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1. Occurrence data for the two cryptic species of Cacopsylla pruni (Hemiptera: Psylloidea)

Author: Nicolas Sauvion, Jean Peccoud, Christine Meynard, David Ouvrard, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), This data paper was conceived within the stimulating framework of the KIM RIVE (Key Initiative Montpellier: Infectious Risks and Vectors, https://muse.edu.umontpellier.fr/key-initiatives-muse/rive), supported by MUSE (Montpellier University of Excellence, https://muse.edu.umontpellier.fr/en/muse-i-site) and the RIVOC key challenge (https://muse.edu.umontpellier.fr/2021/04/19/appel-a-projets-rivoc), supported by the Occitanie Region (France). Part of this work benefitted from a postdoctoral grant to NS funded by an INRA-CIRAD SDIPS grant (Speciation and Molecular Diagnosis of Insect Pest Species Complexes).. Field and molecular work for this study were supported by several projects during 15 years:- ECOGER 'Ecologie et adaptation des insectes phytophages en gestion de leurs populations' founded by 'Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation', France, SEE-ERANET, network 'Phytoplasma epidemiology', funded by the 6th EUFramework Programme for Research and Development (ERA-CT-2004-515805), SPEED@ID 'Accurate SPEciEs Delimitation and IDentification of Eukaryotic biodiversity using DNA markers'. A project proposed by F-BoL, the French Barcode of Life initative - Genoscope Evry-France, PRIMA PHACIE 'Pest risk assessment for the European Community plant health: A comparative approach with case studies', founded by European Food Safety Authority (EFSA), grant agreement CFP⁄EFSA⁄PLH, Bilateral project PIA BOSPHORUS between TUBITAK-Turkey and le Ministère des Affaires étrangères-France 'Role of the vectors (psyllids) in the dissemination of the diseases due to phytoplasma on fruit trees', PHYLOPSYL from the project 'Bibliothèque du vivant' (BdV) funded by three French institutions (the CNRS, INRA and MNHN), E-SPACE project number 1504-004, Improving epidemiosurveillance of Mediterranean and tropical plant diseases, French Agropolis Foundation., European Project, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Laboratoire de la santé des végétaux (LSV), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), INRA-CIRAD SDIPS grant (Speciation and molecular Diagnosis of Insect Pest Species complexes)2005-07: ECOGER 'Ecologie et adaptation des insectes phytophages en gestion de leurs populations' founded by le Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation-France, 2007-08: SEE-ERA.NET, network 'Phytoplasma epidemiology', funded by the 6th EU Frame-work Programme for Research and Development (contract number ERACT- 2004-515805)2009-11: SDIPS 'Mechanisms of Speciation & Molecular Diagnosis of Insect Pest Species complexes' founded by INRA-France, 2010-12: SPEED@ID 'Accurate SPEciEs Delimitation and IDentification of Eukaryotic biodiversity using DNA markers'. A project proposed by F-BoL, the French Barcode of Life initative - Genoscope Evry-France, 2010-12: PRIMA PHACIE 'Pest risk assessment for the European Community plant health: A comparative approach with case studies', founded by European Food Safety Authority (EFSA), grant agreement CFP⁄EFSA⁄PLH⁄2009⁄01, 2010-12: Bilateral project PIA BOSPHORUS between TUBITAK-Turkey and le Ministère des Affaires étrangères-France 'Role of the vectors (psyllids) in the dissemination of the diseases due to phytoplasma on fruit trees', 2011-13: PHYLOPSYL from the project 'Bibliothèque du vivant' (BdV) funded by three French institutions (the CNRS, INRA and MNHN), and 2015-2018: E-SPACE project number 1504-004, Improving epidemiosurveillance of Mediterranean and tropical plant diseases, French Agropolis Foundation.
Subjects: Asia, Insecta, Arthropoda, Cacopsylla pruni, QH301-705.5, Biodiversity & Conservation, Cacopsylla, Evolutionary biology, Horticulture, European stone fruit yellows, vector-borne plant pathogen, Hemiptera, Data analysis & Modelling, Sternorrhyncha, Systematics, Agricultural ecology, Ecology & Environmental sciences, Animalia, phytoplasma, Biology (General), 'Candidatus phytoplasma prunorum', Data Paper (Biosciences), Diseases & Pests, Biota, Psylloidea, psyllid, Europe, ' Candidatus phytoplasma prunorum', [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Psyllidae, Biogeography, Zoology & Animal Biology, Africa, species distribution, epidemiology, vecto, Americas, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Cacopsylla pruniisa psyllid that has been known since 1998 as the vector of the bacterium ‘Candidatus Phytoplasma prunorum’, responsible for the European stone fruit yellows (ESFY), a disease that affects species of Prunus. This disease is one of the major limiting factors for the production of stone fruits, most notably apricot (Prunus armeniaca) and Japanese plum (P. salicina), in all EU stone fruit-growing areas. The psyllid vector is widespread in the Western Palearctic, and evidence for the presence of the phytoplasma that it transmits to species of Prunus has been found in 15 of the 27 EU countries. Recent studies showed that C. pruni is actually composed of two cryptic species, which can be differentiated bymolecular markers. A literature review on the distribution of C. pruni was published in 2012, but it only provided presence or absence information at the country level and without distinction between the two cryptic species. Since 2012, numerous new records of the vector in several European countries have been published. We ourselves have acquired a large amountof data from sampling in France and other European countries. We have also carried out a thorough systematic literature review to find additional records, including all the original sources mentioningC. pruni (or its synonyms) since the first description by Scopoli in 1763. Our aim was to create an exhaustive georeferenced occurrence catalog, in particular in countries that are occasionnaly mentioned in the literature with little detail. Finally, for countries that seem suitable for the proliferation of C. pruni (USA, Canada, Japan, China, etc.), we digged deeper into the literature and reliablesources (e.g. checklist)to better subtanciateits current absence from those regions. Information on the distribution ranges of these vector psyllids is of crucial interest in order to best predict the vulnerability of stone fruit producing countries to the ESFY threat in the foreseeable future. We give free access to a unique file of 1975 records of all occurrence data in our possession concerning C. pruni, which we have gathered through more than twenty years of sampling efforts in Europe or through intensive text mining. We have made every effort to retrieve the source information for the records extracted from litterature (1201 records). Thus, we always give the title of the original reference, together with the page(s) citing C. pruni and, if possible, the year of sampling. To makethe results of this survey publicly available, we give a URL to access the literature sources. In most cases, this link allows to freely download a PDFfile. We also give access to information extracted from GBIF (162 exploitable data points on 245 occurrences found in the database), which we thoroughly checked and often supplemented to make the information more easily exploitable. We give access to our own unpublished georeferenced and genotyped record from 612samples taken over the last 20 years in several European countries (Switzerland, Belgium, Netherlands, Spain, etc.). Theseinclude two countries (Portugal and North Macedonia) for which the presence of C. pruni had notbeen reported before.Asour specimens have been genotyped (74 sites with species A solely, 202 with species B solely, and 310 with species A+B), our new data enable a better view of the geographical distribution of the two species at the Palaearctic scale.
Published: 2021
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2. A spectral correction method for multi-scattering effects in close range hyperspectral imagery of vegetation scenes: application to nitrogen content assessment in wheat

Author: Rabatel, Gilles, Al Makdessi, N., Ecarnot, Martin, Roumet, Pierre, Taylor, James, Cammarano, D., Prashar, A., Hamilton, A., Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-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), 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), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), 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), Agropolis Foundation : 1202-008, France Agrimer, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Agropolis Foundation : 1202-008, ANR-10-LABX-0001-01, and l'Agence Nationale de la Recherche (ANR)
Subjects: 0106 biological sciences, Canopy, 0211 other engineering and technologies, Spectral space, chemistry.chemical_element, Soil science, Context (language use), 02 engineering and technology, 01 natural sciences, PHENOTYPING, Partial least squares regression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MULTIPLE SCATTERING, Projection (set theory), 021101 geological & geomatics engineering, Mathematics, Remote sensing, Scattering, Hyperspectral imaging, 04 agricultural and veterinary sciences, General Medicine, Vegetation, 15. Life on land, Nitrogen, Close range, Data set, Optical phenomena, hyperspectral imagery, CANOPY MODELIZATION, chemistry, [SDE]Environmental Sciences, Content (measure theory), 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, canopy modeling, General Agricultural and Biological Sciences, Subspace topology, 010606 plant biology & botany
Abstract: International audience; In-field hyperspectral imagery is a promising tool for crop phenotyping or monitoring. In association with partial least square regression (PLS-R), it allows building high spatial resolution maps of the chemical content of plant leaves. However, several optical phenomena must be taken into account, due to their influence on collected spectral data. The most challenging is multiple scattering, produced when a leaf is partly illuminated by light reflection or transmission from neighboring leaves. It can induce bias in prediction results. This paper presents a method for multi-scattering correction. Its development has been based on simulation tools: a 3D canopy model of winter wheat was combined with light propagation modeling, in order to simulate the apparent reflectance of every visible leaf in the canopy for a given actual reflectance. Leaf nitrogen content (LNC) prediction has been considered. A data set of reflectance spectra associated with LNC values has been issued from real leaf measurements. A theoretical disturbance subspace representing the spectrum dispersion in the spectral space due to multi-scattering has then been built by considering polynomial combinations of the initial spectra, and a projection along this subspace has been applied to every simulated spectra. Using this strategy, a PLS-R model built on initial spectra was still satisfactory when applied to simulated spectra with multiple scattering. The method has then been applied to real plants in greenhouse and field conditions, and its prediction results compared with those of a standard PLS-R, confirming its efficiency in the presence of various lighting environments.
Published: 2017
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3. Adaptation of genetically monomorphic bacteria: evolution of copper resistance through multiple horizontal gene transfers of complex and versatile mobile genetic elements

Author: Aude Chabirand, Christian Vernière, Pierre Lefeuvre, Olivier Pruvost, Claudine Boyer, Pierre Grygiel, Damien Richard, Virginie Ravigné, Adrien Rieux, Marie Annabelle Terville, Isabelle Robène, B.I. Canteros, Stéphanie Javegny, Benoit Facon, Karine Boyer, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre de Biologie pour la Gestion des Populations (UMR CBGP), 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)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA), Instituto Nacional de Tecnología Agropecuaria (INTA), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), European Regional Development Fund (ERDF), European Agricultural Fund for Rural Development (EAFRD), Conseil Departemental de la Reunion, Region Reunion, Etat francais, French Agropolis Foundation (Labex Agro - Montpellier, E-SPACE) : 1504-004, ANSES, CIRAD, Département Systèmes Biologiques (Cirad-BIOS), 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)-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), The European Regional Development Fund (ERDF) and European Agricultural Fund for Rural Development (EAFRD), Conseil Departemental de la Reunion, Region Reunion, Etat francais, the French Agropolis Foundation (Labex Agro - Montpellier, E-SPACE project number 1504-004), ANSES and CIRAD provided financial support., ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), 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: 0301 basic medicine, Citrus, heavy metal resistance, Xanthomonas campestris citri, Xanthomonas citri, Plasmid, Genetics, biology, Adaptation, Physiological, Épidémiologie, MESH: Copper, Stenotrophomonas, PCR, Organisme génétiquement modifié, Cuivre, Citrus canker, mobile DNA, Martinique, MESH: Interspersed Repetitive Sequences, résistance aux maladies, DNA, Bacterial, Séquence nucléotidique, Xanthomonas, Gene Transfer, Horizontal, Genotype, Argentina, Bacterial genome size, MESH: Xanthomonas, 03 medical and health sciences, stomatognathic system, plasmid, MESH: Drug Resistance, Bacterial, Drug Resistance, Bacterial, protection des plantes, contemporary adaptation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Adaptation, Ecology, Evolution, Behavior and Systematics, H20 - Maladies des plantes, Plant Diseases, Résistance aux pesticides, amélioration génétique, Résistance aux produits chimiques, Xanthomonadaceae, Biologie moléculaire, Microsatellite, biology.organism_classification, Interspersed Repetitive Sequences, resistance to diseases, 030104 developmental biology, Genetics, Population, Gène, Genes, Bacterial, Évaluation, U30 - Méthodes de recherche, Mobile genetic elements, Reunion, Copper, crop protection, Microsatellite Repeats
Abstract: Copper-based compounds are widely used in integrated pest management (1PM) programs aiming at controlling agriculturally important plant bacterial pathogens and the latter have adapted in response to this selective pressure. Copper resistance of Xanthomonas citri pv. citri (Xcc), a major citrus pathogen worldwide causing Asialie citrus canker, was first observed in Argentina two decades ago and subsequently reported as a copLAB-based, plasmid-encoded system. The emergence of resistant strains has since been reported in Réunion (South West lndian Ocean) and Martinique (Eastern Caribbean Sea). Disease severity was found markedly increased in groves established with susceptible cultivars and infected with copper-resistant Xcc. Using tandem repeat-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copperresistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons. ln order to investigate this pattern more closely, we sequenced six copper-resistant Xcc strains from Argentina, Martinique and Réunion, together with reference copper-resistant Xanthomonas and Stenotrophomonas strains using long-read sequencing technology. Genes involved in copper resistance were found to be strain-dependent with the nove! identification in Xcc of copABCD and a eus heavy metal efflux resistance-nodulation-division system. The genes providing the adaptive trait were part of a mobile genetic element similar to Tn3-like transposons and included in a conjugative plasmid. The mining of ail bacterial genomes available from public databases suggested that the mobile elements containing copper resistance genes and their plasmid environments were primarily detected in the Xanthomonadaceae family.
Published: 2016
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4. Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes’ Selective Footprints in the Genes Network Regulating Flowering Time

Author: Nourollah AHMADI, Mamadou Billo BARRY, Julien FROUIN, Miguel de Navascués, Mamadou Aminata Touré, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Développement Adaptatif du Riz [AGAP] (DAR), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut de Recherche Agronomique de Guinée (IRAG), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and Funding institution: AGROPOLIS Foundation. Grant number: 0900-001-1. Grant recipient: Nourollah Ahmadi.
Subjects: Climate changes, Temporal cline, O. glaberrima, Flowering time, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Soil Science, Rice, Plant Science, Selection footprint, Genome scan, Agronomy and Crop Science, O. sativa
Abstract: Passport and phenotypic data of the rice accessions studied are provided Additional file 11: Table S1. Genotypic data can be downloaded in HapMap format from http://tropgenedb.cirad.fr/tropgene/JSP/interface.jsp?module=RICE study Genotypes, study type G-panel_GBS_data.; International audience; Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes' selective footprint in crops.
Published: 2023
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5. Documenting evapotranspiration and surface energy fluxes over rainfed annual crops within a Mediterranean hilly agrosystem

Author: Rim Zitouna-Chebbi, Frédéric Jacob, Laurent Prévot, Marc Voltz, Institut National de Recherche en Génie Rural Eaux et Forêts (INRGREF), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Institution de la Recherche et de l'Enseignement Supérieur Agricoles [Tunis] (IRESA), Laboratoire d'étude des Interactions Sol - Agrosystème - Hydrosystème (UMR LISAH), Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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), The current study was financially supported by the IRRIMED Project (European Union - Fifth Framework Program – Contract ICA3-2002-10080 ), by the Agropolis Foundation (Contract 0901-013 ), by the MISTRALS/SICMED Program , by the French National Research Agency (ANR) TRANSMED program through the ALMIRA project (Contract ANR-12-TMED-0003 ), and by the ALTOS Project (PRIMA 2018 Section 2). It was also supported by the French National Research Institute for Sustainable Development (IRD) through the Department for Support and Training and through the NAILA International Joint Laboratory. It also benefited from experimental support from the OMERE Environmental Research Observatory ., and ANR-12-TMED-0003,ALMIRA,Adaptation des mosaïques paysagères dans les agrosystèmes pluviaux Méditerranéens pour une gestion durable de la production agricole, des ressources en eau et en sol(2012)
Subjects: Evapotranspiration, Eddy covariance times series, [SDV]Life Sciences [q-bio], Mediterranean hilly agrosystems, Soil Science, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Rainfed annual crops Mediterranean hilly agrosystems Evapotranspiration Eddy covariance times series Upwinds/downwinds Seasonal dynamics, Seasonal dynamics, Rainfed annual crops, [SDE]Environmental Sciences, Upwinds/downwinds, Agronomy and Crop Science, Earth-Surface Processes, Water Science and Technology
Abstract: International audience; The current study aims to document evapotranspiration and associated surface energy fluxes for rainfed annual crops within a Mediterranean hilly agrosystem, in order to provide information on crop water use under such little-studied conditions. For this, an experimental study is conducted within the Tunisian study site of the OMERE observatory (French acronym for the Mediterranean Observatory of Water and the Rural Environment), located in the northeastern Cap Bon peninsula. It relies on eddy covariance (EC) measurements at the plot scale. We report that (1) observations are consistent with previous studies under Mediterranean or semi-arid contexts, with time series of energy fluxes that depict classical seasonal dynamics, (2) common flux ratios (i.e., Bowen Ratio, ratio of actual to reference evapotranspiration) may change according to upwinds and downwinds, which requires further investigations about possible changes in aerodynamic conditions, and (3) a reference evapotranspiration value of 4 mm day − 1 seems to be a threshold beyond which actual evapotranspiration decreases systematically and rapidly. In terms of agricultural water management, the current study suggests to look for early sowing species/varieties, in order to reduce the evaporation-based water loss in autumn. Overall, EC measurements seem promising over rainfed annual crops within semiarid hilly agrosystems, for long term observations, environmental modelling and operational purposes. Since the current study is conducted over few small fields within a specific hilly topography, the original results we report here need to be strengthened with complementary studies.
Published: 2023
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6. Biocultural Drivers Responsible for the Occurrence of a Cassava Bacterial Pathogen in Small-Scale Farms of Colombian Caribbean

