Mapping Ethanol Tolerance in Budding Yeast Reveals High Genetic Variation in a Wild Isolate

Abstract

Ethanol tolerance, a polygenic trait of the yeast Saccharomyces cerevisiae, is the primary factor determining industrial bioethanol productivity. Until now, genomic elements affecting ethanol tolerance have been mapped only at low resolution, hindering their identification. Here, we explore the genetic architecture of ethanol tolerance, in the F6 generation of an Advanced Intercrossed Line (AIL) mapping population between two phylogenetically distinct, but phenotypically similar, S. cerevisiae strains (a common laboratory strain and a wild strain isolated from nature). Under ethanol stress, 51 quantitative trait loci (QTLs) affecting growth and 96 QTLs affecting survival, most of them novel, were identified, with high resolution, in some cases to single genes, using a High-Resolution Mapping Package of methodologies that provided high power and high resolution. We confirmed our results experimentally by showing the effects of the novel mapped genes: MOG1, MGS1, and YJR154W. The mapped QTLs explained 34% of phenotypic variation for growth and 72% for survival. High statistical power provided by our analysis allowed detection of many loci with small, but mappable effects, uncovering a novel “quasi-infinitesimal” genetic architecture. These results are striking demonstration of tremendous amounts of hidden genetic variation exposed in crosses between phylogenetically separated strains with similar phenotypes; as opposed to the more common design where strains with distinct phenotypes are crossed. Our findings suggest that ethanol tolerance is under natural evolutionary fitness-selection for an optimum phenotype that would tend to eliminate alleles of large effect. The study provides a platform for development of superior ethanol-tolerant strains using genome editing or selection.

Transcriptional Rewiring, Adaptation, and the Role of Gene Duplication in the Metabolism of Ethanol of Saccharomyces cerevisiae

“…Ethanol also exhibits a general cell toxicity that yeasts used to control competitors’ growth. This duality (nutrient and stressor) generates great concerns in the biotechnological industries (by its applications) and in the scientific community (by its molecular basis), highlighting the importance of systems biology studies (reviewed in references 9 to 12 ).…”

Recent advances in yeast genome evolution with stress tolerance for green biological manufacturing

“…Fifty‐one quantitative trait loci (QTLs) have been found to affect the growth while 96 QTLs to affect the survival of the yeast under ethanol stress. For example, MOG1, MGS1, and YJR154W have been mapped as novel genes for phenotyping of growth variation (34%) and survival (72%) (Haas et al, 2019). In another study, Kluyveromyces marxianus was subjected to adaptive evolution at 6% ethanol concentration for 100 days.…”

Unveiling genetic anchors in Saccharomyces cerevisiae: QTL mapping identifies IRA2 as a key player in ethanol tolerance and beyond

“…Genetic mapping of the variants associated with the phenotype of interest in strain SA-1 utilized a combined approach of individual phenotyping and bulk whole-genome analysis, followed by a bioinformatics pipeline to identify rare NS mutations in the candidate gene. Previous studies employing a QTL mapping strategy to infer causative genes for ethanol tolerance in yeast have already been documented (Haas et al, 2019; Ho et al, 2021; Riles and Fay, 2019; Swinnen et al, 2012). These investigations have proven the following genes are linked to this phenotype: MOG1, MGS1 , and YJR154W (Haas et al, 2019); SEC24 (Riles and Fay, 2019); MKT1 , SWS2 , and APJ1 (Swinnen et al, 2012).…”