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22 results on '"Centre National de la Recherche Appliquée au Développement Rural"'

1. Le potentiel de stockage de carbone du semis direct en comparaison d'autres techniques culturales

Author

Chevallier, T., Metay, A., Arrouays, Dominique, Balesdent, Jérôme, Germon, J Claude, Mary, Bruno, Roger-Estrade, J., Université d'Antananarivo, ., Institut de Recherche Pour Le Développement, ., Fofifa - Centre National de La Recherche Appliquée Au Développement Rural, ., Centre de Coopération Internationale En Recherche Agronomique Pour Le Développement, ., UR SEQBIO, Institut de Recherche pour le Développement (IRD), Ecole Supérieure d’Agro-Développement International (ISTOM), InfoSol (InfoSol), Institut National de la Recherche Agronomique (INRA), Unité de recherche Géochimie des Sols et des Eaux (URGSE), Microbiologie, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Unité de Recherche Agronomie Laon-Reims-Mons (UA LRM), Institut National Agronomique Paris Grignon (INAPG), Université d'Antananarivo, Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], PEDOLOGIE, [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2007

2. Harmonized in situ datasets for agricultural land use mapping and monitoring in tropical countries

Author

A. Jolivot, V. Lebourgeois, L. Leroux, M. Ameline, V. Andriamanga, B. Bellón, M. Castets, A. Crespin-Boucaud, P. Defourny, S. Diaz, M. Dieye, S. Dupuy, R. Ferraz, R. Gaetano, M. Gely, C. Jahel, B. Kabore, C. Lelong, G. le Maire​​​​​​​, D. Lo Seen, M. Muthoni, B. Ndao, T. Newby, C. L. M. de Oliveira Santos, E. Rasoamalala, M. Simoes, I. Thiaw, A. Timmermans, A. Tran, A. Bégué, AUDREY JOLIVOT, CIRAD/TETIS, VALENTINE LEBOURGEOIS, CIRAD/TETIS, LOUISE LEROUX, CIRAD/AIDA/Centre de Suivi Ecologique, MAEL AMELINE, CIRAD/TETIS, VALÉRIE ANDRIAMANGA, CIRAD/Centre National de la Recherche Appliquée au Développement Rural, BEATRIZ BELLÓN, CIRAD/TETIS, MATHIEU CASTETS, CIRAD/TETIS, ARTHUR CRESPIN-BOUCAUD, CIRAD/TETIS, PIERRE DEFOURNY, Université Catholique de Louvain, SANTIANA DIAZ, CIRAD/TETIS, MOHAMADOU DIEYE, Institut Sénégalais de Recherches Agricoles, STÉPHANE DUPUY, CIRAD/TETIS, RODRIGO PECANHA DEMONTE FERRAZ, CNPS, RAFFAELE GAETANO, CIRAD/TETIS, MARIE GELY, CIRAD/TETIS, CAMILLE JAHEL, CIRAD/TETIS, BERTIN KABORE, Independent consultant: Ouagadougou, Burkina Faso, CAMILLE LELONG, CIRAD/TETIS, GUERRIC LE MAIRE, CIRAD/Eco&Sols; DANNY LO SEEN, CIRAD/TETIS, MARTHA MUTHONI, Independent consultant: Nairobi, Kenya, BABACAR NDAO, Centre de Suivi Ecologique/Université Cheikh Anta Diop de Dakar, TERRY NEWBY, Agricultural Research Council, CECÍLIA LIRA MELO DE OLIVEIRA SANTOS, UNICAMP, ELOISE RASOAMALALA, CIRAD/Centre National de la Recherche Appliquée au Développement Rural, MARGARETH GONCALVES SIMOES, CNPS, IBRAHIMA THIAW, Université Cheikh Anta Diop de Dakar, ALICE TIMMERMANS, Université Catholique de Louvain, ANNELISE TRAN, CIRAD/TETIS, AGNÈS BÉGUÉ, CIRAD/TETIS., Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Université Catholique de Louvain = Catholic University of Louvain (UCL), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Embrapa Solos, Ministério da Agricultura, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), Centre de Suivi Ecologique [Dakar] (CSE), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Brazilian Agricultural Research Corporation (Embrapa), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), CNES APR TOSCA projects, SIGMA FP7 grant no. 603719, ESA Sen2Agri grant no. ESRIN 400109979/14/I-AM, CNPq grant nos. 454292/2014-7 and 307560/2016-3, and FAPESP-Microsoft Research grant no. 2014/50715-9, 25 -the SERENA project funded by the CIRAD-INRA metaprogram GloFoodS

Subjects
Environmental sciences, QE1-996.5, Cobertura do Solo, Cropping systems, [SDE]Environmental Sciences, General Earth and Planetary Sciences, GE1-350, Geology, Cropland, Remote sensing, Sistema de Cultivo, Sensoriamento Remoto
Abstract

The availability of crop type reference datasets for satellite image classification is very limited for complex agricultural systems as observed in developing and emerging countries. Indeed, agricultural land use is very dynamic, agricultural censuses are often poorly georeferenced and crop types are difficult to interpret directly from satellite imagery. In this paper, we present a database made of 24 datasets collected in a standardized manner over nine sites within the framework of the international JECAM (Joint Experiment for Crop Assessment and Monitoring) initiative; the sites were spread over seven countries of the tropical belt, and the number of data collection years depended on the site (from 1 to 7 years between 2013 and 2020). These quality-controlled datasets are distinguished by in situ data collected at the field scale by local experts, with precise geographic coordinates, and following a common protocol. Altogether, the datasets completed 27 074 polygons (20 257 crops and 6817 noncrops, ranging from 748 plots in 2013 (one site visited) to 5515 in 2015 (six sites visited)) documented by detailed keywords. These datasets can be used to produce and validate agricultural land use maps in the tropics. They can also be used to assess the performances and robustness of classification methods of cropland and crop types/practices in a large range of tropical farming systems. The dataset is available at https://doi.org/10.18167/DVN1/P7OLAP (Jolivot et al., 2021). Made available in DSpace on 2022-01-06T12:00:36Z (GMT). No. of bitstreams: 1 Harmonized-in-situ-datasets-for-agricultural-land-use-2021.pdf: 1589665 bytes, checksum: d254577e188593e533093fe816e3fe00 (MD5) Previous issue date: 2021

Published
2021
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3. Management of service crops for the provision of ecosystem services in vineyards: A review

Author

Christian Gary, Aude Ripoche, Florian Celette, Léo Garcia, Aurélie Metay, Héctor Valdés-Gómez, Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), ISARA-LYON (ISARA-LYON), Agroécologie et Intensification Durables des cultures annuelles (Cirad-Persyst-UPR 115 AIDA), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Appliquée au Développement Rural (FOFIFA), DSV, Direction des Services Vétérinaires, Ministère de l’Elevage, Departamento de Fruticultura y Enologia, Pontificia Universidad Catolica de Chile, 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)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-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), ISARA-Lyon, Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Pontificia Universidad Católica de Chile (UC), Celette, Florian, Ripoche, Aude, and Valdés Gómez, Héctor

