SNP/InDel-Based GWAS Reveals QTNs and Candidate Genes for Seed Oil and Protein Content in Northern China Soybean Core Accessions

Seed oil and protein content in soybean [ Glycine max (L.) Merr.] are complex quantitative traits controlled by multiple genes and highly susceptible to environmental influences. To investigate the genetic basis of these traits in Northern China, a major soybean-producing area, we re-sequenced 334 core accessions of soybean landraces and elite cultivars from this area. Based on phenotypic data collected over multiple years, a subsequent SNP/InDel-based GWAS for seed oil and protein content identified fifteen quantitative trait nucleotides (QTNs) significantly associated with the traits. Noticeably, qOil05-1 was consistently detected across three years, accounting for 4.8 ~ 14.46% of phenotypic variance (PVE). Within the confidence interval of qOil05-1 , we identified GmHAD1 , a gene encoding a haloacid dehalogenase-like hydrolase, as a strong candidate gene. GmHAD1 expression differed substantially (~ 3.04 fold) between the two major haplotypes (H1 and H2 - 1). Further analysis confirmed that the two major haplotypes of GmHAD1 showed significant or highly significant differences in seed oil and protein content. Overall, our findings offer valuable information into the genetic mechanisms underlying oil and protein accumulation in soybean, providing guidance for future genetic improvement of soybean quality.