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14,575 results on '"010606 plant biology & botany"'

1. Approaches and determinants to sustainably improve crop production

Author: Alain Gojon, Laurent Nussaume, Doan T. Luu, Erik H. Murchie, Alexandra Baekelandt, Vandasue Lily Rodrigues Saltenis, Jean‐Pierre Cohan, Thierry Desnos, Dirk Inzé, John N. Ferguson, Emmanuel Guiderdonni, Anne Krapp, René Klein Lankhorst, Christophe Maurel, Hatem Rouached, Martin A. J. Parry, Mathias Pribil, Lars B. Scharff, Philippe Nacry, 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), Plant Environmental Physiology and Stress Signaling (PEPSS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Nottingham, UK (UON), Universiteit Gent = Ghent University (UGENT), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Copenhagen Plant Science Center (CPSC), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), ARVALIS - Institut du végétal [Paris], University of Cambridge [UK] (CAM), 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, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wageningen University and Research [Wageningen] (WUR), Lancaster Environment Centre, Lancaster University, European Project: 817690,H2020, Gojon, A [0000-0001-5412-8606], Nussaume, L [0000-0002-9445-2563], Luu, DT [0000-0001-9765-2125], Murchie, EH [0000-0002-7465-845X], Baekelandt, A [0000-0003-0816-7115], Rodrigues Saltenis, VL [0000-0002-1455-7171], Cohan, JP [0000-0003-2117-7027], Desnos, T [0000-0002-6585-1362], Inzé, D [0000-0002-3217-8407], Ferguson, JN [0000-0003-3603-9997], Guiderdonni, E [0000-0003-2760-2864], Krapp, A [0000-0003-2034-5615], Klein Lankhorst, R [0000-0003-1845-8733], Maurel, C [0000-0002-4255-6440], Rouached, H [0000-0002-7751-0477], Parry, MAJ [0000-0002-4477-672X], Pribil, M [0000-0002-9174-9548], Scharff, LB [0000-0003-0210-3428], Nacry, P [0000-0001-7766-4989], and Apollo - University of Cambridge Repository
Subjects: 0106 biological sciences, Agriculture and Food Sciences, PHOSPHORUS-ACQUISITION, [SDV]Life Sciences [q-bio], NITROGEN ASSIMILATION, drought, UTILIZATION EFFICIENCY, SALT TOLERANCE, 01 natural sciences, nitrogen, climate change mitigation, salinity, heat stress, 03 medical and health sciences, DROUGHT TOLERANCE, AFFINITY PHOSPHATE TRANSPORTER, Life Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Renewable Energy, TRANSCRIPTION FACTOR, 030304 developmental biology, phosphate, 2. Zero hunger, 0303 health sciences, Sustainability and the Environment, Renewable Energy, Sustainability and the Environment, fungi, BioSolar Cells, Biology and Life Sciences, food and beverages, Forestry, 15. Life on land, WATER-USE, 13. Climate action, ABSCISIC-ACID RECEPTORS, Agronomy and Crop Science, 010606 plant biology & botany, Food Science, HEAT-STRESS
Abstract: International audience; Plant scientists and farmers are facing major challenges in providing food and nutritional security for a growing population, while preserving natural resources and biodiversity. Moreover, this should be done while adapting agriculture to climate change and by reducing its carbon footprint. To address these challenges, there is an urgent need to breed crops that are more resilient to suboptimal environments. Huge progress has recently been made in understanding the physiological, genetic and molecular bases of plant nutrition and environmental responses, paving the way towards a more sustainable agriculture. In this review, we present an overview of these progresses and strategies that could be developed to increase plant nutrient use efficiency and tolerance to abiotic stresses. As illustrated by many examples, they already led to promising achievements and crop improvements. Here, we focus on nitrogen and phosphate uptake and use efficiency and on adaptation to drought, salinity and heat stress. These examples first show the necessity of deepening our physiological and molecular understanding of plant environmental responses. In particular, more attention should be paid to investigate stress combinations and stress recovery and acclimation that have been largely neglected to date. It will be necessary to extend these approaches from model plants to crops, to unravel the relevant molecular targets of biotechnological or genetic strategies directly in these species. Similarly, sustained efforts should be done for further exploring the genetic resources available in these species, as well as in wild species adapted to unfavourable environments. Finally, technological developments will be required to breed crops that are more resilient and efficient. This especially relates to the development of multiscale phenotyping under field conditions and a wide range of environments, and use of modelling and big data management to handle the huge amount of information provided by the new molecular, genetic and phenotyping techniques.
Published: 2023
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2. Editorial - Impact assessment, ecology and management of animal pests affecting field crop establishment: An introduction to the special issue

Author: Jay Ram Lamichhane, AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, post-emergence damage, emergence failure, seed damage, Impact assessment, Ecology (disciplines), [SDV]Life Sciences [q-bio], 04 agricultural and veterinary sciences, Biology, Field crop, 01 natural sciences, seed predation, seedling damage, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, seedling losses, Crop Protection bird damage, Agronomy and Crop Science, Environmental planning, 010606 plant biology & botany
Abstract: International audience; This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Editorial-Impact assessment, ecology and management of animal pests affecting field crop establishment: An introduction to the special issue
Published: 2022
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3. Detection of dynamic QTLs for traits related to organoleptic quality during banana ripening

Author: Frédéric Salmon, Catherine Hervouet, Stella Biabiany, Françoise Carreel, Félicie Lopez-Lauri, Angélique D'Hont, Sébastien Ricci, Emilie Araou, Mathieu Lechaudel, Jean-Claude Efile, Guillaume Martin, Fabien Cormier, 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), Démarche intégrée pour l'obtention d'aliments de qualité (UMR QualiSud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Qualisud - Pôle de La Réunion (Qualisud Réunion ), CIRAD, European Agricultural Fund for Rural Development (EAFRD) 'Plan Banane Durable 2 program, Genoscope/CEA, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), and ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, Locus des caractères quantitatifs, Dynamic QTL, Population, Organoleptic, Context (language use), Horticulture, Quantitative trait locus, Biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Q02 - Traitement et conservation des produits alimentaires, Maturation après récolte, Molecular marker, Cultivar, Dry matter content, education, Mûrissage, 030304 developmental biology, 2. Zero hunger, amélioration génétique, 0303 health sciences, education.field_of_study, Organoleptic banana quality, Qualité des aliments, food and beverages, Ripening, Q01 - Sciences et technologies alimentaires - Considérations générales, Pulp firmness, Propriété organoleptique, chemistry, MusaPulp acidity, 010606 plant biology & botany
Abstract: International audience; Fruit quality traits are directly linked to consumer acceptability, and thus key targets for banana breeding programs. We explored the genetic control of three major organoleptic and ripening-related traits, namely pulp acidity (pH), firmness (PF) and dry matter content (DMC), over a 7-day ripening period and three production cycles in a banana segregating population genotyped by sequencing. Significant broad-sense heritabilities were estimated with 0.77, 0.46 and 0.81 values for pH, PF and DMC, respectively. QTL detection was first performed on the whole dataset to analyze their dynamics. In a second approach, per-cycle data were considered to evaluate the stability across production cycles. Finally, a meta-analysis was performed. Various QTLs were detected, as well as many QTL colocalizations, while 12 of these QTLs were more prominent as they were detected in several approaches and/or explained over 15.0% of the phenotypic variation. Candidate genes were proposed for 10 of these QTLs. The QTL with the largest contribution to pulp acidity (R-2 = 19.3-50.6%) was located on LG1_7 on the genetic map of Pisang Madu, i.e. a parent that is closely related to Cavendish, the world's most cultivated dessert banana cultivar group. This QTL is located on a chromosome derived from a reciprocal translocation that does not recombine in Pisang Madu, which is a favorable context for molecular marker monitoring. These first results will provide a relevant basis for marker-assisted selection in banana improvement programs.
Published: 2022
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4. Calcium-permeable cation channels are involved in uranium uptake in Arabidopsis thaliana

