Genetic architecture of cyst nematode resistance revealed by genome-wide association study in soybean.
BACKGROUND
Bi-parental mapping populations have been commonly utilized to identify and characterize quantitative trait loci (QTL) controlling resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe). Although this approach successfully mapped a large number of SCN resistance QTL, it captures only limited allelic diversity that exists in parental lines, and it also has limitations for genomic resolution. In this study, a genome-wide association study (GWAS) was performed using a diverse set of 553 soybean plant introductions (PIs) belonging to maturity groups from III to V to detect QTL/genes associated with SCN resistance to HG Type 0.


RESULTS
Over 45,000 single nucleotide polymorphism (SNP) markers generated by the SoySNP50K iSelect BeadChip (http// www.soybase.org ) were utilized for analysis. GWAS identified 14 loci distributed over different chromosomes comprising 60 SNPs significantly associated with SCN resistance. Results also confirmed six QTL that were previously mapped using bi-parental populations, including the rhg1 and Rhg4 loci. GWAS identified eight novel QTL, including QTL on chromosome 10, which we have previously mapped by using a bi-parental population. In addition to the known loci for four simple traits, such as seed coat color, flower color, pubescence color, and stem growth habit, two traits, like lodging and pod shattering, having moderately complex inheritance have been confirmed with great precision by GWAS.


CONCLUSIONS
The study showed that GWAS can be employed as an effective strategy for identifying complex traits in soybean and for narrowing GWAS-defined genomic regions, which facilitates positional cloning of the causal gene(s).
Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO, 65211, USA. vuongt@missouri.edu.
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Vuong
Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO, 65211, USA. sonahh@missouri.edu.|Present address: Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Centre de Recherche en Horticulture, Université Laval, Quebec, Canada. sonahh@missouri.edu.
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Sonah
Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO, 65211, USA. meinhardtc@missouri.edu.
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Meinhardt
Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO, 65211, USA. deshmukhr@missouri.edu.|Present address: Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Centre de Recherche en Horticulture, Université Laval, Quebec, Canada. deshmukhr@missouri.edu.
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Deshmukh
Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO, 65211, USA. kadamsu@missouri.edu.
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Kadam
Soybean Maize Germplasm, Pathology, and Genetics Research Unit, USDA, Agricultural Research Service, and Department of Crop Sciences University of Illinois, Urbana, IL, 61801, USA. rlnelson@illinois.edu.
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Nelson
Division of Plant Sciences and NCSB, University of Missouri, Portageville, MO, 63873, USA. shannong@missouri.edu.
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Shannon
Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO, 65211, USA. nguyenhr@missouri.edu.
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Nguyen
D000818:Animals; D002874:Chromosome Mapping; D060467:Disease Resistance; D055106:Genome-Wide Association Study; D010940:Plant Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D013025:Glycine max / Q000235:genetics* / Q000469:parasitology*; D014431:Tylenchoidea / Q000502:physiology
D010940:Plant Proteins