Search

Your search keyword '"Bioversity International [Rome]"' showing total 26 results
Start Over Author "Bioversity International [Rome]" Topic 15. life on land
26 results on '"Bioversity International [Rome]"'

1. GreenPhylDB v5: a comparative pangenomic database for plant genomes

Author

Guignon Valentin, Rouard Mathieu, Conte Matthieu, Toure Abdel, Droc Gaëtan, Dufayard Jean-François, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), French Institute of Bioinformatics (ELIXIR-FR), Syngenta France, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Syngenta Seeds SAS, and CGIAR

Subjects
Crops, Agricultural, 0106 biological sciences, AcademicSubjects/SCI00010, Arabidopsis, Genomics, Biology, computer.software_genre, 01 natural sciences, Genome, 03 medical and health sciences, Gene Expression Regulation, Plant, Databases, Genetic, Protein Interaction Mapping, Genetics, Database Issue, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Gene, Phylogeny, Plant Proteins, 030304 developmental biology, Comparative genomics, Internet, 0303 health sciences, Sequence Homology, Amino Acid, Database, Phylogenetic tree, Molecular Sequence Annotation, Oryza, F70 - Taxonomie végétale et phytogéographie, Plants, 15. Life on land, Plant genomes, Tree (data structure), Gene Ontology, Multigene Family, Corrigendum, Sequence Alignment, computer, Genome, Plant, Software, 010606 plant biology & botany
Abstract

Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.

Published
2020
Full Text
View/download PDF

2. Selecting for useful properties of plants and fungi – Novel approaches, opportunities, and challenges

Author

Valery Malécot, I. Thormann, Paul J. Kersey, Nigel Maxted, Carey L. Metheringham, Jérôme Collemare, Laura J. Kelly, Christopher Cockel, D. K. Das, Eoin P. Lettice, Ehsan Dulloo, Ilia J. Leitch, Westerdijk Fungal Biodiversity Insitute [Utrecht] (WI), Royal Netherlands Academy of Arts and Sciences (KNAW), Bidhan Chandra Krishi Viswavidyalaya, Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Royal Botanic Gardens, Kew, United College Cork (National University of Ireland) (UCC), Department of Chemistry and Environmental Research Institute, University College Cork, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Biological and Chemical Sciences, Queen Mary University of London (QMUL), and Federal Office for Agriculture and Food (BLE)

Subjects
0106 biological sciences, Emerging technologies, Conservation agriculture, Biodiversity, Plant Science, Horticulture, Biology, 01 natural sciences, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Genome editing, lcsh:Botany, Genetic variation, genetic modification, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture, Environmental planning, lcsh:Environmental sciences, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, lcsh:GE1-350, 2. Zero hunger, 0303 health sciences, Genetic diversity, plants, fungi, conservation, food and beverages, Societal impact of nanotechnology, Forestry, genetic diversity, 15. Life on land, crops, lcsh:QK1-989, 13. Climate action, breeding, Biological dispersal, metabolic engineering, 010606 plant biology & botany
Abstract

Societal Impact Statement For millennia, humans have used plants and fungi, as foods, fuels, fibers, and medicines; and have developed techniques for improving their usefulness to our species, mostly through selection of desirable traits. With human populations forecast to rise, the availability of arable land likely to fall amid climate change and increasing urbanization, and modern communications technologies accelerating the dispersal of pathogens, further improvement is urgently needed. However, ensuring long‐term resilience involves conservation of existing genetic diversity in addition to selection. New technologies, particularly those based on molecular biology, are increasingly driving conservation and improvement strategies. Summary Humans use plants and fungi for a wide range of purposes and, over millennia, have improved wild species by selecting for and combining genetic variation. Improvements in DNA sequencing technologies have enhanced our capacity to identify and manipulate genetic diversity, increasing the range of variation that can be utilized, and accelerating the breeding cycle to reduce the time taken to develop and put new varieties to use. Most recently, the CRISPR/Cas9 gene editing technology has greatly increased our capacity to directly introduce novel genetic variants without unwanted associated material. Moreover, increased knowledge of metabolic pathways resulting from genomic analysis can be used to design new varieties with desired properties with increased precision. Selecting for, or engineering, desirable variants has increased the usefulness of plants and fungi to humans, but at the cost of reducing their genetic diversity, decreasing their resilience and reducing the stock of variation available for future use. Conservation of genetic biodiversity is thus an essential counterpart of crop improvement and is essential to ensure that crop species retain resilience to emerging threats. Conservation efforts are focused on orphan crops, wild relatives of crop species, and landraces; in and exsitu efforts are complementary. Informatic approaches can inform use of these materials in breeding programmes even in the absence of genomic information. The application of some of these approaches may be restricted by ethical, legal, or organizational obstacles. If these can be overcome, there is great potential to unlock previously untapped reservoirs of biodiversity for human benefit.

Published
2020
Full Text
View/download PDF

3. Genome-wide and comparative phylogenetic analysis of senescence-associated NAC transcription factors in sunflower (Helianthus annuus)

Author

Bengoa Luoni, Sofia A., Cenci, Alberto, Moschen, Sebastian, Nicosia, Salvador, Radonic, Laura M., Sabio, Julia, Garcia, Langlade, Nicolas B., Vile, Denis, Rovere, Cecilia Vazquez, Fernandez, Paula, Instituto Nacional de Tecnología Agropecuaria (INTA), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INTA PE 1131022, 1131043, ANPCyT Préstamo BID PICT 2012–0390, PICT 2014–0175, PIP CONICET PIP 11220120100262CO, Marie Curie IRSES Project DEANN (PIRSES-GA-2013-612583), CONICET, SUNRISE and Heliagen Project, and ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011)

