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Tenaillon MI, Burban E, Huynh S, Wojcik A, Thuillet AC, Manicacci D, Gérard PR, Alix K, Belcram H, Cornille A, Brault M, Stevens R, Lagnel J, Dogimont C, Vigouroux Y, Glémin S. Crop domestication as a step towards reproductive isolation. Am J Bot 2023:e16173. [PMID: 37087742 DOI: 10.1002/ajb2.16173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Speciation, Darwin's mystery of mysteries, is a continuous process that results in genomic divergence accompanied by the gradual increment of reproductive barriers between lineages. Since the beginning of research on the genetics of speciation, several questions have emerged such as: What are the genetic bases of incompatibilities? How many loci are necessary to prevent hybridization and how are they distributed along genomes? Can speciation occur despite gene flow and how common is ecological speciation? Early stages of divergence are key to understand the ecology and genetics of speciation, and semi-isolated species where hybrids can still be produced are particularly relevant This article is protected by copyright. All rights reserved.
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Affiliation(s)
- M I Tenaillon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 12 route, 128, Gif-sur-Yvette, France
| | - E Burban
- Laboratoire ECOBIO_UMR 6553 UR1-CNRS, Campus de Beaulieu, Rennes, France
| | - S Huynh
- UMR DIADE, Univ Montpellier, IRD, CIRAD, 911 avenue Agropolis, Montpellier, France
| | - A Wojcik
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 12 route, 128, Gif-sur-Yvette, France
| | - A-C Thuillet
- UMR DIADE, Univ Montpellier, IRD, CIRAD, 911 avenue Agropolis, Montpellier, France
| | - D Manicacci
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 12 route, 128, Gif-sur-Yvette, France
| | - P R Gérard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 12 route, 128, Gif-sur-Yvette, France
| | - K Alix
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 12 route, 128, Gif-sur-Yvette, France
| | - H Belcram
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 12 route, 128, Gif-sur-Yvette, France
| | - A Cornille
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 12 route, 128, Gif-sur-Yvette, France
| | - M Brault
- GAFL - Génétique et Amélioration des Fruits et Légumes, INRAE, Allée des Chênes, Montfavet, France
| | - R Stevens
- GAFL - Génétique et Amélioration des Fruits et Légumes, INRAE, Allée des Chênes, Montfavet, France
| | - J Lagnel
- GAFL - Génétique et Amélioration des Fruits et Légumes, INRAE, Allée des Chênes, Montfavet, France
| | - C Dogimont
- GAFL - Génétique et Amélioration des Fruits et Légumes, INRAE, Allée des Chênes, Montfavet, France
| | - Y Vigouroux
- UMR DIADE, Univ Montpellier, IRD, CIRAD, 911 avenue Agropolis, Montpellier, France
| | - S Glémin
- Laboratoire ECOBIO_UMR 6553 UR1-CNRS, Campus de Beaulieu, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
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2
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de la Fuente Cantó C, Diouf MN, Ndour PMS, Debieu M, Grondin A, Passot S, Champion A, Barrachina C, Pratlong M, Gantet P, Assigbetsé K, Kane N, Cubry P, Diedhiou AG, Heulin T, Achouak W, Vigouroux Y, Cournac L, Laplaze L. Genetic control of rhizosheath formation in pearl millet. Sci Rep 2022; 12:9205. [PMID: 35655088 PMCID: PMC9163325 DOI: 10.1038/s41598-022-13234-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/13/2022] [Indexed: 11/09/2022] Open
Abstract
The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub-Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.
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Affiliation(s)
| | - M N Diouf
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.,Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L'Ouest (IESOL), Dakar, Senegal.,Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop, Dakar, Sénégal
| | - P M S Ndour
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.,Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L'Ouest (IESOL), Dakar, Senegal
| | - M Debieu
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - A Grondin
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France.,Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Senegal.,CERAAS, Thiès, Senegal
| | - S Passot
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - A Champion
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | | | - M Pratlong
- Montpellier GenomiX, Montpellier, France
| | - P Gantet
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - K Assigbetsé
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.,Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L'Ouest (IESOL), Dakar, Senegal
| | - N Kane
- Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Senegal
| | - P Cubry
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - A G Diedhiou
- Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Senegal.,Département de Biologie Végétale, Faculté Des Sciences Et Techniques, Université Cheikh Anta Diop, Dakar, Sénégal
| | - T Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France
| | - W Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France
| | - Y Vigouroux
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - L Cournac
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Laplaze
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France. .,Laboratoire Mixte International Adaptation Des Plantes Et Microorganismes Associés Aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Senegal.
