Objective  Vernicia montana, belonging to the genus Vernicia of Euphorbiaceae family, is an important industrial oil tree species, which has received great attention in recent years because it is much more resistant to wilt disease than V. fordii of same genus. However, the current researches on the molecular genetics of V. montana are still very limited due to its short cultivation history and inadequate management of germplasm resources. This study aimed to develop V. montana’s genome SSR markers, and then to carry out its germplasm identification, genetic diversity and population structure analyses.

  Method  Using RAD sequencing technology to obtain a simplified genome of V. montana to develop its SSR markers, based on the SSR markers, a series of methods including the analysis of molecular variance (AMOVA), the unweighted pair group method with arithmetic mean (UPGMA) clustering, principal coordinate analysis (PCoA) and population structure analysis were used to study 105 germplasm resources of V. montana from three different geographical distributions.

  Result  17 polymorphic trinucleotide genomic-SSR markers were developed, which well distinguished all the tested 105 V. montana germplasms. A total of 85 private alleles were detected in 62 germplasms at 15 SSR loci. The AMOVA analysis revealed a moderate degree of genetic differentiation among the populations of V. montana; however, the genetic variation within the populations was much higher than that among the populations. Population structure analysis showed that four different gene pools were present in the three V. montana populations from different geographical distributions, and there was both evolutionary independence and a relatively high degree of genetic admixture among the populations, which was basically consistent with the results of UPGMA and PCoA analyses.

  Conclusion  The newly developed 17 SSR markers effectively identified 105 V. montana germplasms, and revealed the genetic diversity and population genetic structure of the germplasms, which would be very helpful for the conservation of germplasms and breeding program in V. montana.