Author: Célia Baggio, Sylvie Figuet, Jacques Bourguignon, Claude Alban, Manon C.M. Sarthou, Stéphane Ravanel, Fabienne Devime, Plantes, Stress & Métaux (MetalStress), Physiologie cellulaire et végétale (LPCV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), The Toxicology program of the Commissariat à l'energie atomique et aux énergies alternatives (CEA), The Plant Biology and Breeding division from Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), ANR-17-CE34-0007,GreenU,Identification de protéines impliquées dans le devenir de l'uranium chez les plantes(2017), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)
Subjects: 0106 biological sciences, Absorption (pharmacology), Environmental Engineering, Health, Toxicology and Mutagenesis, Mutant, Arabidopsis, chemistry.chemical_element, Calcium, 01 natural sciences, Plant Roots, 03 medical and health sciences, Cations, medicine, Environmental Chemistry, Arabidopsis thaliana, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Waste Management and Disposal, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, Chemistry, Arabidopsis Proteins, Assimilation (biology), biology.organism_classification, Pollution, Bioaccumulation, Biophysics, Verapamil, Uranium, Calcium Channels, 010606 plant biology & botany, medicine.drug
Abstract: Uranium (U) is a non-essential and toxic element that is taken up by plants from the environment. The assimilation pathway of U is still unknown in plants and any other organism. In this study, we provide several evidences that U is taken up by the roots of Arabidopsis thaliana through Ca2+-permeable cation channels. First, we showed that deprivation of Arabidopsis plants with calcium induced a 1.5-fold increase in the capacity of roots to accumulate U, suggesting that calcium deficiency promoted the radionuclide import pathway. Second, we showed that external calcium inhibits U accumulation in roots, suggesting a common route for the uptake of both cations. Third, we found that gadolinium, nifedipine and verapamil inhibit the absorption of U, suggesting that different types of Ca2+-permeable channels serve as a route for U uptake. Last, we showed that U bioaccumulation in Arabidopsis mutants deficient for the Ca2+-permeable channels MCA1 and ANN1 was decreased by 40%. This suggests that MCA1 and ANN1 contribute to the absorption of U in different zones and cell layers of the root. Together, our results describe for the first time the involvement of Ca2+-permeable cation channels in the cellular uptake of U.
Published: 2022
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5. Crystal structure of chloroplast fructose-1,6-bisphosphate aldolase from the green alga Chlamydomonas reinhardtii

Author: Théo Le Moigne, Edoardo Sarti, Antonin Nourisson, Alessandra Carbone, Stéphane D. Lemaire, Julien Henri, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Algorithms, Biology, Structure (ABS), 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), Architecture et Dynamique des Macromolécules Biologiques - Architecture and Dynamics of Biological Macromolecules, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)
Subjects: 0106 biological sciences, 0303 health sciences, 03 medical and health sciences, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 01 natural sciences, 030304 developmental biology, 010606 plant biology & botany
Abstract: The Calvin-Benson cycle fixes carbon dioxide into organic triosephosphates through the collective action of eleven conserved enzymes. Regeneration of ribulose-1,5-bisphosphate, the substrate of Rubisco-mediated carboxylation, requires two lyase reactions catalyzed by fructose-1,6-bisphosphate aldolase (FBA). While cytoplasmic FBA has been extensively studied in non-photosynthetic organisms, functional and structural details are limited for chloroplast FBA encoded by oxygenic phototrophs. Here we determined the crystal structure of plastidial FBA from the unicellular green alga Chlamydomonas reinhardtii (Cr). We confirm that CrFBA folds as a TIM barrel, describe its catalytic pocket and homo-tetrameric state. Multiple sequence profiling classified the photosynthetic paralogs of FBA in a distinct group from non-photosynthetic paralogs. We mapped the sites of thiol- and phospho-based post-translational modifications known from photosynthetic organisms and predict their effects on enzyme catalysis.
Published: 2022

6. Plastoquinone homeostasis in plant acclimation to light intensity

Author: Brigitte Ksas, Jean Alric, Stefano Caffarri, Michel Havaux, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Unite Mixte Rech Biol Vegetale & Microbiol Enviro, Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Photosynthèse & Environnement (P&E), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Luminy Génétique et Biophysique des Plantes (LGBP), Plant Environmental Physiology and Stress Signaling (PEPSS), and Financial support from CEA (Radiobiology 2019 program), CNRS (Metaphores 2020–2021 project) and ECCOREV is acknowledged
Subjects: 0106 biological sciences, 0303 health sciences, Light, Plastoquinone, Acclimatization, [SDV]Life Sciences [q-bio], Arabidopsis, food and beverages, Photosystem II Protein Complex, Cell Biology, Plant Science, General Medicine, 01 natural sciences, Biochemistry, Thylakoids, Electron Transport, 03 medical and health sciences, Homeostasis, Photosynthesis, Oxidation-Reduction, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Arabidopsis plants were grown from seeds at different photon flux densities (PFDs) of white light ranging from 65 to 800 µmol photons m$^{−2}$ s$^{−1}$. Increasing PFD brought about a marked accumulation of plastoquinone (PQ) in leaves. However, the thylakoid photoactive PQ pool, estimated to about 700 pmol mg$^{−1}$ leaf dry weight, was independent of PFD; PQ accumulation in high light mostly occurred in the photochemically non-active pool (plastoglobules, chloroplast envelopes) which represented up to 75% of total PQ. The amounts of PSII reaction center (on a leaf dry weight basis) also were little affected by PFD during growth, leading to a constant PQ/PSII ratio at all PFDs. Boosting PQ biosynthesis by overexpression of a solanesyl diphosphate-synthesizing enzyme strongly enhanced the PQ levels, particularly at high PFDs. Again, this accumulation occurred exclusively in the non-photoactive PQ pool. Mutational suppression of the plastoglobular ABC1K1 kinase led to a selective reduction of the thylakoid PQ pool size to ca. 400 pmol mg$^{−1}$ in a large range of PFDs, which was associated with a restriction of the photosynthetic electron flow. Our results show that photosynthetic acclimation to light intensity does not involve modulation of the thylakoid PQ pool size or the amounts of PSII reaction centers. There appears to be a fixed amount of PQ molecules for optimal interaction with PSII and efficient photosynthesis, with the extra PQ molecules being stored outside the thylakoid membranes, implying a tight regulation of PQ distribution within the chloroplasts.
Published: 2022
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7. eQTLs are key players in the integration of genomic and transcriptomic data for phenotype prediction

