Rachel B. Brem ¹, Gael Yvert ¹, Rebecca Clinton ², Leonid Kruglyak ^1, *

¹ Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, D4-100, Seattle, WA 98109, USA.
² Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

* To whom correspondence should be addressed. E-mail:  leonid@fhcrc.org

To begin to understand the genetic architecture of natural variation in gene expression, we carried out genetic linkage analysis of genome-wide expression patterns in a cross between a laboratory and a wild strain of Saccharomyces cerevisiae. Over 1500 genes were differentially expressed between the parent strains. Expression levels of 570 genes were linked to one or more different loci, with most expression levels showing complex inheritance patterns. The loci detected by linkage fell largely into two categories: cis-acting modulators of single genes and trans-acting modulators of many genes. We found eight such trans-acting loci, each affecting expression of a group of 7-94 genes of related function. 

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