Nucleotide variation 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, Cultivated soybean; W, Wild soybean.π, Nucleotide diversity with Jukes and Cantor correction.Hd, Haplotype diversity.θ, Watterson’s estimator of θ per basepair calculated on the total number of polymorphic sites.θsil, Watterson’s estimator of θ per basepair calculated on the silent sites.Ksil, Average divergence per silent site (with the Jukes and Cantor correction) between cultivars and wild soybean.Dxy, Nucleotide divergence with Jukes and Cantor correction between cultivars and wild soybean.