Comprehensive Genomic Survey of Genes Related to Domestication and Improvement in Soybeans

Soybean (Glycine max) is an important crop, and it is the world's main source of oilseed. Through a large-scale assessment of soybean domestication and improvement by resequencing 302 wild, landrace and improved soybean accessions at >11× depth, we detected 230 selective sweeps and numbers of selected copy number variations. Genome-wide association study revealed associations between 10 selected regions and 9 domestication/improvement traits and identified 13 previously uncharacterized loci relevant to important agronomical traits, such as oil content, plant height and pubescence form. Combined with previous linkage studies on quantitative trait loci (QTL) identification, we found that 96 selected regions fell into reported oil QTLs and 21 selected regions contained fatty acid biosynthesis genes. Moreover, we observed that some traits and loci are associated with particular geographical regions, showing that soybean populations were structured geographically. This study provides unprecedented large-scale information and resources for genetics research and genomics-enabled improvements in soybean breeding.