Many agronomically important traits exhibit modularity and tend to be tightly integrated. Theunderstanding of how traits become associated or correlated is essential in the improvement of complextraits. Soybean is a major crop of agronomic importance as the predominantsource of animal feed protein and cooking oil, which was domesticated from wild soybean in China 5,000 years ago. Dissection the genomic diversity during soybeandomestication/improvement and the genetic basis of agronomic traits is important for soybeanimprovement. By analysis of several hundred resequenced wild, landrace and improved soybeanaccessions, we detect 230 selective sweeps and 162 selected copy number variants. Combined withprevious quantitative trait loci (QTL) information, we find that, of the 230 selected regions, 96correlate with reported oil QTLs and 21 contain fatty acid biosynthesis genes 96 0f which correlatewith reported oil QTLs. Moreover, we detect several hundred association signals via a comprehensiveGWAS for dozens of agronomic traits. Through modeling analyses, we find that amount of associationsites are tightly linked and form a complex network to regulate the modularity of different complextraits. This study provides valuable resources for genomics-enabled improvements in soybeanmolecular breeding.
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