Genetic diversity and structure of local apple cultivars from Northeastern Spain assessed by microsatellite markers

A set of 493 old and local Spanish accessions of apple (Malus x domestica Borkh) maintained at three collections in Northeastern Spain was studied using 16 simple sequence repeats in order to estimate their genetic diversity and to identify the genetic structure and relationships among their accessions. An additional diverse set of 45 apple cultivars, including old Spanish and international cultivars, was added as reference. Genetic analyses performed by Bayesian model-based clustering revealed a very strong differentiation of two major groups. The first one clustered 159 individuals (52 % of unique genotypes) including local accessions and six old Spanish cultivars. The second major group was formed by 145 individuals, including 38 international reference cultivars and one old Spanish cultivar. Nested Bayesian clustering was applied to those two groups and two and four sub-groups were found at each one, respectively. The identification of private and unique alleles, and the remarkable differences in allelic richness among groups and sub-groups constitute further evidence of a clear genetic structure. The results obtained through the factorial correspondence and analyses of molecular variance confirmed those obtained by Bayesian analyses, revealing moderate but significant differentiation among the two major groups (F (ST) = 0.076) and the six sub-groups (F (ST) = 0.111). Our results highlight that the genetic diversity encompassed by currently cultivated apple accounts only for a small fraction of that existing within the species, and that an important part (a parts per thousand 60 %) of the local material analyzed constitutes a good example of genetic distinctness with respect to the main cultivars used in European orchards.