Discriminating ability of molecular markers and morphological characterization in the establishment of genetic relationships in cultivated genotypes of almond and related wild species

Abstract

A total 23 morphological traits, 19 AFLP-primer combinations, 80 RAPD primers and 32 SSR primer pair were used to compare the informativeness and efficiency of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers in establishing genetic relationships among 29 almond cultivars and three related wild species. SSRs presented a high level of polymorphism and greater information content, as assessed by the expected hetrozygosity, compared to AFLPs and RAPDs. The lowest values of expected hetrozygosity were obtained for AFLPs; however AFLPs showed the highest efficiency, owing to their capacity to reveal large numbers of bands per reaction, which led to high values for various types of indices of diversity. All the three techniques discriminated almond genotypes very effectively, except that SSRs failed to discriminate between ‘Monagha’ and ‘Sefied’ almond genotypes. The correlation coefficients of similarity were statistically significant for all the three marker systems, but were lower for the SSR data than for RAPDs and AFLPs. For all the markers, high similarity in dendrogram topologies was obtained, although some differences were observed. All the dendrograms, including that obtained by the combined use of all the marker data, reflect relationships for most of cultivars according to their geographic diffusion. AMOVA detected more variation among cultivated and related wild species of almond within each geographic group. Bootstrap analysis revealed that the number of markers used was sufficient for reliable estimation of genetic similarity and for meaningful comparisons of marker types.