Subjects
0106 biological sciences, H01 - Protection des végétaux - Considérations générales, Soil biodiversity, F08 - Systèmes et modes de culture, agroécologie, Lutte antipollution, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Facteur climatique, 01 natural sciences, Désherbage, Ecosystem services, Protection des plantes, Trade-off management, Agriculture durable, Cropping system, Cover crop, 2. Zero hunger, Ecology, Agroforestry, Environmental resource management, 04 agricultural and veterinary sciences, viticulture, Agricultural sciences, Agroécosystème, Microclimat, P01 - Conservation de la nature et ressources foncières, écosystème, Plante de couverture, Fertilité du sol, Propriété physicochimique du sol, Sustainable viticulture, Agroecology, Service (business), business.industry, Soil organic matter, 15. Life on land, services écosystémiques, 13. Climate action, Vitis vinifera, Sustainability, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Animal Science and Zoology, Business, Agronomy and Crop Science, Sciences agricoles, 010606 plant biology & botany
Abstract

International audience; Service crops are crops grown with the aim of providing non-marketed ecosystem services, i.e. differing from food, fiber and fuel production. Vineyard soils face various agronomic issues such as poor organic carbon levels, erosion, fertility losses, and numerous studies have highlighted the ability of service crops to address these issues. In addition to their ability to increase soil organic matter and fertility, and reduce runoff and erosion processes, service crops provide a large variety of ecosystem services in vineyards such as weed control, pest and disease regulation, water supply, water purification, improvement of field trafficability and maintenance of soil biodiversity. However, associating service crops with grapevines may also generate disservices and impair grape production: competition for soil resources with the grapevine is often highlighted to reject such association. Consequently, vinegrowers have to find a balance between services and disservices, depending on local soil and climate conditions, on their objectives of grape production and on the nature and temporality of the ecosystem services they expect during the grapevine cycle. This study proposes a review of the services and disservices provided by service crops in vineyards, and a framework for their management. Vinegrowers' production objectives and pedoclimatic constraints form the preliminary stage to consider before defining a strategy of service crop management. This strategy assembles management options such as the choice of species, its spatial distribution within the vineyard, the timing of its installation, maintenance and destruction. These management options, defined for both annual and long-term time scales, form action levers which may impact cropping system functioning. Finally, we underline the importance of implementing an adaptive strategy at the seasonal time scale. Such tactical management allows adapting the cropping system to observed climate and state of the biophysical system during the grapevine cycle, in order to provide targeted services and achieve satisfactory production objectives.

Published
2018
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4. Genetic Diversity of the Ralstonia solanacearum Species Complex in the Southwest Indian Ocean Islands

Author

Yahiaoui, Noura, Chéron, Jean-Jacques, Ravelomanantsoa, Santatra, Hamza, Azali A., Petrousse, Bobb, Jeetah, Rajan, Jaufeerally-Fakim, Yasmina, Félicité, Jérôme, Fillâtre, Jacques, Hostachy, Bruno, Guérin, Fabien, Cellier, Gilles, Prior, Philippe, Poussier, Stéphane, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Institut National de la Recherche pour l'Agriculture, la Pêche et l'Environnement, Seychelles Agricultural Agency, Food and Agricultural Research and Extension Institute, University of Mauritius, Commission of Agriculture, Association Réunionnaise pour la Modernisation de l’Economie Fruitière, Légumière et HORticole (ARMEFLHOR), Agropolis Fondation : 1403-011, ANR-10-LABX-0001-01, European Union: European regional development fund (ERDF), Conseil Regional de La Reunion, Centre de Cooperation Internationale en Recherche agronomique pour le Developpement (CIRAD), ANSES, CIRAD, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Association Réunionnaise pour la Modernisation de l’Economie Fruitière Légumière et HORticole, Centre National de la Recherche Appliquée au Développement Rural, UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT - INRA), Institut National de la Recherche Agronomique (INRA), and ANR-10-LABX-0001/10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)

Subjects
MLSA, Phylogénie, Polymorphisme génétique, Plant Science, Variation génétique, Génétique des populations, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Surveillance épidémiologique, Original Research, H20 - Maladies des plantes, [SDV.GEN]Life Sciences [q-bio]/Genetics, clonal complex, Ralstonia solanacearum species complex, P34 - Biologie du sol, genetic diversity, Agricultural sciences, Épidémiologie, Enquête pathologique, Southwest Indian Ocean, epidemiology, diversité génétique, Ralstonia solanacearum, océan indien, Sciences agricoles, MLST
Abstract

Epidemiological surveillance of plant pathogens based on genotyping methods is mandatory to improve disease management strategies. In the Southwest Indian Ocean (SWIO) islands, bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC) is hampering the production of many sustainable and cash crops. To thoroughly analyze the genetic diversity of the RSSC in the SWIO, we performed a wide sampling survey (in Comoros, Mauritius, Reunion, Rodrigues, and Seychelles) that yielded 1,704 isolates from 129 plots, mainly from solanaceous crops. Classification of the isolates to the four major RSSC phylogenetic groups, named phylotypes, showed that 87% were phylotype I, representing the most prevalent strain in each of the SWIO islands. Additionally, 9.7% were phylotype II, and 3.3% were phylotype III; however, these isolates were found only in Reunion. Phylotype IV (2 isolates), known to be restricted to Indonesia-Australia-Japan, was reported in Mauritius, representing the first report of this group in the SWIO. Partial endoglucanase (egl) sequencing, based on the selection of 145 isolates covering the geographic and host diversity in the SWIO (also including strains from Mayotte and Madagascar), revealed 14 sequevars with Reunion and Mauritius displaying the highest sequevar diversity. Through a multilocus sequence analysis (MLSA) scheme based on the partial sequencing of 6 housekeeping genes (gdhA, gyrB, rplB, leuS, adk, and mutS) and 1 virulence-associated gene (egl), we inferred the phylogenetic relationships between these 145 SWIO isolates and 90 worldwide RSSC reference strains. Phylotype I was the most recombinogenic, although recombination events were detected among all phylotypes. A multilocus sequence typing (MLST) scheme identified 29 sequence types (STs) with variable geographic distributions in the SWIO. The outstanding epidemiologic feature was STI-13 (sequevar I-31), which was overrepresented in the SWIO and obviously reflected a lineage strongly adapted to the SWIO environment. A goeBURST analysis identified eight clonal complexes (CCs) including SWIO isolates, four CCs being geographically restricted to the SWIO, and four CCs being widespread beyond the SWIO. This work, which highlights notable genetic links between African and SWIO strains, provides a basis for the epidemiological surveillance of RSSC and will contribute to BW management in the SWIO.

