Discriminating the capabilities and efficiencies of RAPD, ISSR and SSR markers in the assessement of the genetic variation in cultivated Tunisian olives

The olive tree is a typical crop in the Mediterranean basin, where it shows wide genetic variability of the olive germplasm. Therefore, studying the genetic diversity to preserve and conserve local olive tree resources is a challenge. In this context, random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers were used for detecting genetic variation among 13 Tunisian olive cultivars. The effectiveness of the three methods in generating their levels of information on olive genetic relationships and diversity was studied. Furthermore, the polymorphic information content (PIC), effective multiplex ratio (EMR), marker index (MI) and Shannon's diversity index were calculated based on molecular data. The unweighted pair-group method with arithmetic averages (UPGMA) tree obtained from cluster analysis discriminated different major groups of olive genotypes. Bayesian analysis of the population structure for the combined primer data with K = 2 separated the 13 genotypes into two clusters. The RAPD method resulted in 45 bands, 38 of which were polymorphic (84%). ISSR primers amplified 39 bands with a high level of polymorphism (79%), while the highest level of polymorphism was seen with SSR (93%). For SSR, the total number of alleles per locus varied from three to nine, with an average number of 5.33 and a mean polymorphic information content (PIC) of 0.20. The three markers used in this study could potentially provide consistent information on the genetic relationships among olive cultivars. Our results indicate that the SSR method is the most suitable molecular-based technique for fingerprinting and assessing genetic variability and relationship among Tunisian olive cultivars.