Baker's yeast is exposed to various environmental stresses during its production and bread making. To clarify genes crucial for tolerance to these stresses, we performed genome-wide screenings of mutants that showed sensitivity or tolerance to stresses using a complete collection of deletion mutant strains of Saccharomyces cerevisiae. These screenings revealed genes crucial for tolerance to each stress. It is important to note that genes involved in the vacuolar acidification were indispensable for tolerance to multiple stresses. We applied the results of the screenings to select target genes for molecular breeding of stress-tolerant yeasts. Using so-called self-cloning technique, the target gene was disrupted or overexpressed in a derivative of an industrial baker's yeast strain. Results of the genetic modification suggested that this strategy was appropriate for breeding of stress-tolerant yeasts.