Published
2017
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5. Drivers of Rift Valley fever epidemics in Madagascar

Author

Lancelot, Renaud, Béral, Marina, Rakotoharinome, Vincent Michel, Andriamandimby, Soa-Fy, Heraud, Jean-Michel, Coste, Caroline, Apolloni, Andrea, Squarzoni-Diaw, Cécile, De La Rocque, Stéphane, Formenty, Pierre B H, Bouyer, Jérémy, Wint, G R William, Cardinale, Eric, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), Université de La Réunion (UR), Centre National de la Recherche Appliquée au Développement Rural (FOFIFA), DSV [Antananarivo], Direction des Services Vétérinaires, Ministère de l’Elevage, Unité d'Epidémiologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Animal Production and Health Division [Rome], Food and Agriculture Organization of the United Nations, World Organization for Animal Health, International Health Regulations Monitoring Procedure and Information Team, Global Capacity and Response Department, Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Emerging and Epidemic Zoonotic Diseases, Pandemic and Epidemic Disease Department, Department of Zoology, Environmental Research Group Oxford, Cyclotron Réunion Océan Indien (CYROI), Université de La Réunion (UR)-Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), European Project: 613996,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,VMERGE(2013), Department of Zoology [Oxford], University of Oxford [Oxford], World Health Organization, Food and Agriculture Organization of the United Nations through the Central Emergency Response Fund of the United Nations, European Union [FP7-613996], Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and University of Oxford

Subjects
Rift Valley Fever, L73 - Maladies des animaux, Seroepidemiologic Studies, Analyse du risque, Facteur de risque, vector-borne infection, zoonosis, El Nino, cattle trade, One Health, Contrôle de maladies, 000 - Autres thèmes, Fièvre de la Vallée du Rift, Commerce, Facteur du milieu, Biological Sciences, Épidémiologie, Vecteur de maladie, Sérum sanguin, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Commercialisation, L72 - Organismes nuisibles des animaux, Abattoirs, Genre humain, zoonose, Bétail, Ruminant, Cattle Diseases, Virus de la fièvre de la vallée du Rift, Madagascar, Animals, Humans, Surveillance épidémiologique, El Niño, Epidemics, Weather, Transmission des maladies, Bovin, Rift Valley fever virus, Immunoglobulin M, Enquête pathologique, Immunoglobulin G, Cattle
Abstract

International audience; Rift Valley fever (RVF) is a vector-borne viral disease widespread in Africa. The primary cycle involves mosquitoes and wild and domestic ruminant hosts. Humans are usually contaminated after contact with infected ruminants. As many environmental, agricultural, epidemiological, and anthropogenic factors are implicated in RVF spread, the multidisciplinary One Health approach was needed to identify the drivers of RVF epidemics in Madagascar. We examined the environmental patterns associated with these epidemics, comparing human and ruminant serological data with environmental and cattle-trade data. In contrast to East Africa, environmental drivers did not trigger the epidemics: They only modulated local Rift Valley fever virus (RVFV) transmission in ruminants. Instead, RVFV was introduced through ruminant trade and subsequent movement of cattle between trade hubs caused its long-distance spread within the country. Contact with cattle brought in from infected districts was associated with higher infection risk in slaughterhouse workers. The finding that anthropogenic rather than environmental factors are the main drivers of RVF infection in humans can be used to design better prevention and early detection in the case of RVF resurgence in the region.

Published
2017
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6. West Nile virus infection in horses, Indian ocean

Author

Mahmad Reshad Jaumally, Camille Bernard, M. Roger, Marie-Marie Olive, Julie Ravaomanana, Catherine Cetre-Sossah, Stéphan Zientara, Sylvie Lecollinet, Jimmie Melanie, Eric Cardinale, Deodass Meenowa, Vincent Michel Rakotoharinome, Jean-Michel Heraud, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Virologie UMR1161 (VIRO), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA), Direction des Services Vétérinaires, Ministère de l'Agriculture, l'Elevage, la Pêche, Centre National de la Recherche Appliquée au Développement Rural, Ministère des Agro-Industries, Ministère de l’Agriculture et des Ressources Marines, Unité de Virologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), This study was conducted in connection with AnimalRisk/TROI, a research program on emerging animal diseases in the Indian Ocean, funded by FEDER POCT (European Union, Regional Council of Reunion and French government) under the DP One Health-OI., École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and Centre National de Recherche Appliquée au Développement Rural (FOFIFA)

Subjects
Antibody prevalence, Veterinary medicine, viruses, medicine.disease_cause, Antibodies, Viral, L73 - Maladies des animaux, 0403 veterinary science, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Seroepidemiologic Studies, Immunology and Allergy, Indian Ocean, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Transmission (medicine), virus diseases, 04 agricultural and veterinary sciences, General Medicine, 3. Good health, Épidémiologie, Flavivirus, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, West Nile virus, geographic locations, Genre humain, 040301 veterinary sciences, 030231 tropical medicine, Immunology, Enzyme-Linked Immunosorbent Assay, Microbiology, Virus des animaux, Sérologie, 03 medical and health sciences, Neutralization Tests, biology.animal, medicine, Seroprevalence, Animals, Humans, Horses, Transmission des maladies, West Nile Virus Infection, General Veterinary, Animal, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Equidae, Morbidité, biology.organism_classification, nervous system diseases, Indian ocean, Enquête pathologique, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Horse Diseases, West Nile Fever, Cheval
Abstract

International audience; The circulation of West Nile virus (WNV) in horses was investigated in the Southwest Indian ocean. In 2010, blood samples were collected from a total of 303 horses originating from Madagascar, Mauritius, Reunion and the Seychelles and tested for WNV-specific antibodies. An overall seroprevalence of 27.39% was detected in the Indian Ocean with the highest WNV antibody prevalence of 46.22% (95% CI: [37.4–55.2%]) in Madagascar. The age and origin of the horses were found to be associated with the WNV infection risk. This paper presents the first seroprevalence study investigating WN fever in horses in the Southwest Indian Ocean area and indicates a potential risk of infection for humans and animals. In order to gain a better understanding of WN transmission cycles, WNV surveillance needs to be implemented in each of the countries.

Published
2017
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7. Genetic variability of nitrogen use efficiency in rainfed upland rice

Author

Alain Ramanantsoanirina, Nourollah Ahmadi, Pierre Roumet, Tatiana Rakotoson, Philippe Letourmy, Isabelle Ratsimiala Ramonta, Julie Dusserre, Tuong-Vi Cao, Louis-Marie Raboin, Centre National de la Recherche Appliquée au Développement Rural, Agroécologie et Intensification Durables des cultures annuelles (Cirad-Persyst-UPR 115 AIDA), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Faculté des sciences, Université de Goma, 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), Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de la Recherche Agronomique (INRA)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Cariplo Foundation, and Agropolis Foundation

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, madagascar, Disponibilité nutriments (sol), variabilité génétique, Upland rice, 01 natural sciences, F30 - Génétique et amélioration des plantes, Région d'altitude, upland rice, genetic variability, 2. Zero hunger, biology, food and beverages, 04 agricultural and veterinary sciences, Nutrition des plantes, Rendement des cultures, Fertilizer, Génotype, Limiting factor, Efficacité d'utilisation, Intéraction génotype environnement, Azote, low input, Soil Science, Oryza sativa, Context (language use), Teneur en azote, engineering.material, Oryza, Variation génétique, Riz pluvial, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genetic variability, nitrogen utilization efficiency, Panicle, Méthode statistique, Sol, rice, nitrogène, 15. Life on land, biology.organism_classification, F61 - Physiologie végétale - Nutrition, Agronomy, oryza, 040103 agronomy & agriculture, engineering, 0401 agriculture, forestry, and fisheries, nitrogen uptake efficiency, Agronomy and Crop Science, F04 - Fertilisation, 010606 plant biology & botany
Abstract

