Search

Your search keyword '"Philippe Cubry"' showing total 12 results
Start Over Author "Philippe Cubry" Topic 03 medical and health sciences
12 results on '"Philippe Cubry"'

1. Genetic diversity and population structure in Vitis species illustrate phylogeographic patterns in eastern North America

Author

Elisa Peressotti, Andrew Michael Walker, Patrice This, Philippe Cubry, Amandine Launay, Jean-Michel Boursiquot, Didier Merdinoglu, Emilce Prado, Valérie Laucou, Agnes Doligez, Jean-Pierre Péros, Peter Cousins, Sabine Wiedemann-Merdinoglu, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), E&J Gallo Winery, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of California [Davis] (UC Davis), University of California, Santé de la vigne et qualité du vin (SVQV), Université de Strasbourg (UNISTRA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-08-GENM-0002,DLVitis,Structure génétique et déséquilibre de liaison chez 3 espèces du genre Vitis(2008)

Subjects
0106 biological sciences, 0301 basic medicine, Range (biology), Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genus, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Vitis, wine.grape_variety, Phylogeny, Ecology, Evolution, Behavior and Systematics, Genetic diversity, Vitis aestivalis, Resistance (ecology), Ecology, Genetic Variation, 15. Life on land, Texas, Phylogeography, 030104 developmental biology, Oomycetes, Genetic structure, wine, Biological dispersal
Abstract

Geographical distribution and diversity of current plant species have been strongly shaped by climatic oscillations during the Quaternary. Analysing the resulting divergence among species and differentiation within species is crucial to understand the evolution of taxa like the Vitis genus, which provides very useful genetic resources for grapevine improvement and might reveal original recolonization patterns due to growth habit and dispersal mode. Here, we studied the genetic structure in natural populations of three species from eastern North America: Vitis aestivalis, V. cinerea and V. riparia using different marker types. Vitis aestivalis and V. cinerea showed higher diversity than V. riparia. The two former species are less differentiated, confirming an earlier divergence of V. riparia. V. aestivalis and V. riparia exhibited different genetic groups on both sides of the Appalachian Mountains that could mirror different recolonization routes from southern refugia. Genetic structure was stronger in V. cinerea, for which two varieties (var. berlandieri and var. cinerea) are morphologically recognized. Our results confirm this distinction and suggest the existence of three other lineages within var. cinerea. These discontinuities appear linked to adaptation of var. berlandieri to dry and limy areas of Texas and partially to the Mississippi River Valley. Rapid range expansions from refugia upon climate warming are also suggested by the low linkage disequilibrium values observed. Furthermore, large variation for downy mildew resistance was observed in the three species. Our findings appeared consistent with the vegetation history of eastern North America.

Published
2021

2. Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

Author

Christine Tranchant-Dubreuil, Maria Holzinger, Yves Vigouroux, Stefan Jouannic, Hélène Adam, Alain Ghesquière, Philippe Cubry, Kim Nhung Ta, Olivier François, François Sabot, Honoré Kam, Anne-Céline Thuillet, Harold Chrestin, Hélène Pidon, Laurence Albar, and Université Grenoble Alpes (UGA)

Subjects
0106 biological sciences, Candidate gene, RYMV, Flowering time, Rice yellow mottle virus, Climate variation, Quantitative trait locus, Oryza glaberrima, lcsh:Plant culture, 01 natural sciences, Genome, 03 medical and health sciences, lcsh:SB1-1110, Domestication, 030304 developmental biology, Panicle, 2. Zero hunger, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, food and beverages, 15. Life on land, biology.organism_classification, Panicle architecture, Evolutionary biology, Original Article, Adaptation, Genome wide association study, African rice, 010606 plant biology & botany
Abstract

BackgroundAfrican rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species.ResultsUsing a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we demonstrated that we could successfully retrieve known genes from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting QTLs and candidate genes (including Rymv1 for resistance and SP1, Ghd7.1, APO1 and OsMADS1 for panicle architecture). Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations.ConclusionOur results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.

