SCoT markers provide insight into the genetic diversity, population structure and phylogenetic relationships among three Pistacia species of Iran

Genetic variability, phylogenetic relationship and population structure were evaluated among 50 accessions of three Iranian Pistacia species using start codon targeted (SCoT) primers and morphological traits. Genetic similarity and structure of the germplasm were evaluated based on the molecular data and their association with phenotypic characters were estimated by multiple regression analysis. The SCoT primers amplified 76 fragments on the germplasm with high level of polymorphism (98.46%). The average of RP, PIC, and MI were 3.30, 0.38, and 2.12, respectively representing the effectiveness of primer set for genetic discrimination among the Pistacia species. A high level of genetic variability was observed among the accessions. The germplasm belonging to the same species were grouped together using different clustering methods. Among the studied species, P. khinjuk Stocks. proved to be the most diverse species and had the highest gene diversity (h = 0.33) and Shannon’s information indices (I = 0.483) followed by P. atlantica Desf. and P. vera L., respectively. According to results, P. vera and P. khinjuk were the most closely related species, while P. atlantica and P. vera had the highest genetic differentiation. Significant association was observed between some of the morphological attributes and a number of SCoT generated fragments. Three species-specific amplicons were detected in P. atlantica and P. vera which can be used for designing sequence characterized amplification regions (SCAR) primers and subsequent marker assistant selection as well as species assignment in controversial cases. This study indicates the effectiveness of SCoT technique for genetic characterization of Pistacia germplasm, which could be used for genetic diversity and evolutionary assessments, detecting and tagging of agronomically important traits as well as quick, reliable and more precise authentication of Pistacia species.