Subjects
0106 biological sciences, Leaves, Arabidopsis thaliana, Arabidopsis, QH426-470, Senescence, 01 natural sciences, 03 medical and health sciences, Leaf senescence, Factores de Transcripción, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Girasol, Phylogeny, 030304 developmental biology, Plant Proteins, 2. Zero hunger, 0303 health sciences, Leaf Senescence, Research, High throughput phenotyping, Correction, food and beverages, Helianthus annuus, Phylogenetic Analysis, 15. Life on land, HaNAC001, Genética, Plant Senescence, Plant Leaves, Sunflower, Análisis Filogenético, NAC transcriptions factors, Avejentamiento, Hojas, Helianthus, TP248.13-248.65, 010606 plant biology & botany, Biotechnology, Transcription Factors
Abstract

Background: Leaf senescence delay impacts positively in grain yield by maintaining the photosynthetic area during the reproductive stage and during grain filling. Therefore a comprehensive understanding of the gene families associated with leaf senescence is essential. NAC transcription factors (TF) form a large plant-specific gene family involved in regulating development, senescence, and responses to biotic and abiotic stresses. The main goal of this work was to identify sunflower NAC TF (HaNAC) and their association with senescence, studying their orthologous to understand possible functional relationships between genes of different species. Results: To clarify the orthologous relationships, we used an in-depth comparative study of four divergent taxa, in dicots and monocots, with completely sequenced genomes (Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa). These orthologous groups provide a curated resource for large scale protein sequence annotation of NAC TF. From the 151 HaNAC genes detected in the latest version of the sunflower genome, 50 genes were associated with senescence traits. These genes showed significant differential expression in two contrasting lines according to an RNAseq assay. An assessment of overexpressing the Arabidopsis line for HaNAC001 (a gene of the same orthologous group of Arabidopsis thaliana ORE1) revealed that this line displayed a significantly higher number of senescent leaves and a pronounced change in development rate. Conclusions: This finding suggests HaNAC001 as an interesting candidate to explore the molecular regulation of senescence in sunflower. Instituto de Biotecnología Fil: Bengoa Luoni, Sofia Ailin. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Cenci, Alberto. Bioversity International; Francia Fil: Moschen, Sebastian Nicolás. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina. Fil: Nicosia, Salvador. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Radonic, Laura Mabel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Sabio Y Garcia, Julia Veronica. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Langlade, Nicolas B. Université de Toulouse. LIPM-INRA-CNRS; Francia Fil: Langlade, Nicolas B. Université de Montpellier. LEPSE; Francia Fil: Vazquez Rovere, Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Fernandez, Paula Del Carmen. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina.

Published
2021
Full Text
View/download PDF

4. Biodiversity and ecosystem services on the African continent – What is changing, and what are our options?

Author

Laura Pereira, Reinette Biggs, M-C Cormier Salem, Christopher P. Gordon, Benis N. Egoh, Katja Heubach, Emma Archer, Malebajoa A. Maoela, Luthando Dziba, A. Assogbadjo, K.J. Mulongoy, Nadia Sitas, Amy E. Dunham, Mariteuw Chimère Diaw, Fabrice DeClerck, Marwa Waseem A. Halmy, Adelina Mensah, K. A. Harhash, L. Tito de Morais, Michele Walters, Lindsay C. Stringer, Fred Kizito, N Oguge, W.D. Nyingi, Pierre Failler, Robert Kasisi, B. Osman-Elasha, Department of Geography, Geoinformatics and Meteorology [Pretoria], University of Pretoria [South Africa], South African National Parks (SANParks), Nelson Mandela Metropolitan University [Port Elizabeth, South Africa], Institute for Enhanced Livelihoods (IEL), Council for Scientific and Industrial Research [Pretoria] (CSIR), Stellenbosch University, Stockholm University, Institut de Recherche pour le Développement (IRD), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), African Model Forests Network (AMFN), Rice University [Houston], University of Portsmouth, University of Ghana, Biodiversity Central Department, Ministry of Environment, Université de Montréal (UdeM), CIAT, National Museums of Kenya, University of Nairobi (UoN), Banque africaine de développement / African Development Bank (BAD), School of Earth and Environment [Leeds] (SEE), University of Leeds, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Abomey Calavi (UAC), Department of Earth System Science [Irvine] (ESS), University of California [Irvine] (UCI), University of California-University of California, Alexandria University [Alexandrie], Palmengarten der Stadt Frankfurt am Main (PalmenGarten), City University London, and Environmental Governance

Subjects
Value (ethics), 010504 meteorology & atmospheric sciences, Monitoring, Natural resource economics, Geography, Planning and Development, Biodiversity, Climate change, 010501 environmental sciences, Management, Monitoring, Policy and Law, 01 natural sciences, Ecosystem services, Degradation, 11. Sustainability, 0105 earth and related environmental sciences, Planning and Development, Land use, Geography, Policy and Law, ACL, 15. Life on land, Management, 13. Climate action, Sustainability, Africa, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Futures contract
Abstract

International audience; Throughout the world, biodiversity and nature's contributions to people are under threat, with clear changes evident. Biodiversity and ecosystem services have particular value in Africa– yet they are negatively impacted by a range of drivers, including land use and climate change. In this communication, we show evidence of changing biodiversity and ecosystem services in Africa, as well as the current most significant drivers of change. We then consider five plausible futures for the African continent, each underlain by differing assumptions. In three out of the five futures under consideration, negative impacts on biodiversity and ecosystem services are likely to persist. Those two plausible futures prioritizing environment and sustainability, however, are shown as the most likely paths to achieving long term development objectives without compromising the continent's biodiversity and ecosystem services. Such a finding shows clearly that achievement of such objectives cannot be separated from full recognition of the value of such services.