Author: Vincent Segura, Leopoldo Sanchez, Abdou Rahmane Wade, Harold Duruflé, Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office National des Forêts (ONF)-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)-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), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Diversité, Adaptation et Amélioration de la Vigne [AGAP] (DAAV), 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)-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), The NOVELTREE project (EU-FP7-211868). INRAE SELGEN metaprogramme (EPINET project)., NOVELTREE project (EU-FP7-211868). SYBIOPOP project. B4EST project. EPINET project, ANR-13-JSV6-0001,SYBIOPOP,Une approche de biologie intégrative pour améliorer le peuplier en vue de sa valorisation en bio-raffinerie grâce à une meilleure compréhension de l'architecture génétique de la production et de la qualité de la biomasse lignocellulosique(2013), and European Project: 773383,B4EST
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Multi-omics integration, Omics, Computational biology, Biology, eQTL, computer.software_genre, 01 natural sciences, Genome, Polymorphism, Single Nucleotide, Transcriptome, 03 medical and health sciences, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Predictability, 030304 developmental biology, 0303 health sciences, Genomics, Phenotype, Genetic architecture, Genomic Prediction, Expression quantitative trait loci, Trait, Populus nigra, computer, 010606 plant biology & botany, Data integration, Biotechnology
Abstract: Background Multi-omics represent a promising link between phenotypes and genome variation. Few studies yet address their integration to understand genetic architecture and improve predictability. Results Our study used 241 poplar genotypes, phenotyped in two common gardens, with xylem and cambium RNA sequenced at one site, yielding large phenotypic, genomic (SNP), and transcriptomic datasets. Prediction models for each trait were built separately for SNPs and transcripts, and compared to a third model integrated by concatenation of both omics. The advantage of integration varied across traits and, to understand such differences, an eQTL analysis was performed to characterize the interplay between the genome and transcriptome and classify the predicting features into cis or trans relationships. A strong, significant negative correlation was found between the change in predictability and the change in predictor ranking for trans eQTLs for traits evaluated in the site of transcriptomic sampling. Conclusions Consequently, beneficial integration happens when the redundancy of predictors is decreased, likely leaving the stage to other less prominent but complementary predictors. An additional gene ontology (GO) enrichment analysis appeared to corroborate such statistical output. To our knowledge, this is a novel finding delineating a promising method to explore data integration.
Published: 2022
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8. EBEC 2020: The conference that should have taken place!

Author: Schoepp-Cothenet Barbara, Magalon Axel, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Laboratoire de chimie bactérienne (LCB)
Subjects: 0106 biological sciences, 0303 health sciences, 03 medical and health sciences, [SDV]Life Sciences [q-bio], Biophysics, Cell Biology, Periodicals as Topic, 01 natural sciences, Biochemistry, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience
Published: 2022
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9. Promoting crop pest control by plant diversification in agricultural landscapes: A conceptual framework for analysing feedback loops between agro-ecological and socio-economic effects

Author: Aude Vialatte, Anaïs Tibi, Audrey Alignier, Valérie Angeon, Laurent Bedoussac, David A. Bohan, Douadia Bougherara, Alain Carpentier, Bastien Castagneyrol, Stéphane Cordeau, Pierre Courtois, Jean-Philippe Deguine, Jérôme Enjalbert, Frédéric Fabre, Fabienne Féménia, Hélène Fréville, Frédéric Goulet, Régis Grateau, Benoît Grimonprez, Nicolas Gross, Mourad Hannachi, Philippe Jeanneret, Laure Kuhfuss, Pierre Labarthe, Marie Launay, Marianne Lefebvre, Virginie Lelièvre, Stéphane Lemarié, Gilles Martel, Abel Masson, Mireille Navarrete, Manuel Plantegenest, Virginie Ravigné, Adrien Rusch, Frédéric Suffert, Abdoulaye Tapsoba, Olivier Therond, Sophie Thoyer, Vincent Martinet, Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction de l'Expertise scientifique collective, de la Prospective et des Etudes, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche d'Écodéveloppement (ECODEVELOPPEMENT), AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Economie de l'Environnement - Montpellier - UMR 5211 (CEE-M), 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), Structures et Marché Agricoles, Ressources et Territoires (SMART-LERECO), AGROCAMPUS OUEST-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Santé et agroécologie du vignoble (UMR SAVE), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), Département Environnements et Sociétés (Cirad-ES), Economie Publique (ECO-PUB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Etudes et de Coopération Juridique Interdisciplinaire (CECOJI), Université de Poitiers, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Agroscope, University of St Andrews [Scotland], Agroclim (AGROCLIM), Institut National de la Recherche Agronomique (INRA), Groupe de Recherche Angevin en Economie et Management (GRANEM), Institut National de l'Horticulture et du Paysage-AGROCAMPUS OUEST-Université d'Angers (UA), Département agronomie et sciences de l'environnement pour les agroécosystèmes (AgroEcoSystem), Laboratoire d'Economie Appliquée de Grenoble (GAEL), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), AGROCAMPUS OUEST-Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BIOlogie et GEstion des Risques en agriculture (BIOGER), Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Agronomie et Environnement - Antenne Colmar (LAE-Colmar ), Laboratoire Agronomie et Environnement (LAE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-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), Centre d'Economie de l'Environnement - Montpellier (CEE-M), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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 Agrocampus Ouest, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), 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’études et de coopération juridique interdisciplinaire - Université de Poitiers (CECOJI-UP), Université d'Angers (UA)-AGROCAMPUS OUEST-Institut National de l'Horticulture et du Paysage, Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, French Office for Biodiversity (OFB) through the national ECOPHYTO plan, David A. Bohan, Alex J. Dumbrell, Adam J. Vanbergen, 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), AGROCAMPUS OUEST, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de l'Horticulture et du Paysage-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)-Université d'Angers (UA), 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)-Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Gestion des ressources renouvelables et environnement (UPR GREEN), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Angers (UA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de l'Horticulture et du Paysage
Subjects: 2. Zero hunger, 0106 biological sciences, 13. Climate action, 11. Sustainability, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, 04 agricultural and veterinary sciences, 15. Life on land, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, 01 natural sciences, 010606 plant biology & botany, [SHS]Humanities and Social Sciences
Abstract: International audience; Given the negative environmental effects of conventional agricultural techniques, the need for biodiversity-friendly agriculture systems that rely more on ecosystem services and less on chemical inputs is becoming increasingly urgent. In this paper, we focus on crop protection strategies that are alternatives to the use of pesticides. Diversification of the plant component of agricultural areas at different space and time scales has been presented as a powerful socio-economic and agro-ecological mechanism for the sustainable control of pests. Our interdisciplinary group of scientific experts examined the literature on the ecological effects of plant diversification on pests and their natural enemies, as well as the social science literature on the conditions for farmers to adopt the corresponding practices, to assess the potential offered by plant diversification.We developed a conceptual framework that connects the agro-ecological and socio-economic components of an agricultural landscape in a dynamic loop accounting for interactions among elements at different spatial and temporal scales and their feedback effects. This article presents this framework and illustrates its application to the case of wheat production and protection. By explicitly connecting each level of agro-ecological organization with the potential socio-economic drivers and limitations underpinning the adoption and implementation of plant diversification in landscapes, this framework makes it possible to ana yse the synergies and antagonisms between different modes of diversification and the conditions of their deployment. Exploring this framework is a prerequisite to the identification of opportunities and key feed-back loops for designing diversification strategies that unlock the agro-ecological potential of f uture production systems. We conclude that there is a need for interdisciplinary research in experimental landscapes involving farmers and other local stakeholders to design sustainable future agricultural landscapes that deliver high levels of biological control services..
Published: 2022
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10. A combined approach utilizing UAV 3D imaging methods, in-situ measurements, and laboratory experiments to assess water evaporation and trace element uptake by tree species growing in a red gypsum landfill