Author: Pérez, Darío, Duputié, Anne, Vernière, Christian, Szurek, Boris, Caillon, Sophie, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Patrimoines locaux, Environnement et Globalisation (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU), Universidad Nacional de Colombia [Bogotà] (UNAL), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and Agropolis Foundation (Grant No. 1 403-073)
Subjects: seed system, fertilizer use, circulation of propagative propagules, Ecology, cassava bacterial blight (CBB), land property, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, food and beverages, agricultural practices, Xanthomonas phaseoli pv. manihotis, Ecology, Evolution, Behavior and Systematics, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: International audience; Cassava ( Manihot esculenta Crantz) is a primary crop for food security of millions of people worldwide. In Colombia, the Caribbean region contributes about half of the national cassava production, despite major socioeconomic constraints such as unequal land property, omnipresence of middlemen, low and unstable prices, armed conflict, climate change and phytosanitary issues. Among the latter is Cassava Bacterial Blight (CBB), a disease caused by the bacterial pathogen Xanthomonas phaseoli pv. manihotis ( Xpm ) that leads to irreversible damage to plants, impeding growth and productivity. In 2016, we analyzed the role of sociocultural and agricultural practices on CBB prevalence in small-scale fields of a village of the Colombian Caribbean region, where farmers live almost exclusively from the sale of their cassava production. Semi-structured interviews (48) were conducted with all farmers who cultivated cassava to document individual sociodemographic characteristics, cassava farming practices, and perceptions about CBB occurrence. Cassava Bacterial Blight was diagnosed in the field and the presence of Xpm was further confirmed upon laboratory analysis of collected diseased leaf samples. Our data show that (i) according to the risks perceived by farmers, CBB is the main disease affecting cassava crops in the village and it could indeed be detected in about half of the fields visited; (ii) CBB occurrence depends strongly on land property issues, likely because of an inadequate phytosanitary control during acquisition of cuttings when farmers are forced to rent the land; and (iii) there is a strong positive correlation between the use of commercial fertilizers and the occurrence of CBB in the village of Villa López.
Published: 2022
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7. Chemical and biochemical quality of organic and/ or mineral fertilization resources - A dataset from the Highlands of Madagascar

Author: Raminoarison, Manoa, Blanchart, Eric, Razafimbelo-Andriamifidy, Tantely, Thuriès, Laurent, Trap, Jean, Laboratoire des RadioIsotopes (LRI), Université d'Antananarivo, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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), Recyclage et risque (UPR Recyclage et risque), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), project SECuRE (Soil ecological function restoration to enhance agrosystem services in rainfed rice cropping systems in agroecological transition), supported by the Agropolis Foundation under the reference ID 1605-007 through the 'Investissements d'Avenir' program (Labex Agro: ANR-10-LABX-0001-01), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), and ANR-16-IDEX-0006,MUSE,MUSE(2016)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Nitrogen mineralization, Nutrient contents, CO 2 mineralization, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Ferralsols
Abstract: International audience; A basic understanding of the fertilization resources (FR) char-acteristics is required to drive soil functions following the FR application, and to improve crop productivity. The datasets presented include the FR characteristics, i.e. their nutrient contents and biochemical quality, and their effects on soil in carbon (C) and nitrogen (N) mineralization. We selected nineteen FR from local farmers, from laboratory institution and from commercial producers. The soil used in experiment was sampled in Imerintsiatosika locality, located in the Cen-tral Highlands of Madagascar. Nutrient contents of FR were evaluated by measuring total carbon, nitrogen, phosphorus, potassium, calcium, magnesium and sulphur contents. Bio-chemical quality of the products was assayed by fractioning organic matter of organic resources in soluble compartments, hemicelluloses, celluloses and lignin equivalent. Laboratory incubations in microcosm experiments were conducted with the mixture of soil and fertilization resources to determine C and N mineralization rates. Carbon mineralization rate was measured using microgas chromatography, and nitrogen min-eralization rates were analyzed by colorimetry on a continu-ous flow analyzer.
Published: 2022
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8. Increasing plant diversity promotes ecosystem functions in rainfed rice based short rotations in Malagasy highlands

Author: Marie Sauvadet, Patrice Autfray, Jean Trap, Eric Blanchart, Aude Ripoche, Philippe Letourmy, Bodovololona Rabary, Thierry Becquer, Richard Randriamanantsoa, Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), Fonctionnement écologique et gestion durable des agrosystèmes bananiers et ananas (UR GECO), and STRADIV project (STRADIV project no. 1504-003) supported by Agropolis Foundation (France) and partly by CRP Rice Program supported by CGIAR
Subjects: 0106 biological sciences, Agroecosystem, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Rotation culturale, agrobiodiversité, F08 - Systèmes et modes de culture, 01 natural sciences, 7. Clean energy, F07 - Façons culturales, 2. Zero hunger, Ecology, biology, 04 agricultural and veterinary sciences, Legume, Rendement des cultures, Agroécosystème, Diversification, Cover crop, Rotation, Context (language use), Ecological intensification, 010603 evolutionary biology, Crop, Culture en mélange, Riz pluvial, Ecosystem services, Monocropping, 15. Life on land, Crop rotation, Sorghum, biology.organism_classification, services écosystémiques, Agronomy, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Système de culture, Animal Science and Zoology, Soil fertility, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Weed, Agronomy and Crop Science, Agroecology
Abstract: International audience; Plant diversification is one of the main ways to ecologically intensify agroecosystems to improve their sustainability and resilience. Rotations and/or a mixture of crops can mitigate pest and weed infestation, reduce diseases, and improve soil fertility and crop productivity. However, rainfed rice yields in the Malagasy highlands remain low despite the frequent use of cropping systems including crop rotations and mixtures. In this study, we compared three rainfed rice based short rotations with rainfed rice monocropping to quantify the benefits of plant diversification on different ecosystem functions such as weed and nematode control, soil fertility, soil macrofauna abundance and diversity, and rice yield over four cropping seasons. The three rotations were based on rice in rotation with one legume, groundnut (RG), a cereal-legume mixture, sorghum and cowpea (RSC), or a mixture of legumes, velvet bean and crotalaria (RVC). Rice growth, N content and yield, soil N content, weed biomass, nematofauna and macrofauna were assessed and a profitability analysis was performed at rotation scale. The legume mixture had a significant and positive effect on rice growth, N content and yield, soil N content, and weed and nematode control due to high biomass production in the cropping cycle including legume mixture, by limiting weed growth and leaving a large quantity of N-rich residues to enrich the soil for the following rice crop. The nematicide properties of the legume mixture may reduce the infestation of plant-feeding nematodes. The RG and RSC rotations produced intermediate results. While rice yields were higher in these rotations than when rainfed rice was grown alone, weed biomass remained high due to minimal competition with weeds during the crop rotation cycle especially with groundnut. For RSC, nematode control was limited as both sorghum and cowpea are host plants for nematodes. Despite a year with no crop income with the RVC rotation, profitability was higher mainly due to the increased rice yield and reduced field management costs. The choice of species is thus crucial to optimise ecosystem functions adapted to farmers’ context and objectives.
Published: 2021
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9. Population structure and genetic relationships between Ethiopian and Brazilian Coffea arabica genotypes revealed by SSR markers

Author: David Pot, Luiz Filipe Protasio Pereira, Bruna Silvestre Rodrigues da Silva, Leonardo Godoy Androcioli, Gustavo Cesar Sant'ana, Pierre Charmetant, Gustavo Hiroshi Sera, Douglas Silva Domingues, Camila Lucas Chaves, Thierry Leroy, Rafaelle Vecchia Ferreira, Instituto Agronômico do Paraná (IAPAR), Universidade Estadual de Londrina (UEL), UMR AGAP, Montpellier SupAgro, Mestrado em Agricultura Conservacionista, Universidade Estadual Paulista (Unesp), Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Instituto Agronômico do Parana, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, 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), State University of Londrina = Universidade Estadual de Londrina, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior - Brazil (CAPES) : 001, CAPES - Agropolis Foundation : 1203-001 ANR-10-LABX-0001-01, INCT Cafe, CNPq, CAPES, Brazilian Coffee Research Consortium, and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, 0301 basic medicine, Genotyping Techniques, Cultivated and wild gene pools, Coffea, Plant Science, 01 natural sciences, Genetic diversity, F30 - Génétique et amélioration des plantes, Coffea spp, Population structure and relationships, Genotype, Marqueur génétique, Phylogeny, 2. Zero hunger, SSR markers, biology, Coffea arabica, General Medicine, Horticulture, Microsatellite, Populationstructure and relationships, Génotype, Canephora, 010603 evolutionary biology, 03 medical and health sciences, Variation génétique, Genetics, Allele, Structure de la population, Ressource génétique, Polymorphism, Genetic, biology.organism_classification, Plant Breeding, 030104 developmental biology, Genetic distance, Insect Science, Animal Science and Zoology, Microsatellite Repeats
Abstract: Made available in DSpace on 2019-10-06T15:42:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-04-15 Agropolis Fondation Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Information about population structure and genetic relationships within and among wild and brazilian Coffea arabica L. genotypes is highly relevant to optimize the use of genetic resources for breeding purposes. In this study, we evaluated genetic diversity, clustering analysis based on Jaccard’s coefficient and population structure in 33 genotypes of C. arabica and of three diploid Coffea species (C. canephora, C. eugenioides and C. racemosa) using 30 SSR markers. A total of 206 alleles were identified, with a mean of 6.9 over all loci. The set of SSR markers was able to discriminate all genotypes and revealed that Ethiopian accessions presented higher genetic diversity than commercial varieties. Population structure analysis indicated two genetic groups, one corresponding to Ethiopian accessions and another corresponding predominantly to commercial cultivars. Thirty-four private alleles were detected in the group of accessions collected from West side of Great Rift Valley. We observed a lower average genetic distance of the C. arabica genotypes in relation to C. eugenioides than C. canephora. Interestingly, commercial cultivars were genetically closer to C. eugenioides than C. canephora and C. racemosa. The great allelic richness observed in Ethiopian Arabica coffee, especially in Western group showed that these accessions can be potential source of new alleles to be explored by coffee breeding programs. Instituto Agronômico do Paraná (IAPAR), Rodovia Celso Garcia Cid, 375 Km Centro de Ciências Biológicas Área de Genética e Biologia Molecular Universidade Estadual de Londrina (UEL), CP 10.011 CIRAD UMR AGAP AGAP Univ. Montpellier CIRAD INRA INRIA Montpellier SupAgro Departamento de Agronomia Universidade Estadual de Londrina (UEL), CP 6001 Instituto Agronômico do Paraná (IAPAR) Mestrado em Agricultura Conservacionista, CP 481 Instituto de Biociências de Rio Claro Universidade Estadual Paulista (UNESP) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA Café) Laboratório de Biotecnologia de Plantas – IAPAR Embrapa Café, Rodovia Celso Garcia Cid, 375 km Instituto de Biociências de Rio Claro Universidade Estadual Paulista (UNESP)
Published: 2019
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10. Urban collective garden participation and health: a systematic literature review of potential benefits for free-living adults

Author: Marion Tharrey, Nicole Darmon, Montpellier Interdisciplinary center on Sustainable Agri-food systems (Social and nutritional sciences) (UMR MoISA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This research was part of doctoral thesis of M.T. co-funded by INRAE and the Surfood-Foodscape project, the latter being publicly funded through the French National Research Agency under the 'Investissements d’avenir' program (reference ANR-10-LABX-001–01 Labex Agro), and coordinated by the Agropolis Foundation. This research was also supported by the Olga Triballat Institute., ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Adult, media_common.quotation_subject, Well-being, Medicine (miscellaneous), Context (language use), Health Promotion, Community garden, 03 medical and health sciences, 0302 clinical medicine, Environmental health, Vegetables, Humans, 030212 general & internal medicine, Social determinants of health, media_common, 2. Zero hunger, Consumption (economics), Selection bias, 030505 public health, Nutrition and Dietetics, Physical activity, Allotment garden, Gardening, Health indicator, Mental health, Systematic review, Fruit, Fruit and vegetables, 0305 other medical science, Psychology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Gardens
Abstract: Context Collective gardens are increasingly considered a tool to promote health and well-being. Objective In this systematic review, we critically appraise quantitative studies exploring the potential health benefits of urban collective garden participation. Data Sources Articles published between January 2000 and August 2020 were used. Data Extraction All original research studies reporting at least 1 health outcomes associated with urban collective gardening in free-living adults from Western and other high-income countries were included. Of 1261 articles identified, 15 were included in the systematic review. Methodological quality was assessed by applying the criteria of the Quantitative Study Quality Assessment Tool. Analysis A wide range of health indicators was used. Collective gardening was associated with higher fruit and vegetable consumption than was nongardening. Mixed results were found for physical activity and physiological health. A positive association was found in most studies with mental health and social health. However, the vast majority of included studies were cross-sectional and presented selection bias (n = 13 of 15 for both) and very few used objective measurement methods (n = 3 of 15). Conclusions Longitudinal studies allowing the exploration of causal relationships are needed before the health benefits of collective garden participation suggested by existing studies can be confirmed.
Published: 2021
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11. Diversity and Geographical Structure of Xanthomonas citri pv. citri on Citrus in the South West Indian Ocean Region

Author: PRUVOST, Olivier, Richard, Damien, Boyer, Karine, Javegny, Stéphanie, Boyer, Claudine, Chiroleu, Frédéric, Grygiel, Pierre, Parvedy, Evelyne, Robène, Isabelle, Maillot-Lebon, Véronique, Hamza, Azali, Lobin, Kanta Kumar, Naiken, Marc, Vernière, Christian, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-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), Laboratoire de santé des végétaux (LSV Angers), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Institut National de la Recherche pour l'Agriculture, la Pêche et l'Environnement (INRAPE), Food and Agricultural Research and Extension Institute (FAREI), National Biosecurity Agency, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-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), The European Union (ERDF contract GURDT I2016-1731-0006632, ERDF INTERREG IV and INTERREG V), Conseil Régional de La Réunion, the French Agropolis Foundation (Labex Agro—Montpellier, E-SPACE project number 1504-004), ANSES and CIRAD provided financial support., ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Laboratoire de santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: QH301-705.5, [SDV]Life Sciences [q-bio], Pathologie végétale, MESH: Xanthomonas, Xanthomonas campestris citri, molecular epidemiology, citrus, Variation génétique, copper resistance, MESH: Molecular Epidemiology, Surveillance épidémiologique, Biology (General), Variation phénotypique, H20 - Maladies des plantes, Bactérie pathogène, Xanthomonas citri pv citri, aggressiveness, Épidémiologie, Asiatic canker, Citrus medica
Abstract: A thorough knowledge of genotypic and phenotypic variations (e.g., virulence, resistance to antimicrobial compounds) in bacteria causing plant disease outbreaks is key for optimizing disease surveillance and management. Using a comprehensive strain collection, tandem repeat-based genotyping techniques and pathogenicity assays, we characterized the diversity of X. citri pv. citri from the South West Indian Ocean (SWIO) region. Most strains belonged to the prevalent lineage 1 pathotype A that has a wide host range among rutaceous species. We report the first occurrence of genetically unrelated, nonepidemic lineage 4 pathotype A* (strains with a host range restricted to Mexican lime and related species) in Mauritius, Moheli and Réunion. Microsatellite data revealed that strains from the Seychelles were diverse, grouped in three different clusters not detected in the Comoros and the Mascarenes. Pathogenicity data suggested a higher aggressiveness of strains of one of these clusters on citron (Citrus medica). With the noticeable exception of the Comoros, there was no sign of recent interisland movement of the pathogen. Consistent with this finding, the copL gene, a marker for the plasmid-borne copLAB copper resistance that was recently identified in Réunion, was not detected in 568 strains from any islands in the SWIO region apart from Réunion.
Published: 2021
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12. Optimization of a protein extraction method from natural rubber sheets made of Hevea brasiliensis latex

