Discovery and validation of <i>ASG1</i> as a novel determinant of NaCl tolerance in the yeast <i>Saccharomyces cerevisiae</i> through iterative crossing

To dissect the genetic basis of quantitative traits, generation of numerous haploid segregants with diverse genotypes and phenotypes from heterozygous parental strains is a powerful approach. To identify quantitative trait loci (QTLs) associated with NaCl salt tolerance, we employed an iterative crossing strategy using parental strains with contrasting phenotypes. Whole-genome sequencing of selected individual offspring with the most extreme trait value from each generation as well as of the pools of segregants under extreme salt conditions enabled QTL mapping and identification of candidate causative variants. Their effects on phenotypic variation were quantified through a genome-wide screen of generation-dependent reduction of the causative loci and by allele swapping procedure of the putative quantitative trait genes in isogenic strain backgrounds. A combination of these complementary approaches enabled assessment of the causal loci with the strongest effect. We thus confirmed the causative role of the ENA locus, and proposed an additional contribution of the ASG1 gene in NaCl salt tolerance. Asg1 (Activator of Stress Genes 1) has been proposed as a transcriptional regulator of genes involved in lipid metabolism and various stress responses. Previous large-scale studies have indicated that Asg1 could have a negative effect on NaCl tolerance in S. cerevisiae. The results of our study confirm that prediction and further elucidate its previously uncharacterized negative role in NaCl stress adaptation. Our species-wide association analysis supports a universal contribution of ASG1 gene to NaCl tolerance, which had been masked by the dominant influence of the ENA locus in S. cerevisiae.