Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 365716
Title Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme
Author(s) Kiekens, R.; Vercauteren, A.; Moerkerke, B.; Goetghebeur, E.; Daele, H. Van Den; Sterken, R.; Kuiper, M.; Eeuwijk, F.A. van; Vuylsteke, M.
Source Nucleic acids research 34 (2006)13. - ISSN 0305-1048 - p. 3677 - 3686.
DOI https://doi.org/10.1093/nar/gkl510
Department(s) Laboratory of Plant Breeding
PE&RC
Publication type Refereed Article in a scientific journal
Publication year 2006
Keyword(s) human gene-expression - allelic variation - transcriptional regulation - arabidopsis-thaliana - functional genomics - sequence tags - microarray - model - identification - construction
Abstract 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.
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