Plants with altered root architecture, related constructs and methods involving genes encoding exostosin family polypeptides and homologs thereof

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, 21, 23, 25, 27, 29, 31, or 34, 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, 21, 23, 25, 27, 29, 31, or 34, 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 EXST or EXST-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.

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, 21, 23, 25, 27, 29, 31, or 34;
• 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.

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, 21, 23, 25, 27, 29, 31, or 34;
• (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.

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, 21, 23, 25, 27, 29, 31, or 34;
• (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.

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, 21, 23, 25, 27, 29, 31, or 34;
• (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.

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, 21, 23, 25, 27, 29, 31, or 34;
• (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.

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, 21, 23, 25, 27, 29, 31, or 34, 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 EXST or EXST-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.

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, 21, 23, 25, 27, 29, 31, or 34, 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 EXST or EXST-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.

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, 21, 23, 25, 27, 29, 31, or 34, 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 EXST or EXST-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.

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, 21, 23, 25, 27, 29, 31, or 34, 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 EXST or EXST-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.

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, 21, 23, 25, 27, 29, 31, or 34, 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 EXST or EXST-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.

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, 20, 22, 24, 26, 28, 30, or 33;
• or
• (ii) a nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NO:15, 17, 19, 21, 23, 25, 27, 29, 31, or 34;
• 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.

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, 20, 22, 24, 26, 28, 30, or 33;
• or
• (ii) a nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NO:15, 17, 19, 21, 23, 25, 27, 29, 31, or 34;
• 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.