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Nucleic Acids Research 2006 34(13):3677-3686; doi:10.1093/nar/gkl510
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Published online 2 August 2006

Nucleic Acids Research, 2006, Vol. 34, No. 13 3677-3686
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article

Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme

Raphaël Kiekens, Annelies Vercauteren, Beatrijs Moerkerke1, Els Goetghebeur1, Hilde Van Den Daele, Roel Sterken, Martin Kuiper, Fred van Eeuwijk2 and Marnik Vuylsteke*

Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University Technologiepark 927, B-9052 Gent, Belgium 1 Department of Applied Mathematics and Computer Science, Ghent University B-9000 Gent, Belgium 2 Laboratory of Plant Breeding, Wageningen University and Research Centre NL-6700 AJ Wageningen, The Netherlands

*To whom correspondence should be addressed. Tel: +32 9 3313860; Fax: +32 9 3313809; Email: marnik.vuylsteke{at}psb.ugent.be

Received March 23, 2006. Revised June 21, 2006. Accepted July 5, 2006.

Large-scale screening studies carried out to date for genetic variants that affect gene regulation are generally limited to descriptions of differences in allele-specific expression (ASE) detected in vivo. Allele-specific differences in gene expression provide evidence for a model whereby cis-acting genetic variation results in differential expression between alleles. Such gene surveys for regulatory variation are a first step in identifying the specific nucleotide changes that govern gene expression differences, but they leave the underlying mechanisms unexplored. Here, we propose a quantitative genetics approach to perform a genome-wide analysis of ASE differences (GASED). The GASED approach is based on a diallel design that is often used in plant breeding programs to estimate general combining abilities (GCA) of specific inbred lines and to identify high-yielding hybrid combinations of parents based on their specific combining abilities (SCAs). In a context of gene expression, the values of GCA and SCA parameters allow cis- and trans-regulatory changes to be distinguished and imbalances in gene expression to be ascribed to cis-regulatory variation. With this approach, a total of 715 genes could be identified that are likely to carry allelic polymorphisms responsible for at least a 1.5-fold allelic expression difference in a total of 10 diploid Arabidopsis thaliana hybrids. The major strength of the GASED approach, compared to other ASE detection methods, is that it is not restricted to genes with allelic transcript variants. Although a false-positive rate of 9/41 was observed, the GASED approach is a valuable pre-screening method that can accelerate systematic surveys of naturally occurring cis-regulatory variation among inbred lines for laboratory species, such as Arabidopsis, mouse, rat and fruitfly, and economically important crop species, such as corn.

Present address: Annelies Vercauteren, Instituut voor Landbouw-en Visserij Onderzoek, Eenheid Plant/Gewasbescherming, Burg. Van Gansberghelaan 96, B-9820 Merelbeke, Belgium

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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