Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci

J.J.B. Keurentjes, J. Fu, I.R. Terpstra, J.M. Garcia, G. van den Ackerveken, L.B. Snoek, A.J. Peeters, D. Vreugdenhil, M. Koornneef, R.C. Jansen

Research output: Contribution to journalArticleAcademicpeer-review

260 Citations (Scopus)

Abstract

Accessions of a plant species can show considerable genetic differences that are analyzed effectively by using recombinant inbred line (RIL) populations. Here we describe the results of genome-wide expression variation analysis in an RIL population of Arabidopsis thaliana. For many genes, variation in expression could be explained by expression quantitative trait loci (eQTLs). The nature and consequences of this variation are discussed based on additional genetic parameters, such as heritability and transgression and by examining the genomic position of eQTLs versus gene position, polymorphism frequency, and gene ontology. Furthermore, we developed an approach for genetic regulatory network construction by combining eQTL mapping and regulator candidate gene selection. The power of our method was shown in a case study of genes associated with flowering time, a well studied regulatory network in Arabidopsis. Results that revealed clusters of coregulated genes and their most likely regulators were in agreement with published data, and unknown relationships could be predicted.
Original languageEnglish
Pages (from-to)1708-1713
JournalProceedings of the National Academy of Sciences of the United States of America
Volume104
Issue number5
DOIs
Publication statusPublished - 2007

Keywords

  • natural allelic variation
  • flowering time
  • microarray experiments
  • circadian-rhythms
  • linkage analysis
  • thaliana
  • yeast
  • identification
  • pathways
  • population

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