Author: Jérôme Sainte-Beuve, Céline Bottier, Kanthida Wadeesirisak, Siriluck Liengprayoon, Surattiya Srisomboon, Kittipong Rattanaporn, Laurent Vaysse, Natedao Musigamart, Frédéric Bonfils, Kasetsart University (KU), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Graduate Program Scholarship from the Graduate School, Kasetsart University., Agropolis Foundation is thanked for the support to the creation of LipPolGreen-Asia platform in Kasetsart Agricultural and Agro-Industrial Product Improvement Institute, Bangkok., and Hevea Research Platform in Partnership (HRPP).
Subjects: Cyclohexane, Extraction, 02 engineering and technology, Plant Science, chemistry.chemical_compound, Natural rubber, Protein purification, Centrifugation, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Q60 - Traitement des produits agricoles non alimentaires, Caoutchouc, Chromatography, Aqueous solution, Électrophorèse gel polyacrylamide, biology, Chemistry, 020502 materials, Organic Chemistry, Extraction (chemistry), 021001 nanoscience & nanotechnology, biology.organism_classification, U50 - Sciences physiques et chimie, Hevea brasiliensis, Electrophoresis, 0205 materials engineering, visual_art, visual_art.visual_art_medium, 0210 nano-technology, Qualité protéique
Abstract: International audience; A method to extract proteins from natural rubber (NR) samples has been developed to characterize the protein composition of NR by SDS-PAGE electrophoresis. While the incubation of NR pieces in aqueous buffers did not provide satisfactory results (no protein bands detected by SDS-PAGE), the solubilization of NR pieces in an organic solvent, prior to centrifugation and protein extraction from the obtained pellet, was found efficient to highlight protein bands by SDS-PAGE. Pure cyclohexane was used to solubilize NR pieces and resulted in a low share of nitrogen in the pellet (29%). The addition of 10% (v/v) ethanol to cyclohexane allowed to significantly increase this share to 73% and to detect 13 protein bands by SDS-PAGE. The molecular weights of the four most intense bands suggest the presence in NR of the following proteins: rubber elongation factor, small rubber particle protein, hevamine, and β-1-3 glucanase.
Published: 2021
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13. TAL Effector Repertoires of Strains of Xanthomonas phaseoli pv. manihotis in Commercial Cassava Crops Reveal High Diversity at the Country Scale

Author: Zárate-Chaves, Carlos, Osorio-Rodríguez, Daniela, Mora, Rubén, Perez-Quintero, Alvaro, Dereeper, Alexis, Restrepo, Silvia, Lopez, Camilo, Szurek, Boris, Bernal, Adriana, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-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), Universidad de los Andes [Bogota] (UNIANDES), Universidad Nacional de Colombia [Bogotà] (UNAL), Colombian Ministry of Sciences (Former Colciencias), through project No. 315-2013, Universidad de los Andes and its Basic Sciences funding through multiple research projects (seed project NUMBER assigned to CAZ and Project No. INV-2019-84-1855 assigned to AB), Research Program on Roots, Tubers and Bananas, Agropolis Foundation (project #1403-073), doctoral fellowship awarded by the Insitut de Recherche pour le Developpement., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: EBE prediction, transcriptomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], cassava bacterial blight, food and beverages, host target genes, susceptibility, SWEET, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: International audience; Transcription activator-like effectors (TALEs) play a significant role for pathogenesis in several xanthomonad pathosystems. Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of Cassava Bacterial Blight (CBB), uses TALEs to manipulate host metabolism. Information about Xpm TALEs and their target genes in cassava is scarce, but has been growing in the last few years. We aimed to characterize the TALE diversity in Colombian strains of Xpm and to screen for TALE-targeted gene candidates. We selected eighteen Xpm strains based on neutral genetic diversity at a country scale to depict the TALE diversity among isolates from cassava productive regions. RFLP analysis showed that Xpm strains carry TALomes with a bimodal size distribution, and affinity-based clustering of the sequenced TALEs condensed this variability mainly into five clusters. We report on the identification of 13 novel variants of TALEs in Xpm, as well as a functional variant with 22 repeats that activates the susceptibility gene MeSWEET10a, a previously reported target of TAL20(Xam668). Transcriptomics and EBE prediction analyses resulted in the selection of several TALE-targeted candidate genes and two potential cases of functional convergence. This study provides new bases for assessing novel potential TALE targets in the Xpm-cassava interaction, which could be important factors that define the fate of the infection.
Published: 2021
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14. metaXplor: an interactive viral and microbial metagenomic data manager

Author: Sempéré, Guilhem, Pétel, Adrien, Abbé, Magsen, Lefeuvre, Pierre, Roumagnac, Philippe, Mahé, Frédéric, Baurens, Gaël, Filloux, Denis, Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Université de Bordeaux (UB)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-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), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was supported by the Agropolis Foundation grant ESPACE (1504-004)., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Gestion de données, Phylogénie, AcademicSubjects/SCI02254, [SDV]Life Sciences [q-bio], Logiciel, web, génomique, taxonomy, base de données sur le matériel génétique, shotgun, Technical Note, Phylogeny, metagenomics, U10 - Informatique, mathématiques et statistiques, Analyse de données, L60 - Taxonomie et géographie animales, NoSQL, Taxonomie, Genomics, sequence, L10 - Génétique et amélioration des animaux, sample, assignment, metabarcoding, AcademicSubjects/SCI00960, Metagenome, data management, Software
Abstract: International audience; Background: Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and user-friendly tools exist for running various types of analyses (e.g., Qiime, Mothur, Megan, IMG/VR, Anvi'o, Qiita, MetaVir), scientists lack comprehensive software for easily building scalable, searchable, online data repositories on which they can rely during their ongoing research. Results: metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. Being based on a flexible NoSQL data model, it has few constraints regarding dataset contents and thus proves useful for handling outputs from both shotgun and metabarcoding techniques. By supporting incremental data feeding and providing means to combine filters on all imported fields, it allows for exhaustive content browsing, as well as rapid narrowing to find specific records. The application also features various interactive data visualization tools, ways to query contents by BLASTing external sequences, and an integrated pipeline to enrich assignments with phylogenetic placements. The project home page provides the URL of a live instance allowing users to test the system on public data. Conclusion: metaXplor allows efficient management and exploration of metagenomic data. Its availability as a set of Docker containers, making it easy to deploy on academic servers, on the cloud, or even on personal computers, will facilitate its adoption.
Published: 2021
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15. Contrasting Expression of Rhizobial Phytase in Nodules of Two Soybean Cultivars Grown Under Low Phosphorus Availability

Author: Victoria Cerecetto, Elena Beyhaut, Laurie Amenc, Carlos Trives, Nora Altier, Jean-Jacques Drevon, Instituto Nacional de Investigación Agropecuaria (INIA), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Uruguayan Agencia Nacional de Investigación e Innovación (ANII) (grants MOV_CA_2016_1_127378 and POS_NAC_2014_1_102525), Agropolis Foundation Montpellier, France, through Fabatropimed Project under the reference of ID 100-009., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, 0301 basic medicine, symbiotic nitrogen fixation, chemistry.chemical_element, lcsh:TX341-641, phytate mineralization, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Horticulture, Management, Monitoring, Policy and Law, rhizobia, 01 natural sciences, Bradyrhizobium, Rhizobia, 03 medical and health sciences, Phosphorus deficiency, Cultivar, nodule RT-PCR in situ, soybean, Legume, 2. Zero hunger, Global and Planetary Change, lcsh:TP368-456, Ecology, biology, Phosphorus, fungi, food and beverages, sustainability, biology.organism_classification, lcsh:Food processing and manufacture, 030104 developmental biology, Agronomy, chemistry, phytase, Nitrogen fixation, Phytase, lcsh:Nutrition. Foods and food supply, Agronomy and Crop Science, 010606 plant biology & botany, Food Science
Abstract: Phosphorus deficiency can be a major limitation to legume growth when plant nitrogen nutrition depends on symbiotic nitrogen fixation. One possible approach to overcome this constraint is the selection of plant and rhizobial genotypes capable of metabolizing complex forms of phosphorus in the nodules. The aim of this research was to study the rhizobial phytase transcript abundance in nodules of two soybean cultivars (Glycine max (L.) Merr.) grown under two different phosphorus conditions in hydroaeroponic conditions. An in situ RT-PCR of a rhizobial phytase was performed in microtome sections of soybean nodules of two cultivars growing under phosphorus sufficiency vs. phosphorus deficiency. The results showed that the plant cultivar may influence the level of transcript abundance of the bacterial phytase and in consequence affect the phosphorus use efficiency of nitrogen-dependent Bradyrhizobium spp.-soybean symbioses. Thus, the selection of a good combination of plant and rhizobial genotypes should be a priority when breeding for phosphorus deficiency is performed.
Published: 2021
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16. Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history

Author: Adrien, Rieux, Paola, Campos, Arnaud, Duvermy, Sarah, Scussel, Darren, Martin, Myriam, Gaudeul, Pierre, Lefeuvre, Nathalie, Becker, Jean-Michel, Lett, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-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), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Computational Biology Group, Dept Clinical Laboratory Sciences, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IIDMM), This work was financially supported by l'Agence Nationale pour la Recherche (JCJC MUSEOBACT contrat ANR 17-CE35-0009), the European Regional Development Fund (ERDF contract GURDT I2016-1731-0006632), Region Reunion, the French Agropolis Foundation (Labex Agro-Montpellier, E-SPACE Project Number 1504004, MUSEOVIR project number 1600-004), the SYNTHESYS Project http://www.synthesys.info/(Grants GBTAF-6437 and GB-TAF-7130) which is financed by European Community Research Infrastructure Action under the FP7 'Capacities' Program & CIRAD/AI-CRESI-3/2016. PhD of P.C. was co-funded by ED 227, Museum national d'Histoire naturelle et Sorbonne Universite, French Ministry of Higher Education, Research and Innovation, France., ANR-17-CE35-0009,MUSEOBACT,'Une nuit au musée': mieux reconstuire les emergences de bactéries pathogènes des cultures grâce à des échantillons historiques(2017), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), 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), and Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE)
Subjects: Manihot, Science, High-Throughput Nucleotide Sequencing, Bayes Theorem, Genome, Viral, Genomics, Sequence Analysis, DNA, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Article, Computational biology and bioinformatics, Evolution, Molecular, RNA, Plant, Begomovirus, Host-Pathogen Interactions, Medicine, Molecular ecology, Phylogeny, Plant Diseases
Abstract: International audience; Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.
Published: 2021
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17. Comparison of the virome of quarantined sugarcane varieties and the virome of grasses growing near the quarantine station

Author: Daugrois, Jean, Filloux, Denis, Julian, Charlotte, Claude, Lisa, Ferdinand, Romain, Fernandez, Emmanuel, Fontes, Hugo, Rott, Philippe, Roumagnac, Philippe, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de recherche de la Tour du Valat, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Agropolis Foundation (E-Space flagship program, grant number 1504-004), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU)
Subjects: H01 - Protection des végétaux - Considérations générales, quarantaine, Poaceae, Microbiology, Article, Maladie des plantes, sugarcane, Phylogeny, Transmission des maladies, Plant Diseases, H20 - Maladies des plantes, Virome, Virion, Virus des végétaux, QR1-502, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Saccharum, plant quarantine, Quarantine, Mesure phytosanitaire, Metagenome, Metagenomics, viral metagenomics
Abstract: International audience; Visacane is a sugarcane quarantine station located in the South of France, far away from sugarcane growing areas. Visacane imports up to 100 sugarcane varieties per year, using safe control and confinement measures of plants and their wastes to prevent any risk of pathogen spread outside of the facilities. Viruses hosted by the imported material are either known or unknown to cause disease in cultivated sugarcane. Poaceae viruses occurring in plants surrounding the quarantine glasshouse are currently unknown. These viruses could be considered as a source of new sugarcane infections and potentially cause new sugarcane diseases in cases of confinement barrier failure. The aim of this study was to compare the plant virome inside and outside of the quarantine station to identify potential confinement failures and risks of cross infections. Leaves from quarantined sugarcane varieties and from wild Poaceae growing near the quarantine were collected and processed by a metagenomics approach based on virion-associated nucleic acids extraction and library preparation for Illumina sequencing. While viruses belonging to the same virus genus or family were identified in the sugarcane quarantine and its surroundings, no virus species was detected in both environments. Based on the data obtained in this study, no virus movement between quarantined sugarcane and nearby grassland has occurred so far, and the confinement procedures of Visacane appear to be properly implemented.
Published: 2021
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18. First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence

Author: Campos, Paola, Groot Crego, Clara, Boyer, Karine, Gaudeul, Myriam, Baider, Claudia, Richard, Damien, PRUVOST, Olivier, Roumagnac, Philippe, Szurek, Boris, Becker, Nathalie, Gagnevin, Lionel, Rieux, Adrien, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-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), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Ministry of Agro Industry and Food Security, Partenaires INRAE, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-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), This work was financially supported by l’Agence Nationale pour la Recherche (AR: JCJC MUSEOBACT contrat ANR-17-CE35-0009), the European Regional Development Fund (AR, KB, OP, NB: ERDF contract GURDT I2016‐1731‐0006632, FEDER), Région Réunion (AR, KB, OP, NB), the French Agropolis Foundation Labex Agro –Montpellier (AR, OP, PR, BS, NB, LG: E-SPACE project number 1504-004) & (AR, PR, BS, LG: MUSEOVIR project number 1600-004), the SYNTHESYS Project (LG: grant GB-TAF-6437 & AR: grant GB-TAF-7130, ANR-17-CE35-0009,MUSEOBACT,'Une nuit au musée': mieux reconstuire les emergences de bactéries pathogènes des cultures grâce à des échantillons historiques(2017), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), European Project, Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Citrus, Topography, [SDV]Life Sciences [q-bio], Single Nucleotide Polymorphisms, Plant Science, Xanthomonas campestris citri, Biochemistry, Biology (General), Phylogeny, Data Management, Islands, Herbier, Ancient DNA, Phylogenetic Analysis, Genomics, Phylogenetics, Nucleic acids, Mauritius, Research Article, Computer and Information Sciences, Xanthomonas, QH301-705.5, Plant Pathogens, Agent pathogène, Genetics, Evolutionary Systematics, Plant Diseases, Taxonomy, H20 - Maladies des plantes, Evolutionary Biology, Landforms, Génome, Bacteria, Organisms, Biology and Life Sciences, Paleontology, Geomorphology, DNA, RC581-607, History, 20th Century, Plant Pathology, Maladie bactérienne, Earth Sciences, H50 - Troubles divers des plantes, Immunologic diseases. Allergy, Paleogenetics, Genome, Bacterial
Abstract: Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors., Author summary Herbarium collections are a precious resource to plant pathologists, tracking crop diseases on specimens collected in the past centuries. In addition to indicating the presence of a disease at a specific time and locality, recent molecular technologies now allow extraction and microbial DNA sequencing from dead specimens. Despite challenges due to the degraded nature of DNA retrieved from historical samples, we were able to reconstruct the genome of a pathogenic bacterium from a 1937 herbarium specimen collected in Mauritius: Xanthomonas citri pv. citri, responsible for Asiatic citrus canker (ACC, an economically important agricultural disease controlled mostly through prophylactic and quarantine measures). Enhanced knowledge about the epidemiology and evolution of this bacterial pathogen is valuable to improve these measures. We compared the genome of this 1937 bacterial strain to a collection of modern strains, included it in a tree representing their genetic relationships, and calculated both evolutionary mutation rate and divergence times. This “forensic investigation” informs us about how and when the disease developed in the South West Indian Ocean Islands. We hypothesize that there was a single (or a few related) introduction of ACC in Mauritius in the mid-19th century, followed by expansion to the neighbouring islands.
Published: 2021
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19. Epidemics and the future of coffee production