AGAP : équipe GE2pop; In sub-Saharan Africa and in Madagascar, upland rice is mostly grown for subsistence by resource-poor farmers in low-input production systems with low yields. In this context, soil nitrogen availability is a major limiting factor. To determine the appropriate breeding strategy to improve nitrogen use efficiency (NUE), the genetic variability and the level of G × N interaction of NUE need to be evaluated. NUE and its components are complex quantitative traits and the study of their relationship with other simpler traits should help understand the mechanisms involved in NUE and identify ways to improve it. A study was conducted at mid-altitude in Madagascar using 13 adapted tropical japonica rice varieties over three cropping seasons with two contrasted levels of applied N (high N with 90–120 kg N ha−1 as urea and low N without mineral fertilizer) in rainfed upland conditions. Year × N and Year × G interactions were significant due to contrasted rainfall distributions across the three cropping seasons. Agronomic efficiencies of N fertilization were low (11.5 kg grain kg−1 N in the best year) because of N loss through leaching or volatilization. Our results also suggest gaseous loss of N by plants between flowering and harvest, particularly under the high N treatment. The experiment revealed significant genetic variability for NUE, nitrogen uptake efficiency (NUPE) and nitrogen utilization efficiency (NUTE) in both high N and low N treatments but a low level of G × N interaction. The variation in NUPE accounted for more of the variation in NUE than the variation in NUTE. There was no correlation between NUPE and NUTE, either under high N or under low N. We found no negative relationship between grain yield and grain N concentration under low N. The relationship between NUE and agronomic and N-related traits differed from one year to the next, illustrating the plasticity of the contribution of the different agronomic traits to NUE as a function of the contrasted climatic conditions (particularly the rainfall distribution pattern). However, two traits, the number of panicles per m2 and the harvest index were consistently positively correlated with NUE. The difference between total N uptake at flowering and at harvest was positively correlated with NUE, particularly under the low N treatment.

Published
2017
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8. Attractancy of bacterivorous nematodes to root-adhering soils differs according to rice cultivars

Author

Alain Ramanantsoanirina, Mathilde Sester, Eric Blanchart, Laurent Cournac, Jean Trap, Mahafaka Patricia Ranoarisoa, Claude Plassard, Kirsten Vom Brocke, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-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), Laboratoire des Radio Isotopes, Université d'Antananarivo, Institut de Recherche pour le Développement (IRD [France-Ouest]), 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), SRR FOFIFA, Centre National de la Recherche Appliquée au Développement Rural, Agroécologie et Intensification Durables des cultures annuelles (Cirad-Persyst-UPR 115 AIDA), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), UMR Eco&Sols, LMI IESOL, Centre IRD/ISRA de Bel Air, Labex Agro: ANR-10-LabX-001-01, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), 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), Laboratoire des Radio-Isotopes (LRI), Université d'Antananarivo, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), 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 National de Recherche Appliquée au Développement Rural (FOFIFA), Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), LMI IESOL Intensification Ecologique des Sols Cultivés en Afrique de l’Ouest [Dakar] (IESOL), Institut de recherche pour le développement (IRD [Sénégal]), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Laboratoire des RadioIsotopes (LRI), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro

Subjects
0106 biological sciences, exsudat, sol ferrallitique, madagascar, Plant Science, Upland rice cultivar, Acrobeloides sp, Nematode attractancy, Ferrallitic soil, Madagascar, 01 natural sciences, F30 - Génétique et amélioration des plantes, Interactions biologiques, Cultivar, nématode, 2. Zero hunger, Rhizosphere, Vegetal Biology, riziculture, nématode bactériophage, food and beverages, 04 agricultural and veterinary sciences, Physiologie végétale, Horticulture, medicine.symptom, Micro-organisme du sol, Nématode à vie libre, Exudate, Ferralsol, F60 - Physiologie et biochimie végétale, Soil Science, Oryza sativa, Biology, transudates, Invertebrate Zoology, medicine, Riz pluvial, ferrallitic soil, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant breeding, Variété, Inoculation, fungi, 15. Life on land, biology.organism_classification, Zoologie des invertébrés, Amélioration des plantes, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Nematode, Agronomy, Rhizosphère, rice growing, Striga asiatica, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Agronomy and Crop Science, Biologie végétale, 010606 plant biology & botany
Abstract

We tested the ability of root-adhering soils (RAS) from eight rice cultivars to attract a bacterivorous nematode (Acrobeloides sp.) living in a poor-nutrient soil in Madagascar. We showed that the ability of rice to attract bacterivorous nematodes in its rhizosphere is variable among cultivars. FOFIFA 172 was the cultivar with the highest attraction value, the lowest root biomass (RB) and the highest RAS:RB ratio and RAS respiration. In contrast, nematodes exhibited strong repellent response to W880 RAS. Also, nematode attractancy was not related to rice resistance against pests (blast rice disease and Striga asiatica) neither to cultivar ability to grow at specific altitude. Our results suggest a trade-off in carbon allocation between plant biomass and root exudation driving nematode attractancy and raise questions about the impact of plant breeding on cultivar ability to interact with soil mutualists such as bacterivorous nematodes. Further investigations are required into (i) variation in root exudate quantity and composition among the eight cultivars and (ii) the response of rice cultivars to bacterivorous nematode inoculation.

Published
2017
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9. Association mapping of resistance to rice blast in upland field conditions

Author

Nourollah Ahmadi, Julien Frouin, Elsa Ballini, Alain Ramanantsoanirina, Didier Tharreau, Brigitte Courtois, Louis-Marie Raboin, Agroécologie et Intensification Durables des cultures annuelles (Cirad-Persyst-UPR 115 AIDA), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), 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 de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Appliquée au Développement Rural, 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), Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), 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
0301 basic medicine, Résistance génétique, Analyse qualitative, Plant Science, Japonica, F30 - Génétique et amélioration des plantes, Génétique des populations, Marqueur génétique, Association mapping, pathologie végétale, 2. Zero hunger, Genetics, Microbiology and Parasitology, food and beverages, Magnaporthe grisea, Microbiologie et Parasitologie, Magnaporthe, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, regional study, Qualitative resistance, Original Article, rice, blast disease, Genome-Wide Association Study, quantitative resistance, qualitative resistance, protection des cultures, sélection végétale, résistance aux maladies, Locus des caractères quantitatifs, Soil Science, Locus (genetics), Oryza sativa, Biology, Plant disease resistance, Chromosome, 03 medical and health sciences, Quantitative resistance, Analyse quantitative, Variation génétique, Riz pluvial, étude régionale, Variété, H20 - Maladies des plantes, Genetic diversity, Génome, business.industry, Haplotype, biology.organism_classification, Blast disease, Biotechnology, resistance to diseases, 030104 developmental biology, Genetic marker, oryza, Rice, business, Agronomy and Crop Science
Abstract

Background Rice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers. Results The contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240 kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance. Conclusions It was possible to identify three chromosomal regions associated with resistance in the field through GWAS in this study. Future research should concentrate on specific indica markers targeting the identified insertion in the Pi33 zone. Specific experimental designs should also be implemented to dissect quantitative resistance among tropical japonica varieties. Electronic supplementary material The online version of this article (doi:10.1186/s12284-016-0131-4) contains supplementary material, which is available to authorized users.

