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125 results on '"Bioversity International [Rome]"'

51. A Network-Based Method to Detect Patterns of Local Crop Biodiversity: Validation at the Species and Infra-Species Levels CINVESTAV-IPN

Author: Thomas, Mathieu, Verzelen, Nicolas, BARBILLON, Pierre, Coomes, Oliver, Caillon, Sophie, Mckey, Doyle, Elias, Marianne, Garine, Eric, Raimond, Christine, Dounias, Edmond, Jarvis, Devra, Wencélius, Jean, Leclerc, Christian, Labeyrie, Vanesse, Hung Cuong, Pham, Thi Ngoc Hue , Nguyen, Sthapit, Bhuwon, Bahadur Rana, Ram, Barnaud, Adeline, Violon, Chloé, Arias-Reyes, Luis Manuel, Latournerie-Moreno, Luis, de Santis, Paola, Massol, François, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Geography [Montréal], McGill University = Université McGill [Montréal, Canada], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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), Laboratoire d'ethnologie et de sociologie comparative (LESC), Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Washington State University (WSU), Plant Resources Center (PRC), 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]), Instituto Tecnológico de Conkal [Yucatán], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), McGill University, Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-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 la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UPVM), 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 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 la Recherche Agronomique (INRA), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), 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]), 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 National de la Recherche Scientifique (CNRS)-Université Paris Nanterre (UPN), 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), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), and 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)
Subjects: [STAT.AP]Statistics [stat]/Applications [stat.AP], fungi, food and beverages, respiratory system, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities, [SDE.ES]Environmental Sciences/Environmental and Society, [STAT.ME]Statistics [stat]/Methodology [stat.ME], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; AbstractIn this chapter, we develop new indicators and statistical tests to characterize patterns of crop diversity at local scales to better understand interactions between ecological and socio-cultural functions of agroecosystems. Farms, where a large number of crops (species or landraces) is grown, are known to contribute a large part of the locally available diversity of both rare and common crops but the role of farms with low diversity remains little understood: do they grow only common varieties—following a nestedness pattern typical of mutualistic networks in ecology—or do ‘crop–poor’ farmers also grow rare varieties? This question is pivotal in ongoing efforts to assess the local-scale contribution of small farms to global agrobiodiversity. We develop new network-based approaches to characterize the distribution of local crop diversity (species and infra-species) at the village level and to validate these approaches using meta-datasets from 10 countries. Our results highlight the sources of heterogeneity in crop diversity at the village level. We often identify two or more groups of farms based on their different levels of diversity. In some datasets, ‘crop–poor’ farms significantly contribute to the local crop diversity. Generally, we find that the distribution of crop diversity is more heterogeneous at the species than at the infra-species level. This analysis reveals the absence of a general pattern of crop diversity distribution, suggesting strong dependence on local agro-ecological and socio-cultural contexts. These different patterns of crop diversity distribution reflect an heterogeneity in farmers’ self-organized action in cultivating and maintaining local crop diversity, which ensures the adaptability of agroecosystems to global change.
Published: 2015
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52. The coffee genome hub: a resource for coffee genomes

Author: Olivier Garsmeur, Valentin Guignon, Alexis Dereeper, Sébastien Ravel, Christine Tranchant-Dubreuil, Stéphanie Bocs, Philippe Lashermes, Gaëtan Droc, Valérie Poncet, Mathieu Rouard, Résistance des plantes aux bio-agresseurs (UMR RPB), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de Recherche pour le Développement (IRD [France-Sud]), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), 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]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2), and 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)
Subjects: Coffea, Genome browser, Logiciel, Genome, Gene, F30 - Génétique et amélioration des plantes, Phylogenomics, Database Issue, 2. Zero hunger, Genetics, Diversity, U10 - Informatique, mathématiques et statistiques, Genome project, Genomics, C30 - Documentation et information, Système d'information, Tool, Databases, Nucleic Acid, Banque de données, Genome, Plant, Metabolic Networks and Pathways, Framework, Computational biology, Biology, Coffea canephora, Polymorphism, Single Nucleotide, Synteny, génomique, Database, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Ressource génétique végétale, Bioinformatique, Syntenic, Genomes, Whole genome sequencing, Génome, Gene Expression Profiling, Gene Annotation, 15. Life on land, biology.organism_classification, Amélioration des plantes, ComputingMethodologies_PATTERNRECOGNITION, Gène, Arabica, Software
Abstract: The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub ( ext-link-type="uri" xlink:href="http://coffee-genome.org/" xlink:type="simple">http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager.
Published: 2015
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53. SNiPlay3 : a web-based application for exploration and large scale analyses of genomic variations

Author: Felix Homa, Manuel Ruiz, Gautier Sarah, Gwendoline Andres, Guilhem Sempere, Jean-François Dufayard, Alexis Dereeper, Yann Hueber, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), 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), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), International Center for Tropical Agriculture [Colombie] (CIAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Recherche pour le Développement (IRD)-Université de Bordeaux (UB), Bioversity International, Consultative Group on International Agricultural Research [CGIAR], International Center for Tropical Agriculture (CIAT), and Consultative Group on International Agricultural Research (CGIAR)
Subjects: Genotyping Techniques, Genomics, Genome-wide association study, Biology, computer.software_genre, Population stratification, Polymorphism, Single Nucleotide, F30 - Génétique et amélioration des plantes, INDEL Mutation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Web Server issue, Web application, Genetic association, Internet, Variant Call Format, business.industry, Genetic Variation, High-Throughput Nucleotide Sequencing, Workflow, Data mining, business, computer, Software, Genome-Wide Association Study
Abstract: International audience; SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable geno-typing data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.
Published: 2015
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54. Use and transfer of forest reproductive material in Europe in the context of climate change

Author: Konnert, Monika, Fady, Bruno, Gömöry, Dušan, A’Hara, Stuart, Wolter, Frank, Ducci, Fulvio, Koskela, Jarkko, Bozzano, Michèle, Maaten, Tiit, Kowalczyk, Jan, Bavarian Office for Forestry Seed and Plant Breeding, Partenaires INRAE, Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Technical University in Zvolen (TUZVO), Forestry Research, Northern Research Station, Administration de la nature et des forêts, Centro di Ricerca per la Selvicoltura (SEL), Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Estonian University of Life Sciences (EMU), Forest Research Institute, and Commanditaire : European Forest Genetic Resources Programme (Italy)
Subjects: [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Published: 2015

55. Stratégie pan-européenne pour la conservation génétique des arbres forestiers et la mise en place d'un réseau central d'unités de conservation dynamique

Author: De Vries, S.M.G., Alan, M., Bozzano, M., Burianek, V., Collin, E., Cottrell, J., Ivankovic, M., Kelleher, C.T., Koskela, J., Rotach, P., Vietto, L., Yrjänä, Leena, Wageningen University and Research [Wageningen] (WUR), FOREST TREE SEEDS AND TREE BREEDING RESEARCH DIRECTORATE ANKARA TUR, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), FORESTRY AND GAME MANAGEMENT RESEARCH INSTITUTE JILOVISTE CZE, Ecosystèmes forestiers (UR EFNO), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), FOREST RESEARCH NORTHERN RESEARCH STATION ROSLIN GBR, CROATIAN FOREST RESEARCH INSTITUTE JASTREBARSKO HRV, NATIONAL BOTANIC GARDENS DUBLIN IRL, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), COUNCIL FOR AGRICULTURAL RESEARCH AND ECONOMICS CASALE MONFERRATO ITA, and NATURAL RESOURCES INSTITUTE VANTAA FIN
Subjects: EUROPE, CONSERVATION DYNAMIQUE, RESEAU EUROPEEN, [SDE]Environmental Sciences
Abstract: A working group was established by the EUFORGEN Steering Committee to develop the pan-European genetic conservation strategy for forest trees. For each species, the strategy calls for a core network of dynamic conservation units. These units are not interconnected by geneflow, but together capture the current genetic diversity across the European continent. Method: The working group selected 14 pilot tree species representing four categories, depending on their geographical distribution (wide vs restricted) and their ecology (stand-forming vs scattered). The group also created a map of eight environmental zones by amalgamating some of the zones of an accepted environmental zoning classification for Europe. It then sought to identify at least one conservation unit per country for each environmental zone in that country, using a set of criteria to determine the most appropriate unit. This process resulted in the identification of 1836 dynamic conservation units, covering a total area of 205,803 ha and encompassing 2173 populations. Gaps in conservation efforts: To identify gaps in existing conservation efforts, the group compared species distribution maps in each environmental zone in each country with the location of the conservation units. Any species with no unit in an appropriate environmental zone in that country was recorded as a gap, and units were also noted where there was an information gap in the EUFGIS database. Genetic Conservation Strategy: The EUFORGEN Steering Committee will promote implementation, identify additional units once gaps have been filled and will monitor progress. A particular concern is the effect of climate change on phenology, but the detailed effects on long-lived tree species are likely to be variable, complex and difficult to predict. As a result, conservation should focus on the most vulnerable populations and species, for example those near the edge of their environmental limits, which often harbour high genetic diversity. Monitoring such populations should help to reveal key changes in a timely fashion, and management may then be needed to mitigate the effects of climate change.
Published: 2015

56. Implementing the dynamic conservation of elm genetic resources in Europe: case studies and perspectives

Author: Michele Bozzano, E. Collin, Ecosystèmes forestiers (UR EFNO), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), BIOVERSITY EUFORGEN ROME ITA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and Irstea Publications, Migration
Subjects: 0106 biological sciences, Dynamic Conservation, [SDE] Environmental Sciences, EUROPE, CONSERVATION DYNAMIQUE, Ulmus minor, Ulmus laevis, Population, FRANCE, Biology, 010603 evolutionary biology, 01 natural sciences, Riparian forest, lcsh:Forestry, education, European white elm, Nature and Landscape Conservation, education.field_of_study, geography, geography.geographical_feature_category, Ecology, Agroforestry, EUFORGEN, Forestry, ORME LISSE, 15. Life on land, biology.organism_classification, Forest genetic resources, ULMUS MINOR, Habitat, ORME, IN SITU, [SDE]Environmental Sciences, lcsh:SD1-669.5, Dutch elm disease, Elm, ORME CHAMPETRE, GENETIQUE DES POPULATIONS, ORME DE MONTAGNE, Population Genetics, 010606 plant biology & botany
Abstract: International audience; Many European countries have undertaken the static preservation of native elm genotypes in clone collections maintained ex situ. Less development has been devoted to the dynamic conservation of elm populations in situ. Case studies of elm conservation in France are given here as an illustration of methods employed at country level. We also briefly review the process used by the ‘European Forest Genetic Resources Programme’ (EUFORGEN) to monitor elm dynamic conservation in a pan-European perspective. Dynamic conservation methods were promoted by EUFORGEN through leaflets, strategies, Technical Guidelines and the geo-referenced database EUFGIS on Dynamic Conservation Units (DCUs). Because the network of DCUs needs to be representative of the partitioning of adaptive diversity across the species distribution range, a GIS-aided approach has been developed to position DCUs in environmental zones and identify conservation gaps. The two DCUs of European white elm (Ulmus laevis Pall.) selected in riparian forests of two different climatic zones of France show that management oriented toward habitat protection is compatible with dynamic conservation, and that the species can still be conserved in situ in spite of Dutch Elm Disease (DED). Collaboration with habitat conservationists enabled the monitoring of losses to DED and the assessment of within-population diversity for flowering phenology. Collaboration with forest geneticists revealed that the diversity of the Garonne population was low, but that it contained rare DNA variants and adaptive traits. Since 1987, experimental restoration of countryside hedges has been carried out, using field elm clones (U. minor Mill.) selected from the French national collection and tested for lower susceptibility to the agent of DED in artificial inoculation tests. Such plantations can be viewed as a very dynamic form of conservation if they permit the local gene pool to be reinforced with trees able to reach sexual maturity and exchange pollen with elms in the neighbourhood, hence contributing new genotypes that will be submitted to natural selection and provide fuel for ongoing adaptation processes. Initiatives assembling a large consortium of stakeholders, including habitat conservationists and hedge re-constructors, are needed to trigger new conservation projects.
Published: 2015
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57. Vers un paradigme ontologique d'interprétation des images de télédétection

