Plant Molecular Biology Reporter

, Volume 37, Issue 1–2, pp 87–97 | Cite as

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

  • Wen-Jiang Shu
  • Jian-min Tang
  • Zong-You ChenEmail author
  • Yun-Sheng Jiang
  • Zheng-Feng Wang
  • Xiao WeiEmail author
Original Paper


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 (Na = 8.00, He = 0.74, PIC = 0.80, I = 1.67), and reduced genetic variation and heterozygote excess were detected in landrace populations (Na = 5.59, He = 0.71, Ar = 4.11, FIS = − 0.043) when compared with those semi-wild population (Na = 9.7, He = 0.74, Ar = 8.80, FIS = 0.082). A significant bottleneck was detected in two Landraces populations. Moderate differentiation and frequent gene flow were detected among all populations (FST = 0.079, P < 0.05, Nm = 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.


S. japonica SSR marker Genetic diversity Population structure 


Funding Information

This study was supported by the Guangxi Natural Science Foundation Program (2018GXNSFAA138073), Guangxi Youth Science Foundation Project (2017JXNSFBA198011), Guangxi Key Laboratory of Plant Functional Substance Research and Utilization (ZRJJ2016-20), and Guangxi Academy of Sciences Basic Research Business Funding Project (2017YJJ23010).

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Guangxi Institute of BotanyGuangxi Zhuangzu Autonomous Region and the Chinese Academy of SciencesGuilinChina
  2. 2.Baoji Central HospitalBaojiChina
  3. 3.Key Laboratory of Vegetation Restoration and Management of Degraded Systems, South China Botanical GardenChinese Academy of SciencesGuangzhouPeople’s Republic of China

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