title: Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.
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.
authors.affiliation: INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile, Santiago, Chile.
authors.forename: Francisco A
authors.initials: FA
authors.lastname: Cubillos
authors.affiliation: Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tuebingen, Germany European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
authors.forename: Oliver
authors.initials: O
authors.lastname: Stegle
authors.affiliation: INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Grondin
authors.affiliation: INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Canut
authors.affiliation: INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Tisné
authors.affiliation: INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Gy
authors.affiliation: INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France olivier.loudet@versailles.inra.fr.
authors.forename: Olivier
authors.identifier: http://orcid.org/0000-0003-3717-0137
authors.initials: O
authors.lastname: Loudet
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D055864:Droughts; D004777:Environment; D018506:Gene Expression Regulation, Plant; D011110:Polymorphism, Genetic; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*