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

Abstract

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 regionspecific 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.

Genetic diversity of Czech apple cultivars inferred from microsatellite markers analysis

“…Identical microsatellite profiles of cvs Mantet and Glencross could be due to mistake in the reported pedigree or potential documentation error. Similar results were published for known pedigrees (Evans et al 2011) or incorrect documented cultivar names (van Treuren et al 2010) in apple collections using SSR markers. Therefore for apple, microsatellite genotyping appeared a very efficient tool for enhancing collection management of genetic resources and for cultivar identification.…”

“…The dendrogram showed that there was a genotype dependence on pedigree and origin of apple cultivars (Table 1). Therefore SSR markers were useful for parentage study (Kitahara et al 2005;Evans et al 2011) and cultivar identification (Galli et al 2005;van Treuren et al 2010) of apple genotypes. The first group (I.)…”

“…For apple, several hundreds of microsatellite markers were developed (Guilford et al 1997;Hokanson et al 1998;Liebhard et al 2002;Silfverberg-Dilworth et al 2006). SSR markers were used for assessment of genetic diversity in germplasm collections (Hokanson et al 2001;Guarino et al 2006;Pereira-Lorenzo et al 2007;Garkava-Gustavsson et al 2008;Gharghani et al 2009;Patzak et al 2009;Gasi et al 2010), cultivar identification (Galli et al 2005;van Treuren et al 2010), construction of genetic linkage maps (Liebhard et al 2003;Hemmat et al 2003;Silfverberg-Dilworth et al 2006) and for parent identification (Kitahara et al 2005;Evans et al 2011).…”

Identification of duplicates of cassava accessions sampled on the North Region of Brazil using microsatellite markers

“…The identification of duplicates on germplasm banks of vegetatively propagated plants seems to be common (Irish et al 2010;van Treuren et al 2010). This may be due to usual exchanges of propagules among farmers of different regions, especially when the species has economical importance.…”

“…Microsatellite markers, due to high information generated per locus, have been used to identify duplicates on germplasm banks and populations of different species (Robichaud et al 2006;Irish et al 2010;van Treuren et al 2010). Methods of identification that use multiloci profiles of microsatellites are more accurate than the ones based on dominant markers, since genotypes can present a complete coincidence and the probability of casual coincidence can be measured based on allelic frequencies (Paetkau and Strobeck 1994).…”