Author: Grégoire Leclerc, Christopher M. Bacon, Daniel P. Bebber, Chris Knudson, Jacques Avelino, Kevon Rhiney, M. Catherine Aime, Zack Guido, Rutgers University [Camden], Rutgers University System (Rutgers), University of Arizona, University of Hawai'i [Hilo], Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro Agronómico Tropical de Investigación y Enseñanza - Tropical Agricultural Research and Higher Education Center (CATIE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Santa Clara University, Savoirs, ENvironnement et Sociétés (SENS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut de Recherche pour le Développement (IRD), Département Environnements et Sociétés (Cirad-ES), Purdue University [West Lafayette], University of Exeter, National Science Foundation Grant BCS-1539795, project Assessment of Diversification Strategies in Smallholder Coffee Systems (No AF 1507-086 : No FDNC Engt 00063479) supported under the 'Thought for Food' Initiative of the Agropolis Foundation (through the 'Investissements d'avenir' programme with reference number ANR10-LABX-0001-01), Fondazione Cariplo and Daniel & Nina Carasso. Jacques Avelino and Gregoire Leclerc are grateful for financial support by the 'Programa Centroamericano de Gestion Integral de la roya del Cafe ', (PROCAGICA) funded by the EU (DCI-ALA/2015/365-17), and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: 0106 biological sciences, Latin Americans, Coffea, Coffee, 01 natural sciences, Maladie des plantes, media_common, 2. Zero hunger, Industrie du café, 0303 health sciences, Multidisciplinary, biology, 1. No poverty, Hemileia vastatrix, Investment (macroeconomics), Agro-industrie, Épidémiologie, S50 - Santé humaine, Perspective, Financial crisis, Rouille, impact économique, Farms, media_common.quotation_subject, Environment, 03 medical and health sciences, Development economics, Industry, impacts socio-économiques, Epidemics, Socioeconomic status, Crise économique, Plant Diseases, 030304 developmental biology, H20 - Maladies des plantes, E10 - Économie et politique agricoles, SARS-CoV-2, business.industry, Basidiomycota, COVID-19, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Socioeconomic Factors, Agriculture, Unemployment, business, 010606 plant biology & botany
Abstract: International audience; In this perspective, we draw on recent scientific research on the coffee leaf rust (CLR) epidemic that severely impacted several countries across Latin America and the Caribbean over the last decade, to explore how the socioeconomic impacts from COVID-19 could lead to the reemergence of another rust epidemic. We describe how past CLR outbreaks have been linked to reduced crop care and investment in coffee farms, as evidenced in the years following the 2008 global financial crisis. We discuss relationships between CLR incidence, farmer-scale agricultural practices, and economic signals transferred through global and local effects. We contextualize how current COVID-19 impacts on labor, unemployment, stay-at-home orders, and international border policies could affect farmer investments in coffee plants and in turn create conditions favorable for future shocks. We conclude by arguing that COVID-19’s socioeconomic disruptions are likely to drive the coffee industry into another severe production crisis. While this argument illustrates the vulnerabilities that come from a globalized coffee system, it also highlights the necessity of ensuring the well-being of all. By increasing investments in coffee institutions and paying smallholders more, we can create a fairer and healthier system that is more resilient to future social-ecological shocks.
Published: 2021
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20. The Rice DNA-Binding Protein ZBED Controls Stress Regulators and Maintains Disease Resistance After a Mild Drought

Author: Zuluaga, Paola A., Bidzinski, Przemyslaw, Chanclud, Emilie, Ducasse, Aurélie, Cayrol, Bastien, Gomez Selvaraj, Michael, Ishitani, Manabu, Jauneau, Alain, Deslandes, Laurent, Kroj, Thomas, Michel, Corinne, Szurek, Boris, Koebnik, Ralf, Morel, Jean-Benoit, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), International Center for Tropical Agriculture [Colombie] (CIAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), INRA project from the SPE division (Decoy), Agropolis Foundation : 1201-001, Fondazione Cariplo : 1201-001, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Erist, Montpellier, Agricultural Sciences for sustainable Development - - AGRO2010 - ANR-10-LABX-0001 - LABX - VALID, AgreenSkills+ - AGREENSKILLSPLUS - - EC:FP7:PEOPLE2014-05-05 - 2019-05-04 - 609398 - VALID, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national 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), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), and Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: disease resistance, plant-pathogen interactions, [SDV]Life Sciences [q-bio], drought resistance, fungi, plant– pathogen interactions, food and beverages, Magnaporthe oryzae, Plant Science, lcsh:Plant culture, [SDV] Life Sciences [q-bio], lcsh:SB1-1110, Zn-finger BED domains, plant–pathogen interactions, Original Research
Abstract: BGPI : Equipe 4 : Interactions Céréales Agents Pathogènes (ICAP) ; Equipe 2 : Interactions Virus Insecte Plante (VIP); Background: Identifying new sources of disease resistance and the corresponding underlying resistance mechanisms remains very challenging, particularly in Monocots. Moreover, the modification of most disease resistance pathways made so far is detrimental to tolerance to abiotic stresses such as drought. This is largely due to negative cross-talks between disease resistance and abiotic stress tolerance signaling pathways. We have previously described the role of the rice ZBED protein containing three Zn-finger BED domains in disease resistance against the fungal pathogen Magnaporthe oryzae. The molecular and biological functions of such BED domains in plant proteins remain elusive.Results: Using Nicotiana benthamiana as a heterologous system, we show that ZBED localizes in the nucleus, binds DNA, and triggers basal immunity. These activities require conserved cysteine residues of the Zn-finger BED domains that are involved in DNA binding. Interestingly, ZBED overexpressor rice lines show increased drought tolerance. More importantly, the disease resistance response conferred by ZBED is not compromised by drought-induced stress.Conclusions: Together our data indicate that ZBED might represent a new type of transcriptional regulator playing simultaneously a positive role in both disease resistance and drought tolerance. We demonstrate that it is possible to provide disease resistance and drought resistance simultaneously.
Published: 2020
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21. Improving lifestyles sustainability through community gardening: results and lessons learnt from the JArDinS quasi-experimental study

Author: Tharrey, Marion, Sachs, Ashby, Perignon, Marlène, Simon, Chantal, Méjean, Caroline, Litt, Jill, Darmon, Nicole, Marchés, Organisations, Institutions et Stratégies d'Acteurs (UMR MOISA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Colorado [Boulder], Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Instituto de Salud Global - Institute For Global Health [Barcelona] (ISGlobal), This research was part of the Surfood-Foodscape project. This work was publicly funded through ANR (the French National Research Agency) under the 'Investissements d’avenir' programme, reference ANR-10-LABX-001-01 Labex Agro, and coordinated by the Agropolis Foundation. It was also supported by the Olga Triballat Institute. The funders had no role in the design of the study or the collection, analysis and interpretation of data, or in writing the manuscript., ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Perez, Isabelle, Agricultural Sciences for sustainable Development - - AGRO2010 - ANR-10-LABX-0001 - LABX - VALID, Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Adult, Male, Connection to nature, Quasi-experiment, Well-being, Food supply, Humans, Life Style, Qualitative Research, Nutrition, Physical activity, lcsh:Public aspects of medicine, Urban garden, technology, industry, and agriculture, Community Participation, food and beverages, Correction, lcsh:RA1-1270, social sciences, Gardening, Middle Aged, Accelerometer, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Cross-Sectional Studies, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Health promotion, Mental health, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Female, France, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, geographic locations, Research Article
Abstract: Background Despite an increasing number of studies highlighting the health benefits of community gardening, the literature is limited by cross-sectional designs. The “JArDinS” quasi-experimental study aimed to assess the impact of community garden participation on the adoption of more sustainable lifestyles among French adults. Methods Individuals entering a community garden in Montpellier (France) in 2018 (n = 66) were compared with pairwise matched individuals with no experience in community gardening (n = 66). Nutritional quality, environmental impact and cost of monthly household food supplies, level of physical activity measured by accelerometers, as well as mental and social well-being, sensitivity to food waste, and connection with nature were evaluated at baseline (t0) and 12 months later (t1) to explore sustainability of lifestyles in social/health, environmental and economic dimensions. Linear mixed models were used to determine the independent effect of community gardening on investigated lifestyles components. In-depth interviews were conducted at t1 with 15 gardeners to better understand changes that may have occurred in gardeners’ lives during the first year of gardening. Results At t0, gardeners had lower education level, lower BMI and their household reported lower percentage of meals consumed outside of the home compared to non-gardeners (p
Published: 2020
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22. Shade trees have higher impact on soil nutrient availability and food web in organic than conventional coffee agroforestry

Author: Thierry Becquer, Marie Sauvadet, Karel Van den Meersche, Clémentine Allinne, Philippe Tixier, Jean-Michel Harmand, Elias de Melo Virginio Filho, Matthieu Chauvat, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), Agro-écologie, Hydrogéochimie, Milieux et Ressources (AGHYLE), UniLaSalle, Centro Agronomico Tropical de Investigacion y Enseñanza (CATIE), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Étude et compréhension de la biodiversité (ECODIV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), World Agroforesty Centre, CGIAR, Partenaires INRAE, Agropolis Foundation, STRADIV project (no. 1504-003), and Agroforestry Systems with Perennial Crops Scientific Partnership Platform (PCP AFS-PC)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 010504 meteorology & atmospheric sciences, F08 - Systèmes et modes de culture, Biologie du sol, Arbre d'ombrage, Coffea, Agroforesterie, 010501 environmental sciences, Erythrina poeppigiana, 01 natural sciences, Trees, Soil, Nutrient, Soil food web, Soil functions, Soil pH, Waste Management and Disposal, 2. Zero hunger, Organic Agriculture, Agroforestry, Chaîne alimentaire, Forestry, Phosphorus, Coffea arabica, Nitrogen Cycle, Pollution, Food web, Terminalia, Costa Rica, Food Chain, Environmental Engineering, Management practices, Agriculture biologique, Soil fertility, Carbon Cycle, Species Specificity, Fertilité du sol, Environmental Chemistry, Agriculture traditionnelle, Shade type, 0105 earth and related environmental sciences, Shade tree, P35 - Fertilité du sol, P34 - Biologie du sol, 15. Life on land, K10 - Production forestière, 13. Climate action, Soil water, Environmental science
Abstract: International audience; Conventional, intensively managed coffee plantations are currently facing environmental challenges. The use of shade trees and the organic management of coffee crops are welcome alternatives, aiming to reduce synthetic inputs and restore soil biological balance. However, little is known about the impacts of the different types of shade tree species on soil functioning and fauna. In this paper, we assess soil nutrient availability and food web structure on a 17-year old experimental coffee plantation in Turrialba in Costa Rica. Three shade types (unshaded coffee, shaded with Terminalia amazonia, and shaded with Erythrina poepiggiana) combined with two management practices (organic and conventional) were evaluated. Total C and N, inorganic N and Olsen P content, soil pH, global soil fertility, and nematode and microarthropod communities were measured in the top 10 cm soil layer, with the objective of determining how shade tree species impact the soil food web and soil C, N and P cycling under different types of management. We noted a decrease in soil inorganic N content and nematode density under conventional management (respectively -47% and -91% compared to organic management), which suggested an important biological imbalance, possibly caused by the lack of organic amendment. Under conventional management, soil nutrient availability and fauna densities were higher under shade, regardless of the shade tree species. Under organic management, only soils under E. poeppigiana, a heavily pruned. N-2 -fixing species, had increased nutrient availability and fauna density, while T amazonia shade had a null or negative impact. The effects of coffee management and shade type on soil nutrient availability were mirrored by changes in soil food web structure. Higher fertility was recorded in soil with balanced food webs. These results emphasize the importance of the choice of shade tree species for soil functions in low input systems, more so than in fertilized systems
Published: 2019
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23. Pest-regulating networks of the coffee berry borer (Hypothenemus hampei) in agroforestry systems

Author: Leïla Bagny Beilhe, Sacha Roudine, Dominique Carval, José Alcides Quintero Perez, Rémi Mauxion, Djavan Daout, Clémentine Allinne, Bioagresseurs, analyse et maîtrise du risque (UPR Bioagresseurs), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centro Agronómico Tropical de Investigación y Enseñanza - Tropical Agricultural Research and Higher Education Center (CATIE), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fonctionnement écologique et gestion durable des agrosystèmes bananiers et ananas (UR GECO), and The present work was funded by the Agropolis Foundation, STRADIV project (no. 1504-003). The project was carried out within the framework of the Agroforestry Systems with Perennial Crops Scientific Partnership Platform (PCP AFS-PC).
Subjects: 0106 biological sciences, H01 - Protection des végétaux - Considérations générales, F08 - Systèmes et modes de culture, [SDV]Life Sciences [q-bio], Population, Coffea, Berry, Agroforesterie, medicine.disease_cause, 01 natural sciences, Predation, Abundance (ecology), Infestation, medicine, Hypothenemus hampei, education, Lutte intégrée, 2. Zero hunger, education.field_of_study, biology, Agroforestry, Phenology, Integrated pest management, Biodiversity, 15. Life on land, biology.organism_classification, H10 - Ravageurs des plantes, Lutte biologique, 010602 entomology, PEST analysis, Biodiversité, Phénologie, Top down regulation, Agronomy and Crop Science, Bottom up regulation, 010606 plant biology & botany
Abstract: International audience; Highlights:• The most diversified groups of predatory ants had a significant negative top down effect on CBB infestation.• Higher % of shade favours CBB infestation.• Regulation of CBB depends on the balance between the effects of local (in plot) and global (farm level) variables.• Farmers practices could be efficient to manage CBB and to reduce related damage.• Holistic approach is required to characterize more precisely regulating network in agroforestry systems.Abstract:Pest regulation in agroforestry systems (AFS) is beginning to be well-recognized, but the mechanisms implied in the interaction network between the environment, pests and predators in AFS are still not well-described. The aim of this work is to understand how plant diversity associated with AFS regulates the coffee berry borer (CBB) taking into account a tripartite interaction network: pest–predator–environment. It further seeks to understand how farmers' management practices can modify the regulating network. Using field data from coffee-based AFS and structural equation modeling, we assessed the effects of environmental conditions (% shade cover, tree area surface, coffee density) and farm management (conventional, integrated, organic) on (1) ant predatory groups, (2) the abundance and the damage from CBB and (3) their interactions. Percentage of shade cover was positively correlated to CBB initial infestation (through direct effect) and negatively through its effect on coffee phenology. A higher percentage of shade is also negatively related to damage intensity. Farmers’ practices significantly reduced the CBB population without considerable side effects on the ant predatory group, probably due to the high plant diversity within these farms. The abundance of the most diversified ant predatory group has a top-down effect on the peak of the CBB infestation rate. Our approach appears promising for a better understanding of the complex regulating network in coffee AFS and confirms the importance of an integrated management strategy to reduce CBB damage.
Published: 2020
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24. Multi-block classification of chocolate and cocoa samples into sensory poles

Author: Clotilde Hue, Hélène Labouré, Gilles Morel, Nicolas Sommerer, Marie Christine Lahon, Marc Lebrun, Sébastien Preys, Renaud Boulanger, Fabrice Davrieux, Alessandra Biancolillo, Belal Gaci, Noémie Fayeulle, Zoé Deuscher, Jean-Michel Roger, Pierre Costet, Jean-Luc Le-Quere, Véronique Cheynier, Isabelle Maraval, Karine Alary, Università degli Studi dell'Aquila (UNIVAQ), Ondalys, Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), 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), CHEMHOUSE RESEARCH GROUP MONTPELLIER FRA, 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), Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bourgogne Franche-Comté [COMUE] (UBFC), Sciences Pour l'Oenologie (SPO), Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Chocolaterie Valrhona, Démarche intégrée pour l'obtention d'aliments de qualité (UMR QualiSud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Avignon Université (AU)-Université de La Réunion (UR)-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), Agropolis Foundation Valrhona, Projet CHAMAN, and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: Spectroscopie, Chocolat, 01 natural sciences, High-performance liquid chromatography, Mass Spectrometry, Analytical Chemistry, Fève de cacao, Chocolate, Spectroscopy, Chromatography, High Pressure Liquid, Chromatography, Spectroscopy, Near-Infrared, 04 agricultural and veterinary sciences, General Medicine, Q01 - Sciences et technologies alimentaires - Considérations générales, Composition chimique, Classification, Cocoa beans, Multi-block, Sensory analysis, 040401 food science, Analyse organoleptique, Taste, Materials science, Mass spectrometry, Fluorescence spectroscopy, Gas Chromatography-Mass Spectrometry, 0404 agricultural biotechnology, [CHIM]Chemical Sciences, Humans, Least-Squares Analysis, Q04 - Composition des produits alimentaires, Solid Phase Microextraction, Chocolate Flavor, Cacao, 010401 analytical chemistry, Near-infrared spectroscopy, Polyphenols, 0104 chemical sciences, Propriété organoleptique, Spectrometry, Fluorescence, Polyphenol, Chromatographie, U30 - Méthodes de recherche, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Analysis, Food Science
Abstract: International audience; The present study aims at developing an analytical methodology which allows correlating sensory poles of chocolate to their chemical characteristics and, eventually, to those of the cocoa beans used for its preparation. Trained panelists investigated several samples of chocolate, and they divided them into four sensorial poles (characterized by 36 different descriptors) attributable to chocolate flavor. The same samples were analyzed by six different techniques: Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-ToF-MS), Solid Phase Micro Extraction-Gas Chromatography-Mass Spectroscopy (SPME-GC-MS), High-Performance Liquid Chromatography (HPLC) (for the quantification of eight organic acids), Ultra High Performance Liquid Chromatography coupled to triple-quadrupole Mass Spectrometry (UHPLC-QqQ-MS) for polyphenol quantification, 3D front face fluorescence Spectroscopy and Near Infrared Spectroscopy (NIRS). A multi-block classification approach (Sequential and Orthogonalized-Partial Least Squares – SO-PLS) has been used, in order to exploit the chemical information to predict the sensorial poles of samples. Among thirty-one test samples, only two were misclassified.
Published: 2020
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25. Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses

Author: Hennet, Lauriane, Berger, Angélique, Trabanco, Noemi, Ricciuti, Emeline, Dufayard, Jean-François, Bocs, Stéphanie, Bastianelli, Denis, Bonnal, Laurent, Roques, Sandrine, Rossini, Laura, Luquet, Delphine, Terrier, Nancy, Pot, David, 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), Parco Tecnologico Padano, CERSA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Département Environnements et Sociétés (Cirad-ES), Università degli Studi di Milano [Milano] (UNIMI), BIOSORG project - Agropolis foundation AF 1301-010, BIOSORG project - Cariplo foundation FC 2013-1890, Ministry of Higher Education & Scientific Research (MHESR), Dufrenoy Foundation, and ANR-11-BTBR-0006,BFF,Biomasse pour le futur(2011)
Subjects: Paroi cellulaire, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, NAC, [SDV]Life Sciences [q-bio], food and beverages, MYB, Plant Science, co-expression network analysis, gene co-expression network analysis, phylogeny, F30 - Génétique et amélioration des plantes, génomique, cell wallgene, Expression des gènes, cell wall, sorghum, internode, transcription factor, Original Research
Abstract: International audience; Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.
Published: 2020
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26. High yields in a low-P tolerant recombinant inbred line of common bean under field conditions

Author: Mohamed Lazali, Jean-Jacques Drevon, Samira Brahimi, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de 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), Université de Djilali Bounaama Khemis Miliana (univ-DBKM), and Great Federative Project FABATROPIMED, financed by Agropolis Foundation of Montpellier under the reference ID 1001-009.
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, Soil Science, chemistry.chemical_element, Growing season, Plant Science, Nodulation, Soil fertility, 01 natural sciences, law.invention, Dry weight, Inbred strain, law, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Common bean, 2. Zero hunger, biology, Phosphorus, 04 agricultural and veterinary sciences, biology.organism_classification, Horticulture, chemistry, Nutrient efficiency, Shoot, 040103 agronomy & agriculture, Recombinant DNA, 0401 agriculture, forestry, and fisheries, Phaseolus, Agronomy and Crop Science, 010606 plant biology & botany, Field conditions
Abstract: International audience; Low phosphorus (P) availability is a primary factor that limits the production of common bean (Phaseolus vulgaris L.) in many parts of the world, especially when plant growth depends on N2 fixation. In order to understand how common bean copes with this nutritional constraint, two recombinant inbred lines (RILs) of common bean namely RILs 115 and 147 were studied in the field conditions during three growing seasons from 2012 to 2014. At flowering stage, plants were harvested and analyzed for their nodulation, growth, P content and yield. Results showed that for RIL115, the nodulation (43%), shoot (28%) and root growth (32%) was higher than for RIL147 in a low-P availability soil whatever the growing season. In addition, RIL115 had better growth and efficiency in use of P for the rhizobial symbiosis (7.29 mg nodule dry weight mg−1 nodule P) about twice higher may be involved in tolerance to low-P, and to be a useful marker for field data. At harvest, the RIL115 showed higher grain yield (1146 kg ha−1) than the RIL147 (1045 kg ha−1). It is concluded that the genotype of RIL 115 had a higher yield and could best adapt to low-P availability under field condition.
Published: 2018
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27. Synchrotron FTIR and Raman spectroscopy provide unique spectral fingerprints for Arabidopsis floral stem vascular tissues

Author: Federica De Marco, Nelly Wolff, Sylvie Dinant, Christophe Sandt, Emilie Aubry, Rozenn Le Hir, Catherine Bellini, Françoise Vilaine, Lionel Gissot, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Synchrotron SOLEIL, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SOLEIL, French national synchrotron facility [20150210], French State grant [LabEx Saclay Plant Sciences-SPS, ANR-10-LABX512 0040-SPS], managed by the French National Research Agency under an 'Investments for the Future' program [ANR-11-IDEX-0003-02], Agropolis Foundation [ID-1401-005] through the 'Investissements d'Avenir' program [Labex Agro: ANR516 10-LABX-0001-01], Centre National de la Recherche Scientifique (CNRS), Umea Plant Science Centre, Department of Plant Physiology, and Le Hir, Rozenn
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, Spectrum Analysis, Raman, 01 natural sciences, chemistry.chemical_compound, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Spectroscopy, Fourier Transform Infrared, Vascular tissue, Plant Stems, Synchrotron radiation, biology, Cell wall, food and beverages, Raman spectroscopy, CART method, cell wall, floral stem, FTIR, multivariate analysis, phloem, synchrotron radiation, xylem, symbols, Flowers, Phloem, 03 medical and health sciences, symbols.namesake, Xylem, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Hemicellulose, Cellulose, Floral stem, Arabidopsis Proteins, fungi, Membrane Transport Proteins, Biological Transport, biology.organism_classification, 030104 developmental biology, Multivariate analysis, chemistry, Mutation, Biophysics, Sugars, Synchrotrons, 010606 plant biology & botany
Abstract: Preprint publié dans BioRxiv : https://www.biorxiv.org/content/early/2018/06/11/343343 https://prodinra.inra.fr/record/432127; International audience; Cell walls are highly complex structures that are modified during plant growth and development. For example, the development of phloem and xylem vascular cells, which participate in the transport of sugars and water as well as providing support, can be influenced by cell-specific wall composition. Here, we used synchrotron radiation-based Fourier-transform infrared (SR-FTIR) and Raman spectroscopy to analyse the cell wall composition of floral stem vascular tissues of wild-type Arabidopsis and the double-mutant sweet11-1 sweet12-1, which has impaired sugar transport. The SR-FTIR spectra showed that in addition to modified xylem cell wall composition, phloem cell walls in the double-mutant line were characterized by modified hemicellulose composition. Combining Raman spectroscopy with a classification and regression tree (CART) method identified combinations of Raman shifts that could distinguish xylem vessels and fibers. In addition, the disruption of the SWEET11 and SWEET12 genes impacted on xylem wall composition in a cell-specific manner, with changes in hemicelluloses and cellulose observed at the xylem vessel interface. These results suggest that the facilitated transport of sugars by transporters that exist between vascular parenchyma cells and conducting cells is important in ensuring correct phloem and xylem cell wall composition.
Published: 2018
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28. Agroecosystem diversification with legumes or non-legumes improves differently soil fertility according to soil type

Author: Seguy Enock, Clémentine Allinne, Béatrice Rhino, Richard Randriamanantsoa, Patrice Autfray, Thierry Becquer, Stéphane Saj, Gaëlle Damour, Peninna Deberdt, Elias de Melo Virginio Filho, Miora Rakotoarivelo, Elisabeth Rosalie, Aude Ripoche, Philippe Tixier, Marie Sauvadet, Isabelle Bertrand, Mickaël Hedde, Grégoire T. Freschet, Bodovololona Rabary, Eric Blanchart, Raphaël Achard, Claude Plassard, Jean-Michel Harmand, Jean Trap, Jean-Daniel Essobo, Karel Van den Meersche, Fonctionnement écologique et gestion durable des agrosystèmes bananiers et ananas (UR GECO), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centro Agronómico Tropical de Investigación y Enseñanza - Tropical Agricultural Research and Higher Education Center (CATIE), Agrosystèmes Biodiversifiés (UMR ABSys), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Agroécologie et Intensification Durables des cultures annuelles (UPR AIDA), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), World Agroforestry Centre [CGIAR, Cameroun] (ICRAF), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Université d'Antananarivo, Université de Montpellier (UM), The present work was funded by the Agropolis Foundation, STRADIV project (no. 1504-003), CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), IRD (Institut de Recherche pour le Développement). Part of this work was also carried out within the framework of the CGIAR Research Program on Forests, Trees and Agroforestry (FTA)., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM), INRAE l'unité technologie et système d'information (TSCF) du centre de Clermont-Ferrand, Station d'écologie théorique et expérimentale (SETE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Ecole Supérieure des Sciences Agronomiques
Subjects: 0106 biological sciences, Agroecosystem, Nematoda, F08 - Systèmes et modes de culture, [SDV]Life Sciences [q-bio], legumes, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, tropical soils, 01 natural sciences, Soil, Soil pH, plant diversification, functional traits, Biomass, Waste Management and Disposal, Soil Microbiology, 2. Zero hunger, Sol volcanique, food and beverages, Fabaceae, 04 agricultural and veterinary sciences, Soil type, Pollution, Sol tropical, Agroécosystème, Diversification, Environmental Engineering, Indicateur écologique, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Biology, complex mixtures, 010603 evolutionary biology, Fertilité du sol, Animals, Environmental Chemistry, Agroecology, Méthode statistique, fungi, P35 - Fertilité du sol, Plant community, légume, 15. Life on land, Crop rotation, C-N-P cycling, Agronomy, nematodes, Soil water, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, U30 - Méthodes de recherche, Soil fertility, Caractère agronomique
Abstract: International audience; Plant diversification through crop rotation or agroforestry is a promising way to improve sustainability of agroecosystems. Nonetheless, criteria to select the most suitable plant communities for agroecosystems diversification facing contrasting environmental constraints need to be refined. Here, we compared the impacts of 24 different plant communities on soil fertility across six tropical agroecosystems: either on highly weathered Ferralsols, with strong P limitation, or on partially weathered soils derived from volcanic material, with major N limitation. In each agroecosystem, we tested several plant communities for diversification, as compared to a matching low diversity management for their cropping system. Plant residue restitution, N, P and lignin contents were measured for each plant community. In parallel, the soil under each community was analyzed for organic C and N, inorganic N, Olsen P, soil pH and nematode community composition. Soil potential fertility was assessed with plant bioassays under greenhouse controlled climatic conditions. Overall, plant diversification had a positive effect on soil fertility across all sites, with contrasting effects depending on soil type and legumes presence in the community. Communities with legumes improved soil fertility indicators of volcanic soils, which was demonstrated through significantly higher plant biomass production in the bioassays (+18%) and soil inorganic N (+26%) compared to the low diversity management. Contrastingly, communities without legumes were the most beneficial in Ferralsols, with increases in plant biomass production in the bioassays (+39%), soil Olsen P (+46%), soil C (+26%), and pH (+5%). Piecewise structural equation models with Shipley's test revealed that plant diversification impacts on volcanic soil fertility were related to soil N availability, driven by litter N. Meanwhile, Ferralsols fertility was related to soil P availability, driven by litter P. These findings underline the importance of multifactorial and multi-sites experiments to inform trait-based frameworks used in designing optimal plant diversification in agroecological systems.Highlights:• We compared plant diversification impacts on soil fertility across 6 agroecosystems.• Benefits of plant diversification depended on both legume presence and soil type.• Legume-based diversification was mostly beneficial on the younger soils.• Ferralsols' fertility was improved with plant communities' litter P content.• Plant communities' traits were linked with diversification impacts on contrasting soils.
Published: 2021
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29. How plant structure impacts the biochemical leaf traits assessment from in-field hyperspectral images: A simulation study based on light propagation modeling in 3D virtual wheat scenes

Author: Martin Ecarnot, Gilles Rabatel, Nathalie Al Makdessi, Pierre Roumet, Nathalie Gorretta, Pierre-Antoine Jean, Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-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), 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), Agropolis Foundation : 1202-008, 'Investissements d'avenir' program (Labex Agro) : ANR-10-LABX-0001-01, France Agrimer and l'Agence Nationale de la Recherche (ANR) through the Phenoble and Phenome programmes, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Feature vector, simulation models, Soil Science, three dimensional model, modèle de simulation, 01 natural sciences, 3D virtual scenes, modelling, leaf nitrogen content, Partial least squares regression, biochimie végétale, modélisation, triticum durum, 0105 earth and related environmental sciences, Remote sensing, Mathematics, caribu, diffusion de la lumière, Spectrometer, Ecology, canopy light propagation, modèle 3d, Simulation modeling, Hyperspectral imaging, Regression analysis, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Field (geography), multiple scattering, Principal component analysis, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: AGAP : équipe GE2pop (Génomique évolutive et gestion des populations); Light propagation modeling in 3-dimensional virtual scenes has been successfully applied to many fields, including plant canopies. However, its application to detailed analyses on how multiple scattering affects spectral-based biochemistry assessments has never been proposed. In this article, a wheat canopy model has been built using simulation models included in the open source software platform Open-Alea. Adel-Wheat, a 3D dynamic model of the aerial growth of winter wheat, has been associated with spectra collected on wheat leaves with an ASD spectrometer, and then used as input of the Caribu light propagation model. Caribu calculates the proportion of direct and scattered light for all polygons of the 3D scene. Principal component analysis was first applied to analyze the distribution of resulting spectra in the spectral feature space. Then the influence of canopy structure on quantitative regression models has been considered. For this purpose, a typical agronomical problem, i.e. nitrogen content retrieval, was addressed, using a Partial Least Square regression model. This study exhibits some important results concerning the distribution of collected spectra in the spectral feature space due to multiple scattering, and underlines the physical interpretation of these results. In the short term, it shows that satisfactory nitrogen content prediction (error about 0.5% of dry matter) can be obtained at the plant level, when considering only the plant top leaves. Moreover, its paves the way for future researches to develop spectral analysis tools able to overcome such multiple scattering phenomena.
Published: 2017
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30. Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel

Author: Tuong-Vi Cao-Hamadoun, Nilima Kumari, Arvind Kumar, Nitika Sandhu, Nourollah Ahmadi, Jérôme Bartholome, Aditi Bhandari, International Rice Research Institute [Philippines] (IRRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Banasthali Vidyapith, 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), Agropolis Foundation, and Fondazione Cariplo : 1201-006
Subjects: 0106 biological sciences, 0301 basic medicine, Locus des caractères quantitatifs, Quantitative trait loci, Tolérance à la sécheresse, [SDV]Life Sciences [q-bio], Drought tolerance, Soil Science, Oryza sativa, Single-nucleotide polymorphism, Genome-wide association study, Plant Science, lcsh:Plant culture, Biology, Quantitative trait locus, 01 natural sciences, Genetic diversity, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Variation génétique, lcsh:SB1-1110, Allele, Association mapping, 2. Zero hunger, F63 - Physiologie végétale - Reproduction, Diversité génétique (comme ressource), business.industry, fungi, Sélection assistée par marqueurs, food and beverages, 15. Life on land, Reproductive-stage drought, Genetic architecture, Biotechnology, 030104 developmental biology, Original Article, Rice, business, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: Background Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. Results The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. Conclusion These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
Published: 2020
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31. Combining participatory games and backcasting to support collective scenario evaluation : an action research approach for sustainable agroforestry landscape management

Author: Karel Van den Meersche, Clémentine Allinne, Federico Andreotti, E.N. Speelman, Gestion des ressources renouvelables et environnement (UPR GREEN), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Wageningen University and Research [Wageningen] (WUR), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Centro Agronómico Tropical de Investigación y Enseñanza - Tropical Agricultural Research and Higher Education Center (CATIE), STRADIV project (Grant no. 1504-003) funded by Agropolis Foundation, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), and Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Health (social science), Role-playing game, Sociology and Political Science, F08 - Systèmes et modes de culture, Geography, Planning and Development, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, 010501 environmental sciences, Agroforesterie, 01 natural sciences, recherche participative, Laboratory of Geo-information Science and Remote Sensing, 11. Sustainability, Action research, 2. Zero hunger, Global and Planetary Change, Ecology, Agroforestry, 04 agricultural and veterinary sciences, technique de prévision, PE&RC, Natural resource, Landscape planning, Aménagement du paysage, [SDE.MCG]Environmental Sciences/Global Changes, Future studies, Management, Monitoring, Policy and Law, gestion forestière durable, systèmes agroforestiers, Laboratorium voor Geo-informatiekunde en Remote Sensing, Transformative change, Durabilité, 0105 earth and related environmental sciences, Nature and Landscape Conservation, Sustainable development, Sustainable landscaping, business.industry, 15. Life on land, 13. Climate action, Sustainability, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Business, Sustainability transition, Landscape ecology, U30 - Méthodes de recherche, Backcasting, Agroecology, Forecasting
Abstract: The combined and interacting effects of land-use change, resource extraction and climate change threaten the sustainability of millions of mainly smallholder farms in tropical agroforested landscapes. In many of these landscapes, coordinated action among stakeholders at landscape level would help to address challenges such as pests and diseases, price crises and climate change. However, methods to facilitate the co-production of sustainable landscape management in such complex multi-stakeholder systems are currently largely lacking. In this paper, we present a novel approach to explore pathways for the sustainability transition of agroforestry systems. By combining participatory forecasting and backcasting approaches, based on serious games and future vision development, we explore relevant agroforestry management strategies for reaching sustainable future coffee-based agroforestry landscapes. We focused our research on the challenges faced in the main coffee-producing area in Nicaragua. Here, we organized five participatory game sessions to explore farmer decision-making processes, farming strategies and to develop new networks and stimulate social learning among farmers. In the associated backcasting workshop, the most influential game session participants joined technicians, researchers and municipality officials to collectively envision sustainable future landscape management. In all game sessions, farmers developed diversified coffee-based agroforested landscapes characterised by increased density and diversity of shade trees, for the purpose of income diversification as well as forest conservation. During the backcasting workshop, the participants identified policy instruments and community-based solutions for the transition to sustainable landscapes. Our participatory approach facilitated discussion on landscape planning among farmers and other stakeholders and allowed the outline of a pathway towards the collective envisioned future landscape. The combination of participatory forecasting and backcasting proved to be a helpful tool to support multi-stakeholder processes towards sustainable landscape management in this and other complex landscapes.
Published: 2020
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32. Establishing high-density protein banks for livestock in Burkina Faso (West Africa): Agronomic performance under contrasting edaphoclimatic conditions

