Objective  As an endangered native tree species in China, Pinus bungeana has important economic and garden ornamental values. In order to further develop and utilize the species germplasm resources, the study evaluated the genetic diversity of three populations from different provenances in P. bungeana.

  Method  Simple sequence repeats were selected from the transcriptome data in P. bungeana, and then 96 pairs of primers were developed, and the genetic diversity of 60 individuals in Beijing Hot Spring Nursery collected from three different provenances (Beijing, Shandong, and Shanxi) was analyzed, and genetic diversity parameters between intra- and inter-population were analyzed.

  Result  The variation ranges of the observed heterozygosity, expected heterozygosity, polymorphism information content and the number of allele loci for 5 pairs of polymorphic primers were 0.203−0.433, 0.211−0.530, 0.187−0.484 and 2−5, respectively. The number of alleles, effective alleles, Shannon diversity index, observed heterozygosity and fixed index of the three populations ranged in 2.400−3.000, 1.516−1.761, 0.484−0.606, 0.295−0.362 and −0.075−0.081, the average values were 2.677, 1.632, 0.560, 0.333 and −0.007, respectively. The ranges of genetic differentiation coefficient and gene flows were 0.021 6−0.115 3 and 1.399 6−11.340 0, and the average values were 0.090 2 and 2.521 2, respectively. AMOVA analysis showed that genetic variation mainly comed from within the population, with small differences between populations, accounting for only 11%.

  Conclusion  This study obtained 5 pairs of polymorphic EST-SSR primers in P. bungeana, which can be used for subsequent analysis of the population genetic diversity and molecular marker-assisted breeding. Genetic diversity analysis about the three populations of P. bungeana shows that the existing populations in Beijing Hot Spring Nursery have high genetic similarity, and the populations from other provenances should be considered for the future germplasm resource preservation and seedling breeding work.