Genome Wide Association Study of Sclerotinia stem rot in Soybean

Sclerotinia stem rot or white mold (WM) [Sclerotinia sclerotiorum (Lib.) de Bary] is an important fungal disease affecting soybean [Glycine max (L.) Merr.] and causes yield and quality losses. WM is prevalent in cool and moist environments, particularly in the soybean growing regions of Northern United States and Canada. Although sources of complete resistance have not yet been identified, several quantitative trait loci (QTL) for partial resistance have been reported but generally using bi-parental mapping populations. Genome-wide association (GWA) studies have been used to dissect complex disease resistance traits in plants and to identify the genes controlling the expression. We phenotyped 473 diverse plant introduction accessions from the USDA Soybean Germplasm Collection and genotyped with the Illumina Infinium BeadChip with 50K SNP to 1) find sources of WM resistance, 2) identify SNP associated with WM resistance using GWA studies, and 3) determine putative candidate genes for WM resistance. Phenotyping for WM was done under artificial epiphytotic conditions in both field and greenhouse tests. Multiple response variables were recorded at varying growth stages. GWA study was performed in GAPIT using ordinal logistic mixed model to obtain BLUPs. A range of disease responses were recorded among the PI lines. Forty five SNP associated with WM resistance were identified at different growth stages and for multiple response variables. A wide range of candidate genes were identified at the proximity of peak SNPs, which included disease response genes previously reported in the literature as well as previously unreported genes.