The Contributions of Single Alleles to the Biology of Interspecific Hybrid Saccharomyces

Abstract

Interspecific hybrids play integral roles in society and are essential to industries worth hundreds of billions of dollars. They often have dominant genetic networks that allow them to be more fit than either parent, particularly in manmade settings. Hybrid Saccharomyces are amenable for scientific investigation because many hybrids are sterile, but Saccharomyces can grow indefinitely mitotically thereby bypassing this problem. Further, Saccharomyces cerevisiae is perhaps the best studied organism in the world, with countless tools to facilitate research. I sought to understand the genome-wide effects of single allele deletions on hybrids and determine their individual contributions to hybrid fitness. I mated the S. cerevisiae deletion collection, which contains a deletion strain for nearly every ORF, to WT S. uvarum, which is 20% diverged on the amino acid and nucleotide level. I also mated two S. cerevisiae collections with conditional knockouts of essential genes to WT S. uvarum. I then found the fitness of every deletion strain in three chemostat media, and the fitness of the essential genes knockouts on solid YPD. I found the hybrid deletion strains had more within condition and between condition variances than the purebreds, as well as large gene by genetic background effects. The essential genes had significantly less variance between conditions than the nonessential deletions, and significantly less gene by genetic background effects. To investigate the effects on fitness of each ortholog, I performed a reciprocal hemizygosity analysis showing that the effects of single allele deletions are dependent on the ortholog deleted. Together, our results show why hybrids are so abundant in manmade settings. They begin heterotic and they have new ways of exploring fitness landscape that have larger effects. To determine the molecular interactions between hybrid alleles, we developed a method, in conjunction with the Yates lab at Scripps, finding the preferences of particular orthologs in hybrid protein complexes, and showed that key amino acids can dramatically affect interspecific binding. Our findings show that hybrid proteins often have heterogeneous preferences for orthologs, which have been shown to confer heterosis. Lastly, I determined whether there are genes essential only to interspecific mating by mating the deletion collection to S. uvarum, and generating mating scores for every strain. Our findings did not identify any complete hybrid-specific mating incompatibilities, though there were significant incompatibilities suggesting it is possible to create a S. cerevisiae strain that does not mate with S. uvarum but that does mate with itself.