ISSR analysis of cultivars of pear and suitability of molecular markers for clone discrimination

Inter-simple sequence repeat (ISSR) markers were used for cultivar identifi cation and for determination of the phenetic relationships among 24 pear cu ltivars (Pyrus communis L.). The ability of several molecular marker system s including randomly amplified polymorphic DNA (RAPD), amplified fragment l ength polymorphisms (AFLP), inter-simple sequence repeats (ISSR), simple se quence repeats (SSR), and selective amplification of microsatellite polymor phic loci (SAMPL) to detect variation among clones of the most significant Portuguese cultivar, Rocha, was also investigated. Each of the eight ISSR p rimers tested was able to distinguish the 24 pear cultivars. The ISSR prime rs generated 337 markers, 79.5% of which were polymorphic. The cultivar den drogram obtained with the ISSR marker data was very similar to that obtaine d with previous RAPD+AFLP analysis, confirming the genetic divergence of 'P erola','Carvalhal' and 'Lawson' from the other cultivars. Eight out of 15 a pple [Malus sylvestris (L.) Mill. var domestica (Borkh.) Mansf.] SSR primer s tested also amplified microsatellites in pear. None of the five molecular marker systems analyzed (with a total of 1082 markers) detected reproducib le polymorphisms among the nine 'Rocha' clones, in spite of the presence of clear phenotypic differences.