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402 results on '"Écophysiologie des Plantes sous Stress environnementaux (LEPSE)"'

1. Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues

Author: Nathalie Leblanc-Fournier, Denis Vile, Zhanwu Dai, Philippe Gallusci, Arnaud Gauffretau, Michel Génard, Céline Richard-Molard, Sophie Brunel-Muguet, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Laboratoire de Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Ecophysiologie Végétale, Agronomie et Nutritions (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), 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), Unité de recherche Plantes et Systèmes de Culture Horticoles ( PSH ), Institut National de la Recherche Agronomique ( INRA ), Laboratoire de Physique et Physiologie Intégratives de l'Arbre Fruitier et Forestier ( PIAF ), Institut National de la Recherche Agronomique ( INRA ) -Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes ( ECOSYS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Écophysiologie des Plantes sous Stress environnementaux ( LEPSE ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Ecophysiologie Végétale, Agronomie et Nutritions ( EVA ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)
Subjects: 0106 biological sciences, 0301 basic medicine, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Process (engineering), plasticité phénotypique, régulateur du développement des plantes, intensive husbandry, adaptation, Plant Science, Breeding, Biology, phenotypic plasticity, 01 natural sciences, Epigenesis, Genetic, modelling, 03 medical and health sciences, épigénétique, adaptation au changement, plant breeding, variation epigénétique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Epigenetics, development, modélisation, 2. Zero hunger, Genetic diversity, Phenotypic plasticity, Variation épigénétique, epigenetics, business.industry, fungi, food and beverages, modeling, Plants, 15. Life on land, Heritability, contrôle de processus, Adaptation, Physiological, Biotechnology, 030104 developmental biology, Evolutionary biology, Adaptation, changement environnemental, business, environment, élevage intensif, amélioration des plantes, 010606 plant biology & botany
Abstract: Epigenetic variations are involved in the control of plant developmental processes and participate in shaping phenotypic plasticity to the environment. Intense breeding has eroded genetic diversity, and epigenetic diversity now emerge as a new source of phenotypic variations to improve adaptation to changing environments and ensure the yield and quality of crops. Here, we review how the characterization of the stability and heritability of epigenetic variations is required to drive breeding strategies, which can be assisted by process-based models. We propose future directions to hasten the elucidation of complex epigenetic regulatory networks that should help crop modelers to take epigenetic modifications into account and assist breeding strategies for specific agronomical traits.
Published: 2017

2. Genetic variability and plasticity of plant allometry

Author: François Vasseur, Cyrille Violle, Brian J. Enquist, Denis Vile, 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, 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), University of Arizona, Santa Fe Institute, Association Nationale de la Recherche et de la Technologie, Grant/Award Number: 0398/2009-09 42 008, H2020 European Research Council, Grant/Award Number: ERC-StG-2020-949843 PHENOVIGOUR, Région Occitanie Pyrénées-Méditerranée, Grant/Award Number: FEDER FSE IEJ 2014- 2020, ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: high temperature, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, water stress, Arabidopsis thaliana, intraspecific trait variability, plasticity, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, growth rate, metabolic scaling theory, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; The metabolic scaling theory (MST) predicts quasi-universal trait-size relationships in plants, characterised by a unique allometric exponent within and across large taxonomic scales. However, recent studies have identified variability in allometric relationships, without a clear understanding of the modulating role played by genetic variation and environment.Here, we investigated (1) the allometric relationships for two central traits of MST, namely total leaf area and plant growth rate, in the model species Arabidopsis thaliana, (2) the variability of plant allometries between genotypes and (3) the plastic responses of plant allometries under water deficit, high temperature and their interaction.Using a population of 120 genotypes, we found that intraspecific allometries adhered on average with MST predictions. However, a broad variability but a moderate plasticity in the allometric exponents was observed across genotypes and environments. Allometric exponents were impacted significantly, yet weakly, by water deficit, but not by high temperature. Moreover, genotypes that deviated from MST predictions exhibited more plasticity in trait-size relationships than genotypes that followed MST predictions.Our study suggests that plant allometry is genetically variable and might be related to different adaptive strategies to cope with stressing conditions. Thus, our results highlights the need of assessing trait-size relationships within species to understand the mechanisms of plant adaptation to contrasted environments.
Published: 2023

3. Sucrose is an early modulator of the key hormonal mechanisms controlling bud outgrowth in Rosa hybrida

Author: Marion Lecerf, Thomas Péron, François Barbier, Stéphanie Boutet-Mercey, Jessica Bertheloot, Benoit Porcheron, Sylvie Citerne, Hanaé Roman, Soulaiman Sakr, Quentin Barrière, Jakub Rolčík, Rémi Lemoine, José Gentilhomme-Le Gourrierec, Nathalie Leduc, Maria-Dolores Perez-Garcia, Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratory of Growth Regulators, Palacky University and Institute of Experimental Botany ASCR, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de catalyse en chimie organique (LACCO), Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), SFR QUASAV 4207, Lab Biol & Pathol Vegetales, PRES Université Nantes Angers Le Mans (UNAM), Centre de Recherche des Cordeliers (CRC), Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universidad de Salamanca, Salamanca, Spain, Universidad de Salamanca, Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), 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), Laboratory of Growth Regulators [Univ Palacký] (LGR), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Sucres & Echanges Végétaux-Environnement (SEVE), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Écophysiologie des Plantes sous Stress environnementaux ( LEPSE ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Université Nantes Angers Le Mans, Centre de Recherche des Cordeliers ( CRC ), Université Paris Diderot - Paris 7 ( UPD7 ) -École pratique des hautes études ( EPHE ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Institut Jean-Pierre Bourgin ( IJPB ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Ecologie et biologie des interactions ( EBI ), Université de Poitiers-Centre National de la Recherche Scientifique ( CNRS ), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Sucrose, sugar signaling, Physiology, Mutant, Flowers, strigolactones, Plant Science, Biology, Rosa, Rosa sp, Bud burst, Pisum, chemistry.chemical_compound, Plant Growth Regulators, Gene Expression Regulation, Plant, Auxin, shoot branching, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, Sugar, ComputingMilieux_MISCELLANEOUS, Plant Proteins, 2. Zero hunger, chemistry.chemical_classification, Indoleacetic Acids, fungi, food and beverages, Biological Transport, sugar signalling, biology.organism_classification, Hedgehog signaling pathway, cytokinins, chemistry, Biochemistry, sugar, Cytokinin, auxin, Research Paper, Signal Transduction
Abstract: Highlight Recent research shows that sugar availability triggers bud outgrowth. This paper further demonstrates that the effect of sucrose involves changes in the hormonal network related to bud outgrowth, and identifies potential hormones involved in sugar control., Sugar has only recently been identified as a key player in triggering bud outgrowth, while hormonal control of bud outgrowth is already well established. To get a better understanding of sugar control, the present study investigated how sugar availability modulates the hormonal network during bud outgrowth in Rosa hybrida. Other plant models, for which mutants are available, were used when necessary. Buds were grown in vitro to manipulate available sugars. The temporal patterns of the hormonal regulatory network were assessed in parallel with bud outgrowth dynamics. Sucrose determined bud entrance into sustained growth in a concentration-dependent manner. Sustained growth was accompanied by sustained auxin production in buds, and sustained auxin export in a DR5::GUS-expressing pea line. Several events occurred ahead of sucrose-stimulated bud outgrowth. Sucrose upregulated early auxin synthesis genes (RhTAR1, RhYUC1) and the auxin efflux carrier gene RhPIN1, and promoted PIN1 abundance at the plasma membrane in a pPIN1::PIN1-GFP-expressing tomato line. Sucrose downregulated both RwMAX2, involved in the strigolactone-transduction pathway, and RhBRC1, a repressor of branching, at an early stage. The presence of sucrose also increased stem cytokinin content, but sucrose-promoted bud outgrowth was not related to that pathway. In these processes, several non-metabolizable sucrose analogues induced sustained bud outgrowth in R. hybrida, Pisum sativum, and Arabidopsis thaliana, suggesting that sucrose was involved in a signalling pathway. In conclusion, we identified potential hormonal candidates for bud outgrowth control by sugar. They are central to future investigations aimed at disentangling the processes that underlie regulation of bud outgrowth by sugar.
Published: 2015

4. Similar estimates of temperature impacts on global wheat yield by three independent methods

Author: Frank Ewert, Jakarat Anothai, P. V. Vara Prasad, Davide Cammarano, Curtis D. Jones, Elias Fereres, Margarita Garcia-Vila, Soora Naresh Kumar, Eckart Priesack, Phillip D. Alderman, Andrew J. Challinor, Reimund P. Rötter, Alex C. Ruane, Christian Folberth, Gerrit Hoogenboom, Pierre Martre, Roberto C. Izaurralde, Fulu Tao, Pramod K. Aggarwal, Mohamed Jabloun, Jordi Doltra, Joshua Elliott, Christoph Müller, Bing Liu, Iurii Shcherbak, Jeffrey W. White, Bruno Basso, Senthold Asseng, Pierre Stratonovitch, Peter J. Thorburn, Claas Nendel, Taru Palosuo, Joost Wolf, Ann-Kristin Koehler, Thilo Streck, Jørgen E. Olesen, David B. Lobell, Kurt Christian Kersebaum, Delphine Deryng, L. A. Hunt, Garry O'Leary, Katharina Waha, Giacomo De Sanctis, Daniel Wallach, Yan Zhu, James W. Jones, Elke Stehfest, Mikhail A. Semenov, Christian Biernath, Claudio O. Stöckle, Thomas A. M. Pugh, Matthew P. Reynolds, Enli Wang, Bruce A. Kimball, Erwin Schmid, Iwan Supit, Zhigan Zhao, Michael J. Ottman, Sebastian Gayler, Cynthia Rosenzweig, Ehsan Eyshi Rezaei, Gerard W. Wall, National Engineering and Technology Center for Information Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricutural University, Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Potsdam Institute for Climate Impact Research (PIK), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Leibniz-Zentrum für Agrarlandschaftsforschung (ZALF), Leibniz Association, Center for Climate Systems Research [New York] (CCSR), Columbia University [New York], Computation Institute, Loyola University of Chicago, Department of Environmental Earth System Science and Center on Food Security and the Environment, Stanford University, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, CGIAR Research Program on Climate Change, Agriculture and Food Security, Borlaug Institute for South Asia, CIMMYT, Consultative Group on International Agricultural Research (CGIAR), Department of Plant and Soil Sciences, Mississippi State University [Mississippi], Department of Plant Science, Faculty of Natural Resources, Prince of Songkla University (PSU), Department of Geological Sciences, University of Oregon [Eugene], W. K. Kellogg Biological Station (KBS), Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Institute of Soil Ecology [Neuherberg] (IBOE), Helmholtz-Zentrum München (HZM), The James Hutton Institute, Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, CGIAR-ESSP Program on Climate Change, Agriculture and Food Security, International Center for Tropical Agriculture, European Commission - Joint Research Centre [Ispra] (JRC), Cantabrian Agricultural Research and Training Centre, Department of Agronomy, Purdue University [West Lafayette], Department of Geography, University of Liverpool, Ecosystem Services and Management Program, International Institute for Applied Systems Analysis (IIASA), Institute of Soil Science and Land Evaluation, University of Hohenheim, AgWeatherNet Program, Washington State University (WSU), Department of Plant Agriculture, University of Guelph, Department of Geographical Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, Texas A and M AgriLife Research, Texas A&M University System, Department of Agroecology, Aarhus University [Aarhus], US Arid-Land Agricultural Research Center, United States Department of Agriculture, Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute (IARI), Institute of Landscape Systems Analysis, Leibniz Centre for Agricultural Landscape Research, Landscape & Water Sciences, Department of Environment of Victoria, The School of Plant Sciences, University of Arizona, Natural resources institute Finland, Institute of Ecology, German Research Center for Environmental Health, Institut für Meteorologie und Klimaforschung - Atmosphärische Umweltforschung (IMK-IFU), Karlsruher Institut für Technologie (KIT), School of Geography, Earth and Environmental Sciences [Birmingham], University of Birmingham [Birmingham], Birmingham Institute of Forest Research (BIFoR), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Center for Development Research (ZEF), Environmental Impacts Group, Georg-August-University [Göttingen], Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Computational and Systems Biology Department, Rothamsted Research, Biotechnology and Biological Sciences Research Council, Netherlands Environmental Assessment Agency, Department of Biological Systems Engineering, University of Wisconsin-Madison, PPS, WSG and CALM, Wageningen University and Research [Wageningen] (WUR), Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences [Beijing] (CAS), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), USDA-ARS, Arid-Land Agricultural Research Center, China Agricultural University (CAU), National High-Tech Research and Development Program of China (2013AA100404), the National Natural Science Foundation of China (31271616, 31611130182, 41571088 and 31561143003), the National Research Foundation for the Doctoral Program of Higher Education of China (20120097110042), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), China Scholarship Council., IFPRI through the Global Futures and Strategic Foresight project, the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), the CGIAR Research Program on Wheat, the Agricultural Model Intercomparison and Improvement Project (AgMIP), Agricultural & Biological Engineering Department, University of Florida [Gainesville], Institute of Crop Science and Resource Conservation, University of Bonn-Division of Plant Nutrition, Stanford University [Stanford], Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Prince of Songkla University, Texas A&M AgriLife Research and Extension Center, Natural Resources Institute Finland, Georg-August-Universität Göttingen, Wageningen University and Research Center (WUR), China Agricultural University, Division of Plant Nutrition-University of Bonn, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), University of Florida, Potsdam Institute for Climate Impact Research ( PIK ), Leibniz Centre for Agricultural Landscape Research, Institute for Landscape Biogeochemistry, Center for Climate Systems Research [New York] ( CCSR ), Écophysiologie des Plantes sous Stress environnementaux ( LEPSE ), 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 ), NASA Goddard Institute for Space Studies ( GISS ), NASA Goddard Space Flight Center ( GSFC ), Consultative Group on International Agricultural Research ( CGIAR ), W.K. Kellogg Biological Station, Institute of Soil Ecology [Neuherberg] ( IBOE ), Helmholtz-Zentrum München ( HZM ), James Hutton Institute, Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, European Commission - Joint Research Centre [Ispra] ( JRC ), International Institute for Applied Systems Analysis ( IIASA ), Washington State University ( WSU ), Texas A and M University ( TAMU ), Leibniz Centre for Agricultural Landscape Research (ZALF), Centre for Environment Science and Climate Resilient Agriculture ( CESCRA ), Indian Agricultural Research Institute ( IARI ), Institut für Meteorologie und Klimaforschung - Atmosphärische Umweltforschung ( IMK-IFU ), Karlsruher Institut für Technologie ( KIT ), School of Geography, Earth & Environmental Science and Birmingham Institute of Forest Research, University of Birmingham, International Maize and Wheat Improvement Center ( CIMMYT ), Bonn Universität [Bonn], University of Natural Resources and Life Sciences, University of Wisconsin-Madison [Madison], Wageningen University and Research Center ( WUR ), Chinese Academy of Sciences [Beijing] ( CAS ), Commonwealth Scientific and Industrial Research Organisation, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Université de Toulouse (UT)-Université de Toulouse (UT), Helmholtz Zentrum München = German Research Center for Environmental Health, Natural Resources Institute Finland (LUKE), Georg-August-University = Georg-August-Universität Göttingen, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Biotechnology and Biological Sciences Research Council (BBSRC), and Institute of geographical sciences and natural resources research [CAS] (IGSNRR)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, régression statistique, 010504 meteorology & atmospheric sciences, impact sur le rendement, klim, Atmospheric sciences, 01 natural sciences, incertitude, wheat, uncertainty, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, 2. Zero hunger, changement climatique, Regression analysis, statistical regression, simulation, PE&RC, [ SDE.MCG ] Environmental Sciences/Global Changes, sécurité alimentaire, Plant Production Systems, modèle de récolte, Yield (finance), comparaison de modèles, [SDE.MCG]Environmental Sciences/Global Changes, Climate change, Environmental Science (miscellaneous), Earth System Science, blé, température, Life Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, réchauffement climatique, global change, 0105 earth and related environmental sciences, Hydrology, WIMEK, Global temperature, business.industry, Crop yield, Global warming, Climate Resilience, 13. Climate action, Agriculture, Klimaatbestendigheid, Plantaardige Productiesystemen, Environmental science, Leerstoelgroep Aardsysteemkunde, Climate model, business, Social Sciences (miscellaneous), 010606 plant biology & botany
Abstract: The potential impact of global temperature change on global crop yield has recently been assessed with different methods. Here we show that grid-based and point-based simulations and statistical regressions (from historic records), without deliberate adaptation or CO2 fertilization effects, produce similar estimates of temperature impact on wheat yields at global and national scales. With a 1 °C global temperature increase, global wheat yield is projected to decline between 4.1% and 6.4%. Projected relative temperature impacts from different methods were similar for major wheat-producing countries China, India, USA and France, but less so for Russia. Point-based and grid-based simulations, and to some extent the statistical regressions, were consistent in projecting that warmer regions are likely to suffer more yield loss with increasing temperature than cooler regions. By forming a multi-method ensemble, it was possible to quantify ‘method uncertainty’ in addition to model uncertainty. This significantly improves confidence in estimates of climate impacts on global food security. The potential impact of global temperature change on global crop yield has recently been assessed with different methods. Here we show that grid-based and point-based simulations and statistical regressions (from historic records), without deliberate adaptation or CO2 fertilization effects, produce similar estimates of temperature impact on wheat yields at global and national scales. With a 1 °C global temperature increase, global wheat yield is projected to decline between 4.1% and 6.4%. Projected relative temperature impacts from different methods were similar for major wheat-producing countries China, India, USA and France, but less so for Russia. Point-based and grid-based simulations, and to some extent the statistical regressions, were consistent in projecting that warmer regions are likely to suffer more yield loss with increasing temperature than cooler regions. By forming a multi-method ensemble, it was possible to quantify ‘method uncertainty’ in addition to model uncertainty. This significantly improves confidence in estimates of climate impacts on global food security.
Published: 2016