Published
2020

3. New insights on spatial genetic structure and diversity of Coffea canephora (Rubiaceae) in Upper Guinea based on old herbaria

Author

Jean-Pierre Labouisse, Ronan Rivallan, Philippe Cubry, Hong Anh Nguyen, Frédéric Austerlitz, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche pour le Développement (IRD), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), H.A. Nguyen’s scholarship was supported by a grant from the CULTIVAR project funded by Agropolis Fondation (ID 1504-007) through the Investissements d’Avenir program (Labex Agro:ANR-10-LABX-0001-01) under the frame of I-SITE MUSE (ANR-16-IDEX-0006), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), ANR-16-IDEX-0006,MUSE,MUSE(2016), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Éco-Anthropologie (EAE), H.A. Nguyen's scholarship was supported by a grant from the CULTIVAR project funded by Agrop-d'Avenir program (Labex Agro ANR-10-LABX-001-01) under the frame of I-SITE MUSE (ANR-16-IDEX-0006)., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, 0301 basic medicine, Germplasm, Rubiaceae, Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, F30 - Génétique et amélioration des plantes, Génétique des populations, population genetic structure, herbarium, Herbier, population genetic, SSR markers, education.field_of_study, robusta coffee, genetic diversity, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Guinea herbarium, Genetic structure, Distribution géographique, Canephora, Population, Zoology, Biology, Coffea canephora, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Variation génétique, structure, education, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], West African forest, 15. Life on land, biology.organism_classification, Cote d'Ivoire, 030104 developmental biology, Herbarium, Guinea, 010606 plant biology & botany
Abstract

International audience; Backgrounds and aims - Previous studies showed that robusta coffee (Coffea canephora Pierre ex A.Froehner), one of the two cultivated coffee species worldwide, can be classified in two genetic groups: the Guinean group originating in Upper Guinea and the Congolese group in Lower Guinea and Congolia. Although C. canephora of the Guinean group is an important resource for genetic improvement of robusta coffee, its germplasm is under-represented in ex situ gene banks and its genetic diversity and population structure have not yet been investigated.Methods - To overcome the limitations of living collections, we explored old herbarium specimens collected in Guinea and Cote d'Ivoire and conserved at the Museum National d'Histoire Naturelle, Paris. First, we reviewed the history of collection missions in both countries and how the C. canephora herbaria from the Museum were assembled. Then, using 23 nuclear microsatellite markers, factorial and model-based Bayesian analyses, we investigated the genetic diversity of 126 specimens and 36 controls, analysed their distribution among the Congolese and Guinean groups, and estimated admixture proportions for each individual.Key results - For the first time, we detected population genetic structure within the Guinean group of C. canephora. The Guinean genotypes can be assigned to five sub-groups with distinct geographic distribution especially in Guinea where two sub-groups (Maclaudii and Game) are characterized by a low level of admixture due to geographical isolation.Conclusions - We showed how combining a literature review and genetic data from old herbarium specimens can shed light on previous observations made by botanists and guide further actions to better preserve native coffee plants in forest remnants of West Africa.

Published
2020

4. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Author

Ndjido Ardo Kane, Yves Vigouroux, Denisa Šimoníková, Leila Zekraoui, Jaroslav Dolezel, Nagarajan Kathiresan, Sandrine Causse, Michael Abrouk, Thomas Wicker, Sandrine Arribat, Claire Billot, Stéphane Cauet, Simon G. Krattinger, Jana Cizkova, Sylvie Vancoppenolle, Adeline Barnaud, E. Hribova, Hélène Bergès, Philippe Cubry, Jan Bettgenhaeuser, Mathieu Gueye, Hanin Ibrahim Ahmed, Liubov Gapa, Nora Scarcelli, Yveline Pailles, Jan J. Wieringa, Christian Leclerc, Marie Couderc, University of Zurich, Barnaud, Adeline, Krattinger, Simon G, King Abdullah University of Science and Technology (KAUST), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Naturalis Biodiversity Center [Leiden], Institut Fondamental d'Afrique Noire (IFAN), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Senegalese Agricultural Research Institute, LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE), Institut de Recherche pour le Développement (IRD), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universität Zürich [Zürich] = University of Zurich (UZH), European Regional Development Fund OPVVV project 'Plants as a tool for sustainable development' CZ.02.1.01/0.0/0.0/16_019/0000827, ANR-16-IDEX-0006,MUSE,MUSE(2016), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Digitaria, General Physics and Astronomy, 580 Plants (Botany), 01 natural sciences, Plant breeding, F30 - Génétique et amélioration des plantes, Domestication, 0302 clinical medicine, 10126 Department of Plant and Microbial Biology, lcsh:Science, 2. Zero hunger, Molecular breeding, 0303 health sciences, Multidisciplinary, Diversité génétique (comme ressource), Agroforestry, Domestication des plantes, phytogénétique, food and beverages, Agriculture, 3100 General Physics and Astronomy, Genome, Plant, Agricultural genetics, Plant domestication, Science, Climate Change, Context (language use), 1600 General Chemistry, Genetics and Molecular Biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, génomique, Evolution, Molecular, 03 medical and health sciences, Ressource génétique végétale, Variation génétique, Species Specificity, 1300 General Biochemistry, Genetics and Molecular Biology, 10211 Zurich-Basel Plant Science Center, Selection, Genetic, 030304 developmental biology, Changement climatique, Genetic diversity, business.industry, Genetic Variation, Molecular Sequence Annotation, Digitaria exilis, General Chemistry, 15. Life on land, biology.organism_classification, Amélioration des plantes, 030104 developmental biology, Crop diversity, 13. Climate action, General Biochemistry, Africa, lcsh:Q, business, Edible Grain, 030217 neurology & neurosurgery, 010606 plant biology & botany
Abstract

