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

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...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2007-01, Vol.104 (5), p.1708-1713
Main Authors: Keurentjes, Joost J.B, Fu, Jingyuan, Terpstra, Inez R, Garcia, Juan M, van den Ackerveken, Guido, Snoek, L. Basten, Peeters, Anton J.M, Vreugdenhil, Dick, Koornneef, Maarten, Jansen, Ritsert C
Format: Article
Language:English
Subjects:
Arabidopsis - genetics
Arabidopsis - metabolism
Arabidopsis thaliana
Bioinformatics
Biological Sciences
Botany
Chromosome Mapping
circadian-rhythms
expression quantitative trait loci
flowering
flowering time
Flowers & plants
Gene expression
Gene expression regulation
Gene Expression Regulation, Plant
Gene loci
Genes
Genes, Plant
Genetic Linkage
Genetic loci
Genetic mapping
Genetic Markers
Genetic variation
genome
Genome, Plant
genome-wide gene expression quantitative trait loci
Heritability
identification
linkage analysis
microarray experiments
Models, Genetic
Models, Statistical
natural allelic variation
Oligonucleotide Array Sequence Analysis
P values
pathways
phenology
Physical Chromosome Mapping
population
Quantitative Trait Loci
recombinant inbred lines
thaliana
yeast
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Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0610429104