The averaged numbers of alleles per locus for SNPs and SSRs were 1.648 and 6.657, respectively, and the PIC values for SNPs and SSRs were 0.198 and 0.605, respectively (Table 2). The genetic diversity of SNP (0.250) is less than that of SSR (0.646), which is likely due to the difference of the bi-allele nature of SNP and the multi-allele nature of SSR. However, because the total number of SNPs is 29.7 times as high as that of SSR, indicating that SSR can provide more genetic information than SNP for assessment of genetic relatedness. The Fst between the two sub-populations defined by the STRUCTURE were 0.023 and 0.029 for SSRs and SNPs, respectively, which were similar to that between soybean breeding lines and landraces (0.0267) in a previous study . Low population differentiation indicated a narrow genetic background in modern soybean cultivars.Table 2The genetic diversity of soybean population based on SSR and SNP markersMarkerSNPsSSRsMajor Allele Frquency0.8060.481Alleles per locus1.6486.657Gene Diversity0.2500.646Heterozygosity0.0730.023PIC0.1980.605 Fst 0.0290.023