Published
2021
Full Text
View/download PDF

5. Filling the gaps in gene banks: Collecting, characterizing, and phenotyping wild banana relatives of Papua New Guinea

Author

Catherine Breton, Julie Sardos, Janet Paofa, Simon Kallow, Claude Welcker, Bart Panis, David Eyland, Steven Janssens, François Tardieu, Sebastien Carpentier, Rony Swennen, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Royal Botanic Gardens [Kew], Bioversity International [Belgique], International Institute of Tropical Agriculture (IITA-Tanzania), International Institute of Tropical Agriculture [Nigeria] (IITA), PNG National Agricultural Research Institute (NARI), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Meise Botanic Garden [Belgium] (Plantentuin), 'Adapting Agriculture to Climate Change: Collecting, Pro-tecting and Preparing Crop Wild Relatives,' which is supported by the Government of Norway., Global Crop Diversity Trust in part-nership with national and international gene banks and plant breeding institutes around the world (http://www.cwrdiversity.org/)., The Deutsche Gesellschaft für Interna-tionale Zusammenarbiet GIZ, scholarship funded by the Global TRUST foundation project 'Crop wild Relatives Evaluation of drought tolerance in wild bananas from Papua New Guinea', CGIAR Fund (https://www.cgiar.org/funders/), CGIAR Research Program Roots, Tubers and Bananas (RTB-CRP), Belgian Development Cooperation project ‘‘More fruit for food security: Developing climate-smart bananas for the African Great Lakes region.', European Project: 731013 ,EPPN2020(2017), Royal Botanic Gardens, Kew, Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Botanic Garden Meise

Subjects
2. Zero hunger, 0106 biological sciences, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Vapour Pressure Deficit, business.industry, Drought tolerance, Plant genetics, 15. Life on land, Biology, biology.organism_classification, 01 natural sciences, Musa peekelii, Crop, 03 medical and health sciences, Horticulture, Gene bank, Agriculture, Shoot, business, Agronomy and Crop Science, 030304 developmental biology, 010606 plant biology & botany
Abstract

International audience; Since natural habitats are disappearing fast, there is an urgent need to collect, characterize, and phenotype banana (Musa spp.) crop wild relatives to identify unique genotypes with specific traits that fill the gaps in our gene banks. We report on a collection mission in Papua New Guinea carried out in 2019. Seed containing bunches were collected from Musa peekelii ssp. angustigemma (N.W.Simmonds) Argent (3), M. schizocarpa N. W. Simmonds (4), M. balbisiana Colla (3), M. acuminata ssp. banksii (F. Muell.) Simmonds (14), M. boman Argent (3), M. ingens Simmonds (2), M. maclayi ssp. maclayi F.Muell. ex Mikl.-Maclay (1), and M. lolodensis Cheesman (1). This material, together with the seeds collected during a previous mission in 2017, form the basis for the development of a wild banana seed bank. For characterization and phenotyping, we focused on the most ubiquitous indigenous species of Papua New Guinea: M. acuminata ssp. banksii, the ancestor of most edible bananas. We calculated that the median genomic dissimilarity of the M. acuminata ssp. banksii accessions was 4% and that they differed at least 5% from accessions present in the International Transit Centre, the world's largest banana gene bank. High-throughput phenotyping revealed drought avoidance strategies with significant differences in root/shoot ratio, soil water content sensitivity, and response towards vapor pressure deficit (VPD). We deliver a proof of principle that the wild diversity is not yet fully covered in the gene banks and that wild M. acuminata ssp. banksii populations contain individuals with unique traits, useful for drought tolerance breeding programs.

Published
2021
Full Text
View/download PDF

6. Genetics to the rescue: managing forests sustainably in a changing world

Author

Filippos A. Aravanopoulos, Barbara Vinceti, Marcus Lindner, Raquel Benavides, Fernando Valladares, Bruno Fady, Christian Rellstab, Santiago C. González-Martínez, Delphine Grivet, Martin Lascoux, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aristotle University of Thessaloniki, Spanish National Research Council [Madrid] (CSIC), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INIA MADRID ESPAGNE, 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), Uppsala Universitet [Uppsala], European Forest Institute (EFI), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome] (Alliance), and This publication is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 676876 (GenTree).

Subjects
0106 biological sciences, phenotype, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Biodiversity, Climate change, policy, Horticulture, Biology, Diversification (marketing strategy), 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genetics, Lagging, Molecular Biology, 030304 developmental biology, media_common, 0303 health sciences, Genetic diversity, Natural selection, Genomic diversity, conservation, Forestry, 15. Life on land, 13. Climate action, breeding, Sustainability, [SDE]Environmental Sciences, environment, Diversity (politics)
Abstract

International audience; There is growing concern that the implementation of political agreements on climate change and biodiversity will not be enough to protect forests in the short run and up to the end of the 21st century. As mitigation efforts are lagging behind self-imposed, reasonable targets, genetic diversity will have a large and significant part to play in the process of adapting forests to climate change. Genetic diversity, the raw material of evolution, can be used for adaptation by natural selection and artificial breeding, in naturally regenerated and plantation forests alike. The two-day scientific conference: “#rescueforests: Genetics to the rescue - Managing forests sustainably in a changing world”, addressed the genetic diversity of forests. More specifically, the conference was about natural as well as assisted adaptive processes, their spatial scale, from fine grain to landscape and ecoregions, and how much of the genome it involves. It also dealt with phenotypes and how much of their variation is determined by underlying genetic diversity. And finally, and perhaps most importantly, the conference emphasized the importance of conservation and sustainable use of this genetic diversity as a nature-based solution to adapt under the fast pace of climate change. The conference demonstrated how improved knowledge on genomic diversity and evolutionary mechanisms can help to rescue forests, either naturally or by means of management.

Published
2020
Full Text
View/download PDF

7. Managing forest genetic resources as a strategy to adapt forests to climate change: perceptions of European forest owners and managers

Author

Marcus Lindner, Mattia Manica, Barbara Vinceti, Bruno Fady, Pieter Johannes Verkerk, Nina Lauridsen, Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), European Forest Institute (EFI), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome] (Alliance), Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, and This research was part of the GenTree project which has received funding from the European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No. 676876.

