Development of polymorphic microsatellite markers for tree peony Paeonia delavayi (Paeoniaceae) using ddRAD-seq data.

Microsatellite markers were developed for the tree peony Paeonia delavayi to investigate fine scale population genetics of this species. Using ddRAD-seq data from twenty individuals of P. delavayi, we identified 529 polymorphic microsatellite loci, of which 195 were suitable for designing microsatellite primers. Of the 120 microsatellite loci selected for validation, 20 were successfully amplified with clear peaks and displayed polymorphism. Three populations were genotyped using the 20 polymorphic microsatellites. The number of alleles per locus ranged from two to thirteen. Observed and expected heterozygosity ranged from 0 to 0.941 and 0 to 0.834 respectively. The cross-species amplification test using five individuals from a population of P. ludlowii showed that 15 of the 20 polymorphic loci were successfully amplified, and four loci showed polymorphism. Among the 22 alleles occurring in P. ludlowii across fifteen loci, eight alleles across five loci were exclusive to P. ludlowii. The results demonstrate that ddRAD-seq is an efficient method for the development of microsatellite markers for non-model organisms with large genomes. The newly developed markers will be valuable tools to investigate the genetic diversity, genetic structure, and gene flow of P. delavayi from local to regional spatial scales.