Integration of GWAS and transcriptome and haplotype analyses to identify QTNs and candidate genes controlling oil content in soybean seeds

The oil content (OC) of soybean is a critical trait with important applications in the development of both food and industrial products. Consequently, enhancing OC has consistently remained a significant objective in soybean breeding programs. In this research, a four-way recombinant inbred line (FW-RIL) population containing 144 lines developed from the cross (Kenfeng14 × Kenfeng15) × (Kenfeng19 × Heinong48) was planted in ten environments to investigate the phenotypic data for OC in seeds. On the basis of the genotype data for 109,676 nonredundant single-nucleotide polymorphism (SNP) markers obtained in previous studies, important quantitative trait nucleotides (QTNs) controlling OC in soybean were identified via five multilocus genome-wide association study (GWAS) methods. A total of 54 significant QTNs were detected by the five methods, including 21 QTNs identified by multiple methods and 2 QTNs detected in two environments. By combining pathway analysis, transcriptome sequencing and gene annotation information, two candidate genes, Glyma.18G027100 and Glyma.03G021800, which are likely related to oil synthesis and metabolism in soybean seeds, were identified, and they were then verified via haplotype analysis. Additionally, 12 of the 23 important QTNs were found for the first time in this study. These results not only contribute to the understanding of the genetic control of OC in soybean seeds but are also helpful in marker-assisted selection (MAS) for breeding high-oil varieties of soybean.