Analysis of Genetic Diversity and Population Structure in Sophora japonica Linn. in China With Newly Developed SSR Markers

Sophora japonica is a medium-sized deciduous native tree to China. Its flower buds and fruits have special medicinal value. By using 26 highly variable nuclear microsatellites, newly reported here, we assessed the genetic diversity and population structure of 10 representative populations (180 individuals in total) within the species. The results revealed a relatively high genetic diversity in S. japonica (N_a?=?8.00, H_e?=?0.74, PIC?=?0.80, I?=?1.67), and reduced genetic variation and heterozygote excess were detected in landrace populations (N_a?=?5.59, H_e?=?0.71, A_r?=?4.11, F_IS?=???0.043) when compared with those semi-wild population (N_a?=?9.7, H_e?=?0.74, A_r?=?8.80, F_IS?=?0.082). A significant bottleneck was detected in two Landraces populations. Moderate differentiation and frequent gene flow were detected among all populations (F_ST?=?0.079, P?<?0.05, N_m?=?2.893). Mantel test detected a marginal significant pattern of isolation by distance (r?=?0.009, P?=?0.50), and strong differentiation was observed between most southern and northern populations both by the STRUCTURE clustering and principal coordinate analysis (PCoA), indicating that geographic isolation played a key role in the genetic differentiation of the species. The results from this study will benefit the breeding and conservation of S. japonica, other congener species, and tree species with similar life history traits.