5. Solving the grand challenge of phenotypic integration: allometry across scales

Author: François Vasseur, Adrianus Johannes Westgeest, Denis Vile, Cyrille Violle, 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, 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), PHENOVIGOUR grant ERC-StG-2020-949843, ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: Genome size, Allometry, Phenotype, Phenotypic integration, Insect Science, Metabolic scaling, Genetics, Body Size, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Animal Science and Zoology, Plant Science, General Medicine, Trait relationships
Abstract: Phenotypic integration is a concept related to the cascade of trait relationships from the lowest organizational levels, i.e. genes, to the highest, i.e. whole-organism traits. However, the cause-and-effect linkages between traits are notoriously difficult to determine. In particular, we still lack a mathematical framework to model the relationships involved in the integration of phenotypic traits. Here, we argue that allometric models developed in ecology offer testable mathematical equations of trait relationships across scales. We first show that allometric relationships are pervasive in biology at different organizational scales and in different taxa. We then present mechanistic models that explain the origin of allometric relationships. In addition, we emphasized that recent studies showed that natural variation does exist for allometric parameters, suggesting a role for genetic variability, selection and evolution. Consequently, we advocate that it is time to examine the genetic determinism of allometries, as well as to question in more detail the role of genome size in subsequent scaling relationships. More broadly, a possible—but so far neglected—solution to understand phenotypic integration is to examine allometric relationships at different organizational levels (cell, tissue, organ, organism) and in contrasted species.
Published: 2022

6. AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana

Author: Maria Stefania Przybylska, Cyrille Violle, Denis Vile, J. F. Scheepens, Benoit Lacombe, Xavier Le Roux, Lisa Perrier, Lou Sales-Mabily, Mariette Laumond, Mariona Vinyeta, Pierre Moulin, Gregory Beurier, Lauriane Rouan, Denis Cornet, François Vasseur, 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, 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Goethe-University Frankfurt am Main, Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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, Agence National de la Recherche (ANR, European Research Council (ERC) Starting Grant Project 'Ecophysiological and biophysical constraints on domestication in crop plants' (Grant ERC-StG-2014- 639706-CONSTRAINTS, European Research Council (ERC) Starting Grant Project 'PHENOVIGOUR' (Grant ERC-StG-2020-949843), ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: Statistics and Probability, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Library and Information Sciences, Statistics, Probability and Uncertainty, Computer Science Applications, Education, Information Systems
Abstract: Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana’s intraspecific variability that can be explored to address questions at the interface of genetics and ecology.
Published: 2023

7. RhizoTubes as a new tool for high throughput imaging of plant root development and architecture: test, comparison with pot grown plants and validation

Author: Hoai Nam Truong, Marion Prudent, Virginie Bourion, Christophe Baussard, Mickael Lamboeuf, Simeng Han, Barbara Pivato, Daniel Wipf, Sophie Trouvelot, Frédéric Cointault, Anne-Sophie Voisin, Céline Bernard, Marielle Adrian, Hughes Busset, Delphine Moreau, Christophe Salon, Eric Bernaud, Christian Jeudy, Llorenç Cabrera-Bosquet, Vanessa Vernoud, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Inoviaflow, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), National Research Agency and the 'Programme d’Investissements d’Avenir' (PIA) (ANR-11-INBS-0012), Phenome-FPPN, Inra EA et INRA BAP, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Écophysiologie des Plantes sous Stress environnementaux ( LEPSE ), and Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro )
Subjects: 0106 biological sciences, 0301 basic medicine, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Root system, Plant Science, Growth, Nitrogen availability, root architecture, 01 natural sciences, Sativum, architecture racinaire, pisum sativum, 2. Zero hunger, Abiotic component, Rhizosphere, Vegetal Biology, Plant–microorganism interactions, medicago truncatula, plateforme de phénotypage, Phenotyping, Shoot, interaction plante microorganisme, Biotechnology, abiotic stress, High-throughput, Biology, rhizotron, brassica napus, 03 medical and health sciences, Plant roots, vitis vinifera, RhizoCab, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, triticum aestivum, stress abiotique, Drought, Abiotic stress, Rhizotron, Methodology, Image acquisition, 15. Life on land, RhizoTubes, 030104 developmental biology, vulpia, Agronomy, peas, acquisition d'image, Weed, Biologie végétale, 010606 plant biology & botany
Abstract: Background In order to maintain high yields while saving water and preserving non-renewable resources and thus limiting the use of chemical fertilizer, it is crucial to select plants with more efficient root systems. This could be achieved through an optimization of both root architecture and root uptake ability and/or through the improvement of positive plant interactions with microorganisms in the rhizosphere. The development of devices suitable for high-throughput phenotyping of root structures remains a major bottleneck. Results Rhizotrons suitable for plant growth in controlled conditions and non-invasive image acquisition of plant shoot and root systems (RhizoTubes) are described. These RhizoTubes allow growing one to six plants simultaneously, having a maximum height of 1.1 m, up to 8 weeks, depending on plant species. Both shoot and root compartment can be imaged automatically and non-destructively throughout the experiment thanks to an imaging cabin (RhizoCab). RhizoCab contains robots and imaging equipment for obtaining high-resolution pictures of plant roots. Using this versatile experimental setup, we illustrate how some morphometric root traits can be determined for various species including model (Medicago truncatula), crops (Pisum sativum, Brassica napus, Vitis vinifera, Triticum aestivum) and weed (Vulpia myuros) species grown under non-limiting conditions or submitted to various abiotic and biotic constraints. The measurement of the root phenotypic traits using this system was compared to that obtained using “classic” growth conditions in pots. Conclusions This integrated system, to include 1200 Rhizotubes, will allow high-throughput phenotyping of plant shoots and roots under various abiotic and biotic environmental conditions. Our system allows an easy visualization or extraction of roots and measurement of root traits for high-throughput or kinetic analyses. The utility of this system for studying root system architecture will greatly facilitate the identification of genetic and environmental determinants of key root traits involved in crop responses to stresses, including interactions with soil microorganisms.
Published: 2016

8. Plant–herbivore interactions: Experimental demonstration of genetic variability in plant–plant signalling

Author: Aurélien Estarague, Cyrille Violle, Denis Vile, Anaïs Hany, Thibault Martino, Pierre Moulin, François Vasseur, 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, 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Centre de Recherche sur les Médiations (Crem), Université de Lorraine (UL), European Research Council (ERC) ‘PHENOVIGOUR’: grant ERC-StG-2020-949843)., ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Cornu aspersum, genome-wide association study, Arabidopsis thaliana, herbivory, Genetics, intraspecific diversity, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, General Agricultural and Biological Sciences, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Plant-herbivore interactions mediated by plant-plant signalling have been documented in different species but its within-species variability has hardly been quantified. Here, we tested if herbivore foraging activity on plants was influenced by a prior contact with a damaged plant and if the effect of such plant-plant signalling was variable across 113 natural genotypes of Arabidopsis thaliana. We filmed the activity of the generalist herbivore Cornu aspersum during 1 h on two plants differing only in a prior contact with a damaged plant or not. We recorded each snails' first choice, and measured its first duration on a plant, the proportion of time spent on both plants and leaf consumption. Overall, plant-plant signalling modified the foraging activity of herbivores in A. thaliana. On average, snails spent more time and consumed more of plants that experienced a prior contact with a damaged plant. However, the effects of plant-plant signalling on snail behaviour was variable: depending on genotype identity, plant-plant signalling made undamaged plants more repellant or attractive to snails. Genome-wide associations revealed that genes related to stress coping ability and jasmonate pathway were associated to this variation. Together, our findings highlight the adaptive significance of plant-plant signalling for plant-herbivore interactions.
Published: 2023

9. Improving crop Yield potential: Underlying biological processes and future prospects

Author: Burgess, Alexandra, Masclaux-Daubresse, Céline, Strittmatter, Günter, Weber, Andreas, Taylor, Samuel Harry, Harbinson, Jeremy, Yin, Xinyou, Long, Stephen, Paul, Matthew, Westhoff, Peter, Loreto, Francesco, Ceriotti, Aldo, Saltenis, Vandasue, Pribil, Mathias, Nacry, Philippe, Scharff, Lars, Jensen, Poul Erik, Muller, Bertrand, Cohan, Jean‐pierre, Foulkes, John, Rogowsky, Peter, Debaeke, Philippe, Meyer, Christian, Nelissen, Hilde, Inzé, Dirk, Klein Lankhorst, René, Parry, Martin, Murchie, Erik, Baekelandt, Alexandra, University of Nottingham, UK (UON), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ)-Universität zu Köln = University of Cologne, Lancaster Environment Centre, Lancaster University, Wageningen University and Research [Wageningen] (WUR), University College of London [London] (UCL), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Copenhagen = Københavns Universitet (UCPH), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Food Science [Copenhagen] (UCPH FOOD), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), ARVALIS - Institut du végétal [Paris], Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), European Commission 817690, and European Project: 817690,ERC
Subjects: food supply, photosynthesis, [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, crop yield, nutrient remobilisation, crop improvement, organ growth
Abstract: International audience; The growing world population and global increases in the standard of living both result in an increasing demand for food, feed and other plant- derived products. In the coming years, plant- based research will be among the major drivers ensuring food security and the expansion of the bio- based economy. Crop productivity is determined by several factors, including the available physical and agricultural resources, crop management, and the resource use efficiency, quality and intrinsic yield potential of the chosen crop. This review focuses on intrinsic yield potential, since understanding its determinants and their biological basis will allow to maximize the plant's potential in food and energy production. Yield potential is determined by a variety of complex traits that integrate strictly regulated processes and their underlying gene regulatory networks. Due to this inherent complexity, numerous potential targets have been identified that could be exploited to increase crop yield. These encompass diverse metabolic and physical processes at the cellular, organ and canopy level. We present an overview of some of the distinct biological processes considered to be crucial for yield determination that could further be exploited to improve future crop productivity.
Published: 2023

10. Evidence for increasing global wheat yield potential

Author: Jose Rafael Guarin, Pierre Martre, Frank Ewert, Heidi Webber, Sibylle Dueri, Daniel Calderini, Matthew Reynolds, Gemma Molero, Daniel Miralles, Guillermo Garcia, Gustavo Slafer, Francesco Giunta, Diego N L Pequeno, Tommaso Stella, Mukhtar Ahmed, Phillip D Alderman, Bruno Basso, Andres G Berger, Marco Bindi, Gennady Bracho-Mujica, Davide Cammarano, Yi Chen, Benjamin Dumont, Ehsan Eyshi Rezaei, Elias Fereres, Roberto Ferrise, Thomas Gaiser, Yujing Gao, Margarita Garcia-Vila, Sebastian Gayler, Zvi Hochman, Gerrit Hoogenboom, Leslie A Hunt, Kurt C Kersebaum, Claas Nendel, Jørgen E Olesen, Taru Palosuo, Eckart Priesack, Johannes W M Pullens, Alfredo Rodríguez, Reimund P Rötter, Margarita Ruiz Ramos, Mikhail A Semenov, Nimai Senapati, Stefan Siebert, Amit Kumar Srivastava, Claudio Stöckle, Iwan Supit, Fulu Tao, Peter Thorburn, Enli Wang, Tobias Karl David Weber, Liujun Xiao, Zhao Zhang, Chuang Zhao, Jin Zhao, Zhigan Zhao, Yan Zhu, Senthold Asseng, University of Florida [Gainesville] (UF), Center for Climate Systems Research [New York] (CCSR), Columbia University [New York], Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Universidad Austral de Chile, International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), KWS Momont SAS, Universitad de Buenos Aires = University of Buenos Aires [Argentina], Instituto de Investigaciones Fisiologicas y Ecologicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Agronomía [Buenos Aires], Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Universitat de Lleida, Institució Catalana de Recerca i Estudis Avançats (ICREA), Università degli Studi di Sassari = University of Sassari [Sassari] (UNISS), Pir Mehr Ali Shah Arid Agriculture University = PMAS-Arid Agriculture University Rawalpindi (AAUR), Swedish University of Agricultural Sciences (SLU), Oklahoma State University [Stillwater] (OSU), Michigan State University [East Lansing], Michigan State University System, Instituto Nacional de Investigación Agropecuaria (INIA), Department of Agriculture, Food, Environment and Forestry (DAGRI), Università degli Studi di Firenze = University of Florence (UniFI), Georg-August-University = Georg-August-Universität Göttingen, Purdue University [West Lafayette], Institute of geographical sciences and natural resources research [CAS] (IGSNRR), Chinese Academy of Sciences [Beijing] (CAS), Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidad de Córdoba = University of Córdoba [Córdoba], University of Hohenheim, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), University of Guelph, Global Change Research Centre (CzechGlobe), University of Potsdam = Universität Potsdam, Aarhus University [Aarhus], Natural Resources Institute Finland (LUKE), Helmholtz Zentrum München = German Research Center for Environmental Health, Universidad de Castilla-La Mancha = University of Castilla-La Mancha (UCLM), Centro de Estudios e Investigación para la Gestión de Riesgos Agrarios y Medioambientales (CEIGRAM), Universidad Politécnica de Madrid (UPM), Centre for Biodiversity and Sustainable Land-use [University of Göttingen] (CBL), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), Washington State University (WSU), Wageningen University and Research [Wageningen] (WUR), Universität Kassel [Kassel], Zhejiang University, Nanjing Agricultural University (NAU), Building artificial Intelligence between trust, Responsibility and Decision (BIRD), Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Beijing Normal University (BNU), China Agricultural University (CAU), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), International Wheat Yield Partnership (IWYP, Grant IWYP115) and the International Maize and Wheat Improvement Center (CIMMYT)., IWYP, CIMMYT (Mexico), and the Chilean Technical and Scientific Research Council (CONICYT) by FONDECYT Project 1141048, National Natural Science Foundation of China (Project Nos. 31761143006 and 41571493), Ministry of Education, Youth and Sports of Czech Republic through SustEs (CZ.02.1.01/0.0/0.0/16_019/000797), Biotechnology and Biological Sciences Research Council (BBSRC) through Designing Future Wheat (BB/P016855/1) and Achieving Sustainable Agricultural Systems (NE/N018125/1)., International Wheat Yield Partnership, International Maize and Wheat Improvement Center, Comisión Nacional de Investigación Científica y Tecnológica (Chile), Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), National Natural Science Foundation of China, Ministry of Education, Youth and Sports (Czech Republic), and Biotechnology and Biological Sciences Research Council (UK)
Subjects: Crop Population, Crop Model Ensemble, Global Food Security Supplementary Material For This Article Is Available Online, Radiation Use Efficiency, Wheat Potential Yield, Yield Increase, Climate, Global Food Security, crop model ensemble, Grain Number, global food security Supplementary material for this article is available online, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Photosynthesis, yield increase, General Environmental Science, WIMEK, radiation use efficiency, Renewable Energy, Sustainability and the Environment, Spring Wheat, Public Health, Environmental and Occupational Health, Letter, wheat potential yield, global food security, Food Demand, ddc, Solar-Radiation, Water Systems and Global Change, Biomass Accumulation
Abstract: Wheat is the most widely grown food crop, with 761 Mt produced globally in 2020. To meet the expected grain demand by mid-century, wheat breeding strategies must continue to improve upon yield-advancing physiological traits, regardless of climate change impacts. Here, the best performing doubled haploid (DH) crosses with an increased canopy photosynthesis from wheat field experiments in the literature were extrapolated to the global scale with a multi-model ensemble of process-based wheat crop models to estimate global wheat production. The DH field experiments were also used to determine a quantitative relationship between wheat production and solar radiation to estimate genetic yield potential. The multi-model ensemble projected a global annual wheat production of 1050 ± 145 Mt due to the improved canopy photosynthesis, a 37% increase, without expanding cropping area. Achieving this genetic yield potential would meet the lower estimate of the projected grain demand in 2050, albeit with considerable challenges., This study was a part of the Agricultural Model Intercomparison and Improvement Project (AgMIP) Wheat Phase 4. The study was supported by the International Wheat Yield Partnership (IWYP, Grant IWYP115) and the International Maize and Wheat Improvement Center (CIMMYT). Experiments carried out in Valdivia (Chile) were funded by IWYP, CIMMYT (Mexico), and the Chilean Technical and Scientific Research Council (CONICYT) by FONDECYT Project 1141048. The experimental work conducted at Valdivia by Dr Jaime Herrera (UACh) is appreciated. F T was supported by the National Natural Science Foundation of China (Project Nos. 31761143006 and 41571493). K C K was supported by the Ministry of Education, Youth and Sports of Czech Republic through SustEs (CZ.02.1.01/0.0/0.0/16_019/000797). Rothamsted Research receives support from the Biotechnology and Biological Sciences Research Council (BBSRC) through Designing Future Wheat (BB/P016855/1) and Achieving Sustainable Agricultural Systems (NE/N018125/1).
Published: 2022

11. Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition

Author: Houssein Zhour, Fabrice Bray, Israa Dandache, Guillaume Marti, Stéphanie Flament, Amélie Perez, Maëlle Lis, Llorenç Cabrera-Bosquet, Thibaut Perez, Cécile Fizames, Ezekiel Baudoin, Ikram Madani, Loubna El Zein, Anne-Aliénor Véry, Christian Rolando, Hervé Sentenac, Ali Chokr, Jean-Benoît Peltier, Bray, Fabrice, Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-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), Faculty of Sciences [Lebanese University] | Faculté des Sciences [Université Libanaise], Lebanese University [Beirut] (LU), Miniaturisation pour la Synthèse, l’Analyse et la Protéomique - UAR 3290 (MSAP), Université de Lille-Centre National de la Recherche Scientifique (CNRS), MetaToul Agromix, MetaboHUB-MetaToul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), 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)-Université Toulouse III - Paul Sabatier (UT3), 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)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), 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, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), 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)-Université Toulouse III - Paul Sabatier (UT3), 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)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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 de Recherche en Sciences Végétales (LRSV), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and 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)
Subjects: plant–microbiome communication, Organic Chemistry, diazotroph, durum wheat, PGPR, bacterial exudate, metabolomics, proteomics, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Catalysis, Computer Science Applications, Inorganic Chemistry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.
Published: 2022

12. Non-autonomous stomatal control by pavement cell turgor via the K+ channel subunit AtKC1

Author: Manuel Nieves-Cordones, Farrukh Azeem, Yuchen Long, Martin Boeglin, Geoffrey Duby, Karine Mouline, Eric Hosy, Alain Vavasseur, Isabelle Chérel, Thierry Simonneau, Frédéric Gaymard, Jeffrey Leung, Isabelle Gaillard, Jean-Baptiste Thibaud, Anne-Aliénor Véry, Arezki Boudaoud, Hervé Sentenac, Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-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), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CEA Cadarache, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), and Université de Montpellier (UM)
Subjects: Regular Issue, Arabidopsis Proteins, [SDV]Life Sciences [q-bio], fungi, Plant Stomata, Arabidopsis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cell Biology, Plant Science
Abstract: Stomata optimize land plants’ photosynthetic requirements and limit water vapor loss. So far, all of the molecular and electrical components identified as regulating stomatal aperture are produced, and operate, directly within the guard cells. However, a completely autonomous function of guard cells is inconsistent with anatomical and biophysical observations hinting at mechanical contributions of epidermal origins. Here, potassium (K+) assays, membrane potential measurements, microindentation, and plasmolysis experiments provide evidence that disruption of the Arabidopsis thaliana K+ channel subunit gene AtKC1 reduces pavement cell turgor, due to decreased K+ accumulation, without affecting guard cell turgor. This results in an impaired back pressure of pavement cells onto guard cells, leading to larger stomatal apertures. Poorly rectifying membrane conductances to K+ were consistently observed in pavement cells. This plasmalemma property is likely to play an essential role in K+ shuttling within the epidermis. Functional complementation reveals that restoration of the wild-type stomatal functioning requires the expression of the transgenic AtKC1 at least in the pavement cells and trichomes. Altogether, the data suggest that AtKC1 activity contributes to the building of the back pressure that pavement cells exert onto guard cells by tuning K+ distribution throughout the leaf epidermis.
Published: 2022

13. Impact of Olive Trees on the Microclimatic and Edaphic Environment of the Understorey Durum Wheat in an Alley Orchard of the Mediterranean Area

Author: Anna Panozzo, Hsin-Ya Huang, Bruno Bernazeau, Florence Meunier, Olivier Turc, Robin Duponnois, Yves Prin, Teofilo Vamerali, Dominique Desclaux, Università degli Studi di Padova = University of Padua (Unipd), DIASCOPE, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Padova BIRD210158/21, and European Project: 613520,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,AGFORWARD(2014)
Subjects: air temperature, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, intercropping, agroforestry, PAR, water conservation, arbuscular mycorrhizal fungi, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Agronomy and Crop Science
Abstract: In the current context of climate change, the impact of trees in agroforestry systems is expected to mitigate water and heat stresses, particularly in semi-arid environments. Within this framework, in a two-year trial conducted at INRAE in Southern France, the dynamics of microclimatic parameters and the edaphic environment of durum wheat were investigated under a yearly-pruned (AF) and a never-pruned (AF+) 6-m apart alley olive orchard, in comparison with controls under full sun. Here it was recorded a reduction of photosynthetic active radiation (PAR) by 30% and 51% in AF and AF+, respectively, during the wheat cycle, together with a marked reduction of wind speed compared to controls (–85% in AF and −99% in AF+). A significant buffer effect was also highlighted for air temperature, averagely +1.7 °C during the night and −3.2 °C during the daytime under the moderate shading of AF. The positive effect of trees on soil water conservation increased with the intensity of shading, particularly during the critical wheat stage of grain filling, with benefits on wheat root mycorrhization, and NH4+ and NO3− abundance in the arable layer. Despite some of the environmental modifications being favorable for the understorey wheat, these were not translated into yield improvements, suggesting that the severe shading associated with the small inter-row and evergreen trees has a prevailing effect, that requires to be managed through appropriate tree pruning.
Published: 2022

14. A Perspective on Plant Phenomics: Coupling Deep Learning and Near-Infrared Spectroscopy

Author: François Vasseur, Denis Cornet, Grégory Beurier, Julie Messier, Lauriane Rouan, Justine Bresson, Martin Ecarnot, Mark Stahl, Simon Heumos, Marianne Gérard, Hans Reijnen, Pascal Tillard, Benoît Lacombe, Amélie Emanuel, Justine Floret, Aurélien Estarague, Stefania Przybylska, Kevin Sartori, Lauren M. Gillespie, Etienne Baron, Elena Kazakou, Denis Vile, Cyrille Violle, 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, 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), 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, University of Waterloo [Waterloo], Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Tübingen, Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), ANR-17-CE02-0018-01 Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l’espèce modèle Arabidopsis thaliana – AraBreed, Centre National de la Recherche Scientifique (CNRS)European Commission, German Research Foundation (DFG)INST 37/696-1 FUGG, ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: multivariate analysis, machine learning, Arabidopsis thaliana, [SDV]Life Sciences [q-bio], near-infrared spectroscopy (NIRS), trait-based ecology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, functional traits, Plant Science, metabolomics
Abstract: International audience; The trait-based approach in plant ecology aims at understanding and classifying the diversity of ecological strategies by comparing plant morphology and physiology across organisms. The major drawback of the approach is that the time and financial cost of measuring the traits on many individuals and environments can be prohibitive. We show that combining near-infrared spectroscopy (NIRS) with deep learning resolves this limitation by quickly, non-destructively, and accurately measuring a suite of traits, including plant morphology, chemistry, and metabolism. Such an approach also allows to position plants within the well-known CSR triangle that depicts the diversity of plant ecological strategies. The processing of NIRS through deep learning identifies the effect of growth conditions on trait values, an issue that plagues traditional statistical approaches. Together, the coupling of NIRS and deep learning is a promising high-throughput approach to capture a range of ecological information on plant diversity and functioning and can accelerate the creation of extensive trait databases.
Published: 2022

15. Do leaf nitrogen resorption dynamics align with the slow‐fast continuum? A test at the intraspecific level

Author: Kevin Sartori, Cyrille Violle, Denis Vile, François Vasseur, Pierre de Villemereuil, Justine Bresson, Lauren Gillespie, Leila Rose Fletcher, Lawren Sack, Elena Kazakou, 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, 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), 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), University of California [Los Angeles] (UCLA), University of California (UC), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), and European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015)
Subjects: association genetics, Arabidopsis thaliana, leaf nitrogen, fungi, food and beverages, population genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, resorption, Ecology, Evolution, Behavior and Systematics, resource-use strategies
Abstract: International audience; The links between internal nitrogen recycling through the process of resorption from senescing leaves, whole-plant resource-use strategies and performance remain elusive. Indeed, tests of such potential linkages are hampered by the classical evaluation of plant nitrogen resorption efficiency (REN) based on ‘snapshots’ of leaf nitrogen concentration from adult and senescent leaves. We significantly increased the resolution for measuring leaf nitrogen resorption by non-destructively tracking time courses of nitrogen concentration in leaves of 137 natural Arabidopsis thaliana genotypes native to a wide range of climates across Europe, grown in a greenhouse. In addition to the classical measurement of resorption efficiency, we computed the relative maximum resorption rate of nitrogen (RRN), that is, the amount of nitrogen remobilized by a leaf per unit time and per unit nitrogen, together with slow–fast syndrome traits at the leaf and whole-plant levels. Across genotypes, high rates and efficiencies of nitrogen resorption were associated with low specific leaf area and late flowering. The RRN showed significant heritability, genetic associations and was negatively correlated with the mean annual temperature of the native populations. By contrast, despite the evidence of a correlation with temperature, REN showed lower heritability and no evidence of genetic association, questioning the mechanisms of nitrogen resorption. Overall, our results suggest a much stronger adaptive role for leaf nitrogen resorption than previously uncovered.
Published: 2022

16. A two-stage approach for the spatio-temporal analysis of high-throughput phenotyping data

Author: Diana M. Pérez-Valencia, María Xosé Rodríguez-Álvarez, Martin P. Boer, Lukas Kronenberg, Andreas Hund, Llorenç Cabrera-Bosquet, Emilie J. Millet, Fred A. van Eeuwijk, Basque Center for Applied Mathematics (BCAM), Basque Center for Applied Mathematics, Universidad del Pais Vasco / Euskal Herriko Unibertsitatea [Espagne] (UPV/EHU), Ikerbasque - Basque Foundation for Science, Wageningen University and Research [Wageningen] (WUR), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Project MTM2017-82379-R (AEI/FEDER, UE), by the Basque Government (BERC 2018-2021 program), by the Spanish Ministry of Science, Innovation, and Universities (BCAM Severo Ochoa accreditation SEV-2017-0718), the Swiss National Foundation (SNF) project PhenoCOOL (project no. 169542)., and European Project: 731013 ,EPPN2020(2017)
Subjects: Agricultural genetics, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, Statistics, PE&RC, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Wiskundige en Statistische Methoden - Biometris, Plant breeding, 2417.14 Genética Vegetal, Biometris, FOS: Mathematics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Life Science, 1209.03 Análisis de Datos, P-splines, mixed models, spatio-temporal modelling, hierarquical modelling, Mathematical and Statistical Methods - Biometris
Abstract: High throughput phenotyping (HTP) platforms and devices are increasingly used for the characterization of growth and developmental processes for large sets of plant genotypes. Such HTP data require challenging statistical analyses in which longitudinal genetic signals need to be estimated against a background of spatio-temporal noise processes. We propose a two-stage approach for the analysis of such longitudinal HTP data. In a first stage, we correct for design features and spatial trends per time point. In a second stage, we focus on the longitudinal modelling of the spatially corrected data, thereby taking advantage of shared longitudinal features between genotypes and plants within genotypes. We propose a flexible hierarchical three-level P-spline growth curve model, with plants/plots nested in genotypes, and genotypes nested in populations. For selection of genotypes in a plant breeding context, we show how to extract new phenotypes, like growth rates, from the estimated genotypic growth curves and their first-order derivatives. We illustrate our approach on HTP data from the PhenoArch greenhouse platform at INRAE Montpellier and the outdoor Field Phenotyping platform at ETH Zürich., Scientific Reports, 12 (1), ISSN:2045-2322
Published: 2022

17. Connecting plant phenotyping and modelling communities: lessons from science mapping and operational perspectives

Author: Clément Saint Cast, Guillaume Lobet, Llorenç Cabrera-Bosquet, Valentin Couvreur, Christophe Pradal, François Tardieu, Xavier Draye, Interactions Sol Plante Atmosphère (UMR ISPA), Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain = Catholic University of Louvain (UCL), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Earth and Life Institute - Environmental Sciences (ELIE), European Project: 731013 ,EPPN2020(2017), Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), European Project: 739514,EMPHASIS-PREP, and UCL - SST/ELI/ELIA - Agronomy
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, data and model integration, F40 - Écologie végétale, [SHS.INFO]Humanities and Social Sciences/Library and information sciences, Phénotype, Analyse de réseau, Genetics and Molecular Biology (miscellaneous), Plant Science, Biochemistry, Biochemistry, Genetics and Molecular Biology (miscellaneous), Analyse de système, F30 - Génétique et amélioration des plantes, Bibliometric analyses, modelling, plant phenotyping, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Modélisation environnementale, Modélisation des cultures, imaging, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, C30 - Documentation et information, Modeling and Simulation, network, Bibliométrie, Plante, U30 - Méthodes de recherche, ddc:004, Banque de données, Agronomy and Crop Science, Génotype, Modèle mathématique
Abstract: Plant phenotyping platforms generate large amounts of high-dimensional data at different scales of plant organization. The possibility to use this information as inputs of models is an opportunity to develop models that integrate new processes and genetic inputs. We assessed to what extent the phenomics and modelling communities can address the issues of interoperability and data exchange, using a science mapping approach (i.e. visualization and analysis of a broad range of scientific and technological activities as a whole). In this paper, we (i) evaluate connections, (ii) identify compatible and connectable research topics and (iii) propose strategies to facilitate connection across communities. We applied a science mapping approach based on reference and term analyses to a set of 4332 scientific papers published by the plant phenomics and modelling communities from 1980 to 2019, retrieved using the Elsevier’s Scopus database and the quantitative-plant.org website. The number of papers on phenotyping and modelling dramatically increased during the past decade, boosted by progress in phenotyping technologies and by key developments at hardware and software levels. The science mapping approach indicated a large diversity of research topics studied in each community. Despite compatibilities of research topics, the level of connection between the phenomics and modelling communities was low. Although phenomics and modelling crucially need to exchange data, the two communities appeared to be weakly connected. We encourage these communities to work on ontologies, harmonized formats, translators and connectors to facilitate transparent data exchange.
Published: 2022

18. Simulating the effect of flowering time on maize individual leaf area in contrasting environmental scenarios

Author: Lacube, Sebastien, Manceau, Loïc, Welcker, Claude, Millet, Emilie J, Gouesnard, Brigitte, Palaffre, Carine, Ribaut, Jean-Marcel, Hammer, Graeme, Parent, Boris, Tardieu, François, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wageningen University and Research [Wageningen] (WUR), 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), Unité expérimentale du maïs (BORDX ST-MARTIN UE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Queensland [Brisbane], ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010), ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011), European Project: 244374,EC:FP7:KBBE,FP7-KBBE-2009-3,DROPS(2010), 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 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
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Leaf growth, Light, Whole plant, whole plant, Zea mays, Wiskundige en Statistische Methoden - Biometris, Soil, genetic variability, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Mathematical and Statistical Methods - Biometris, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, model, Drought, AcademicSubjects/SCI01210, Temperature, Water, temperature, PE&RC, Research Papers, whole-plant, Europe, Plant Leaves, Plant—Environment Interactions, leaf growth, Genetic variability, light, Model
Abstract: The quality of yield prediction is linked to that of leaf area. We first analysed the consequences of flowering time and environmental conditions on the area of individual leaves in 127 genotypes presenting contrasting flowering times in fields of Europe, Mexico, and Kenya. Flowering time was the strongest determinant of leaf area. Combined with a detailed field experiment, this experiment showed a large effect of flowering time on the final leaf number and on the distribution of leaf growth rate and growth duration along leaf ranks, in terms of both length and width. Equations with a limited number of genetic parameters predicted the beginning, end, and maximum growth rate (length and width) for each leaf rank. The genotype-specific environmental effects were analysed with datasets in phenotyping platforms that assessed the effects (i) of the amount of intercepted light on leaf width, and (ii) of temperature, evaporative demand, and soil water potential on leaf elongation rate. The resulting model was successfully tested for 31 hybrids in 15 European and Mexican fields. It potentially allows prediction of the vertical distribution of leaf area of a large number of genotypes in contrasting field conditions, based on phenomics and on sensor networks., Flowering time affects all processes governing whole-plant leaf area, namely rates, durations, and sensitivity to environmental conditions. Genotype dependency was assessed via large phenomic datasets in field and controlled conditions.
Published: 2020

