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ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Publications at this Location » Publication #325722
Title: Characterization of disease resistance loci in the USDA soybean germplasm collection using genome-wide association studies

Author
item CHANG, HAO-XUN - University Of Illinois
item LIPKA, ALEXANDER - University Of Illinois
item Domier, Leslie
item Hartman, Glen

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/21/2016
Publication Date: 8/10/2016
Citation: Chang, H., Lipka, A.E., Domier, L.L., Hartman, G.L. 2016. Characterization of disease resistance loci in the USDA soybean germplasm collection using genome-wide association studies. Phytopathology. 106(10):1139-1151. http://dx.doi.org/10.1094/PHYTO-01-16-0042-FI.

Interpretive Summary: Genetic resistance is a key strategy for soybean disease management. In past decades, soybean germplasm has been characterized for resistance to many different pathogens. Even though genes for resistance have been incorporated into elite breeding lines and commercial cultivars, high-throughput techniques to associate regions of chromosomes with disease resistance have been lacking. Recently, genome-wide association studies using high-quality genetic markers and information on plant responses to pathogen infection have become powerful tools to identify those chromosomal regions in unrelated germplasm lines. The objective of our study was to use the data in the United States Department of Agriculture, Agricultural Research Service, Germplasm Resources Information Network (USDA-ARS-GRIN) on responses to pathogen infection and a set of high quality genetic markers to identify chromosomal regions associated with disease resistance. In this study we report the association of genetic markers with resistance to one bacterial disease, five fungal diseases, two diseases caused by nematodes, and three viral diseases. Some of the genetic markers were in pathogen resistance-like genes, and many were proximal to chromosomal regions previously associated with disease resistance. We review and present a global view of soybean resistance loci against multiple diseases, and discuss the power and the challenges of genome-wide association to discover disease resistance utilizing the USDA-ARS-GRIN soybean database. This information is important to scientists and producers interested in research on managing soybean diseases through host-plant resistance.

Technical Abstract: Genetic resistance is a key strategy for soybean disease management. In past decades, soybean germplasm has been phenotyped for resistance to many different pathogens and genes for resistance have been incorporated into elite breeding lines often resulting in commercial cultivars with disease resistance. While biparental mapping has identified disease resistance loci, genome-wide association studies have become a powerful tool to associate high-density and high-quality single nucleotide polymorphism (SNP) markers with phenotypes. The objective of our study was to associate the soybean phenotypic data deposited in the United States Department of Agriculture, Agricultural Research Service, Germplasm Resources Information Network (USDA-ARS-GRIN) with SoySNP50K markers. We report on the association of SNPs with one bacterial disease, five fungal diseases, two diseases caused by nematodes, and three viral diseases. In the process, we identified SNPs within coding sequences of defense-related candidate genes, and proximal to previously reported quantitative trait loci for disease resistances. We review and present a global view of soybean resistance loci against multiple diseases, and discuss the power and the challenges of genome-wide association to discover disease resistances utilizing the USDA-ARS-GRIN soybean database.