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BR-122020000568-B1 - METHODS OF OBTAINING AND PRODUCING SOYBEAN PLANTS COMPRISING A GENOTYPE ASSOCIATED WITH A PHENOTYPE WITHOUT YELLOW FLASH

BR122020000568B1BR 122020000568 B1BR122020000568 B1BR 122020000568B1BR-122020000568-B1

Abstract

The present invention relates to methods and compositions for identifying and selecting loci that modulate phenotypic expression of a herbicide tolerance trait in plant breeding. Furthermore, methods are provided for classifying germplasm entries for the performance and expression of this trait.

Inventors

  • Liesa Cerny
  • Kunsheng Wu
  • Tom Floyd

Assignees

  • MONSANTO TECHNOLOGY LLC

Dates

Publication Date
20260310
Application Date
20110901
Priority Date
20100903

Claims (14)

  1. 1. Method for obtaining a soybean plant comprising in its genome at least one non-flash locus, characterized in that it comprises the steps of: a. To genotype a plurality of soybean plants with respect to at least one yellow flash locus in a linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) by identifying at least one polymorphic allele of at least one marker in said linkage group L region selected from the group consisting of M0129138 (SEQ ID NO: 4), M0101742 (SEQ ID NO: 5), M0093116 (SEQ ID NO: 6), and M0129925 (SEQ ID NO: 7) that is associated with a non-flash phenotype, wherein the plurality of soybean plants comprises a population containing plants comprising a transgene conferring glyphosate tolerance that is obtained by: i) crossing a parental plant comprising at least one non-flash locus with a parental plant comprising at least one yellow flash locus wherein at least one of said soybean plants comprises a transgene conferring glyphosate tolerance; or ii) obtaining seed or progeny from a parent plant segregating for at least one non-flash locus; and, b. selecting a soybean plant comprising in its genome at least one non-flash locus comprising a genotype associated with a non-flash phenotype, wherein the selected plant exhibits a non-flash phenotype.
  2. 2. Method according to claim 1, characterized in that the genotype associated with a non-flash phenotype comprises at least one polymorphic allele of at least one marker in a first subregion of the L linkage group region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16), wherein the marker is M0129138 (SEQ ID NO: 4) or M0101742 (SEQ ID NO: 5); and/or at least one polymorphic allele of at least one marker in a second subregion of the L linkage group region that is flanked by loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14), where the marker is M0093116 (SEQ ID NO: 6) or M0129925 (SEQ ID NO: 7).
  3. 3. Method according to claim 1 or 2, characterized in that the phenotype associated with a non-flash phenotype in the selected plant from step (b) comprises at least one polymorphic allele of at least one marker in the first region of the L linkage group, the first subregion, or the second subregion where the marker is selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6) and M0129925 (SEQ ID NO:7).
  4. 4. Method according to claim 1, characterized in that said population contains plants comprising a transgene that confers tolerance to glyphosate.
  5. 5. A method according to any one of claims 1 to 3, characterized in that it comprises the assay step for the presence of at least one additional marker, wherein said additional marker is either linked or not linked to said genomic region of the L-linkage group.
  6. 6. A method according to any one of claims 1 to 4, characterized in that said plurality of soybean plants, said soybean plant, and/or its progeny are exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety.
  7. 7. Method for producing a soybean plant comprising in its genome at least one introgressed non-flash locus, characterized in that it comprises the steps of: a. crossing a first non-flash soybean plant with a second soybean plant, wherein the second soybean plant comprises a yellow flash locus in a first genomic region of the L linkage group flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14), and at least one linked polymorphic locus not present in the first non-flash soybean plant, and wherein at least one of said first or second soybean plants comprises a transgene conferring glyphosate tolerance, to obtain a population that segregates for the non-flash loci and said linked polymorphic locus; b. To detect at least two polymorphic nucleic acids in a seed or progeny plant from at least one soybean plant from the population, wherein at least one of said polymorphic nucleic acids is located in said linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) and is detected by identifying at least one polymorphic allele of at least one marker in said linkage group L region selected from the group consisting of M0129138 (SEQ ID NO: 4), M0101742 (SEQ ID NO: 5), M0093116 (SEQ ID NO: 6), and M0129925 (SEQ ID NO: 7) that is associated with a non-flash phenotype and wherein at least one of the polymorphic nucleic acids is a polymorphic locus linked not present in the aforementioned first flashless soybean plant; and, c. select a soybean seed or progeny plant from step (b) by its genotype, wherein the selected progeny soybean seed or plant comprises a genotype from the first L linkage group that is flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) that is associated with a flashless phenotype and at least one linked marker found in the aforementioned second soybean plant comprising a yellow flash locus but not in the aforementioned first flashless soybean plant, thereby obtaining a soybean plant comprising in its genome at least one introgressed flashless locus.
  8. 8. Method according to claim 7, characterized in that said population, said selected soybean plant and/or progeny of selected soybean plant is exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety.
  9. 9. Method according to claim 7, characterized in that the yellow flash locus comprises at least one polymorphic allele of at least one marker in a first subregion of the L linkage group region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16), wherein the marker is M0129138 (SEQ ID NO: 4) or M0101742 (SEQ ID NO: 5); and/or at least one polymorphic allele of at least one marker in a second subregion of the L linkage group region that is flanked by loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14), where the marker is M0093116 (SEQ ID NO: 6) or M0129925 (SEQ ID NO: 7).
  10. 10. Method according to claim 7, characterized in that said polymorphic nucleic acid is detected in step (b) with at least one marker selected from the group consisting of M0101742 (SEQ ID NO:5) and M0129925 (SEQ ID NO:7).
  11. 11. Method according to claim 7, characterized in that two polymorphic nucleic acids located in said L region of the first linking group that is flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) are detected with marker M0101742 (SEQ ID NO: 5) and with marker M0129925 (SEQ ID NO: 7).
  12. 12. A method according to any one of claims 7 to 11, characterized in that the linked polymorphic locus is detected with a genotypic marker, a phenotypic marker, or both.
  13. 13. Method according to claim 12, characterized in that the linked polymorphic locus is detected with a marker that is located at approximately 1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) from said non-flash locus.
  14. 14. Method according to claim 13, characterized in that the linked polymorphic locus is detected with at least one marker selected from the group consisting of M0205928 (SEQ ID NO:3), M0205537 (SEQ ID NO:8), M0202715 (SEQ ID NO:9), M0206286 (SEQ ID NO:10), M0206054 (SEQ ID NO:11) and M0205375 (SEQ ID NO:12).