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments., Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.

Published
2020

5. Coalescent Models of Demographic History: Application to Plant Domestication

Author

Olivier François, Concetta Burgarella, Philippe Cubry, Yves Vigouroux, Université Grenoble Alpes (UGA), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Biologie Computationnelle et Modélisation (TIMC-BCM ), and Université Grenoble Alpes (UGA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )

Subjects
0106 biological sciences, 2. Zero hunger, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Range (biology), Demographic history, food and beverages, Inference, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, Field (geography), Coalescent theory, 03 medical and health sciences, Evolutionary biology, Approximate Bayesian computation, Domestication, ComputingMilieux_MISCELLANEOUS, Selection (genetic algorithm), 030304 developmental biology
Abstract

A detailed understanding of the origins of domesticated species is important for many disciplines. Recent advances in this field have been made with the use of genome-wide polymorphisms and improved statistical methods. In this chapter, we review the most important developments of coalescent models for the inference of demographic history from genome-wide data. These methods include sequential Markovian models, range expansion models, and approximate Bayesian computation. We summarize the applications of the methods to some major cultivated cereals, including rice, maize, and millet. Then we discuss extensions of these methods that would better incorporate the interaction of demographic processes with selection and inclusion of gene flow with wild related species.

Published
2020

6. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Author

Jun Wang, Katrien M. Devos, Jianping Wang, Andrew H. Paterson, Cédric Mariac, Xinming Liang, Wenbin Chen, Dadakhalandar Doddamani, Sunil Gupta, Om Parkash Yadav, Rattan Yadav, Eric Lyons, Rajeev K. Varshney, Arindam Ghatak, Wolfram Weckwerth, C. Tom Hash, He Zhang, Mame Codou Gueye, Dev Paudel, Abhishek Rathore, Palak Chaturvedi, R. S. Mahala, Christian Dupuy, Xun Xu, Jeffrey L. Bennetzen, Guangyi Fan, Swapan K. Datta, Yusheng Zhao, Somashekhar Punnuri, Annapurna Chitikineni, Ndjido Ardo Kane, Mohan A. V. S. K. Katta, Falalou Hamidou, Francesca Sparvoli, Jason G. Wallace, Mahendar Thudi, Edward S. Buckler, Joann A. Conner, Prasad Bajaj, Xiyin Wang, Ramanjulu Sunkar, Peggy Ozias-Akins, Marie Couderc, Bharat P. Singh, Trilochan Mohapatra, Stefania Grando, Xin Liu, Bénédicte Rhoné, Vanika Garg, K. D. Mungra, Hari D. Upadhyaya, Chengcheng Shi, Peng Qi, Philippe Cubry, Yong Jiang, Hao Wang, Karen R. Harris-Shultz, Sabarinath Subramaniam, Yves Vigouroux, Jérémy Clotault, Cécile Berthouly-Salazar, Shifeng Cheng, Jochen C. Reif, Neetin Desai, Rakesh K. Srivastava, Institut des Mondes Africains (IMAF), Université Paris 1 Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), ANR-13-BSV7-0017,AfriCrop,Etude de l'histoire évolutive des plantes domestiquées africaines(2013), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Numerical modeling and high performance computing for evolution problems in complex domains and heterogeneous media (NACHOS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Alexandre Dieudonné (JAD), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Unité de Mécanique (UME), École Nationale Supérieure de Techniques Avancées (ENSTA Paris), State Key Laboratory of Fine Chemicals, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Alexandre Dieudonné (LJAD), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, genome sequence, [SDV]Life Sciences [q-bio], adaptation, Applied Microbiology and Biotechnology, hybridism, Conserved Sequence, 2. Zero hunger, Agriculture, Staple food, genetic diversity, Genomics, hybridations, Phenotype, diversité génétique, pennisetum glaucum, Molecular Medicine, Desert Climate, pearl millet, Genome, Plant, Biotechnology, Agricultural genetics, Pennisetum, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Drought tolerance, Biomedical Engineering, Bioengineering, Biology, Genes, Plant, milieu aride, Article, domestication, 03 medical and health sciences, Quantitative Trait, Heritable, Mil (Cenchrus americanus), Genetic variation, Plant breeding, Domestication, Millet (Cenchrus americanus), Genetic diversity, Base Sequence, Genetic Variation, Molecular Sequence Annotation, 15. Life on land, Arid, arid environment, Plant Breeding, 030104 developmental biology, Agronomy, Next-generation sequencing, Hybridization, Genetic, Genome-Wide Association Study
Abstract

