Genetic diversity in a collection of ancient cultivars of apple (Malus x domestica Borkh.) as revealed by SSR-based fingerprinting

A collection of 48 accessions of Malus X domestica Borkh. from the apple germplasm repository of the Campania Region in Italy, several of which were suspected to be synonyms, was screened together with eight ancient well-known cultivars, added for reference, using a set of nine microsatellite or Simple Sequence Repeat (SSR) primer pairs to determine genetic identities, to estimate genetic diversity and to identify genetic relationships between the accessions. All microsatellite (SSR) primers revealed polymorphism, with seven to 14 alleles per main locus and the expected heterozygosity (H,,) ranging from 0.713-0.884. Three SSRs (CH01h02, CH02c11 and CH04c06) amplified a second locus that was less polymorphic and clearly distinguished from the main locus. The frequency of each allele at the main loci was generally low, with many alleles detected in only one or a few cultivars. Of the 56 genotypes studied, as many as 27 were identified as synonyms and were excluded from the genetic analysis. Synonymy not only included accessions classified with the same name, but also accessions with different names. In a few cases, accessions with the same name resulted in absolutely different SSR marker profiles. The remaining 29 unique genotypes showed great genetic diversity, with the eight reference cultivars ('Belle de Boskoop','Calville blanc','Delicious','Golden delicious', 'Limoncella', 'McIntosh', 'Permain doree', and 'Stark splendor') distributed throughout the dendrogram. Finally, this paper discusses the problems in dealing with incorrect allele-sizing and binning, which still do not allow comparison of SSR-based profiles produced by different laboratories.