eQTL Mapping of the Yeast Ethanol Response

In a previous study, we identified extensive natural variation in the response to acute ethanol treatment in three yeast strains: a lab strain derived from the commonly used S288c (DBY8268), vineyard isolate M22, and oak soil strain YPS163. Many expression differences persisted across several modules of co-regulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. To understand the genetic basis for these expression differences, we performed eQTL mapping analysis of the response to acute ethanol stress in ~100 F2 strains from two crosses: DBY8268x M22 and DBY8268 x YPS163. We measured the gene expression response to acute ethanol stress (5% for 30 min) in 6 replicates for the parental strains, and in biological duplicate for the eQTL mapping population. Dye swaps were performed in the replicates to control for dye-specific effects.