Draft genome, 994 re-sequenced lines and GWAS for yield-traits provide a resource of genetics and genomics tools for pearl millet researchers and breeders. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users., Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users.

Published
2017

7. Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

Author

Wei Yang, Dawen Xu, Chellapilla Bharadwaj, David Edwards, Lakshmanan Krishnamurthy, Kadambot H. M. Siddique, Rajeev K. Varshney, Jun Wang, Paul Kimurto, Yves Vigouroux, Vanika Garg, Henry T. Nguyen, Prasad Bajaj, Tim Sutton, Mahendar Thudi, Aamir W. Khan, Timothy D. Colmer, José Crossa, Kavi Kishor B. Polavarapu, Annapurna Chitikineni, Eric von Wettberg, Hari D. Upadhyaya, Philippe Cubry, G. P. Dixit, Suk-Ha Lee, R. Varma Penmetsa, Asnake Fikre, Sheshshayee M. Sreeman, Xin Liu, Sushil K. Chaturvedi, Dadakhalandar Doddamani, Abhishek Rathore, Xun Xu, Manish Roorkiwal, Pooran M. Gaur, Weiming He, Jianbo Jian, Shailesh Tripathi, Gangarao V. P. R. Nadigatla, Narendra Singh, International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Beijing Genomics Institute [Shenzhen] (BGI), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), The University of Western Australia (UWA), Osmania University, Indian Council of Agricultural Research (ICAR), Egerton University, Seoul National University [Seoul] (SNU), University of California [Davis] (UC Davis), University of California, International Maize and Wheat Improvement Center (CIMMYT), University of Missouri [Columbia] (Mizzou), University of Missouri System, University of South Australia [Adelaide], University of Vermont [Burlington], and R.K.V. acknowledges the funding support from CGIAR Generation Challenge Programme, Department of Science and Technology Government of India under the Australia-India Strategic Research Fund, Ministry of Agriculture and Farmers Welfare, Government of India and Bill & Melinda Gates Foundation, USA. Shenzhen Municipal Government of China (grant no. JCYJ20150831201643396 and no. JCYJ20170817145512476 under the Basic Research Program) and the Guangdong Provincial Key Laboratory of Genome Read and Write (grant no. 2017B030301011) are acknowledged to provide support to X.X. and X.L. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals.

Subjects
Germplasm, Candidate gene, Hight-throughput sequencing, DNA, Plant, Quantitative Trait Loci, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Linkage Disequilibrium, Plant breeding, Domestication, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Population genomics, 03 medical and health sciences, 0302 clinical medicine, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genetic variation, Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Genetic diversity, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Cicer, Center of origin, Evolutionary biology, Genetic markers, Genome-wide Association Studies, Genome, Plant, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

International audience; We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.