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3
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Mariac C, Vigouroux Y, Duponchelle F, García-Dávila C, Nunez J, Desmarais E, Renno J. Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms. PLoS One 2018; 13:e0202976. [PMID: 30208069 PMCID: PMC6135497 DOI: 10.1371/journal.pone.0202976] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/13/2018] [Indexed: 12/04/2022] Open
Abstract
The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.
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Affiliation(s)
- C. Mariac
- Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Montpellier, France
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
- * E-mail:
| | - Y. Vigouroux
- Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Montpellier, France
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
| | - F. Duponchelle
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), MNHN—CNRS-7208—UPMC—UCBN—IRD-207, Montpellier, France
| | - C García-Dávila
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
- Instituto de Investigaciones de la Amazonía Peruana (IIAP), Laboratorio de Biología y Genética Molecular (LBGM), Iquitos, Perú
| | - J. Nunez
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), MNHN—CNRS-7208—UPMC—UCBN—IRD-207, Montpellier, France
| | - E. Desmarais
- Institut des Sciences de l’Évolution (UMR ISEM), Université Montpellier—CNRS—IRD—EPHE, Place Eugène Bataillon—France
| | - J.F. Renno
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP—UAGRM—IRD, UMR BOREA, Paris, France
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), MNHN—CNRS-7208—UPMC—UCBN—IRD-207, Montpellier, France
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Fustier MA, Brandenburg JT, Boitard S, Lapeyronnie J, Eguiarte LE, Vigouroux Y, Manicacci D, Tenaillon MI. Signatures of local adaptation in lowland and highland teosintes from whole-genome sequencing of pooled samples. Mol Ecol 2017; 26:2738-2756. [DOI: 10.1111/mec.14082] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 02/21/2017] [Indexed: 01/01/2023]
Affiliation(s)
- M.-A. Fustier
- Génétique Quantitative et Evolution - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; Ferme du Moulon F-91190 Gif-sur-Yvette France
| | - J.-T. Brandenburg
- Génétique Quantitative et Evolution - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; Ferme du Moulon F-91190 Gif-sur-Yvette France
| | - S. Boitard
- GenPhySe; Université de Toulouse, INRA, INPT, INP-ENVT; 24 chemin de Borde-Rouge - Auzeville Tolosane; F-31326 Castanet Tolosan France
| | - J. Lapeyronnie
- GenPhySe; Université de Toulouse, INRA, INPT, INP-ENVT; 24 chemin de Borde-Rouge - Auzeville Tolosane; F-31326 Castanet Tolosan France
| | - L. E. Eguiarte
- Departamento de Ecología Evolutiva; Instituto de Ecología; Universidad Nacional Autónoma de México; Apartado Postal 70-275 Coyoacán 04510 México D.F. Mexico
| | - Y. Vigouroux
- Institut de Recherche pour le développement (IRD); UMR Diversité, Adaptation et Développement des plantes (DIADE); Université de Montpellier; 911 avenue Agropolis, F-34394 Montpellier Cedex 5 France
| | - D. Manicacci
- Génétique Quantitative et Evolution - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; Ferme du Moulon F-91190 Gif-sur-Yvette France
| | - M. I. Tenaillon
- Génétique Quantitative et Evolution - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; Ferme du Moulon F-91190 Gif-sur-Yvette France
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5
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Ousseini IS, Bakasso Y, Kane NA, Couderc M, Zekraoui L, Mariac C, Manicacci D, Rhoné B, Barnaud A, Berthouly-Salazar C, Assoumane A, Moussa D, Moussa T, Vigouroux Y. Myosin XI is associated with fitness and adaptation to aridity in wild pearl millet. Heredity (Edinb) 2017; 119:88-94. [PMID: 28295033 DOI: 10.1038/hdy.2017.13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 01/09/2017] [Accepted: 01/12/2017] [Indexed: 11/09/2022] Open
Abstract
Phenotypic changes in plants can be observed along many environmental gradients and are determined by both environmental and genetic factors. The identification of alleles associated with phenotypic variations is a rapidly developing area of research. We studied the genetic basis of phenotypic variations in 11 populations of wild pearl millet (Pennisetum glaucum) on two North-South aridity gradients, one in Niger and one in Mali. Most of the 11 phenotypic traits assessed in a common garden experiment varied between the populations studied. Moreover, the size of the inflorescence, the number of flowers and aboveground dry mass co-varied positively with a decrease in rainfall. To decipher the genetic basis of these phenotypes, we used an association mapping strategy with a mixed model. We found two SNPs on the same myosin XI contig significantly associated with variations in the average number of flowers. Both the allele frequency of the two SNPs and the average number of flowers co-varied with the rainfall gradient on the two gradients. Interestingly, this gene was also a target of selection during domestication. The Myosin XI gene is thus a good candidate for fitness-related adaptation in wild populations.
