A Genome-Wide Association Study to Identify Loci Associated with Seed Protein Concentration in Soybean

Genome-Wide Association Studies (GWAS) are applied to detect the location of qualitative genes and quantitative trait loci using the correlation between DNA marker alleles or haplotypes and the phenotypic expression of a trait of interest. In this research, GWAS was performed to detect loci controlling seed protein concentration in soybean. A total of 42,368 SNPs were analyzed in a diverse set of Glycine max (L.) Merr. germplasm accessions from the USDA Soybean Germplasm Collection. Field tests were conducted to evaluate seed protein concentration of the accessions using a randomized complete block design with four replicates at Beltsville, MD and two replicates at Lincoln, NE. Total seed nitrogen was determined using a LECO CHM 2000 analyzer (LECO, St. Joseph, MI) in order to obtain an estimate of seed protein concentration. Analysis of variance was conducted and population structure of the 302 accessions was estimated by the Admixture program v. 1.22 (Alexander et al. 2009). Association analysis was performed with the mixed linear model approach implemented by TASSEL (Bradbury et al. 2007). GWAS detected 17 loci on 10 chromosomes showing significant association (-logP>3) with seed protein concentration including associations at the 27-30 Mbp region on Gm20, at 14.7 Mbp on Gm06, and at 8.9 Mbp on Gm17. Of the 17 associations, 12 corresponded with the location of previously reported seed protein QTL. This result indicates that GWAS was successful in identifying loci controlling seed protein concentration in soybean germplasm accessions.