Layers of Cryptic Genetic Variation Underlie a Yeast Complex Trait

Genetics
Jonathan T LeeIan M Ehrenreich

Abstract

Cryptic genetic variation may be an important contributor to heritable traits, but its extent and regulation are not fully understood. Here, we investigate the cryptic genetic variation underlying a Saccharomyces cerevisiae colony phenotype that is typically suppressed in a cross of the laboratory strain BY4716 (BY) and a derivative of the clinical isolate 322134S (3S). To do this, we comprehensively dissect the trait's genetic basis in the BYx3S cross in the presence of three different genetic perturbations that enable its expression. This allows us to detect and compare the specific loci that interact with each perturbation to produce the trait. In total, we identify 21 loci, all but one of which interact with just a subset of the perturbations. Beyond impacting which loci contribute to the trait, the genetic perturbations also alter the extent of additivity, epistasis, and genotype-environment interaction among the detected loci. Additionally, we show that the single locus interacting with all three perturbations corresponds to the coding region of the cell surface gene FLO11 While nearly all of the other remaining loci influence FLO11 transcription in cis or trans, the perturbations tend to interact with loci in different p...Continue Reading

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Citations

Sep 14, 2019·Molecular Biology and Evolution·Zebin ZhangRike Stelkens
Mar 24, 2020·Heredity·Michael P Shahandeh, Thomas L Turner

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Datasets Mentioned

BETA
PRJNA503265

Methods Mentioned

BETA
gene knockouts
genetic modifications
Synthetic Genetic Array
SGA
PCR
GTPase

Software Mentioned

MOST
custom
GPa
GPb
HMM
statsmodels
Python
R

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