Author: Andrés, Samuel, ARVOR, Damien, Libourel Rouge, Thérèse, Mougenot, Isabelle, Laporte, Marie-Angélique, Durieux, Laurent, UMR 228 Espace-Dev, Espace pour le développement, Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), Littoral, Environnement, Télédétection, Géomatique (LETG - Rennes), Littoral, Environnement, Télédétection, Géomatique UMR 6554 (LETG), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université d'Angers (UA)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Brest (UBO)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Géographie et d'Aménagement Régional de l'Université de Nantes (IGARUN), Université de Nantes (UN)-Université de Nantes (UN)-Université de Caen Normandie (UNICAEN), Université de Nantes (UN)-Université de Nantes (UN), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and Institut de Recherche pour le Développement (IRD)
Subjects: remote sensing, [INFO.INFO-FL]Computer Science [cs]/Formal Languages and Automata Theory [cs.FL], télédétection, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], Ontologies, observation de la terre, earth observation, [SHS.GEO]Humanities and Social Sciences/Geography, satellite images, images satellitaires, ACM: H.: Information Systems/H.1: MODELS AND PRINCIPLES
Abstract: International audience; Le traitement de l'information doit prendre en compte l'explicitation de la connais-sance. Cela semble une évidence, mais comment intégrer celle-ci dans le cycle de constitution de l'information? L'essor actuel des systèmes à base de connaissance incite à formuler cette question dans la perspective de paramétrer les traitements par une connaissance formalisée et partageable. En télédétection, la connaissance intervient en particulier dans l'interprétation sémantique des images satellitaires. En nous appuyant sur les ontologies, nous présentons dans cet article une démarche méthodologique originale. Celle-ci permet de voir sous un jour nou-veau le rapport de l'expert avec les outils de classification qu'il est possible de paramétrer avec une connaissance conceptuelle formalisée en OWL. ABSTRACT. The information processing must take into consideration the knowledge elicitation. This may seem obvious, but how to integrate it in the cycle of constitution of the information? The current development of knowledge-based systems encourages to formulate this question in prospect to set processing by a formal and sharable knowledge. In remote sensing, knowledge takes place in particular in the semantic interpretation of satellite images. Leaning on onto-logies, we present in this paper an original methodological approach. This one allows to see in a new light the relationships between the expert and the classification tools which can be parametrized with a conceptual knowledge formalized in OWL.
Published: 2014
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58. A Semantic Web Faceted Search System for Facilitating Building of Biodiversity and Ecosystems Services

Author: Isabelle Mougenot, Ulrike Stahl, Lutz Maicher, Marie-Angélique Laporte, Eric Garnier, Jens Kattge, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), UMR 228 Espace-Dev, Espace pour le développement, Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), 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]), Max Planck Institute for Biogeochemistry (MPI-BGC), Max-Planck-Gesellschaft, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Bioversity International, Consultative Group on International Agricultural Research [CGIAR], Université des Antilles (UA)-Université de Guyane (UG)-Université de Montpellier (UM)-Université de La Réunion (UR)-Avignon Université (AU)-Université de Perpignan Via Domitia (UPVD)-Institut de Recherche pour le Développement (IRD), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Friedrich-Schiller-Universität Jena, and Mougenot, Isabelle
Subjects: [INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], 0106 biological sciences, [INFO.INFO-WB] Computer Science [cs]/Web, Computer science, Context (language use), 02 engineering and technology, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], 020204 information systems, Controlled vocabulary, 0202 electrical engineering, electronic engineering, information engineering, Semantic Web, ComputingMilieux_MISCELLANEOUS, Thesaurus (information retrieval), [INFO.INFO-WB]Computer Science [cs]/Web, ACM: H.: Information Systems/H.2: DATABASE MANAGEMENT/H.2.1: Logical Design/H.2.1.0: Data models, Data discovery, computer.file_format, Linked data, 15. Life on land, Data science, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Simple Knowledge Organization System, Faceted search, Data mining, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer
Abstract: To address biodiversity issues in ecology and to assess the consequences of ecosystem changes, large quantities of long-term observational data from multiple datasets need to be integrated and characterized in a unified way. Linked open data initiatives in ecology aim at promoting and sharing such observational data at the web-scale. Here we present a web infrastructure, named Thesauform, that fully exploits the key principles of the semantic web and associated key data standards in order to guide the scientific community of experts to collectively construct, manage, visualize and query a SKOS thesaurus. The study of a thesaurus dedicated to plant functional traits demonstrates the potential of this approach. A point of great interest is to provide each expert with the opportunity to generate new knowledge and to draw novel plausible conclusions from linked data sources. Consequently, it is required to consider both the scientific topic and the objects of interest for a community of expertise. The goal is to enable users to deal with a small number of familiar and conceptual dimensions, or in other terms, facets. In this regard, a faceted search system, based on SKOS collections and enabling thesaurus browsing according to each end-users requirements is expected to greatly enhance data discovery in the context of biodiversity studies.
Published: 2014
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59. Agricultural biodiversity, social-ecological systems and sustainable diets

Author: Bruce Cogill, Guillermo Flichman, Paolo Prosperi, Thomas Allen, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM), Dipartimento di Gestione dei Sistemi Agroalimentari e Ambientali (DiGeSA), Università degli studi di Catania [Catania], 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), and Consultative Group on International Agricultural Research [CGIAR] (CGIAR)
Subjects: ECOSYSTEME, Food policy, Medicine (miscellaneous), Food Supply, AGROFOOD SYSTEM, Sustainable development, Bio-economic modelling, ECOSYSTEMS, Food Industry, Integrated assessment, MODELE BIOECONOMIQUE, 2. Zero hunger, Nutrition and Dietetics, Food security, SECURITE ALIMENTAIRE, Environmental resource management, FOOD SECURITY, Biodiversity, NUTRITION HUMAINE, language, Food systems, Crops, Agricultural, Conservation of Natural Resources, Nutrition-sensitive agriculture, Nutritional Status, Crops, Sustainable Agriculture Innovation Network, 12. Responsible consumption, HUMAN NUTRITION, BIOECONOMIC MODEL, Humans, COMPORTEMENT ALIMENTAIRE, Environmental planning, Ecosystem, Agricultural, Dietary diversity, SYSTEME AGROALIMENTAIRE, business.industry, Feeding Behavior, Diet, [SDV.SA.AEP]Life Sciences [q-bio]/Agricultural sciences/Agriculture, economy and politics, 15. Life on land, RESILIENCE, AGROBIODIVERSITE, ALIMENTATION DURABLE, language.human_language, 13. Climate action, Agriculture, SUSTAINABLE FOOD, Sustainability, Environmental science, AGROBIODIVERSITY, Agricultural biodiversity, FEEDING HABITS, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: Conference on Sustainable Diet and Food Security, 2013/05/28-29, Lille (France); International audience; The stark observation of the co-existence of undernourishment, nutrient deficiencies and overweight and obesity, the triple burden of malnutrition, is inviting us to reconsider health and nutrition as the primary goal and final endpoint of food systems. Agriculture and the food industry have made remarkable advances in the past decades. However, their development has not entirely fulfilled health and nutritional needs, and moreover, they have generated substantial collateral losses in agricultural biodiversity. Simultaneously, several regions are experiencing unprecedented weather events caused by climate change and habitat depletion, in turn putting at risk global food and nutrition security. This coincidence of food crises with increasing environmental degradation suggests an urgent need for novel analyses and new paradigms. The sustainable diets concept proposes a research and policy agenda that strives towards a sustainable use of human and natural resources for food and nutrition security, highlighting the preeminent role of consumers in defining sustainable options and the importance of biodiversity in nutrition. Food systems act as complex social–ecological systems, involving multiple interactions between human and natural components. Nutritional patterns and environment structure are interconnected in a mutual dynamic of changes. The systemic nature of these interactions calls for multidimensional approaches and integrated assessment and simulation tools to guide change. This paper proposes a review and conceptual modelling framework that articulate the synergies and tradeoffs between dietary diversity, widely recognised as key for healthy diets, and agricultural biodiversity and associated ecosystem functions, crucial resilience factors to climate and global changes.
Published: 2014
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60. Vulnerability of dynamic genetic conservation units of forest trees in Europe to climate change

Author: Jarkko Koskela, Hojka Kraigher, Jason Hubert, Wolfgang Falk, Roman Longauer, Michele Bozzano, François Lefèvre, Ditte Christina Olrik, Silvio Schueler, Federal Research and Training Centre for Forests Natural Hazards and Landscape, Bavarian State Institute of Forestry, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Northern Research Station, Forest Research, Slovenian Forestry Institute, National Forest Centre - Národné lesnícke centrum [Zvolen], Ministry of the Danish Environment, Partenaires INRAE, European Commission under Council Regulation (EC) (EUFGIS action) [870/2004, AGRI-2006-0261], and EUFORGEN Programme
Subjects: Conservation of Natural Resources, velocity of climate change, genetic conservation unit, Climate Change, [SDV]Life Sciences [q-bio], Species distribution, Niche, Vulnerability, Climate change, Forests, Models, Biological, Trees, Species Specificity, Forest ecology, Environmental Chemistry, favourability function, forest ecology, FORESTRY, climate niche modelling, General Environmental Science, Global and Planetary Change, Ecology, Climate risk, forest genetic resources, Gap analysis (conservation), 15. Life on land, Forest genetic resources, Europe, Geography, 13. Climate action, gap analysis
Abstract: International audience; A transnational network of genetic conservation units for forest trees was recently documented in Europe aiming at the conservation of evolutionary processes and the adaptive potential of natural or man-made tree populations. In this study, we quantified the vulnerability of individual conservation units and the whole network to climate change using climate favourability models and the estimated velocity of climate change. Compared to the overall climate niche of the analysed target species populations at the warm and dry end of the species niche are underrepresented in the network. However, by 2100, target species in 33-65% of conservation units, mostly located in southern Europe, will be at the limit or outside the species' current climatic niche as demonstrated by favourabilities below required model sensitivities of 95%. The highest average decrease in favourabilities throughout the network can be expected for coniferous trees although they are mainly occurring within units in mountainous landscapes for which we estimated lower velocities of change. Generally, the species-specific estimates of favourabilities showed only low correlations to the velocity of climate change in individual units, indicating that both vulnerability measures should be considered for climate risk analysis. The variation in favourabilities among target species within the same conservation units is expected to increase with climate change and will likely require a prioritization among co-occurring species. The present results suggest that there is a strong need to intensify monitoring efforts and to develop additional conservation measures for populations in the most vulnerable units. Also, our results call for continued transnational actions for genetic conservation of European forest trees, including the establishment of dynamic conservation populations outside the current species distribution ranges within European assisted migration schemes.
Published: 2014
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61. New methodological frontiers for sustainability assessment: A multidimensional vulnerability framework for the agrofood system

Author: Paolo Prosperi, Thomas Allen, Padilla, M., Luri Peri, Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Università degli studi di Catania [Catania], Italian Society of Agricultural Economics (SIDEA)., and Gennaro B. de (ed.), Nardone G. (ed.)
Subjects: INDICATORS, VULNERABILITY, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q0 - General/Q.Q0.Q01 - Sustainable Development, SYSTEME AGROALIMENTAIRE, metrics,sustainability,resilience,decision-making,causal-factors,food systems,food and Nutrition Security, DURABILITE, RESILIENCE, DECISION SUPPORT, VULNERABILITE, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, MEASUREMENT, AGROFOOD SYSTEM, Economies et finances, Economies and finances, SUSTAINABILITY, INDICATEUR, JEL: Q - Agricultural and Natural Resource Economics • Environmental and Ecological Economics/Q.Q1 - Agriculture/Q.Q1.Q18 - Agricultural Policy • Food Policy, food and Nutrition Security, decision-making, resilience, sustainability, metrics, causal-factors, food systems, MESURE, JEL: C - Mathematical and Quantitative Methods/C.C1 - Econometric and Statistical Methods and Methodology: General/C.C1.C18 - Methodological Issues: General, AIDE A LA DECISION
Abstract: International audience; Sustainable Food Security and Sustainable Diets are widely acknowledged and studied by the international community. The links between food regimes of populations and the environmental and socioeconomic issues concerning individuals, countries and geographical areas, are nowadays recognized and proved. Nevertheless, identifying metrics for a multidimensional analysis remains a challenging task. This methodological paper proposes a revisited vulnerability approach for an innovative application to food security and sustainability issues in the agrofood system. The aim is to identify qualitative and quantitative methods to consider the interrelating factors leading to vulnerability, in order to inform decision-making and adaptive strategies. An original methodological framework of the integrated vulnerability approach to analyze food insecurity and unsustainability is presented together with a metric methodology.
Published: 2013

