Genomic atlas of 8,105 accessions reveals stepwise domestication, global dissemination, and improvement trajectories in soybean

After millennia of domestication, dissemination, and improvement, soybean has evolved into a globally significant leguminous crop. Addressing how soybeans adapt to diverse planting environments and breeding objectives will facilitate future breeding advancements. Here, we systematically investigated the genes under selection of 8,105 soybean accessions underlying domestication, dissemination, and improvement. The analyses revealed that black soybeans serve as a critical domestication intermediate, and soybean domestication traits were selected in a stepwise manner. Comparisons across accessions from diverse geographical areas and historical eras identified numerous selected genes that have contributed to trait enhancement and environmental adaptation during the global dissemination and unveiled a temporal shift of breeding priorities in soybean improvement in China. To highlight the allele utilization among soybean varieties, we constructed a variation map and quantitative trait nucleotide (QTN) library. Our findings provide valuable insights and serve as a critical resource for understanding soybean domestication and informing breeding strategies.