Novel diagnostic marker genes differentiate Saccharomyces with respect to their potential application

Marker genes are widely used to differentiate and classify yeast at a species level. Diagnostic marker genes (DMGs) derived from a whole genome comparison allow the differentiation of strains of Saccharomyces cerevisiae according to their potential application. This approach, which has not been previously described, uses the software tool BIAst Diagnostic Gene Finder (BADGE). We compared the genome sequences of 25 brewing yeast strains to predict DMGs for the discrimination of Saccharomyces yeasts according to their brewing style. Two promising DMGs were chosen for PCR screening in order to test the presence of these genes in 83 yeast strains. A first PCR screening of 25 top-fermenting S. cerevisiae strains, using the DMG-specific primer pairs for wheat beer marker I (putative AMD2) and wheat beer marker II (GEX1), distinguished yeast strains of the wheat beer style from all other beer styles. The PCR screening of an extended set of 83 yeast strains displayed a more variable distribution of the selected DMGs to different potential applications. Furthermore, 60 out of 83 yeast strains were positive for at least one DMG. The diagnostic marker genes proved to be useful for the differentiation of wheat beer strains (100% positive identification for both genes) to German Alt-Kölsch and ale yeasts (87.5% negative identification for both genes).