Published
2016
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10. Gestion de la résistance aux maladies à l’échelle des territoires cultivés

Author

Lannou, Christian, Papaix, Julien, Monod, Herve, Raboin, L.M., Goyeau, Henriette, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche Mathématiques et Informatique Appliquées (MIA), Institut National de la Recherche Agronomique (INRA), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Centre National de la Recherche Appliquée au Développement Rural

Subjects
diversité fonctionnelle, épidémiologie du paysage, [SDV]Life Sciences [q-bio], parasites des cultures, contrôle des épidémies, biodiversité
Abstract

présentation orale suite à la conférence du CIAG: La diversité génétique, une ressource pour l’agriculture de demain, le 18-06-2013 à Versailles; En épidémiologie végétale, l'idée de développer des stratégies de gestion des variétés résistantes à l'échelle des paysages est de plus en plus explorée. Après une revue de la littérature, nous montrons, sur la base d'une analyse de jeux de données acquis à l'échelle de la France, que la résistance des variétés cultivées, telle qu'elle est observée au champ, est influencée par la composition variétale du paysage dans son ensemble. De plus, nous montrons que la prise en compte des aspects quantitatifs de la relation hôte – parasite est indispensable pour expliquer l'évolution de la population pathogène à cette échelle. Pour aller plus loin dans cette exploration, nous avons construit un ensemble de modèles et exploré l'effet des caractéristiques du paysage sur la dynamique de la population pathogène. Nous avons montré que la fragmentation du paysage peut conduire à une réduction globale des épidémies mais aussi, sous certaines conditions, à une augmentation de la sévérité de maladie sur des variétés à résistance quantitative. Enfin, la structure du paysage a un effet fort sur l'évolution de la population parasite vers des formes spécialistes ou généralistes.

Published
2013

11. A survey of mangiferin and hydroxycinnamic acid ester accumulation in coffee (Coffea) leaves: biological implications and uses

Author

Aaron P. Davis, Philippe La Fisca, Laurence Mondolot, Emmanuel Couturon, Arsene Rakotondravao, Christian Jay-Allemand, Jean-Jacques Rakotomalala, Annick Gargadennec, Claudine Campa, Luc P. R. Bidel, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour le Développement (IRD [France-Sud]), Laboratoire de Biochimie, Centre National de Recherche Appliquée au Développement Rural (FOFIFA), 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), Royal Botanic Gardens, Kew, Agence Universitaire Francophone (AUF), 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), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Centre National de la Recherche Appliquée au Développement Rural, Royal Botanic Gardens Kew, and 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])

Subjects
0106 biological sciences, Arabica coffee, Coumaric Acids, Canephora, Xanthones, [SDV]Life Sciences [q-bio], C. arabica, Coffea, Plant Science, phenolic compounds, Biology, hydroxycinnamic acids, Photosynthesis, phylogeny, 01 natural sciences, mangiferin, 03 medical and health sciences, chemistry.chemical_compound, Species Specificity, Phylogenetics, chlorogenic acids, Botany, Hydroxybenzoates, Madagascar, Mangiferin, hybridization, 030304 developmental biology, Hybrid, chemistry.chemical_classification, 0303 health sciences, C. canephora, robusta coffee, Genetic Variation, Esters, Original Articles, 15. Life on land, biology.organism_classification, Hydroxycinnamic acid, coffeeleaf tea, Plant Leaves, chemistry, Fruit, Africa, Crop Wild Relatives (CWRs), Composition (visual arts), 010606 plant biology & botany
Abstract

BACKGROUND AND AIMS The phenolic composition of Coffea leaves has barely been studied, and therefore this study conducts the first detailed survey, focusing on mangiferin and hydroxycinnamic acid esters (HCEs). METHODS Using HPLC, including a new technique allowing quantification of feruloylquinic acid together with mangiferin, and histochemical methods, mangiferin content and tissue localization were compared in leaves and fruits of C. pseudozanguebariae, C. arabica and C. canephora. The HCE and mangiferin content of leaves was evaluated for 23 species native to Africa or Madagascar. Using various statistical methods, data were assessed in relation to distribution, ecology, phylogeny and use. KEY RESULTS Seven of the 23 species accumulated mangiferin in their leaves. Mangiferin leaf-accumulating species also contain mangiferin in the fruits, but only in the outer (sporophytic) parts. In both leaves and fruit, mangiferin accumulation decreases with ageing. A relationship between mangiferin accumulation and UV levels is posited, owing to localization with photosynthetic tissues, and systematic distribution in high altitude clades and species with high altitude representatives. Analyses of mangiferin and HCE content showed that there are significant differences between species, and that samples can be grouped into species, with few exceptions. These data also provide independent support for various Coffea lineages, as proposed by molecular phylogenetic analyses. Sampling of the hybrids C. arabica and C. heterocalyx cf. indicates that mangiferin and HCE accumulation may be under independent parental influence. CONCLUSIONS This survey of the phenolic composition in Coffea leaves shows that mangiferin and HCE accumulation corresponds to lineage recognition and species delimitation, respectively. Knowledge of the spectrum of phenolic accumulation within species and populations could be of considerable significance for adaptation to specific environments. The potential health benefits of coffee-leaf tea, and beverages and masticatory products made from the fleshy parts of Coffea fruits, are supported by our phenolic quantification.

Published
2012
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12. Urban agriculture and land use in cities : An approach with the multi-functionality and sustainability concepts in the case of Antananarivo (Madagascar)

Author

Marie-Hélène Dabat, Josette Rakotondraibe, Josélyne Ramamonjisoa, R. Lilia Rabeharisoa, Jacqueline Rakotoarisoa, Christine Aubry, Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Departement of geography, Université d'Antananarivo, Acteurs, Ressources et Territoires dans le Développement (UMR ART-Dev), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Paul-Valéry - Montpellier 3 (UPVM)-Université de Perpignan Via Domitia (UPVD)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of rice research, Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Department of Science, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre National de la Recherche Scientifique (CNRS)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Université de Perpignan Via Domitia (UPVD)-Université Paul-Valéry - Montpellier 3 (UPVM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Paul-Valéry - Montpellier 3 (UM3)-Université de Perpignan Via Domitia (UPVD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Centre National de la Recherche Appliquée au Développement Rural

Subjects
Geography, Planning and Development, 0211 other engineering and technologies, Urban density, 02 engineering and technology, 010501 environmental sciences, urban agriculture, 01 natural sciences, E14 - Économie et politique du développement, Environmental protection, Viabilité économique, 11. Sustainability, Sustainability organizations, 2. Zero hunger, Utilisation des terres, 021107 urban & regional planning, Forestry, sustainability, E11 - Économie et politique foncières, Agriculture urbaine, Zone urbaine, Management, Monitoring, Policy and Law, urban planning, 12. Responsible consumption, Urban planning, Urbanization, multi-functionality, Urban agriculture, Environmental planning, 0105 earth and related environmental sciences, Nature and Landscape Conservation, [SHS.ARCHI]Humanities and Social Sciences/Architecture, space management, Land use, business.industry, 15. Life on land, Développement régional, 13. Climate action, Agriculture, Développement durable, Sustainability, Exploitation agricole, Business, U30 - Méthodes de recherche
Abstract

