Retrotransposon insertional polymorphism and genetic diversity in cultivated and wild grape genotypes

In the current investigation, inter retrotransposon amplified polymorphism (IRAP) and retrotransposon microsatellite amplified polymorphism (REMAP) markers were used to study the insertional polymorphism of retrotransposon families Tvv1, Edel, Vine1, Gentil and Huben and genetic diversity in 67 grape (Vitis vinifera L.) cultivars and wild genotypes. Totally, 103 loci generated using 2 IRAP and 13 REMAP primers which 83 (80.58%) was polymorphic. The mean of Nei’s diversity index for primers ranged from 0 (Gentil-A7) to 0.38 (Tvv1-808), averaging 0.27 for the studied grape collection. The Dice similarity coefficients varied from 0.57 (H6 and Dastarchin) to 1 (Rasha-SeyahMamoli) with a mean value of 0.78. The maximum values of Nei’s diversity index (0.32), number of effective alleles (Ne=1.54) and Shannon’s information index (I=0.47) was for retrotransposon Tvv1, showing its high activity and insertional polymorphism in the studied grape collection. Cluster analysis using Dice similarity coefficients and UPGMA algorithm grouped cultivars in 6 main clusters and differentiated cultivated and wild grapes. The UPGMA classification of the studied cultivars was confirmed using model-based methods, implemented in software Structure 2.3.1. It was concluded that used retrotransposon families especially Tvv1 are transpositionally active and could make insertional polymorphism in grape genome; hence molecular markers developed based on this retrotransposon could be used in grapevine genotypes and cultivar identifications.