Evolution of neutral and flowering genes along pearl millet ([i]Pennisetum glaucum[/i]) domestication
2012
Lakis, Ghayas | Navascués, Miguel | Sekima, Samah | Simon, Mathieu | Remigereau, Marie-Stanislas | Leveugle, Magalie | Takvorian, Najat | Lamy, Françoise | Depaulis, Frantz | Robert, Thierry | Ecologie Systématique et Evolution (ESE) ; Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS) | Centre de Biologie pour la Gestion des Populations (UMR CBGP) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [Occitanie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) | Institut Jean-Pierre Bourgin (IJPB) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Molecular & Computational Biology ; University of Southern California (USC) | Université Pierre et Marie Curie - Paris 6 (UPMC) | Laboratoire Ecologie et évolution ; École normale supérieure - Paris (ENS-PSL) ; Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS) | Agence Nationale pour la Recherche Scientifique [ANR-07Biodiv-005-04, ANR-06-BDIV-003-01]
Background : Pearl millet landraces display an important variation in their cycle duration. This diversity contributes to the stability of crop production in the Sahel despite inter-annual rainfall fluctuation. Conservation of phenological diversity is important for the future of pearl millet improvement and sustainable use. Identification of genes contributing to flowering time variation is therefore relevant. In this study we focused on three flowering candidate genes, PgHd3a, PgDwarf8 and PgPHYC. We tested for signatures of past selective events within polymorphism patterns of these three genes that could have been associated with pearl millet domestication and/or landraces differentiation. In order to implement ad hoc neutrality tests, a plausible demographic history of pearl millet domestication was inferred through Approximate Bayesian Computation by using eight neutral STS loci.Results : Domesticated pearl millet exhibited 84% of the nucleotide diversity level found in the wild population. No specific polymorphisms were found either in the wild or in the domestic populations. The Bayesian approach and previous studies suggest that gene flow between wild relatives and domesticated pearl millets is a main factor explaining these results. Early and late landraces did not show significant genetic differentiation at both the neutral and the candidate loci. A positive selection was evidenced in PgHd3a and PgDwarf8 genes of domestic forms but not in the wild population.Conclusion: Our results strongly suggest that PgHd3a and PgDwarf8 were likely targeted by selection during domestication. However, a potential role of any of the three candidate genes in the phenological differentiation between early and late landraces was not supported by our data. Reasons why these results contrast with previous results that have shown a slight but significant association between PgPHYC polymorphisms and variation in flowering time in pearl millet are discussed.
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