Three previously described highly polymorphic SSR (microsatellite) primer pairs in 126 sweet cherry (Prunus avium L.) accessions were tested using two microsatellite marker detection methods: ASCE (automated sequencer capillary electrophoresis) and PAGE (polyacrylamide gel electrophoresis) in screening of sweet cherry germplasm collections. It was determined that ASCE provided more precise genotyping. In the case of PAGE, due to possible manual scoring errors, a higher number of putative alleles was observed, which overestimated the level of polymorphism and hence the genetic diversity. This should be taken into account when comparing results obtained in different investigations. The ASCE detection method generally is considered as expensive, it requires more advanced and expensive equipment, and is available mostly in mid- to high-throughput laboratories. Nevertheless, the detection precision and possibility of complete unification of laboratory protocols among laboratories makes it a very useful tool in the identification and characterisation of sweet cherry breeding material, especially in large, diverse collecions.
