The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiae

Saccharomyces cerevisiae is the main microorganism responsible for wine alcoholic fermentation. The oenological phenotypes resulting from fermentation, such as the production of acetic acid, glycerol, and residual sugar concentration are regulated by multiple genes and vary quantitatively between different strain backgrounds. With the aim of identifying the quantitative trait loci (QTLs) that regulate oenological phenotypes, we performed linkage analysis using three crosses between highly diverged S. cerevisiae strains. Segregants from each cross were used as starter cultures for 20-day fermentations, in synthetic wine must, to simulate actual winemaking conditions. Linkage analysis on phenotypes of primary industrial importance resulted in the mapping of 18 QTLs. We tested 18 candidate genes, by reciprocal hemizygosity, for their contribution to the observed phenotypic variation, and validated five genes and the chromosome II right subtelomeric region. We observed that genes involved in mitochondrial metabolism, sugar transport, nitrogen metabolism, and the uncharacterized ORF YJR030W explained most of the phenotypic variation in oenological traits. Furthermore, we experimentally validated an exceptionally strong epistatic interaction resulting in high level of succinic acid between the Sake FLX1 allele and the Wine/European MDH2 allele. Overall, our work demonstrates the complex genetic basis underlying wine traits, including natural allelic variation, antagonistic linked QTLs and complex epistatic interactions between alleles from strains with different evolutionary histories.

酿酒酵母（Saccharomyces cerevisiae）是介导葡萄酒酒精发酵的核心微生物。发酵产生的酿酒表型（oenological phenotypes），如乙酸、甘油生成量与残糖浓度，受多基因调控，且在不同菌株背景中呈现数量化差异。本研究旨在定位调控酿酒表型的数量性状位点（quantitative trait loci，QTLs），通过三对高度分化的酿酒酵母菌株开展杂交连锁分析。将每个杂交组合产生的分离子作为发酵起始菌种，在合成葡萄酒基质（synthetic wine must）中进行20天发酵，以模拟实际酿酒环境。针对具有核心工业价值的表型开展连锁分析，最终定位到18个QTLs。我们通过正反交半合子分析（reciprocal hemizygosity）对18个候选基因的表型贡献进行验证，成功确认5个基因以及II号染色体右端亚端粒区域的调控功能。研究发现，参与线粒体代谢、糖转运、氮代谢的基因以及未注释开放阅读框ORF YJR030W可解释酿酒性状的大部分表型变异。此外，我们通过实验验证了一种极强的上位互作：清酒来源FLX1等位基因与酿酒/欧洲来源MDH2等位基因共同作用可导致高水平琥珀酸（succinic acid）生成。综上，本研究揭示了酿酒性状背后复杂的遗传基础，包括天然等位基因变异、拮抗连锁QTLs以及不同进化背景菌株间等位基因的复杂上位互作。