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Affiliation(s)
- I S Ousseini
- Institut de Recherche pour le Développement, Montpellier, France.,Université Abdou Moumouni de Niamey, Niamey, Niger.,Université de Montpellier, Montpellier, France.,Institut Sénégalais de la Recherche Agronomique, Campus de Bel Air, Dakar, Sénégal
| | - Y Bakasso
- Université Abdou Moumouni de Niamey, Niamey, Niger
| | - N A Kane
- Institut Sénégalais de la Recherche Agronomique, Campus de Bel Air, Dakar, Sénégal.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal
| | - M Couderc
- Institut de Recherche pour le Développement, Montpellier, France
| | - L Zekraoui
- Institut de Recherche pour le Développement, Montpellier, France.,Institut Sénégalais de la Recherche Agronomique, Campus de Bel Air, Dakar, Sénégal.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal
| | - C Mariac
- Institut de Recherche pour le Développement, Montpellier, France
| | - D Manicacci
- Université Paris-Sud, UMR 0320 / UMR 8120 Génétique Quantitative et Évolution - Le Moulon, Gif-sur-Yvette, France
| | - B Rhoné
- Institut de Recherche pour le Développement, Montpellier, France.,Centre National de la Recherche Scientifique, Lyon, France
| | - A Barnaud
- Institut de Recherche pour le Développement, Montpellier, France.,Institut Sénégalais de la Recherche Agronomique, Campus de Bel Air, Dakar, Sénégal.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal
| | - C Berthouly-Salazar
- Institut de Recherche pour le Développement, Montpellier, France.,Institut Sénégalais de la Recherche Agronomique, Campus de Bel Air, Dakar, Sénégal.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal
| | - A Assoumane
- Université Abdou Moumouni de Niamey, Niamey, Niger.,Institut de Recherche pour le Développement, Niamey, Niger
| | - D Moussa
- Institut de Recherche pour le Développement, Niamey, Niger
| | - T Moussa
- Institut de Recherche pour le Développement, Niamey, Niger
| | - Y Vigouroux
- Institut de Recherche pour le Développement, Montpellier, France.,Université de Montpellier, Montpellier, France.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LMI LAPSE), Centre de Recherche de Bel Air, Dakar, Sénégal
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6
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Ta KN, Sabot F, Adam H, Vigouroux Y, De Mita S, Ghesquière A, Do NV, Gantet P, Jouannic S. miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species. Rice (N Y) 2016; 9:10. [PMID: 26969003 PMCID: PMC4788661 DOI: 10.1186/s12284-016-0082-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/06/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii. RESULTS Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems. CONCLUSION Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.
