Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae

Abstract

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.

Figure 1

Growth of strains on rich medium (YPD) and rich medium supplemented with different concentrations of copper sulfate (CuSO₄). For each condition, a 10^-3 and a 10^-4 dilution of cells from an overnight YPD culture are shown.

Figure 2

Hierarchical clustering of differentially expressed genes. Genes with significant expression differences among strains in both media (strain), in copper-sulfate medium (strain*CuSO₄), in rich medium (strain*YPD), and between copper sulfate and rich medium reference pools (YPD vs CuSO₄) for p < 0.05 (yellow) and p < 0.01 (blue). Groups of functionally related genes are also shown.

Figure 3

The average growth rates from three replicates of strains in rich medium and rich medium with 1 mM copper sulfate. Relative growth rates were measured by the slope of the linear regression of cell density on time.

Figure 4

Genes associated with resistance to copper sulfate. (a) Genes correlated with sensitivity to copper sulfate (r > 0.8, p < 0.01) that are differentially expressed among strains in the presence of copper sulfate or between the rich medium and copper sulfate reference pools. (b) Genes differentially expressed and annotated as functioning in copper homeostasis, protein folding or response to oxidative stress.

Figure 5

Genes with different expression levels in the copper sulfate compared to the rich medium reference pool. Groups of genes enriched for functions in protein folding (red bar) and stress response and metabolism (blue bar) are shown.

Figure 6

Genes correlated (r > 0.8, p < 0.01) with rust coloration and differentially expressed among strains in the presence of copper sulfate.

Figure 7

Relative rates of growth at 30°C subsequent to a -30°C compared to a 4°C treatment. Growth rates were measured as the change in OD₆₀₀ over 4 h. Error bars are one standard deviation.

Figure 8

DNA sequence differences found in three genes (SUP35, MBP1, HHT2). Intergenic (i), amino-acid-altering (a), and synonymous (s) polymorphic sites are shown in reference to the S. paradoxus sequence. d indicates an insertion or deletion and N indicates missing data.

Figure 9

Pairwise differences in gene expression compared to pairwise DNA sequence divergence. (a) Genes differentially expressed among strains, and (b) genes different between copper-sulfate and rich medium. Distances with S288C (green) and with YPS163 (red) are distinguished.