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Diverse genetic architectures lead to the same cryptic phenotype in a yeast cross

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  • Matthew B. Taylor

    (Molecular and Computational Biology Section, University of Southern California
    Present address: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA)

  • Joann Phan

    (Molecular and Computational Biology Section, University of Southern California
    Present address: Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, USA)

  • Jonathan T. Lee

    (Molecular and Computational Biology Section, University of Southern California)

  • Madelyn McCadden

    (Molecular and Computational Biology Section, University of Southern California)

  • Ian M. Ehrenreich

    (Molecular and Computational Biology Section, University of Southern California)

Abstract

Cryptic genetic variants that do not typically influence traits can interact epistatically with each other and mutations to cause unexpected phenotypes. To improve understanding of the genetic architectures and molecular mechanisms that underlie these interactions, we comprehensively dissected the genetic bases of 17 independent instances of the same cryptic colony phenotype in a yeast cross. In eight cases, the phenotype resulted from a genetic interaction between a de novo mutation and one or more cryptic variants. The number and identities of detected cryptic variants depended on the mutated gene. In the nine remaining cases, the phenotype arose without a de novo mutation due to two different classes of higher-order genetic interactions that only involve cryptic variants. Our results may be relevant to other species and disease, as most of the mutations and cryptic variants identified in our study reside in components of a partially conserved and oncogenic signalling pathway.

Suggested Citation

  • Matthew B. Taylor & Joann Phan & Jonathan T. Lee & Madelyn McCadden & Ian M. Ehrenreich, 2016. "Diverse genetic architectures lead to the same cryptic phenotype in a yeast cross," Nature Communications, Nature, vol. 7(1), pages 1-6, September.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms11669
    DOI: 10.1038/ncomms11669
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    Cited by:

    1. Joseph J. Hale & Takeshi Matsui & Ilan Goldstein & Martin N. Mullis & Kevin R. Roy & Christopher Ne Ville & Darach Miller & Charley Wang & Trevor Reynolds & Lars M. Steinmetz & Sasha F. Levy & Ian M. , 2024. "Genome-scale analysis of interactions between genetic perturbations and natural variation," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Takeshi Matsui & Martin N. Mullis & Kevin R. Roy & Joseph J. Hale & Rachel Schell & Sasha F. Levy & Ian M. Ehrenreich, 2022. "The interplay of additivity, dominance, and epistasis on fitness in a diploid yeast cross," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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