Published
2019

8. The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes

Author

Bénédicte Rhoné, Patrick Wincker, Christine Tranchant-Dubreuil, Yves Vigouroux, Pierre Larmande, Christian Dupuy, Philippe Cubry, François Sabot, Karine Labadie, Nora Scarcelli, Concetta Burgarella, Anne-Céline Thuillet, Stefan Engelen, Olivier François, Cécile Monat, Marie-Noelle Ndjiondjop, Corinne Cruaud, Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre d'Etudes des Mondes Africains (CEMAf), Université Paris 1 Panthéon-Sorbonne (UP1)-Université de Provence - Aix-Marseille 1-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Paris 1 Panthéon-Sorbonne (UP1)-Université de Provence - Aix-Marseille 1-École Pratique des Hautes Études (EPHE), ANR-13-BSV7-0017,AfriCrop,Etude de l'histoire évolutive des plantes domestiquées africaines(2013), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Université Panthéon-Sorbonne (UP1)-Université de Provence - Aix-Marseille 1-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, 0301 basic medicine, Crops, Agricultural, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Oryza barthii, Climate Change, [SDV]Life Sciences [q-bio], Population, Population Dynamics, Middle Niger Valley, Biology, Oryza glaberrima, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Population genomics, Crop, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, domestication, moyenne vallée du Niger, Domestication, education, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, education.field_of_study, Oryza sativa, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, business.industry, food and beverages, protohistoire, Oryza, protohistory, 15. Life on land, biology.organism_classification, Phylogénétique, Phylogenetics, 030104 developmental biology, Agriculture, Africa, General Agricultural and Biological Sciences, business, Genome, Plant, riz africain (Oryza glaberrima), 010606 plant biology & botany, African rice (Oryza glaberrima)
Abstract

International audience; African rice (Oryza glaberrima) was domesticated independently from Asian rice. The geographical origin of its domestication remains elusive. Using 246 new whole-genome sequences, we inferred the cradle of its domestication to be in the Inner Niger Delta. Domestication was preceded by a sharp decline of most wild populations that started more than 10.000 years ago. The wild population collapse occurred during the drying of the Sahara. This finding supports the hypothesis that depletion of wild resources in the Sahara triggered African rice domestication. African rice cultivation strongly expanded 2.000 years ago. During the last five centuries, a sharp decline of its cultivation coincided with the introduction of Asian rice in Africa. The gene PROG1 associated with an erect plant architecture phenotype, showed convergent selection in two rice cultivated species, Oryza glaberrima from Africa and Oryza sativa from Asia. In contrast, the shattering gene SH5 showed selection signature during African rice domestication, but not during Asian rice domestication. Overall, our genomic data reveal a complex history of African rice domestication influenced by important climatic changes in the Saharan area, by the expansion of African agricultural society, and by recent replacement by another domesticated species.; Le riz africain (Oryza glaberrima) a été domestiqué indépendamment du riz asiatique. L'origine géographique de sa domestication restait obscure. En utilisant 246 nouvelles séquences du génome complet, nous avons déduit que le berceau de sa domestication se trouvait dans le delta intérieur du Niger. Sa domestication a été précédée d'un fort déclin de la plupart des populations sauvages qui s’est amorcé il y a plus de 10.000 ans. L'effondrement des populations sauvages s'est produit pendant l'assèchement du Sahara. Cette découverte confirme l'hypothèse selon laquelle l'épuisement des ressources sauvages dans le Sahara a déclenché la domestication du riz africain. La culture du riz en Afrique s'est fortement développée il y a 2.000 ans. Au cours des cinq derniers siècles, le fort déclin de sa culture a coïncidé avec l'introduction du riz asiatique en Afrique. Le gène PROG1 associé à un phénotype d'architecture végétale érigée, a montré une sélection convergente pour deux espèces de riz cultivées, à savoir pour Oryza glaberrima d'Afrique et Oryza sativa d'Asie. En revanche, le gène d'éclatement SH5 a montré une signature de sélection pendant la domestication du riz africain, mais pas pendant la domestication du riz asiatique. Pour résumer, nos données génomiques révèlent une histoire complexe de la domestication du riz africain, influencée par les importants changements climatiques qu’a connu le Sahara, par une expansion des pratiques agricoles africaines, puis par le remplacement de cette céréale autochtone par des espèces domestiquées en Asie.