Author: Michel Chalot, Jean-Michel Colin, Fabienne Tatin-Froux, bdoulaye Mahamat Malabad, Gilles Gallinet, Julien Parelle, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Faculté des Sciences et Technologies [Université de Lorraine] (FST ), and Université de Lorraine (UL)
Subjects: 0106 biological sciences, Stomatal conductance, Environmental Engineering, Gypsum, Unmanned Aerial Devices, UAV remote sensing, Health, Toxicology and Mutagenesis, Context (language use), engineering.material, 01 natural sciences, Calcium Sulfate, Trees, Transpiration, Ostrya carpinifolia, Imaging, Three-Dimensional, Environmental Chemistry, Leachate, Waste Management and Disposal, Betula, biology, Canopy conductance, Water, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, Pollution, Trace Elements, LAI, Waste Disposal Facilities, Agronomy, 13. Climate action, Betula pendula, [SDE]Environmental Sciences, 040103 agronomy & agriculture, engineering, 0401 agriculture, forestry, and fisheries, Environmental science, Laboratories, 010606 plant biology & botany
Abstract: International audience; The extractive industry is increasingly faced with problems of managing contaminated sites. The red gypsum landfill at the Ochsenfeld site is representative of the typology byproduct storage of the Ti-extraction activity. The management of the elemental content and the water body are the issues at this site. The aim of this study was to evaluate the canopy conductance (gcmax) of various tree species and the content of elements in the leaves, utilizing the opportunity of a demonstration plantation setup in 2014 with sixteen tree species, combined with a growth chamber experiment. We combined the gas exchange measurements with the data from two multispectral cameras with RGB and NIR bands embarked on an unmanned aerial vehicle (UAV). In the field, Ostrya carpinifolia, Maclura pomifera, and Rhus copallina had the highest gcmax of all planted tree species, and the high transpiration rate in O. carpinifolia was confirmed in a pot-based controlled experiment. Except R. copallina, the species with a high Mn content (O. carpinifolia, Betula pendula, and Salix aquatica grandis) had high stomatal conductance. O. carpinifolia could therefore be a species to exploit in the management of landfill leachates, especially in the context of climate change since this species is well adapted to dry environments.
Published: 2022
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11. Co-localised phosphorus mobilization processes in the rhizosphere of field-grown maize jointly contribute to plant nutrition

Author: Michael Santangeli, Eva Oburger, Gabrielle Daudin, Isabelle Bertrand, Doris Vetterlein, Walter W. Wenzel, Jakob Santner, Sandra Spielvogel, Bahar S. Razavi, Eva Lippold, Nataliya Bilyera, Christina Hummel, Steffen Schlüter, Xuechen Zhang, Christian-Albrechts University of Kiel, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Georg-August-University = Georg-August-Universität Göttingen, Department Soil System Science [UFZ Leipzig], Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Martin-Luther-University Halle-Wittenberg, University of Natural Resources and Life Sciences (BOKU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and University of Göttingen - Georg-August-Universität Göttingen
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Soil zymography, Soil Science, chemistry.chemical_element, Root hair, Diffusive gradients in thin films (DGT), 01 natural sciences, Microbiology, Planar pH optodes, Soil pH, Soil texture, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Root hairs, Root cap, 2. Zero hunger, Rhizosphere, biology, Phosphorus, Acid phosphatase, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, Horticulture, Root window, chemistry, Loam, 040103 agronomy & agriculture, biology.protein, 0401 agriculture, forestry, and fisheries, Plant nutrition, 010606 plant biology & botany
Abstract: International audience; Understanding phosphorus (P) dynamics in the rhizosphere is crucial for sustainable crop production. P mobilization processes in the rhizosphere include the release of plant and microbially-derived protons and extracellular phosphatases. We investigated the effect of root hairs and soil texture on the spatial distribution and intensity of P mobilizing processes in the rhizosphere of Zea mays L. root-hair defective mutant (rth3) and wildtype (WT) grown in two substrates (loam, sand). We applied 2D-chemical imaging methods in custom-designed root windows installed in the field to visualize soil pH (optodes), acid phosphatase activity (zymography), and labile P and Mn fluxes (diffusive gradients in thin films, DGT). The average rhizosphere extent for phosphatase activity and pH was greater in sand than in loam, while the presence of root-hairs had no impact. Acidification was significantly stronger at young root tissue (4 cm from root cap) and stronger in WT than rth3. Accompanied with stronger acidification, higher P flux was observed mainly around young, actively growing root tissues for both genotypes. Our results indicate that acidification was linked to root growth and created a pH optimum for acid phosphatase activity, i.e., mineralization of organic P, especially at young root tissues which are major sites of P uptake. Both genotypes grew better in loam than in sand; however, the presence of root hairs generally resulted in higher shoot P concentrations and greater shoot biomass of WT compared to rth3. We conclude that soil substrate had a larger impact on the extent and intensity of P solubilization processes in the rhizosphere of maize than the presence of root hairs. For the first time, we combined 2D-imaging of soil pH, phosphatase activity, and nutrient gradients in the field and demonstrated a novel approach of stepwise data integration revealing the interplay of various P solubilizing processes in situ.
Published: 2022
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12. Plants playing at home: Advantage of native plant seeds for ski slope revegetation in the French Pyrenees

Author: B. Dupin, B. Durand, Nathalie Fromin, J. Cambecèdes, Conservatoire Botanique National des Pyrénées et Midi-Pyrénées, Conservatoire Botanique National des Pyrénées et de Midi-Pyrénées (CBNP MP), 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), 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), and This work was supported by the programme ECOVARS led by the Conservatoire National botanique des Pyrénées et de Midi Pyrénées, with the financial support of the European
Subjects: 0106 biological sciences, Environmental Engineering, Prairie restoration, reclamation, native seeds, [SDE.MCG]Environmental Sciences/Global Changes, Introduced species, Management, Monitoring, Policy and Law, 01 natural sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, exogeneous seeds, Poaceae, Ecosystem, Revegetation, soil microbial activity, Nature and Landscape Conservation, prairie restoration, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, Native plant, Agronomy, subalpine grassland, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Plant cover, Environmental science, Seeding, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Machine levelling for the creation or maintenance of ski slopes is a major source of disturbance in high elevation ecosystems. Traditional, exogenous seed mixtures can help restoring plant cover and mitigate soil erosion, but they comprise species that are not ecologically adapted to high elevation conditions. Here, the use of local seed mixtures, harvested at nearby sites, was compared to that of exogenous seed mixtures for revegetation of three machine-graded ski runs with different soil conditions in the French Pyrenees. The plant cover, biomasses and associated soil microbial activity were recorded for four years following seeding. The results showed that the establishment of the plant cover was highly dependent of the soil conditions and strongly differed between paired plots that had received local or exogenous seed mixtures. In both seed treatments, some Poaceae dominated the plant cover, allowing the settlement of several spontaneous native species. But the plant cover established more rapidly and more densely, and included a larger cover of target, native species after seeding with local compared to exogenous seed mixtures.
Published: 2022
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13. An epi‐evolutionary model for predicting the adaptation of spore‐producing pathogens to quantitative resistance in heterogeneous environments

