Genome‐wide association mapping and candidate gene analysis for saturated fatty acid content in soybean seed

Abstract

AbstractSaturated fatty acids (FA), an important component of soybean oil, plays a crucial role in the nutritional value of soybean oil through different concentration and relative proportions. In this study, an association population of 185 diverse soybean accessions was used to identify quantitative trait nucleotide (QTN) and scan candidate genes via genome‐wide association analysis (GWAS), which was based on high throughout single‐nucleotide polymorphisms (SNPs) developed via the Specific Locus Amplified Fragment Sequencing (SLAF‐seq) approach. A total of 33,149 SNPs were identified with minor allele frequencies (MAF) >4%, which covered 97% of the soybean whole genome. For the two saturated FA concentration, including palmitic acid (PA) and stearic acid (SA), up to 65 SNPs were verified via GWAS. Among them, 35 and 16 SNPs loci were the novel loci for PA and SA, respectively. There were other six loci for PA and eight loci for SA overlapped or located in the linked genomic regions reported by the previous study. Furthermore, many loci were repeated in more than two environments, and four pair of pleiotropic loci (PA‐3‐2 and SA‐3‐2, PA‐11‐2 and SA‐11‐1, PA‐12‐2 and SA‐12‐1, and PA‐17‐1 and SA‐17‐2) had similar genomic regions, which might control both PA and SA simultaneously. A total of 49 genes, which could participate in lipid biosynthesis pathway or hormone metabolism, were identified as the potential candidate genes associated with saturated FA. The identified loci with beneficial alleles and the candidate genes would be valuable for studying the molecular mechanisms of saturated FA and further for improving nutritional value of soybean oil.