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

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.

Fig. 1.

Distribution of mapped genes versus the position of their accompanying eQTL. Positions of detected eQTL are plotted against the position of the gene for which that eQTL was found. Chromosomal borders are depicted as horizontal and vertical lines. Mb, megabase.

Fig. 2.

Regulatory network of genes involved in the transition to flowering. Flower genes (green dots) are connected to their most likely regulator (blue dots) by directional edges. Arrows, stimulative regulation; bars, repressive regulation.