Genetic diversity investigation of the apple germplasm available at the Fondazione Edmund Mach

Analysis of the genetic diversity harboured within a germplasm collection is a fundamental aspect for breeding, capable of providing information on the availability of an allelic pool potentially valuable for the creation of novel cultivars. The germplasm analysed in our study comprised 1639 Malus accessions available at the experimental orchards of Fondazione Edmund Mach (FEM), of which 1127 are unique accessions of Malus × domestica. This germplasm was collected to incorporate the maximum genetic variability of M. × domestica and to include representatives from other species of the genus Malus. In addition, the collection has been extended with the FEMRSQUOs advanced selections and interspecific hybrids. Genetic identities and genetic diversity were investigated using a set of 17 simple sequence repeat (SSR) markers selected from the microsatellite inventory already available for apple, considering a representative for each apple chromosome. Markers were chosen on the base of important criteria, such as single locus targeting and high allelic variability. A total of 343 alleles were identified, with an average of 20 alleles for each SSR. Considering only M. × domestica, it was possible to identify all the cultivars unambiguously with just seven markers. The genetic stratification of the germplasm was investigated with principal component analysis (PCA) and model-based clustering, which allowed a clear separation of the domesticated and wild material. This analysis revealed a low level of structure and high admixture within the domesticated apple.