Microsatellite genotyping of apple (Malus × domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification

A highly informative set of 16 microsatellite markers was used to fingerprint 695 apple accessions from eight Dutch collections. Among the total sample, 475 different genotypes were distinguished based on multi-locus microsatellite variation, revealing a potential redundancy within the total sample of 32%. The majority of redundancies were found between collections, rather than within collections. No single collection covered the total observed diversity well, as each collection consisted of about 50% of unique accessions. These findings reflected the fact that most collection holders focus on common Dutch varieties, as well as on region-specific diversity. Based on the diversity patterns observed, maintenance of genetic resources by a network of co-operating collection holders, rather than by collecting the total diversity in a single collection appears to be an efficient approach. Comparison of microsatellite and passport data showed that for many accessions the marker data did not provide support for the registered variety names. Verification of accessions showed that discrepancies between passport and molecular data were largely due to documentation and phenotypic determination errors. With the help of the marker data the varietal names of 45 accessions could be corrected. Microsatellite genotyping of apple appears to be an efficient tool in the management of collections and in variety identification. The development of a marker database was considered relevant as a reference instrument in variety identification and as a source of information about thus far unexplored diversity that could be of interest in the development of new apple varieties.