High resolution QTL mapping and candidate gene mining for seed oil content and fatty acid composition in soybean

Soybean oil plays crucial roles in both food and biodiesel industries. Increasing oil content and improving the fatty acid composition are critical objectives in soybean breeding programs. In this study, we performed high-resolution QTL mapping for oil content and fatty acid composition using 192 F_2:7-8 recombinant inbred lines (RILs) based on a high-density genetic map. We detected a total of 66 QTL, including 14 for oil content and 52 for individual fatty acids. Among these, seven QTL were stable across multiple environments, with qPA-05 and qLA-06 being novel loci for palmitic and linoleic acids, respectively. A total of 34 QTL were grouped into seven clusters. Through candidate gene mining for Cluster05-2 and qLNA-14 using single-locus ANOVA in 1025 soybean accessions, combined with gene expression profiling and annotation, we identified the MOTHER OF FT AND TFL1 (MFT) gene (Glyma.05G244100), the 2-acylglycerol O-acyltransferase (MGAT) gene (Glyma.05G248100), and three ubiquitination-related genes (Glyma.05g237500, Glyma.05G238500, and Glyma.05G238900) in Cluster05-2 as strong candidate genes for oil content, and the ω-3 fatty acid desaturase (FAD3A) gene (Glyma.14G194300) in qLNA-14 as strong candidate gene for linolenic acid. Haplotype analyses of these candidate genes revealed significant influence of specific haplotypes on oil and linolenic acid content, respectively. Notably, for MGAT, the frequency of the high-oil haplotype (Hap1-TA) exhibited a clear decreasing trend from north to south in China among the soybean accessions, which is consistent with the distribution trend of soybean oil content across China. The discovery of stable QTL and candidate genes associated with oil and fatty acid contents will enhance the efficiency of molecular breeding programs aimed at improving soybean quality.