Author: Ramsès Djidjou-Demasse, Frédéric Fabre, Sébastien Lion, Arnaud Ducrot, Quentin Richard, Jean-Baptiste Burie, Santé et agroécologie du vignoble (UMR SAVE), 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), Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques Appliquées du Havre (LMAH), Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU), 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), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Conseil Interprofessionnel du Vin de BordeauxMarie-Curie FP7 COFUND People Programme. Grant Number: FP7-609398, ANR-16-CE35-0012,STEEP,Structuration spatiale, traitements et épidémiologie évolutive des parasites(2016), ANR-18-CE32-0004,ArchiV,Architecture génétique des caractères quantitatifs dans les interactions plante-virus: conséquences pour la gestion des variétés résistantes et/ou tolérantes à l'échelle du paysage.(2018), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), 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), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, quantitative resistance, Evolution, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Biology, integro-differential equations, 01 natural sciences, 03 medical and health sciences, basic reproduction number, Genetics, QH359-425, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Resistance (ecology), fungi, integro‐differential equations, Original Articles, Spore, adaptive dynamics, Evolutionary biology, spore‐producing pathogens, spore-producing pathogens, Original Article, Adaptation, General Agricultural and Biological Sciences, Basic reproduction number, resistance durability, 010606 plant biology & botany
Abstract: International audience; We have modeled the evolutionary epidemiology of spore-producing plant pathogens in heterogeneous environments sown with several cultivars carrying quantitative resistances. The model explicitly tracks the infection-age structure and genetic composition of the pathogen population. Each strain is characterized by pathogenicity traits determining its infection efficiency and a time-varying sporulation curve taking into account lesion aging. We first derived a general expression of the basic reproduction number urn:x-wiley:17524571:media:eva13328:eva13328-math-0001 for fungal pathogens in heterogeneous environments. We show that the evolutionary attractors of the model coincide with local maxima of urn:x-wiley:17524571:media:eva13328:eva13328-math-0002 only if the infection efficiency is the same on all host types. We then studied the contribution of three basic resistance characteristics (the pathogenicity trait targeted, resistance effectiveness, and adaptation cost), in interaction with the deployment strategy (proportion of fields sown with a resistant cultivar), to (i) pathogen diversification at equilibrium and (ii) the shaping of transient dynamics from evolutionary and epidemiological perspectives. We show that quantitative resistance affecting only the sporulation curve will always lead to a monomorphic population, whereas dimorphism (i.e., pathogen diversification) can occur if resistance alters infection efficiency, notably with high adaptation costs and proportions of the resistant cultivar. Accordingly, the choice of the quantitative resistance genes operated by plant breeders is a driver of pathogen diversification. From an evolutionary perspective, the time to emergence of the evolutionary attractor best adapted to the resistant cultivar tends to be shorter when resistance affects infection efficiency than when it affects sporulation. Conversely, from an epidemiological perspective, epidemiological control is always greater when the resistance affects infection efficiency. This highlights the difficulty of defining deployment strategies for quantitative resistance simultaneously maximizing epidemiological and evolutionary outcomes.
Published: 2022
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14. Participative design of the spatial and temporal development of improved cocoa agroforestry systems for yield and biodiversity

Author: Olivier Deheuvels, Christian Gary, Martin Notaro, Agrosystèmes Biodiversifiés (UMR ABSys), 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), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Center for Development of Agriculture and Forestry (CEDAF), We thank the Cacao Forest project, a partnership combining stakeholders from the agri-food industry, NGO and research, especially chocolate manufacturers and craftsmen, who funded this research (Valrhona, Bjorg Bonneterre & Cie, Weiss, Révillon and the Relais Desserts)., and Cacao Forest project
Subjects: 0106 biological sciences, Gestion fondée sur la participation, F08 - Systèmes et modes de culture, Biodiversity, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Plant Science, Agroforesterie, 01 natural sciences, Co-design, productivité agricole, Productivity, 2. Zero hunger, Planting density, Agroforestry, 04 agricultural and veterinary sciences, Rendement des cultures, Work (electrical), Diversification, Process (engineering), Soil Science, Diversification (marketing strategy), systèmes agroforestiers, Theobroma cacao, Spatial arrangement, business.industry, 15. Life on land, approches participatives, Agriculture, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Système de culture, Working group, business, Agronomy and Crop Science, Cropping, Agroecology, 010606 plant biology & botany, Espacement
Abstract: International audience; Highlights:• Cocoa-based agroforestry systems were co-designed to increase their productivity and generated income.• Various participative tools were combined in an original co-design approach.• Innovations focused on diversity, density and spatial arrangement of crop species.• This co-design method is generic and can be applied to other complex systems.Abstract: Farmers constantly adapt cropping systems to meet their needs. Cocoa farming is frequently associated with low incomes and little access to technical innovations for the small farmers and their families who are responsible for most cocoa production around the world. A collaborative approach, including different professionals working in the Dominican cocoa sector, led to the emergence of many technical innovations designed to modify the current agroforestry systems (AFS) in order to increase their overall productivity while maintaining a high level of biodiversity. Two types of original results are presented: (i) the co-design method that combined different participatory tools drawn from the literature and (ii) the results of applying the method for the co-design of complex AFS in four working groups. Compared to current AFS, a first level of innovation that emerged during the workshops involves the diversity and density of associated crops in AFS. The second level of innovation deals with the evolution over time and location of the different species selected for the AFS plots. This participatory work led to the formulation of four AFS prototypes whose crop species and densities follow spatio-temporal dynamics anticipated to be capable of providing better revenues while maintaining a high level of crop biodiversity. The different technical and management innovations of these prototypes are described and discussed. The AFS prototypes resulting from the co-design process will be established on farm to assess their agronomic, ecological and economic performances.
Published: 2022
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15. One Health concepts and challenges for surveillance, forecasting and mitigation of plant disease beyond the traditional scope of crop production

Author: Nicolas Sauvion, Claire Nédellec, Ghislain Géniaux, Cindy E. Morris, Samuel Soubeyrand, Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche d'Écodéveloppement (ECODEVELOPPEMENT), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Biostatistique et Processus Spatiaux (BioSP), ANR-17-CE32-0004,SPREE,Stratégie préemptive de surveillance de l'air et de l'eau pour anticiper l'émergence de maladies des plantes liés aux changements paysagers(2017), ANR-20-PCPA-0002,BEYOND,Building epidemiological surveillance and prophylaxis with observations both near and distant(2020), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, agroecology, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, long distance dissemination, spillover, virulence drivers, Context (language use), Plant Science, Disease, Horticulture, Biology, 01 natural sciences, 03 medical and health sciences, disease forecasting, Genetics, Environmental planning, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Disease surveillance, Scope (project management), Health management system, 15. Life on land, Plant disease, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, One Health, 13. Climate action, Sustainable management, knowledge inference, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; The One Health approach to understanding disease epidemiology and achieving surveillance and prevention is holistic all while focusing on zoonotic diseases. Many of its principles are similar to those espoused in Agroecology, begetting the question of what One Health can contribute - in practice - to preventing plant disease. Here we describe four knowledge challenges for plant health management that have arisen from the One Health experience for zoonotic diseases that could boost prospects for novel approaches to plant disease surveillance, prediction and prevention. The challenges are to i) uncover reservoirs and revise pathogen life histories, ii) elucidate drivers of virulence beyond the context of direct host-pathogen interactions, iii) account for the natural highways of long distance dissemination (i.e., surface water and air mass movement), and iv) update disease forecasts in the face of changing land use, cultivation practices and climate. Furthermore, we note that implementation of a One Health approach to disease surveillance and prevention will require mobilization of tools to deal with the representation and accessibility of massive and heterogeneous data and knowledge; with knowledge inference, data science, modelling, and pattern recognition; and multi-actor approaches that unite different sectors of society as well as different scientific disciplines. The infrastructure to build and the obstacles to overcome for a bona fide One Health approach to disease surveillance and prevention are the key commonalities where actors in the efforts to prevent zoonotic diseases and plant disease can work together for human, animal and plant health and sustainable management of biodiversity.
Published: 2022
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16. First report of grapevine virus L infecting grapevine in southeast France