Published
2018

9. Population Genomics of Crop Domestication: Current State and Perspectives

Author

Philippe Cubry and Yves Vigouroux

Subjects
0106 biological sciences, 0301 basic medicine, media_common.quotation_subject, food and beverages, Genomics, 01 natural sciences, Data science, Crop, Population genomics, 03 medical and health sciences, 030104 developmental biology, Ancient DNA, Geography, State (polity), Domestication, 010606 plant biology & botany, media_common
Abstract

Genomics has enabled access to unprecedented amounts of genomic and transcriptomic data. Studies of crop domestication have benefited from these datasets for deeper insights into when, where, and how crops were domesticated. Although genomics makes it possible to answer such questions, it also creates new technical and methodological challenges. Such large genomic and transcriptomic datasets provide the opportunity to advance from descriptive to hypothesis testing studies. Several model-based methods are now available to test hypotheses and to trace the history of crops. Studies of gene expression and of ancient DNA are new very active fields which hold great promise. Here, we review some key questions concerning crop domestication and discuss how genomics can help answer these questions and what interesting new approaches could be used in the future. As genomics data continue to become available, domestication studies will advance our knowledge not only of well-known domestication models, such as rice and maize, but also of other currently less widely studied crops. We will then be able to test general hypotheses associated with domestication across species.

Published
2018

10. Generalization of the QST framework in hierarchically structured populations: Impacts of inbreeding and dominance

Author

Sylvie Oddou-Muratorio, Ivan Scotti, François Lefèvre, Philippe Cubry, Ecologie des Forêts Méditerranéennes [Avignon] (URFM 629), Institut National de la Recherche Agronomique (INRA), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), ANR-12-ADAP-0007- 01 FLAG, Ecologie des Forêts Méditerranéennes (URFM), This work was supported by Agence Nationale de la Recherche (ANR) under the FLAG project ANR-12-ADAP-0007., and ANR-12-ADAP-0007,FLAG,Génétique écologique des arbres forestiers : interactions entre flux de gènes et variabilité environnementale dans la détermination de l'adaptation locale et du potentiel d'adaptation(2012)

Subjects
0301 basic medicine, quantitative genetics, [SDV]Life Sciences [q-bio], hierarchical F-statistics, Biology, différenciation génétique, 03 medical and health sciences, quantitative, Genetic variation, Statistics, genetics, variance génétique, 10. No inequality, Ecology, Evolution, Behavior and Systematics, filtrage statistique, Dominance (genetics), Ecology, Quantitative genetics, hierarchical Q-statistics, Genetic differentiation, genêtic differentiation, 030104 developmental biology, Trait, Inbreeding, Biotechnology
Abstract

Q(ST) is a differentiation parameter based on the decomposition of the genetic variance of a trait. In the case of additive inheritance and absence of selection, it is analogous to the genic differentiation measured on individual loci, F(ST). Thus, Q(ST)−F(ST) comparison is used to infer selection: selective divergence when Q(ST) > F(ST), or convergence when Q(ST) < F(ST). The definition of Q-statistics was extended to two-level hierarchical population structures with Hardy–Weinberg equilibrium. Here, we generalize the Q-statistics framework to any hierarchical population structure. First, we developed the analytical definition of hierarchical Q-statistics for populations not at Hardy–Weinberg equilibrium. We show that the Q-statistics values obtained with the Hardy–Weinberg definition are lower than their corresponding F-statistics when F(IS) > 0 (higher when FIS < 0). Then, we used an island model simulation approach to investigate the impact of inbreeding and dominance on the Q(ST)−F(ST) framework in a hierarchical population structure. We show that, while differentiation at the lower hierarchical level (Q(SR)) is a monotonic function of migration, differentiation at the upper level (Q(RT)) is not. In the case of additive inheritance, we show that inbreeding inflates the variance of Q(RT), which can increase the frequency of Q(RT) > F(RT) cases. We also show that dominance drastically reduces Q-statistics below F-statistics for any level of the hierarchy. Therefore, high values of Q-statistics are good indicators of selection, but low values are not in the case of dominance.

Published
2017

11. Development and characterization of a new set of 164 polymorphic EST-SSR markers for diversity and breeding studies in rubber tree (Hevea brasiliensisMüll. Arg.)