62. Proceedings of the 1st International Workshop on Semantics for Biodiversity

Author: Larmande, Pierre, Arnaud, Elizabeth, Mougenot, Isabelle, Jonquet, Clement, Libourel Rouge, Thérèse, Ruiz, Manuel, 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), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), UMR 228 Espace-Dev, Espace pour le développement, Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), Système Multi-agent, Interaction, Langage, Evolution (SMILE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), 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), 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), ANR-12-JS02-0010, Pierre Larmande, Elizabeth Arnaud, Isabelle Mougenot, Clement Jonquet, Thérèse Libourel, Manuel Ruiz, ANR-12-JS02-0010,SIFR,Indexation sémantique de ressources biomédicales francophones(2012), 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)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Bioversity International, Consultative Group on International Agricultural Research [CGIAR], Université des Antilles (UA)-Université de Guyane (UG)-Université de Montpellier (UM)-Université de La Réunion (UR)-Avignon Université (AU)-Université de Perpignan Via Domitia (UPVD)-Institut de Recherche pour le Développement (IRD), and 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)
Subjects: Local knowledge about the value of agricultural and wild biodiversity, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Text mining, Linked data, Plant diseases and plant-pathogen relationships, [INFO.INFO-WB]Computer Science [cs]/Web, Genomics and phenomics, Environment, Agro-ecology and ecosystem services, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Biomass recycling, Ontology engineering and applications, Mobile devices, Remote sensors, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genetic resources, Visualization tools, Knowledge engineering
Abstract: International audience; Semantic web standards, tools, ontologies and related technologies have considerably matured in the recent years. Nowadays, accessing a wide catalogue of biological, social, environmental, and ecological data sources helps stakeholders working on biodiversity to answer their complex questions. Will the real time access to web resources effectively support the definition of strategies to conserve and manage biodiversity? How might semantic web technologies help us to handle the complex and heterogeneous big data related to biodiversity? The workshop aims to identify the key challenges faced by the bioinformatics community, discuss potential solutions and identify the opportunities emerging from the trans-disciplinary interactions between Plant Science and Informatics experts. Therefore, we expect the bioinformatics experts to explain how they apply semantic web standards and tools to their scientific topic, from biology, agriculture, agro-ecology, genomics, environmental studies, to social sciences, citizen sciences. Research papers presenting various aspects of semantic web technologies applied to biodiversity data, ranging from position papers to implemented systems descriptions and their evaluation, will be selected. We are particularly interested in the use of the semantic technologies to design and develop systems that supports research on agricultural and wild biodiversity conservation and management for food security. Examples may include strategies for resilience to climate change pressures, sustainability of productive ecosystems, ecosystems services monitoring or territories management, rather than systems supporting only research on climate patterns or soil erosion.
Published: 2013

63. Wheat Crop Ontology: A Species Specific Trait Ontology. Use Case: The URGI Information System

Author: Pommier, Cyril, Alaux, Michael, Kimmel, Erik, Steinbach, Delphine, Arnaud, Elizabeth, Le Gouis, Jacques, Quesneville, Hadi, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Bioversity International [Montpellier], Bioversity International [Rome], and Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR)
Subjects: [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2013

64. Conservation dynamique des Ressources Génétiques Forestières dans 33 pays d'Europe

Author: Lefèvre, Francois, Koskela, J., Hubert, J., Kraigher, H., Longauer, R., Olrik, D., Schüler, S., Bozzano, M., Alizoti, Paraskevi, Bakys, R., Baldwin, C., Ballian, D., Black Samuelsson, S., Bednarova, D., Bordács, S., Collin, E., De Cuyper, Bart, De Vries, S., Eysteinsson, T., Frydl, J., Haverkamp, M., Institut National de la Recherche Agronomique (INRA), Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), FOREST RESEARCH NORTHERN RESEARCH STATION ROSLIN GBR, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), SLOVENIAN FORESTRY INSTITUTE LJUBLJANA SVN, NATIONAL FOREST CENTRE ZVOLEN SVK, MINISTRY OF THE DANISH ENVIRONMENT NATURE AGENCY GRAESTED DNK, FEDERAL RESEARCH AND TRAINING CENTRE FOR FORESTS NATURAL HAZARDS AND LANDSCAPES VIENNA AUT, Aristotle University of Thessaloniki, SEED AND PLANT SERVICE GIRIONYS LTU, UNIVERSITY OF SARAJEVO SARAJEVO BIH, SWEDISH FOREST AGENCY UPPSALA SWE, CENTRAL AGRICULTURAL OFFICE BUDAPEST HUN, Ecosystèmes forestiers (UR EFNO), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), RESEARCH INSTITUTE FOR NATURE AND FOREST GERAARDSBERGEN BEL, Wageningen University and Research [Wageningen] (WUR), ICELAND FOREST SERVICE EGILSSTADIR ISL, FORESTRY AND GAME MANAGEMENT RESEARCH INSTITUTE JILOVISTE CZE, FEDERAL AGENCY FOR AGRICULTURE AND FOOD BONN DEU, and European Commission [870/2004, AGRI-2006-0261]
Subjects: EUROPE, CONSERVATION DYNAMIQUE, RESEAU EUROPEEN, [SDE]Environmental Sciences, ARBRES FORESTIERS, INDICATEURS
Abstract: International audience; Dynamic conservation of forest genetic resources (FGR) means maintaining the genetic diversity of trees within an evolutionary process and allowing generation turnover in the forest. We assessed the network of forests areas managed for the dynamic conservation of FGR (conservation units) across Europe (33 countries). On the basis of information available in the European Information System on FGR (EUFGIS Portal), species distribution maps, and environmental stratification of the continent, we developed ecogeographic indicators, a marginality index, and demographic indicators to assess and monitor forest conservation efforts. The pan-European network has 1967 conservation units, 2737 populations of target trees, and 86 species of target trees. We detected a poor coincidence between FGR conservation and other biodiversity conservation objectives within this network. We identified 2 complementary strategies: a species-oriented strategy in which national conservation networks are specifically designed for key target species and a site-oriented strategy in which multiple-target units include so-called secondary species conserved within a few sites. The network is highly unbalanced in terms of species representation, and 7 key target species are conserved in 60% of the conservation units. We performed specific gap analyses for 11 tree species, including assessment of ecogeographic, demographic, and genetic criteria. For each species, we identified gaps, particularly in the marginal parts of their distribution range, and found multiple redundant conservation units in other areas. The Mediterranean forests and to a lesser extent the boreal forests are underrepresented. Monitoring the conservation efficiency of each unit remains challenging; however
Published: 2013
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65. Seed exchange networks for agrobiodiversity conservation. A review

Author: Oliver T. Coomes, François Massol, Doyle McKey, Sara Tramontini, Marc Delêtre, Clélia Soler, Thomas F. Döring, Sophie Caillon, Marco Pautasso, Shawn McGuire, Devra I. Jarvis, Hélène Joly, Adeline Barnaud, Guntra A. Aistara, Christine Padoch, Pascal Clouvel, Mathieu Thomas, Paola De Santis, Selim Louafi, Isabelle Goldringer, Laure Emperaire, Eric Garine, Christian Leclerc, Elise Demeulenaere, Pierre Martin, Ludivine Eloy, Forest Pathology and Dendrology, Institute of Integrative Biology, Department of Environmental Sciences and Policy, Central European University [Budapest, Hongrie] (CEU), Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Dynamiques socio-environnementales et gouvernance des ressources (199), Systèmes de Cultures Annuelles (UPR SCA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), McGill University = Université McGill [Montréal, Canada], Botany Department, Trinity College Dublin (TCD), Trinity College Dublin, Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Biodiversity International, Acteurs, Ressources et Territoires dans le Développement (UMR ART-Dev), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Perpignan Via Domitia (UPVD)-Université Paul-Valéry - Montpellier 3 (UPVM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Patrimoines Locaux et Gouvernance (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD), Laboratoire d'ethnologie et de sociologie comparative (LESC), Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), Génétique Végétale (GV), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS), European Space Research and Technology Centre (ESTEC), European Space Agency (ESA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-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 la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UPVM), 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), 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), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), School of International Development, University of East Anglia [Norwich] (UEA), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), European Food Safety Authority (EFSA), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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]), Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Organic Research Centre (ORC), 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), Center for International Forestry Research (CIFOR), French Foundation for Research on Biodiversity (FRB), Centre de Synthese et d'Analyse sur la Biodiversite (CESAB), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7), 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 la Recherche Agronomique (INRA), Diversité et génomes des plantes cultivées [UMR DGPC], Systèmes de Cultures Annuelles [UPR SCA], Eco-Anthropologie et Ethnobiologie [EAE], Acteurs, Ressources et Territoires dans le Développement [UMR ART-Dev], Patrimoines Locaux et Gouvernance [PALOC], Génétique Végétale [GV], European Space Research and Technology Centre [ESTEC], Centre d’Ecologie Fonctionnelle et Evolutive [CEFE], Amélioration génétique et adaptation des plantes méditerranéennes et tropicales [UMR AGAP], Centre de Coopération Internationale en Recherche Agronomique pour le Développement [Cirad], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], Institut Universitaire de France [IUF], Environnements, Dynamiques et Territoires de Montagne [EDYTEM], European Food Safety Authority [EFSA], 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]), 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), Centre National de la Recherche Scientifique (CNRS)-Université Paris Nanterre (UPN), 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), School of International Development, University of East Anglia, Norwich, United Kingdom, Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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 de Recherche pour le Développement (IRD [France-Sud]), and 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)
Subjects: 0106 biological sciences, collecte de semences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, agrobiodiversité, Biodiversity, DIVERSITE SPECIFIQUE, Review, 01 natural sciences, Global change, ComputingMilieux_MISCELLANEOUS, media_common, 2. Zero hunger, FACTEUR SOCIOECONOMIQUE, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, Participation, [SHS.GEO]Humanities and Social Sciences/Geography, Simulation models, CONSERVATION DES RESSOURCES GENETIQUES, GRAINE, Agroécosystème, Seeds, P01 - Conservation de la nature et ressources foncières, Environmental Engineering, Agriculteur, Participatory approaches, media_common.quotation_subject, ECHANGE, Analyse de réseau, Complex networks, 010603 evolutionary biology, Landscape genetics, SEMENCE, PLANTE CULTIVEE, Conservation des ressources, Scenarios, Variété indigène, F03 - Production et traitement des semences, Variété, Environnement socioculturel, Environmental planning, Semence, Sustainable development, Changement climatique, business.industry, Modèle de simulation, AGRICULTEUR, 15. Life on land, AGROBIODIVERSITE, MODELISATION, Methods in ecology and evolution, [SDE.ES]Environmental Sciences/Environmental and Society, Cultural heritage, Conceptual framework, approches participatives, 13. Climate action, Agriculture, Sustainability, Agricultural biodiversity, U30 - Méthodes de recherche, Plante de culture, business, Agronomy and Crop Science, 010606 plant biology & botany, Diversity (politics)
Abstract: International audience; The circulation of seed among farmers is central to agrobiodiversity conservation and dynamics. Agrobiodiversity, the diversity of agricultural systems from genes to varieties and crop species, from farming methods to landscape composition, is part of humanity’s cultural heritage. Whereas agrobiodiversity conservation has received much attention from researchers and policy makers over the last decades, the methods available to study the role of seed exchange networks in preserving crop biodiversity have only recently begun to be considered. In this overview, we present key concepts, methods, and challenges to better understand seed exchange networks so as to improve the chances that traditional crop varieties (landraces) will be preserved and used sustainably around the world. The available literature suggests that there is insufficient knowledge about the social, cultural, and methodological dimensions of environmental change, including how seed exchange networks will cope with changes in climates, socio-economic factors, and family structures that have supported seed exchange systems to date. Methods available to study the role of seed exchange networks in the preservation and adaptation of crop specific and genetic diversity range from meta-analysis to modelling, from participatory approaches to the development of bio-indicators, from genetic to biogeographical studies, from anthropological and ethnographic research to the use of network theory. We advocate a diversity of approaches, so as to foster the creation of robust and policy-relevant knowledge. Open challenges in the study of the role of seed exchange networks in biodiversity conservation include the development of methods to (i) enhance farmers’ participation to decision-making in agro-ecosystems, (ii) integrate ex situ and in situ approaches, (iii) achieve interdisciplinary research collaboration between social and natural scientists, and (iv) use network analysis as a conceptual framework to bridge boundaries among researchers, farmers and policy makers, as well as other stakeholders.
Published: 2013
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66. Translating conservation genetics into management: pan-European minimum requirements for dynamic conservation units of forest tree genetic diversity