Author: L. Svanella-Dumas, T. Candresse, M. Lefebvre, J. Lluch, S. Valiere, P. Larignon, A. Marais, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), 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)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Français de la Vigne et du Vin (IFV), 'Plan National Dépérissement du Vignoble' (Mycovir project), Université Toulouse III - Paul Sabatier (UT3), and 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)
Subjects: 0106 biological sciences, 2. Zero hunger, Viruses and viroids, 0303 health sciences, Subject Areas, [SDV]Life Sciences [q-bio], Pathogen detection, Plant Science, Causal Agent, 01 natural sciences, grapevine, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 03 medical and health sciences, Agronomy and Crop Science, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Grapevine virus L (GVL) is a recently described vitivirus (family Betaflexiviridae) with a positive-sense single-stranded RNA genome. It has so far been reported from China, Croatia, New-Zealand, the United States and Tunisia (Debat et al. 2019; Diaz-Lara et al. 2019; Alabi et al. 2020; Ben Amar et al. 2020). It has significant genetic variability (up to 26% of nucleotide divergence between isolates) and the existence of four phylogroups has been proposed (Alabi et al. 2020). In the frame of a project investigating the possible links between grapevine trunk diseases and grapevine virome, viral high throughput sequencing (HTS)-based testing was performed on symptomatic and asymptomatic grapevines collected in July 2019 in vineyards of four areas in France (Bourgogne, Charentes, Gard, Gironde) corresponding to five cultivars of Vitis vinifera (Cabernet franc, Cabernet Sauvignon, Chardonnay, Sauvignon, Ugni blanc). Total RNAs were purified from powder of 105 trunk wood samples using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, Saint-Quentin-Fallavier, France) and RNA-seq libraries were prepared using Zymo-Seq RiboFree Total RNA Library Prep Kit (Ozyme, Saint Cyr l’Ecole, France). HTS was performed on a S4 lane of Illumina NovaSeq 6000 using a paired-end read length of 2x150 bp. The trimmed sequence reads obtained from Chardonnay plants CH30-75M (99.9 M) and CH37-19S (114 M) from a vineyard in Gard were analyzed using CLC Genomics Workbench v21 (Qiagen, Courtaboeuf, France) and revealed complex mixed infections. Besides contigs representing a complete GVL genome (average scaffold coverage: 6,197x and 2,970x, respectively), contigs from grapevine rupestris stem pitting virus (1,697x ; 1,124x), grapevine virus A (82x ; 95x), grapevine pinot gris virus (1,475x ; 866x), grapevine leafroll-associated virus 3 (5,122x ; 1,042x), hop stunt viroid (13,783x ; 29,514x) and grapevine yellow speckle viroid 1 (690x ; 1158x) were also identified. Plant CH37-19S was also co-infected by grapevine rupestris vein feathering virus (164x). The GVL contigs integrated respectively 320,000 and 152,000 reads (corresponding to 0.32% and 0.11% of filtered/trimmed reads, respectively). The GVL genomic sequences from each sample (7,616 nt) have been deposited in GenBank (Accession nos. OK042110 and OK042111, respectively). The two contigs are nearly identical (99.9% nt identity) and share respectively 97.5% and 95.9% with GVL-KA from the USA (MH643739) and GVL-RS from China (MH248020), the closest isolates present in GenBank. To confirm the presence of GVL, the original grapevines were resampled in the field and total RNAs were extracted as described above from cambial scrappings and leaves. Total RNAs were used for RT-PCR tests using primers targeting a 279-bp fragment corresponding to the 3’ end of the coat protein gene and part of the nucleic acid binding protein gene (Debat et al. 2019). The Sanger-derived sequences from the amplicons shared 100% nt identities with the corresponding sequences of the HTS assembled genomes, confirming the presence of GVL in both tissues of both grapevine samples. To our knowledge, this represents the first report of the occurrence of GVL in vineyards in France. Given the complex mixed infection present in the two analyzed grapevines, no conclusions can be drawn on the pathogenicity of GVL. Further efforts are needed to better understand GVL distribution and its potential pathogenicity to grapevine. References Alabi, O J., et al. 2020. Arch. of Virol. 165:1905-1909. Ben Amar, A., et al. 2020. Plant disease 104:3274. Debat, H., et al. 2019. Eur J Plant Pathol. 155:319. Diaz-Lara, A., et al. 2019. Arch. of Virol. 164:2573. Acknowledgments The authors are grateful to the “Plan National Dépérissement du Vignoble” (Mycovir project) for the financial support
Published: 2022
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17. Growth and root-knot nematode infection of tomato are influenced by mycorrhizal fungi and earthworms in an intercropping cultivation system with leeks

Author: Caroline Djian-Caporalino, Jeremy Detrey, Laurence Maurousset, Julia Clause, Nathalie Pourtau, Nathalie Marteu, Didier Bouchon, Joan Doidy, Valentin Cognard, Cécile Vriet, Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Ecologie, Evolution, Symbiose (EES), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), and Sucres & Echanges Végétaux-Environnement (SEVE)
Subjects: 0106 biological sciences, Rhizophagus irregularis, [SDV]Life Sciences [q-bio], Soil Science, 01 natural sciences, 03 medical and health sciences, medicine, Meloidogyne incognita, Gall, Root-knot nematode, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Ecology, biology, medicine.disease, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), Horticulture, Nematode infection, Shoot, Monoculture, Solanum, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: In a greenhouse experiment, we investigated the influence of leek (Allium porrum) intercropping, mycorrhizal fungi and earthworms on the root-knot nematode infection by Meloidogyne incognita (RKN) and the growth and development of tomato plants (Solanum lycopersicum). Tomato plants were grown in pots, intercropped with leeks or in monoculture, and earthworms and/or arbuscular mycorrhizal fungi (AMF) were introduced. The effects of these two treatments on root-knot nematode infection and tomato plant growth and development were assessed i) by counting the galls induced by the nematodes and the number of egg masses on their roots, and ii) by measuring their height increase, shoot and root dry biomasses and flowering time. Tomato growth was increased with leek compared to the monoculture (e.g., +82% shoot biomass), probably due to a lower plant-plant competition, although a facilitation effect cannot be excluded. The presence of leeks did not reduce the number of galls (per g of root). The presence of AMF (Rhizophagus irregularis) increased the overall infection of M. incognita (e.g., +36% egg masses) and induced more galls with multiple egg masses in the leek-tomato association (+71%) but did not increase plant biomass. On the other hand, it increased plant height in presence of the compost earthworms (Eisenia andrei) compared to earthworms alone with RKN (+2%). It also delayed the flowering compared to RKN alone (+7.6 days in average). Competition between the two tomato plants in monoculture probably strongly impacted plant growth, flowering time and thereby the RKN infection, but leek-tomato interactions should be further examined. The overall increased number of multiple egg masses per gall in presence of AMF is contrary to its protective effect reported in the litterature.
Published: 2022
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18. 'Je t'aime moi non plus': A love-hate relationship between iron and phosphate

