Microsatellite high resolution melting (SSR-HRM) analysis for authenticity testing of protected designation of origin (PDO) sweet cherry products

DNA based methods have been employed recently for plant species identification and their ingredients in the final food products. The aim of this work was to setup a microsatellite-based method not only to distinguish sweet cherry cultivars but also to compare different techniques for DNA isolation and DNA fragment analysis for verifying the presence of protected designation of origin (PDO) sweet cherry, at the cultivar level, in sweet cherry processed products. Thirteen microsatellites were tested and the combination of the amplification profiles of six of them, characterised by high polymorphism and simple electrophoretic patterns, enabled to distinguish and identify a PDO sweet cherry cultivar used for sweet cherry products. The obtained amplicons were all in the range of 68–258 bp, and were analyzed by capillary electrophoresis (CE) and High Resolution Melting (HRM) analysis. We compare the results obtained by both methods and analyze the differences observed. Dendrograms were constructed using data from HRM analysis and fragment analysis indicating a higher resolution capacity of the HRM method compared to fragment analysis. Moreover, costs, throughput and difficulties to implement HRM analysis and CE methods in the laboratory are discussed. In conclusion HRM analysis can be a cost effective alternative method, with higher resolution, not only to genotype sweet cherry cultivars but also to extend the use to process sweet cherry products using microsatellite markers.