Urban planners are increasingly interested in agriculture around cities and have to decide whether to maintain or not areas of agricultural land use within and close to growing cities. There is therefore a need for researchers to design tools to guide public decision-making on land use. Various approaches, originating from different disciplines, may be adopted in this respect. We designed an interdisciplinary research program in order to test two related concepts: the "sustainability" and the "multi-functionality" of agriculture. We show that these concepts provide a useful framework for obtaining appropriate knowledge about urban agriculture, which urban planners could apply in real situations. In close collaboration with urban planners, we applied an interdisciplinary research methodology, based on common farm surveys and territorial approaches, to the Antananarivo area (Madagascar). The main functions analyzed were the food production and environmental roles of urban agriculture. Two aspects of sustainability were assessed: the farm sustainability and the territorial sustainability, with expert scores. This approach identified a wide diversity of farming systems that performed differently, depending on their intra- or suburban location. The food supply function appeared to be important not only for fresh produce but also for rice consumption. The function of protection against flooding is now important and this importance will increase with climate change. A diagnosis of sustainability was made and discussed with urban planners: several farming systems and zones were identified in which agriculture was considered important as a means of maintaining or developing the food supply, employment and incomes, and even landscape or environmental quality. We also identified other areas in which poor production conditions and/or the negative effects of urbanization on agriculture jeopardized its sustainability. This methodology appeared to be useful for determining the most appropriate role of urban agriculture in the land-use planning of this city. Our study raises new questions on the subject and should lead to more focused research programmes. We discuss several points of interest and the limitations and possible extension of this method.

Published
2012
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13. Le réseau régional AnimalRisk : de la surveillance à la recherche dans l'Océan Indien

Author

Eric Cardinale, Matthieu Roger, Nohal Elissa, Abdourahime Faharoudine, Sébastien Girard, Mohamed Halifa, Jaumally, Mahmad R., Jean-Michel HERAUD, Lalaonirina, B. A., Laurette, S., Lasnes, L., Séverine Licciardi, Marianne Maquart, Mélanie, J., Deodass Meenowa, Marie-Marie Olive, Rakotoharinome, M., Rakotondravao, M., Ravaomanana, J., Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), Université de La Réunion (UR), 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), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), Ministère de l’Agriculture, Ministère de l’Agriculture, de la technologie alimentaire et des ressources naturelles, Ministère de l’Agriculture et des Ressources Marines, Direction de l’Alimentation, de l’Agriculture et de la Forêt, Département de Recherches Zootechniques et Vétérinaires, Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Appliquée au Développement Rural, and Univ, Réunion

Subjects
[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, network, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Océan Indien, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Ermerging diseases, Maladies émergentes, Indian Ocean, réseau
Abstract

The Animal Risk regional network: surveillance and research in the Indian Ocean. To meet the challenges of emerging diseases in the Indian Ocean region, in 2009 animal health stakeholders set up the Animal Risk-OI network, designed to provide technicaland scientific support to surveillance systems and to suggest ways of improving health risk control in the area. The network is supported by OIE referring bodies for the Indian Ocean—veterinary services and animal health research organizations. Animal Risk-OI is not intended to replace current monitoring systems but to help consider arising issues through bimonthly webconferences, annual meetings and quarterly newsletters, and to provide information for research aiming to clarify theepidemiology of certain diseases and recommend suitable control measures. This paper presents the preliminary findings following the monitoring and investigation of diseases considered by network partners to be of top priority. Apart from pursuing synergy between surveillance and research activities, the network aims to bridge the gap between animal and human health to instigate ajoint, standardized approach to the assessment and control of health risks in the Indian Ocean region., Pour répondre aux défis lancés par les maladies émergentes dans l’Océan Indien, les acteurs de la santé animale ont mis en place depuis début 2009 le réseau AnimalRisk-OI. Ce réseau a pour objectif d’apporter un soutien technique et scientifique aux systèmes de surveillance et de proposer des réponses pour une meilleure gestion des risques sanitaires dans la zone. Les partenaires sont les référents de l’OIE dans l’Océan Indien, à savoir les services vétérinaires ainsi que les structures de recherché impliquées en santé animale. Le réseau AnimalRisk-OI n’a pas pour vocation de se substituer aux systèmes de surveillance existants, mais il est chargé d’animer une réflexion autour des problématiques observées par des téléweb conférences bimensuelles, des réunions annuelles et des bulletins d’information trimestriels et de nourrir des actions de recherche qui visent à mieux comprendre l’épidémiologie de certaines maladies et donc de proposer des mesures de gestion adéquates pour mieux les maîtriser. Les premiers résultats de la surveillance et des investigations sur certaines maladies considérées prioritaires par les partenaires sont présentés ici. Les orientations envisagées, outre la poursuite de la synergie entre les actions de surveillance et de recherche, sont un rapprochement avec la santé humaine pour permettre une approche commune et harmonisée de l’appréciation et de la gestion des risques sanitaires dans l’Océan Indien.

Published
2011

14. Is soil fauna an important driver of key soil function ? the case of denitrifier communities in tropical soils

Author

Brauman, Alain, Philippot, Laurent, Baudoin, Ezékiel, Djigal, Djibril, Gueye, M., Rabary, B., Assigbetse, K., Lensi, R., Villenave, Cécile, Blanchart, Eric, UR SEQBIO, Institut de Recherche pour le Développement (IRD), Microbiologie du Sol et de l'Environnement (MSE), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Centre National de la Recherche Appliquée au Développement Rural, Institut de Recherche pour le Développement ( IRD ), Microbiologie du Sol et de l'Environnement ( MSE ), and Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB )

Subjects
[ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], tropical soil, denitrifier community, soil fauna
Abstract

Affiche, résuméAffiche, résumé; According to recent estimations, soil animals represent as much as 23% of the total diversity of living organisms. If the importance of soil fauna on soil global microbial processes like mineralization is widely recognized, their impact on composition of soil microbial guilds, like denitrifiers, remains questionable. This study will resume several works undertaken on the influence of keystone tropical soil species (nematodes, termites, earthworms) on different parameters (activity- density and genetic structure or diversity) of the denitrifying bacterial communities. In order to take into account the main different interactions between fauna and microorganisms, the exposed studies focus on bacterial-feeding nematodes (grazing effect) earthworms and termites (engineering effect ; modification of soil structure and/or physico-chemical properties). Their respective impact was measured on the activity (potential denitrification activity), genetic structure (fingerprinting and cloning sequencing) and density (real time PCR) of the targeted functional communities. The soil feeding termite mound is characterized by an increase in the denitrification potential activity and shift in the diversity of the nitrate reducers performing the first step of the denitrification process with enrichment of actinomycetes. Contrarily, earthworms reduced the soil potential denitrification activity but do not modify composition nor density of the denitrifier community. The inoculation of the nematodes led to a decrease in the potential denitrifying activity and a slight modification of the genetic structure of the denitrifier community. These results underline that besides the plants, soil fauna represent also a key factor of regulation of the functional soil microbial activities.

