Originally published as Genetics Published Articles Ahead of Print on April 19, 2006.

Genetics, Vol. 173, 1347-1355, July 2006, Copyright © 2006
doi:10.1534/genetics.105.051474

Segregating Variation in the Transcriptome: Cis Regulation and Additivity of Effects

Kimberly A. Hughes^*,,1, Julien F. Ayroles^,2, Melissa M. Reedy^*, Jenny M. Drnevich^*,3, Kevin C. Rowe^*,4, Elizabeth A. Ruedi, Carla E. Cáceres^* and Ken N. Paige^*

^* School of Integrative Biology, Institute for Genome Biology, Department of Natural Resources and Environmental Sciences and Program in Ecology and Evolutionary Biology, University of Illinois, Urbana, Illinois 61801

¹ Corresponding author: School of Integrative Biology, University of Illinois, 515 Morrill Hall, 505 S. Goodwin Ave., Urbana, IL 61801.
E-mail: kahughes{at}life.uiuc.edu

Properties of genes underlying variation in complex traits are largely unknown, especially for variation that segregates within populations. Here, we evaluate allelic effects, cis and trans regulation, and dominance patterns of transcripts that are genetically variable in a natural population of Drosophila melanogaster. Our results indicate that genetic variation due to the third chromosome causes mainly additive and nearly additive effects on gene expression, that cis and trans effects on gene expression are numerically about equal, and that cis effects account for more genetic variation than do trans effects. We also evaluated patterns of variation in different functional categories and determined that genes involved in metabolic processes are overrepresented among variable transcripts, but those involved in development, transcription regulation, and signal transduction are underrepresented. However, transcripts for proteins known to be involved in protein–protein interactions are proportionally represented among variable transcripts.

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