Analysis of genetic diversity and population structure of Pinellia ternata using EST-SSR markers

Abstract

Pinellia ternata (Thunb.) Breit. is a widely used Chinese Medicinal Material with economic and medicinal value. Few molecular studies have been conducted on P. ternata, resulting in a lack of applicable molecular markers. This present research analyzed the genetic diversity of 255 P. ternata germplasm resources from China, including 117 wild germplasm resources and 138 cultivated germplasm resources. Following the development of 17 pairs of highly polymorphic primers, 126 alleles were found; the average polymorphism was 99.21 %. The average number of observed alleles (Na), effective alleles (Ne) were 1.98 and 1.36, respectively. The mean of the Nei genetic diversity index (H), the Shannon's information index (I) and the polymorphic information content (PIC) were 0.23, 0.36 and 0.6482, respectively. The population structure of P. ternata germplasm resources was categorized into two groups, designated as Group 1 and Group 2. The majority of wild germplasm resources was clustered in Group 1. Phylogenetic and population structure analyses produced similar results. A comparison of the genetic diversity parameters of wild and cultivated germplasm revealed that the genetic diversity was higher in the former, while the genetic differentiation level of the two types of germplasm was low. Analysis of molecular variance (AMOVA) demonstrated that 9 % of the genetic variation was between populations and 91 % of the genetic variation was within populations. Principal coordinate analysis (PCoA) served to corroborate the findings of the cluster and population structure analysis. It was found that P. ternata with tubers having red epidermis was more separated from other germplasm resources. Association analysis based on the generalized linear model (GLM) detected four EST-SSR markers significantly associated with P. ternata tuber color. This study will be helpful for P. ternata germplasm resource conservation, identification and trait-specific breeding programs.