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Affiliation(s)
- K. N. Ta
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
| | - F. Sabot
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - H. Adam
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - Y. Vigouroux
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - S. De Mita
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />Present address: INRA, Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, F-54280 Champenoux, France
| | - A. Ghesquière
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - N. V. Do
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
| | - P. Gantet
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
- />Université de Montpellier, UMR DIADE, Place Eugène Bataillon, F-34095 Montpellier, Cedex 5 France
| | - S. Jouannic
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
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7
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Faye A, Deblauwe V, Mariac C, Richard D, Sonké B, Vigouroux Y, Couvreur TLP. Phylogeography of the genus Podococcus (Palmae/Arecaceae) in Central African rain forests: Climate stability predicts unique genetic diversity. Mol Phylogenet Evol 2016; 105:126-138. [PMID: 27521478 DOI: 10.1016/j.ympev.2016.08.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 11/16/2022]
Abstract
The tropical rain forests of Central Africa contain high levels of species diversity. Paleovegetation or biodiversity patterns suggested successive contraction/expansion phases on this rain forest cover during the last glacial maximum (LGM). Consequently, the hypothesis of the existence of refugia e.g. habitat stability that harbored populations during adverse climatic periods has been proposed. Understory species are tightly associated to forest cover and consequently are ideal markers of forest dynamics. Here, we used two central African rain forest understory species of the palm genus, Podococcus, to assess the role of past climate variation on their distribution and genetic diversity. Species distribution modeling in the present and at the LGM was used to estimate areas of climatic stability. Genetic diversity and phylogeography were estimated by sequencing near complete plastomes for over 120 individuals. Areas of climatic stability were mainly located in mountainous areas like the Monts de Cristal and Monts Doudou in Gabon, but also lowland coastal forests in southeast Cameroon and northeast Gabon. Genetic diversity analyses shows a clear North-South structure of genetic diversity within one species. This divide was estimated to have originated some 500,000years ago. We show that, in Central Africa, high and unique genetic diversity is strongly correlated with inferred areas of climatic stability since the LGM. Our results further highlight the importance of coastal lowland rain forests in Central Africa as harboring not only high species diversity but also important high levels of unique genetic diversity. In the context of strong human pressure on coastal land use and destruction, such unique diversity hotspots need to be considered in future conservation planning.
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Affiliation(s)
- A Faye
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France; Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon.
| | - V Deblauwe
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France; Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon
| | - C Mariac
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France
| | - D Richard
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France
| | - B Sonké
- Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon
| | - Y Vigouroux
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France
| | - T L P Couvreur
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France; Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon; Naturalis Biodiversity Centre, Botany Section, Darwinweg 2, 2333 CR Leiden, The Netherlands
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8
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Scarcelli N, Mariac C, Couvreur TLP, Faye A, Richard D, Sabot F, Berthouly‐Salazar C, Vigouroux Y. Intra‐individual polymorphism in chloroplasts from
NGS
data: where does it come from and how to handle it? Mol Ecol Resour 2015; 16:434-45. [DOI: 10.1111/1755-0998.12462] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/07/2015] [Accepted: 08/21/2015] [Indexed: 01/11/2023]
Affiliation(s)
- N. Scarcelli
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
| | - C. Mariac
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
| | - T. L. P. Couvreur
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
- Département des Sciences Biologiques Laboratoire de Botanique Systématique et d'Ecologie Ecole Normale Supérieure Université de Yaoundé I BP 047 Yaoundé Cameroon
| | - A. Faye
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
| | - D. Richard
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
| | - F. Sabot
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
| | - C. Berthouly‐Salazar
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
- Route des Hydrocarbures Centre de Recherche de Bel‐Air IRD/ISRA BP 1386 – 18524 Dakar Senegal
| | - Y. Vigouroux
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
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9
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Deu M, Sagnard F, Chantereau J, Calatayud C, Vigouroux Y, Pham JL, Mariac C, Kapran I, Mamadou A, Gérard B, Ndjeunga J, Bezançon G. Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger. Theor Appl Genet 2010; 120:1301-13. [PMID: 20062963 DOI: 10.1007/s00122-009-1257-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 12/19/2009] [Indexed: 05/12/2023]
Abstract
The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. Sorghum is the second staple cereal in Niger, a centre of diversity for this crop. Niger was submitted to recurrent drought period and to major social changes during these last decades. We report here on a spatio-temporal analysis of sorghum genetic diversity, conducted in 71 villages covering the rainfall gradient and range of agro-ecological conditions in Niger's agricultural areas. We used 28 microsatellite markers and applied spatial and genetic clustering methods to investigate change in genetic diversity over a 26-year period (1976-2003). Global genetic differentiation between the two collections was very low (F (st) = 0.0025). Most of the spatial clusters presented no major differentiation, as measured by F (st), and showed stability or an increase in allelic richness, except for two of them located in eastern Niger. The genetic clusters identified by Bayesian analysis did not show a major change between the two collections in the distribution of accessions between them or in their spatial location. These results suggest that farmers' management has globally preserved sorghum genetic diversity in Niger.