Author: Koskela, Jarkko, Lefèvre, Francois, Schueler, Silvio, Kraigher, Hojka, Olrik, Ditte C., Hubert, Jason, Longauer, Roman, Bozzano, Michele, Yrjänä, Leena, Alizoti, Paraskevi, Rotach, Peter, Vietto, Lorenzo, Bordács, Sándor, Myking, Tor, Eysteinsson, Thröstur, Souvannavong, Oudara, Fady, Bruno, De Cuyper, Bart, Heinze, Berthold, von Wühlisch, Georg, Ducousso, Alexis, Ditlevsen, Bjerne, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Federal Research and Training Centre for Forests Natural Hazards and Landscape, Slovenian Forestry Institute, Ministry of the Danish Environment, Partenaires INRAE, Forestry Research, Northern Research Station, National Forest Centre - Národné lesnícke centrum [Zvolen], Finnish Forest Research Institute, Aristotle University of Thessaloniki, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Agricultural Research Council (CRA), Central Agricultural Office, Veterinary Diagnostic Directorate, Norwegian Forest and Landscape Institute, Forest Service, Food and Agriculture Organization, Research Institute for Nature and Forest (INBO), Federal Research Institute for Rural Areas, Forestry and Fisheries, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), and European Commission under Council Regulation (EC) No. 870/2004 (EUFGIS action, Contract No. AGRI-2006-0261), EUFORGEN Programme
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, ressources génétiques forestières
Abstract: International audience; This paper provides a review of theoretical and practical aspects related to genetic management of forest trees. The implementation of international commitments on forest genetic diversity has been slow and partly neglected. Conservation of forest genetic diversity is still riddled with problems, and complexities of national legal and administrative structures. Europe is an example of a complex region where the dis- tribution ranges of tree species extend across large geographical areas with profound environmental dif- ferences, and include many countries. Conservation of forest genetic diversity in Europe has been hampered by a lack of common understanding on the management requirements for genetic conserva- tion units of forest trees. The challenge resides in integrating scientific knowledge on conservation genet- ics into management of tree populations so that recommendations are feasible to implement across different countries. Here, we present pan-European minimum requirements for dynamic conservation units of forest genetic diversity. The units are natural or man-made tree populations which are managed for maintaining evolutionary processes and adaptive potential across generations. Each unit should have a designated status and a management plan, and one or more tree species recognized as target species for genetic conservation. The minimum sizes of the units are set at 500, 50 or 15 reproducing individuals depending on tree species and conservation objectives. Furthermore, silvicultural interventions should be allowed to enhance genetic processes, as needed, and field inventories carried out to monitor regen- eration and the population size. These minimum requirements are now used by 36 countries to improve management of forest genetic diversity.
Published: 2013
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67. Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources

Author: Hari D. Upadhyaya, Rolf T. Folkertsma, Ping Lu, Jean-Louis Noyer, Laëtitia Gardes, C. Thomas Hash, Sophie Bouchet, Yu Li, Monique Deu, Jacques Chantereau, Elizabeth Arnaud, Jean-François Rami, Claire Billot, Jean-Christophe Glaszmann, Ronan Rivallan, Punna Ramu, Tianyu Wang, 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), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Institute of Crop Science, Rheinische Friedrich-Wilhelms-Universität Bonn, Chinese Academy of Agricultural Sciences (CAAS), Bioversity International, Consultative Group on International Agricultural Research [CGIAR], Generation Challenge Programme (GCP), Council of Scientific and Industrial Research (CSIR), New Delhi, India Microsoft Corporation, 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), 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), International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), 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), Génétique Diversité et Ecophysiologie des Céréales (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: 0106 biological sciences, Germplasm, Plant Evolution, [SDV]Life Sciences [q-bio], ADN, sorgho, lcsh:Medicine, Plant Science, Plant Genetics, 01 natural sciences, Gene flow, F30 - Génétique et amélioration des plantes, Génétique des populations, Plant Genomics, Marqueur génétique, lcsh:Science, Phylogeny, 2. Zero hunger, 0303 health sciences, Multidisciplinary, biology, food and beverages, Agriculture, Genomics, F70 - Taxonomie végétale et phytogéographie, Sorghum bicolor, Phylogeography, genetic resources, Provenance, Microsatellite, marqueur ssr, génotype, Research Article, Locus des caractères quantitatifs, DNA, Plant, Genotype, Distribution géographique, Cereals, Crops, ressource génétique, diversity, 03 medical and health sciences, Ressource génétique végétale, Variation génétique, Genetic variation, Genetics, Plant breeding, Biology, Alleles, 030304 developmental biology, diversité, Genetic diversity, Polymorphism, Genetic, Population Biology, business.industry, lcsh:R, Computational Biology, Genetic Variation, Bayes Theorem, échelle mondiale, Sorghum, biology.organism_classification, Biotechnology, Gestion des ressources, Genetic Loci, Collection de matériel génétique, Genetic Polymorphism, marqueur de sélection, Plant Biotechnology, lcsh:Q, sorghum, U30 - Méthodes de recherche, business, Sweet sorghum, Population Genetics, 010606 plant biology & botany, Microsatellite Repeats
Abstract: Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity.
Published: 2013
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68. Modelling agri-food policy impact at farm-household level in developing countries (FSSIM-Dev): application to Sierra Leone

Author: Louhichi, K., Paloma, S., Belhouchette, Hatem, Allen, T., Fabre, J., Blanco Fonseca, M., Chenoune, R., Acs, S., Flichman, G., Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and DIATAE
Subjects: FAMILY FARMS, SECURITE ALIMENTAIRE, FOOD SECURITY, [SDV.SA.AEP]Life Sciences [q-bio]/Agricultural sciences/Agriculture, economy and politics, RURAL DEVELOPMENT, AGRICULTURAL HOUSEHOLD, MENAGE AGRICOLE, PAUVRETE, SOUTIEN DES PRIX, POVERTY, [SHS]Humanities and Social Sciences, PAYS EN DEVELOPPEMENT, DEVELOPING COUNTRIES, EXPLOITATION AGRICOLE FAMILIALE, SIERRA LEONE, BIOECONOMIC MODEL, PRICE SUPPORT, GESTION DE L'EXPLOITATION AGRICOLE, FARM MANAGEMENT, RICE, MODELE BIOECONOMIQUE, DEVELOPPEMENT RURAL, RIZ
Abstract: Scientific and Technical Research Reports: EUR 25962. Final report: FSSIM-AFRICA.; International audience; This report presents a farm household model for use in the context of developing countries to gain knowledge on food security and rural poverty alleviation under different economic conditions and agri-food policy options. This model, called FSSIM-Dev (Farming System Simulator for Developing Countries), is an extension of the FSSIM model developed within the SEAMLESS project for impact assessment of agricultural and environmental policies on farm performances across Europe. FSSIM-Dev is conceived to be applied for family agriculture where farm household production, consumption and labour allocation decisions are non-separable due to market imperfections. Contrary to most well-known household models which are econometric-based, FSSIM-Dev is a non-linear optimization model which simultaneously solves a set of microeconomic models reproducing the behaviour of representative farm households. FSIM-Dev is designed to capture five key features of developing countries' agriculture: non-separability of production and consumption decisions; interaction among farm households for market factors; heterogeneity of farm households with respect to their both consumption baskets and resource endowments; inter-linkage between transaction costs and market participation decisions; and the seasonality of farming activities and resource use. Model use is illustrated in this report with an analysis of the combined effects of rice support policy and improved rice cropping management on the livelihood of representative farm households in Sierra Leone. Results show that both the rice support policy and the improved crop management would significantly increase rice productivity and boost household income but they are not sufficient to fight poverty since most of the farm household types would continue to live below the extreme poverty line of 1 USD-equivalent per day.
Published: 2013
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69. Chado controller: advanced annotation management with a community annotation system

Author: Olivier Garsmeur, Claire Poiron, Stéphanie Bocs, Valentin Guignon, Tim Carver, Gaëtan Droc, Michael Alaux, Franc-Christophe Baurens, Mathieu Rouard, 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), 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), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), The Wellcome Trust Sanger Institute [Cambridge], Guignon, Valention, and Bocs, Stéphanie
Subjects: 0106 biological sciences, Computer science, [SDV]Life Sciences [q-bio], Application des ordinateurs, Banque de gènes, Ontology (information science), computer.software_genre, 01 natural sciences, Biochemistry, F30 - Génétique et amélioration des plantes, Documentation, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), computer.programming_language, base de données, 0303 health sciences, Database, Database schema, Genomics, Computer Science Applications, Computational Mathematics, Applications Note, C30 - Documentation et information, Computational Theory and Mathematics, annotation, Vocabulary, Controlled, Système d'information, Sandbox (software development), management, Statistics and Probability, Chado database schema, Databases and Ontologies, annotation génomique, 03 medical and health sciences, Annotation, Control theory, Controlled vocabulary, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, 030304 developmental biology, Génome, Computational Biology, Molecular Sequence Annotation, Database Management Systems, U30 - Méthodes de recherche, Perl, computer, Software, 010606 plant biology & botany
Abstract: Summary: We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl. Availability: The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form Contact: valentin.guignon@cirad.fr; stephanie.sidibe-bocs@cirad.fr Supplementary information: Supplementary data are available at Bioinformatics online.
Published: 2012
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70. More efficient conservation and use of vegetable genetic resources in Europe: ECPGR achievement and perspectives

Author: Emmanuel Geoffriau, R. van Treuren, Ferdinando Branca, K. Smékalova, E. R. J. Keller, T. Kotlinska, D. Astley, Charlotte J. Allender, María José Díez, W. van Dooijeweert, Lorenzo Maggioni, M. C. Daunay, N. Bas, Johannes M.M. Engels, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Wageningen University and Research [Wageningen] (WUR), Universitat Politècnica de València (UPV), Leibniz Institute of Plant Genetics and Crop Plant Research, Department of vegetables and special crops, Crop Research Institute, University of Warwick, Università degli Studi di Catania (UniCT), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-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), Plant genetic resources laboratory, Research institute of vegetables crops (RIVC), Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Wageningen University and Research Centre [Wageningen] (WUR), Universitat Politecnica de Valencia (UPV), Regional office for Europe bioversity international, and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: 0106 biological sciences, Leafy vegetables, Centre for Genetic Resources, The Netherlands, [SDV]Life Sciences [q-bio], Centre for Genetic Resources, Brassica, Horticulture, 01 natural sciences, resource preservation, ressource génétique, biodiversité, Allium, Genetic resources, Vegetables, conservation des ressources, vegetable, European cooperation, Environmental planning, Solanaceae, 2. Zero hunger, collection botanique, Cucurbits, The Netherlands, 04 agricultural and veterinary sciences, légume, 15. Life on land, vegetables, genetic resources, European cooperation, Brassica, Allium, Geography, Centrum Genetische Bronnen Nederland, Umbellifers, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, plant collections, Curcubitaceae, 010606 plant biology & botany
Abstract: The European Cooperative Programme for Plant Genetic Resources (ECPGR) is a regional network funded by the European countries and coordinated by Bioversity International. The Vegetables Network with representatives of 42 countries, is one of the crop specific ECPGR networks (http://www.ecpgr.cgiar.org/ networks/vegetables.html). It consists of six Working Groups (WGs), i.e., on Allium, Brassica, Cucurbits, Leafy Vegetables, Solanaceae and Umbellifer Crops. Sharing responsibilities for the ex situ conservation of European vegetable crops genetic resources is the highest priority of the Vegetables Network. It is foreseen that the rationalization of the collections will lead to higher cost-efficiency, and improvement of plant genetic resources documentation and quality. These efforts will be continued within the framework of the AEGIS initiative (A European Genebank Integrated System) (http://www.aegis.cgiar.org/). Challenges for the Vegetables Network include the identification of the so-called Most Appropriate Accessions (MAA) for each crop for their inclusion in the decentrally managed European Collection, and the development of agreed crop specific technical standards for conservation. Achievements of the Network in recent years include the development of European Central Crop Databases (ECCDBs), quality standards for collection man-agement of seed-propagated crops and cryopreserved material, safety duplication improvement and definition of minimum characterization descriptors. Several EU-funded projects have initiated and accelerated the activities of the WGs. Apart from further improvements within the framework of AEGIS, the Network is planning a number of other initiatives, such as improving collaboration at the global level (Allium), developing molecular characterization protocols (lettuce), filling the gaps in the conservation of wild relatives (Brassica and Umbellifer Crops), and improving the Network’s communication with the scientific community and the public at large.
Published: 2011