19. The case for improving crop carbon sink strength or plasticity for a CO2-rich future

Author: Matthew J. Paul, Michaël Dingkuhn, Denis Fabre, Bertrand Muller, Xinyou Yin, Delphine Luquet, 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Wageningen University and Research [Wageningen] (WUR), Rothamsted Research, strategic funding from the Biotechnological Sciences Research Council of the UK, Designing Future Wheat Strategic Programme (BB/P016855/1), and CGIAR Research Program Rice (CRP-RICE)
Subjects: 0106 biological sciences, 0301 basic medicine, Crop Physiology, F60 - Physiologie et biochimie végétale, Plant Science, Biology, Photosynthesis, 01 natural sciences, Acclimatization, Sink (geography), 03 medical and health sciences, Life Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, Génie génétique, 2. Zero hunger, Abiotic component, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, geography, Phenotypic plasticity, geography.geographical_feature_category, Carbon sink, genetic engineering, Ideotype, 15. Life on land, PE&RC, Amélioration des plantes, source-sink interactions, séquestration du carbone, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, Agronomy, Atmospheric CO2, 010606 plant biology & botany
Abstract: Atmospheric CO2 concentration [CO2] has increased from 260 to 280 μmol mol−1 (level during crop domestication up to the industrial revolution) to currently 400 and will reach 550 μmol mol−1 by 2050. C3 crops are expected to benefit from elevated [CO2] (e-CO2) thanks to photosynthesis responsiveness to [CO2] but this may require greater sink capacity. We review recent literature on crop e-CO2 responses, related source-sink interactions, how abiotic stresses potentially interact, and prospects to improve e-CO2 response via breeding or genetic engineering. Several lines of evidence suggest that e-CO2 responsiveness is related either to sink intrinsic capacity or adaptive plasticity, for example, involving enhanced branching. Wild relatives and old cultivars mostly showed lower photosynthetic rates, less downward acclimation of photosynthesis to e-CO2 and responded strongly to e-CO2 due to greater phenotypic plasticity. While reverting to such archaic traits would be an inappropriate strategy for breeding, we argue that substantial enhancement of vegetative sink vigor, inflorescence size and/or number and root sinks will be necessary to fully benefit from e-CO2. Potential ideotype features based on enhanced sinks are discussed. The generic 'feast-famine' sugar signaling pathway may be suited to engineer sink strength tissue-specifically and stage-specifically and help validate ideotype concepts. Finally, we argue that models better accounting for acclimation to e-CO2 are needed to predict which trait combinations should be targeted by breeders for a CO2-rich world.
Published: 2020

20. VviPLATZ1 is a major factor that controls female flower morphology determination in grapevine

Author: Mark R. Thomas, Pat Iocco-Corena, Laurent Torregrosa, Harley M. S. Smith, Jamila Chaïb, Don Mackenzie, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), HM. CLAUSE Iberica SA, Diversité, Adaptation et Amélioration de la Vigne [AGAP] (DAAV), 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)-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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Wine Australia (CSP 06/01), and CSIRO Agriculture and Food.
Subjects: Agricultural genetics, 0106 biological sciences, Genotype, Science, Dioecy, Stamen, General Physics and Astronomy, Flowers, Biology, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, Domestication, Magnoliopsida, Self incompatability, 03 medical and health sciences, Hermaphrodite, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Vitis, Allele, Gene, Alleles, Plant Proteins, 030304 developmental biology, Gene Editing, Genetics, 0303 health sciences, Multidisciplinary, Reproduction, Homozygote, fungi, Plant morphogenesis, food and beverages, Cell Differentiation, General Chemistry, Mating system, Phenotype, DNA-Binding Proteins, Differentiation, 010606 plant biology & botany
Abstract: Plant genetic sex determinants that mediate the transition to dioecy are predicted to be diverse, as this type of mating system independently evolved multiple times in angiosperms. Wild Vitis species are dioecious with individuals producing morphologically distinct female or male flowers; whereas, modern domesticated Vitis vinifera cultivars form hermaphrodite flowers capable of self-pollination. Here, we identify the VviPLATZ1 transcription factor as a key candidate female flower morphology factor that localizes to the Vitis SEX-DETERMINING REGION. The expression pattern of this gene correlates with the formation reflex stamens, a prominent morphological phenotype of female flowers. After generating CRISPR/Cas9 gene-edited alleles in a hermaphrodite genotype, phenotype analysis shows that individual homozygous lines produce flowers with reflex stamens. Taken together, our results demonstrate that loss of VviPLATZ1 function is a major factor that controls female flower morphology in Vitis., Unlike wild Vitis species, which produce either female or male flowers, modern grapevine cultivars form hermaphrodite flowers for self-pollination. Here, the authors report that the VviPLATZ1 (plant AT-rich sequence-and zinc-binding protein1) transcription factor functions in controlling female flower morphology determination.
Published: 2021

21. Physiological and genetic control of transpiration efficiency in African rice, Oryza glaberrima Steud

Author: Pablo Affortit, Branly Effa-Effa, Mame Sokhatil Ndoye, Daniel Moukouanga, Nathalie Luchaire, Llorenç Cabrera-Bosquet, Maricarmen Perálvarez, Raphaël Pilloni, Claude Welcker, Antony Champion, Pascal Gantet, Abdala Gamby Diedhiou, Baboucarr Manneh, Ricardo Aroca, Vincent Vadez, Laurent Laplaze, Philippe Cubry, Alexandre Grondin, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Centre national de la recherche scientifique et technologique (CENAREST), Centre d'Etude Regional Pour l'Amelioration de l'Adaptation A la Secheresse (CERAAS), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Africa Rice Center (AfricaRice), Sahel Regional, Africa Rice Center [Côte d'Ivoire] (AfricaRice), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE), Institut de Recherche pour le Développement (IRD), International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Institut de Recherche pour le Développement, the CGIAR Research Program (CRP) on rice-agrifood systems (RICE, 2017-2022), French Ministry of Higher Education (doctoral fellowship), Centre National de la Recherche Scientifique et Technologique of Gabon, ANR-17-MPGA-0011,ICARUS,Improve Crops in Arid Regions and future climates(2017), European Project: 731013 ,EPPN2020(2017), Agence Nationale de la Recherche (France), European Commission, and Centre National de la Recherche Scientifique (France)
Subjects: roots, Physiology, rice, food and beverages, Water, Oryza, Plant Transpiration, Plant Science, transpiration, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Plant Breeding, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, high-throughput phenotyping, Genome-Wide Association Study
Abstract: Improving crop water use efficiency, the amount of carbon assimilated as biomass per unit of water used by a plant, is of major importance as water for agriculture becomes scarcer. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand remain unknown. These traits were measured in 2019 in a panel of 147 African rice (Oryza glaberrima) genotypes known to be potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly contrasted genotypes in terms of biomass accumulation and transpiration confirmed these associations and suggested that root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency, and its residuals, with links to genes involved in water transport and cell wall patterning. Our data suggest that root-shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies., This work was supported by the Institut de Recherche pour le Développement, the CGIAR Research Program (CRP) on rice-agrifood systems (RICE, 2017-2022) and the Agence Nationale de la Recherche (grant ANR-17-MPGA-0011 to VV). Financial support by the Access to Research Infrastructures activity in the Horizon 2020 Programme of the EU (EPPN2020 Grant Agreement 731013) is gratefully acknowledged. PA was supported by a doctoral fellowship from the French Ministry of Higher Education. BEE was supported by the Centre National de la Recherche Scientifique et Technologique of Gabon. The authors acknowledge the IRD iTrop HPC (South Green Platform) at IRD Montpellier for providing HPC resources (https://bioinfo.ird.fr, http://www.southgreen.fr).
Published: 2021

22. The shoot system architecture of Vitis vinifera ssp. sativa

Author: Laurent Torregrosa, Alain Carbonneau, Jean-Jacques Kelner, Diversité, Adaptation et Amélioration de la Vigne [AGAP] (DAAV), 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)-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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF)
Subjects: Branching, Apical dominance, Horticulture, Biology, Acrotony, 03 medical and health sciences, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, Vitis vinifera, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Biomass (ecology), Syllepsis, 04 agricultural and veterinary sciences, 15. Life on land, Phyllotaxis, Prolepsis, Shoot, Shoot primary growth, 040103 agronomy & agriculture, Systems architecture, 0401 agriculture, forestry, and fisheries, Winter bud, Sink (computing)
Abstract: International audience; Conversely to many other woody perennial crops, the Vitis vinifera grapevine does not display self-supporting and limited-in-space aerial architectures, but rather develops extended shoot systems relying on external mechanical supports. This behavior results from both structural factors, i.e. stem anatomy, bud and phytomer organisation, and also specificities in the modulation of primary growth and branching, i.e. phyllotaxis, apical dominance and acrotony. To mitigate the most limiting biological properties for cultivation, the grapevine domestication need a range of practices to facilitate plant management and improve agronomic performances. The structure and the functioning of the shoot system regulate not only the potential of biomass accumulation and source/sink balance and but also the canopy microclimate with effects on fruit quality and organ fungus susceptibility. This paper reviews the main biological processes and management practices that regulate grapevine shoot system architecture and development, revisiting the associated terminology.
Published: 2021

23. Functional–Structural Plant Modeling Highlights How Diversity in Leaf Dimensions and Tillering Capability Could Promote the Efficiency of Wheat Cultivar Mixtures

Author: Emmanuelle Blanc, Pierre Barbillon, Christian Fournier, Christophe Lecarpentier, Christophe Pradal, Jérôme Enjalbert, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-20-PCPA-0006,MoBiDiv,Mobilizing and Breeding Intra and inter-specific crop Diversity for a systemic change towards pesticide-free agriculture(2020), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), and 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
Subjects: 0106 biological sciences, Canopy, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, F08 - Systèmes et modes de culture, [SDV]Life Sciences [q-bio], Plant Science, Agricultural engineering, Performance de culture, 01 natural sciences, F50 - Anatomie et morphologie des plantes, SB1-1110, sensitivity analysis, Cultivar, functional traits, Original Research, Mathematics, 2. Zero hunger, competition for light, Tallage, U10 - Informatique, mathématiques et statistiques, 04 agricultural and veterinary sciences, tillering plasticity, Anatomie végétale, Diversification, Trait, Interception, Assembly rules, Triticum aestivum, Crop, aerial architecture, variety mixture, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Variété, Leaf area index, Morphologie végétale, Modélisation des cultures, Plant culture, 15. Life on land, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Cropping, 010606 plant biology & botany
Abstract: International audience; Increasing the cultivated diversity has been identified as a major leverage for the agroecological transition as it can help improve the resilience of low input cropping systems. For wheat, which is the most cultivated crop worldwide in terms of harvested area, the use of cultivar mixtures is spreading in several countries, but studies have seldom focused on establishing mixing rules based on plant architecture. Yet, the aerial architecture of plants and the overall canopy structure are critical for field performance as they greatly influence light interception, plant interactions and yield. The very high number of trait combinations in wheat mixtures makes it difficult to conduct experimentations on this issue, which is why a modeling approach appears to be an appropriate solution. In this study, we used WALTer, a functional structural plant model (FSPM), to simulate wheat cultivar mixtures and try to better understand how differences between cultivars in key traits of the aerial architecture influence mixture performance. We simulated balanced binary mixtures of cultivars differing for different critical plant traits: final height, leaf dimensions, leaf insertion angle and tillering capability. Our study highlights the impact of the leaf dimensions and the tillering capability on the performance of the simulated mixtures, which suggests that traits impacting the plants' leaf area index (LAI) have more influence on the performance of the stand than traits impacting the arrangement of the leaves. Our results show that the performance of mixtures is very variable depending on the values of the explored architectural traits. In particular, the best performances were achieved by mixing cultivars with different leaf dimensions and different tillering capability, which is in agreement with numerous studies linking the diversity of functional traits in plant communities to their productivity. However, some of the worst performances were also achieved by mixing varieties differing in their aerial architecture, which suggests that diversity is not a sufficient criterion to design efficient mixtures. Overall, these results highlight the importance of simulation-based explorations for establishing assembly rules to design efficient mixtures.
Published: 2021

24. The unique and extreme vineyards of Santorini Island (Cyclades)

Author: Xyrafis, Efstratios Guillaume, DELOIRE, Alain, Petoumenou, Despoina, Paraskevopoulos, Ioannis, Biniari, Katerina, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and SupagroMontpellier
Subjects: Agriculture (General), Plant culture, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, S1-972, SB1-1110
Abstract: International audience; Own-rooted and phylloxera-free vines have been cultivated on the volcanic soil of Santorini for thousands of years. All this time, vines have been cultivated by using two traditional training systems, the ‘Κouloura’, and the ‘Κladeftiko’, which are well-adapted to the specific climatic conditions of the island. This first report aims to share the scarce existing knowledge on Santorini’s training and pruning systems, looking at some important quantitative and qualitative ripening parameters over four consecutive seasons (2017-2020) and revealing similarities regarding their adaptation to climate conditions on the island.; Des vignes franches de pied et exemptes de phylloxéra sont cultivées sur le sol volcanique de Santorin depuis des milliers d’années. Deux systèmes de conduite traditionnels ont toujours été utilisés pour cultiver ces vignes : ‘Κouloura’ et ‘Κladeftiko’, tous deux parfaitement adaptés aux conditions climatiques spécifiques de l’île. Cette première étude vise à partager les rares connaissances existant sur les systèmes de conduite et de taille de Santorin, par l’observation de certains paramètres quantitatifs et qualitatifs importants de la maturation, sur une période de quatre millésimes consécutifs (2017-2020). L’étude révèle des similitudes concernant l’adaptation de ces systèmes aux conditions climatiques de l’île.
Published: 2021

25. Rappels sur la vigne et le déficit hydrique. Quels leviers au vignoble à courts et moyens termes ?

Author: DELOIRE, Alain, Pellegrino, Anne, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SupagroMontpellier, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract: International audience; In the context of climate change, most wine-growing regions are experiencing periods of water deficit, or even water stress, as well as heatwaves. The proven increase in average temperatures has led to a shift in the phenological stages of the vine. In the Mediterranean regions of the south of France, more frequent thunderstorms in the fall and lower rainfall in winter have led to reduced filling of soil water holding capacity before budburst. In addition, rainfall over the growing cycle is decreasing while evapotranspiration is increasing. This combination of climate changes (rainfall × temperature) has an impact on vine cultural practices, berry composition and the aromatic profile of wines. As such, it seems useful to share a bullet-point list of the possible consequences of increased water deficit and heat peaks on the physiology of the vine and its fruit and to point out some potential solutions in the short and medium term, especially when planting young vines.; Dans le cadre de l’évolution du climat, la majorité des régions viticoles subissent des périodes de contraintes hydriques voire de stress hydrique et des vagues de chaleurs. L’augmentation des températures moyennes est avérée, décalant les stades phénologiques de la vigne. Dans les régions méditerranéennes du sud de la France, les orages plus fréquents en automne et la plus faible pluviométrie en hiver réduisent le remplissage de la réserve utile des sols pré débourrement. Par ailleurs, la pluviométrie sur le cycle cultural diminue alors que l’évapotranspiration augmente. L’ensemble de ces évolutions climatiques (pluies x températures) a des effets sur le fonctionnement de la vigne, la composition des baies et le profil aromatique des vins. À ce titre, il nous semble intéressant de partager sous forme de « dot points » les conséquences possibles de l’augmentation du déficit hydrique et des pics de chaleur sur la physiologie de la vigne et de ses fruits et de rappeler quelques solutions potentielles à mettre en œuvre à court et moyen terme, notamment lors de la plantation de jeunes vignes.
Published: 2021

26. Breeding custom‐designed crops for improved drought adaptation

Author: Rajeev K. Varshney, Rutwik Barmukh, Manish Roorkiwal, Yiping Qi, Jana Kholova, Roberto Tuberosa, Matthew P. Reynolds, Francois Tardieu, Kadambot H. M. Siddique, International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Murdoch University, University of Maryland [College Park], University of Maryland System, University of Bologna, International Maize and Wheat Improvement Center (CIMMYT), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The University of Western Australia (UWA), Bill & Melinda Gates Foundation, USA, Department of Biotechnology, Ministry of Science & Technology, and Ministry of Agriculture & Farmers Welfare of Government of India, Science & Engineering Research Board (SERB) of Department of Science & Technology (DST), Government of India for National Fellowship (SB/S9/Z-13/2019), Council of Scientific and Industrial Research (CSIR), Government of India, for the award of a research fellowship, and NSF grants (IOS-1758745 and IOS2029889) and USDA-NIFA grants (2018-33522-28789, 2020-33522-32274 and 2020-70029-33161).
Subjects: 2. Zero hunger, root system architecture, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Genomic breeding, drought physiology, fungi, food and beverages, 15. Life on land, Biochemistry, context-dependent optimization, 03 medical and health sciences, 0302 clinical medicine, 13. Climate action, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], speed breeding, Genetics, genome editing, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: International audience; The current pace of crop improvement is inadequate to feed the burgeoning human population by 2050. Higher, more stable and sustainable crop production is required against a backdrop of drought stress, which causes significant losses in crop yields. Tailoring crops for drought adaptation may hold the key to address these challenges and provide resilient production systems for future harvests. Understanding the genetic and molecular landscape of the functionality of alleles associated with adaptive traits will make designer crop breeding the prospective approach for crop improvement. Here, we highlight the potential of genomics technologies combined with crop physiology for high-throughput identification of the genetic architecture of key drought-adaptive traits and explore innovative genomic breeding strategies for designing future crops.
Published: 2021