Author: Laurent Nussaume, Thierry Desnos, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Plant Environmental Physiology and Stress Signaling (PEPSS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), ANR-18-CE20-0023,BioPhyt,Mode d'action de phytostimulants biosourcés sur une voie de signalisation multi-stress(2018), ANR-21-CE12-0016,ULTIM,Elucider la perception du Phosphate chez les plantes grâce au développement de l'imagerie en temps réelle de la transcription(2021), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Signalisation de l'Adaptation des Végétaux à l'Environnement (SAVE)
Subjects: 0106 biological sciences, 0303 health sciences, Iron, [SDV]Life Sciences [q-bio], Plant Science, Biology, Phosphate, 01 natural sciences, Adaptation, Physiological, Phosphates, 03 medical and health sciences, chemistry.chemical_compound, chemistry, Stress, Physiological, Love–hate relationship, Theology, Molecular Biology, Plant Physiological Phenomena, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience
Published: 2022
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19. A European perspective on opportunities and demands for field-based crop phenotyping

Author: Juan Manuel Herrera, Alison R. Bentley, Emilie J. Millet, Peter Lootens, Merlijn Morisse, Michela Janni, Francesco Cellini, Onno Muller, Darren M. Wells, Morten Lillemo, Sven Fahrner, Universiteit Gent = Ghent University (UGENT), University of Nottingham, UK (UON), 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), Wageningen University and Research [Wageningen] (WUR), Norwegian University of Life Sciences (NMBU), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura (Alsia), Research Institute for Agricultural, Fisheries and Food (ILVO), Agroscope, International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Istituto dei Materiali per l'Elettronica ed il Magnetismo [Genova] (IMEM-CNR), the Foundation for Research Levy on Agricultural Products (FFL), the Agricultural Agreement Research Fund (JA) in Norway through NFR grant grants 267806 and 320090, Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2070 – 390732324., European Project: 739514,EMPHASIS-PREP, European Project: 731013 ,EPPN2020(2017), Universiteit Gent = Ghent University [Belgium] (UGENT), 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 Consiglio Nazionale delle Ricerche (CNR)
Subjects: 0106 biological sciences, Phenotyping networks, IMPACT, Computer science, Soil Science, User requirements document, Wiskundige en Statistische Methoden - Biometris, 01 natural sciences, Field (computer science), Plant breeding, ISO-9000 CERTIFICATION, 03 medical and health sciences, Field based, PLANT, Mathematical and Statistical Methods - Biometris, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Food security, Perspective (graphical), Stakeholder, Biology and Life Sciences, 15. Life on land, Remote sensing, Plant phenotyping, Data science, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Software deployment, ddc:640, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; The challenges of securing future food security will require deployment of innovative technologies to accelerate crop production. Plant phenotyping methods have advanced significantly, spanning low-cost hand-held devices to large-scale satellite imaging. Field-based phenotyping aims to capture plant response to the environment, generating data that can be used to inform breeding and selection requirements. This in turn requires access to multiple representative locations and capacities for collecting useful information. In this paper we identify the current challenges in access to field phenotyping in multiple locations in Europe based on stakeholder feedback. We present a map of current infrastructure and propose opportunities for greater integration of existing facilities for meeting different user requirements. We also review the currently available technology and data requirements for effective multi-location field phenotyping and provide recommendations for ensuring future access and coordination. Taken together we provide an overview of the current status of European field phenotyping capabilities and provides a roadmap for their future use to support crop improvement. This provides a wider framework for the analysis and planning of field phenotyping activities for crop improvement worldwide.
Published: 2022
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20. Root traits of crop species contributing to soil shear strength

Author: Matthieu Forster, Carolina Ugarte, Mathieu Lamandé, Michel-Pierre Faucon, Agro-écologie, Hydrogéochimie, Milieux et Ressources (AGHYLE), UniLaSalle, and Aarhus University [Aarhus]
Subjects: 2. Zero hunger, 0106 biological sciences, crop species, [SDV]Life Sciences [q-bio], Soil Science, 04 agricultural and veterinary sciences, Soil cohesion, Crop species, compaction, Root traits, 15. Life on land, 01 natural sciences, Angle of internal friction, root traits, 040103 agronomy & agriculture, soil shear strength, 0401 agriculture, forestry, and fisheries, compaction, angle of internal friction, Soil shear strength, 010606 plant biology & botany
Abstract: Roots of annual species would be able to conserve soil properties during traffic induced compaction. The objective of this study was to determine and compare root traits and soil shear strength for three crop species with contrasted root types and morphological traits to see if roots of annual species are able to increase soil shear strength and thus explain the soil properties conservation. The experiment was performed under controlled conditions in steel cylinders containing a repacked loamy sand, with initial dry bulk density of 1.2 g cm−3 and that was kept moist. Soil shear strength parameters, i.e. cohesion and angle of internal friction, were determined from direct shear tests for soil cores at a soil matric potential of −10 kPa (i.e. water content at field capacity). The direct shear tests were performed with six external normal stress levels (25, 34, 44, 63, 83 and 93 kPa) and at a constant shear rate of 3 mm.min−1, and applying Mohr Coulomb equation. The difference of root type, root length density, root density, specific root length and root dry matter content among crop species was not related to a difference in soil shear strength. The root volume density was the main trait involved in both soil cohesion and the angle of internal friction. This study highlights the effect of roots of annual crop species on soil shear strength by comparing their root traits to the apparent cohesion of soil core where they grow. Vicia faba would be a good candidate to improve soil shear strength for soil conservation. This study constitutes a step towards improving the understanding of plants’ effects on soil shear strength with regards to selecting species and designing cropping systems for soil conservation.
Published: 2022
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21. Assessment of the combined effects of beef cattle manure and lemon peel waste on soil-plant biochemical properties and phosphorus uptake by ryegrass

Author: Cecilia Paredes, Rodrigo Rodriguez, María de la Luz Mora, Siobhan Staunton, Paola Duran, Universidad de la frontera [Chile], Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and FONDECYT 1181050.
Subjects: 0106 biological sciences, Amendment, Soil Science, chemistry.chemical_element, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, 01 natural sciences, complex mixtures, Organic residues, Soil health, Plant nutrition, 2. Zero hunger, Ecology, Chemistry, Phosphorus, fungi, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, Agricultural and Biological Sciences (miscellaneous), Manure, Soil quality, 6. Clean water, Agronomy, 13. Climate action, Oxidative stress, Soil water, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Soil fertility, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Organic fertilizer, 010606 plant biology & botany
Abstract: International audience; Agroindustrial waste-derived amendments may be used as substitutes for synthetic fertilizers to improve soil physicochemical and biological properties and crop production. Microbial activity plays an essential role in the beneficial effects of organic amendments on soil quality. In this study, we investigated the combined effects of two different agroindustrially-derived amendments, namely, beef cattle manure (CM) and lemon peel (LP), on soil biological properties, plant nutrition and antioxidant responses in ryegrass to evaluate their putative use as organic phosphorus fertilizers. A combined amendment of CM + LP was more effective than each amendment used separately. For example, the microbial biomass in the CM + LP group was more than 4 times that of the control. This can be largely attributed to the fungal community because the richness biodiversity index was greater than that of the bacterial and fungal biomass. The bacterial biodiversity index of the treated soils was lower than that of the control but was less dominant and more changeable with soil chemical parameters such as Al content and pH. Interestingly, ryegrass yield and phosphorus uptake significantly increased with the addition of combined CM + LP (43% and 44%, respectively) with respect to treatments with synthetic supertriple phosphate fertilizer (STP). Less oxidative stress was observed in treatments with CM + LP supplementation than in treatments with supertriple phosphate fertilizer. In conclusion, the combined application of CM + LP showed a beneficial effect on P uptake and oxidative stress with a concomitant increase in plant productivity, indicating that the combined amendment could be used as an organic fertilizer to improve the soil fertility and sustainability of agricultural production systems.
Published: 2022
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22. Next biotechnological plants for addressing global challenges: The contribution of transgenesis and new breeding techniques

