Yeast Saccharomyces cerevisiae is one of the most useful microorganisms in biological fermentation fields, such as winemaking, baking, brewing, and bioethanol production. The bioconversion of cellulosic biomass to ethanol is a promising technology to address fossil fuels shortages and greenhouse gas over-emission (Koutinas et al. 2016). To release the sugars that are trapped inside the cross-linking structure of cellulose, pretreatment processes (such steam explosion and dilute acid treatment) are always required prior to the enzymatic hydrolysis (Jönsson et al. 2013; Silveira et al. 2015). Unfortunately, pretreatment processes give rise to certain inhibitors (including acetic acid, furan derivatives, and phenolic compounds) that would greatly inhibit the viability of yeast cells during ethanol fermentation (Jönsson et al. 2013; Sindhu et al. 2016; Zheng et al. 2017). In the past two decades, a great amount of functional genomic studies on S. cerevisiae using the reference genome of strain S288c (the first sequenced eukaryote) have greatly enriched our knowledge of how yeast cells respond to external stimuli (Kitichantaropas et al. 2016). However, S. cerevisiae strains isolated from different sources generally show extensive phenotypic diversity (Fay et al. 2004; Strope et al. 2015). It was shown that certain industrial strains are more tolerant to specific environments stresses compared with S288c-derived laboratory strains (Zheng et al. 2012, 2016). Using highthroughput sequencing technology, the genetic diversity between S288c and other strains has been widely determined (Borneman et al. 2011; Coi et al. 2017; Nijkamp et al. 2012; Strope et al. 2015; Zheng et al. 2012; Zhu et al. 2016). Additionally, great efforts have been devoted to exploring how genomic variations (point mutations, chromosomal rearrangements, and novel ORFs) affect stress tolerance and ethanol fermentation performance among different S. cerevisiae strains. For example, a nonsense mutation in the gene AQY2 would result in higher osmotic resistance in many non-S288c strains (Will et al. 2010). The unique genes AWA1 and BIO6 in sake strains are responsible for foam formation in sake mash and biotin synthesis, respectively (Akao et al. 2011; Hall and Dietrich 2007).