IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v9y2018i1d10.1038_s41467-018-06023-5.html
   My bibliography  Save this article

The complex underpinnings of genetic background effects

Author

Listed:
  • Martin N. Mullis

    (University of Southern California)

  • Takeshi Matsui

    (University of Southern California)

  • Rachel Schell

    (University of Southern California)

  • Ryan Foree

    (University of Southern California)

  • Ian M. Ehrenreich

    (University of Southern California)

Abstract

Genetic interactions between mutations and standing polymorphisms can cause mutations to show distinct phenotypic effects in different individuals. To characterize the genetic architecture of these so-called background effects, we genotype 1411 wild-type and mutant yeast cross progeny and measure their growth in 10 environments. Using these data, we map 1086 interactions between segregating loci and 7 different gene knockouts. Each knockout exhibits between 73 and 543 interactions, with 89% of all interactions involving higher-order epistasis between a knockout and multiple loci. Identified loci interact with as few as one knockout and as many as all seven knockouts. In mutants, loci interacting with fewer and more knockouts tend to show enhanced and reduced phenotypic effects, respectively. Cross–environment analysis reveals that most interactions between the knockouts and segregating loci also involve the environment. These results illustrate the complicated interactions between mutations, standing polymorphisms, and the environment that cause background effects.

Suggested Citation

  • Martin N. Mullis & Takeshi Matsui & Rachel Schell & Ryan Foree & Ian M. Ehrenreich, 2018. "The complex underpinnings of genetic background effects," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06023-5
    DOI: 10.1038/s41467-018-06023-5
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-018-06023-5
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-018-06023-5?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    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.
    3. Solip Park & Fran Supek & Ben Lehner, 2021. "Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers," Nature Communications, Nature, vol. 12(1), pages 1-10, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06023-5. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.