Genetic differentiation between cultivated and wild soybean at <i>IFS1</i>, <i>IFS2</i>, <i>F3H</i> genes and reference genes, only CDS were considered.

R1 represents plant-environment interaction related reference genes, which include EU450800, the disease resistance gene Rps1-k-1; L20310, nodulin (nod-20) gene and D13505, early nodulin related gene; R2 signifies other fourteen reference genes. C, Cultivars; W, Wild soybean. Fixed, the number of fixed differences between cultivated and wild soybeans; In W, Mutations that are polymorphic in wild soybeans, but monomorphic in cultivars; In C, Mutations that are polymorphic in cultivars, but monomorphic in wild soybean; Shared, the total number of shared mutations. RM, the minimum number of recombination events [25], both coding and noncoding sequences were considered. *P<0.05, **P<0.01, ***P<0.001.