Genetic diversity, germplasm identification and population structure of Diospyros kaki Thunb. from different geographic regions in China using SSR markers

Abstract

Persimmons (Diospyros kaki Thunb.), originated in China, have a long history of cultivation and domestication in East Asia. In China, as one of most important fruit crops, the persimmon is utilized as fresh or dried fruit as well as an important timber and ornamental plant. There were more than 1000 germplasms and abundant morphological resources distributed in different geographic regions of China. To date, the genetic diversity of the main persimmon cultivars has been characterized, but the detailed information for the fruits in different regions in China remains unknown. Here, 228 persimmon accessions from different regions in China were analyzed to illustrate their genetic relationships and genetic diversities using simple sequence repeat (SSR) markers. Among the 228 samples, 33 were collected from North China (NC), 47 from East China (EC), 66 from South and Central China (SCC), 58 from Northwest China (NWC) and 24 from Southwest China (SWC). A total of 143 alleles were obtained from 12 highly polymorphic SSR markers, and these markers displayed rich polymorphisms for the genetic study of 228 samples. Relationship and structure studies and analysis of molecular variance (AMOVA) in different geographic regions showed that the intraspecific gene exchange of persimmons was frequent among/within the samples from five regions. The unweighted pair-group method with arithmetic means (UPGMA) analysis of persimmons within geographic regions revealed that samples in five regions displayed relatively higher genetic diversity. Moreover, we identified 13 combinations of synonyms and 16 genotypes of homonyms. Three synonyms were successfully further confirmed by combining genetic relationships from SSR markers with morphological traits. Additionally, 12 SSR markers exhibited high transferability in some related species of Diospyros. Taken together, these SSR markers provide new insight for a relatively accurate understanding of the genetic diversity and geographically structured distribution of persimmon germplasms and potentially promote the breeding program of persimmon.