Originally published as Genetics Published Articles Ahead of Print on December 18, 2006.

Genetics, Vol. 175, 1441-1450, March 2007, Copyright © 2007
doi:10.1534/genetics.106.064972

Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

Marilyn A. L. West^*, Kyunga Kim, Daniel J. Kliebenstein^*, Hans van Leeuwen^*, Richard W. Michelmore^*,, R. W. Doerge and Dina A. St. Clair^*,1

^* Department of Plant Sciences, University of California, Davis, California 95616-8780, Department of Statistics, Purdue University, West Lafayette, Indiana 47907-2067 and The Genome Center, University of California, Davis, California 95616

¹ Corresponding author: Department of Plant Sciences, University of California, Mail Stop 3, 1 Shields Ave., Davis, CA 95616-8780.
E-mail: dastclair{at}ucdavis.edu

The genetic architecture of transcript-level variation is largely unknown. The genetic determinants of transcript-level variation were characterized in a recombinant inbred line (RIL) population (n = 211) of Arabidopsis thaliana using whole-genome microarray analysis and expression quantitative trait loci (eQTL) mapping of transcript levels as expression traits (e-traits). Genetic control of transcription was highly complex: one-third of the quantitatively controlled transcripts/e-traits were regulated by cis-eQTL, and many trans-eQTL mapped to hotspots that regulated hundreds to thousands of e-traits. Several thousand eQTL of large phenotypic effect were detected, but almost all (93%) of the 36,871 eQTL were associated with small phenotypic effects (R² < 0.3). Many transcripts/e-traits were controlled by multiple eQTL with opposite allelic effects and exhibited higher heritability in the RILs than their parents, suggesting nonadditive genetic variation. To our knowledge, this is the first large-scale global eQTL study in a relatively large plant mapping population. It reveals that the genetic control of transcript level is highly variable and multifaceted and that this complexity may be a general characteristic of eukaryotes.

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