Microsatellite (SSR) variation in a collection of Malus (apple) species and hybrids

A collection of 142 accessions of 23 Malus species, derived hybrids and cul tivar accessions from the USDA-ARS Plant Genetic Resources Unit's core coll ection, which represents an extensive range of Malus species, was screened with a set of previously described SSR (simple sequence repeat) markers. Th e markers were used to determine genetic identities, estimate genetic diver sity, identify genetic relationships among the accessions, and determine th e utility of SSR primers developed from Malus x domestica for making geneti c assessments across the whole Malus genus. All eight primer pairs amplifie d multiple fragments when used in polymerase chain reactions with DNA from these accessions. High levels of variation were detected with a mean of 26. 4 alleles per locus and a mean direct count heterozygosity across all eight loci equal to 0.623. The eight primer pairs used in this study unambiguous ly differentiated all but five pairs of accessions in this collection of 14 2 accessions of 23 Malus species, derived hybrids and cultivars. These SSR data were not useful in identifying genetic relationships among this divers e collection of accessions, with the majority of the accessions not cluster ing in ways concordant with taxonomic information and/or geographic origin. The resulting phenogram resolved only two meaningful clusters, for the tax onomically isolated Section Chloromeles and for M. fusca accessions, reflec ting genetic relationships arising from geographic origin. The detection of identical accessions in the collection, which were previously considered t o be unique, highlights the critical need to further bolster collections of certain Malus species.