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, Settore AGR/05 - ASSESTAMENTO FORESTALE E SELVICOLTURA, media_common.quotation_subject, Climate change, Plant Science, 010603 evolutionary biology, 01 natural sciences, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Effects of global warming, Order (exchange), Perception, Forest genetic resources, Forest ecology, Quality (business), Adaptation, 0105 earth and related environmental sciences, media_common, Forest management, business.industry, Environmental resource management, Forestry, 15. Life on land, Forest reproductive material, 13. Climate action, Psychological resilience, Business
Abstract

Managing genetic diversity is of key importance in fostering resilience of forest ecosystems to climate change. We carried out a survey reaching over 200 forest owners and managers from 15 European countries to understand their perceptions of the main threats to forest ecosystems, their knowledge of forest genetic resources (FGR) and their attitude toward actively managing these resources to strengthen the resilience of forest ecosystems to climate change. Respondents perceived pests and diseases to be the top-ranking threats to forests, followed by windstorms and drought, with differences across countries. They stated to be aware of the potential offered by managing FGR and indicated that they paid attention to origin and quality in their choice of planting material. Generally, respondents showed a positive attitude in using forest reproductive material foreign to the planting site, to better match the projected future climate conditions, introducing either a new native tree species or a new non-local genotype of a species already planted (keeping the same species but changing the source of planting material). However, forest reproductive material from local sources was largely preferred over non-local material (both genetically improved and not improved). Forest managers and owners may need to be exposed to more evidence of the potential benefits deriving from active adaptation and mitigation management of FGR before implementing adaptive measures. Also, more efforts should be invested in understanding perceptions and motivations of European forest owners and managers, in order to better tailor advice on optimal measures to counteract the detrimental effects of climate change.

Published
2020
Full Text
View/download PDF

8. Towards a thesaurus of plant characteristics

Author

Eric Garnier, Pedro Jaureguiberry, Stefan Klotz, J. Hans C. Cornelissen, Marie-Angélique Laporte, Gerhard Bönisch, Evan Weiher, Bernard Amiaud, Lutz Maicher, Sandra Díaz, Mark Schildhauer, Sophie Gachet, Christian Wirth, Baptiste Laporte, Ingolf Kühn, Farshid S. Ahrestani, Natalia Pérez-Harguindeguy, Ulrike Stahl, Hendrik Poorter, Cyrille Violle, Ian J. Wright, Bill Shipley, Sandra Lavorel, Isabelle Mougenot, Jens Kattge, Michael Kleyer, Daniel E. Bunker, Brian J. Enquist, Publica, Systems Ecology, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), 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), Centre de Synthèse et d’Analyse sur la Biodiversité (CESAB), Fondation pour la recherche sur la Biodiversité (FRB), Max Planck Institute for Biogeochemistry (MPI-BGC), Max-Planck-Gesellschaft, German Centre for Integrative Biodiversity Research (iDiv), Helmholtz Centre for Environmental Research (UFZ), Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR], Département Environnement et Ressources [Montpellier] (ESPACE-DEV), Université de Montpellier (UM)-Université de La Réunion (UR)-Université des Antilles et de la Guyane (UAG), Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Department of Ecology, Evolution and Environmental Biology, Columbia University [New York], Frontier Wildlife Conservation [Mumbai], New Jersey Institute of Technology [Newark] (NJIT), Vrije Universiteit Amsterdam [Amsterdam] (VU), Instituto Multidisciplinario de Biología Vegetal [Córdoba] (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas, Físicas y Naturales [Córdoba], Universidad Nacional de Córdoba [Argentina]-Universidad Nacional de Córdoba [Argentina], Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Faculty 5, Institute of Biology and Environmental Sciences, AG Zoosystematics, University of Oldenburg, Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Friedrich-Schiller-Universität Jena, Fraunhofer Center for International Management and Knowledge Economics (Fraunhofer MOEZ), Forschungszentrum Jülich GmbH, National Center for Ecological Analysis and Synthesis (NCEAS), Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada, Université de Sherbrooke, University of Wisconsin - Eau Claire (UWEC), Universität Leipzig [Leipzig], Dpt Biological Sciences, Macquarie University, Macquarie University, GDR 2574 (‘Traits’)of CNRS (France), the TraitNet Research Coordination Network (US NationalScience Foundation Grant No. 0639161), the SONet effort (US NSF Grant No.0753144), the project ‘Towards a unifying system of plant trait definition andmeasurement’ (the German Centre for Integrative Biodiversity Research (iDiv)Halle-Jena-Leipzig/Deutsche Forschungsgemeinschaft via Grant No. 50170649_#16), the German Federation for Biological Data - GFBio (DeutscheForschungsgemeinschaft via Grant No. KA 3323/2-2), and FONCyT, CONICET,Universidad Nacional de Cordoba and Inter-American Institute for GlobalChange Research (CRN 2015 and SGP-CRA2015, supported by NS grantsGEO-0452325 and GEO-1138881)

Subjects
0106 biological sciences, thesaurus, PLANT CHARACTERISTICS, Computer science, Otras Ciencias Biológicas, plant trait, Context (language use), CONTROLLED VOCABULARY, Plant Science, Ontology (information science), ECOLOGY, Semantics, 010603 evolutionary biology, 01 natural sciences, Terminology, Ciencias Biológicas, INFORMATICS, PLANT TRAIT, SEMANTICS, Controlled vocabulary, plant environmental association, informatics, THESAURUS, ontology, Semantic Web, semantics, Ecology, Evolution, Behavior and Systematics, biodiversity, Thesaurus (information retrieval), Ecology, Biological Ontologies, 15. Life on land, PLANT ENVIROMENTAL ASSOCIATION, ONTOLOGY, 13. Climate action, BIODIVERSITY, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ecology, CIENCIAS NATURALES Y EXACTAS, plant characteristics, 010606 plant biology & botany, controlled vocabulary
Abstract

