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CN-121986169-A - Maize plants comprising resistance to southern corn rust, and compositions and methods for selecting and producing the same

CN121986169ACN 121986169 ACN121986169 ACN 121986169ACN-121986169-A

Abstract

Provided herein are methods for selecting maize plants comprising QTLs associated with resistance to southern rust. Methods of producing plants or plant cells comprising QTLs associated with resistance to southern rust are also provided. Resistant plants or plant cells themselves, as well as resistant plant seeds, are also provided.

Inventors

  • M.T. Carl Jung
  • S. Thatcher
  • G. M. Taber
  • LEONARD APRIL L.

Assignees

  • 先锋国际良种公司

Dates

Publication Date
20260505
Application Date
20240917
Priority Date
20230918

Claims (20)

  1. 1. A method for identifying a maize plant comprising a sequence associated with resistance to southern rust, the method comprising: a. obtaining a sample comprising nucleic acid from a maize plant, B. Screening said sample for a protein or a nucleic acid encoding said protein, wherein said protein comprises an amino acid sequence having at least 95% sequence identity to SEQ ID NO. 30, and C. detecting the protein or nucleic acid encoding the protein, thereby identifying the maize plant as comprising a sequence associated with resistance to southern rust.
  2. 2. The method of claim 1, wherein the protein has 100% amino acid sequence identity to SEQ ID NO. 30.
  3. 3. The method of claim 1 or 2, wherein the method comprises A. Obtaining a sample comprising nucleic acid from each of a plurality of maize plants, B. Screening each sample for the protein or nucleic acid encoding the protein; c. detecting said protein or a nucleic acid encoding said protein in at least one sample, thereby identifying at least one maize plant from which said sample was obtained as comprising said sequence associated with resistance to southern rust, and D. selecting the at least one maize plant identified as comprising the sequence associated with resistance to southern rust.
  4. 4. A method for producing a maize plant comprising a sequence associated with resistance to southern rust, the method comprising selecting a maize plant according to claim 3, and further comprising: c. crossing the at least one maize plant selected in (d) with a second maize plant, and D. obtaining a progeny plant comprising the sequence associated with resistance to southern rust.
  5. 5. The method of any one of claims 1-4, wherein the nucleic acid sequence has at least 95% nucleotide sequence identity to SEQ ID No. 28 or 35.
  6. 6. The method of any one of claims 1-5, wherein the nucleic acid sequence comprises SEQ ID No. 28 or 35.
  7. 7. A method for producing a modified maize plant or modified maize plant cell, the method comprising: Providing an unmodified maize plant or one or more cells thereof susceptible to SR; introducing a heterologous NLR01 nucleic acid sequence encoding a protein having at least 95% amino acid sequence identity with SEQ ID NO. 30 into the genome of said plant or one or more cells thereof, thereby producing one or more modified plants or plant cells thereof comprising said heterologous NLR01 sequence, and Selecting at least one of the modified maize plant or modified maize plant cell.
  8. 8. The method of claim 7, wherein the method comprises: a) Site-specific modification of at least one target site in the genome of said susceptible maize plant or one or more cells thereof, and B) Introducing a polynucleotide modification template comprising the heterologous NLR01 sequence into the susceptible maize plant or one or more maize plant cells thereof, thereby producing the modified maize, or modified maize plant cell.
  9. 9. The method of claim 7 or 8, wherein the method comprises: a) Site-specific modification of the native NLR01 gene of said susceptible maize plant or cell thereof, and B) Altering the native NLR01 gene sequence to produce the modified maize plant or modified maize plant cell.
  10. 10. The method of claim 7,8 or 9, wherein the site-specific modification is induced by a CRISPR-associated endonuclease.
  11. 11. The method of any one of claims 7-10, wherein the method comprises producing one or more modified maize plant cells, and further comprising growing a modified maize plant from the selected maize plant cells, wherein the modified plant exhibits increased resistance to southern rust relative to the unmodified maize plant.
  12. 12. The method of any one of claims 7-11, wherein the unmodified maize plant comprises an endogenous susceptible NLR01 sequence, and the heterologous NLR01 sequence replaces the endogenous susceptible NLR01 sequence.
  13. 13. The method of any one of claims 7,8, 10 and 11, wherein the heterologous NLR01 sequence is inserted into a locus that does not naturally comprise a native NLR01 gene sequence.
  14. 14. The method of any one of claims 7-13, wherein the heterologous NLR gene sequence comprises a nucleotide sequence having at least 95% identity to SEQ ID No. 28 or 35.
  15. 15. The method of claim 14, wherein the heterologous NLR gene sequence comprises the nucleotide sequence of SEQ ID No. 28 or 35.
  16. 16. The method of claim 11, further comprising: crossing the modified maize plant with a maize plant susceptible to SR and lacking the heterologous NLR01 sequence, and Selecting a progeny plant that is more resistant to SR than the susceptible maize plant and that comprises the heterologous NLR01 sequence for further breeding or maize production.
  17. 17. A recombinant maize plant seed comprising a heterologous nucleic acid sequence encoding a protein having at least 95% amino acid sequence identity to SEQ ID No. 30.
  18. 18. The recombinant maize plant seed of claim 17, wherein said protein has 100% amino acid sequence identity to SEQ ID No. 30.
  19. 19. The recombinant maize plant seed of claim 17 or 18, wherein said heterologous nucleic acid sequence has at least 95% nucleotide sequence identity to SEQ ID No. 28 or 35.
  20. 20. The recombinant seed of any one of claims 17-19, wherein the heterologous nucleic acid comprises the nucleotide sequence of SEQ ID No. 28 or 35.

