Genetic Diversity and Population Structure Analysis of Tree Peony (Paeonia Section Moutan DC.) Germplasm Using Sixteen Functional SSR Markers

Abstract

Tree peony (Paeonia section Moutan DC.) is a traditional ornamental flower of China, which has thousands of varieties with different flower colors and types after a long history of natural selection and artificial breeding. However, tree peony is a perennial woody plant with a long breeding, and there are still significant challenges to accelerate the process of genetic improvement of important ornamental traits. In this study, a total of sixteen primer pairs with high polymorphism and good universality were selected from the initial pool of 115 SSR markers. The SSR marker set was derived from published papers on the genetic linkage map and association analysis of tree peony. Furthermore, we conducted a genetic diversity and population structure analysis on 322 tree peony cultivars using molecular markers with functional. These SSRs amplified a total of 391 alleles, the average number of different alleles was 5.113 alleles across all loci. The average Shannon’s information index, gene diversity and polymorphism information content were 0.842, 0.532, and 0.503 over all loci, respectively. Population genetic diversity analysis indicated that the average expected heterozygosity of the total population was larger than the observed heterozygosity, showing the presence of a certain degree of heterozygous deletion phenomenon. The Japan varieties had the richest diversity with the highest H (0.508) and PIC (0.479) values. The Zhongyuan varieties showed the greatest variation may be related to its longstanding cultivation history. Moreover, the STRUCTURE and principal coordinate analyses indicated that 322 tree peony individuals from five populations were grouped into two clusters. An analysis of molecular variance demonstrated significant genetic diversity among different populations. This research may contribute to the sustainable management, conservation, and utilization of tree peony resources.