The context of Open Biological Ontologies; (ii) whenever possible, the Entities and Qualities aretaken from existing terminology standards, mainly the Plant Ontology (PO) and Phenotypic QualityOntology (PATO) ontologies; and (iii) whenever a characteristic already has a definition, if appropriate,it is reused and referenced. The development of TOP, which complies with semantic web principles,was carried out through the involvement of experts from both the ecology and the semanticsresearch communities. Regular updates of TOP are planned, based on community feedback andinvolvement.3. TOP provides names, definitions, units, synonyms and related terms for about 850 plant characteristics.TOP is available online (www.top-thesaurus.org), and can be browsed using an alphabeticallist of characteristics, a hierarchical tree of characteristics, a faceted and a free-text search, andthrough an Application Programming Interface.4. Synthesis. Harmonizing definitions of concepts, as proposed by TOP, forms the basis for betterintegration of data across heterogeneous data sets and terminologies, thereby increasing the potentialfor data reuse. It also allows enhanced scientific synthesis. TOP therefore has the potential toimprove research and communication not only within the field of ecology, but also in related fieldswith interest in plant functioning and distribution Fil: Garnier, Eric. Université de Montpellier. Centre d'Ecologie Fonctionnelle et Evolutive; Francia Fil: Stahl, Ulrike. German Centre for Integrative Biodiversity Research; Alemania. Max-Planck-Institute for Biogeochemistry; Alemania. Department of Community Ecology, Helmholtz Centre for Environmental Research; Alemania Fil: Laporte, Marie-Angelique. Université de Montpellier. Centre d'Ecologie Fonctionnelle et Evolutive; Francia. German Centre for Integrative Biodiversity Research; Alemania. Bioversity International; Italia Fil: Kattge, Jens. Max-Planck-Institute for Biogeochemistry; Alemania. German Centre for Integrative Biodiversity Research; Alemania Fil: Mougenot, Isabelle. Maison de la Télédétection; Francia Fil: Kuhn, Ingolf. German Centre for Integrative Biodiversity Research; Alemania Fil: Laporte, Baptiste. Centre for the Synthesis and Analysis of Biodiversity; Francia Fil: Amiaud, Bernard. Université de Lorraine; Francia Fil: Ahrestani, Farshid S.. Columbia University; Estados Unidos Fil: Bonisch, Gerhard. Max-Planck-Institute for Biogeochemistry; Alemania Fil: Bunker, Daniel E.. New Jersey Institute of Technology. Department of Biological Sciences; Estados Unidos Fil: Cornelissen, Johannes H. C.. Vrije Universteit; Países Bajos Fil: Díaz, Sandra Myrna. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina Fil: Enquist, Brian J.. University of Arizona; Estados Unidos Fil: Gachet, Sophie. Avignon Université Avignon Université. Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale; Francia Fil: Jaureguiberry, Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina Fil: Kleyer, Michael. University of Oldenburg. Institute of Biology and Environmental Sciences; Alemania Fil: Lavorel, Sandra. Université Joseph Fourier; Francia Fil: Maicher, Lutz. Universitat Jena; Alemania Fil: Pérez Harguindeguy, Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina Fil: Poorter, Hendrik. Forschungszentrum Jülich; Alemania Fil: Schildhauer, Mark. University of California. National Center for Ecological Analysis and Synthesis; Estados Unidos Fil: Shipley, Bill. Université de Sherbrooke; Canadá Fil: Violle, Cyrille. Université de Montpellier; Francia Fil: Weiher, Evan. University of Wisconsin; Estados Unidos Fil: Wirth, Christian. German Centre for Integrative Biodiversity Research; Alemania Fil: Wright, Ian J.. Macquarie University; Australia Fil: Klotz, Stefan. Helmholtz Centre for Environmental Research; Alemania

Published
2017
Full Text
View/download PDF

9. Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy

Author

Bertrand Pitollat, Imène Chentli, Pierre Larmande, Clement Jonquet, Valentin Guignon, Nordine El Hassouni, Ndomassi Tando, Gildas Tagny, Aravind Venkatesan, Gaëtan Droc, Mathieu Rouard, Manuel Ruiz, 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), 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), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), WEB Architecture x Semantic WEB x WEB of Data (WEB3), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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]), Computational Biology Institute of Montpellier : ANR-11-INBS-0013, IA-11-BINF-0002, Institut Francais de Bioinformatique : ANR-11-INBS-0013, IA-11-INBS-0013, Labex Agro : ANR-10LABX-001-01, IA-10-LABX-0001, ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), 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), 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), WEB-CUBE, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), 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 National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
Proteomics, Agronomie, Computer science, Knowledge Bases, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Social Sciences, ontologie de domaine, Ontology (information science), Logiciel, Infographics, Computer Architecture, F30 - Génétique et amélioration des plantes, Database and Informatics Methods, 0302 clinical medicine, Phenomics, céréale, Psychology, Ensembl, Génétique, Data Management, Language, 2. Zero hunger, 0303 health sciences, Gene Ontologies, Agriculture, Genomics, computer.file_format, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-TT]Computer Science [cs]/Document and Text Processing, Knowledge base, C30 - Documentation et information, Information Retrieval, Medicine, Recherche de l'information, Graphs, Functional genomics, Biologie, Genome, Plant, Research Article, Computer and Information Sciences, Science, Crops, Phenome, Research and Analysis Methods, 03 medical and health sciences, Ontologies, Genetics, RDF, Semantic Web, 030304 developmental biology, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], business.industry, Data Visualization, [INFO.INFO-WB]Computer Science [cs]/Web, Cognitive Psychology, Biology and Life Sciences, Computational Biology, 15. Life on land, Genome Analysis, Data science, Agronomy, [INFO.INFO-IR]Computer Science [cs]/Information Retrieval [cs.IR], Cognitive Science, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, 030217 neurology & neurosurgery, User Interfaces, Neuroscience, Crop Science, Cereal Crops
Abstract

Exploring the links between genetic and phenotypic traits is an important area of research in agronomy. One of the main objectives of this is to accelerate the development of important traits that can positively impact the agricultural economy. However, due to the existence of complex molecular interactions, to gain complete understanding will warrant data analyses performed at different molecular and environmental levels for a given (plant) subject. For instance, to understand how rice genes involved in metabolism or signaling of growth regulators control the rice panicle architecture. While high-throughput technologies have played a key role in accelerating and generating the much-needed data, these can only partially capture the dynamics in genotypephenotype relations. Consequently, our knowledge of the complex relationships between the different molecular actors responsible for the expression of the phenome in various plant systems remains fragmented. Hence, there is an urgent need to effectively integrate and assimilate complementary information to understand the biological system in its entirety. We have developed AgroLD [1] (www.agrold.org), a knowledge graph system that exploits the Semantic Web technology and FAIR principles [2], to integrate information to integrate data about plant species of high interest for the plant science community e.g., rice, wheat, Arabidopsis and in this way facilitating the formulation of new scientific hypotheses. We present some integration results of the project, which currently focused on genomics, proteomics and phenomics. AgroLD is now an RDF knowledge base of 900M triples created by annotating and integrating more than 100 datasets coming from 15 data sources –such as Ensembl plants [3], Gramene.org [4] and TropGeneDB [5]– with 15 ontologies –such as the Gene Ontology [6] and Plant Ontology [7]. Our objective is to offer a domain specific knowledge platform to solve complex biological and agronomical questions related to the implication of genes in, for instances, plant disease resistance or high yield traits. We expect the resolution of these questions to facilitate the formulation of new scientific hypotheses to be validated with a knowledge-oriented approach.