Description

Maize plants comprising resistance to southern corn rust, and compositions and methods for selecting and producing the same Technical Field The present disclosure relates to maize plants comprising resistance to southern corn rust and compositions and methods for selecting and producing the same. Reference to sequence Listing The official copy of the sequence listing was submitted electronically as an XML file named "108486-WO-SEC-1 Sequence Listing" created at 9, 17, 2024. The XML file is 74,908 bytes in size and the sequence table is filed concurrently with this specification. The sequence listing contained in this XML file document is part of this specification and is incorporated herein by reference in its entirety. Background Southern rust ("SR") is a maize plant disease caused by the fungal pathogen puccinia polytricha (Puccinia polysora). In many corn producing areas, the rust of the piles cannot survive over winter, but under appropriate climatic conditions, the pathogen can spread from warmer, more humid areas to colder areas in winter. SR is a concern for farmers and grain producers because it may reduce the yield and/or quality of maize crops. SR can be particularly detrimental to corn because of the potential for rapid development and propagation under favorable conditions. While there are techniques to reduce the impact of SR on maize crops, there is still a need to additionally develop new techniques to manage and minimize the potential impact of SR. Disclosure of Invention The present disclosure provides maize plants comprising resistance to southern rust ("SR"). Resistance may be provided via QTL as disclosed herein and NLR01 gene as disclosed herein. Breeding and/or genetic engineering techniques can be used to produce plants comprising resistance provided via QTL and NLR01 genes. When SR is a problem, the plants provided herein can increase agricultural yield and/or reduce or eliminate the need for fungicide applications. Provided herein is a method for selecting a maize plant comprising a QTL disclosed herein that is associated with SR resistance. The method comprises obtaining nucleic acid from one or more maize plants, and screening the nucleic acid for QTL on maize chromosome 10, including for one or more of the marker alleles (e.g., haplotypes) disclosed in table 1, and selecting a maize plant comprising one or more of the marker alleles (e.g., haplotypes), thereby selecting a maize plant comprising the QTL. Also provided herein is a method for selecting a maize plant comprising QTL associated with resistance to southern rust. The method comprises obtaining nucleic acids from one or more maize plants. The method comprises screening nucleic acids for haplotypes on maize chromosome 10 that comprise one or more of the marker alleles disclosed in table 1 (e.g., haplotypes) and/or one or more of (a) a "at C01800-1 corresponding to position 201 of SEQ ID NO: 3, (b) a" G "at C06790-1 corresponding to position 201 of SEQ ID NO: 4, or (C) a" T "at C00429-801 corresponding to position 84 of SEQ ID NO: 8. The method comprises selecting a maize plant comprising the haplotype, thereby selecting a maize plant comprising the QTL. Also provided herein is a method for selecting a maize plant comprising QTL associated with resistance to southern rust. The method comprises obtaining nucleic acid from one or more maize plants, and screening the nucleic acid for a haplotype on maize chromosome 10, the haplotype comprising one or more of the marker alleles disclosed in table 1 and/or one or more of (d) a "T" at C00431-802 corresponding to position 210 of SEQ ID NO: 5, (e) a "C" at C002TCN-001 corresponding to position 61 of SEQ ID NO: 6, (f) a "T" at C002TCM-001 corresponding to position 61 of SEQ ID NO: 9, or (g) a "at C06817-1 corresponding to position 201 of SEQ ID NO: 10. The method comprises selecting a maize plant comprising the haplotype, thereby selecting a maize plant comprising the QTL. Also provided herein is a method for selecting a maize plant comprising resistance to SR. The method comprises screening a population of maize plants for a gene or a protein encoded by the gene, wherein the protein comprises an amino acid sequence having at least 95% sequence identity to SEQ ID No. 30. The method comprises selecting a maize plant comprising the gene or a protein encoded thereby. Also provided herein is a method for producing a recombinant maize plant or cell thereof comprising a heterologous gene associated with anti-SR resistance. The method comprises introducing a heterologous NLR gene sequence encoding a protein having at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% amino acid sequence identity with SEQ ID NO. 30 into one or more cells derived from a first maize plant, thereby producing at least one modified cell comprising the heterologous NLR gene sequence in the genome of the modified cell. The method comprises selecting at least one of the modified maize plant c