Fig. 2

Apple evolutionary map. a Apple evolutionary map along the west and east bounds of the Silk Route with center of origin at Kazakhstan in central Asia. b Decay of linkage disequilibrium (LD) measured as the squared correlation coefficient (r 2) by pairwise physical distance in M. domestica, M. sieversii in Kazakhstan, M. sieversii in Xinjiang, M. sylvestris, and other wild species. c Multidimensional scaling (MDS) plot for the pairwise F ST matrix. The Euclidean distances between each pair of groups significantly represent the corresponding F ST values (Spearman rank-sum correlation ρ = 0.95; p < 10−14). d Major alleles of scion and rootstock cultivars derived from M. sieversii in Kazakhstan and M. sylvestris. Asi M. asiatica, Bac M. baccata, Dom M. domestica, Hup M. hupehensis, Rob M. robusta, Sie_K M. sieversii in Kazakhstan, Sie_X M. sieversii in Xinjiang, Syl M. sylvestris