Published
2018
Full Text
View/download PDF

10. Developing data interoperability using standards : a wheat community use case

Author

Sophie Aubin, Hanna Ćwiek-Kupczyńska, Alex Whan, Michael Alaux, Aravind Venkatesan, Patrice Buche, Laurel Cooper, Clement Jonquet, Marie-Angélique Laporte, Elizabeth Arnaud, Rosemary Shrestha, Richard Fulss, Pierre Larmande, Vassilis Protonotarios, Robert P. Davey, Cyril Pommier, Imma Subirats, Ute Baumann, Esther Dzale Yeumo, Hadi Quesneville, Carmen Reverte, Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), School of Agriculture, Food and Wine, University of Adelaide, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), 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 international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Graphs for Inferences on Knowledge (GRAPHIK), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Department of Botany and Plant Pathology, Oregon State University (OSU), Earlham Institute [Norwich], International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Stanford Center for BioMedical Informatics Research (BMIR), Stanford University, Système Multi-agent, Interaction, Langage, Evolution (SMILE), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Neuropublic S.a., Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), 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), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), ANR-12-JS02-0010,SIFR,Indexation sémantique de ressources biomédicales francophones(2012), European Project: 701771,H2020,H2020-MSCA-IF-2015,SIFRm(2016), 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 de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), 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 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), Institute of Agrifood Research and Technology (IRTA), 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], Department of Biometry and Bioinformatics, Institute of Plant Genetics (IPG), Polish Academy of Sciences (PAN)-Polish Academy of Sciences (PAN), Stanford University [Stanford], 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), Food and Agricultural Organization of the United Nations (FAO), United Nations Organization, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, 0301 basic medicine, Data Sharing, Best practice, Data management, Interoperability, Agriculture & Biotechnology, Knowledge organization system, Ontology (information science), 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Data interoperability, Data standards, Wheat, Bio-ontologies, Ontology repository, 03 medical and health sciences, General Pharmacology, Toxicology and Pharmaceutics, 2. Zero hunger, Metadata, General Immunology and Microbiology, business.industry, [INFO.INFO-WB]Computer Science [cs]/Web, Articles, General Medicine, Opinion Article, Data formats, 15. Life on land, Data science, Data sharing, Open data, 030104 developmental biology, Standard vocabularies, business, 010606 plant biology & botany
Abstract

In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently facilitate the extraction of new information from existing and new datasets. During a period of more than 18 months, the RDA Wheat Data Interoperability Working Group (WDI-WG) surveyed the wheat research community about the use of data standards, then discussed and selected a set of recommendations based on consensual criteria. The recommendations promote standards for data types identified by the wheat research community as the most important for the coming years: nucleotide sequence variants, genome annotations, phenotypes, germplasm data, gene expression experiments, and physical maps. For each of these data types, the guidelines recommend best practices in terms of use of data formats, metadata standards and ontologies. In addition to the best practices, the guidelines provide examples of tools and implementations that are likely to facilitate the adoption of the recommendations. To maximize the adoption of the recommendations, the WDI-WG used a community-driven approach that involved the wheat research community from the start, took into account their needs and practices, and provided them with a framework to keep the recommendations up to date. We also report this approach’s potential to be generalizable to other (agricultural) domains.

Published
2017
Full Text
View/download PDF

11. Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests

Author

Bruno Fady, Filippos A. Aravanopoulos, Suchitra Changtragoon, Giovanni G. Vendramin, Zohra Bennadji, Judy Loo, Lars Graudal, Lolona Ramamonjisoa, Erik Dahl Kjær, Forest & Landscape Denmark, Faculty of Life Sciences, World Agroforestry Centre, Aristotle University of Thessaloniki, Instituto Nacional de Investigación Agropecuaria (INIA), National Park Wild Life and Plant Conservation Department, Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Silo National des Graines Forestières, Antananarivo, Consiglio Nazionale delle Ricerche (CNR), ANR (ANR-08-BDVA-0006), FAO, Consortium Research Programme of the CGIAR on Forests, Trees and Agroforestry (FTA), EUFORGEN, Judy Loo, Oudara Souvannavong, and Ian Dawson

Subjects
knowledge, productivity, Resource (biology), Types of indicators, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Biodiversity, Biology, Management, Monitoring, Policy and Law, Ecosystem services, biodiversité, productivité, Ecosystem diversity, Genetic variability, pilotage strategique, Genetic erosion, media_common, Nature and Landscape Conservation, 2. Zero hunger, Diversity, Genetic diversity, arbre, Genetic and demographic verifiers, The genecological approach, Diversity, productivity, knowledge, management, business.industry, Environmental resource management, Forestry, 15. Life on land, échelle, diversité génétique, business, indicateur, human activities, management, Diversity (politics)
Abstract