71. Genetic characterization of two traditional leafy vegetables (Sesamum radiatum Thonn. ex Hornem and Ceratotheca sesamoides Endl.) of Benin, using flow cytometry and amplified fragment length polymorphism (AFLP) markers

Author: null Adeacute oti, null K, null Rival, null A, null Dansi, null Santoni, null S, null Brown, null Beule, null T, null Nato, null Henry, null Y, Vodouhe R, null Loko, Y L, null Sanni, Université d'Abomey-Calavi, University of Abomey Calavi (UAC), 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]), 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), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Université d’Abomey-Calavi = University of Abomey Calavi (UAC), and 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)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Polymorphisme génétique, ADN, légumes à feuilles, 01 natural sciences, Applied Microbiology and Biotechnology, F30 - Génétique et amélioration des plantes, Marqueur génétique, leafy vegetables, 0303 health sciences, medicine.diagnostic_test, biology, ploidy, F70 - Taxonomie végétale et phytogéographie, genetic diversity, Nuclear DNA, Légume feuille, Amplified fragment length polymorphism (AFLP) markers, Ceratotheca sesamoides, flow cytometry, genetic diversity, ploidy, Sesamum radiatum, leafy vegetables, Ploidy, Ceratotheca sesamoides, Biotechnology, Sesamum radiatum, Flow cytometry, 03 medical and health sciences, Botany, Genetics, medicine, Molecular Biology, Genome size, 030304 developmental biology, Genetic diversity, cytométrie en flux, flow cytometry, biology.organism_classification, Amplified fragment length polymorphism, amplified fragment length polymorphism (AFLP) markers, U30 - Méthodes de recherche, stratégies de reproduction, fragments amplifiés, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: AGAP : Equipe AFEF ‘Architecture et Fonctionnement des Espèces fruitières’ ; Team AFFS ‘Architecture and Functioning of Fruit Species’ Contact : adansi2001@gmail.com; International audience; Amplified fragment length polymorphism (AFLP) markers and flow cytometry were applied for the genetic characterization of wild and cultivated accessions of Sesamum radiatum and Cerathoteca sesamoides; two neglected and underutilized species of traditional leafy vegetable consumed in Benin. The average 2C nuclear DNA content per nucleus was found to be 1.99 +/- 0.06 and 1.05 +/- 0.06 pg for S. radiatum and C. sesamoides, respectively which correspond to estimated genome size of 1946,22 Mpb for S. radiatum and 1026,9 Mpb for C. sesamoides. No variation in DNA content could be detected within accessions from each analysed species. Also, no relation was found between nuclear DNA content, ecogeographical origin and the status (cultivated or wild) of the analyzed accessions. AFLP markers revealed low diversity within the accessions analyzed. Results from the study contributed to a better characterization of S. radiatum and C. sesamoides accessions and will help in defining both genetic resources conservation and breeding strategies.
Published: 2011
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72. Forest ecosystem genomics and adaptation EVOLTREE conference report

Author: J. Turok, Bernd Degen, Silvia Fluch, Antoine Kremer, Barbara Vinceti, Gerhard Mueller-Starck, Birgit Ziegenhagen, Gail Taylor, Ricardo Alía, Jarkko Koskela, Christophe Plomion, François Lefèvre, Jaroslav Burczyk, Hans Peter Koelewijn, Michele Morgante, Felix Gugerli, Dušan Gömöry, Outi Savolainen, Stephen Cavers, Reiner Finkeldey, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), University of Bydgoszcz (KWUB), Natural Environment Research Council (NERC), Federal Research Centre for Forestry and Forest Products, Georg-August-University [Göttingen], ARC Seibersdorf Res, Technical University in Zvolen (TUZVO), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Wageningen University and Research Centre (WUR), International Plant Genetic Resources Institute, Partenaires INRAE, Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Università degli Studi di Udine - University of Udine [Italie], Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), University of Southampton, Department of Biology, University of Oulu, and Philipps University of Marburg
Subjects: 0106 biological sciences, Service (systems architecture), Climate change, Context (language use), adaptation, Biology, Horticulture, 01 natural sciences, Session (web analytics), 03 medical and health sciences, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Forest ecology, CE - Molecular Ecology Ecotoxicology and Wildlife Management, Genetics, genomics, Wageningen Environmental Research, Adaptation, Adaptation (computer science), Molecular Biology, 030304 developmental biology, 0303 health sciences, business.industry, End user, Environmental resource management, genomique, Stakeholder, Forestry, Genomics, 15. Life on land, climate change, 13. Climate action, business, Life Sciences, Plant Breeding/Biotechnology, Biotechnology, Tree Biology, Plant Genetics & Genomics, 010606 plant biology & botany
Abstract: article présenté lors de l'International conference "Forest ecosystem genomics and adaptation" EVOLTREE ; Madrid (Espagne) - (2010-06-09 - 2010-06-11) / Conférence; International audience; This article is a summary report of the international conference "Forest ecosystem genomics and adaptation" organized by the EVOLTREE Network of Excellence in San Lorenzo de El Escorial (Madrid), Spain, from 9 to 11 June 2010. Main achievements and results of the network are presented for the eight thematic sessions and a stakeholder session. The conference has shown that adaptive responses of trees to biotic or abiotic selection pressures can now be investigated at the gene level for traits of adaptive significance. Candidate genes have been catalogued for phenological and drought-related traits in important tree families (Salicaceae, Fagaceaea and Pinaceae), and their variation in natural populations is being explored. Genomics can now be integrated in ecological research to investigate evolutionary response to climate changes in a wide range of species. New avenues of research were also highlighted as the exploration of gene networks involved in adaptive responses and the combination of experimental and modelling approaches to disentangle components of evolutionary changes triggered by climate change. The main focus of the conference was the adaptation of trees to environmental changes. The conference was organized in eight thematic sessions ranging from genomic approaches aiming at identifying genes of adaptive significance to practical issues regarding mitigation options for combating climate change. A dialogue between scientists and end users took place in the form of an ad hoc stakeholder session. A panel of end users from various forest and policy-making institutions expressed their expectations, and the discussions with the scientists addressed the potential applications of research findings to the management of genetic resources in the context of climate changes. The conference was introduced by two keynote speakers Dr. Pierre Mathy from the European Commission, Directorate General of Research, and Dr. Allen Solomon, former National Program Leader for Global Change, US Forest Service. All the thematic sessions were introduced by high-level invited speakers from the respective fields.
Published: 2011
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73. Climate change and forest genetic resources – State of knowledge, risks and opportunities

Author: Loo, Judy, Fady, Bruno, Dawson, Ian, Vinceti, Barbara, Baldinelli, Giulia, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), and Commanditaire : Food and Agriculture Organization
Subjects: [SDV]Life Sciences [q-bio]
Abstract: This paper is one of several requested by the Commission on Genetic Resources for Food and Agriculture that seek to review and examine the impacts of climate change on genetic resources of organisms that are important for human well-being, and the potential role of these resources in mitigating and adapting to change. This paper, which focuses on forest genetic resources (FGR), does so in the context of trees in natural forests, plantations and agroforestry systems. The paper is structured to match those being prepared by the other sectors and consists of a review of the current state of knowledge, followed by the identification of gaps and priorities for action. A glossary is included to clarify terms
Published: 2011

74. A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes

Author: Cedric Chauve, Aïda Ouangraoua, Sylvie Hamel, Valentin Guignon, Bioinformatics and Sequence Analysis (BONSAI), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Département d'Informatique et de Recherche Opérationnelle [Montreal] (DIRO), Université de Montréal (UdeM), Department of Mathematics [Burnaby] (SFU), and Simon Fraser University (SFU.ca)
Subjects: Scheme (programming language), String-to-string correction problem, Theoretical computer science, General Computer Science, 0206 medical engineering, Sequence alignment, Needleman–Wunsch algorithm, 0102 computer and information sciences, 02 engineering and technology, Wagner–Fischer algorithm, Dynamic programming, 01 natural sciences, Theoretical Computer Science, [INFO]Computer Science [cs], Mathematics, computer.programming_language, Hierarchy (mathematics), Arc-annotated sequences, 010201 computation theory & mathematics, Edit distance, Algorithm, computer, 020602 bioinformatics, Computer Science(all)
Abstract: International audience; In this paper, we propose a new algorithm for the alignment of nested arc-annotated sequences, having applications in the comparison of RNA secondary structures without pseudo-knots. We use a general edit distance model between arc-annotated sequences, that considers classical sequences of edit operations and structural edit operations on arcs. In this model, the general edit distance problem under a non-constrained weight scheme, is NP-hard. Recently, a hierarchy of arc-annotated sequence alignment problems that highlights less general, but tractable, problems was introduced. We refine this hierarchy of alignment problems and extend the class of tractable alignment problems. Up to date, the alignment problem we solve is the most general one that is known to be tractable in the considered edit distance model and under arbitrary weight schemes. This algorithm is efficient, as its asymptotic time and space complexities are the same as the complexities of the best previously published algorithm.
Published: 2011
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75. Climate change and forest genetic resources (FGR): state of knowledge, risks and opportunities

Author: Fady, Bruno, Loo, Judy, Dawson, Ian, Vinceti, Barbara, Baldinelli, Julia, Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Bioversity International [Montpellier], Bioversity International [Rome], and Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR)
Subjects: arbre forestier, changement climatique, regénération naturelle, [SDV]Life Sciences [q-bio], diversité génétique, adaptation, ComputingMilieux_MISCELLANEOUS, sécheresse
Abstract: International audience
Published: 2011

76. Construction collective de standards de données en écologie : standards de données en écologie

Author: Laporte, Marie-Angélique, Garnier, Eric, Mougenot, Isabelle, Mougenot, Isabelle, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), 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]), Models And Reuse Engineering, Languages (MAREL), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Bioversity International, Consultative Group on International Agricultural Research [CGIAR], Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: [INFO.INFO-AI] Computer Science [cs]/Artificial Intelligence [cs.AI], [SDE] Environmental Sciences, [INFO.INFO-WB] Computer Science [cs]/Web, web de données, [INFO.INFO-WB]Computer Science [cs]/Web, Data models, modèles de données, Web of data, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Functional ecology, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, thésaurus, écologie fonctionnelle, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Lack of data standards in functional ecology inhibits the most efficient use of long-term observational data. Such data standards however, would be accepted by the whole community if they reflect the opinion and experience of the majority. Here we propose an approach to this problem that is based on models, which integrate web of data resources to guide a community of experts in the collaborative and joint construction of a generally accepted thesaurus. Our practical approach is based on the design of a vocabulary that is dedicated to functional traits in plants. Once the thesaurus has been stabilized, it will be mobilized on the web of data, with the expectation that this approach will lead to a domain ontology in functional ecology., L'écologie fonctionnelle manque de standards de données, pour pouvoir pleinement faire usage des données, issues des observations menées sur le long terme. Ces standards ne seront acceptés par l'ensemble de la communauté, que si ils reflètent la perception du plus grand nombre. Nous proposons une approche centrée sur les modèles, qui exploite les ressources généralistes du web de données afin de guider une communauté d'experts dans la construction collective d'un thésaurus. La démarche est mise en pratique au travers de la construction du thésaurus dédié aux traits fonctionnels chez les plantes. Le thésaurus, une fois stabilisé, sera à son tour mobilisable sur le web et viendra amorcer la construction d'une ontologie de domaine en écologie fonctionnelle.
Published: 2011

77. More efficient conservation and use vegetable genetic resources in Europe: ECPGR achievements

Author: Daunay, M-Christin, Allender, C., Astley, D., Bas, N., Branca, Francesco, Diez-Niclos, M.J., Van Dooijeweer, W., Geoffriau, Emmanuel, Keller, J., Kotlinska, T., Smekalova, K., Van Treuren, R., Engels Maggioni, J.L., Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), University of Warwick, Wageningen University and Research Centre (WUR), Università degli Studi di Catania (UniCT), Universitat Politècnica de València (UPV), Unité mixte de recherche génétique et horticulture Genhort, Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-Institut National d'Horticulture, Leibniz Institute of Plant Genetics and Crop Plant Research, Research institute of vegetables crops (RIVC), Crop research institute, Bioversity International [Montpellier], Bioversity International [Rome], and Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR)
Subjects: [SDV]Life Sciences [q-bio], SOLANACEAE, GENBANK, CUCURBITS, ALLIUM, ComputingMilieux_MISCELLANEOUS, BRASSICA, UMBELLIFER, ECPGR
Abstract: International audience
Published: 2010

