Pomegranate ( Punica granatum L.) is one of the oldest fruits known to mankind and is one of the most important endemic horticultural plants in Iran. According to historical evidences, it seems that Iran has been the origin of pomegranate and it has spread from this region to the other parts of the world. Long historic cultivation of pomegranate in Iran has led to synonymies and homonymies among genotypes cultivated in different regions. A precise method for determination and discrimination of the genotypes is requested for breeding and commercialization of Iranian pomegranate cultivars and it can be achieved using molecular markers and morphology characters. With the development of modern biotechnology, molecular markers are used more than morphology character because they are not affected by environment. Molecular studies of the pomegranate have been restricted to examinations of nuclear genomic to investigate the population dynamics of these economically important cultivars. Among all of these molecular markers in nuclear genome, microsatellite markers showed higher efficiency than others to separate the pomegranate genotypes. The SSR markers derived from chloroplast genome generally show simple, uniparental modes of inheritance, haploid nature and high copy number, which make them better than genomic microsatellite. Therefore, to characterize the genetic diversity and population structures of pomegranate in Iran, cRs were studied on 52 cultivars from different geographical regions to reveal the cpDNA variation among and within populations. In the present research the investigation of the genetic diversity of pomegranate was done based on cRs markers on 52 Iranian genotypes of pomegranate, among which 16 cR primer pairs amplified 21 loci and 16 loci (80%) were shown to be polymorphic. The average number of alleles for each cR locus was 2.44. The average values of PIC and Nei's gene diversity ( He ) for all loci were 0.24 and 0.37, respectively. The cophenetic correlation coefficient based on Dice’s similarity coefficients by UPGMA algorithm was accounted high ( r = 0.88) indicating that the dendrogram was a good representation of the similarity matrix. Cluster analysis was able to cluster 52 genotypes based on cultivation somedeal, as cultivated and wild genotypes almost similarity was observed between wild and cultivated groups. This research indicates that the level of polymorphism among pomegranate genotypes is appreciably high in Iran, and also the results of this study suggested that cR marker offers a powerful means to analyze the genetic diversity within and among populations.
