Genetic differentiation between cultivated and wild soybean at IFS1, IFS2, F3H 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**P***P