Ilex chinensis Sims. is an evergreen tree species native to China and mainly distributed in the region south of the Qinling Mountains and the Huai River. This species has important ornamental, medicinal, ecological, and economic values, and plays a positive role in improving the environment and people’s lives. To reveal the genetic diversity and genetic structure of 401 individuals from 14 populations in the major distribution area of I. chinensis, 11 pairs of SSR primers were selected for PCR amplification. The products were then subjected to capillary electrophoresis, and the genetic diversity of Ilex individuals was analyzed using relevant software. The results showed that the genetic diversity of I. chinensis was at a moderate-to-high level. A total of 54 alleles were detected at 11 SSR loci in the 14 Ilex populations, with an average of 4.831 alleles per locus. AMOVA analysis indicated that the genetic variation of I. chinensis populations mainly originated within populations. A STRUCTURE analysis divided the 401 I. chinensis individuals into four different genetic clusters. The unweighted pair group methods using arithmetic averages (UPGMA) clustering based on Nei’s genetic distance revealed that the population from Xinping of Yuxi, Yunnan Province (XP), and the population from Longan of Qianxinan, Guizhou Province (LoA) were located in the outermost layer of the phylogenetic tree, indicating the furthest genetic relationship between these two population and other populations. The remaining populations could be roughly divided into two groups. Principal coordinate analysis (PCoA) demonstrated that the 401 individuals were clearly divided into three groups, which was consistent with the results of the STRUCTURE analysis and UPGMA clustering. This study identified the hotspots of genetic diversity of I. chinensis, as well as units for the conservation of individuals. It also revealed the patterns of genetic variation and population distribution of I. chinensis in different regions, providing a molecular basis for the geographical zoning and formulation of breeding programs for I. chinensis, as well as germplasm resource management.
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