Author

Valérie Pujade-Renaud, Sandra Espeout, Marc Seguin, Françoise Granet, Dominique Garcia, Vincent Le Guen, Philippe Cubry, Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Laboratoire de Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Société Michelin, 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, Résistance génétique, Polymorphisme génétique, Microcyclus ulei, rflp, Population genetics, Plant Science, 01 natural sciences, Genome, microsatellites, F30 - Génétique et amélioration des plantes, Genotype, wild, hevea, 2. Zero hunger, Genetics, 0303 health sciences, Vegetal Biology, biology, plants, Dendrogram, food and beverages, genetic-linkage map, Hevea brasiliensis, EST-SSR, rubber tree, Hevea spp, microsatellite markers, disequilibrium, association, populations, sequences, Microsatellite, Restriction fragment length polymorphism, Génotype, microsatellite, Séquence nucléotidique, Plant disease resistance, arbre à caoutchouc, 03 medical and health sciences, Variation génétique, Bioinformatique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, H20 - Maladies des plantes, 030304 developmental biology, Génie génétique, Biologie moléculaire, Résistance aux maladies, biology.organism_classification, Amélioration des plantes, U30 - Méthodes de recherche, Agronomy and Crop Science, Biologie végétale, 010606 plant biology & botany
Abstract

Plant Breed.ISI Document Delivery No.: AJ4WPTimes Cited: 0Cited Reference Count: 31Cited References: Argout X, 2008, BMC GENOMICS, V9, DOI 10.1186/1471-2164-9-512 BESSE P, 1994, THEOR APPL GENET, V88, P199, DOI 10.1007/BF00225898 Conesa A, 2005, BIOINFORMATICS, V21, P3674, DOI 10.1093/bioinformatics/bti610 Cubry P, 2013, BMC GENOMICS, V14, DOI 10.1186/1471-2164-14-10 Ellis JR, 2007, HEREDITY, V99, P125, DOI 10.1038/sj.hdy.6801001 Feng SP, 2009, MOL BREEDING, V23, P85, DOI 10.1007/s11032-008-9216-0 Garcia D, 2011, PHYSIOL MOL PLANT P, V76, P126, DOI 10.1016/j.pmpp.2011.07.006 Gupta PK, 2005, PLANT MOL BIOL, V57, P461, DOI 10.1007/s11103-005-0257-z Gupta S, 2013, PLANT BREEDING, V132, P367, DOI 10.1111/pbr.12070 Kumar Yadav H., 2010, TREE GENET GENOMES, V7, P207 Le Guen V., 2008, EXPLORATION DIVERSIT Le Guen V, 2011, PLANT BREEDING, V130, P294, DOI 10.1111/j.1439-0523.2010.01774.x Le Guen V, 2009, TREE GENET GENOMES, V5, P673, DOI 10.1007/s11295-009-0218-9 Lespinasse D, 2000, THEOR APPL GENET, V100, P127, DOI 10.1007/s001220050018 Li DJ, 2012, BMC GENOMICS, V13, DOI 10.1186/1471-2164-13-192 Liu KJ, 2005, BIOINFORMATICS, V21, P2128, DOI 10.1093/bioinformatics/bti282 Ohyama A, 2009, MOL BREEDING, V23, P685, DOI 10.1007/s11032-009-9265-z Perovic D, 2009, MOL BREEDING, V23, P641, DOI 10.1007/s11032-009-9262-2 Perrier Xavier, 2003, P31 Perrier X., 2006, DARWIN SOFTWARE Pootakham W, 2012, PLANT BREEDING, V131, P555, DOI 10.1111/j.1439-0523.2012.01982.x Rafalski JA, 2010, CURR OPIN PLANT BIOL, V13, P174, DOI 10.1016/j.pbi.2009.12.004 Rozen S, 2000, Methods Mol Biol, V132, P365 SAITOU N, 1987, MOL BIOL EVOL, V4, P406 Seguin Marc, 2003, P277 Souza LM, 2009, CONSERV GENET RESOUR, V1, P75, DOI 10.1007/s12686-009-9018-7 Triwitayakorn K, 2011, DNA RES, V18, P471, DOI 10.1093/dnares/dsr034 Tyrka M, 2008, J APPL GENET, V49, P127, DOI 10.1007/BF03195605 Varshney RK, 2005, TRENDS BIOTECHNOL, V23, P48, DOI 10.1016/j.tibtech.2004.11.005 Vigouroux Y, 2005, GENETICS, V169, P1617, DOI 10.1534/genetics.104.032086 Wen Mingfu, 2010, BMC Res Notes, V3, P42, DOI 10.1186/1756-0500-3-42Cubry, Philippe Pujade-Renaud, Valerie Garcia, Dominique Espeout, Sandra Le Guen, Vincent Granet, Francoise Seguin, MarcFrench National Research Agency (Agence Nationale pour la Recherche; contrat ANR/Genoplante) [GPLA07017C]This work was performed as part of the CIRAD - Michelin collaborative project 'Genesalb' supported by a grant from the French National Research Agency (Agence Nationale pour la Recherche; contrat ANR/Genoplante no GPLA07017C). We thank the Montpellier Languedoc-Roussillon Grand plateau technique regional for hosting the SSR genotyping activities. ESTtik database was made available by the SouthGreen bioinformatics platform at http://southgreen.cirad.fr/. We thank Ronan Rivallan for technical help, Xavier Argout for computational procedures and data retrieving, Gerald Oliver for keeping some vegetal material in a greenhouse in Montpellier, Jean-Marc Thevenin and Fabien Doare for providing us with some fresh material from CIRAD's Pointe Combi Centre (French Guyana) collection.Wiley-blackwellHoboken; Despite its economic importance and recent genome release, the need for molecular tools for Hevea brasiliensis is high. In the frame of a disease resistance study, EST sequences were retrieved from public database or generated by sequencing SSH libraries. Sequences were trimmed and microsatellite motifs searched using an ad hoc bioinformatic pipeline, and pairs of primers for the amplification of candidate markers were generated. We found a total of 10499 unigenes from both sources of sequences, and 673 microsatellites motifs were detected using the default parameters of the pipeline. Two hundred sixty-four primer pairs were tested and 226 (85.6%) successfully amplified. Out of the amplified candidate markers, 164 exhibited polymorphism. Relationships based on dendrograms using simple matching index and diversity statistics based on EST-SSRs were compared with Genomic SSRs, showing the potentialities of EST-derived microsatellites for resistance studies but also for population genetics approaches.