Author: Marlen Navarro, Mélanie Blanchard, Eliel Gonzalez-Garcia, Eric Vall, Ollo Sib, Valérie M.C. Bougouma-Yameogo, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), 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), IDR (Institut de développement rural), Université Nazi Boni, Estación Experimental 'Indio Hatuey', Universidad de Matanzas, 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), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de Recherche sur les Productions Animales, Centre International de Recherche-Développement sur l'Elevage en zone Subhumide, Centre international de recherche-développement sur l'élevage en zone sub-humide (CIRDES), Département Environnements et Sociétés (Cirad-ES), Institut de Recherche pour le Développement (IRD), Université Polytechnique Nazi Boni Bobo-Dioulasso (UNB), and Financial grant STRADIV (System approach for the TRAnsition to bio-DIVersified agroecosystems) from Agropolis Foundation (France) (Grant No. 1405-018)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, [SDV]Life Sciences [q-bio], F08 - Systèmes et modes de culture, Performance de culture, 01 natural sciences, Leucaena leucocephala, Établissement de la plante, Coppicing, Leucaena, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, F01 - Culture des plantes, 2. Zero hunger, Biomass (ecology), biology, Forestry, 04 agricultural and veterinary sciences, Facteur édaphique, Morus alba, Céréale fourragère, Rendement des cultures, western Africa, Livestock, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, Forage, alimentation du bétail, edaphoclimatic conditions, Production végétale, Fodder, establishment, Banque de céréales, trees and shrubs, L02 - Alimentation animale, business.industry, protein bank, Sowing, plant growth, 15. Life on land, biology.organism_classification, Agronomy, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, business, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: West African livestock keepers need forage sources to feed animals without degrading the local fragile ecosystems. Establishing high-density forage protein banks for animal feeding was evaluated in three contrasting zones of Burkina Faso. The agronomic performance of the fodder species Leucaena leucocephala (leucaena) and Morus alba (mulberry), planted for intensive forage production (25,000 plants/ha) was monitored through plant height (HEI), stem diameter (DIA), branch number (BrN) and branch length (BrL). Once plots were considered established (at 7 months) all trees were coppiced. Biomass yield subsequently was monitored over three bi-monthly harvests which began approximately 1 year after planting. For both species, a highly significant interaction between experimental site and dates was observed for all variables except BrN. Average HEI (103 cm) were similar. DIA (7 +/- 0.4 cm) and BrL (55 +/- 2.2 cm) were higher in mulberry (6 +/- 0.1 and 29 +/- 1.0 cm, respectively), whereas the BrN remained higher in leucaena (7 +/- 0.2 vs. 2 +/- 0.1 cm). No differences were observed in HEI between sites from June to August. However, from September to October, both species displayed a stronger growth rate at site 1. The biomass yields (t DM/ha/year) in three consecutive harvests were lower than values reported in other tropical regions (1.8 +/- 1.2 and 8.1 +/- 3.9, for mulberry and leucaena, respectively). Differences between sites were due mainly to soil properties, rainfall pattern and termite attacks. This study demonstrated that L. leucocephala and M. alba, planted in high-density forage banks, successfully establish and have high forage yield across several edaphoclimatic conditions in Burkina Faso. Our findings suggest that this technology could significantly contribute to livestock feeding systems in the region, thus reducing negative effects of over-grazing on landscape degradation.
Published: 2020
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33. Multiple-nutrient limitation of upland rainfed rice in ferralsols: a greenhouse nutrient-omission trial

Author: Tovohery Rakotoson, Eric Blanchart, Thierry Becquer, Tantely Razafimbelo, Manoa Raminoarison, Jean Trap, Université d'Antananarivo, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), project SECuRE (Soil ecological function restoration to enhance agrosystem services in rainfed rice cropping systems in agroecological transition), Agropolis Foundation under the reference ID 1605-007 through the 'Investissements d'Avenir' program (Labex Agro: ANR-10-LABX-0001-01), I-SITE MUSE (ANR-16-IDEX-0006)., ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), and ANR-16-IDEX-0006,MUSE,MUSE(2016)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Physiology, Greenhouse, Upland rainfed rice, Upland rice, 01 natural sciences, Nutrient, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Rice cultivars, cultivars, Madagascar, upland rainfed rice, 2. Zero hunger, nutrient limitation, Greenhouse trial, Nutrient management, rice, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, ferralsols, Agronomy, Nutrient limitation, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Ferralsols, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; To optimize the nutrient management of upland rice production on tropical ferralsols, a greenhouse experiment was established using the multi-nutrient omission approach. A reciprocal soil origin-rice cultivar transplant experiment was also conducted to better understand the relative contributions of the soil origin and the rice cultivar in rice nutrient limitation. We tested the deficiency of seven major and secondary nutrients [nitrogen (N), phosphorus (P), potassium (K), sulfur (S), calcium (Ca), magnesium (Mg), and silicon (Si)] and a solution of six micronutrients (B, Mn, Cu, Co, Na, Mo) likely to limit the growth of two upland rice cultivars, Chhomrong Dan and Nerica 4, on two Ferralsols from the highlands of Madagascar. We found severe multiple nutrient deficiencies. For both cultivars, P, Ca, N, Mg omission significantly depressed the shoot and root dry biomass and their amounts in plant tissues. However, the main limiting nutrients were not the same in both soils. We conclude that the multinutrient deficiencies observed for rice growth in the Ferralsols are site-specific, even though P limitation appears to be in common, and requires a holistic consideration of the mineral fertility, including micronutrients.
Published: 2020
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34. Nitrogen supply reduces the earthworm-silicon control on rice blast disease in a Ferralsol

Author: M. Razafindrakoto, Jean Trap, Harinjaka Raveloson, Thierry Becquer, Laetitia Bernard, Eric Blanchart, Mathilde Sester, Tantely M. Razafimbelo, Onja Ratsiatosika, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), Laboratoire des Radio-Isotopes (LRI), Université d'Antananarivo, Université d'Antananarivo, Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), project SECuRE (Soil ecological function restoration to enhance agrosystem services in rainfed rice cropping systems in agroecological transition) supported by Agropolis Foundation under the reference ID 1605-007, 'Investissements d'Avenir' programme (Labex Agro: ANR-10-LABX-0001-01), I-SITE MUSE (ANR-16-IDEX-0006)., ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), ANR-16-IDEX-0006,MUSE,MUSE(2016), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Laboratoire des RadioIsotopes (LRI)
Subjects: 0106 biological sciences, 01 natural sciences, Ver de terre, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Pyricularia oryzae, Plant nutrition, Cover crop, Pontoscolex corethrurus, 2. Zero hunger, Biomass (ecology), Ecology, food and beverages, 04 agricultural and veterinary sciences, Agricultural and Biological Sciences (miscellaneous), Nutrition des plantes, Tillage, Fertilizer, pyriculariose du riz, Ferralsol, Conservation agriculture, Soil biology, Azote, Soil Science, Biology, engineering.material, Fertilisation, Madagascar, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Disease severity, H20 - Maladies des plantes, Earthworm, Oryza, 15. Life on land, biology.organism_classification, F61 - Physiologie végétale - Nutrition, Agronomy, 13. Climate action, 040103 agronomy & agriculture, engineering, 0401 agriculture, forestry, and fisheries, Belowground-aboveground relationships, 010606 plant biology & botany, F04 - Fertilisation
Abstract: International audience; Revealing belowground-aboveground relationships (BAR) is essential to drive ecological processes to address agriculture dysfunctions, especially in the management of aboveground plant diseases. Earthworms are one of the most important soil organisms involved in BAR, and silicon (Si) has been identified as a crucial element regulating aboveground plant health. How earthworm-Si interactions induce BAR in poor- and rich-nutrient soil contexts is still poorly understood, despite a growing interest in agricultural sustainability. We investigated the potential of BAR induced by the earthworm-silicon interaction to control the severity of rice blast disease in a Ferralsol in Madagascar, with or without NPK fertilization. We conducted a greenhouse microcosm experiment in which we manipulated the presence of the endogeic earthworm Pontoscolex corethrurus and the fungus Pyricularia oryzae in a Ferralsol supplied or not with Si and fertilized with macronutrients (nitrogen, phosphorus and potassium, i.e., NPK). After eight weeks of growth, plant biomass, nutrition and disease severity were measured. Our results validated the hypothesis that a dual treatment of earthworm inoculation and Si fertilization in a nutrient-poor tropical soil confers a higher tolerance of rainfed rice to P. oryzae, in comparison with treatments with only earthworms or Si, providing the optimal agronomic balance between a gain in biomass (and nutrition) and a reduction in disease severity. The supply of macronutrients altered this positive BAR by favouring the phenomenon of N-induced susceptibility. The aboveground plant C:N ratio of 15 is a threshold below which any increase in N per C unit likely enhances blast disease. The role of belowground interactions to counteract agricultural dysfunctions is supported by our study. To accomplish ecological intensification and provision of ecosystem services such as disease regulation, our findings recommend replacing excessive use of macronutrient fertilizer with sustained agricultural practices promoting the development of earthworm populations, such as organic matter inputs, superficial or no tillage, and the use of cover crops or conservation agriculture.
Published: 2020
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35. Yam genomics supports West Africa as a major cradle of crop domestication

Author: Scarcelli, Nora, Cubry, Philippe, Akakpo, Roland, Thuillet, Anne-Céline, Obidiegwu, Jude, Baco, Mohamed N., Otoo, Emmanuel, Sonké, Bonaventure, Dansi, Alexandre, Djedatin, Gustave, Mariac, Cédric, Couderc, Marie, Causse, Sandrine, Alix, Karine, Chaïr, Hâna, François, Olivier, Vigouroux, Yves, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), National Root Crops Research Institute, Université de Parakou (UP), Centre for Scientific and Industrial Research, Partenaires INRAE, University of Yaoundé [Cameroun], National University of Sciences, Technologies, Engineering and Mathematics of Abomey, 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), Université de Montpellier (UM), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Agence Nationale de la Recherche (ANR) : AFRICROP ANR-13-BSV7-0017, ANR : ANR-10-INBS-09, ARCAD project - Agropolis foundation, FEDER program, 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]), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)
Subjects: Crops, Agricultural, Pennisetum, Séquence nucléotidique, [SDV]Life Sciences [q-bio], Forests, Polymorphism, Single Nucleotide, F30 - Génétique et amélioration des plantes, génomique, Domestication, Evolution, Molecular, Rivers, Igname, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, B50 - Histoire, Research Articles, Histoire naturelle, Evolutionary Biology, Models, Statistical, Base Sequence, Whole Genome Sequencing, Dioscorea, Domestication des plantes, SciAdv r-articles, Agriculture, Oryza, F70 - Taxonomie végétale et phytogéographie, Genomics, Plant Leaves, Africa, Western, Provenance, Genome, Plant, Research Article
Abstract: Yam, a tuber crop, was domesticated alongside some African cereals and defines a cradle of domestication in West Africa., While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River was a major cradle of African agriculture.
Published: 2019
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36. Earthworm Inoculation Improves Upland Rice Crop Yield and Other Agrosystem Services in Madagascar

Author: Onja Ratsiatosika, Jean Trap, Michel Rabenarivo, Laetitia Bernard, Thierry Becquer, Eric Blanchart, Tantely Razafimbelo, Malalatiana Razafindrakoto, Laboratoire des Radio-Isotopes (LRI), Université d'Antananarivo, Université d'Antananarivo, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-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), project SECuRE (Soil ecological function restoration to enhance agrosystem services in rainfed rice cropping systems in agroecological transition), supported by the Agropolis Foundation under the reference ID 1605-007 through the 'Investissements d’Avenir' program (Labex Agro: ANR-10-LABX-0001-01) under the framework I-SITE MUSE (ANR-16-IDEX-0006)., IRD (French Institute of Research for the Development) also contributed to the funding via the ERA-Net ARD II call (2012), CAMES Project (Impacts of Conservation Agriculture on Macrofauna diversity and related Ecosystem Services for improved farmer’s cropping systems and livelihoods in Highlands of Madagascar)., ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), ANR-16-IDEX-0006,MUSE,MUSE(2016), Laboratoire des RadioIsotopes (LRI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, rice growth, Conservation agriculture, Plant Science, Biology, Upland rice, 03 medical and health sciences, Pontoscolex corethrurus, lcsh:Agriculture (General), soil ecological intensification, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Inoculation, Crop yield, Earthworm, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, lcsh:S1-972, rice yield, Tillage, Agronomy, soil macroaggregates, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ferralsols, Agronomy and Crop Science, Cropping, Food Science
Abstract: The effects of earthworm inoculation and cropping systems on upland rice systems were examined over a four-year period in the Highlands of Madagascar. Each year, endogeic earthworms Pontoscolex corethrurus (Rhinodrilidae) were inoculated (EW+) at a density of 75 ind m&minus, 2 or were not inoculated (EW0). Inoculation was tested in three cropping systems: conservation agriculture (CA) and traditional tillage with or without residues restitution. Soil and plant properties were measured during the first three years while soil biological properties were assessed at the fourth year. At the end of the experiment, earthworm density was three-fold higher in EW+ than in EW0, demonstrating the success of the inoculation. Earthworm density was more important in CA than in tillage systems. Earthworm inoculation had higher significant effects on soil and plant properties than cropping systems. Earthworm inoculation had positive effects on soil macroaggregation (+43%), aboveground biomass (+27%), rice grain yield (+45%), and N grain amount (+43%). Intensifying earthworm activity in field conditions to meet the challenge of ecological transition is supported by our study.
Published: 2021
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37. Engineering meiotic recombination pathways in rice

Author: Fayos, Ian, Mieulet, Delphine, Petit, Julie, Meunier, Anne Cecile, Perin, Christophe, Nicolas, Alain, Guiderdoni, Emmanuel, 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), Université Paris sciences et lettres (PSL), Meiogenix, Meiogenix Company, French National Research Agency (ANR), CGIAR research program RICE (CRP RICE), and Agropolis Foundation (RicE FUnctional GEnomics (REFUGE) platform project)
Subjects: Crossing over, Arabidopsis, Reviews, Oryza sativa, Review, Genes, Plant, F30 - Génétique et amélioration des plantes, crossovers, meiosis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Homologous Recombination, Vegetal Biology, rice, fungi, food and beverages, Oryza, recombination, Apomixie, Gène, apomixis, Méiose, Genetic Engineering, Biologie végétale
Abstract: International audience; In the last 15 years, outstanding progress has been made in understanding the function of meiotic genes in the model dicot and monocot plants Arabidopsis and rice (Oryza sativa L.), respectively. This knowledge allowed to modulate meiotic recombination in Arabidopsis and, more recently, in rice. For instance, the overall frequency of crossovers (COs) has been stimulated 2.3- and 3.2-fold through the inactivation of the rice FANCM and RECQ4 DNA helicases, respectively, two genes involved in the repair of DNA double-strand breaks (DSBs) as noncrossovers (NCOs) of the Class II crossover pathway. Differently, the programmed induction of DSBs and COs at desired sites is currently explored by guiding the SPO11-1 topoisomerase-like transesterase, initiating meiotic recombination in all eukaryotes, to specific target regions of the rice genome. Furthermore, the inactivation of 3 meiosis-specific genes, namely PAIR1, OsREC8 and OsOSD1, in the Mitosis instead of Meiosis (MiMe) mutant turned rice meiosis into mitosis, thereby abolishing recombination and achieving the first component of apomixis, apomeiosis. The successful translation of Arabidopsis results into a crop further allowed the implementation of two breakthrough strategies that triggered parthenogenesis from the MiMe unreduced clonal egg cell and completed the second component of diplosporous apomixis. Here, we review the most recent advances in and future prospects of the manipulation of meiotic recombination in rice and potentially other major crops, all essential for global food security.
Published: 2019
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38. Deciphering the growth form variation of the Mediterranean chamaephyte Thymus vulgaris L. using architectural traits and their relations with different habitats