Published
2008

15. L’agriculture à Antananarivo (Madagascar) : une approche interdisciplinaire

Author

Josélyne Ramamonjisoa, Josette Rakotondraibe, Marie-Hélène Dabat, Jacqueline Rakotoarisoa, Christine Aubry, R. Lilia Rabeharisoa, Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Faculté des lettres et sciences humaines, Université d'Antananarivo, Systèmes de culture et rizicultures durables (URP SCRID), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université d'Antananarivo-Centre National de Recherche Appliquée au Développement Rural (FOFIFA)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Africa Rice Center [Côte d'Ivoire] (AfricaRice), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Département des Recherches rizicoles, Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Faculté des Sciences, Ecole Supérieur des Sciences Agronomiques, Institut de Recherche pour le Développement (IRD)-Université d'Antananarivo-Africa Rice Center (AfricaRice)-FOFIFA-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Consultative Group on International Agricultural Research [CGIAR], Centre National de la Recherche Appliquée au Développement Rural, and Aubry, Christine

Subjects
interdisciplinarité, madagascar, [SDV]Life Sciences [q-bio], 0211 other engineering and technologies, 02 engineering and technology, urban agriculture, agriculture urbaine, multifonctionnalité, interdisciplinarity, Analyse de système, General Biochemistry, Genetics and Molecular Biology, 12. Responsible consumption, 11. Sustainability, Durabilité, E10 - Économie et politique agricoles, riz, General Environmental Science, 2. Zero hunger, Culture maraîchère, Système de production, General Social Sciences, 021107 urban & regional planning, Analyse économique, 04 agricultural and veterinary sciences, 15. Life on land, Classification, Produit alimentaire, 6. Clean water, Approvisionnement en eau, 13. Climate action, E16 - Économie de la production, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, General Earth and Planetary Sciences, General Agricultural and Biological Sciences
Abstract

La durabilité de l'agriculture urbaine d'Antananarivo (Madagascar) a été questionnée dans le cadre d'un projet de recherche pluridisciplinaire à visée opérationnelle. Six thèmes de recherche articulent quatre disciplines (agronomie, économie, géographie, chimie) autour de sites, de systèmes de production ou de produits communs. On montre que la diversité des systèmes d'activités et de production, dont on propose une typologie, est principalement liée à la distance à la ville et à l'accès quantitatif et qualitatif à l'eau. On quantifie la fonction alimentaire de cette agriculture, forte pour les produits maraîchers et non négligeable pour le riz. La lutte contre les inondations en plaine et l'érosion dans les collines bâties justifient aussi certaines décisions de maintien local de l'activité agricole, alors que les performances agricoles, quantitatives et qualitatives (risques sanitaires) sont diminuées par les effluents industriels et urbains. La durabilité intrinsèque et exogène de l'agriculture est approchée en première analyse en proposant une hiérarchie entre les systèmes de production et entre les sites. Cependant, les questions liées à la qualité sanitaire variable de certains produits agricoles issus de l'agriculture urbaine, à la segmentation croissante de certaines filières ou aux risques liés à de nouvelles fonctions de l'agriculture ont émergé dans ce projet, mais ouvrent surtout de nouveaux champs de recherche., An interdisciplinary program (ADURAA) analyzes the sustainability and the urban functions of agriculture inside and around Antananarivo. Its aim is to develop knowledge and to help public decisions about the interest, limits and conditions of the local maintenance of agriculture, compared with other land uses. Six research themes were identified based on a typology of urban farms; they contribute knowledge on three main functions of this agriculture, viz. food supply, land use and risk prevention, and the emerging role of urban waste reuse. A wide diversity of activities systems and agricultural production systems has been identified in relation to distance to the town and water availability. This urban agriculture significantly contributes to the vegetables supply of the district as well as to its rice supply. Flooding in the lowland and erosion in the hills are also e ciently contained by agricultural land use, but anarchic building and the use of agricultural soil for brick making largely counteract this role. Uncontrolled discharge of industrial liquid wastes into the irrigation network greatly reduces rice production and has even led to the desertion of some intra-urban rice-growing areas, while domestic pollution strongly a ects the sanitary quality of intra-urban vegetables. However a positive externality could be developed by using some urban solid waste as fertilisers for the growing horticultural sector. Emerging questions such as the quality of urban produce and potential new risks open up new avenues for future research on this agriculture.

Published
2008
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16. Activity, size and structure of the nitrate reducer community in relation to land-use and fertilization regime in Madagascar

Author

Chèneby, Dominique, Brauman, Alain, Rabary, B., Philippot, Laurent, Microbiologie du Sol et de l'Environnement (MSE), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), UR 179 SeqBio, Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Appliquée au Développement Rural, ProdInra, Archive Ouverte, Microbiologie du Sol et de l'Environnement ( MSE ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), Institut de Recherche pour le Développement ( IRD ), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), and Ville service.

Subjects
[SDV] Life Sciences [q-bio], cycle de l'azote, stomatognathic diseases, dénitrification, [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], nitrate réduction, résidue, labour
Abstract

Communication orale, résumé; absent

Published
2007

17. Contrasting genetic diversity and structure among Malagasy Ralstonia pseudosolanacearum phylotype I populations inferred from an optimized Multilocus Variable Number of Tandem Repeat Analysis scheme.

Author

Rasoamanana H, Ravelomanantsoa S, Yahiaoui N, Dianzinga N, Rébert E, Gauche MM, Pecrix Y, Costet L, Rieux A, Prior P, Robène I, Cellier G, Guérin F, and Poussier S

Subjects
Genotype, Bacterial Typing Techniques, Genetic Variation, Multilocus Sequence Typing, Phylogeny, Ralstonia classification, Ralstonia genetics, Tandem Repeat Sequences genetics
Abstract

The Ralstonia solanacearum species complex (RSSC), composed of three species and four phylotypes, are globally distributed soil-borne bacteria with a very broad host range. In 2009, a devastating potato bacterial wilt outbreak was declared in the central highlands of Madagascar, which reduced the production of vegetable crops including potato, eggplant, tomato and pepper. A molecular epidemiology study of Malagasy RSSC strains carried out between 2013 and 2017 identified R. pseudosolanacearum (phylotypes I and III) and R. solanacearum (phylotype II). A previously published population biology analysis of phylotypes II and III using two MultiLocus Variable Number of Tandem Repeats Analysis (MLVA) schemes revealed an emergent epidemic phylotype II (sequevar 1) group and endemic phylotype III isolates. We developed an optimized MLVA scheme (RS1-MLVA14) to characterize phylotype I strains in Madagascar to understand their genetic diversity and structure. The collection included isolates from 16 fields of different Solanaceae species sampled in Analamanga and Itasy regions (highlands) in 2013 (123 strains) and in Atsinanana region (lowlands) in 2006 (25 strains). Thirty-one haplotypes were identified, two of them being particularly prevalent: MT007 (30.14%) and MT004 (16.44%) (sequevar 18). Genetic diversity analysis revealed a significant contrasting level of diversity according to elevation and sampling region. More diverse at low altitude than at high altitude, the Malagasy phylotype I isolates were structured in two clusters, probably resulting from different historical introductions. Interestingly, the most prevalent Malagasy phylotype I isolates were genetically distant from regional and worldwide isolates. In this work, we demonstrated that the RS1-MLVA14 scheme can resolve differences from regional to field scales and is thus suited for deciphering the epidemiology of phylotype I populations., Competing Interests: The authors have declared that no competing interests exist.

Published
2020
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18. Genetic Diversity of the Ralstonia solanacearum Species Complex in the Southwest Indian Ocean Islands.

