Monitoring genetic diversity across Pinus tabuliformis seed orchard generations using SSR markers

Abstract

The maintenance of genetic diversity across seed orchard generations is an important management objective. Here, we used Pinus tabuliformis Carrière as a model to explore the extent of genetic diversity across the species’ breeding activities through their corresponding seed orchard generations. We utilized a large number of simple sequence repeat (SSR) markers selected from P. tabuliformis transcriptomic data, and then assessed the effect of marker number on genetic diversity and genetic relationships of individuals across orchard generations. In total, we designed 125 SSR markers, of which 39 were polymorphic and used in the present study. The genetic diversity and genetic distance parameters tended to increase with an increase in loci number and a stable trend was reached at 24 SSRs. The selected optimal 24 SSR markers were further used to assess the genetic diversity across seed orchard generations, and a decreasing trend was detected with the advancement of orchard’s generations. Genetic distance analysis indicated that individuals in the 2nd generation orchard were more closely related compared with those of the 1st generation and the 1.5 generation. This study provided valuable information on the effect of selection and breeding on genetic diversity and highlighted its role for effective seed orchard management.