27. Ontological Formalisation of Mathematical Equations for Phenomic Data Exploitation

Author: Felipe Vargas-Rojas, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Ruben Verborgh, Anastasia Dimou, Aidan Hogan, Claudia d'Amato, Ilaria Tiddi, Arne Bröring, Simon Mayer, Femke Ongenae, Riccardo Tommasini, Mehwish Alam, and ANR-16-CONV-0004,DIGITAG,Institut Convergences en Agriculture Numérique(2016)
Subjects: Structure (mathematical logic), Mathematical equations, 0303 health sciences, Information retrieval, Computer science, Conversion of units, Inference, 04 agricultural and veterinary sciences, Domain (software engineering), [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Metadata, 03 medical and health sciences, Phenomics, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ontological reasoning, Plant phenomics, Semantic Web, 030304 developmental biology
Abstract: International audience; In recent years, plant phenomics community has adopted Semantic Web technologies in order to harmonise heterogeneous, multi-scale and multi-source datasets. Semantic Web provides inference services for representing logic relationships in an unambiguous, homogeneous and clean manner, which enhances data harmonisation. However, mathematical relationships involving numerical attributes are poorly formalised, despite the fact that they are supported for a theoretical and well-defined structure. For instance, whilst unit ontologies (e.g. UO, OM, QUDT) provide relationships and annotations to perform unit conversion, they are not effectively used for automating the integration of heterogeneous measurements. Here we propose an ontological framework for representing mathematical equations supporting the automatised use of inference services, metadata, domain ontologies, and the internal structure of mathematical equations. This approach is evaluated using two plant phenomics case studies involving the calculation of unit conversions and thermal time.
Published: 2021

28. Impact de la variabilité intra- et inter-spécifique des réponses à la température et au déficit hydrique dans la diversité des scénarios E x M

Author: Parent, Boris, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM), FRA., Alain Ourry, and Ausset, Aurélien
Subjects: déficit hydrique, température, temperature, variabilité intra-et inter-spécifique, scénarios E x M, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, E x M scenarios, intra- and inter-specific variability, water deficit
Abstract: Impact de la variabilité intra-et inter-spécifique des réponses à la température et au déficit hydrique dans la diversité des scénarios E x M
Published: 2021

29. An exploration of the variability of physiological responses to soil drying in relation with C/N balance across three species of the under‐utilized genus Vigna

Author: Julie Guiguitant, Hélène Marrou, Martha Ramirez, Michel Edmond Ghanem, Thomas R. Sinclair, Denis Vile, Deepti Pradhan, 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Mohammed VI Polytechnic University [Marocco] (UM6P), AgroBioSciences, Université Mohammed VI Polytechnique, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), United States Department of Agriculture (USDA), This work has been funded with the support of the European Union through the Arimnet program and of the Occitanie Province in France awarding doctoral grant. The authors particularly acknowledge the French Academy of Agriculture for supporting travel expenses to the USA, awarding the Jean and Marie-Louise Dufresnoy Grant., European Project: 618127,EC:FP7:KBBE,FP7-ERANET-2013-RTD,ARIMNET2(2014), 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, 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 Agro - Montpellier SupAgro, and Université Mohammed VI Polytechnique [Ben Guerir] (UM6P)
Subjects: 0106 biological sciences, 0301 basic medicine, leaf traits, Physiology, Radiata, Plant Science, 01 natural sciences, transpiration, Crop, Vigna, Soil, 03 medical and health sciences, Genus, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Soil drying, Transpiration, 2. Zero hunger, biology, response to soil drying, Fabaceae, Cell Biology, General Medicine, 15. Life on land, biology.organism_classification, Droughts, Plant Leaves, 030104 developmental biology, Taxon, Agronomy, N fixation, 010606 plant biology & botany
Abstract: International audience; The genus Vigna (Fabaceae) is an agriculturally important taxon, which includes several crop species such as cowpea (Vigna unguiculata L), mung bean (Vigna radiata) and azuki bean (Vigna angularis). Most studies have focused on cowpea (Vigna unguiculata (L.) as a drought‐resistant crop, although insights on the mechanisms that confer this species the ability to grow in dry environment are still not fully resolved. The diversity of this rich genus has been overlooked in many physiological studies. This study explores the physiological mechanisms of response to soil drying (N2 fixation, transpiration rate and changes in C and N allocation) across three species of the Vigna genus: Vigna radiata, Vigna unguiculata, Vigna vexillata (tuber cowpea). A significant variability among the studied Vigna accessions was found for the threshold in decline of N2 fixation with soil drying. Less variability was observed in the transpiration threshold. Through the analysis of leaf traits variation under well‐watered and water‐deficit conditions, we were able to relate the variability in N2 fixation and transpiration response to C/N metabolism modifications resulting in different allocation of carbon and nitrogen to leaves under water deficit.
Published: 2021

30. To clean or not to clean phenotypic datasets for outlier plants in genetic analyses?

Author: François Tardieu, Claude Welcker, Santiago Alvarez Prado, Llorenç Cabrera-Bosquet, Isabelle Sanchez, Antonin Grau, Nadine Hilgert, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), 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), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011), European Project: 244374,EC:FP7:KBBE,FP7-KBBE-2009-3,DROPS(2010), European Project: 731013 ,EPPN2020(2017), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), and Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Quantitative Trait Loci, Genome-wide association study, Plant Science, genetic analysis, Biology, Quantitative trait locus, eXtra Botany, 01 natural sciences, Genetic analysis, Polymorphism, Single Nucleotide, 03 medical and health sciences, fréquence des allèles, statistical analysis, Gene Frequency, faux positif, Statistics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Allele, Allele frequency, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Alleles, Genetic association, Plant Proteins, Vegetal Biology, analyse statistique, outliers, Biologie du développement, Outliers, Phenomics, Quantitative trait loci, Statistical analysis, food and beverages, nutritional and metabolic diseases, phenomics, Development Biology, Minor allele frequency, plateforme de phénotypage, Viewpoints, 030104 developmental biology, Outlier, Biologie végétale, analyse génétique, 010606 plant biology & botany, Genome-Wide Association Study
Abstract: Excluding outlier plants (biological replicates deviating from the expected distribution on a multi-criteria basis) from phenotypic datasets is necessary to avoid false-positive associations between genome markers and traits., Based on case studies, we discuss the extent to which genome-wide association studies (GWAS) are affected by outlier plants, i.e. those deviating from the expected distribution on a multi-criteria basis. Using a raw dataset consisting of daily measurements of leaf area, biomass, and plant height for thousands of plants, we tested three different cleaning methods for their effects on genetic analyses. No-cleaning resulted in the highest number of dubious quantitative trait loci, especially at loci with highly unbalanced allelic frequencies. A trade-off was identified between the risk of false-positives (with no-cleaning and/or a low threshold for minor allele frequency) and the risk of missing interesting rare alleles. Cleaning can lower the risk of the latter by making it possible to choose a higher threshold in GWAS.
Published: 2019

31. Do metabolic changes underpin physiological responses to water limitation in alfalfa (Medicago sativa) plants during a regrowth period?

Author: Llorenç Cabrera-Bosquet, José Luis Araus, Iker Aranjuelo, Gemma Molero, Guillaume Tcherkez, Caroline Mauve, Salvador Nogués, Regina Roca, European Commission, Ministerio de Ciencia y Tecnología (España), Consejo Superior de Investigaciones Científicas (España), Ministerio de Educación y Ciencia (España), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Barcelona, Australian National University (ANU), Serveis Cientificotècnics (SCT), Universitat de Barcelona (UB), Plateforme Métabolisme-Métabolome (IFR87), Université Paris-Sud - Paris 11 (UP11), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA), the Spanish Ministry of Science and Technology (CGL2009-13079-C02), i-COOP-suelos y legumbres (2016SU0016) funded by the National Research Council, (Programa Nacional de Formacion de Personal Universitario, AP2005-2916) sponsored by the Spanish Ministry of Education and Science., European Project: 602139,EC:FP7:HEALTH,FP7-HEALTH-2013-INNOVATION-1,PERMED(2013), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Universitat de Barcelona
Subjects: Physiology, Water stress, Metabolite, Sequeres, 0208 environmental biotechnology, Growth (Plants), Soil Science, Crops, 02 engineering and technology, Photosynthesis, chemistry.chemical_compound, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Proline, Medicago sativa, Creixement (Plantes), Earth-Surface Processes, Water Science and Technology, 2. Zero hunger, chemistry.chemical_classification, Pinitol, Chemistry, Alfalfa, fungi, food and beverages, 04 agricultural and veterinary sciences, Metabolism, 15. Life on land, Droughts, 020801 environmental engineering, Amino acid, Conreu, 15N-labeling, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Photorespiration, Agronomy and Crop Science, Metabolite profile
Abstract: Drought is one of the most limiting factors on crop productivity under Mediterranean conditions, where the leguminous species alfalfa (Medicago sativa L.) is extensively cultivated. Whereas the effect of drought on plant performance has been widely described at leaf and nodule levels, less attention has been given to plant-nodule interactions and their implication on metabolites exchange during a regrowth period, when water is limiting. For this purpose, physiological characterization and metabolite profiles in different plant organs and nodules were undertaken under water deficit, including regrowth after removal of aerial parts. In order to study in more detail how nitrogen (N) metabolism was affected by water stress, plants were labelled with N-enriched isotopic air (15N2) using especially designed chambers. Water stress affected negatively water status and photosynthetic machinery. Metabolite profile and isotopic composition analyses revealed that, water deficit induced major changes in the accumulation of amino acids (proline, asparagine, histidine, lysine and cysteine), carbohydrates (sucrose, xylose and pinitol) and organic acids (fumarate, succinate and maleic acid) in the nodules in comparison with other organs. The lower 15N-labeling observed in serine, compared with other amino acids, was related with its high turnover rate, which in turn, indicates its potential implication in photorespiration. Isotopic analysis of amino acids also revealed that proline synthesis in the nodule was a local response to water stress and not associated with a feedback inhibition from the leaves. Water deficit induced extensive reprogramming of whole-plant C and N metabolism, including when the aerial part was removedto trigger regrowth., This study was supported in part by the European research project PERMED (INCO- CT-2004-509140), the Spanish Ministry of Science and Technology (CGL2009-13079-C02) and i-COOP-suelos y legumbres (2016SU0016) funded by the National Research Council. GM was the recipient of a doctoral fellowship (Programa Nacional de Formación de Personal Universitario, AP2005–2916) sponsored by the Spanish Ministry of Education and Science.
Published: 2019

32. Climate change impact and adaptation for wheat protein

Author: Mohamed Jabloun, Pierre Martre, Garry O'Leary, Dominique Ripoche, Bruno Basso, Pramod K. Aggarwal, Daniel Wallach, Matthew P. Reynolds, Marijn van der Velde, John R. Porter, Heidi Webber, Enli Wang, Frank Ewert, Joost Wolf, Christian Klein, Belay T. Kassie, Christian Biernath, Margarita Garcia-Vila, M. Ali Babar, Pierre Stratonovitch, Yujing Gao, Glenn J. Fitzgerald, Davide Cammarano, Bing Liu, Peter J. Thorburn, Fulu Tao, Andrew J. Challinor, Reimund P. Rötter, Christine Girousse, Zhigan Zhao, Christoph Müller, Ann-Kristin Koehler, Jørgen E. Olesen, Elias Fereres, Iwan Supit, Andrea Maiorano, Marco Bindi, Sebastian Gayler, Kurt Christian Kersebaum, Giacomo De Sanctis, Alex C. Ruane, Rosella Motzo, Juraj Balkovic, Manuel Montesino San Martin, Roberto Ferrise, Mikhail A. Semenov, Claudio O. Stöckle, Soora Naresh Kumar, Gerrit Hoogenboom, Benjamin Dumont, Ehsan Eyshi Rezaei, Mukhtar Ahmed, Senthold Asseng, Thilo Streck, Yan Zhu, R. Cesar Izaurralde, Katharina Waha, Ahmed M. S. Kheir, Taru Palosuo, Liujun Xiao, Sara Minoli, Eckart Priesack, Heidi Horan, Curtis D. Jones, Francesco Giunta, Zhao Zhang, Claas Nendel, International Food Policy Research Institute (US), CGIAR (France), European Commission, Institut National de la Recherche Agronomique (France), National Natural Science Foundation of China, Federal Ministry of Food and Agriculture (Germany), Biotechnology and Biological Sciences Research Council (UK), Innovation Fund Denmark, China Scholarship Council, Ministero delle Politiche Agricole Alimentari e Forestali, Academy of Finland, Finnish Ministry of Agriculture and Forestry, Federal Ministry of Education and Research (Germany), Department of Agriculture and Water Resources (Australia), University of Melbourne, Grains Research and Development Corporation (Australia), National Institute of Food and Agriculture (US), German Research Foundation, Gorgan University, Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), European Food Safety Authority = Autorité européenne de sécurité des aliments, Tropical Plant Production and Agricultural Systems Modelling (TROPAGS), Georg-August-University = Georg-August-Universität Göttingen, Centre for Biodiversity and Sustainable Land-use [University of Göttingen] (CBL), Department of Economic Drt and Resources, Grains Innovation Park, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, Faculty of Veterinary and Agricultural Science [Melbourne], Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Department of Agricultural Sciences, University of Naples Federico II = Università degli studi di Napoli Federico II, World Food Crops Breeding, Department of Agronomy, IFAS, University of Florida [Gainesville] (UF), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Soils, Water and Environment Research Institute, Agricultural Research Center (ARC), Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), International Maize and Wheat Improvement Centre [Inde] (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Biological Systems Engineering, University of Wisconsin-Madison, Department of Agronomy, University of El-Tarf, Ecosystem Services and Management Program, International Institute for Applied Systems Analysis (IIASA), Department of Soil Science, Faculty of Natural Sciences, Comenius University in Bratislava, W. K. Kellogg Biological Station (KBS), Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Department of Earth and Environmental Sciences [Ann Arbor], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Institute of Biochemical Plant Pathology, Research Center for Environmental Health, Helmholtz Zentrum München = German Research Center for Environmental Health, Department of Agri‐food Production and Environmental Sciences (DISPAA), Università degli Studi di Firenze = University of Florence (UniFI), The James Hutton Institute, Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, Collaborative Research Program from CGIAR and Future Earth on Climate Change, Agriculture and Food Security (CCAFS), International Center for Tropical Agriculture, GMO Unit, European Food Safety Authority, Department Terra & AgroBioChem, Gembloux Agro‐Bio Tech, Université de Liège, Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Department of Crop Sciences, Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Soil Science and Land Evaluation, University of Hohenheim, Food Systems Institute [Gainesville] (UF|IFAS), Department of Geographical Sciences, College Park, University of Maryland [College Park], University of Maryland System-University of Maryland System, Texas A and M AgriLife Research, Texas A&M University System, Department of Agroecology, Aarhus University [Aarhus], Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Institute of Biochemical Plant Pathology [Neuherberg], German Research Center for Environmental Health - Helmholtz Center München (GmbH), National Engineering and Technology Center for Information Agriculture, Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricutural University, Member of the Leibniz Association, Potsdam Institute for Climate Impact Research (PIK), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Centre for Environment Science and Climate Resilient Agriculture [New Delhi], Indian Agricultural Research Institute (IARI), Natural Resources Institute Finland (LUKE), 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), University of Lincoln, Agroclim (AGROCLIM), Institut National de la Recherche Agronomique (INRA), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), Water & Food and Water Systems & Global Change Group, Wageningen University and Research [Wageningen] (WUR), Institute of geographical sciences and natural resources research [CAS] (IGSNRR), Chinese Academy of Sciences [Beijing] (CAS), Joint Research Centre (IPTS), Commission Européenne, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), CSIRO Agriculture and Food (CSIRO), Plant Production Systems, State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University (BNU), Department of Agronomy and Biotechnology, China Agricultural University (CAU), National Research Foundation for the Doctoral Program of Higher Education of China, Grant/Award Number: 20120097110042, International Food Policy, European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Georg-August-University [Göttingen], Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen - Georg-August-Universität Göttingen, University of Naples Federico II, Helmholtz-Zentrum München (HZM), Universtiy of Florence, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Natural Resources Institute Finland, 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), Wageningen University, Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Agricultural & Biological Engineering Department, University of Florida [Gainesville], Georg-August-Universität Göttingen, University of Goettingen, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Research Program on Climate Change, Agriculture and Food Security, BISA‐CIMMYT, Consultative Group on International Agricultural Research (CGIAR), Comenius University [Bratislava], Helmholtz Zentrum München, Institute of Crop Science and Resource Conservation INRES, University of Bonn, IAS‐CSIC, Universidad de Cordoba, Institute for Sustainable Food Systems, Texas A&M AgriLife Research and Extension Center, Aarhus University, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), UE Agroclim (UE AGROCLIM), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Wageningen University and Research Center (WUR), Beijing Normal University, and China Agricultural University
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, 010504 meteorology & atmospheric sciences, Water en Voedsel, 01 natural sciences, grain protein, adaptation au milieu, climate change adaptation, climate change impact, food security, wheat, Co2 concentration, adaptation to the environment, Triticum, General Environmental Science, 2. Zero hunger, changement climatique, Global and Planetary Change, Food security, Ecology, Temperature, food and beverages, Adaptation, Physiological, Droughts, Nitrogen, Climate Change, Climate change, 010603 evolutionary biology, blé, Crop production, Food Quality, Grain quality, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Environmental Chemistry, Grain Proteins, global change, 0105 earth and related environmental sciences, WIMEK, Water and Food, Global change, Carbon Dioxide, Models, Theoretical, 15. Life on land, Agronomy, 13. Climate action, Grain yield, Environmental science, Water Systems and Global Change, Protein concentration
Abstract: Wheat grain protein concentration is an important determinant of wheat quality for human nutrition that is often overlooked in efforts to improve crop production. We tested and applied a 32‐multi‐model ensemble to simulate global wheat yield and quality in a changing climate. Potential benefits of elevated atmospheric CO2 concentration by 2050 on global wheat grain and protein yield are likely to be negated by impacts from rising temperature and changes in rainfall, but with considerable disparities between regions. Grain and protein yields are expected to be lower and more variable in most low‐rainfall regions, with nitrogen availability limiting growth stimulus from elevated CO2. Introducing genotypes adapted to warmer temperatures (and also considering changes in CO2 and rainfall) could boost global wheat yield by 7% and protein yield by 2%, but grain protein concentration would be reduced by −1.1 percentage points, representing a relative change of −8.6%. Climate change adaptations that benefit grain yield are not always positive for grain quality, putting additional pressure on global wheat production., B.L received support from the International Food Policy Research Institute (IFPRI) through the Global Futures and Strategic Foresight project, the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS) and the CGIAR Research Program on Wheat. A.M. received support from the EU Marie Curie FP7 COFUND People Programme, through an AgreenSkills fellowship under grant agreement no. PCOFUND‐GA‐2010‐267196. PM, A.M., D.R., and D.W. acknowledge support from the FACCE JPI MACSUR project (031A103B) through the metaprogram Adaptation of Agriculture and Forests to Climate Change (AAFCC) of the French National Institute for Agricultural Research (INRA). L.X. and Y.Z. were supported by the National High‐Tech Research and Development Program of China (2013AA100404), the National Natural Science Foundation of China (31271616), the National Research Foundation for the Doctoral Program of Higher Education of China (20120097110042), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). F.T. and Z.Z. were supported by the National Natural Science Foundation of China (41571088, 41571493 and 31561143003). R.R. received support from the German Ministry for Research and Education (BMBF) through project SPACES‐LLL. Rothamsted Research receives support from the Biotechnology and Biological Sciences Research Council (BBSRC) Designing Future Wheat programme [BB/P016855/1]. M.J. and J.E.O. were supported by Innovation Fund Denmark through the MACSUR project. L.X. and Y.G. acknowledge support from the China Scholarship Council. M.B and R.F. were funded by JPI FACCE MACSUR2 through the Italian Ministry for Agricultural, Food and Forestry Policies and thank A. Soltani from Gorgan Univ. of Agric. Sci. & Natur. Resour. for his support. R.P.R., T.P., and F.T. received financial support from the FACCE MACSUR project funded through the Finnish Ministry of Agriculture and Forestry (MMM) and from the Academy of Finland through the projects NORFASYS (decision nos. 268277 and 292944) and PLUMES (decision nos. 277403 and 292836). K.C.K. and C.N. received support from the German Ministry for Research and Education (BMBF) within the FACCE JPI MACSUR project. S.M. and C.M. acknowledge financial support from the MACMIT project (01LN1317A) funded through BMBF. G.J.O. and G.J.F. acknowledge support from the Victorian Department of Economic Development, Jobs, Transport and Resources, the Australian Department of Agriculture and Water Resources, The University of Melbourne and the Grains Research Development Corporation, Australia. P.K.A.'s work was implemented as part of the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), which is carried out with support from the CGIAR Trust Fund and through bilateral funding agreements. For details please visit https://ccafs.cgiar.org/donors. The views expressed in this document cannot be taken to reflect the official opinions of these organizations.. B.B. received financial support from USDA NIFA‐Water Cap Award 2015‐68007‐23133. F.E. acknowledges support from the FACCE JPI MACSUR project through the German Federal Ministry of Food and Agriculture (2815ERA01J) and from the German Science Foundation (project EW 119/5‐1).
Published: 2019