78. GnpAnnot community annotation system: features, qualifiers, values

Author: Sidibe-Bocs, Stéphanie, Legeai, Fabrice, Droc, Gaëtan, Rouard, Mathieu, Alaux, Michael, Leroy, P., Fournier, Philippe, Terrier, Nancy, Baurens, Franc-Christophe, Garsmeur, Olivier, Poiron, Claire, Guignon, V., Simon, A., Hoede, Claire, Steinbach, Delphine, Lebrun, Marc-Henri, Tagu, Denis, Quesneville, Hadi, Amselem, Joelle, Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Biologie Intégrative et Virologie des Insectes [Univ. de Montpellier II] (BIVI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Sciences Pour l'Oenologie (SPO), Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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 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)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: [SDV] Life Sciences [q-bio], Génie génétique, C30 - Documentation et information, [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, [SDV]Life Sciences [q-bio], [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [SDV.IDA] Life Sciences [q-bio]/Food engineering, H10 - Ravageurs des plantes, F30 - Génétique et amélioration des plantes
Abstract: Correspondance: stephanie.sidibe-bocs@cirad.fr; International audience; In January 2009, 991 complete genomes have been already published and 3376 genome sequencing projects are ongoing, leading to an explosion of data that needs to be stored, curated and analyzed. GnpAnnot is a project on green genomics which intends to develop a system of structural and functional annotation supported by comparative genomics and dedicated to plant and bio-aggressor genomes allowing both automatic predictions and manual curations of genomic objects. The core of GnpAnnot is a community annotation system (CAS) based on GMOD components: Chado / GBrowse / Apollo / Artemis. The system should also enable to browse comparative genomics results, to build queries and to export sets of gene lists and gene reports in various formats. The system should allow the annotation reconciliation, history, integrity, consistency and update and the management of public and private projects. To facilitate the work of the curators, four steps are crucial: 1. To provide homogeneous features, qualifiers and values for genomic objects; 2. To share a strong CAS: run high quality combiners / pipelines to predict automatically genomic objects which are stored in a relational database management system and then available from graphical and textual fast browsers and powerful editors; 3. To define annotation rules, train the annotators and organize annotation jamborees; 4. To submit the results in public sequence knowledge bases in an easy way. In this work we focus on the first and third steps. A mapping between different known sources: sequence ontology, DDBJ / EMBL / GenBank feature definition, GFF3, Chado, gene nomenclatures, transposable element classification and annotation guidelines from various genome project consortia is described. Homogeneous feature keys, qualifiers and value format with a maximum of controlled vocabularies for genes and transposable elements are proposed. Rules to annotate, in a coherent way, the structure and the function of genes and the structure and the classification of transposable elements are proposed. These rules could be useful both for automatic predictions and manual curation. Examples of annotations on a BAC sequence of a monocot are presented.
Published: 2009

79. Insights into the genome of Musa (banana), a giant herb bearing fleshy fruits

Author: d'Hont, Angélique, Piffanelli, Pietro, Lescot, Magali, Town, Chris, Leebens-Mack, Jim, Blanc, Guillaume, Souza, Manoel, Pappas, Giorgio, Sasaki, Takuji, Roux, Nicolas, Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), J. Craig Venter Institute [La Jolla, USA] (JCVI), Department of Plant Biology, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), CENARGEN, Brazilian Agricultural Research Corporation (Embrapa), Universidade Católica de Brasília (UCB), National Institute of Agrobiological Sciences, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), ProdInra, Migration, and Universidade Católica de Brasília=Catholic University of Brasília (UCB)
Subjects: PAYS EN DEVELOPPEMENT, [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, BANANIER, [SDV.IDA]Life Sciences [q-bio]/Food engineering, food and beverages, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [SDV.IDA] Life Sciences [q-bio]/Food engineering, RIZ, GENOMIQUE
Abstract: International audience; Musa species, comprising dessert and cooking bananas, represent the fourth most important crop in developing countries. They are monocotyledons of the Musa species, comprising dessert and cooking bananas, represent the fourth most important crop in developing countries. They are monocotyledons of the Zingiberales order and the Musaceae family. We have compared genomic sequence in two Musa species with orthologous regions in the rice genome. We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. Further sequencing efforts should be focused first on the A genome of M. acuminata, which has a major contribution to banana and plantain diversity. This will enable: - alignment of the Musa genome in relation to major grasses, including rice and sorghum- phylogenomic analysis of gene families and metabolic pathways among monocots- use as a template for positional cloning of genes of agricultural interest- use as a support to develop genomic tools for whole-genome expression analysis- use as a template for re-sequencing and deep diversity analysis in the Musa gene pool.
Published: 2009

80. Heterozygosity In Diploid Musa Lines: Implications For Marker Development, Genomics, Sequencing And Breeding Vegetatively Propagated Crops

Author: Heslop Harrison, Pat, Cheung, Foo, Moskal, William A., Hippolyte, Isabelle, Baurens, Franc-Christophe, Bakry, Frédéric, Sasaki, Takuji, Matsumoto, Takashi, Rouard, Mathieu, Schwarzacher, Trude, Roux, Nicolas, Town, Christopher, University of Leicester, J. Craig Venter Institute [La Jolla, USA] (JCVI), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), National Institute of Agrobiological Sciences, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and ProdInra, Migration
Subjects: [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, [SDV.IDA]Life Sciences [q-bio]/Food engineering, BANANIER PLANTAIN, food and beverages, Musa, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [SDV.IDA] Life Sciences [q-bio]/Food engineering, DIVERSITE GENETIQUE, GENOMIQUE, F30 - Génétique et amélioration des plantes
Abstract: International audience; Musa species (bananas and plantains) are usually vegetatively propagated, and we have measured the levels and nature of heterozygosity within various accessions to examine genetic and genomic diversity, to compare heterozygosity with other species which are in-breeding, to investigate the feasibility of shot-gun sequencing approaches in potentially heterozygous plants, to optimise marker development, and to better characterize a single doubled-haploid Musa accession. We studied genic regions, areas flanking SSRs, and non-gene, non-SSR fragments of the genome. We analysed heterozygosity in single plants of various accessions of diploid banana (Musa) accessions by two approaches: PCR amplification of fragments of genomic DNA and sequencing, and by comparison of sequenced BACs from homologous chromosome regions from single plants. The study was carried out with a focus on Musa acuminata ‘Calcutta 4’, ‘Pahang’ and another a Musa malaccensis accession, and a doubled haploid line derived from ‘Pahang’, along with some sequences from M. schizocarpa and M. balbisiana
Published: 2008

81. Quantitative trait loci associated with adaptation to Mediterranean dryland conditions in barley

Author: M. von Korff, Salvatore Ceccarelli, A. Del Greco, Dominique This, Stefania Grando, Michael Baum, International Center for Agricultural Research in the Dry Areas [Syrie] (ICARDA), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Développement et amélioration des plantes (UMR DAP), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genetic Markers, 0106 biological sciences, Candidate gene, Rain, Quantitative Trait Loci, Plant genetics, Population, Drought tolerance, Biology, Quantitative trait locus, Genes, Plant, 01 natural sciences, 03 medical and health sciences, Genetics, Cultivar, education, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, Mediterranean Region, fungi, Water, food and beverages, Hordeum, General Medicine, 15. Life on land, Adaptation, Physiological, Plant Leaves, Agronomy, Genetic marker, Seeds, Hordeum vulgare, Agronomy and Crop Science, 010606 plant biology & botany, Biotechnology
Abstract: Correspondance: m.baum@cgiar.org; UMR DAP équipe SEG; International audience; The objective of the present study was to identify quantitative trait loci (QTL) influencing agronomic performance across rain fed Mediterranean environments in a recombinant inbred line (RIL) population derived from the barley cultivars ER/Apm and Tadmor. The population was tested in four locations (two in Syria and two in Lebanon) during four consecutive years. This allowed the analysis of marker main effects as well as of marker by location and marker by year within location interactions. The analysis demonstrated the significance of crossover interactions in environments with large differences between locations and between years within locations. Alleles from the parent with the higher yield potential, ER/ Apm, were associated with improved performance at all markers exhibiting main effects for grain yield. The coincidence of main effect QTL for plant height and yield indicated that average yield was mainly determined by plant height, where Tadmor’s taller plants, being susceptible to lodging, yielded less. However, a number of crossover interactions were detected, in particular for yield, where the Tadmor allele improved yield in the locations with more severe drought stress. The marker with the highest number of cross-over interactions for yield and yield component traits mapped close to the flowering gene Ppd-H2 and a candidate gene for drought tolerance HVA1 on chromosome 1H. Effects of these candidate genes and QTL may be involved in adaptation to severe drought as frequently occurring in the driest regions in the Mediterranean countries. Identification of QTL and genes affecting field performance of barley under drought stress is a first step towards the understanding of the genetics behind drought tolerance.
Published: 2008
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82. I-GOST a phylogenomic tool for plant comparative genomics

Author: Conte, Matthieu, Rouard, Mathieu, Droc, Gaëtan, Perin, Christophe, ProdInra, Migration, Polymorphismes d'intérêt agronomique (UMR PIA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Bioversity International [Montpellier], Bioversity International [Rome], and Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR)
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], RIZ, GENOMIQUE, F30 - Génétique et amélioration des plantes
Abstract: International audience; I-GOST (Iterative GreenPhyl Orthologous Search Tool) is a fast and user friendly comparative genomic program using a phylogeny-based method to infer orthologs and paralogs in plants. This tools use precomputed phylogeny develops on Oryza sativa and Arabidopsis thaliana full genomes from GreenPhylDB (http://greenphyl.cirad.fr). I-GOST intends to provide a reliable tool for sequence annotation, gene functional analysis or candidate gene search for any plant genome. I-GOST improves time processing performance by using pre calculated phylogenetic analyses available for more than 4000 of validated families from GreenPhylDB database. I-GOST gives clear phylogenetic scores, ranked by bootstrap confidence from a list of plant genes. I-GOST is a publicly accessible tool available on-line (http://greenphyl.cines.fr/cgi-bin/i-gost.cgi)
Published: 2008

83. Sustainability and Food & Nutrition Security

Author: Martine Padilla, Bruce Cogill, Paolo Prosperi, Iuri Peri, Thomas Allen, Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and Università degli studi di Catania [Catania]
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Biodiversité et Ecologie, Vulnerability, VULNERABILITE, INDICATEUR COMPOSITE, Social Sciences (all), AGROFOOD SYSTEM, résilience, alimentation durable, Methods and statistics, VOLATILITE DES PRIX, 11. Sustainability, food systems, sustainable diets, environment, metrics, resilience, système alimentaire, crise alimentaire, alimentation durablerégime alimentaire, résiliencedurabilité, Sustainability organizations, Etudes de l'environnement, 2. Zero hunger, [SHS.STAT]Humanities and Social Sciences/Methods and statistics, Food security, food systems,sustainable diets,environment,metrics,resilience, General Arts and Humanities, Environmental resource management, 1. No poverty, General Social Sciences, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Agricultural sciences, Food systems, Santé publique et épidémiologie, régime alimentaire, Environment, Metrics, Resilience, Sustainable diets, Arts and Humanities (all), NUTRITION HUMAINE, Alimentation et Nutrition, food systems, sustainable diets, environment, metrics, resilience, système alimentaire, Social sustainability, Food systems, sustainable diets, resilience, metrics, HUMAN FEEDING, 12. Responsible consumption, Economies et finances, Biodiversity and Ecology, HUMAN NUTRITION, Vulnerability assessment, Food and Nutrition, FOOD SUPPLY, REGION MEDITERRANEENNE, Environmental studies, VULNERABILITY, Sustainable development, ALIMENTATION HUMAINE, SYSTEME AGROALIMENTAIRE, business.industry, COMPOSITE INDICATOR, ADAPTATION AU CHANGEMENT, Environmental and Society, durabilité, COMPORTEMENT, RESILIENCE, 15. Life on land, ADAPTATION TO CHANGE, [SDE.ES]Environmental Sciences/Environmental and Society, Méthodes et statistiques, DISPONIBILITE ALIMENTAIRE, Economies and finances, crise alimentaire, SUSTAINABLE FOOD, 13. Climate action, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, Sustainability, ALIMENTAIRE, DEVELOPPEMENT DURABLE, SUSTAINABLE DEVELOPMENT, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, FEEDING HABITS, MEDITERRANEAN REGION, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environnement et Société, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Sciences agricoles
Abstract: International audience; Recurrent food crises and climate change, along with habitat loss and micronutrient deficiencies, are global issues of critical importance that have pushed food security and environmental sustainability to the top of the political agenda. Analyses of the dynamic linkages between food consumption patterns and environmental concerns have recently received considerable attention from the international and scientific community. Using the lens of a broad sustainability approach, this conceptual article aims at developing a multidimensional framework to evaluate the sustainability of food systems and diets, applicable to countries of the Mediterranean region. Derived from natural disaster and sustainability sciences, a vulnerability approach, enhanced by inputs from the resilience literature, has been adapted to analyze the main issues related to food and nutrition security. Through causal factor analysis, the resulting conceptual framework improves the design of information systems or metrics assessing the interrelated environmental, economic, social, and health dynamics of food systems.
Published: 2014
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84. Urbanization and food security ! in Mediterranean countries: ! A multidimensional vulnerability approach

