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Originally published as Genetics Published Articles Ahead of Print on October 3, 2005.
Genetics, Vol. 172, 1179-1189, February 2006, Copyright © 2006
doi:10.1534/genetics.105.049353
Genomic Survey of Gene Expression Diversity in Arabidopsis thaliana
Daniel J. Kliebenstein*,1,
Marilyn A. L. West*,1,
Hans van Leeuwen*,
Kyunga Kim
,
R. W. Doerge,
Richard W. Michelmore*,
and
Dina A. St. Clair*,2
* 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
2 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
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 and their associated variation. 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, and 52 hr 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. Upward of 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.
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