33. Leaf elongation response to blue light is mediated by stomatal-induced variations in transpiration in Festuca arundinacea

Author: Didier Combes, Pierre Martre, Abraham J. Escobar-Gutiérrez, Jean-Louis Durand, Romain Barillot, Tom De Swaef, Cédric Perrot, Elzbieta Frak, Eric Roy, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Research Institute for Agricultural, Fisheries and Food (ILVO), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Region Poitou-Charentes, European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), 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: Festuca, 0106 biological sciences, 0301 basic medicine, Vapor Pressure, Physiology, Vapour Pressure Deficit, Water flow, stomata, Irradiance, Tiller (botany), Plant Science, 01 natural sciences, hydraulic model, transpiration, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transpiration, biology, Chemistry, fungi, Water, food and beverages, Plant Transpiration, plant hydraulics, biology.organism_classification, photomorphogenesis, Plant Leaves, Horticulture, 030104 developmental biology, grasses, leaf elongation, Plant Stomata, Photomorphogenesis, Elongation, light, Festuca arundinacea, 010606 plant biology & botany, Blue light
Abstract: Reduced blue light irradiance is known to enhance leaf elongation rate (LER) in grasses, but the mechanisms involved have not yet been elucidated. We investigated whether leaf elongation response to reduced blue light could be mediated by stomata-induced variations of plant transpiration. Two experiments were carried out on tall fescue in order to monitor LER and transpiration under reduced blue light irradiance. Additionally, LER dynamics were compared with those observed in the response to vapour pressure deficit (VPD)-induced variations of transpiration. Finally, we developed a model of water flow within a tiller to simulate the observed short-term response of LER to various transpiration regimes. LER dramatically increased in response to blue light reduction and then reached new steady states, which remained higher than the control. Reduced blue light triggered a simultaneous stomatal closure which induced an immediate decrease of leaf transpiration. The hydraulic model of leaf elongation accurately predicted the LER response to blue light and VPD, resulting from an increase in the growth-induced water potential gradient in the leaf growth zone. Our results suggest that the blue light signal is sensed by stomata of expanded leaves and transduced to the leaf growth zone through the hydraulic architecture of the tiller.
Published: 2021

34. Physiological roles of Casparian strips and suberin in the transport of water and solutes

Author: Marc S. Frenger, Christopher Hidalgo-Shrestha, Zoe Ribeyre, Patrick Diehl, Christophe Maurel, Thierry Simonneau, David E. Salt, Guilhem Reyt, Rochus Franke, Myriam Dauzat, Bertrand Muller, Monica Calvo-Polanco, Yann Boursiac, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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), Universidad de Salamanca, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Nottingham, UK (UON), University of Bonn, ERA-NET Coordinating Action in Plant Sciences program project ERACAPS13.089_RootBarriers, the German Research Foundation (DFG, grant FR 1721/2-1 to R.B.F), FEDER-Junta de Castilla y León, CLU-2018-04., Transnational Cooperation within the PLANT-KBBE Initiative, with funding from the German Federal Ministry of Education to RBF, ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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 Universität Bonn = University of Bonn
Subjects: 0106 biological sciences, water transport, Arabidopsis thaliana, Physiology, Arabidopsis, Aquaporin, Plant Science, solutes diffusion, 01 natural sciences, Plant Roots, 03 medical and health sciences, suberin, Suberin, Cell Wall, Casparian strips, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, aquaporins, 030304 developmental biology, 0303 health sciences, Water transport, biology, Chemistry, fungi, Plant physiology, food and beverages, Water, biology.organism_classification, Lipids, Apoplast, apoplastic barriers, Biophysics, root hydraulic conductivity, Endodermis, Casparian strip, 010606 plant biology & botany
Abstract: International audience; The formation of Casparian strips (CS) and the deposition of suberin at the endodermis of plant roots are thought to limit the apoplastic transport of water and ions. We investigated the specific role of each of these apoplastic barriers in the control of hydro-mineral transport by roots and the consequences on shoot growth.A collection of Arabidopsis thaliana mutants defective in suberin deposition and/or CS development was characterized under standard conditions using a hydroponic system and the Phenopsis platform.Mutants altered in suberin deposition had enhanced root hydraulic conductivity, indicating a restrictive role for this compound in water transport. In contrast, defective CS directly increased solute leakage and indirectly reduced root hydraulic conductivity. Defective CS also led to a reduction in rosette growth, which was partly dependent on the hydro-mineral status of the plant. Ectopic suberin was shown to partially compensate for defective CS phenotypes. Altogether, our work shows that the functionality of the root apoplastic diffusion barriers greatly influences the plant physiology, and that their integrity is tightly surveyed.
Published: 2021

35. Le flétrissement, la perte d’eau et la mort cellulaire des baies de raisin : un défi grandissant pour les viticulteurs dans le contexte du changement climatique

Author: DELOIRE, Alain, Rogiers, Suzy, Šuklje, Katja, Antalick, Guillaume, Zeyu, Xiao, Pellegrino, Anne, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and SupagroMontpellier
Subjects: [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, lcsh:Agriculture (General), lcsh:Plant culture, lcsh:S1-972
Abstract: International audience; Late ripening berry dehydration is an important phenomenon that occurs through grape berry water loss due to the alteration of the fruit water budget when transpiration and potential water back ﬂow to the plant exceed the import of water into the berry through the phloem and xylem. Berry shrivelling can have a signiﬁcant economic impact, reducing yields by ≥25 % with consequences on berry composition and the resulting wine. Its occurrence and consequences are expected to increase due to predicted climate change, shifting grape development and ripening into warmer periods (i.e., heat waves and drought events).; La déshydratation des baies en fin de maturation est un phénomène majeur causé par la perte d’eau des baies par suite d’une altération de leur balance hydrique. Cette altération apparaît quand les flux liés à la transpiration et au reflux potentiel d’eau vers la plante excèdent ceux de l’entrée d’eau dans la baie via le phloème et le xylème. Le flétrissement des baies peut avoir un impact économique significatif, avec une réduction des rendements ≥25 %, et des conséquences sur la composition des baies et sur le vin qui en résulte. L’apparition de ce phénomène et ses conséquences seraient amenées à s’intensifier à cause du changement climatique prévu, lequel causerait un décalage des stades de développement et de maturation des baies vers des périodes plus chaudes (c’est-à-dire des canicules et des épisodes de sécheresse).
Published: 2021

36. Cache-aware scheduling of scientific workflows in a multisite cloud

Author: Esther Pacitti, François Tardieu, Christophe Pradal, Gaëtan Heidsieck, Patrick Valduriez, Daniel de Oliveira, Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Universidade Federal Fluminense [Rio de Janeiro] (UFF), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, ANR-16-CONV-0004,DIGITAG,Institut Convergences en Agriculture Numérique(2016), ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Centre 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), and Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Multisite cloud, Exploit, Computer Networks and Communications, Computer science, Distributed computing, Workflow System, Cloud computing, 02 engineering and technology, Reuse, Scheduling (computing), Distributed Caching, processus, Workflow Scheduling, 0202 electrical engineering, electronic engineering, information engineering, Code (cryptography), Workflow scheduling, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], business.industry, U10 - Informatique, mathématiques et statistiques, Scientific Workflow, 020206 networking & telecommunications, Informatique, Workflow, Hardware and Architecture, 020201 artificial intelligence & image processing, Cache, business, Software
Abstract: International audience; Many scientific experiments today are performed using scientific workflows, which become more and more data-intensive. We consider the efficient execution of such workflows in a multisite cloud, leveraging heterogeneous resources available at multiple geo-distributed data centers. Since it is common for workflow users to reuse code or data from previous workflows, a promising approach for efficient workflow execution is to cache intermediate data in order to avoid re-executing entire workflows. However, caching intermediate data and scheduling workflows to exploit such caching in a multisite cloud is complex. In particular, workflow scheduling must be cache-aware, in order to decide whether reusing cache data or re-executing workflows entirely. In this paper, we propose a solution for cache-aware scheduling of scientific workflows in a multisite cloud. Our solution includes a distributed and parallel architecture and new algorithms for adaptive caching, cache site selection, and dynamic workflow scheduling. We implemented our solution in the OpenAlea workflow system, together with cache-aware distributed scheduling algorithms. Our experimental evaluation in a three-site cloud with a real application in plant phenotyping shows that our solution can yield major performance gains, reducing total time up to 42% with 60% of the same input data for each new execution.
Published: 2021

37. Natural variation at FLM splicing has pleiotropic effects modulating ecological strategies in Arabidopsis thaliana

Author: Justine Bresson, Elodie Marchadier, Mathieu Hanemian, Cyrille Violle, Isabelle Gy, Olivier Loudet, François Vasseur, Elodie Gilbault, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-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), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), 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), 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), European Project: 243359,EC:FP7:ERC,ERC-2009-StG,DECODE(2010), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), 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, 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 Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro
Subjects: 0301 basic medicine, Arabidopsis, General Physics and Astronomy, 02 engineering and technology, Gene Expression Regulation, Plant, lcsh:Science, education.field_of_study, Multidisciplinary, Temperature, food and beverages, Genetic Pleiotropy, 021001 nanoscience & nanotechnology, Phenotype, 0210 nano-technology, Plant genetics, RNA Splicing, Science, Quantitative Trait Loci, Population, MADS Domain Proteins, Locus (genetics), Biology, Article, Evolutionary genetics, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Plant development, Genetic variation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Allele, education, Alleles, Arabidopsis Proteins, Human evolutionary genetics, fungi, Genetic Variation, General Chemistry, Quantitative genetics, 15. Life on land, biology.organism_classification, Introns, Plant Leaves, Natural variation in plants, 030104 developmental biology, Evolutionary biology, lcsh:Q
Abstract: Investigating the evolution of complex phenotypes and the underlying molecular bases of their variation is critical to understand how organisms adapt to their environment. Applying classical quantitative genetics on a segregating population derived from a Can-0xCol-0 cross, we identify the MADS-box transcription factor FLOWERING LOCUS M (FLM) as a player of the phenotypic variation in plant growth and color. We show that allelic variation at FLM modulates plant growth strategy along the leaf economics spectrum, a trade-off between resource acquisition and resource conservation, observable across thousands of plant species. Functional differences at FLM rely on a single intronic substitution, disturbing transcript splicing and leading to the accumulation of non-functional FLM transcripts. Associations between this substitution and phenotypic and climatic data across Arabidopsis natural populations, show how noncoding genetic variation at a single gene might be adaptive through pleiotropic effects., FLOWERING LOCUS M (FLM) is known as a repressor of Arabidopsis flowering. Here, the authors show that a single intronic substitution of FLM modulates leaf color and plant growth strategy along the leaf economics spectrum, as well as plays a role in plant adaptation.
Published: 2020

38. Enabling reusability of plant phenomic datasets with MIAPPE 1.1

Author: François Tardieu, Cyril Pommier, Célia Michotey, Bruno Costa, Stephan Weise, Bert Droesbeke, Graham J.W. King, Astrid Junker, Philippe Rocca-Serra, Guillaume Cornut, Hanna Ćwiek-Kupczyńska, Markus Oppermann, Célia Miguel, Daniel Faria, Björn Usadel, Cristobal Uauy, Paweł Krajewski, Jochen C. Reif, Susanna-Assunta Sansone, Živa Ramšak, Uwe Scholz, Richard G. F. Visser, Evangelia Papoutsoglou, Ioannis N. Athanasiadis, Daniel Arend, Inês Chaves, Hendrik Poorter, Richard Finkers, Marie-Angélique Laporte, Kristina Gruden, Elizabeth Arnaud, Ricardo H. Ramirez-Gonzalez, Paul J. Kersey, Anne-Françoise Adam-Blondon, Frederik Coppens, Richard Ostler, Matthias Lange, Wageningen University and Research [Wageningen] (WUR), Instituto Gulbenkian de Ciência [Oeiras] (IGC), Fundação Calouste Gulbenkian, Instituto de Engenharia de Sistemas e Computadores (INESC), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Geo-Information Science and Remote Sensing Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Instituto de Biologia Experimental e Tecnológica (IBET), Department of plant Biotechnology and Bioinformatics, University of Gent, VIBUGent Center for Plant Systems Biology, Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BioISI, Universidade de Lisboa (ULISBOA), Polish Academy of Sciences, Institute of Plant Genetics, Department of Integrative Plant Biology, Partenaires INRAE, Department of Biotechnology and Systems Biology, National Institute of Biology [Ljubljana] (NIB), Southern Cross Plant Science, Southern Cross University (SCU), Computational and Analytical Sciences, Rothamsted Research, Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, University North Ryde, John Innes Centre [Norwich], University of Oxford [Oxford], Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RWTH Aachen University, Royal Botanic Gardens, Kew Richmond, European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), European Project: 739514,EMPHASIS-PREP, European Project: 634107,H2020,H2020-PHC-2014-two-stage,MULTIMOT(2015), European Project: 654241,H2020,H2020-EINFRA-2014-2,PhenoMeNal(2015), Universiteit Gent = Ghent University (UGENT), Universidade de Lisboa = University of Lisbon (ULISBOA), Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), Biotechnology and Biological Sciences Research Council (BBSRC), University of Oxford, 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 Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH)
Subjects: 0106 biological sciences, 0301 basic medicine, Computer science, Physiology, Interoperability, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, WASS, interoperability, Plant Science, MINIMUM INFORMATION, 01 natural sciences, Domain (software engineering), law.invention, 03 medical and health sciences, plant phenotyping, Laboratorium voor Plantenveredeling, Knowledge extraction, Laboratory of Geo-information Science and Remote Sensing, law, Methods, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Laboratorium voor Geo-informatiekunde en Remote Sensing, Implementation, Reusability, Research, metadata, Biology and Life Sciences, phenomics, Plants, findability, PE&RC, Data science, ONTOLOGIES, Metadata, Plant Breeding, 030104 developmental biology, ddc:580, Data model, VOCABULARY, CLARITY, reusability, standards, EPS, 010606 plant biology & botany, REPOSITORY
Abstract: The new phytologist 227(1), 260-273 (2020). doi:10.1111/nph.16544, Published by Wiley-Blackwell, Oxford [u.a.]
Published: 2020