International audience; There is a general trend of biodiversity loss at global, regional, national and local levels. To monitor this trend, international policy processes have created a wealth of indicators over the last two decades. However, genetic diversity indicators are regrettably absent from comprehensive bin-monitoring schemes. Here, we provide a review and an assessment of the different attempts made to provide such indicators for tree genetic diversity from the global level down to the level of the management unit. So far, no generally accepted indicators have been provided as international standards, nor tested for their possible use in practice. We suggest that indicators for monitoring genetic diversity and dynamics should be based on ecological and demographic surrogates of adaptive diversity as well as genetic markers capable of identifying genetic erosion and gene flow. A comparison of past and present genecological distributions (patterns of genetic variation of key adaptive traits in the ecological space) of selected species is a realistic way of assessing the trend of intra-specific variation, and thus provides a state indicator of tree genetic diversity also able to reflect possible pressures threatening genetic diversity. Revealing benefits of genetic diversity related to ecosystem services is complex, but current trends in plantation performance offer the possibility of an indicator of benefit. Response indicators are generally much easier to define, because recognition and even quantification of, e.g., research, education, breeding, conservation, and regulation actions and programs are relatively straightforward. Only state indicators can reveal genetic patterns and processes, which are fundamental for maintaining genetic diversity. Indirect indicators of pressure, benefit, or response should therefore not be used independently of state indicators. A coherent set of indicators covering diversity-productivity-knowledge-management based on the genecological approach is proposed for application on appropriate groups of tree species in the wild and in cultivation worldwide. These indicators realistically reflect the state, trends and potentials of the world's tree genetic resources to support sustainable growth. The state of the genetic diversity will be based on trends in population distributions and diversity patterns for selected species. The productivity of the genetic resource of trees in current use will reflect the possible potential of mobilizing the resource further. Trends in knowledge will underpin the potential capacity for development of the resource and current management of the genetic resource itself will reveal how well we are actually doing and where improvements are required. (C) 2014 The Authors. Published by Elsevier B.V.

Published
2014
Full Text
View/download PDF

12. The role of forest genetic resources in responding to biotic and abiotic factors in the context of anthropogenic climate change

Author

Tore Skrøppa, Judy Loo, Roberto Lindig-Cisneros, Barbara Vinceti, Ian K. Dawson, Cuauhtémoc Sáenz-Romero, Bruno Fady, Giovanni G. Vendramin, Richard A. Fleming, Trevor Q. Murdock, René I. Alfaro, Carlos Navarro, Yousry A. El-Kassaby, Giulia Baldinelli, Canadian Forest Service, Natural Resources Canada (NRCan), Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche [Roma] (CNR), World Agroforestry Centre, Universidad Michoacana de San Nicolás de Hidalgo (UMICH), Centro de Investigaciones en Ecosistemas, Universidad Nacional Autónoma de México (UNAM), Pacific Climate Impacts Consortium, University of Victoria [Canada] (UVIC), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Azuero Earth Project, Partenaires INRAE, Norwegian Forest and Landscape Institute, University of London, Department of Forest and Conservation Sciences, Faculty of Forestry, and University of British Columbia (UBC)

Subjects
arbre forestier, [SDV]Life Sciences [q-bio], Climate change, Context (language use), Management, Monitoring, Policy and Law, Natural disturbances, ressource génétique végétale, Tree genetic variation, Adaptation, Nature and Landscape Conservation, 2. Zero hunger, Abiotic component, Phenotypic plasticity, changement climatique, business.industry, Ecology, Global warming, Environmental resource management, Forestry, 15. Life on land, Forest genetic resources, Geography, Habitat, 13. Climate action, adaptation au changement climatique, business
Abstract

International audience; The current distribution of forest genetic resources on Earth is the result of a combination of natural processes and human actions. Over time, tree populations have become adapted to their habitats including the local ecological disturbances they face. As the planet enters a phase of human-induced climate change of unprecedented speed and magnitude, however, previously locally-adapted populations are rendered less suitable for new conditions, and 'natural' biotic and abiotic disturbances are taken outside their historic distribution, frequency and intensity ranges. Tree populations rely on phenotypic plasticity to survive in extant locations, on genetic adaptation to modify their local phenotypic optimum or on migration to new suitable environmental conditions. The rate of required change, however, may outpace the ability to respond, and tree species and populations may become locally extinct after specific, but as yet unknown and unquantified, tipping points are reached. Here, we review the importance of forest genetic resources as a source of evolutionary potential for adaptation to changes in climate and other ecological factors. We particularly consider climate-related responses in the context of linkages to disturbances such as pests, diseases and fire, and associated feedback loops. The importance of management strategies to conserve evolutionary potential is emphasised and recommendations for policy-makers are provided.

Published
2014
Full Text
View/download PDF

13. Translating conservation genetics into management: Pan-European minimum requirements for dynamic conservation units of forest tree genetic diversity

Author

Peter Rotach, Oudara Souvannavong, Lorenzo Vietto, Hojka Kraigher, Sándor Bordács, François Lefèvre, Silvio Schueler, Alexis Ducousso, Jason Hubert, Bjerne Ditlevsen, Ditte Christina Olrik, Roman Longauer, Tor Myking, Berthold Heinze, Michele Bozzano, Georg von Wühlisch, Paraskevi Alizoti, Jarkko Koskela, Thröstur Eysteinsson, Leena Yrjänä, Bart De Cuyper, Bruno Fady, 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), European Commission under Council Regulation (EC) No. 870/2004 (EUFGIS action, Contract No. AGRI-2006-0261), EUFORGEN Programme, and Koskela, Jarkko

Subjects
ressource forestière, chloroplaste adn, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, Conservation genetics, arbre forestier, Distribution (economics), Biology, 010603 evolutionary biology, 01 natural sciences, Unit (housing), adaptation au milieu, ressource génétique végétale, Regeneration (ecology), FORESTRY, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, changement climatique, Genetic diversity, conservation génétique, business.industry, Population size, Environmental resource management, in situ, gestion des ressources forestières, ressources génétiques forestières, 15. Life on land, Forest genetic resources, conservation de gènes, Agricultural sciences, Tree (data structure), adaptation locale, diversité génétique, conservation des ressources génétiques, europe, business, picea abies, Sciences agricoles, gestion génétique, 010606 plant biology & botany
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
Full Text
View/download PDF