Published
2014

12. An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis

Author

Magali Dufour, Komlan Avia, Thierry Leroy, David Pot, Fabien De Bellis, Philippe Cubry, Hyacinthe Legnaté, Sophie Bouchet, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Dept Biol, University of Bergen (UiB), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre National de Recherche Agronomique de Côte d'Ivoire (CNRA), French Grant from the research ministry, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, Linkage disequilibrium, [SDV]Life Sciences [q-bio], MULTILOCUS GENOTYPE DATA, DIVERSITY, Coffea, SOFTWARE, Sélection récurrente, SSR MARKERS, 01 natural sciences, Genetic diversity, F30 - Génétique et amélioration des plantes, Génétique des populations, Genetics, 0303 health sciences, biology, F70 - Taxonomie végétale et phytogéographie, Genomics, Microsatellite, Biotechnology, Research Article, Genetic Markers, Genotype, lcsh:QH426-470, Canephora, lcsh:Biotechnology, Coffea canephora, Africa, Association studies, POPULATION-STRUCTURE, HAPLOTYPE RECONSTRUCTION, ASSOCIATION GENETICS, INFERENCE, MAIZE, GRAPEVINE, 03 medical and health sciences, Variation génétique, lcsh:TP248.13-248.65, Genetic variation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Genetic association, Génome, Genetic Variation, biology.organism_classification, Amélioration des plantes, lcsh:Genetics, Evolutionary biology, 010606 plant biology & botany, Microsatellite Repeats
Abstract

Background A reciprocal recurrent selection program has been under way for the Coffea canephora coffee tree for approximately thirty years in the Ivory Coast. Association genetics would help to speed up this program by more rapidly selecting zones of interest in the genome. However, prior to any such studies, the linkage disequilibrium (LD) needs to be assessed between the markers on the genome. These data are essential for guiding association studies. Results This article describes the first results of an LD assessment in a coffee tree species. Guinean and Congolese breeding populations of C. canephora have been used for this work, with the goal of identifying ways of using these populations in association genetics. We identified changes in the LD along the genome within the different C. canephora diversity groups. In the different diversity groups studied, the LD was variable. Some diversity groups displayed disequilibria over long distances (up to 25 cM), whereas others had disequilibria not exceeding 1 cM. We also discovered a fine structure within the Guinean group. Conclusions Given these results, association studies can be used within the species C. canephora. The coffee recurrent selection scheme being implemented in the Ivory Coast can thus be optimized. Lastly, our results could be used to improve C. arabica because one of its parents is closely related to C. canephora.

Published
2013

Catalog

Books, media, physical & digital resources
See catalog results