombinant DNA construct.   
     
     
         23 . The method of  claim 22 , wherein said determining step comprises determining whether the transgenic plant exhibits an alteration of at least one agronomic characteristic when compared, under varying environmental conditions, to a control plant not comprising the recombinant DNA construct. 
     
     
         24 . A method of determining an alteration of an agronomic characteristic in a plant, comprising:
 (a) introducing into a regenerable plant cell a suppression DNA construct comprising at least one regulatory element operably linked to:
 (i) all or part of: (A) a nucleic acid sequence encoding a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36, or (B) a full complement of the nucleic acid sequence of (a)(i)(A); or 
 (ii) a region derived from all or part of a sense strand or antisense strand of a target gene of interest, said region having a nucleic acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to said all or part of a sense strand or antisense strand from which said region is derived, and wherein said target gene of interest encodes a LLRK or LLRK-like polypeptide; 
   (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the suppression DNA construct; and   (c) determining whether the transgenic plant exhibits an alteration of at least one agronomic characteristic when compared to a control plant not comprising the suppression DNA construct.   
     
     
         25 . The method of  claim 24 , wherein said determining step comprises determining whether the transgenic plant exhibits an alteration of at least one agronomic characteristic when compared, under varying environmental conditions, to a control plant not comprising the suppression DNA construct. 
     
     
         26 . The method of  claim 25 , further comprising:
 (d) obtaining a progeny plant derived from the transgenic plant, wherein the progeny plant comprises in its genome the suppression DNA construct; and   (e) determining whether the progeny plant exhibits an alteration of at least one agronomic characteristic when compared to a control plant not comprising the suppression DNA construct.   
     
     
         27 . The method of  claim 26 , wherein said determining step (e) comprises determining whether the progeny plant exhibits an alteration of at least one agronomic characteristic when compared, under varying environmental conditions, to a control plant not comprising the suppression DNA construct. 
     
     
         28 . A method of determining an alteration of an agronomic characteristic in a plant, comprising:
 (a) introducing into a regenerable plant cell a suppression DNA construct comprising at least one regulatory element operably linked to:
 (i) all or part of: (A) a nucleic acid sequence encoding a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36, or (B) a full complement of the nucleic acid sequence of (a)(i)(A); or 
 (ii) a region derived from all or part of a sense strand or antisense strand of a target gene of interest, said region having a nucleic acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to said all or part of a sense strand or antisense strand from which said region is derived, and wherein said target gene of interest encodes a LLRK or LLRK-like polypeptide; 
   (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the suppression DNA construct and exhibits altered root architecture when compared to a control plant not comprising the suppression DNA construct;   (c) obtaining a progeny plant derived from the transgenic plant, wherein the progeny plant comprises in its genome the suppression DNA construct; and   (d) determining whether the progeny plant exhibits an alteration of at least one agronomic characteristic when compared to a control plant not comprising the suppression DNA construct.   
     
     
         29 . The method of  claim 28 , wherein said determining step comprises determining whether the transgenic plant exhibits an alteration of at least one agronomic characteristic when compared, under varying environmental conditions, to a control plant not comprising the recombinant DNA construct. 
     
     
         30 . A method of altering root architecture in a plant, comprising:
 (a) introducing into a regenerable plant cell a suppression DNA construct comprising at least one regulatory element operably linked to:
 (i) all or part of: (A) a nucleic acid sequence encoding a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36, or (B) a full complement of the nucleic acid sequence of (a)(i)(A); or 
 (ii) a region derived from all or part of a sense strand or antisense strand of a target gene of interest, said region having a nucleic acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to said all or part of a sense strand or antisense strand from which said region is derived, and wherein said target gene of interest encodes a LLRK or LLRK-like polypeptide; and 
   (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the suppression DNA construct and wherein the transgenic plant exhibits altered root architecture when compared to a control plant not comprising the suppression DNA construct.   
     
     
         31 . The method of  claim 30 , further comprising:
 (c) obtaining a progeny plant derived from the transgenic plant, wherein said progeny plant comprises in its genome the recombinant DNA construct and wherein the progeny plant exhibits altered root architecture when compared to a control plant not comprising the suppression DNA construct.   
     
     
         32 . A method of evaluating root architecture in a plant, comprising:
 (a) introducing into a regenerable plant cell a suppression DNA construct comprising at least one regulatory element operably linked to:
 (i) all or part of: (A) a nucleic acid sequence encoding a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36, or (B) a full complement of the nucleic acid sequence of (a)(i)(A); or 
 (ii) a region derived from all or part of a sense strand or antisense strand of a target gene of interest, said region having a nucleic acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to said all or part of a sense strand or antisense strand from which said region is derived, and wherein said target gene of interest encodes a LLRK or LLRK-like polypeptide; 
   (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the suppression DNA construct; and   (c) evaluating root architecture of the transgenic plant compared to a control plant not comprising the suppression DNA construct.   
     
