QTL/Segment Mapping and Candidate Gene Analysis for Oil Content Using a Wild Soybean Chromosome Segment Substitution Line Population

Annual wild soybean, the ancestor of cultivated soybean, underwent a significant increase in seed oil content during domestication. To elucidate the genetic basis of this change, a chromosome segment substitution line population (177 lines) constructed with cultivated soybean <i>NN1138-2</i> as recipient and wild soybean <i>N24852</i> as donor was used in this study. Phenotypic evaluation across three distinct environments led to the identification of two major QTL/segments, <i>qOC14</i> on chromosome 14 and <i>qOC20</i> on chromosome 20, which collectively explained 39.46% of the phenotypic variation, with individual contributions of 17.87% and 21.59%, respectively. Both wild alleles exhibited negative additive effects, with values of -0.35% and -0.42%, respectively, consistent with the inherently low oil content of wild soybeans. Leveraging transcriptome and genome data from the two parents, two candidate genes were predicted. Notably, <i>Glyma.14G179800</i> is a novel candidate gene encoding a PHD-type zinc finger domain-containing protein, and the hap-A haplotype exhibits a positive effect on oil content. In contrast, <i>Glyma.20G085100</i> is a reported <i>POWR1</i> gene, known to regulate protein and oil content. Our findings not only validate the role of known gene but, more importantly, unveil a new candidate gene, offering valuable genetic resources and theoretical targets for molecular breeding of high-oil soybean.