Author: Paolo Prosperi, Allen, T., Peri, I., Padilla, M., Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and Arnal C. (ed.), Perrin C. (ed.)
Subjects: Biodiversité et Ecologie, système alimentaire, VULNERABILITE, AGROFOOD SYSTEM, [SHS]Humanities and Social Sciences, Biodiversity and Ecology, SUSTAINABILITY, Methods and statistics, Food and Nutrition, REGION MEDITERRANEENNE, securité alimentaire, ComputingMilieux_MISCELLANEOUS, Environmental studies, Etudes de l'environnement, VULNERABILITY, food systems, sustainability, metrics, cities, resilience, urbanisation, SECURITE ALIMENTAIRE, SYSTEME AGROALIMENTAIRE, FOOD SECURITY, Environmental and Society, durabilité, [SDV.SA.AEP]Life Sciences [q-bio]/Agricultural sciences/Agriculture, economy and politics, URBANIZATION, DURABILITE, ALIMENTATION DURABLE, Méthodes et statistiques, Agricultural sciences, SUSTAINABLE FOOD, Alimentation et Nutrition, ville, MEDITERRANEAN REGION, Environnement et Société, région méditerranéenne, Sciences agricoles
Abstract: International audience

85. Metrics of sustainable diets and food systems: insights from a multi-institutional research partnership

Author: Martine Padilla, Paolo Prosperi, Bruce Cogill, Thomas Allen, Luri Peri, Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM), Marchés, Organisations, Institutions et Stratégies d'Acteurs, 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)-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), Di3A, Universitat Politècnica de Catalunya [Barcelona] (UPC), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), and University of Catania [Italy]
Subjects: INDICATORS, ALIMENTATION HUMAINE, SECURITE ALIMENTAIRE, SYSTEME AGROALIMENTAIRE, FOOD SECURITY, [SDV.SA.AEP]Life Sciences [q-bio]/Agricultural sciences/Agriculture, economy and politics, HUMAN FEEDING, DURABILITE, RESILIENCE, AGROFOOD SYSTEM, DIET, MEASUREMENT, REGIME ALIMENTAIRE, [SHS]Humanities and Social Sciences, SUSTAINABILITY, INDICATEUR, Sustainable Food Systems, EVALUATION, MESURE, Metrics, MEDITERRANEAN REGION, Sustainable Diets, REGION MEDITERRANEENNE, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The Metrics of Sustainable Diets and Food Systems project is a multi-institutional initiative realized in partnership by Bioversity International and CIHEAM-Montpellier (2013-2014) that aims at exploring the different approaches to the assessment of sustainability of diets and food systems, establishing a multidisciplinary taskforce of experts and identifying a shortlist of indicators for sustainable diets and food systems to inform policy-makers. The initial focus was on the Mediterranean region. The research approach builds on the assumptions that sustainability assessment aims at capturing the ability of a system to maintain and enhance its essential functions over time, and that sustainability addresses threats to preserving life support systems, including their capacity to withstand and adjust.

86. Assessing food security and environmental sustainability in the Mediterranean region: a vulnerability participatory approach for a multidimensional framework

Author: Paolo Prosperi, Allen, T., Padilla, M., Peri, I., Bioversity International [Montpellier], Bioversity International [Rome], and Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR)
Subjects: VULNERABILITY, INDICATORS, SECURITE ALIMENTAIRE, ALIMENTATION HUMAINE, SYSTEME AGROALIMENTAIRE, FOOD SECURITY, [SDV.SA.AEP]Life Sciences [q-bio]/Agricultural sciences/Agriculture, economy and politics, HUMAN FEEDING, DURABILITE, RESILIENCE, VULNERABILITE, ALIMENTATION DURABLE, MEASUREMENT, AGROFOOD SYSTEM, [SHS]Humanities and Social Sciences, SUSTAINABILITY, INDICATEUR, SUSTAINABLE FOOD, MESURE, ComputingMethodologies_GENERAL, MEDITERRANEAN REGION, REGION MEDITERRANEENNE, ComputingMilieux_MISCELLANEOUS
Abstract: Poster; International audience

87. An approach to the multidimensional assessment of food security and environmental sustainability: a vulnerability framework for the Mediterranean region

Author: Paolo Prosperi, Allen, T., Padilla, M., Peri, I., Cogill, B., Bioversity International [Montpellier], Bioversity International [Rome], and Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR)
Subjects: VULNERABILITY, INDICATORS, SECURITE ALIMENTAIRE, ALIMENTATION HUMAINE, FOOD SECURITY, [SDV.SA.AEP]Life Sciences [q-bio]/Agricultural sciences/Agriculture, economy and politics, HUMAN FEEDING, DURABILITE, VULNERABILITE, ALIMENTATION DURABLE, MEASUREMENT, [SHS]Humanities and Social Sciences, SUSTAINABILITY, INDICATEUR, SUSTAINABLE FOOD, MESURE, ComputingMethodologies_GENERAL, ComputingMilieux_MISCELLANEOUS
Abstract: Poster; International audience

88. Women's empowerment, household dietary diversity, and child anthropometry among vulnerable populations in Odisha, India.

Author: Ogutu S, Mockshell J, Garrett J, Ritter T, Labarta R, Alvarez D, Nedumaran S, Gonzalez C, and Gotor E
Subjects: Humans, India epidemiology, Female, Adult, Child, Male, Nutritional Status, Child, Preschool, Vulnerable Populations psychology, Vulnerable Populations statistics & numerical data, Diet, Empowerment, Anthropometry, Family Characteristics
Abstract: Women's empowerment has been promoted by researchers and development practitioners as one of the most promising strategies to address widespread hunger and malnutrition. However, the relationship between women's empowerment and dietary diversity and child nutrition has rarely been studied among vulnerable populations or individuals at greater risk of poor physical and social health status. Moreover, the effects of different domains of women's empowerment on nutritional outcomes, including dietary diversity and child anthropometry, have rarely been examined, especially with panel data. Using two rounds of panel data from 1900 households and fixed effects regression models, we analyze the effect of women's empowerment on household dietary diversity score (HDDS) and child anthropometry among the particularly vulnerable tribal groups in Odisha, India. We also estimate the effects of various decision-making domains of women's empowerment on HDDS and child anthropometry to understand which empowerment domains matter for nutrition. Results show that women's empowerment is positively associated with HDDS (coef. 0.41 food groups; p < 0.1) and reduces the prevalence of underweight (coef. 39%; p < 0.05) and wasting (coef. 56%; p < 0.1) in children but has no effect on the prevalence of child stunting. Women's empowerment in agricultural input use; output sales; income; food purchases; and credit, group membership, and employment contribute to improved dietary diversity and child nutrition. We conclude that women's empowerment contributes to improved dietary diversity and child nutrition and is a promising strategy to improve farm household diets and child nutrition among vulnerable populations. Strengthening women's empowerment through the promotion of women's access to land and other agricultural inputs, market participation, access to information, capital, and credit is important., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Ogutu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Published: 2024
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89. Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species.

Author: Xu WQ, Ren CQ, Zhang XY, Comes HP, Liu XH, Li YG, Kettle CJ, Jalonen R, Gaisberger H, Ma YZ, and Qiu YX
Subjects: China, Adaptation, Physiological genetics, Gene Flow, Genetics, Population, Genomics, Reproductive Isolation, Phylogeny, Genetic Variation, Climate, Genetic Speciation, Genome, Plant genetics
Abstract: Understanding the genetic basis of population divergence and adaptation is an important goal in population genetics and evolutionary biology. However, the relative roles of demographic history, gene flow, and/or selective regime in driving genomic divergence, climatic adaptation, and speciation in non-model tree species are not yet fully understood. To address this issue, we generated whole-genome resequencing data of Liquidambar formosana and L. acalycina, which are broadly sympatric but altitudinally segregated in the Tertiary relict forests of subtropical China. We integrated genomic and environmental data to investigate the demographic history, genomic divergence, and climatic adaptation of these two sister species. We inferred a scenario of allopatric species divergence during the late Miocene, followed by secondary contact during the Holocene. We identified multiple genomic islands of elevated divergence that mainly evolved through divergence hitchhiking and recombination rate variation, likely fostered by long-term refugial isolation and recent differential introgression in low-recombination genomic regions. We also found some candidate genes with divergent selection signatures potentially involved in climatic adaptation and reproductive isolation. Our results contribute to a better understanding of how late Tertiary/Quaternary climatic change influenced speciation, genomic divergence, climatic adaptation, and introgressive hybridization in East Asia's Tertiary relict flora. In addition, they should facilitate future evolutionary, conservation genomics, and molecular breeding studies in Liquidambar, a genus of important medicinal and ornamental values., (© 2024 Society for Experimental Biology and John Wiley & Sons Ltd.)
Published: 2024
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90. Decision support tools for agricultural adaptation in Africa.

Author: Rosenstock TS, Joshi N, Segnon AC, Cramer L, Mwongera C, Nowak AC, Njuguna L, Dossou-Yovo ER, Steward P, and Ramirez-Villegas J
Subjects: Africa epidemiology, Agriculture
Published: 2024
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91. A systematic review of the methodology of trade-off analysis in agriculture.

Author: Breure TS, Estrada-Carmona N, Petsakos A, Gotor E, Jansen B, and Groot JCJ
Abstract: Trade-off analysis (TOA) is central to policy and decision-making aimed at promoting sustainable agricultural landscapes. Yet, a generic methodological framework to assess trade-offs in agriculture is absent, largely due to the wide range of research disciplines and objectives for which TOA is used. In this study, we systematically reviewed 119 studies that have implemented TOAs in landscapes and regions dominated by agricultural systems around the world. Our results highlight that TOAs tend to be unbalanced, with a strong emphasis on productivity rather than environmental and socio-cultural services. TOAs have mostly been performed at farm or regional scales, rarely considering multiple spatial scales simultaneously. Mostly, TOAs fail to include stakeholders at study development stage, disregard recommendation uncertainty due to outcome variability and overlook risks associated with the TOA outcomes. Increased attention to these aspects is critical for TOAs to guide agricultural landscapes towards sustainability., (© 2024. The Author(s).)
Published: 2024
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92. Author Correction: Periodic Table of Food Initiative for generating biomolecular knowledge of edible biodiversity.

Author: Jarvis A, Gallo-Franco J, Portilla J, German B, Debouck D, Rajasekharan M, Khoury C, Herforth A, Ahmed S, Tohme J, Arnaud E, Golden CD, Dawid C, de Haan S, DeClerck F, Feskens EJM, Fogliano V, Fritz G, Hald C, Hall R, Hart R, Henry A, Huang S, Hunter D, Imanbaeva B, Lowe A, Turner NJ, Jia G, Johnson E, Kalaiah G, Karboune S, Klade S, La Cerva GR, Lal V, Levy AA, Longvah T, Maeda-Yamamoto M, Minnis P, Nuti M, Octavio M, Osorio C, Pawera L, Peter S, Prasad R, Quave C, Shapiro HY, Sreeman S, Srichamnong W, Steiner R, Turdieva M, Ulian T, van Andel T, Wang R, Weissgold L, Yan J, and de la Parra J
Published: 2024
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93. Periodic Table of Food Initiative for generating biomolecular knowledge of edible biodiversity.