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Affiliation(s)
- Monique Deu
- CIRAD, UMR DAP, Avenue Agropolis, TA-A 96/03, 34398, Montpellier, France.
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10
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Deu M, Sagnard F, Chantereau J, Calatayud C, Hérault D, Mariac C, Pham JL, Vigouroux Y, Kapran I, Traore PS, Mamadou A, Gerard B, Ndjeunga J, Bezançon G. Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers. Theor Appl Genet 2008; 116:903-13. [PMID: 18273600 DOI: 10.1007/s00122-008-0721-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Accepted: 01/23/2008] [Indexed: 05/08/2023]
Abstract
Understanding the geographical, environmental and social patterns of genetic diversity on different spatial scales is key to the sustainable in situ management of genetic resources. However, few surveys have been conducted on crop genetic diversity using exhaustive in situ germplasm collections on a country scale and such data are missing for sorghum in sub-Saharan Africa, its centre of origin. We report here a genetic analysis of 484 sorghum varieties collected in 79 villages evenly distributed across Niger, using 28 microsatellite markers. We found a high level of SSR diversity in Niger. Diversity varied between eastern and western Niger, and allelic richness was lower in the eastern part of the country. Genetic differentiation between botanical races was the first structuring factor (Fst = 0.19), but the geographical distribution and the ethnic group to which farmers belonged were also significantly associated with genetic diversity partitioning. Gene pools are poorly differentiated among climatic zones. The geographical situation of Niger, where typical western African (guinea), central African (caudatum) and eastern Sahelian African (durra) sorghum races converge, explained the high observed genetic diversity and was responsible for the interactions among the ethnic, geographical and botanical structure revealed in our study. After correcting for the structure of botanical races, spatial correlation of genetic diversity was still detected within 100 km, which may hint at limited seed exchanges between farmers. Sorghum domestication history, in relation to the spatial organisation of human societies, is therefore key information for sorghum in situ conservation programs in sub-Saharan Africa.
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Affiliation(s)
- M Deu
- CIRAD, UMR DAP, Avenue Agropolis, TA A 96/03, 34398 Montpellier, France.
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11
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Scarcelli N, Tostain S, Vigouroux Y, Agbangla C, Daïnou O, Pham JL. Farmers' use of wild relative and sexual reproduction in a vegetatively propagated crop. The case of yam in Benin. Mol Ecol 2006; 15:2421-31. [PMID: 16842416 DOI: 10.1111/j.1365-294x.2006.02958.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The impact of traditional farmers' management on genetic diversity of vegetatively propagated crops is poorly documented. In this study, we analysed the impact of ennoblement of spontaneous yams, an original traditional farmers' practice, on the genetic diversity of yam (Dioscorea sp.) in Benin. We used 11 microsatellite markers on yam tubers from a small village in northern Benin and demonstrated that wild x cultivated hybrids are spontaneously formed. Many of the spontaneous yams collected by farmers from surrounding savannah areas for ennoblement were shown to be of wild and hybrid genotypes. Moreover, we demonstrated that some yam varieties have a wild or hybrid signature. Lastly, we performed a broader ranging genetic analysis on yam material from throughout Benin and showed that this practice is used in different ecological and ethno-linguistic regions. Through this practice, farmers create new varieties with new genetic combinations via sexual reproduction of wild and cultivated yams. This system, whereby a sexual cycle and asexual propagation are mixed, ensures potential large-scale cultivation of the best genotypes while preserving the potential for future adaptation.
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Affiliation(s)
- N Scarcelli
- Equipe DYNADIV, UMR 1097 Diversité et Génomes des Plantes Cultivées, Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier cedex 5, France.
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12
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Abstract
Formulae were derived for the genetic differentiation between populations within a metapopulation (F(SM)), and between metapopulations (F(MT)) as functions of migration and mutation rates, size and number of populations and metapopulations. We show that F(MT) = 1 divided by (1+4 N(e)m), where N(e) is the effective size of a metapopulation, and where the migration rate between metapopulations is m. The formulae for F(MT) and F(SM) were more general than previously proposed since we have relaxed some previously made hypotheses and we included the effect of the mutation rate. Using our formula, some unexpected result of estimation of gene flow, previously obtained, can be explained readily.