14. Towards decoding the conifer giga-genome

Author

Dolores Abarca, John MacKay, Silvia Fluch, Francisco M. Cánovas, Carmen Díaz-Sala, Pär K. Ingvarsson, Barbara Vinceti, Nathalie Pavy, Christophe Plomion, Daniel G. Peterson, María-Teresa Cervera, Outi Savolainen, Jeffrey F. D. Dean, M. Ángeles Guevara, Université Laval [Québec] (ULaval), University of Georgia [USA], Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Mississippi State University [Mississippi], Universidad de Málaga [Málaga] = University of Málaga [Málaga], Umeå University, Department of Biology and Biocenter Oulu, University of Oulu, Austrian Institute of Technology (AIT), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Universidad de Alcalá - University of Alcalá (UAH), and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA)

Subjects
0106 biological sciences, Chromosomes, Artificial, Bacterial, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Context (language use), Plant Science, Computational biology, comparative genomics, Biology, Breeding, 01 natural sciences, Genome, Polymorphism, Single Nucleotide, giga-genome sequencing, Giga, 03 medical and health sciences, Genetics, Genetic Association Studies, 030304 developmental biology, Plant Proteins, Comparative genomics, 0303 health sciences, Ecology, Gene Expression Profiling, Chromosome Mapping, General Medicine, Genomics, 15. Life on land, Tracheophyta, integrative studies, RNA, Plant, conifers, Multigene Family, RNA, Small Untranslated, Transcriptome, Agronomy and Crop Science, functional genomics, Genome, Plant, 010606 plant biology & botany
Abstract

International audience; Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to describe the context for these new initiatives. A knowledge foundation has been acquired in several conifers of commercial and ecological interest through large-scale cDNA analyses, construction of genetic maps and gene mapping studies aiming to link phenotype and genotype. Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing. The hope is that recent and pending developments in sequencing technology will contribute to rapidly filling the knowledge vacuum surrounding their structure, contents and evolution. Researchers are also making plans to use comparative analyses that will help to turn the data into a valuable resource for enhancing and protecting the world's conifer forests.

Published
2016
Full Text
View/download PDF

15. Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species

Author

Isabel Rodríguez-Quilón, Ricardo Alía, Santiago C. González-Martínez, María Jesús Serra-Varela, Jarkko Koskela, Luis Santos-del-Blanco, Department of Forest Ecology and GeneticsForest Research Centre, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Department of Ecology and Evolution, Université de Lausanne (UNIL), Sustainable Forest Management Research Institute, Universitad de Valladolid, Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Biodiversité, Gènes & Communautés (BioGeCo), and Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)

Subjects
0106 biological sciences, 0301 basic medicine, Conservation genetics, Genetic Markers, Conservation of Natural Resources, Quantitative genetic differentiation, [SDV]Life Sciences [q-bio], Population, Biodiversity, Outcrossing, Pinus pinaster, Phenotypic plasticity, Biology, Forests, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Species Specificity, Genetic variation, Single nucleotide polymorphisms (SNP), Genetic variability, Dynamic conservation, education, Microsatellites, Demography, Genetic diversity, education.field_of_study, Ecology, Genetic Variation, 15. Life on land, Pinus, Europe, 030104 developmental biology, 13. Climate action, Gene pool
Abstract

Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available. © 2016 by the Ecological Society of America.

Published
2016
Full Text
View/download PDF

16. Adaptive genetic diversity of trees for forest conservation in a future climate: a case study on Norway spruce in Austria

Author

Michael Mengl, Heino Konrad, Silvio Schueler, Hojka Kraigher, Thomas Geburek, Michele Bozzano, Jarkko Koskela, Stefan Kapeller, Jason Hubert, François Lefèvre, Roman Longauer, Ditte Christina Olrik, Federal Research and Training Centre for Forests Natural Hazards and Landscape, 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), Forestry Research, Northern Research Station, Slovenian Forestry Institute, National Forest Centre - Národné lesnícke centrum [Zvolen], Danish Forest and Nature Agency, and Partenaires INRAE

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, changement climatique, Genetic diversity, Ecology, [SDE.MCG]Environmental Sciences/Global Changes, Biodiversity, Gap analysis (conservation), ressources génétiques forestières, 15. Life on land, Forest genetic resources, 010603 evolutionary biology, 01 natural sciences, Geography, 13. Climate action, Genetic variation, Forest ecology, Adaptation, Ecology, Evolution, Behavior and Systematics, 010606 plant biology & botany, Nature and Landscape Conservation, Local adaptation
Abstract

Genetic resources of forest trees are considered as a key factor for the persistence of forest ecosystems because the ability of tree species to survive under changing climate depends strongly on their intraspecific variation in climate response. Therefore, utilizing available genetic variation in climate response and planting alternative provenances suitable for future climatic conditions is considered as an important adaptation measure for forestry. On the other hand, the distribution of adaptive genetic diversity of many tree species is still unknown and the predicted shift of ecological zones and species’ distribution may threaten forest genetic resources that are important for adaptation. Here, we use Norway spruce in Austria as a case study to demonstrate the genetic variation in climate response and to analyse the existing network of genetic conservation units for its effectiveness to safeguard the hotspots of adaptive and neutral genetic diversity of this species. An analysis of the climate response of 480 provenances, clustered into 9 groups of climatically similar provenances, revealed high variation among provenance groups. The most productive and promising provenance clusters for future climates originate from three regions that today depict the warmest and driest areas of the natural spruce distribution in Austria. Gap analysis of the Austrian genetic conservation units in the EUFGIS Portal suggests adequate coverage of the genetic hotspots in southern parts of Austria, but not in eastern and northern Austria. Therefore conservation measures and sustainable utilization of the valuable genetic resources in these regions need to be expanded to cover their high adaptive genetic variation and local adaptation to a warmer climate. The study shows that current conservation efforts need to be evaluated for their effectiveness to protect genetic resources that are important for the survival of trees in a future climate.

Published
2012
Full Text
View/download PDF

17. 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
Full Text
View/download PDF

18. 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
Full Text
View/download PDF

19. 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
Full Text
View/download PDF

20. 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
Full Text
View/download PDF

21. 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
Full Text
View/download PDF

22. 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
Full Text
View/download PDF

23. 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

24. 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
Full Text
View/download PDF

25. 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
Full Text
View/download PDF

26. 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
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results