title: No Excess of Cis-Regulatory Variation Associated with Intraspecific Selection in Wild Pearl Millet (Cenchrus americanus).
abstract: Several studies suggest that cis-regulatory mutations are the favorite target of evolutionary changes, one reason being that cis-regulatory mutations might have fewer deleterious pleiotropic effects than protein-coding mutations. A review of the process also suggests that this bias towards adaptive cis-regulatory variation might be less pronounced at the intraspecific level compared with the interspecific level. In this study, we assessed the contribution of cis-regulatory variation to adaptation at the intraspecific level using populations of wild pearl millet (Cenchrus americanus ssp. monodii) sampled along an environmental gradient in Niger. From RNA sequencing of hybrids to assess allele-specific expression, we identified genes with cis-regulatory divergence between two parental accessions collected in contrasted environmental conditions. This revealed that ∼15% of transcribed genes showed cis-regulatory variation. Intersecting the gene set exhibiting cis-regulatory variation with the gene set identified as targets of selection revealed no excess of cis-acting mutations among the selected genes. We additionally found no excess of cis-regulatory variation among genes associated with adaptive traits. As our approach relied on methods identifying mainly genes submitted to strong selection pressure or with high phenotypic effect, the contribution of cis-regulatory changes to soft selection or polygenic adaptive traits remains to be tested. However our results favor the hypothesis that enrichment of adaptive cis-regulatory divergence builds up over time. For short evolutionary time-scales, cis-acting mutations are not predominantly involved in adaptive evolution associated with strong selective signal.
authors.affiliation: Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Institut de Recherche pour le Développement, Montpellier, France.|Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, Lyon, France.
authors.forename: Bénédicte
authors.initials: B
authors.lastname: Rhoné
authors.affiliation: Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Institut de Recherche pour le Développement, Montpellier, France.
authors.forename: Cédric
authors.initials: C
authors.lastname: Mariac
authors.affiliation: Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Institut de Recherche pour le Développement, Montpellier, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Couderc
authors.affiliation: Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Institut de Recherche pour le Développement, Montpellier, France.|Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal.
authors.forename: Cécile
authors.initials: C
authors.lastname: Berthouly-Salazar
authors.affiliation: Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Institut de Recherche pour le Développement, Montpellier, France.|Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal.|Biology Department, Unité Mixte de Recherche Diversité Adaptation et Développement des plantes (UMR DIADE), Université Montpellier, France.|Université Abdou Moumouni de Niamey, Niger.
authors.forename: Issaka Salia
authors.initials: IS
authors.lastname: Ousseini
authors.affiliation: Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Institut de Recherche pour le Développement, Montpellier, France.|Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal.|Biology Department, Unité Mixte de Recherche Diversité Adaptation et Développement des plantes (UMR DIADE), Université Montpellier, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Vigouroux
mesh_terms: D000222:Adaptation, Physiological; D000483:Alleles; D019143:Evolution, Molecular; D017343:Genes, Plant; D000066928:Millets / Q000235:genetics*; D009154:Mutation; D011110:Polymorphism, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012641:Selection, Genetic
keywords: Cenchrus americanus; allele-specific expression; cis-regulation; environmental gradient; local adaptation; selection