Genetics. Published Articles Ahead of Print: December 18, 2006, Copyright © 2006
doi:10.1534/genetics.106.064972


A more recent version of this article appeared on March 1, 2007.

REGULAR RESEARCH PAPERS

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

Marilyn A.L. West 1, Kyunga Kim 2, Daniel J. Kliebenstein 1, Hans van Leeuwen 1, Richard W. Michelmore 1, R. W. Doerge 2 and Dina A. St.Clair 1*

1 University of California-Davis
2 Purdue University

* To whom correspondence should be addressed. E-mail: dastclair{at}ucdavis.edu.

Submitted on August 17, 2006
Revised on October 2, 2006
Accepted on 1 December 2006


Abstract

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 QTL (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-eQTLs and many trans-eQTLs mapped to "hotspots" that regulated hundreds to thousands of e-traits. Several thousand eQTLs of large phenotypic effect were detected, but almost all (93%) of the 36,871 eQTLs were associated with small phenotypic effects (R2 < 0.3). Many transcripts/e-traits were controlled by multiple eQTLs with opposite allelic effects and exhibited higher heritability in the RILs than their parents, suggesting non-additive 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.

Key Words: Arabidopsis, expression QTL (eQTL), functional genomics, quantitative genetics, recombinant inbred population




This article has been cited by other articles:


Home page
 GeneticsHome page
A. R. Whiteley, N. Derome, S. M. Rogers, J. St-Cyr, J. Laroche, A. Labbe, A. Nolte, S. Renaut, J. Jeukens, and L. Bernatchez
The Phenomics and Expression Quantitative Trait Locus Mapping of Brain Transcriptomes Regulating Adaptive Divergence in Lake Whitefish Species Pairs (Coregonus sp.)
Genetics, September 1, 2008; 180(1): 147 - 164.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
A. G. Pisabarro, G. Perez, J. L. Lavin, and L. Ramirez
Genetic networks for the functional study of genomes
Brief Funct Genomic Proteomic, June 25, 2008; (2008) eln026v1.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
H. C. Rowe, B. G. Hansen, B. A. Halkier, and D. J. Kliebenstein
Biochemical Networks and Epistasis Shape the Arabidopsis thaliana Metabolome
PLANT CELL, May 1, 2008; 20(5): 1199 - 1216.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
N. A. Eckardt
Epistasis and Genetic Regulation of Variation in the Arabidopsis Metabolome
PLANT CELL, May 1, 2008; 20(5): 1185 - 1186.
[Full Text] [PDF]

Home page
 Plant Physiol.Home page
R. M. Stupar, P. J. Hermanson, and N. M. Springer
Nonadditive Expression and Parent-of-Origin Effects Identified by Microarray and Allele-Specific Expression Profiling of Maize Endosperm
Plant Physiology, October 1, 2007; 145(2): 411 - 425.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
N. M. Springer and R. M. Stupar
Allele-Specific Expression Patterns Reveal Biases and Embryo-Specific Parent-of-Origin Effects in Hybrid Maize
PLANT CELL, August 1, 2007; 19(8): 2391 - 2402.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
H. van Leeuwen, D. J. Kliebenstein, M. A.L. West, K. Kim, R. van Poecke, F. Katagiri, R. W. Michelmore, R. W. Doerge, and D. A. St.Clair
Natural Variation among Arabidopsis thaliana Accessions for Transcriptome Response to Exogenous Salicylic Acid
PLANT CELL, July 1, 2007; 19(7): 2099 - 2110.
[Abstract] [Full Text] [PDF]