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Here, we describe mitochondrial genome variation in 96 diverse S. cerevisiae strains and assess associations between mitochondrial genotype and phenotypes as well as nuclear-mitochondrial epistasis. We associate sensitivity to the ATP synthase inhibitor oligomycin with SNPs in the mitochondrially encoded ATP6 gene. We describe the use of iso-nuclear F1 pairs, the mitochondrial genome equivalent of reciprocal hemizygosity analysis, to identify and analyze mitochondrial genotype-dependent phenotypes. Using iso-nuclear F1 pairs, we analyze the oligomycin phenotype-ATP6 association and find extensive nuclear-mitochondrial epistasis. Similarly, in iso-nuclear F1 pairs, we identify many additional mitochondrial genotype-dependent respiration phenotypes, for which there was no association in the 96 strains, and again find extensive nuclear-mitochondrial epistasis that likely contributes to the lack of association in the 96 strains. Finally, in iso-nuclear F1 pairs, we identify novel mitochondrial genotype-dependent nonrespiration phenotypes: resistance to cycloheximide, ketoconazole, and copper. We discuss potential mechanisms and the implications of mitochondrial genotype and of nuclear-mitochondrial epistasis effects on respiratory and nonrespiratory quantitative traits.<\/jats:p>","DOI":"10.1534\/genetics.118.301546","type":"journal-article","created":{"date-parts":[[2018,11,30]],"date-time":"2018-11-30T04:25:10Z","timestamp":1543551910000},"page":"773-786","source":"Crossref","is-referenced-by-count":20,"title":["Mitochondrial Genome Variation Affects Multiple Respiration and Nonrespiration Phenotypes in <i>Saccharomyces cerevisiae<\/i>"],"prefix":"10.1093","volume":"211","author":[{"given":"Sriram","family":"Vijayraghavan","sequence":"first","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stanislav G","family":"Kozmin","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710"},{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pooja K","family":"Strope","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710"},{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel A","family":"Skelly","sequence":"additional","affiliation":[{"name":"Department of Biology, Duke University, Durham, North Carolina 27708"},{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenguo","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Biology, Saint Louis University, Missouri 63103"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Kennell","sequence":"additional","affiliation":[{"name":"Department of Biology, Saint Louis University, Missouri 63103"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul M","family":"Magwene","sequence":"additional","affiliation":[{"name":"Department of Biology, Duke University, Durham, North Carolina 27708"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fred S","family":"Dietrich","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John H","family":"McCusker","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,11,29]]},"reference":[{"key":"2022011200270823900_bib1","doi-asserted-by":"publisher","first-page":"241","DOI":"10.2741\/4098","article-title":"The power of yeast to model diseases of the powerhouse of the cell.","volume":"18","author":"Baile","year":"2013","journal-title":"Front. 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