Efficient genes identification via quantitative trait loci analysis by crossbreeding of sake and laboratory yeast

Saccharomyces cerevisiae, a unicellular eukaryotic microorganism, includes various strains used in alcoholic beverage production, like sake, shochu/awamori, and wine yeasts. Despite being the same "Saccharomyces cerevisiae", each strain has unique genes and mutations that make them suitable for specific production processes. We focused on sake yeast, Saccharomyces cerevisiae, suitable for sake making. To identify genes and mutations contributing to sake yeast's characteristics more efficiently, we improved the quantitative trait loci (QTL) analysis system. This genetic statistical method used spore-separating haploid strains (F1 segregant haploids) from crossing sake yeast and laboratory yeast haploid strains. We increased the number of F1 segregant haploids for QTL analysis from 100 to 400 and set DNA markers uniformly across the genome (approximately 12 Mbp) at 5,267 locations using single nucleotide polymorphisms (SNPs) spaced about 3 kb apart. Additionally, a small-scale sake making test using 400 F1 segregant haploids and QTL analysis of ethanol concentration in sake sample identified the PBS2 gene and its causative mutation (amino acid substitution at position 545). The PBS2 gene was also implicated in producing organic acids (fumaric, succinic, and malic acids) and inorganic acids (phosphoric acid) for sake. These findings validated the improved QTL analysis system as effective genes screening method. KEY POINTS: • A new QTL analysis system was constructed using sake and laboratory yeast. • PBS2 gene involved in the ethanol-producing capacity of Saccharomyces cerevisiae was identified. • PBS2 gene was also involved in the organic acid concentration in sake.