Author: Jarvis A, Gallo-Franco J, Portilla J, German B, Debouck D, Rajasekharan M, Khoury C, Herforth A, Ahmed S, Tohme J, Arnaud E, Golden CD, Dawid C, de Haan S, DeClerck F, Feskens EJM, Fogliano V, Fritz G, Hald C, Hall R, Hart R, Henry A, Huang S, Hunter D, Imanbaeva B, Lowe A, Turner NJ, Jia G, Johnson E, Kalaiah G, Karboune S, Klade S, La Cerva GR, Lal V, Levy AA, Longvah T, Maeda-Yamamoto M, Minnis P, Nuti M, Octavio M, Osorio C, Pawera L, Peter S, Prasad R, Quave C, Shapiro HY, Sreeman S, Srichamnong W, Steiner R, Turdieva M, Ulian T, van Andel T, Wang R, Weissgold L, Yan J, and de la Parra J
Subjects: Allergens, Biodiversity, Food
Published: 2024
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94. Examining linkages among multiple sustainable development outcomes: does the productive safety net program increase on-farm agrobiodiversity?

Author: Kozicka M, Gotor E, Pagnani T, Occelli M, and Caracciolo F
Abstract: In Ethiopia, on-farm agrobiodiversity and the Productive Safety Net Program (PSNP) play a key role in building smallholders' resilience. However, the impact of PSNP on on-farm agrobiodiversity is not yet well investigated. In this paper, we develop an analytical framework that links PSNP participation to on-farm agrobiodiversity. Both diverse farming systems and PSNP require labour inputs while providing income stabilization, which might result in a negative relationship between the two. Conversely, higher income from PSNP might allow farmers to increase their long-term on-farm investments, as opposed to the strategies oriented toward the highest immediate profit or calorie intake outcome. We base our empirical analysis on the World Bank's Ethiopian Socioeconomic Survey, a panel dataset encompassing nearly 3000 respondents and a Tobit model, based on Difference-in-Difference and the Propensity-Score Matching methods. We find that Ethiopia's PSNP has a negative impact on farm labour input, both in terms of labour intensity and duration. Furthermore, our results show that participation in the program is associated, on average, with lower on-farm crop diversity. We conclude that the PSNP participation may be crowding-out production stabilizing farming activities, such as intercropping or cover cropping, that are more labour intensive. Our findings call for embedding tools in the new phase of the PSNP (2021-2025) that could incentivise on-farm resilience-oriented investments, in particular leading to higher crop diversification., Competing Interests: Conflict of interestThe authors have no conflicts of interest to declare that are relevant to the content of this article., (© The Author(s) 2023.)
Published: 2023
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95. Home gardens of Central Asia: Reservoirs of diversity of fruit and nut tree species.

Author: Vinceti B, Elias M, Azimov R, Turdieva M, Aaliev S, Bobokalonov F, Butkov E, Kaparova E, Mukhsimov N, Shamuradova S, Turgunbaev K, Azizova N, and Loo J
Subjects: Asia, Fruit, Nuts, Gardens, Trees
Abstract: Central Asia is an important center of origin for many globally valued fruit and nut tree species. Forest degradation and deforestation are cause for concern for the conservation of these valuable species, now confined to small remnant populations. Home gardens have the important function of sustaining household food consumption and income generation, and can potentially play a critical role in conserving diversity of fruit and nut trees. These systems have been very poorly documented in the scientific literature. This study contributes to filling this gap by describing the diversity of fruit and nut trees in home gardens of Kyrgyzstan, Uzbekistan, and Tajikistan, examining their dynamic flow of planting material and its sources, understanding their future prospects, and looking at significant differences between the three countries. Home gardens show a similar portfolio of the most abundant tree species (apple, apricot, walnut, pear, and plum). Although the diversity of tree species and varieties recorded is significant, small population sizes can limit future possibilities for this diversity to thrive, given the pressure on natural stands and on habitats where the preferred species are found. Furthermore, the selection of species and varieties to be planted in home gardens is increasingly influenced by market opportunities and availability of exotic material. Some of the most abundant tree species recorded are represented largely by exotic varieties (apple, pear), while others (e.g., apricot, walnut, plum) are still mainly characterized by traditional local varieties that are not formally registered. Home gardens continue to play a critical role in rural livelihoods and in national economies, and many rural inhabitants still aspire to maintain them. Thus, home gardens should be integrated in national research and extension systems and closely linked to national conservation efforts. Changes and possible declines in the diversity they host, their health status, and resilience should be carefully monitored., Competing Interests: The authors have declared that no competing interests exist.
Published: 2022
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96. Tropical and subtropical Asia's valued tree species under threat.

Author: Gaisberger H, Fremout T, Kettle CJ, Vinceti B, Kemalasari D, Kanchanarak T, Thomas E, Serra-Diaz JM, Svenning JC, Slik F, Eiadthong W, Palanisamy K, Ravikanth G, Bodos V, Sang J, Warrier RR, Wee AKS, Elloran C, Ramos LT, Henry M, Hossain MA, Theilade I, Laegaard S, Bandara KMA, Weerasinghe DP, Changtragoon S, Yuskianti V, Wilkie P, Nghia NH, Elliott S, Pakkad G, Tiansawat P, Maycock C, Bounithiphonh C, Mohamed R, Nazre M, Siddiqui BN, Lee SL, Lee CT, Zakaria NF, Hartvig I, Lehmann L, David DBD, Lillesø JB, Phourin C, Yongqi Z, Ping H, Volkaert HA, Graudal L, Hamidi A, Thea S, Sreng S, Boshier D, Tolentino E Jr, Ratnam W, Aung MM, Galante M, Isa SFM, Dung NQ, Hoa TT, Le TC, Miah MD, Zuhry ALM, Alawathugoda D, Azman A, Pushpakumara G, Sumedi N, Siregar IZ, Nak HK, Linsky J, Barstow M, Koh LP, and Jalonen R
Subjects: Climate Change, Conservation of Natural Resources, Forests, Thailand, Ecosystem, Trees
Abstract: Tree diversity in Asia's tropical and subtropical forests is central to nature-based solutions. Species vulnerability to multiple threats, which affect provision of ecosystem services, is poorly understood. We conducted a region-wide, spatially explicit assessment of the vulnerability of 63 socioeconomically important tree species to overexploitation, fire, overgrazing, habitat conversion, and climate change. Trees were selected for assessment from national priority lists, and selections were validated by an expert network representing 20 countries. We used Maxent suitability modeling to predict species distribution ranges, freely accessible spatial data sets to map threat exposures, and functional traits to estimate threat sensitivities. Species-specific vulnerability maps were created as the product of exposure maps and sensitivity estimates. Based on vulnerability to current threats and climate change, we identified priority areas for conservation and restoration. Overall, 74% of the most important areas for conservation of these trees fell outside protected areas, and all species were severely threatened across an average of 47% of their native ranges. The most imminent threats were overexploitation and habitat conversion; populations were severely threatened by these factors in an average of 24% and 16% of their ranges, respectively. Our model predicted limited overall climate change impacts, although some study species were likely to lose over 15% of their habitat by 2050 due to climate change. We pinpointed specific natural areas in Borneo rain forests as hotspots for in situ conservation of forest genetic resources, more than 82% of which fell outside designated protected areas. We also identified degraded areas in Western Ghats, Indochina dry forests, and Sumatran rain forests as hotspots for restoration, where planting or assisted natural regeneration will help conserve these species, and croplands in southern India and Thailand as potentially important agroforestry options. Our results highlight the need for regionally coordinated action for effective conservation and restoration., (© 2021 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)
Published: 2022
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97. The determinants of common bean variety selection and diversification in Colombia.

Author: Botero H, Barnes AP, Perez L, Rios D, and Ramirez-Villegas J
Abstract: Variety selection and diversification are climate change adaptation practices pursued by Colombian common bean producers. We investigate the drivers behind common bean variety selection and diversification in one of the most important common bean production regions in Colombia -Santander. The effects of climate change on this region are expected to be elevation driven. Exploiting the relationship between elevation-driven weather variations and climate change perception in Santander, we estimate an alternative-specific conditional logistic regression model to identify the determinants of common bean variety selection from a survey of producers. Using an ordered-logistic regression model, we also investigate the drivers behind common bean variety diversification within this farming community. We find that farms' elevation, household composition, and seed certification are some of the most important drivers behind farmers' common bean variety selection in Santander. We also find that varieties that sell at higher prices and have shorter vegetative cycles tend to be more preferred by farmers. Finally, farmers who receive more help from family members and own a tractor tend to grow more than one variety in the same production cycle. Common bean breeding programmes can exploit these drivers to design communication strategies to maximize uptake of newly developed common bean phenotypes., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors.)
Published: 2021
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98. Agrobiodiversity Index scores show agrobiodiversity is underutilized in national food systems.

Author: Jones SK, Estrada-Carmona N, Juventia SD, Dulloo ME, Laporte MA, Villani C, and Remans R
Abstract: The diversity of plants, animals and microorganisms that directly or indirectly support food and agriculture is critical to achieving healthy diets and agroecosystems. Here we present the Agrobiodiversity Index (based on 22 indicators), which provides a monitoring framework and informs food systems policy. Agrobiodiversity Index calculations for 80 countries reveal a moderate mean agrobiodiversity status score (56.0 out of 100), a moderate mean agrobiodiversity action score (47.8 out of 100) and a low mean agrobiodiversity commitment score (21.4 out of 100), indicating that much stronger commitments and concrete actions are needed to enhance agrobiodiversity across the food system. Mean agrobiodiversity status scores in consumption and conservation are 14-82% higher in developed countries than in developing countries, while scores in production are consistently low across least developed, developing and developed countries. We also found an absence of globally consistent data for several important components of agrobiodiversity, including varietal, functional and underutilized species diversity., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)
Published: 2021
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99. Estimates of dietary quality in infants and young children (6-23 mo): Evidence from demographic and health surveys of 49 low- and middle-income countries.

Author: Baye K and Kennedy G
Subjects: Child, Child, Preschool, Diet, Ethnicity, Health Surveys, Humans, Infant, Socioeconomic Factors, Developing Countries, Malnutrition epidemiology
Abstract: Objective: Dietary diversity in early life can prevent all forms of malnutrition and can establish a healthier dietary pattern for later life. However, multicountry national estimates are lacking. The aim of this study was to estimate the proportion of infants and young children (IYC) meeting the minimum dietary diversity (MMD), minimum meal frequency (MMF), and minimum acceptable diet (MAD)., Methods: We calculated the proportion of IYC (6-23 mo of age) meeting the updated MDD, MMF, and MAD for 49 low- and middle-income countries. We calculated the proportion of IYC meeting the MDD by region, rural/urban residence, and wealth quintile. The proportion of stunting cases that would have been averted if 90% of the IYC met their MDD was estimated., Results: The proportion of IYC meeting MDD, MMF, and MAD was very low. Only 4 of 49 countries had >50% of IYC meeting MDD. The lowest MDD was for the sub-Saharan African region (18%) and the highest was for the Latin America and Caribbean (54%) region. Stark inequalities exist between countries, rural/urban residence, and wealth quintiles. A significant proportion (>11 million) of stunting cases could have been averted if ≥90% of IYC had met the MDD. MDD proportions increased with higher gross national income purchasing power parity, maternal literacy, and food supply diversity (P < 0.05)., Conclusions: Closing the gap in dietary inequalities between and within countries is urgently needed to prevent wider, long-term socioeconomic and health inequalities. Diet-quality targets should be set and monitored routinely to promote dietary diversity and prevent all forms of malnutrition., (Copyright © 2020 Elsevier Inc. All rights reserved.)
Published: 2020
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100. Conceptual Links between Landscape Diversity and Diet Diversity: A Roadmap for Transdisciplinary Research.

Author: Gergel SE, Powell B, Baudron F, Wood SLR, Rhemtulla JM, Kennedy G, Rasmussen LV, Ickowitz A, Fagan ME, Smithwick EAH, Ranieri J, Wood SA, Groot JCJ, and Sunderland TCH
Abstract: Malnutrition linked to poor quality diets affects at least 2 billion people. Forests, as well as agricultural systems linked to trees, are key sources of dietary diversity in rural settings. In the present article, we develop conceptual links between diet diversity and forested landscape mosaics within the rural tropics. First, we summarize the state of knowledge regarding diets obtained from forests, trees, and agroforests. We then hypothesize how disturbed secondary forests, edge habitats, forest access, and landscape diversity can function in bolstering dietary diversity. Taken together, these ideas help us build a framework illuminating four pathways (direct, agroecological, energy, and market pathways) connecting forested landscapes to diet diversity. Finally, we offer recommendations to fill remaining knowledge gaps related to diet and forest cover monitoring. We argue that better evaluation of the role of land cover complexity will help avoid overly simplistic views of food security and, instead, uncover nutritional synergies with forest conservation and restoration., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Institute of Biological Sciences.)
Published: 2020
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