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Affiliation(s)
- Y Vigouroux
- Unité de malherbologie et d'agronomie, Institut national de la recherche agronomique, BV 1540, 17 rue Sully, 21000 Dijon, France.
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13
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Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci U S A 2002; 99:9650-5. [PMID: 12105270 PMCID: PMC124964 DOI: 10.1073/pnas.112324299] [Citation(s) in RCA: 224] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2002] [Accepted: 05/29/2002] [Indexed: 11/18/2022] Open
Abstract
Crop species experienced strong selective pressure directed at genes controlling traits of agronomic importance during their domestication and subsequent episodes of selective breeding. Consequently, these genes are expected to exhibit the signature of selection. We screened 501 maize genes for the signature of selection using microsatellites or simple sequence repeats (SSRs). We applied the Ewens-Watterson test, which can reveal deviations from a neutral-equilibrium model, as well as two nonequilibrium tests that incorporate the domestication bottleneck. We investigated two classes of SSRs: those known to be polymorphic in maize (Class I) and those previously classified as monomorphic in maize (Class II). Fifteen SSRs exhibited some evidence for selection in maize and 10 showed evidence under stringent criteria. The genes containing nonneutral SSRs are candidates for agronomically important genes. Because demographic factors can bias our tests, further independent tests of these candidates are necessary. We applied such an additional test to one candidate, which encodes a MADS box transcriptional regulator, and confirmed that this gene experienced a selective sweep during maize domestication. Genomic scans for the signature of selection offer a means of identifying new genes of agronomic importance even when gene function and the phenotype of interest are unknown.
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Affiliation(s)
- Y Vigouroux
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
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14
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Naciri Y, Vigouroux Y, Dallas J, Desmarais E, Delsert C, Bonhomme F. Identification and inheritance of (GA/TC)n and (AC/GT)n repeats in the European flat oyster Ostrea edulis (L.). Mol Mar Biol Biotechnol 1995; 4:83-9. [PMID: 7749469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Twelve microsatellites were isolated from a partial genomic library of Ostrea edulis using (GA/TC)n and (AC/GT)n probes and were subsequently sequenced. We estimate that, on average, 12,700 (GA/TC)n and 3900 (AC/GT)n microsatellites could be found in the genome assuming a random distribution. These estimates are high enough for the construction of a saturated genetic map. Primers were designed for three microsatellite loci, and analyses of polymorphism in a wild cohort revealed that one was suitable for population genetics studies (5 alleles), while the other two were highly polymorphic (between 17 and 48 alleles) and thus were more useful for paternity testing. Mendelian inheritance was tested on two full-sib families, and significant distortions of genotypic frequencies were found, although the gametic distributions seemed to be in agreement with Mendelian expectations. We interpret this as evidence for zygotic selection.
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Affiliation(s)
- Y Naciri
- IFREMER Unité de Recherche en Génétique et Ecloserie, La Tremblade, France
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15
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Corpet DE, Bellier R, Petrowitsch S, Vigouroux Y. Digestion and fermentation of proteins in rats fed keratin, albumin, cooked casein and antibiotics. Reprod Nutr Dev 1994; 34:57-64. [PMID: 7510493 DOI: 10.1051/rnd:19940106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Dietary cooked casein promotes colon cancer in rats. We speculated and tested the hypothesis that cooking reduces the digestibility of casein, and increases the yield of bacterial metabolites, which are potential promoters of cancer. We investigated dietary means to manipulate nitrogen transfer and fermentation in the caecum. The caecal digestion of casein (cooked or not), keratin (hydrolysed or not) and bovine serum albumin (oxidized or not) was measured in rats. Protein fermentation was estimated by assaying caecal ammonia and branched-chain fatty acids. Keratin and cooked casein were digested to a very low extent, and were poorly fermented. Rats given cooked casein had 2-3 times more ammonia in their caecum than animals given the other proteins. Antibiotics (bacitracin, chlortetracycline, neomycin and spiramycin, at either 20 and 80 micrograms/ml water) decreased caecal ammonia in rats eating cooked casein, with spiramycin being most efficient. These data support the hypothesis given above, and provide ways to manipulate caecal ammonia.
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Affiliation(s)
- D E Corpet
- Ecole Nationale Vétérinaire, Toulouse, France
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