Linkage disequilibrium was analysed using SNPs with a minor allele frequency more than 5% and missing data less than 24%, the linkage disequilibrium of the population was decayed to r 2 = 0.2 within approximately 300 kb (Fig. 2). The result was consistent with the previous studies in soybean (125 kb -600 kb) .Fig. 2The estimated average linkage disequilibrium decay of soybean genome. The dashed line in red indicates the position where r 2 is 0.2