The Identification of Significant Single Nucleotide Polymorphisms for Shoot Sulfur Accumulation and Sulfur Concentration Using a Genome-Wide Association Analysis in Wild Soybean Seedlings

Abstract

To understand the genetic basis of soybean sulfur utilization, a genome-wide association study (GWAS) and transcriptome analysis were used to discover new sulfur utilization genes in 121 wild soybeans. The shoot sulfur accumulation (SA) and shoot sulfur concentration (SC) of 121 wild soybean seedlings growing in a Hoagland nutrient solution for 14 days were evaluated in a greenhouse. The maximum coefficients of variation of SA and SC were 66.79% and 49.74%, respectively. An analysis of variance revealed that SA and SC had significant differences among materials. Compared with SC, SA had higher heritability (68%) and was significantly positively correlated with multiple agronomic traits. According to the GWAS, 33 and 18 single nucleotide polymorphisms (SNPs) were significantly associated with SA and SC, respectively. Six quantitative trait loci containing ten SNPs associated with SA were mapped in two or three environments on chromosome 9, 12, 13, 14, 15, and 19. Twenty-seven candidate genes were identified in the six stable loci by searching the low-sulfur-induction soybean transcriptome. A genetic diversity analysis of the ribosomal gene GsRPL35, a candidate gene on chromosome 15, revealed 10 haplotypes (Hap1-10) based on 7 SNPs in 99 wild soybeans. Wild soybeans carrying Hap2 had a higher SA than those carrying Hap6. In general, the results provide novel sulfur accumulation loci and candidate genes for sulfur utilization improvements in soybean in the future.