Population structure and phylogenetic relationship of Peach [Prunus persica (L.) Batsch] and Nectarine [Prunus persica var. nucipersica (L.) C.K. Schneid.] based on retrotransposon markers

For effective varietal improvement of horticultural crops peach (Prunus persica) and nectarine (Prunus persica var. nucipersica), information about their population structure and genetic relatedness plays an important role. In this study we used retrotransposon-based markers (iPBS) to estimate the genetic diversity and population structure of 48 peach and nectarine genotypes from various distinct geographical regions of Punjab and Khyber Pakhtunkhwa, Pakistan. A total of 461 alleles were identified from PCR amplicons derived from nine iPBS primer pairs with an average of 8.5 alleles/locus. Among all four groups the genotypes collected from Swat and Hunza had the highest and the lowest expected heterozygosity, unbiased expected heterozygosity and Shannon’s information index, respectively. We constructed a Neighbour-Joining dendrogram and performed principal coordinate analysis based on the distance matrices, and both forms of analysis grouped the 48 genotypes into two distinct clusters. The STRUCTURE software distributed the forty-eight genotypes into two main populations (k = 2) indicating a low diversity between genotypes collected from Chakwal, Swat, Mansehra and Hunza.