Comparison of RAPDs, AFLPs and SSR markers for the genetic analysis of yeast strains of Saccharomyces cerevisiae

Abstract We evaluated the usefulness of different molecular techniques for the genetic analysis of Saccharomyces cerevisiae strains. Three commonly used PCR-derived genetic methods, random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphism (AFLPs) and simple sequence repeats (SSRs; microsatellites), were used to characterize 27 wine yeast strains of S. cerevisiae from the “Denominacion de Origen Vinos de Madrid” (Spain). Using these methods, we were able to overcome certain limitations associated with classical taxonomic methods. Based on the presence or absence of amplified fragments for each genotype, AFLPs and SSRs showed a similar discriminatory power superior to that of the RAPDs. Genetic relationships between strains were also estimated using the three methods. In general, very poor correlations were found, reflecting the different genomic regions for which the methods are screened. Results are discussed in terms of which molecular technique is most appropriate for use with a particular aspect of genetic evaluation.