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Title: Genetic background effects in quantitative genetics: gene-by-system interactions

Abstract

Proper cell function depends on networks of proteins that interact physically and functionally to carry out physiological processes. Thus, it seems logical that the impact of sequence variation in one protein could be significantly influenced by genetic variants at other loci in a genome. Nonetheless, the importance of such genetic interactions, known as epistasis, in explaining phenotypic variation remains a matter of debate in genetics. Recent work from our lab revealed that genes implicated from an association study of toxin tolerance in Saccharomyces cerevisiae show extensive interactions with the genetic background: most implicated genes, regardless of allele, are important for toxin tolerance in only one of two tested strains. The prevalence of background effects in our study adds to other reports of widespread genetic-background interactions in model organisms. We suggest that these effects represent many-way interactions with myriad features of the cellular system that vary across classes of individuals. Such gene-by-system interactions may influence diverse traits and require new modeling approaches to accurately represent genotype–phenotype relationships across individuals.

Authors:
 [1];  [2]
+ Show Author Affiliations
  1. Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center
  2. Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center, and Lab. of Genetics
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1459533
Grant/Contract Number:  
SC0018409
Resource Type:
Accepted Manuscript
Journal Name:
Current Genetics
Additional Journal Information:
Journal Volume: 64; Journal Issue: 6; Journal ID: ISSN 0172-8083
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; Genetic architecture; Epistasis; Quantitative genetics; Biofuels; Stress tolerance

Citation Formats

Sardi, Maria, and Gasch, Audrey P. Genetic background effects in quantitative genetics: gene-by-system interactions. United States: N. p., 2018. Web. doi:10.1007/s00294-018-0835-7.
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Sardi, Maria, & Gasch, Audrey P. Genetic background effects in quantitative genetics: gene-by-system interactions. United States. https://doi.org/10.1007/s00294-018-0835-7
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Sardi, Maria, and Gasch, Audrey P. Wed . "Genetic background effects in quantitative genetics: gene-by-system interactions". United States. https://doi.org/10.1007/s00294-018-0835-7. https://www.osti.gov/servlets/purl/1459533.
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@article{osti_1459533,
title = {Genetic background effects in quantitative genetics: gene-by-system interactions},
author = {Sardi, Maria and Gasch, Audrey P.},
abstractNote = {Proper cell function depends on networks of proteins that interact physically and functionally to carry out physiological processes. Thus, it seems logical that the impact of sequence variation in one protein could be significantly influenced by genetic variants at other loci in a genome. Nonetheless, the importance of such genetic interactions, known as epistasis, in explaining phenotypic variation remains a matter of debate in genetics. Recent work from our lab revealed that genes implicated from an association study of toxin tolerance in Saccharomyces cerevisiae show extensive interactions with the genetic background: most implicated genes, regardless of allele, are important for toxin tolerance in only one of two tested strains. The prevalence of background effects in our study adds to other reports of widespread genetic-background interactions in model organisms. We suggest that these effects represent many-way interactions with myriad features of the cellular system that vary across classes of individuals. Such gene-by-system interactions may influence diverse traits and require new modeling approaches to accurately represent genotype–phenotype relationships across individuals.},
doi = {10.1007/s00294-018-0835-7},
journal = {Current Genetics},
number = 6,
volume = 64,
place = {United States},
year = {2018},
month = {4}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1007/s00294-018-0835-7
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Figures / Tables:

Figure 1 Figure 1: Different gene products can be required for stress tolerance in different strains. The figure represents a cellular network of interacting proteins (circles) and the output of their functions (shapes). Blue nodes represent proteins involved in toxin tolerance in both of two different strains, whereas red and green nodesmore » represent proteins differentially required in the strains. The star represents a cofactor required for tolerance in both strains. If Strain 1 has a surplus of cofactor whereas Strain 2 lacks availability, then genes influencing cofactor abundance or recycling may be important in Strain 2 but not Strain 1. Genetic variants in the green protein nodes could produce additive phenotypic effects across strains in the same ‘systems’ class as Strain 2 while having no impact in strains from the same systems class as Strain 1.« less
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