Molecular characterisation of cultivars of apple (Malus x domestica Borkh.) using microsatellite (SSR and ISSR) markers

In this study, two microsatellite-based methodologies (SSR and ISSR) were e valuated for potential use in fingerprinting and determination of the simil arity degree between 41 commercial cultivars of apple previously characteri sed using RAPD and AFLP markers. A total of 13 SSR primer sets was used and 84 polymorphic alleles were amplified. Seven ISSR primers yielded a total of 252 bands, of which 176 (89.1%) were polymorphic. Except for cultivars o btained from somatic mutations, all cultivars were easily distinguishable e mploying both methods. The similarity coefficient between cultivars ranged from 0.20 to 0.87 for SSR analysis and from 0.71 to 0.92 using the ISSR met hodology. Dendrograms constructed using UPGMA cluster analysis revealed a p henetic classification that emphasises the existence of a narrow genetic ba se among the cultivars used, with the Portuguese cultivars revealing higher diversity. This study indicates that the results obtained based on the RAP D, AFLP, SSR and ISSR techniques are significantly correlated. The marker i ndex, based on the effective multiplex ratio and expected heterozygosity, w as calculated for both analyses (MI = 1.7 for SSR and MI = 8.4 for ISSR ass ays) and the results obtained were directly compared with previous RAPD and AFLP data from the same material. The SSR and ISSR markers were found to b e useful for cultivar identification and assessment of phenetic relationshi ps, revealing advantages, due to higher reproducibility, over other commonl y employed PCR-based methods, namely RAPD and AFLP.