Genetic characterization of cultivated apple (Malus x domestica Borkh.) in Morocco using microsatellite (SSR) markers

Genetic diversity of 27 apple genotypes from four geographical regions of Morocco was analyzed using 26 simple sequence repeat (SSR) primers. In total, 195 polymorphic SSR alleles were detected, with sizes ranging from 78 to 209 bp. The results obtained for the average number of alleles per locus (7.5), effective number of alleles (4.62), Shannon information index (1.66), expected heterozygosity (0.76), observed heterozygosity (0.74) and polymorphism information content (0.76) showed a moderate level of polymorphism, which suggests that Moroccan apple cultivars exhibit significant genetic diversity. Over the 26 SSR loci used, the probability of identity P (ID) was 4.62 10−29 indicating that most markers were highly discriminating and powerful for cultivars characterization. The principal coordinate analysis and hierarchical classification suggested the presence of four well defined groups, which was confirmed later by model based population structure. Furthermore, strong genetic differentiation between these four groups was also detected (FST = 0.28). Most of the individuals segregated into the four groups showing a membership coefficient greater than 0.80, which indicates their better genetic integrity. A parentage analysis, however, shows that cultivars from the four regions are minimally hybridized. After comparing SSR profiles and genotypes names, we conclude that the problem of homonyms and/or labeling errors appear in the studied cultivars.Thus, based on genetic profiles, two individuals (Beldi 1/Beldi 2 and Laakri 5/Laakri 6) found to be duplicated. Additionally, some cultivars with the same name are grouped in different clusters suggesting the existence of possible homonymy. Lastly, the present work confirms the usefulness of SSR markers for the elimination of duplications and characterization of diversity and hybrid characters of apple genotypes in Morocco.