Soybean is a primary source of plant-based oil and protein for human diets. Seed size and weight are important agronomic traits that significantly influence soybean yield. Despite their importance, the genetic mechanisms underlying soybean seed size and weight remain to be fully elucidated. In order to identify additional, major quantitative trait loci (QTL) associated with seed size and weight, we developed segregating populations by crossing a large-seeded soybean variety “Kebaliang” with a small-seeded soybean variety “SUZUMARU”. We evaluated seed length, width, thickness, and hundred-seed weight across two generations, F₄ and F₅, in 2022 and 2023. Employing bulked segregate analysis with whole-genome resequencing (BSA-seq), we detected 18 QTLs in the F₄ population and 12 QTLs in the F₅ population. Notably, six QTLs showed high stability between the two generations, with five derived from two pleiotropic loci (qSS4-1 and qSS20-1) and one specific to seed width (qSW14-1). Further validation and refinement of these loci were carried out through linkage mapping using molecular markers in the F₅ population. Additionally, we identified 18 candidate genes within these stable loci and analyzed their sequence variations and expression profiles. Together, our findings offered a foundational reference for further soybean seed size research and unveiled novel genetic loci and candidate genes that could be harnessed for the genetic enhancement of soybean production.

Glycine soja is the wild relative species of cultivated soybean. In this study, we investigated the population divergence and genetic basis of the local adaptation of wild soybean in China using genome-wide single-nucleotide polymorphisms (SNPs) of a population of 72 G. soja accessions. Using phylogenetic analysis, we observed that G. soja accessions clustered into three distinct groups, each corresponding to a specific geographic region, the northeastern region (NER), central region (CR), and southern region (SR), consistent with previous studies. Notably, we found a significant positive correlation between genetic and geographic distances. Further population structure analysis revealed each group was associated with an ancestral population and a specific geographic area. By utilizing the genome sequencing data of accessions from 16 different locations, we inferred the population history of these wild soybean groups. Our results indicate that the three groups diverged ~25,000 years ago, coinciding with the time of the last glacial maximum. The effective population size of the SR group expanded first, and subsequently, the NER and CR groups expanded approximately 5000 and 2500 years ago, respectively. Moreover, 83, 104, and 101 significant associated loci (SALs) were identified using genome-wide association analysis for annual mean temperature, annual precipitation, and latitude, respectively. Functional analysis of genes located in SALs highlighted candidate genes related to local adaptation. This study highlights the significant role of geographic isolation and environmental factors in shaping the genetic structure and adaptability of wild soybean populations. Furthermore, it emphasizes the value of wild soybean as a crucial genetic resource for enhancing the adaptability of cultivated soybeans, which have experienced a loss of genetic diversity due to domestication and intensive breeding practices. The insights gained from our research provide valuable information for the protection, conservation, and utilization of this important genetic resource.