Genetic diversity and population genetic structure of Paeonia suffruticosa by chloroplast DNA simple sequence repeats (cpSSRs)

Paeonia suffruticosa Andr. is an endemic shrub flower in China with 2n = 10. This study used 228 cultivars from four populations, i.e., Jiangnan, Japan, Northwest, and Zhongyuan, as materials to explore the genetic diversity levels among different populations of tree peony varieties. The results showed that 34 bands were amplified using five pairs of cpSSR primers, with an average of 6.8 bands per primer pair. The average number of different alleles (Na), effective alleles (Ne), Shannon's information index (I), diversity (H), and polymorphic information content (PIC) were 3.600, 2.053, 0.708, 0.433, and 0.388, respectively. The PIC value was between 0.250 and 0.500, indicating a moderate level of polymorphism for the five cpSSR primer pairs. The genetic diversity levels of peony cultivars varied among different populations, with the Northwest population showing relatively lower levels (I = 0.590, H = 0.289, and PIC = 0.263). A total of 52 haplotypes were identified in the four examined populations, and the number of haplotypes per population ranged from 11 to 22. Forty-four private haplotypes were detected across populations, and the Northwest population exhibiting the highest count of private haplotypes with 17. The mean number of effective number of haplotypes (Neh), haplotypic richness (Rh), and diversity (H) were 8.351, 6.824, and 0.893, respectively. Analysis of molecular variance indicated that genetic variation within tree peony germplasm was greater than that between germplasm resources, and the main variation was found within individuals of peony germplasm. Cluster analysis, principal coordinate analysis, and genetic structure analysis classified tree peonies from different origins into two groups, indicating a certain degree of genetic differentiation among these four tree peony cultivation groups. This study provides a theoretical basis for the exploration, utilization, and conservation of peony germplasm resources, as well as for research on the breeding of excellent varieties.