     
         33 . The method of  claim 32 , further comprising:
 (d) obtaining a progeny plant derived from the transgenic plant, wherein the progeny plant comprises in its genome the suppression DNA construct; and   (e) evaluating root architecture of the progeny plant compared to a control plant not comprising the suppression DNA construct.   
     
     
         34 . A method of evaluating root architecture in a plant, comprising:
 (a) introducing into a regenerable plant cell a suppression DNA construct comprising at least one regulatory element operably linked to:
 (i) all or part of: (A) a nucleic acid sequence encoding a polypeptide having an amino acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 22, or 36, or (B) a full complement of the nucleic acid sequence of (a)(i)(A); or 
 (ii) a region derived from all or part of a sense strand or antisense strand of a target gene of interest, said region having a nucleic acid sequence of at least 50% sequence identity, based on the Clustal V method of alignment, when compared to said all or part of a sense strand or antisense strand from which said region is derived, and wherein said target gene of interest encodes a LLRK or LLRK-like polypeptide; 
   (b) regenerating a transgenic plant from the regenerable plant cell after step (a), wherein the transgenic plant comprises in its genome the suppression DNA construct;   (c) obtaining a progeny plant derived from the transgenic plant, wherein the progeny plant comprises in its genome the suppression DNA construct; and   (d) evaluating root architecture of the progeny plant compared to a control plant not comprising the suppression DNA construct.   
     
     
         35 . An isolated polynucleotide comprising a nucleic acid sequence encoding a LLRK or LLRK-like polypeptide having an amino acid sequence of at least 80% sequence identity, when compared to SEQ ID NO:15, or 19, or of at least 85% sequence identity, when compared to SEQ ID NO:17, based on the Clustal V method of alignment, or a full complement of said nucleic acid sequence. 
     
     
         36 . The polynucleotide of  claim 35 , wherein the amino acid sequence of the polypeptide and the amino acid sequence of SEQ ID NO:15, or 19 have at least 85% sequence identity, or the amino acid sequence of SEQ ID NO:17 have at least 90% identity, based on the Clustal alignment method. 
     
     
         37 . The polynucleotide of  claim 36 , wherein the amino acid sequence of the polypeptide and the amino acid sequence of SEQ ID NO:15, or 19 have at least 90% sequence identity, or the amino acid sequence of SEQ ID NO:17 have at least 95% identity, based on the Clustal alignment method. 
     
     
         38 . The polynucleotide of  claim 35 , wherein the amino acid sequence of the polypeptide and the amino acid sequence of SEQ ID NO:15, or 19 have at least 95% sequence identity, based on the Clustal alignment method. 
     
     
         39 . The polynucleotide of  claim 35 , wherein the amino acid sequence of the polypeptide comprises SEQ ID NO:15, 17, 19, or 22. 
     
     
         40 . The polynucleotide of  claim 35 , wherein the nucleic acid sequences comprise SEQ ID NO: 14, 16, 18, or 21. 
     
     
         41 . A vector comprising the polynucleotide of  claim 35 . 
     
     
         42 . A recombinant DNA construct comprising the polynucleotide of  claim 35  operably linked to at least one regulatory sequence. 
     
     
         43 . A method for transforming a cell, comprising transforming a cell with the polynucleotide of  claim 35 . 
     
     
         44 . A cell comprising the recombinant DNA construct of  claim 43 . 
     
     
         45 . A method for producing a plant comprising transforming a plant cell with the polynucleotide of  claim 35  and regenerating a plant from the transformed plant cell. 
     
     
         46 . A method of mapping genetic variations exhibiting an alteration in root architecture and/or an alteration in at least one agronomic characteristic in plants comprising:
 (a) crossing two plant varieties; and   (b) evaluating genetic variations with respect to a nucleic acid sequence selected from the group consisting of SEQ ID 14, 16, 18, 21, or 36; or
 (ii) a nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NO: 15, 17, 19, 22, or 36; 
   
       in progeny plants resulting from the cross of step (a), wherein the evaluation is made using a method selected from the group consisting of RFLP analysis, SNP analysis, and PCR-based analysis. 
     
     
         47 . A method of molecular breeding to alter root architecture and/or altering at least one agronomic characteristic in plants comprising:
 (a) crossing two plant varieties; and   (b) evaluating genetic variations with respect to
 (i) a nucleic acid sequence selected from the group consisting of SEQ ID NO:14, 16, 18, 21, or 36; or 
 (ii) a nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NO: 15, 17, 19, 22, or 36; 
   
       in progeny plants resulting from the cross of step (a), wherein the evaluation is made using a method selected from the group consisting of RFLP analysis, SNP analysis, and PCR-based analysis.