Genome-Wide Association and RNA-Seq Analyses Reveal a Potential Candidate Gene Related to Oil Content in Soybean Seeds

Abstract

Soybean is a crucial crop globally, serving as a significant source of unsaturated fatty acids and protein in the human diet. However, further enhancements are required for the related genes that regulate soybean oil synthesis. In this study, 155 soybean germplasms were cultivated under three different environmental conditions, followed by phenotypic identification and genome-wide association analysis using simplified sequencing data. Genome-wide association analysis was performed using SLAF-seq data. A total of 36 QTLs were significantly associated with oil content (−log10(p) > 3). Out of the 36 QTLs associated with oil content, 27 exhibited genetic overlap with previously reported QTLs related to oil traits. Further transcriptome sequencing was performed on extreme high–low oil soybean varieties. Combined with transcriptome expression data, 22 candidate genes were identified (|log2FC| ≥ 3). Further haplotype analysis of the potential candidate genes showed that three potential candidate genes had excellent haplotypes, including Glyma.03G186200, Glyma.09G099500, and Glyma.18G248900. The identified loci harboring beneficial alleles and candidate genes likely contribute significantly to the molecular network’s underlying marker-assisted selection (MAS) and oil content.