The genetic diversity of 279 indivdiuals from 10 populations in Shandong Province was investigated using inter-simple sequence repeat (ISSR) markers. As a result, 116 bands were amplified by 10 informative and reliable primers, of which 101 were polymorphic loci. A relatively high level of genetic diversity was revealed: PPL = 87.07, He = 0.2697, H0 = 0.3999 (at the species level); PPL = 64.58, He = 0.2004, H0 = 0.3010 (at the population level). A higher level of genetic differentiation was detected among populations with Nei's G(ST) analysis and the analysis of molecular variance (AMOVA; G(ST) = 0.2414, F(ST) = 0.2224). Habitat fragmentation and gene flow may result in genetic differentiation. UPGMA cluster analysis indicated that the four populations from Linshu, Junan, Tancheng and Feixian grouped together, whereas Laiyang populations clustered in an isolated clade. The results showed that a mixed mating system was possibly the main factor influencing the genetic structure of this species. These results, combined with other information about Castanea mollissima, may provide a valuable basis for proposing conservation strategies.
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