For her thesis project, Katie is taking a quantitative genomic approach in elucidating the genetic basis of survival in a complex environment by comparing divergent Saccharomyces cerevisiae strains that grow on fruit or oak soil. These environments are quite different in their carbon, nitrogen, metal, and acid contents. Furthermore, strains isolated from these two niches are of distinct lineages with little gene flow. She is ultimately interested in finding the loci important to surviving in these two very different environments. She found many ecologically relevant phenotypes that distinguish these two groups of strains including tartaric acid stress, heat stress, ethanol stress, low sugar conditions, and even growth in grape juice. She will study these complex phenotypes by  mapping individual ecologically relevant phenotypes and  mapping combinatorial phenotypic differences including survival in the complex environment itself (growth in grape juice). To do this, she will use a modified bulk segregant analysis (extreme QTL or X-QTL mapping) approach. Millions of progeny between an oak and a vineyard strain cross will be collected, pooled, and phenotyped. Only segregants with the proper alleles for surviving the phenotyping conditions will survive. Sequencing and comparing the selected genomes to the starting pool will reveal loci important for the phenotype. Shecan then use the vast number of yeast genetic tools to validate my loci. She hopes that her comparative QTL approach will allow her to elucidate the complex genetic architecture of ecologically relevant phenotypes.
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