Author

Yahiaoui N, Chéron JJ, Ravelomanantsoa S, Hamza AA, Petrousse B, Jeetah R, Jaufeerally-Fakim Y, Félicité J, Fillâtre J, Hostachy B, Guérin F, Cellier G, Prior P, and Poussier S

Abstract

Epidemiological surveillance of plant pathogens based on genotyping methods is mandatory to improve disease management strategies. In the Southwest Indian Ocean (SWIO) islands, bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC) is hampering the production of many sustainable and cash crops. To thoroughly analyze the genetic diversity of the RSSC in the SWIO, we performed a wide sampling survey (in Comoros, Mauritius, Reunion, Rodrigues, and Seychelles) that yielded 1,704 isolates from 129 plots, mainly from solanaceous crops. Classification of the isolates to the four major RSSC phylogenetic groups, named phylotypes, showed that 87% were phylotype I, representing the most prevalent strain in each of the SWIO islands. Additionally, 9.7% were phylotype II, and 3.3% were phylotype III; however, these isolates were found only in Reunion. Phylotype IV (2 isolates), known to be restricted to Indonesia-Australia-Japan, was reported in Mauritius, representing the first report of this group in the SWIO. Partial endoglucanase ( egl ) sequencing, based on the selection of 145 isolates covering the geographic and host diversity in the SWIO (also including strains from Mayotte and Madagascar), revealed 14 sequevars with Reunion and Mauritius displaying the highest sequevar diversity. Through a multilocus sequence analysis (MLSA) scheme based on the partial sequencing of 6 housekeeping genes ( gdhA, gyrB, rplB, leuS, adk , and mutS ) and 1 virulence-associated gene ( egl ), we inferred the phylogenetic relationships between these 145 SWIO isolates and 90 worldwide RSSC reference strains. Phylotype I was the most recombinogenic, although recombination events were detected among all phylotypes. A multilocus sequence typing (MLST) scheme identified 29 sequence types (STs) with variable geographic distributions in the SWIO. The outstanding epidemiologic feature was STI-13 (sequevar I-31), which was overrepresented in the SWIO and obviously reflected a lineage strongly adapted to the SWIO environment. A goeBURST analysis identified eight clonal complexes (CCs) including SWIO isolates, four CCs being geographically restricted to the SWIO, and four CCs being widespread beyond the SWIO. This work, which highlights notable genetic links between African and SWIO strains, provides a basis for the epidemiological surveillance of RSSC and will contribute to BW management in the SWIO.

Published
2017
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19. Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini-Core Collection Using DArTseq.

Author

Ndjiondjop MN, Semagn K, Gouda AC, Kpeki SB, Dro Tia D, Sow M, Goungoulou A, Sie M, Perrier X, Ghesquiere A, and Warburton ML

Abstract

The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97-99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1-89.2% attributable to differences within groups.

Published
2017
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20. West Nile virus infection in horses, Indian ocean.

Author

Cardinale E, Bernard C, Lecollinet S, Rakotoharinome VM, Ravaomanana J, Roger M, Olive MM, Meenowa D, Jaumally MR, Melanie J, Héraud JM, Zientara S, and Cêtre-Sossah C

Subjects
Animals, Antibodies, Viral blood, Enzyme-Linked Immunosorbent Assay, Horse Diseases immunology, Horse Diseases virology, Horses, Humans, Indian Ocean epidemiology, Neutralization Tests, Seroepidemiologic Studies, West Nile Fever epidemiology, West Nile Fever transmission, West Nile Fever virology, West Nile virus immunology, Horse Diseases epidemiology, West Nile Fever veterinary
Abstract

The circulation of West Nile virus (WNV) in horses was investigated in the Southwest Indian ocean. In 2010, blood samples were collected from a total of 303 horses originating from Madagascar, Mauritius, Reunion and the Seychelles and tested for WNV-specific antibodies. An overall seroprevalence of 27.39% was detected in the Indian Ocean with the highest WNV antibody prevalence of 46.22% (95% CI: [37.4-55.2%]) in Madagascar. The age and origin of the horses were found to be associated with the WNV infection risk. This paper presents the first seroprevalence study investigating WN fever in horses in the Southwest Indian Ocean area and indicates a potential risk of infection for humans and animals. In order to gain a better understanding of WN transmission cycles, WNV surveillance needs to be implemented in each of the countries., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Published
2017
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21. High Prevalence of West Nile Virus in Domestic Birds and Detection in 2 New Mosquito Species in Madagascar.

Author

Maquart M, Boyer S, Rakotoharinome VM, Ravaomanana J, Tantely ML, Heraud JM, and Cardinale E

Subjects
Animals, Animals, Domestic virology, Madagascar, Prevalence, Seroepidemiologic Studies, Birds virology, Culicidae virology, West Nile Fever virology, West Nile virus isolation & purification
Abstract

West Nile virus is an arthropod-borne zoonosis transmitted by a large number of mosquito species, and birds play a key role as reservoir of the virus. Its distribution is largely widespread over Africa, Asia, the Americas and Europe. Since 1978, it has frequently been reported in Madagascar. Studies described a high seroprevalence level of the virus in humans in different areas of the island and a human fatal case of WNV infection was reported in 2011. Despite these reports, the epidemiology of WNV in Madagascar, in particular, viral circulation remains unclear. To explore the transmission of WNV in two rural human populations of Madagascar, we investigated local mosquitoes and poultry for evidence of current infections, and determined seroprevalence of candidate sentinel species among the local poultry. These 2 areas are close to lakes where domestic birds, migratory wild birds and humans coexist. Serological analysis revealed WNV antibodies in domestic birds (duck, chicken, goose, turkey and guinea fowl) sampled in both districts (Antsalova 29.4% and Mitsinjo 16.7%). West Nile virus nucleic acid was detected in one chicken and in 8 pools of mosquitoes including 2 mosquito species (Aedeomyia madagascarica and Anopheles pauliani) that have not been previously described as candidate vectors for WNV. Molecular analysis of WNV isolates showed that all viruses detected were part of the lineage 2 that is mainly distributed in Africa, and were most closely matched by the previous Malagasy strains isolated in 1988. Our study showed that WNV circulates in Madagascar amongst domestic birds and mosquitoes, and highlights the utility of poultry as a surveillance tool to detect WNV transmission in a peri-domestic setting.

Published
2016
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22. [Epidemiology of Newcastle disease in village poultry farming in Madagascar].

Author

Maminiaina OF, Koko M, Ravaomanana J, and Rakotonindrina SJ

Subjects
Animal Husbandry methods, Animals, Madagascar epidemiology, Newcastle Disease mortality, Newcastle Disease transmission, Poultry, Poultry Diseases mortality, Poultry Diseases transmission, Seroepidemiologic Studies, Antibodies, Viral blood, Newcastle Disease epidemiology, Newcastle disease virus immunology, Poultry Diseases epidemiology
Abstract

An epidemiological investigation into Newcastle disease in village poultry farming was carried out for 12 months (from May 1999 to June 2000) in Ambohimangakely and Moramanga, two agro-ecologic zones of Madagascar. The thirty families that were surveyed stated that they had incurred losses from an epizootic with high mortality rates at least once prior to the investigation. The results of serological tests and virus isolation showed that the disease, responsible for 44.3% of all the mortality recorded during the twelve-month period, was Newcastle disease. Maximum incidence of the disease (71%), affecting 75% of the families, occurred in October 1999, and seroprevalence often reached 100% after the outbreak had ended. The infection was brought to the villages either by newly introduced hens or recovered birds. All forms of Newcastle disease (epidemic, endemic and asymptomatic) were observed. The way farmers reacted contributed to the spread of the virus within a village and to neighbouring locations.

Published
2007

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