Comparison of genetic diversity between ancient and common populations of Docynia delavayi (Franch.) Schneid

•SSR markers were used for the first time to analyze and compare the genetic diversity and population structure of ancient and common D. delavayi populations.•The D. delavayi common population showed higher genetic diversity than ancient population.•Genetic variation in ancient populations and common populations occurs mainly among individuals.•Based on these findings, strategies of protecting and utilization for D. delavayi ancient populations were proposed. Docynia delavayi (Franch.) Schneid. (D. delavayi), is a wild fruit tree which combines edible, medicinal, ecological and ornamental uses. In this study, ancient and common populations of D. delavayi were examined for genetic diversity and structure using SSR markers. As a result, a total of 136 alleles were detected at 18 SSR loci, with the mean of 7.56 alleles. The value of Na, Ne, I, He and Nm of the ancient populations were lower than those of the common populations except for Ho and Fst. It indicates that the genetic diversity of the common populations is higher than that in ancient populations. The genetic differences between ancient populations were slightly greater than those between common populations, which demonstrated less gene flow between ancient populations. According to the analysis of molecular variance (AMOVA), the genetic variation within the common population was greater than that in the ancient population, indicating that there was a higher genetic diversity within the common population. Also, the clustering heatmap results are partially consistent with the principal coordinate analysis (PCoA) results. Moreover, the mantel test showed an extremely significant correlation between genetic and geography distance (r = 0.214, p