Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae.
BACKGROUND
The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits.


RESULTS
We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes, 20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2.


CONCLUSIONS
Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation.
Fay
Justin C
JC
Department of Genome Sciences, Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley, CA 94720, USA. jfay@genetics.wustl.edu
McCullough
Heather L
HL
Sniegowski
Paul D
PD
Eisen
Michael B
MB
D003116:Color; D019327:Copper Sulfate / Q000494:pharmacology; D020869:Gene Expression Profiling / Q000379:methods; D015966:Gene Expression Regulation, Fungal / Q000187:drug effects / Q000235:genetics*; D005800:Genes, Fungal / Q000502:physiology; D014644:Genetic Variation / Q000235:genetics*; D006657:Histones / Q000235:genetics; D008715:Methionine / Q000378:metabolism; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D018384:Oxidative Stress / Q000235:genetics; D010454:Peptide Termination Factors; D010641:Phenotype; D011328:Prions / Q000235:genetics / Q000502:physiology; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000502:physiology; D013045:Species Specificity; D013455:Sulfur / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000502:physiology
D006657:Histones; C083209:MBP1 protein, S cerevisiae; D010454:Peptide Termination Factors; D011328:Prions; C068068:SUP35 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D013455:Sulfur; D008715:Methionine; D019327:Copper Sulfate