Description

CROSS-REFERENCE TO RELATED REQUESTS [0001] The present invention claims the benefit of US provisional application 61/380,024, filed September 3, 2010, and incorporated herein by reference in its entirety. Embedding sequence listing [0002] A sequence listing containing the file named "46_21_54534_SeqListing.txt" which is 19,743 bytes in size (measured in MS-Windows®) and was created on August 26, 2011, comprising 32 nucleotide sequences, is filed herewith and is hereby incorporated by reference in its entirety. Also incorporated herein by reference are 32 nucleotide sequences and pertinent identifying information from the sequence listing containing the file named "46_21_54534.txt" which is 18,477 bytes in size (measured in MS-Windows®), created on August 30, 2010 and filed with US Provisional Application 61/380,024 on September 3, 2010. Incorporation of table 2 [0003] A listing of various soybean L (chromosome 19) linkage group markers is provided with this Descriptive Report as Table 2. Also incorporated herein by reference is the listing of various soybean L (chromosome 19) linkage group markers that was provided in the document "Appendix to the Specification as Table 2" which was 4,541,064 bytes (as measured in MS-Windows®), filed with U.S. Provisional Application Serial No. 61/380024 on September 3, 2010. Table 2 appears on the final pages of the Descriptive Report. Background of the invention [0004] "Yellow flash" is an undesirable phenotype observed in certain soybean varieties comprising a transgene that confers tolerance to the broad-spectrum herbicide glyphosate. After glyphosate application, or glyphosate applications under certain environmental conditions such as elevated temperature, the leaves of certain soybean plant varieties comprising the glyphosate-tolerant transgene may exhibit a yellowish color (hence the term "Yellow flash"). The Yellow Flash phenotype can be observed approximately one week after herbicide application in certain soybean varieties comprising the glyphosate-tolerant transgene. The Yellow Flash phenotype is undesirable as it leads to a visually unpleasant yellow leaf color in soybean plants exposed to glyphosate. Summary of the invention [0005] Although the Yellow Flash phenotype can be observed approximately one week after herbicide application in certain soybean varieties comprising the glyphosate-tolerant transgene, distinct soybean varieties comprising the same glyphosate-tolerant transgene integrated at the same chromosomal locus (i.e., the same transgenic event) may show varying degrees of Yellow Flash after exposure to high doses of glyphosate. Some varieties comprising the glyphosate-tolerant transgene insertion are highly resistant to high doses of glyphosate, showing no Yellow Flash phenotype (i.e., a "no-flash phenotype"), while other varieties comprising the same glyphosate-tolerant transgene insertion are highly susceptible to high doses of glyphosate, showing a severe Yellow Flash phenotype. Soybean plants comprising an introgressed genomic region associated with a no-flash phenotype are provided here. Also provided here are markers that reside outside of a genomic region associated with a non-flash phenotype and that facilitate breeding activities that include, but are not limited to, introgression of this genomic region. Markers and specific alleles thereof that are associated with a non-flash phenotype are also provided. Methods for obtaining a soybean plant exhibiting a non-flash phenotype and methods for obtaining a soybean plant comprising in its genome at least one non-flash locus are also provided. Methods that provide the introgression of a genomic region associated with a non-flash phenotype into soybean germplasm that has a genomic region associated with a yellow flash phenotype are also provided. The identification of molecular markers associated with loci that confer the non-flash phenotype has significant economic value. By using markers associated with the non-flash trait, producers can select soybean varieties with the favorable alleles (i.e., alleles that are not associated with the yellow flash trait) for use in trait integration. They can also use the markers to help eliminate unfavorable alleles (i.e., alleles that are associated with the yellow flash trait) in unfavorable soybean alleles. The present invention thus provides commercially desirable transgenic soybean lines that carry a genomic region that is associated with a "no-flash" phenotype and tolerate high doses of glyphosate. [0006] Methods for identifying a soybean plant comprising a genotype associated with a non-flash phenotype are thus provided. In certain embodiments, the methods for identifying a soybean plant comprising a genotype associated with a non-flash phenotype comprise: detecting in the soybean plant an allele at least at one yellow flash marker locus associated with the non-flash phenotype wherein the yellow flash marker locus is in a genomic region of the L linkage