SSU1Checkup, a Rapid Tool for Detecting Chromosomal Rearrangements Related to theSSU1Promoter inSaccharomyces cerevisiae: An Ecological and Technological Study on Wine Yeast

Chromosomal rearrangements (CR) such as translocations, duplications and inversions play a decisive role in the adaptation of microorganisms to specific environments. In enologicalSaccharomyces cerevisiaestrains, CR involving the promoter region of the geneSSU1lead to a higher sulfite tolerance by enhancing the SO(2)efflux. To date, three differentSSU1associated CR events have been described, including translocations XV-t-XVI and VIII-t-XVI and inversion inv-XVI. In the present study, we developed a multiplex PCR method (SSU1checkup) that allows a rapid characterization of these three chromosomal configurations in a single experiment. Nearly 600S. cerevisiaestrains collected from fermented grape juice were genotyped by microsatellite markers. We demonstrated that alleles of theSSU1promoter are differently distributed according to the wine environment (cellar versus vineyard) and the nature of the grape juice. Moreover, rearrangedSSU1promoters are significantly enriched among commercial starters. In addition, the analysis of nearly isogenic strains collected in wine related environments demonstrated that the inheritance of these CR shapes the genetic diversity of clonal populations. Finally, the link between the nature ofSSU1promoter and the tolerance to sulfite was statistically validated in natural grape juice containing various SO(2)concentrations. TheSSU1checkup is therefore a convenient new tool for addressing population genetics questions and for selecting yeast strains by using molecular markers.