Evaluation of the genetic diversity of Pinus koraiensis by EST-SSR and its management, utilization and protection

Abstract Pinus koraiensis is an important economic species in China. With a gradual decrease in their natural population and the increasing demand for wood, there is an urgent need to collect P. koraiensis germplasm resources and explore their genetic diversity for better management and protection. In this study, 11 pairs of EST-SSR primers were synthesized based on RNA-seq technology. The average polymorphism information content (PIC) was 0.48, which indicated that the primers had good polymorphism. 11 pairs of EST-SSR primers were used to study the genetic diversity in 26 provenances of P. koraiensis. Molecular variance analyses showed that 50% of the variations occurred among the provenances. The average Shannon diversity index (I) was 0.39, which indicated moderate genetic diversity. The observed number of alleles (Na = 41), effective number of alleles (Ne = 2.28), expected heterozygosity (He = 0.47), and Shannon diversity index (I = 0.86) of DST provenance were the maximum, which indicated that the genetic diversity in DST provenance was relatively abundant. The genetic distance was 0.002–1.729. The coefficient of genetic differentiation was 0.010–0.847. Based on genetic structure analyses, through principal coordinate analysis (PCoA) and neighbor-joining method analysis (NJ) 26 provenances were clustered into six categories. The results of this study may provide the reference primers for P. koraiensis and related tree species, and useful genetic information for strategies for improvement, management, and protection of P. koraiensis.