Genome-wide distribution of simple sequence repeats in pomegranate and their application to the analysis of genetic diversity

Abstract

Pomegranate (Punica granatum L.) germplasm collections are increasingly appreciated as a repository for the genetic improvement of species, and their genetic analysis is an essential prerequisite for their utilization in pomegranate breeding. Sufficient markers are a prerequisite for genetic analysis. In this study, we identified 36,792 simple sequence repeat (SSR) markers in the pomegranate genome. Dinucleotide repeats are the most abundant SSRs, and of the mono-, di-, tri-, and tetranucleotide repeats, A/T, AT/AT, AAT/ATT, and AAAT/ATTT were the most dominant motif type. There were only 1.80% SSR motifs located in the coding regions, while most (98.20%) SSR motifs were located in noncoding regions. We confirmed the reliability of 50 SSR markers by PCR amplification, from which 11 highly polymorphic SSR markers were selected to study the genetic diversity of 218 pomegranate accessions. A total of 63 alleles was detected for the 11 SSR primers, ranging from 2 (PG152) to 9 (PG093, PG080) across the pomegranate accessions. The polymorphism information content values of each SSR primer pair ranged from 0.22 to 0.70, with a mean value of 0.45. Based on population structure analysis, these accessions were clustered into three main populations and 42 accessions were chosen as the core set. The availability of these SSR markers and the clustering result for the pomegranate germplasm provide new important information for pomegranate genetics and breeding programs.