Genome-wide association mapping for seed protein and oil contents using a large panel of soybean accessions

Soybean is globally cultivated primarily for its protein and oil. The protein and oil contents of the seeds are quantitatively inherited traits determined by the interaction of numerous genes. In order to gain a better understanding of the molecular foundation of soybean protein and oil content for the marker-assisted selection (MAS) of high quality traits, a population of 185 soybean germplasms was evaluated to identify the quantitative trait loci (QTLs) associated with the seed protein and oil contents. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 12,072 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) ≥ 0.05 were detected across the 20 chromosomes (Chr), with a marker density of 78.7 kbp. A total of 31 SNPs located on 12 of the 20 soybean chromosomes were correlated with seed protein and oil content. Of the 31 SNPs that were associated with the two target traits, 31 beneficial alleles were identified. Two SNP markers, namely rs15774585 and rs15783346 on Chr 07, were determined to be related to seed oil content both in 2015 and 2016. Three SNP markers, rs53140888 on Chr 01, rs19485676 on Chr 13, and rs24787338 on Chr 20 were correlated with seed protein content both in 2015 and 2016. These beneficial alleles may potentially contribute towards the MAS of favorable soybean protein and oil characteristics. •Using a diverse collection of soybean germplasm samples, the QTLs associated with seed protein and oil content in this study were identified using a GWAS mapping approach and sequence-based SNP maps. Thirty-one QTLs were identified in total. Of these two stable SNP markers, rs53140888 and rs15774585, constituted novel loci underlying soybean seed protein content and were identified for the first time in the present study.•Previous studies documented a series of pleiotropic QTLs underlying soybean seed and oil compositions. In the present study, rs12328685, rs49097495, rs29457452, and rs29979450 were pleiotropic for soybean seed protein and oil content. It is therefore essential to clarify the effects of the loci for the two target traits before initiating MAS programs.•Using specific length amplified fragment sequencing technology, a total of 12,072 single nucleotide polymorphisms with a minor allele frequency ≥ 0.05 were detected across the 20 chromosomes, with a marker density of 78.7 kbp. A total of 31 SNPs located on 12 of the 20 soybean chromosomes were correlated with seed protein a