Fine mapping and candidate gene analysis of a major QTL qHSW_11 for seed weight in soybean

qHSW_11, a major quantitative trait locus controlling seed weight in soybean, was fine-mapped to a 340-kb region on chromosome 11, and Glyma.11G239000 is the candidate gene responsible for seed weight. A KASP marker could therefore be useful for selecting high-seed-weight lines in soybean breeding. Seed weight is a critical determinant of yield in soybean. The mechanism underlying seed weight remains poorly understood in soybean. In this study, a recombinant inbred line (RIL) population derived from the cross between Jidou17 and Zhonghuang13 was employed to identify QTLs associated with seed weight. A major locus, qHSW_11, which was consistently detected across three consecutive years, explained 9.51-15.13% of the phenotypic variance. To further refine this locus, we developed a BC₁F₄ population, which narrowed qHSW_11 to a 340-kb genomic interval harboring four putative candidate genes. Among them, Glyma.11G239000, a soybean homolog of ETHYLENE INSENSITIVE 3 (EIN3), carried an 8-bp insertion within the EIN3 DNA-binding domain and six SNPs distinguishing the parental alleles and exhibited differential expression between the parents during seed development stages. Haplotype analysis revealed that Hap2 (Zhonghuang13) was significantly associated with higher seed weight compared with Hap1 (Jidou17). Furthermore, we designed a site-specific Kompetitive Allele-Specific PCR (KASP) marker based on resequencing data of Glyma.11G239000 and confirmed its effectiveness in a germplasm collection comprising 247 soybean accessions. Overall, the comprehensive results provide new insights into the genetic regulation of seed weight and establish a functional marker for marker-assisted selection to enhance soybean yield.