Yeast growth plasticity is regulated by environment-specific multi-QTL interactions.
For a unicellular, nonmotile organism like Saccharomyces cerevisiae, carbon sources act as nutrients and as signaling molecules; consequently, these sources affect various fitness parameters, including growth. It is therefore advantageous for yeast strains to adapt their growth to carbon source variation. The ability of a given genotype to manifest different phenotypes in varying environments is known as phenotypic plasticity. To identify quantitative trait loci (QTL) that drive plasticity in growth, two growth parameters (growth rate and biomass) were measured for a set of meiotic recombinants of two genetically divergent yeast strains grown in different carbon sources. To identify QTL contributing to plasticity across pairs of environments, gene-environment interaction mapping was performed, which identified several QTL that have a differential effect across environments, some of which act antagonistically across pairs of environments. Multi-QTL analysis identified loci interacting with previously known growth affecting QTL as well as novel two-QTL interactions that affect growth. A QTL that had no significant independent effect was found to alter growth rate and biomass for several carbon sources through two-QTL interactions. Our study demonstrates that environment-specific epistatic interactions contribute to the growth plasticity in yeast. We propose that a targeted scan for epistatic interactions, such as the one described here, can help unravel mechanisms regulating phenotypic plasticity.
Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854.
Aatish
A
Bhatia
Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India.
Anupama
A
Yadav
European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.
Chenchen
C
Zhu
Gene Center, Ludwig-Maximilians-Universität, 81377 Munich, Germany.
Julien
J
Gagneur
Aparna
A
Radhakrishnan
European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304.
Lars M
LM
Steinmetz
Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854 Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854 Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903 Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey 08540.
Gyan
G
Bhanot
Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India hsinha@tifr.res.in.
Himanshu
H
Sinha
D002244:Carbon / Q000378:metabolism; D002874:Chromosome Mapping; D004777:Environment; D004843:Epistasis, Genetic; D059647:Gene-Environment Interaction; D040641:Quantitative Trait Loci; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000254:growth & development; D015003:Yeasts / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism
D002244:Carbon
carbon source variation; gene-environment interaction; gene–gene interaction; growth plasticity; quantitative trait locus