title: Characterization of Disease Resistance Loci in the USDA Soybean Germplasm Collection Using Genome-Wide Association Studies.
abstract: Genetic resistance is a key strategy for disease management in soybean. Over the last 50 years, soybean germplasm has been phenotyped for resistance to many pathogens, resulting in the development of disease-resistant elite breeding lines and commercial cultivars. While biparental linkage mapping has been used to identify disease resistance loci, genome-wide association studies (GWAS) using high-density and high-quality markers such as single nucleotide polymorphisms (SNPs) has become a powerful tool to associate molecular markers and phenotypes. The objective of our study was to provide a comprehensive understanding of disease resistance in the United States Department of Agriculture Agricultural Research Service Soybean Germplasm Collection by using phenotypic data in the public Germplasm Resources Information Network and public SNP data (SoySNP50K). We identified SNPs significantly associated with disease ratings from one bacterial disease, five fungal diseases, two diseases caused by nematodes, and three viral diseases. We show that leucine-rich repeat (LRR) receptor-like kinases and nucleotide-binding site-LRR candidate resistance genes were enriched within the linkage disequilibrium regions of the significant SNPs. We review and present a global view of soybean resistance loci against multiple diseases and discuss the power and the challenges of using GWAS to discover disease resistance in soybean.
authors.affiliation: All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana.
authors.forename: Hao-Xun
authors.initials: HX
authors.lastname: Chang
authors.affiliation: All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana.
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Lipka
authors.affiliation: All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana.
authors.forename: Leslie L
authors.initials: LL
authors.lastname: Domier
authors.affiliation: All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana.
authors.forename: Glen L
authors.initials: GL
authors.lastname: Hartman
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D060467:Disease Resistance / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D010935:Plant Diseases / Q000276:immunology*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D013025:Glycine max / Q000235:genetics* / Q000276:immunology
chemical_list: D005819:Genetic Markers