Understanding the Effects of Genetic Variation on Osmo-adaptation Dynamics Across S. cerevisiae using Bulk Segregant Analysis and Whole Genome Sequencing

Abstract

<p>Adapting to environmental changes (i.e. an increase in osmolarity) is critical for cell survival. How cells respond and adapt to osmotic stress has been well-studied in the model eukaryote Saccharomyces cerevisiae. Although the molecular and systems properties of osmo-adaptation have been well studied, few studies have focused on the effects of genetic variation. Understanding how genetic variation affects molecular pathways and their dynamics, which translates to variation in cellular and organismal phenotypes, is a key step towards understanding important phenomena such as complex gene by gene interactions and the mapping of genotype to phenotype. The challenge is to causally connect genetic differences with cellular function and differences in complex traits between individuals. As a first step towards addressing this challenge, my dissertation research investigates how natural genetic variation affects osmo-adaptation dynamics in budding yeast, Saccharomyces cerevisiae. </p><p>First, I characterized the natural variation in osmo-adaptation dynamics across S. cerevisiae. I showed that individual strains were highly variable in adaptation time and relative maximum growth rate after adapting to stress. Analysis of a broad set of genes involved in osmo-adaptation did not reveal any obvious genetic differences that could account for the observed variation. To identify alleles associated with the variation, I measured osmo-adaptation dynamics in progeny generated from a cross between two closely related lab strains. Identified alleles were outside the core signaling pathway and affected both adaptation time and relative maximum growth rate. Finally, I built a novel mapping panel and measured osmo-adaptation dynamics to obtain a more global, species-wide view. The panel showed an increased amount of variation in osmo-adaptation dynamics and a subset of progeny were phenotypically more extreme than their parents. Mapping the variation in this panel will generate a comprehensive list of alleles that affect osmo-adaptation. The strains in the mapping panel have a low number of mutations predicted to have strong effects in HOG pathway genes. Given our earlier results from the pairwise cross, I expect that many osmo-adaptation alleles discovered from the mapping panel will be outside the HOG pathway.</p>