Genetic diversity and population structure of the endangered medicinal plant Phellodendron amurense in China revealed by SSR markers

• Genetic diversity and structure of an endangered species were investigated using eight SSR primer pairs.
• A relatively high level of genetic diversity and low genetic differentiation among populations were identified.
• Bayesian clustering and UPGMA supported grouping the populations into two groups.
• The conservation measures were proposed for this species.

Phellodendron amurense is an endangered tree with important medicinal and economic value in China. In this study, eight nuclear SSR primer pairs were employed to assess the genetic diversity and structure of 22 natural populations, including 516 individuals. A total of 66 alleles were detected with an average of 8.3 alleles per locus ranging from 3 to 17. The expected heterozygosity (He) of each SSR locus varied from 0.347 to 0.877 (average 0.627). Analysis of molecular variance (AMOVA) revealed that the main variation component existed within populations (95.11%) rather than among populations (4.89%). The Wilcoxon's sign-rank tests did not show any recent bottleneck effect in any population. A Mantel test displayed a significant correlation between the geographic distances and genetic distances for all populations (r = 0.566, P = 0.0001), indicating conformity to the isolation by distance model. Bayesian clustering and UPGMA supported grouping the populations into two groups. The present genetic structure of P. amurense may be explained by geographical isolation. The lack of genetic structure and genetic diversity decreased with increasing latitude within the Northeast China group may be due to postglacial northward expansion from a single refugium. Proper conservation measures are proposed for this species.