Originally published as Genetics Published Articles Ahead of Print on July 14, 2005.

Genetics, Vol. 171, 1267-1275, November 2005, Copyright © 2005
doi:10.1534/genetics.105.041509

Genetic Analysis of Variation in Gene Expression in Arabidopsis thaliana

Marnik Vuylsteke^*,1, Fred van Eeuwijk, Paul Van Hummelen, Martin Kuiper^* and Marc Zabeau^*

^* Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Gent, Belgium, Laboratory of Plant Breeding, Wageningen University and Research Centre, NL-6700 AJ Wageningen, The Netherlands and Microarray Facility, Flanders Interuniversity Institute for Biotechnology (VIB), B-3000 Leuven, Belgium

¹ Corresponding author: Department of Plant Systems Biology, VIB2-Universiteit Gent, Technologiepark 927, B-9052 Gent, Belgium.
E-mail: marnik.vuylsteke{at}psb.ugent.be

In Arabidopsis thaliana, significant efforts to determine the extent of genomic variation between phenotypically divergent accessions are under way, but virtually nothing is known about variation at the transcription level. We used microarrays to examine variation in transcript abundance among three inbred lines and two pairs of reciprocal F₁ hybrids of the highly self-fertilizing species Arabidopsis. Composite additive genetic effects for gene expression were estimated from pairwise comparisons of the three accessions Columbia (Col), Landsberg erecta (Ler), and Cape Verde Islands (Cvi). For the pair Col and Ler, 27.0% of the 4876 genes exhibited additive genetic effects in their expression ( = 0.001) vs. 32.2 and 37.5% for Cvi with Ler and Col, respectively. Significant differential expression ranged from 32.45 down to 1.10 in fold change and typically differed by a factor of 1.56. Maternal or paternal transmission affected only a few genes, suggesting that the reciprocal effects observed in the two crosses analyzed were minimal. Dominance effects were estimated from the comparisons of hybrids with the corresponding midparent value. The percentage of genes showing dominance at the expression level in the F₁ hybrids ranged from 6.4 to 21.1% ( = 0.001). Breakdown of these numbers of genes according to the magnitude of the dominance ratio revealed heterosis for expression for on average 9% of the genes. Further advances in the genetic analysis of gene expression variation may contribute to a better understanding of its role in affecting quantitative trait variation at the phenotypic level.

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