39. Maize adaptation across temperate climates was obtained via expression of two florigen genes

Author: Castelletti, Sara, Coupel-Ledru, Aude, Granato, Italo, Palaffre, Carine, Cabrera-Bosquet, Llorenç, Tonelli, Chiara, Nicolas, Stéphane D., Tardieu, François, Welcker, Claude, Conti, Lucio, Department of Biosciences [Milano], Università degli Studi di Milano [Milano] (UNIMI), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité expérimentale du maïs (BORDX ST-MARTIN UE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), FLORIMAIZE 'Role of florigen proteins in maizedevelopmental reprogramming under droughtstress' Project (FC ID 2013-1889, AF ID 1301-006) jointly supported by Agropolis Fondation (through the 'Investissements d’avenir' programme with reference number ANR-10-LABX-0001-01') and Fondazione Cariplo, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011), and ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010)
Subjects: Leaves, Single Nucleotide Polymorphisms, Acclimatization, Photoperiod, Quantitative Trait Loci, Maïs Zea mays L, Bioengineering, Plant Science, Flowers, QH426-470, Research and Analysis Methods, Plant Genetics, Zea mays, Model Organisms, Plant and Algal Models, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Genome-Wide Association Studies, Plant Genomics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Humans, Grasses, Molecular Biology Techniques, Molecular Biology, Florigen, Plant Proteins, floraison, Plant Anatomy, Gene Mapping, Organisms, Biology and Life Sciences, Eukaryota, Computational Biology, Human Genetics, Genomics, Plants, Genome Analysis, Adaptation, Physiological, Maize, Cold Temperature, Experimental Organism Systems, Genetic Loci, Animal Studies, Engineering and Technology, Plant Biotechnology, Research Article, Biotechnology
Abstract: Expansion of the maize growing area was central for food security in temperate regions. In addition to the suppression of the short-day requirement for floral induction, it required breeding for a large range of flowering time that compensates the effect of South-North gradients of temperatures. Here we show the role of a novel florigen gene, ZCN12, in the latter adaptation in cooperation with ZCN8. Strong eQTLs of ZCN8 and ZCN12, measured in 327 maize lines, accounted for most of the genetic variance of flowering time in platform and field experiments. ZCN12 had a strong effect on flowering time of transgenic Arabidopsis thaliana plants; a path analysis showed that it directly affected maize flowering time together with ZCN8. The allelic composition at ZCN QTLs showed clear signs of selection by breeders. This suggests that florigens played a central role in ensuring a large range of flowering time, necessary for adaptation to temperate areas., Author summary The cultivation of maize in temperate climates required the suppression of photoperiod sensitivity and the selection of a wide range of flowering time for the adaptation to local environmental constraints. Photoperiodic flowering requires the production of a systemic protein signal referred to as the florigen, which is transcriptionally activated in leaves. A key question is to what extent the expression of the florigen gene can explain flowering time variability of temperate maize, where photoperiod sensitivity has been eliminated by artificial selection. Our results reveal large variability in two related florigen genes which is strongly correlated with variability in flowering time. Using association genetics approaches we could detect genomic regions responsible for the expression of the two florigens that precisely co-localise with flowering time-related regions, thereby supporting the significance of quantitative changes in florigen levels in driving flowering time variability. Markers associated with florigen expression/flowering time display significant signatures of selection indicating that variable patterns of florigen accumulation underpin the adaptation of temperate maize flowering.
Published: 2020

40. Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks

Author: Anthony Venon, Julien Rozière, Johann Joets, Olivier Turc, Stéphanie Pateyron, Marieke L. Kuijjer, Maike Stam, Clémentine Vitte, Maud Fagny, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre for Molecular Medicine Norway (NCMM), Faculty of Medicine [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Rigshospitalet [Copenhagen], Copenhagen University Hospital-Copenhagen University Hospital, Leiden University Medical Center (LUMC), Swammerdam Institute for Life Sciences (SILS), University of Amsterdam [Amsterdam] (UvA), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), Investment for the Future ANR-10-BTBR-01-01 Amaizing program, Amaizing, Plant Development & (Epi)Genetics (SILS, FNWI), Universiteit Leiden, 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 Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Systems biology, Gene regulatory network, Computational biology, Biology, Zea mays, 01 natural sciences, 03 medical and health sciences, mite, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene expression, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, TIR transposon, Enhancer, gene regulatory networks, Transcription factor, Gene, Original Research, 030304 developmental biology, Epigenomics, 2. Zero hunger, 0303 health sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], husk, Maize, DNA binding site, transcription factor binding sites, enhancers, transposable elements, 010606 plant biology & botany
Abstract: Enhancers are important regulators of gene expression during numerous crucial processes including tissue differentiation across development. In plants, their recent molecular characterization revealed their capacity to activate the expression of several target genes through the binding of transcription factors. Nevertheless, identifying these target genes at a genome-wide level remains a challenge, in particular in species with large genomes, where enhancers and target genes can be hundreds of kilobases away. Therefore, the contribution of enhancers to regulatory network is still poorly understood in plants. In this study, we investigate the enhancer-driven regulatory network of two maize tissues at different stages: leaves at seedling stage and husks (bracts) at flowering. Using a systems biology approach, we integrate genomic, epigenomic and transcriptomic data to model the regulatory relationship between transcription factors and their potential target genes. We identify regulatory modules specific to husk and V2-IST, and show that they are involved in distinct functions related to the biology of each tissue. We evidence enhancers exhibiting binding sites for two distinct transcription factor families (DOF and AP2/ERF) that drive the tissue-specificity of gene expression in seedling immature leaf and husk. Analysis of the corresponding enhancer sequences reveals that two different transposable element families (TIR transposon Mutator and MITE Pif/Harbinger) have shaped the regulatory network in each tissue, and that MITEs have provided new transcription factor binding sites that are involved in husk tissue-specificity.SignificanceEnhancers play a major role in regulating tissue-specific gene expression in higher eukaryotes, including angiosperms. While molecular characterization of enhancers has improved over the past years, identifying their target genes at the genome-wide scale remains challenging. Here, we integrate genomic, epigenomic and transcriptomic data to decipher the tissue-specific gene regulatory network controlled by enhancers at two different stages of maize leaf development. Using a systems biology approach, we identify transcription factor families regulating gene tissue-specific expression in husk and seedling leaves, and characterize the enhancers likely to be involved. We show that a large part of maize enhancers is derived from transposable elements, which can provide novel transcription factor binding sites crucial to the regulation of tissue-specific biological functions.
Published: 2020

41. Natural variation of Arabidopsis thaliana responses to Cauliflower mosaic virus infection upon water deficit

Author: Bergès, Sandy, Vasseur, François, Bediée, Alexis, Rolland, Gaëlle, Masclef, Diane, Dauzat, Myriam, van Munster, Manuella, Vile, Denis, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), 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, 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, rant #2015005464 from European Union and the Region LanguedocRoussillon 'Chercheur d'Avenir' (FEDER FSE IEJ 2014-2020, Project APSEVIR)., Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Leaves, Genotype, QH301-705.5, Arabidopsis Thaliana, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Pathogens, Plant Science, Brassica, Research and Analysis Methods, Microbiology, Plant Viral Pathogens, Model Organisms, Caulimovirus, Plant and Algal Models, Virology, Plant Resistance to Abiotic Stress, Plant-Environment Interactions, Natural Resources, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Defenses, Biology (General), Flowering Plants, ComputingMilieux_MISCELLANEOUS, Plant Diseases, Dehydration, Ecology, Plant Anatomy, Plant Ecology, Ecology and Environmental Sciences, fungi, Organisms, Genetic Variation, Biology and Life Sciences, Eukaryota, food and beverages, Plants, Plant Pathology, RC581-607, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Experimental Organism Systems, Plant Physiology, Animal Studies, Water Resources, Immunologic diseases. Allergy, Viral Transmission and Infection, Research Article
Abstract: Plant virus pathogenicity is expected to vary with changes in the abiotic environment that affect plant physiology. Conversely, viruses can alter the host plant response to additional stimuli from antagonism to mutualism depending on the virus, the host plant and the environment. Ecological theory, specifically the CSR framework of plant strategies developed by Grime and collaborators, states that plants cannot simultaneously optimize resistance to both water deficit and pathogens. Here, we investigated the vegetative and reproductive performance of 44 natural accessions of A. thaliana originating from the Iberian Peninsula upon simultaneous exposure to soil water deficit and viral infection by the Cauliflower mosaic virus (CaMV). Following the predictions of Grime’s CSR theory, we tested the hypothesis that the ruderal character of a plant genotype is positively related to its tolerance to virus infection regardless of soil water availability. Our results showed that CaMV infection decreased plant vegetative performance and annihilated reproductive success of all accessions. In general, water deficit decreased plant performance, but, despite differences in behavior, ranking of accessions tolerance to CaMV was conserved under water deficit. Ruderality, quantified from leaf traits following a previously published procedure, varied significantly among accessions, and was positively correlated with tolerance to viral infection under both well-watered and water deficit conditions, although the latter to a lesser extent. Also, in accordance with the ruderal character of the accession and previous findings, our results suggest that accession tolerance to CaMV infection is positively correlated with early flowering. Finally, plant survival to CaMV infection increased under water deficit. The complex interactions between plant, virus and abiotic environment are discussed in terms of the variation in plant ecological strategies at the intraspecific level., Author summary Virus pathogenicity may be influenced by changes in the abiotic environment. A common change is decrease in soil water availability, which is detrimental to plant productivity and the occurrence of which is expected to increase due to climate change, has recently been shown to interfere with plant–virus interactions. We investigated the performance of 44 natural accessions of the plant species Arabidopsis thaliana infected by Cauliflower mosaic virus under well-watered and water deficit conditions. We showed that viral infection decreased plant vegetative performance and annihilated reproductive success of all accessions, and that these pathogenic effects were increased by water deficit. Intrinsic characteristics of the accessions were related to their tolerance to the virus so that accessions with low leaf tissue density and rapid growth rate were more tolerant to viral infection regardless of watering condition. Finally, plant survival upon viral infection increased under water deficit. We discuss the role of intrinsic plant characteristics, seen as ecological strategies, in plant tolerance to viral infections under contrasting environmental conditions, and the consequences for the study of viral epidemiology.
Published: 2020

42. Duravitis opens breeding strategies for grapevine facing T° rises

Author: Laurent Torregrosa, Antoine Bigard, Agnes Doligez, David Lecourieux, Markus Rienth, Nathalie Luchaire, Philippe Pieri, Ratthaphon Chatbanyong, Rezth Shahood, Marc Farnos, Catherine Roux, Angelique Adiveze, Jérémy Pillet, Yannick Sire, Emmanuelle Zumstein, Mélanie Veyret, Loic Lecunff, Fatma Lecourieux, Nicolas Saurin, Bertrand Muller, Hernan Ojeda, Cléa Houel, Jean-Pierre Peros, Patrice This, Anne Pellegrino, Charles Romieu, Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Unité expérimentale de Pech-Rouge (PECH ROUGE), Institut National de la Recherche Agronomique (INRA), Institut Français de la Vigne et du Vin (IFV), and ProdInra, Migration
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, Protéomique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Vigne, [SDV.BDLR] Life Sciences [q-bio]/Reproductive Biology, ComputingMilieux_MISCELLANEOUS, Réchauffement climatique
Abstract: National audience
Published: 2020

43. Why do crop models diverge substantially in climate impact projections? A comprehensive analysis based on eight barley crop models

Author: Kurt Christian Kersebaum, Frank Ewert, Carlos Gregorio Hernández Díaz-Ambrona, Pierre Martre, Fulu Tao, Tapio Salo, Camilla Dibari, Xenia Specka, Lucía Rodríguez, Roberto Ferrise, Amit Kumar Srivastava, G. Padovan, Taru Palosuo, Davide Cammarano, Margarita Ruiz-Ramos, M. Ines Minguez, Alan H. Schulman, Mikhail A. Semenov, Thomas Gaiser, Claas Nendel, Reimund P. Rötter, Jukka Höhn, Viikki Plant Science Centre (ViPS), Institute of Biotechnology, Natural Resources Institute Finland (LUKE), Georg-August-University [Göttingen], Centre for Biodiversity and Sustainable Land Use (CBL), Universidad Politécnica de Madrid (UPM), Rothamsted Research, Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Department of Agronomy, Purdue University [West Lafayette], Crop Science Group, INRES, Rheinische Friedrich-Wilhelms-Universität Bonn, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Helsinki, FACCE-MACSUR knowledge hub (031A103B), Academy of Finland through projects AI-CropPro (decision no. 316172), DivCSA (decision no. 316215), Natural Resources Institute Finland through strategic projects ClimSmartAgri and Boost-IA, German Federal Ministry of Education and Research, ‘Limpopo Living Landscapes’ project within the SPACES program (grant number 01LL1304A), IMPAC^3 project funded by the German Federal Ministry of Education and Research (FKZ 031A351A), MULCLIVAR CGL2012-38923-C02-02 from MINECO and by MACSUR01-UPM from INIA within FACCE-JPI, German Federal Ministry of Food and Agriculture (BMEL) through the Federal Office for Agriculture and Food (BLE), (2851ERA01J), German Ministry of Education and Research (BMBF), 031B0039C, FACCE-MACSUR project (031A103B) through the metaprogramme on Adaptation of Agriculture and Forests to Climate Change (AAFCC) of the French National Institute for Agricultural Research (INRA), FACCE-JPI project ClimBar (Academy of Finland decision 284987), JPI FACCE MACSUR2 through the Italian Ministry for Agricultural, Food, and Forestry Policies, Biotechnology and Biological Sciences Research Council (BBSRC) Designing Future Wheat project (BB/P016855/1)., European Project: 613556,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,WHEALBI(2014), Georg-August-University = Georg-August-Universität Göttingen, Biotechnology and Biological Sciences Research Council (BBSRC), Università degli Studi di Firenze = University of Florence (UniFI), 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 Helsingin yliopisto = Helsingfors universitet = University of Helsinki
Subjects: 0106 biological sciences, Mediterranean climate, Atmospheric Science, 010504 meteorology & atmospheric sciences, AIR CO2 ENRICHMENT, Climate change, Crop growth simulation, Agricultural engineering, SIMULATION-MODELS, 01 natural sciences, NITROGEN DYNAMICS, Evapotranspiration, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Precipitation, ATMOSPHERIC CO2, FIELD EXPERIMENT, TEMPERATURE, 1172 Environmental sciences, 0105 earth and related environmental sciences, 2. Zero hunger, Global and Planetary Change, Biomass (ecology), RICE PHENOLOGY, WHEAT GROWTH, Crop growth stimulation, business.industry, Model improvement, Global warming, Uncertainty, Forestry, Agriculture, 15. Life on land, 11831 Plant biology, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Impact, Boreal, 13. Climate action, 415 Other agricultural sciences, Environmental science, business, ELEVATED CO2, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Robust projections of climate impact on crop growth and productivity by crop models are key to designing effective adaptations to cope with future climate risk. However, current crop models diverge strongly in their climate impact projections. Previous studies tried to compare or improve crop models regarding the impact of one single climate variable. However, this approach is insufficient, considering that crop growth and yield are affected by the interactive impacts of multiple climate change factors and multiple interrelated biophysical processes. Here, a new comprehensive analysis was conducted to look holistically at the reasons why crop models diverge substantially in climate impact projections and to investigate which biophysical processes and knowledge gaps are key factors affecting this uncertainty and should be given the highest priorities for improvement. First, eight barley models and eight climate projections for the 2050s were applied to investigate the uncertainty from crop model structure in climate impact projections for barley growth and yield at two sites: Jokioinen, Finland (Boreal) and Lleida, Spain (Mediterranean). Sensitivity analyses were then conducted on the responses of major crop processes to major climatic variables including temperature, precipitation, irradiation, and CO2, as well as their interactions, for each of the eight crop models. The results showed that the temperature and CO2 relationships in the models were the major sources of the large discrepancies among the models in climate impact projections. In particular, the impacts of increases in temperature and CO2 on leaf area development were identified as the major causes for the large uncertainty in simulating changes in evapotranspiration, above-ground biomass, and grain yield. Our findings highlight that advancements in understanding the basic processes and thresholds by which climate warming and CO2 increases will affect leaf area development, crop evapotranspiration, photosynthesis, and grain formation in contrasting environments are needed for modeling their impacts.
Published: 2020

