Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis  . Issue 11 (26th November 2014)

• Record Type: Journal Article
• Authors: Cubillos, Francisco A.; Stegle, Oliver; Grondin, Cécile; Canut, Matthieu; Tisné, Sébastien; Gy, Isabelle; Loudet, Olivier
• Is Part Of: The Plant Cell. Volume 26:Issue 11(2014)
• Page Start: 4298
• Page End: 4310
• Publication Date: 2014-11-26
• DOI: 10.1105/tpc.114.130310
• Languages: English
• ISSNs: 1040-4651

Abstract

Abstract : A major source of variation between and within species is that originating from changes in the amount of transcript accumulation from specific genes. New approaches and technologies can reveal such variation at the genome scale; this work shows the extent of allele-specific expression differences in hybrids between two distantly related wild strains of Arabidopsis thaliana . Abstract: cis - and trans- acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE ) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans- regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11, 003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis -acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE ) interactions, mostly cis x E interactions with magnitude changes in ASE . We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans -regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis - and trans -regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.