Genetic diversity and population structure of endangered endemic Paeonia jishanensis in China and conservation implications

•Paeonia jishanensis is an endangered endemic species in China.•Moderate genetic diversity levels and high genetic differentiation among populations were revealed using EST-SSRs.•The patterns of genetic variation may be due to limited gene flow, geographic isolation and the breeding system.•Some implications for the conservation and utilization of the genetic wealth of endemic species were proposed.

Paeonia jishanensis, one of the most important ancestral species of cultivated tree peonies, is an endangered ornamental and medicinal plant endemic to China. A total of 236 individuals of P. jishanensis from 10 extant populations were analysed using 21 EST-SSR markers to assess their genetic diversity and population structure. Moderate genetic diversity levels (HE = 0.340) and high genetic differentiation among populations (FST = 0.335) were revealed. Combining the results of STRUCTURE, PCoA and neighbour-joining analyses, the 10 populations were divided into four genetic groups that were significantly related to their geographical origins, which was further supported by hierarchical AMOVA showing the highest variation of 17.9% among groups. The Mantel test showed a significant positive correlation between genetic distance and geographic distance among populations (r = 0.873, P < 0.0001). The genetic structure of P. jishanensis may be due to limited gene flow hindered by vicariance and its breeding system: facultative vegetative reproduction. This study carries significant implications for the conservation and utilization of this endangered species.