Author: Nick P. Rowe, Claude Edelin, Mathieu Millan, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut Français de Pondichéry (IFP), Centre National de la Recherche Scientifique (CNRS)-Ministère de l'Europe et des Affaires étrangères (MEAE), Agropolis Foundation and SYSTRA (ID 1200-014), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, Mediterranean climate, Thymus vulgaris, Context (language use), Plant Science, Woodland, Chemotype, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Module, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Ecology, biology, Plant architecture, fungi, food and beverages, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Shrub, Variation (linguistics), Habitat, Habitat preference, Trait, Reiteration, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany, Woody plant
Abstract: International audience; There is a growing interest for methods in plant biology that summarize different plant growth forms and which can identify patterns of growth form variability at ecological scale in a global context. The use of detailed architectural descriptions can bring valuable information for understanding what developmental features underlie the transitions from one growth form to another. In this paper, we investigate the developmental attributes responsible for growth form variation in Thymus vulgaris and whether they are linked to habitat preference. We analysed architectural development in T. vulgaris from 12 populations in southern France, which includes two contrasting habitats of the species. Architectural development in T. vulgaris is based on three hierarchical levels of organization, which include the module, the branched complex and the whole plant. T. vulgaris is found as three different growth forms that can vary from basally branched to more apically branched growth forms. Differences in growth form result from variations in the sequential repetition of branched complexes and are also linked to the type of habitat. Individuals growing in hot, dry, rocky habitats are dominated by plants that display mostly a basally branched (basitonic) architecture – a potentially adaptive architectural trait for exploiting space in open woodland. Individuals growing in colder, more humid habitats that are dominated by tall grasses display mostly apically branched (mesotonic and acrotonic) architectures resulting in more elevated growth forms. The architectural method provides additional insight into how variations in form are developed in small-bodied woody plants such as Thymus. We found that reiteration processes are important for forming different organisational levels and variations in growth form. Architectural traits provide additional markers for ecological studies that wish to understand how living space is exploited by the whole plant. The study represents a promising approach for identifying whole plant traits at the community level.
Published: 2019
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39. Modelling tiller growth and mortality as a sink-driven process using Ecomeristem: Implications for biomass sorghum ideotyping

Author: Grégory Beurier, Sandrine Roques, Jean-Christophe Soulie, Damien Fumey, Florian Larue, Delphine Luquet, Lauriane Rouan, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ITK, 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), BIOSORG project - Agropolis foundation : AF 1301-010 BIOSORG, project - Cariplo foundation : FC 2013-1890, French National Research Agency (ANR) : ANR-11-BTBR-0006-BFF, and ANR-11-BTBR-0006,BFF,Biomasse pour le futur(2011)
Subjects: 0106 biological sciences, Light conversion efficiency, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, F62 - Physiologie végétale - Croissance et développement, Plant Science, 01 natural sciences, Sink (geography), (non-)structural carbohydrates, F30 - Génétique et amélioration des plantes, ideotyping, Biomass, 2. Zero hunger, Tallage, geography.geographical_feature_category, tiller mortality, biology, U10 - Informatique, mathématiques et statistiques, food and beverages, Ideotype, 04 agricultural and veterinary sciences, Facteur du milieu, Sorghum bicolor, ecophysiological modelling, Phenotype, Trait, Génotype, Sorghum bicolor (L.) Moench, Carbone, Genotype, stem biomass, C source-sink relationships, tillering, Genetic model, Croissance, Sorghum, Genetic diversity, geography, Modélisation des cultures, Sowing, Original Articles, 15. Life on land, biology.organism_classification, Relation source puits, Agronomy, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Edible Grain, 010606 plant biology & botany
Abstract: Background and AimsPlant modelling can efficiently support ideotype conception, particularly in multi-criteria selection contexts. This is the case for biomass sorghum, implying the need to consider traits related to biomass production and quality. This study evaluated three modelling approaches for their ability to predict tiller growth, mortality and their impact, together with other morphological and physiological traits, on biomass sorghum ideotype prediction.MethodsThree Ecomeristem model versions were compared to evaluate whether tillering cessation and mortality were source (access to light) or sink (age-based hierarchical access to C supply) driven. They were tested using a field data set considering two biomass sorghum genotypes at two planting densities. An additional data set comparing eight genotypes was used to validate the best approach for its ability to predict the genotypic and environmental control of biomass production. A sensitivity analysis was performed to explore the impact of key genotypic parameters and define optimal parameter combinations depending on planting density and targeted production (sugar and fibre).Key ResultsThe sink-driven control of tillering cessation and mortality was the most accurate, and represented the phenotypic variability of studied sorghum genotypes in terms of biomass production and partitioning between structural and non-structural carbohydrates. Model sensitivity analysis revealed that light conversion efficiency and stem diameter are key traits to target for improving sorghum biomass within existing genetic diversity. Tillering contribution to biomass production appeared highly genotype and environment dependent, making it a challenging trait for designing ideotypes.ConclusionsBy modelling tiller growth and mortality as sink-driven processes, Ecomeristem could predict and explore the genotypic and environmental variability of biomass sorghum production. Its application to larger sorghum genetic diversity considering water deficit regulations and its coupling to a genetic model will make it a powerful tool to assist ideotyping for current and future climatic scenario.
Published: 2019
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40. Tailoring chemoenzymatic oxidation via in situ peracids

Author: James J. La Clair, Michael D. Burkart, Johanna C. Proessdorf, Maeva Subileau, Rebecca N. Re, 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), 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), Montpellier SupAgro scientific council, Agropolis Foundation (International Mobility Fellowship, Labex Agro, France), Department of Energy grant EE0008246, and NIH T32 GM067550.
Subjects: chemistry.chemical_classification, In situ, Olefin fiber, Molecular Structure, Sulfide, 010405 organic chemistry, Chemistry, Organic Chemistry, époxydation, Alkenes, Sulfides, 010402 general chemistry, Lipids, 01 natural sciences, Biochemistry, Combinatorial chemistry, ingénierie enzymatique, Article, 0104 chemical sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Epoxy Compounds, Physical and Theoretical Chemistry, Oxidation-Reduction
Abstract: Epoxidation chemistry often suffers from the challenging handling of peracids and thus requires in situ preparation. Here, we describe a two-phase enzymatic system that allows the effective generation of peracids and directly translate their activity to the epoxidation of olefins. We demonstrate the approach by application to lipid and olefin epoxidation as well as sulfide oxidation. These methods offer useful applications to synthetic modifications and scalable green processes.
Published: 2019
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41. The lca4csa framework: Using life cycle assessment to strengthen environmental sustainability analysis of climate smart agriculture options at farm and crop system levels

Author: Ivonne Acosta-Alba, Nadine Andrieu, Eduardo Chia, International Center for Tropical Agriculture [Colombie] (CIAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Evalivo, Partenaires INRAE, Université de Montpellier (UM), Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), 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), FONTAGRO program [FTG/RF-14837-RG, 80], Agropolis Foundation [1502-006], CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), 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: agriculture familiale, 010504 meteorology & atmospheric sciences, P40 - Météorologie et climatologie, Cash crop, F08 - Systèmes et modes de culture, [SDV]Life Sciences [q-bio], agroécologie, adaptation aux changements climatiques, Coffea, 7. Clean energy, 01 natural sciences, 12. Responsible consumption, [SHS]Humanities and Social Sciences, mitigation, 11. Sustainability, Sustainable agriculture, environmental sustainability, Life-cycle assessment, Environmental planning, 0105 earth and related environmental sciences, 2. Zero hunger, Upstream (petroleum industry), Changement climatique, Food security, business.industry, 04 agricultural and veterinary sciences, 15. Life on land, 13. Climate action, Agriculture, Greenhouse gas, Sustainability, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Animal Science and Zoology, Système de culture, Canne à sucre, crop system, Business, P01 - Conservation de la nature et ressources foncières, Agronomy and Crop Science, farm
Abstract: International audience; Climate Smart Agriculture (CSA) seeks to meet three challenges: improve the adaptation capacity of agricultural systems to climate change, reduce the greenhouse gas emissions of these systems, and ensure local and global food security. Many CSA assessment methods that consider these three challenges have emerged, but to better assess the environmental resilience of farming systems, other categories of environmental impacts beyond climate change need to be considered. To meet this need, we propose the LCA4CSA method, which was tested in southern Colombia for family farming systems including coffee, cane and small livestock production. This methodological framework is based on Life Cycle Assessment (LCA) and multi-criteria assessment methods. It integrates CSA-related issues through the definition of Principles, Criteria and Indicators, and involves farmers in the assessment of the effects of CSA practices. To reflect the complexity of farming systems, the method proposes a dual level of analysis: the farm and the main cash crop/livestock production system. After creating a typology of the farming systems, the initial situation is compared to the situation after the introduction of a CSA practice. In this case, the practice was the use of compost made from coffee processing residues. The assessment at the crop system level made it possible to quantify the mitigation potential related to the use of compost (between 22 and 41%) by taking into account operations that occur on and upstream of the farm. However, it showed that pollution transfers exist between impact categories, especially between climate change, acidification and terrestrial eutrophication indicators. The assessment made at the fanning system level showed that farms with livestock units could further limit their emissions by modifying the feeding of animals due to the large quantities of imported cereals. The mitigation potential of compost was only 3% for these farms. This article demonstrates the merits of using life cycle thinking that can be used to inform stakeholder discussions concerning the implementation of CSA practices and more sustainable agriculture.
Published: 2019
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42. An Optimized Microsatellite Scheme for Assessing Populations of Xanthomonas phaseoli pv. manihotis

Author: Ralf Koebnik, Silvia Restrepo, Adriana Bernal, Boris Szurek, Cesar Trujillo, Carolina Flores, Leidy Rache, Christian Vernière, Laurence Blondin, Universidad de Los Andes, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université de Montpellier (UM), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Faculty of Sciences from Universidad de los Andes-Bogota, Colombia : 2014-10, 2015-20, UMR Interactions Plantes Microorganismes Environement, Agropolis Foundation (project PAIX), Montpellier, France : 1403-073, ECOS Nord programme : C15A01, and Departamento Administrativo de Ciencia, Tecnologia e Innovacion-Colciencias : 528
Subjects: Xanthomonas, Pathologie végétale, Plant Science, Computational biology, Multiple Loci VNTR Analysis, Biology, Agent pathogène, 03 medical and health sciences, chemistry.chemical_compound, Maladie des plantes, Variation génétique, Tandem repeat, Molecular marker, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Marqueur génétique, Genetic variability, Xanthomonas phaseoli, H20 - Maladies des plantes, 030304 developmental biology, molecular marker, 0303 health sciences, Genetic diversity, 030306 microbiology, biology.organism_classification, Épidémiologie, tandem repeat, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, pathogen diversity, Xanthomonas campestris phaseoli, Microsatellite, H50 - Troubles divers des plantes, epidemiology, Agronomy and Crop Science
Abstract: International audience; Diverse molecular markers have been used to analyze the genetic diversity of plant pathogens. Compared with traditional fingerprinting methods, multiple loci variable number of tandem repeat analyses (MLVAs) have gained importance recently due to their reproducibility, high discriminatory power, ease of performance, low cost, and throughput potential. These characteristics are desirable for continuous pathogen monitoring, especially for pathogens with relatively low genetic diversity, and for disease epidemiology studies. Genetic diversity studies of Xanthomonas phaseoli pv. manihotis, which is the causal agent of cassava bacterial blight, have shown variability and changes in the bacterial population over time. Thus, an easy and fast method needs to be developed to type populations of this pathogen in different countries of the world, especially on small scales. In this study, we developed an MLVA scheme to analyze X. phaseoli pv. manihotis variability on a local scale. The MLVA-15 scheme comprises 15 variable number of tandem repeat loci grouped into four multiplex polymerase chain reaction pools. We showed that the MLVA-15 scheme had slightly higher discriminatory ability at the locality level when compared with amplified fragment length polymorphisms. The MLVA-15 scheme allowed for an accurate determination of the number of genotypes in the sample and showed reproducibility and portability. Additionally, this scheme could be used to analyze numerous strains in a reasonable timeframe. The MLVA-15 scheme was highly specific to X. phaseoli but up to eight tandem repeat loci could be amplified from other Xanthomonas spp. Finally, we assessed the utility of the scheme for analyses of X. phaseoli pv. manihotis genetic variability in the Colombian Caribbean region. MLVA-15 distinguished 88.9% of the haplotypes in our sample. Strains originating from the same field and isolated at the same time could be discriminated. In this study, the advantages of the MLVA-15 scheme targeting 6- or 7-bp repeats were demonstrated. Moreover, this scheme was a fast method that was appropriate for routine monitoring of X. phaseoli pv. manihotis populations on a local scale and, thus, was useful for addressing epidemiological questions.
Published: 2019
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43. Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice

Author: Nilima Kumari, Arvind Kumar, Tuong-Vi Cao-Hamadoun, Bhandari Bhandari, Jérôme Bartholomé, Julien Frouin, Nourollah Ahmadi, International Rice Research Institute [Philippines] (IRRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Banasthali University, 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), Agropolis Foundation, and Cariplo Foundation : 201-006
Subjects: 0106 biological sciences, Marker Selection, Plant Science, 01 natural sciences, Linkage Disequilibrium, Marqueur génétique, 0303 health sciences, education.field_of_study, Vegetal Biology, Statistics, Eukaryota, food and beverages, Genomics, Plants, Phenotypes, Physical Sciences, Medicine, Genotype, Science, Drought tolerance, Environment, Molecular Genetics, 03 medical and health sciences, Plant and Algal Models, Genome-Wide Association Studies, Genetics, SNP, Plant Defenses, Grasses, Statistical Methods, education, Molecular Biology, Plant Ecology, Ecology and Environmental Sciences, fungi, Organisms, Biology and Life Sciences, Computational Biology, Oryza, Plant Pathology, 15. Life on land, Biotechnology, Molecular biology techniques, Genetics, Population, Résistance à la sécheresse, Animal Studies, Mathematics, Biologie végétale, Cereal Crops, Linkage disequilibrium, Sélection, F30 - Génétique et amélioration des plantes, Mathematical and Statistical Techniques, Plant Resistance to Abiotic Stress, riz, 2. Zero hunger, Ecology, Agriculture, Phenotype, Experimental Organism Systems, Plant Physiology, Trait, Genome, Plant, Research Article, F60 - Physiologie et biochimie végétale, Population, Crops, DNA construction, Biology, Research and Analysis Methods, Cross-validation, génomique, Quantitative Trait, Heritable, Plant-Environment Interactions, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection, Genetic, Selection (genetic algorithm), 030304 developmental biology, Models, Genetic, business.industry, Human Genetics, Genome Analysis, bacteria, Gene-Environment Interaction, Rice, business, Predictive modelling, Forecasting, Crop Science, 010606 plant biology & botany
Abstract: Developing high yielding rice varieties that are tolerant to drought stress is crucial for the sustainable livelihood of rice farmers in rainfed rice cropping ecosystems. Genomic selection (GS) promises to be an effective breeding option for these complex traits. We evaluated the effectiveness of two rather new options in the implementation of GS: trait and environment-specific marker selection and the use of multi-environment prediction models. A reference population of 280 rainfed lowland accessions endowed with 215k SNP markers data was phenotyped under a favorable and two managed drought environments. Trait-specific SNP subsets (28k) were selected for each trait under each environment, using results of GWAS performed with the complete genotype dataset. Performances of single-environment and multi-environment genomic prediction models were compared using kernel regression based methods (GBLUP and RKHS) under two cross validation scenario: availability (CV2) or not (CV1) of phenotypic data for the validation set, in one of the environments. The most realistic trait-specific marker selection strategy achieved predictive ability (PA) of genomic prediction was up to 22% higher than markers selected on the bases of neutral linkage disequilibrium (LD). Tolerance to drought stress was up to 32% better predicted by multi-environment models (especially RKHS based models) under CV2 strategy. Under the less favorable CV1 strategy, the multi-environment models achieved similar PA than the single-environment predictions. We also showed that reasonable PA could be obtained with as few as 3,000 SNP markers, even in a population of low LD extent, provided marker selection is based on pairwise LD. The implications of these findings for breeding for drought tolerance are discussed. The most resource sparing option would be accurate phenotyping of the reference population in a favorable environment and under a managed drought, while the candidate population would be phenotyped only under one of those environments.
Published: 2019
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44. A stage-structured hierarchical Bayes model for the babassu palm tree population dynamics – Estimated from anthropogenic open area data sets

Author: Patrice Loisel, Danielle Mitja, Bénédicte Fontez, Alessio Moreira dos Santos, Thérèse Libourel, Nikolay Sirakov, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), UMR 228 Espace-Dev, Espace pour le développement, Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA), Université de Montpellier (UM), SARH – Instituto Ambiental e de Recursos Hídricos, Universidade Federal Rural da Amazônia (UFRA), This research work has been accomplished as a part of the Open Science research project (under the reference ID 1403-026) financed by the Agropolis Foundation and by the French National Institute of Agronomical Research (INRA) and 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), 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), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), and 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)
Subjects: 0106 biological sciences, Population dynamics, Population, Bayesian statistics, palmier, 010603 evolutionary biology, 01 natural sciences, Bottleneck, Bayes' theorem, modèle mathématique, Deforestation, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Attalea speciosa, population dynamics, mathematical modelling, education, estimation statistique, education.field_of_study, Mathematical modelling, biology, Amazon rainforest, Agroforestry, 010604 marine biology & hydrobiology, Ecological Modeling, 15. Life on land, biology.organism_classification, modèle bayésien, Tree (data structure), statistical estimation, dynamique des populations, Geography, palm tree, Babassu palm tree, mathematical model
Abstract: The babassu palm tree (Attalea speciosa Mart. ex Spreng.) is an endemic species of Amazon forests, and has social and economical impact/utility. Deforestation highlights this palm tree in anthropogenic open areas (pastures and cultivated fields). Simultaneously, knowledge concerning the sustainable functioning of the species within these manmade environments is sorely lacking: its life cycle is not well known, and its population dynamics remains unstudied. In this study, our objective was to generate a model of the population dynamics of the babassu palm tree, validated by in situ analysis, to understand how babassu, a forest species, adapts to pastureland and, under certain conditions, becomes invasive. We propose a random matrix model with aggregated variables based on the biological stages of the species as the input. The probabilities of the between-stage transition matrix were modelled using a Dirichlet-multinomial model with a hierarchy taking geographical organization, i.e. transect level, into account. The integration of prior information was formulated through a Bayesian approach. This Bayesian hierarchical matrix model enabled us to demonstrate a bottleneck in the population dynamics and a high year-dependent mortality rate at an early stage.
Published: 2019
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45. A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits

Author: TA, Kim Nhung, KHONG, Ngan Giang, HA, Thi Loan, NGUYEN, Dieu Thu, MAI, Duc Chung, HOANG, Thi Giang, PHUNG, Thi Phuong Nhung, BOURRIE, Isabelle, COURTOIS, Brigitte, TRAN, Thi Thu Hoai, DINH, Bach Yen, LA, Tuan Nghia, DO, Nang Vinh, LEBRUN, Michel, GANTET, Pascal, JOUANNIC, Stefan, National Institute of Genetics (NIG), Université de Montpellier (UM), University of sciences and technologies of hanoi (USTH), Palacky University Olomouc, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Plant Resource Center, Partenaires INRAE, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Vietnam National Foundation for Science and Technology Development (NAFOSTED) : 106-NN.02-2016.60, Agropolis Foundation through the 'Investissements d'avenir' programme : ANR-10-LABX-0001-01, Fondazione Cariplo : EVOREPRICE 1201-004, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), and University of Science and Technology of Hanoi (USTH)
Subjects: Locus des caractères quantitatifs, Yield, Genotyping Techniques, [SDV]Life Sciences [q-bio], Meristem, Quantitative Trait Loci, Oryza sativa, Flowers, F50 - Anatomie et morphologie des plantes, F30 - Génétique et amélioration des plantes, Image analysis, lcsh:Botany, Architecture, GWAS, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, genomic features [EN], riz, amélioration génétique, food and beverages, Oryza, Panicle, lcsh:QK1-989, Plant Breeding, Phenotype, Vietnam, Panicule, Rice, Research Article, Genome-Wide Association Study
Abstract: Context Yield improvement is an important issue for rice breeding. Panicle architecture is one of the key components of rice yield and exhibits a large diversity. To identify the morphological and genetic determinants of panicle architecture, we performed a detailed phenotypic analysis and a genome-wide association study (GWAS) using an original panel of Vietnamese landraces. Results Using a newly developed image analysis tool, morphological traits of the panicles were scored over two years: rachis length; primary, secondary and tertiary branch number; average length of primary and secondary branches; average length of internode on rachis and primary branch. We observed a high contribution of spikelet number and secondary branch number per panicle to the overall phenotypic diversity in the dataset. Twenty-nine stable QTLs associated with seven traits were detected through GWAS over the two years. Some of these QTLs were associated with genes already implicated in panicle development. Importantly, the present study revealed the existence of new QTLs associated with the spikelet number, secondary branch number and primary branch number traits. Conclusions Our phenotypic analysis of panicle architecture variation suggests that with the panel of samples used, morphological diversity depends largely on the balance between indeterminate vs. determinate axillary meristem fate on primary branches, supporting the notion of differences in axillary meristem fate between rachis and primary branches. Our genome-wide association study led to the identification of numerous genomic sites covering all the traits studied and will be of interest for breeding programs aimed at improving yield. The new QTLs detected in this study provide a basis for the identification of new genes controlling panicle development and yield in rice. Electronic supplementary material The online version of this article (10.1186/s12870-018-1504-1) contains supplementary material, which is available to authorized users.
Published: 2018
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46. The YTH Domain Protein ECT2 Is an m 6 A Reader Required for Normal Trichome Branching in Arabidopsis

Author: Scutenaire, Jérémy, Deragon, Jean-Marc, Jean, Viviane, BENHAMED, Moussa, RAYNAUD, Cécile, Favory, Jean-Jacques, Merret, Rémy, Bousquet-Antonelli, Cécile, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Agropolis Foundation (international mobility program) [1502-003], CNRS, University of Perpignan Via Domitian, Institut Universitaire de France, Bio-Environnement platform through utilization of the confocal microscope, Agence Nationale pour la Recherche [ANR HEAT-EpiRNA, ANR-17-CE20-0007-01 and ANR HEAT-Adapt, ANR-14- CE10-0015], University of Perpignan Via Domitia, Doctoral School [ED305], and ANR-17-CE20-0007,HEAT-EpiRNA,Lecture de l'épitranscriptome du stress thermique chez Arabidopsis(2017)
Subjects: Arabidopsis Proteins, [SDV]Life Sciences [q-bio], Arabidopsis, Intracellular Signaling Peptides and Proteins, Trichomes, Research Articles, ComputingMilieux_MISCELLANEOUS, Protein Binding
Abstract: International audience; Methylations at position N-6 of internal adenosines (m(6)As) are the most abundant and widespread mRNA modifications. These modifications play crucial roles in reproduction, growth, and development by controlling gene expression patterns at the posttranscriptional level. Their function is decoded by readers that share the YTH domain, which forms a hydrophobic pocket that directly accommodates the m(6)A residues. While the physiological and molecular functions of YTH readers have been extensively studied in animals, little is known about plant readers, even though m(6)As are crucial for plant survival and development. Viridiplantae contains high numbers of YTH domain proteins. Here, we performed comprehensive evolutionary analysis of YTH domain proteins and demonstrated that they are highly likely to be actual readers with redundant as well as specific functions. We also show that the ECT2 protein from Arabidopsis thaliana binds to m(6)A-containing RNAs in vivo and that this property relies on the m(6)A binding pocket carried by its YTH domain. ECT2 is cytoplasmic and relocates to stress granules upon heat exposure, suggesting that it controls mRNA fate in the cytosol. Finally, we demonstrate that ECT2 acts to decode the m(6)A signal in the trichome and is required for their normal branching through controlling their ploidy levels.
Published: 2018
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47. Two ancestral genes shaped the Xanthomonas campestris TAL effector gene repertoire

Author: Sébastien Carrère, Nicolas Denancé, Boris Szurek, Aude Cerutti, Ahmed Hajri, Matthieu Arlat, Tristan Boureau, Emmanuelle Lauber, Lisa Fontaine-Bodin, Erin L. Doyle, Laurent D. Noël, Adam J. Bogdanove, Endrick Guy, Stéphane Poussier, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Iowa State University (ISU), Doane University, 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), French Ministry of National Education and Research, ANR-10-GENM-0013,XANTHOMIX,Etude comparative des génomes et des transcriptomes de Xanthomonas phytopathogènes(2010), ANR-14-CE19-0002,CROpTAL,Ingénierie de la résistance des plantes cultivées aux pathogènes basée sur le TALome(2014), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), French Guyana grant, Agence Nationale de la Recherche : XANTHOMIX ANR-2010-GENM-013-02, CROpTAL ANR-14-CE19-0002-01, NSF Plant Genome Research Program award, IOS 1238189 Agropolis Foundation : 1200-003, French Laboratory of Excellence project : TULIP ANR-10-LABX-41, ANR-11-IDEX-0002-02, COST Actions : FA1208, CA16107, Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Physiology, [SDV]Life Sciences [q-bio], black rot, Brassica, Plant Science, Xanthomonas campestris, Genome, 03 medical and health sciences, TAL effector, Xanthomonas, Transcription (biology), [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], TALE, Gene, Phylogeny, Transcription Activator-Like Effectors, Plant Diseases, Genetics, biology, Effector, Brassica rapa, DNA-binding domain, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Hax, Host-Pathogen Interactions, Brassicaceae, Genome, Bacterial
Abstract: International audience; Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome). The 53 sequenced tal genes encode 21 distinct DNA binding domains that sort into seven major DNA binding specificities. In silico analysis of the Brassica rapa promoterome identified a repertoire of predicted TALE targets, five of which were experimentally validated using quantitative reverse transcription polymerase chain reaction. The Xc TALome shows multiple signs of DNA rearrangements that probably drove its evolution from two ancestral tal genes. We discovered that Tal12a and Tal15a of Xcc strain Xca5 contribute together in the development of disease symptoms on susceptible B. oleracea var. botrytis cv Clovis. This large and polymorphic repertoire of TALEs opens novel perspectives for elucidating TALE-mediated susceptibility of Brassicaceae to black rot disease and for understanding the molecular processes underlying TALE evolution.
Published: 2018
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48. Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L

Author: Gustavo C, Sant'Ana, Luiz F P, Pereira, David, Pot, Suzana T, Ivamoto, Douglas S, Domingues, Rafaelle V, Ferreira, Natalia F, Pagiatto, Bruna S R, da Silva, Lívia M, Nogueira, Cintia S G, Kitzberger, Maria B S, Scholz, Fernanda F, de Oliveira, Gustavo H, Sera, Lilian, Padilha, Jean-Pierre, Labouisse, Romain, Guyot, Pierre, Charmetant, Thierry, Leroy, 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), Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, State University of Londrina = Universidade Estadual de Londrina, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Brazilian Coffee Research Consortium, CAPES-Agropolis Foundation through the 'Investissements d'avenir' program (Labex Agro) : 1203-001 ANR-10-LABX-0001-01, CAPES :015/13 FAPESP, Ciencia sem Fronteiras, CAPES PVE 084/13, Brazilian Coffee Research Consortium, INCT Cafe, CNPq, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), 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), Inst Agron Parana, CIRAD, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Universidade Estadual Paulista (Unesp), and Univ Montpellier
Subjects: F60 - Physiologie et biochimie végétale, Quantitative Trait Loci, lcsh:Medicine, Coffea, Polymorphism, Single Nucleotide, Article, F30 - Génétique et amélioration des plantes, Plante sauvage, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Teneur en lipides, Diterpénoïde, lcsh:Science, Plant Proteins, Génome, Lipide, lcsh:R, Sequence Analysis, DNA, Coffea arabica, Lipids, Amélioration des plantes, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Biosynthetic Pathways, Agricultural sciences, lcsh:Q, Diterpenes, Fève de café, Sciences agricoles, Genome-Wide Association Study
Abstract: Made available in DSpace on 2018-11-26T15:46:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-11 Brazilian Coffee Research Consortium Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Ciencia sem Fronteiras Brazilian Coffee Research Consortium, INCT Cafe Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley. Inst Agron Parana, Lab Biotecnol Vegetal, BR-86047902 Londrina, PR, Brazil CIRAD, UMR AGAP, F-34398 Montpellier, France Empresa Brasileira Pesquisa Agr, BR-0770901 Brasilia, DF, Brazil Univ Estadual Paulista, Inst Biociencias, BR-13506900 Rio Claro, SP, Brazil Univ Montpellier, IRD, CIRAD, IPME, BP 64501, F-34394 Montpellier, France Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France Univ Estadual Paulista, Inst Biociencias, BR-13506900 Rio Claro, SP, Brazil CAPES: 1203-001 CAPES: ANR-10-LABX-0001-01 CAPES: 015/13 Ciencia sem Fronteiras: CAPES PVE 084/13
Published: 2018
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49. Spatial organisation of habitats in agricultural plots affects per-capita predator effect on conservation biological control: An individual based modelling study

Author: Philippe Tixier, Dominique Carval, Claire Lavigne, Blanche Collard, Thomas Delattre, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and STRADIV project - Agropolis foundation, France 1504-003
Subjects: 0106 biological sciences, [SDE.MCG]Environmental Sciences/Global Changes, Population, Foraging, habitat, Correlated random walk, Biology, 010603 evolutionary biology, 01 natural sciences, Predation, Plante sauvage, education, Predator, Edge length, 2. Zero hunger, education.field_of_study, Ravageur des plantes, U10 - Informatique, mathématiques et statistiques, Modélisation des cultures, business.industry, Ecology, Ecological Modeling, Pest control, Musa, 15. Life on land, Euborellia caraibea, Generalist predators, H10 - Ravageurs des plantes, Lutte biologique, Spatially explicit modelling, 010602 entomology, Habitat, Spatial ecology, Landscape ecology, business, Banana fields, Écosystème
Abstract: International audience; A highly advocated approach to enhance pest control by indigenous predators is to add or maintain appropriate non-crop plant habitats in agrosystems. Although the addition of non-crop plant habitats can enhance the number of predators in crop by increasing their food resources or shelter, the effect is often insufficient to reduce pest abundance or damage. A number of explanations were identified in previous studies; the ability of such habitats to enhance predators, in particular, is affected by the spatial organisation of the habitats at the land-scape level. Here, we explore how intra-plot spatial patterns of non-crop habitats affect the per-capita predator effect on pest control. We use a spatially explicit and individual-based model to simulate the foraging movements of an earwig-like predator in a banana field. Predator movements within a day were based on a simple non-specific behavioural assumption: movement is a correlated random walk affected by habitats and edges. Population dynamic processes occurring at larger time or spatial scales, such as reproduction and immigration, were not considered. In this model, non-crop habitats added to plots were considered favourable to predators: movements were slower and more sinuous in non-crop habitat than in unfavourable habitats. The intra-plot spatial patterns of the non-crop habitat were built and characterised using landscape ecology concepts and metrics. We found that the per-capita predator effect was strongly affected by a spatial dilution of predators, induced by non-crop habitat addition, but this negative effect could be partially or fully mitigated by the spatial organisation of the non-crop habitat. At the banana plant level, a long edge length between the crop and non-crop habitat can compensate for this dilution effect by reducing the duration of the periods between predator visits to the banana plant. At the plot level, the best plots (i.e., those in which all banana plants were often visited by predators) were those with non-crop strips in the banana plant rows. Overall, the results support the idea that the spatial organisation of non-crop habitats at the plot level, characterised by the metric edge length in particular, can be managed to minimise the negative impact of the dilution effect.
Published: 2018
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50. Evaluating four gap-filling methods for eddy covariance measurements of evapotranspiration over hilly crop fields

Author: Nissaf Boudhina, Rim Zitouna-Chebbi, Insaf Mekki, Frédéric Jacob, Nétij Ben Mechlia, Moncef Masmoudi, Laurent Prévot, Laboratoire d'étude des Interactions Sol - Agrosystème - Hydrosystème (UMR LISAH), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National Agronomique de Tunisie (INAT), Université de Carthage - University of Carthage, IRD JEAI JASMIN-Tunisia project (INRGREF), IRD JEAI JASMIN-Tunisia project (INAT), IRD JEAI JASMIN-Tunisia project (LISAH), IRD/ARTS program, MISTRALS/SICMED project, Agropolis Foundation [0901-013], ANR TRANSMED ALMIRA project [ANR-12-TMED-000301], and ANR-12-TMED-0003,ALMIRA,Adaptation des mosaïques paysagères dans les agrosystèmes pluviaux Méditerranéens pour une gestion durable de la production agricole, des ressources en eau et en sol(2012)
Subjects: 2. Zero hunger, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences
Abstract: International audience; Estimating evapotranspiration in hilly watersheds is paramount for managing water resources, especially in semiarid/subhumid regions. The eddy covariance (EC) technique allows continuous measurements of latent heat flux (LE). However, time series of EC measurements often experience large portions of missing data because of instrumental malfunctions or quality filtering. Existing gap-filling methods are questionable over hilly crop fields because of changes in airflow inclination and subsequent aerodynamic properties. We evaluated the performances of different gap-filling methods before and after tailoring to conditions of hilly crop fields. The tailoring consisted of splitting the LE time series beforehand on the basis of upslope and downslope winds. The experiment was setup within an agricultural hilly watershed in northeastern Tunisia. EC measurements were collected throughout the growth cycle of three wheat crops, two of them located in adjacent fields on opposite hillslopes, and the third one located in a flat field. We considered four gap-filling methods: the REddyProc method, the linear regression between LE and net radiation (Rn), the multi-linear regression of LE against the other energy fluxes, and the use of evaporative fraction (EF). Regardless of the method, the splitting of the LE time series did not impact the gap-filling rate, and it might improve the accuracies on LE retrievals in some cases. Regardless of the method, the obtained accuracies on LE estimates after gap filling were close to instrumental accuracies, and they were comparable to those reported in previous studies over flat and mountainous terrains. Overall, REddyProc was the most appropriate method, for both gap-filling rate and retrieval accuracy. Thus, it seems possible to conduct gap filling for LE time series collected over hilly crop fields, provided the LE time series are split beforehand on the basis of upslope-downslope winds. Future works should address consecutive vegetation growth cycles for a larger panel of conditions in terms of climate, vegetation, and water status.
Published: 2018
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