44. Modification of the expression of the aquaporin ZmPIP2;5 affects water relations and plant growth

Author: François Chaumont, Adel Meziane, Boris Parent, Dirk Inzé, François Tardieu, Valentin Couvreur, Thomas Milhiet, Xavier Draye, Mieke Van Lijsebettens, Stijn Aesaert, Hilde Nelissen, Lei Ding, Université Catholique de Louvain = Catholic University of Louvain (UCL), Universiteit Gent = Ghent University [Belgium] (UGENT), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Belgian National Fund for Scientific 44Research (FNRS, FRFC 2.4.501.06F), the Interuniversity Attraction Poles Programme-Belgian Science Policy(grant IAP7/29), the 'Communauté française de Belgique-Actions de Recherches Concertées' (grants ARC11/16-036 and ARC16/21-075), the Pierre and Colette Bauchau Award, Incoming Post-doc Move-in Louvain Fellowships co-funded by the Marie Curie Actions, research fellow at the Fonds de Formation à la Recherche dans l’Industrie et l’Agriculture, the FNRS 50(FC 84104)., UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, and UCL - SST/ELI/ELIA - Agronomy
Subjects: 0106 biological sciences, Physiology, Leaf Hydraulic Conductance, Aquaporin, Transport, Plant Science, Aquaporins, 01 natural sciences, Plant Roots, Zea mays, Plasma-membrane Aquaporins, Hydraulic conductivity, Gene Expression Regulation, Plant, Xylem, Exodermis, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Research Articles, Conductivity, Drought, Chemistry, Primary Root, fungi, Wild type, Plant physiology, Water, Biology and Life Sciences, food and beverages, Plant Transpiration, Vascular bundle, Apoplast, Plant Leaves, Biophysics, Evaporative Demand, Growth-rate, Bundle-sheath, lipids (amino acids, peptides, and proteins), Endodermis, Cell, 010606 plant biology & botany
Abstract: The maize plasma membrane PIP2;5 aquaporin plays a role in controlling root radial water movement, leaf hydraulic conductivity, and plant growth. The plasma membrane intrinsic protein PIP2;5 is the most highly expressed aquaporin in maize (Zea mays) roots. Here, we investigated how deregulation of PIP2;5 expression affects water relations and growth using maize overexpression (OE; B104 inbred) or knockout (KO; W22 inbred) lines. The hydraulic conductivity of the cortex cells of roots grown hydroponically was higher in PIP2;5 OE and lower in pip2;5 KO lines compared with the corresponding wild-type plants. While whole-root conductivity decreased in the KO lines compared to the wild type, no difference was observed in OE plants. This paradox was interpreted using the MECHA hydraulic model, which computes the radial flow of water within root sections. The model hints that the plasma membrane permeability of the cells is not radially uniform but that PIP2;5 may be saturated in cell layers with apoplastic barriers, i.e. the endodermis and exodermis, suggesting the presence of posttranslational mechanisms controlling the abundance of PIP in the plasma membrane in these cells. At the leaf level, where the PIP2;5 gene is weakly expressed in wild-type plants, the hydraulic conductance was higher in the PIP2;5 OE lines compared with the wild-type plants, whereas no difference was observed in the pip2;5 KO lines. The temporal trend of leaf elongation rate, used as a proxy for that of xylem water potential, was faster in PIP2;5 OE plants upon mild stress, but not in well-watered conditions, demonstrating that PIP2;5 may play a beneficial role in plant growth under specific conditions.
Published: 2020

45. The Transcription Factor bHLH121 Interacts with bHLH105 (ILR3) and its Closest Homologs to Regulate Iron Homeostasis in Arabidopsis

Author: Valérie Rofidal, Nathalia Navarro, Frédéric Gaymard, Esther Izquierdo, Christian Dubos, Kevin Robe, Florence Vignols, Véronique Santoni, Fei Gao, Hannetz Roschzttardtz, Mathilde Bettembourg, China Agricultural University (CAU), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0301 basic medicine, Iron, Ubiquitin-Protein Ligases, Mutant, Arabidopsis, Basic helix-loop-helix leucine zipper transcription factors, Plant Science, 01 natural sciences, Plant Roots, In Brief, 03 medical and health sciences, Gene Knockout Techniques, Hydroponics, Gene Expression Regulation, Plant, Basic Helix-Loop-Helix Transcription Factors, Arabidopsis thaliana, Homeostasis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene Regulatory Networks, Transcription factor, Cellular localization, ComputingMilieux_MISCELLANEOUS, Regulation of gene expression, biology, Arabidopsis Proteins, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Nuclear Proteins, Cell Biology, biology.organism_classification, Plants, Genetically Modified, Cell biology, 030104 developmental biology, Transcription Factor Gene, Transcriptome, 010606 plant biology & botany, Transcription Factors
Abstract: Iron (Fe) is an essential micronutrient for plant growth and development. Any defects in the maintenance of Fe homeostasis will alter plant productivity and the quality of their derived products. In Arabidopsis (Arabidopsis thaliana), the transcription factor ILR3 plays a central role in controlling Fe homeostasis. In this study, we identified bHLH121 as an ILR3-interacting transcription factor. Interaction studies showed that bHLH121 also interacts with the three closest homologs of ILR3 (i.e., basic-helix-loop-helix 34 [bHLH34], bHLH104, and bHLH115). bhlh121 loss-of-function mutants displayed severe defects in Fe homeostasis that could be reverted by exogenous Fe supply. bHLH121 acts as a direct transcriptional activator of key genes involved in the Fe regulatory network, including bHLH38, bHLH39, bHLH100, bHLH101, POPEYE, BRUTUS, and BRUTUS LIKE1, as well as IRONMAN1 and IRONMAN2. In addition, bHLH121 is necessary for activating the expression of transcription factor gene FIT in response to Fe deficiency via an indirect mechanism. bHLH121 is expressed throughout the plant body, and its expression is not affected by Fe availability. By contrast, Fe availability affects the cellular localization of bHLH121 protein in roots. Altogether, these data show that bHLH121 is a regulator of Fe homeostasis that acts upstream of FIT in concert with ILR3 and its closest homologs.
Published: 2020

46. Environmental and trophic determinism of fruit abscission and outlook with climate change in tropical regions

Author: Tisné, S., Denis, M., Domonhédo, H., Pallas, B., Cazemajor, M., Tranbarger, Timothy, Morcillo, F., Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut National de Recherche Agricole du Bénin (INRAB), INRAB, PalmElit, 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]), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), PalmElit SAS/IRD/CIRAD/CRA-PP, 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), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)
Subjects: Changement climatique, Abscission, ZONE TROPICALE, P40 - Météorologie et climatologie, Facteur lié au site, F60 - Physiologie et biochimie végétale, [SDV]Life Sciences [q-bio], Facteur du milieu, Facteur climatique, BENIN, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Elaeis guineensis, Adaptation physiologique
Abstract: International audience; Fruit abscission facilitates the optimal conditions and timing of seed dispersal. Environmental regulation of tropical fruit abscission has received little attention, even though climate change may have its strongest impacts in tropical regions. In this study, oil palm fruit abscission was monitored during multiple years in the Benin Republic to take advantage of the climatic seasonality and the continuous fruit production by this species. An innovative multivariable statistical method was used to identify the best predictors of fruit abscission among a set of climate and ecophysiological variables, and the stage of inflorescence and fruit bunch development when the variables are perceived. The effects of climate scenarios on fruit abscission were then predicted based on the calibrated model. We found complex regulation takes place at specific stages of inflorescence and bunch development, even long before the fruit abscission zone is competent to execute abscission. Among the predictors selected, temperature variations during inflorescence and fruit bunch development are major determinants of the fruit abscission process. Furthermore, the timing of ripe fruit drop is determined by temperature in combination with the trophic status. Finally, climate simulations revealed that the abscission process is robust and is more affected by seasonal variations than by extreme scenarios. Our investigations highlighted the central function of the abscission zone as the sensor of environmental signals during reproductive development. Coupling ecophysiological and statistical modeling was an efficient approach to disentangle this complex environmental regulation. K E Y W O R D S climate change, Elaeis guineensis, environmental regulation, fruit abscission, multivariable models
Published: 2020

47. Traité de la vigne : physiologie, terroir, culture

Author: CARBONNEAU, Alain, Torregrosa, Laurent, DELOIRE, Alain, Pellegrino, Anne, Pantin, Florent, Romieu, Charles, Jaillard, Benoît, Metay, Aurelie, Ojeda, Hernan, Abbal, Philippe, 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), Diversité, Adaptation et Amélioration de la Vigne [AGAP] (DAAV), 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)-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), IHEV Institut des hautes études de la vigne et du vin, 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), 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), Unité Expérimentale de Pech-Rouge (PECH ROUGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sciences Pour l'Oenologie (SPO), Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Carbonneau Alain, and Torregrosa Laurent
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, amélioration de la vigne, technique culturale, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, viticulture, terroir viticole, [SDV.BDD]Life Sciences [q-bio]/Development Biology, physiologie de la vigne
Abstract: International audience; Le Traité de la vigne propose une étude détaillée de l’état des connaissances scientifiques sur la biologie de la vigne. Pédagogique et richement illustré, il rassemble théorie et pratique au service d’une nouvelle vision de la viticulture. La remière partie traite du fonctionnement de la vigne à partir du concept fondamental de « triptyque biologique » (signal – structure – système de régulation). Les effets de l’eau, du CO2, du rayonnement solaire, de la température et des éléments minéraux sur la physiologie de la vigne sont précisément décrits. Les connaissances de base concernant les métabolismes du raisin et la génétique de la vigne sont développées. Enfin, sont présentées les bases des applications techniques. La seconde partie est consacrée aux aspects environnementaux et technologiques de la culture de la vigne : climat, changement climatique, agrométéorologie, caractéristiques des sols ; aménagement, entretien des sols et relation avec les racines ; système cultural, irrigation et conduite de la plante ; nouvelle approche climatologique ; nouvelles technologies au service des terroirs ; nouvelle théorie de la maturation du raisin. Cette troisième édition entièrement réactualisée s’est enrichie d’un cahier couleur. Fruit d’une collaboration interdisciplinaire, le Traité de la Vigne s’adresse aux étudiants en agronomie, mais aussi aux professionnels souhaitant approfondir ou mettre à jour leurs connaissances scientifiques et techniques.
Published: 2020

48. A 3D architectural model of grass shoot morphogenesis and plasticity, driven by organ metabolite concentrations and coordination rules

Author: Marion Gauthier, Romain Barillot, Anne Schneider, Camille Chambon, Christian Fournier, Christophe Pradal, Bruno Andrieu, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ITK [Clapiers], Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Hochschule Geisenheim University, University of Hannover, Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM)
Subjects: carbon, plasticity, leaf growth, fungi, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, food and beverages, metabolism, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, nitrogen
Abstract: Introduction - Phenotypic plasticity - the ability of one genotype to produce different phenotypes depending on growth conditions - is a core aspect of the interactions between plants and their environment. For instance, leaf traits define the ability of plants to capture light, as well as their exposition and responses to various signals and stresses. In turn, leaf traits such as dimensions, composition and mass are highly regulated by growth conditions. The explicit description of shoot architecture in functional-structural models (FSPM) open new possibilities to express these feedback loops, which regulate plant fitness and productivity. However, formalizing into models the processes that build the plastic responses of traits to growth conditions is a major bottleneck to date. Most FSPMs that address the coupling between resources availability and growth consider only carbon (C) and drive resource allocation by sink priorities defined from empirical relations. Besides, the determinism of traits such as the areal density, which links mass growth with dimension growth, are poorly understood, so that these traits are frequently approximated as constant, while they have been shown to vary widely with growth conditions. Finally, the lack of process-based formalisms of existing models impairs our ability to simulate morphogenesis under contrasting growth conditions. As a step toward more mechanistic approaches to simulate shoot morphogenesis, we propose a plantscale FSPM of C and nitrogen (N) economy of the growing grass in which the morphogenesis is fully integrated with the plant metabolism. Model description - The model represents the plant as a collection of tillers made of several growing and mature shoot phytomers (identifying lamina, sheath and internode mature tissues and growth zones), a single roots compartment and a shared pool mimicking the phloem. Each compartment has a structural mass and concentrations in mobile and storage metabolites. The plant is seen as a self-regulated system which relies on two processes: i) local C and N concentrations in the growth zones drive organ elongation rate, specific structural mass and width, ii) coordination rules link the timing of extension of the organs between successive phytomers. These processes were implemented into CN-Wheat (Barillot et al., 2016ab), a detailed FSPM of C and N metabolism previously developed for a culm with a static architecture. The new version of CN-Wheat presented here is the coupling of (i) a model of leaf, internode and root growth, (ii) a dynamic representation of the 3D geometry of plants which builds on the ADEL-Wheat model (Fournier et al., 2003), (iii) a model of light distribution (Chelle and Andrieu, 1998), and finally (iv) a model simulating photosynthesis, N acquisition, synthesis and allocation of C and N metabolites, and senescence at the organ level, which extends the initial version of CN-Wheat. All above mentionned processes are regulated, at organ scale, by the environmental conditions and the concentrations in C and N metabolites. Results and Discussion - The model was calibrated for wheat during the vegetative stages (from seedling emergence to the beginning of stem extension). First, the model was evaluated in field conditions representative of North-Western Europe, which resulted in realistic patterns of leaf dimensions, extension and senescence dynamics, organ mass and composition. A key result was the ability of the model to simulate, as emerging properties, key plant and agronomic traits e.g. the phyllochron, shoot/roots ratio dynamic, N dilution and radiation use efficiency. Then, we evaluated the model's ability to simulate plant plasticity under different scenarios of plant density, incoming light and soil nitrate concentration. The model simulated realistic responses of leaf traits such as dimensions, specific leaf area and specific leaf N; the figure illustrates the simulated variations of lamina dimensions and N vertical gradient with N resources. Conclusion - Our model is innovative by the high level of explicitation of the processes underlying shoot morphogenesis, which provides new possibilities to link the phenotypic plasticity of plants to their C and N metabolic status at the place and time where traits are built. The approach could be extended to include other factors involved in plasticity, such as hormones or direct responses to the environment perceived. The genericity of the modelling frame makes it also applicable to explore shoot morphogenesis in other grass species.
Published: 2020

49. FG-iRODS : un service de gestion de données pour les communautés scientifiques à l'échelle nationale et européenne basé une infrastructure fédérée

Author: Medernach, Emmanuel, Pansanel, Jérôme, Flores, Raphaël, Gondrand, Christine, Moreau, Patrick, Negre, Vincent, Romier, Geneviève, Centre National de la Recherche Scientifique (CNRS), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Laboratoire de Physique Subatomique et de Cosmologie (LPSC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), and Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: analyse de données, france grilles, calcul, stockage, irods, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, infrastructure, ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract: International audience
Published: 2019

50. Parameterising wheat leaf and tiller dynamics for faithful reconstruction of wheat plants by structural plant models

Author: Tino Dornbusch, Bruno Andrieu, Camille Chambon, Christian Fournier, David Gouache, Benoit de Solan, Mariem Abichou, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre 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), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ARVALIS - Institut du végétal [Paris], National Research Agency (Wheatamix project ANR-13-AGRO-0008), ANR-13-AGRO-0008,WHEATAMIX,Augmenter la diversité génétique au sein des parcelles de blé pour renforcer la multifonctionnalité et la durabilité de la production dans le Bassin Parisien(2013), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0106 biological sciences, plant architecture, Population, croissance foliaire, Soil Science, Growing season, Structural plant model, Tiller (botany), Biology, three dimensional model, 01 natural sciences, modèle structure fonction, Crop, blé, wheat, Architecture, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Phyllochron, triticum aestivum, Cultivar, education, 2. Zero hunger, education.field_of_study, modèle 3d, Sowing, 04 agricultural and veterinary sciences, 15. Life on land, Phenotype, Agronomy, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Agronomy and Crop Science, architecture de la plante, 010606 plant biology & botany, Main stem
Abstract: International audience; Structural 3D plant models aim at mimicking the dynamics of plant and crop structure based on experimental data. Such models can be interfaced with physical models to investigate plant-environment interactions. This work aimed at defining functions that represent the leaf and tiller development of individual wheat plants, and that could be fitted to the specific traits produced in a broad range of situations.A dataset of the dynamics of wheat plant (Triticum aestivum) architecture was collected for 55 experimental situations, including 11 growing seasons, three sowing densities, three sowing dates, and 13 commercial cultivars. Data were analysed to identify conserved patterns in the dynamics of leaf emergence and of tiller emergence and senescence.The broad range of conditions tested allowed us to evaluate the robustness of relationships proposed in previous studies and to identify novel patterns. Amongst them, we observed: (i) that leaf emergence dynamics may follow either a linear or a bilinear pattern for the same genotype. When a change in phyllochron occurred, it coincided with the initiation of the flag leaf; (ii) the delay between leaf and tiller emergence was not constant, but increased very regularly for successive phytomers; (iii) the number of leaves emerged at tillering cessation decreased with plant density but depended also on the final number of leaves on the main stem (MS) and marked differences existed between cultivars. Finally, we defined functions representing leaf and tiller dynamics with parameters that have a simple botanical interpretation and are easy to derive from field measurements. Assessing plant density, crop leaf stage at 5–6 dates and tiller population at 2 dates during the cycle provide the required data.This study defines a rationale to analyse and represent the dynamics of the architecture of individual wheat plants. The method can be used to determine the dynamics of architecture in 3D models and should be transposable to a wide range of cereal species.
Published: 2018

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