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doi:10.1534/genetics.105.049353
A more recent version of this article appeared on February 1, 2006.
REGULAR RESEARCH PAPERS |
Genomic survey of gene expression diversity in Arabidopsis thaliana
Daniel J. Kliebenstein 1, Marilyn A. L. West 1, Hans van Leeuwen 1, Kyunga Kim 2, R. W. Doerge 2, Richard W. Michelmore 1 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 12, 2005
Revised on September 10, 2005
Accepted on 27 September 2005
Differential gene expression controls variation in numerous plant traits, such as flowering time and plant/pest interactions, but little is known about the genomic distribution of the determinants of transcript levels. Affymetrix ATH1 GeneChip microarrays representing 22,810 genes were used to survey the transcriptome of seven Arabidopsis thaliana accessions in the presence and absence of exogenously applied salicylic acid (SA). These accessions encompassed ~80% of the moderate-to-high frequency nucleotide polymorphisms in Arabidopsis. A factorial design, consisting of three biological replicates per accession for the two treatments at three time points (4, 28, 52 hour post treatment), and a total of 126 microarrays were used. Between any pair of Arabidopsis accessions, we detected on average 2234 genes (ranging from 1428 to 3334) that were significantly differentially expressed under the conditions of this experiment, using a split-plot analysis of variance. Up to 6433 genes were differentially expressed between at least one pair of accessions. These results suggest that analysis of additional genetic, developmental, and environmental conditions may show that a significant fraction of the Arabidopsis genome is differentially expressed. Examination of sequence diversity demonstrated a significant positive association with diversity in gene expression.
Key Words: Arabidopsis thaliana, diversity, expression level polymorphism, microarray, sequence polymorphism
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