The population structure was assessed by STRUCTURE v.2.3.1 software based on SSR and SNP markers and the most likely number of sub-populations were consistent based on the two types of markers. When K = 2, the ad hoc quantity (ΔK) estimation had the highest value (Fig. 1a, Fig. 1b, Additional file 4: Figure S2a and Additional file 4: Figure S2b) . The first sub-population contained 46 cultivars, a majority of which were from the late maturity groups in the Huang-Huai-Hai River Valley, and south China (95.7%). The cultivar ‘Altana’ from the US was also in this group. The second sub-population consisted of 45 cultivars of the early maturity groups (93.3%), which were from northeast China (60%) and the US (33.3%). A cluster analysis and PCA also showed that the genotypes were classified into two groups (Fig. 1c, Fig. 1d, Additional file 4: Figure S2c and Additional file 4: Figure S2d).Fig. 1Population structure of 91 soybean cultivars using 5107 SNP markers. a Estimation of the number of sub-populations. The left figure was a plot of ln (probability of data) vs. K ranging from 1 to 10 and the right figure was a plot of subpopulation number vs. delta K values. b Population structure of 91 soybean cultivars based on SNP markers. The x-axis indicates the cultivars, and the y-axis indicates the Q value from STRUCTURE 2.3.1. The red color represents one sub-group, the green color represents another. c PCA of 91 soybean cultivars with the top two principal components. d Neighbor-joining tree of the 91 soybean cultivars