Author: Bleuenn Rault, Victor C. Pallares, Marcel Kuntz, Agnès E. Ricroch, Jacqueline Martin-Laffon, AgroParisTech, Université Paris-Saclay, Plantes, Stress & Métaux (MetalStress), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), COST Association (European Cooperation in Science and Technology), COST Action PlantEd (CA18111), and ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017)
Subjects: 0106 biological sciences, ISAAA: International Service for the Acquisition of Agribiotech Applications, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Coronavirus disease 2019 (COVID-19), TALEN: Transcription, Bioengineering, molecular farming, Biology, Crop species, 01 natural sciences, edible vaccine BBTV: Banana bunchy top virus, 03 medical and health sciences, Genome editing, Biofuel, Marketed products, CRISPR-Cas: Clustered Regularly Interspaced Short Palindromic Repeats, genome editing, ODM: Oligonucleotide-Directed Mutagenesis, Molecular Biology, 030304 developmental biology, 2. Zero hunger, Gene Editing, 0303 health sciences, Vaccines, Food security, Global challenges, business.industry, EU: European Union, Public sector, Gene Transfer Techniques, CBDS: Cassava Brown Streak Disease, General Medicine, Plants, Genetically Modified, Recombinant Proteins, Biotechnology, Transgenesis, Plant Breeding, CBI: Corporate Business Information, Edible vaccine, CRISPR-Cas Systems, CRISPR-Cas9, business, Genome, Plant, 010606 plant biology & botany
Abstract: International audience; The aim of this survey is to identify and characterize new products in plant biotechnology since 2015, especially in relation to the advent of New Breeding Techniques (NBTs) such as gene editing based on the CRISPR-Cas system. Transgenic (gene transfer or gene silencing) and gene edited traits which are approved or marketed in at least one country, or which have a non-regulated status in the USA, are collected, as well as related patents worldwide. In addition, to shed light on potential innovation for Africa, field trials on the continent are examined. The compiled data are classified in application categories, including agronomic improvements, industrial use and medical use, namely production of recombinant therapeutic molecules or vaccines (including against Covid-19). The data indicate that gene editing appears to be an effective complement to 'classical' transgenesis, the use of which is not declining, rather than a replacement, a trend also observed in the patenting landscape. Nevertheless, increased use of gene editing is apparent. Compared to transgenesis, gene editing has increased the proportion of some crop species and decreased others amongst approved, non-regulated or marketed products. A similar differential trend is observed for breeding traits. Gene editing has also favored the emergence of new private companies. China, and prevalently its public sector, overwhelmingly dominates the patenting landscape, but not the approved/marketed one, which is dominated by the USA. The data point in the direction that regulatory environments will favor or discourage innovation.
Published: 2022
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23. Steneotarsonemus ananas (Acari: Tarsonemidae): a complementary description from Australian pineapples and a new pest on Neoregelia spp. (Bromeliaceae) in Costa Rica

Author: Hugo Aguilar-Piedra, Ana María Solano-Guevara, Ronald Ochoa, Owen D. Seeman, Laboratorio de Acarología, Centro de Investigación en Protección de Cultivos (CIPROC), Escuela de Agronomía, Facultad de Ciencias Agroalimentarias, Universidad de Costa Rica, PO Box 2060, San José, Costa Rica., Queensland Museum, PO Box 3300, South Brisbane 4101, Australia., and SEL, ARS, USDA, BARC-W, 10300 Baltimore Ave, Bldg 005, Room 137, Beltsville, Maryland 20705, USA.
Subjects: 0106 biological sciences, Bromeliaceae, Costa Rica, USA (California, food.ingredient, mites, Arthropoda, Aacriformes, [SDV]Life Sciences [q-bio], Trombidiformes, Colombia, Acariformes, Tarsonemidae, 01 natural sciences, Hawaii), food, Aechmea, Arachnida, Botany, Animalia, Acari, Ananas, Neoregelia, Taxonomy, Steneotarsonemus, biology, Steneotarsonemus ananas, Australia, Biodiversity, biology.organism_classification, Guatemala, 010602 entomology, Insect Science, 010606 plant biology & botany
Abstract: International audience; The pineapple tarsonemid mite Steneotarsonemus ananas (Tryon), 1898 is associated with pineapple around the world, including Costa Rica. Here, we report its association with Neoregelia sp. (Bromeliaceae) for the first time. These mites damaged the plantlets considerably, affecting the esthetic quality of the product and thus causing economic losses to the local growers. This discovery prompted us to redescribe the adult females and males from the type host and locality (pineapple in Queensland, Australia) and compare it with the original description, subsequent descriptions, and material collected from the USA, Costa Rica, and Colombia on pineapple, Neoregelia, and an unidentified bromeliad. Further specimens from pineapple in Guatemala were identified as the same species and represent the first record for this country. We concur with previous observations that the original description by Tryon is not the same species in subsequent descriptions. We tentatively consider all specimens examined the same as those described as S. ananas in succeeding descriptions, i.e., Steneotarsonemus ananas Tryon sensu Beer.
Published: 2021
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24. Editorial feature: Meet the PCP editor—Yonghua Li-Beisson

Author: Yonghua Li-Beisson, Environnement, Bioénergie, Microalgues et Plantes (EBMP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bioénergie et Microalgues (EBM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0303 health sciences, 03 medical and health sciences, Physiology, [SDV]Life Sciences [q-bio], Cell Biology, Plant Science, General Medicine, 01 natural sciences, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Yonghua Li-Beisson received a B.Sc. from Henan University of Technology, China, and a Ph.D. from the University of Hull (England), where her work highlighted the importance of reducing power for lipid synthesis in oleaginous fungi. She then conducted postdoctoral research at Michigan State University focusing on understanding seed oil biosynthesis as well as dissecting the molecular pathways of lipid polyester synthesis and assembly. Since 2009, Yonghua is a staff scientist at the French Atomic and Alternative Energies Commission in France. Her current work focuses on dissecting lipid metabolism in microalgae, in particular using the model green microalga Chlamydomonas reinhardtii (Li-Beisson et al. 2019). In addition to leading her research team, she is also a director of the lipidomics platform HelioBiotec (https://www.cite-des-energies.fr/biam/plateformes-technologiques/heliobiotec/). Since 2016, Yonghua is a serving editor for Plant and Cell Physiology and handles papers in the area of plant and algal lipid metabolism and physiology
Published: 2021
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25. Co-inoculation with arbuscular mycorrhizal fungi differing in carbon sink strength induces a synergistic effect in plant growth

Author: Xinlu Zhang, Maria M. Martignoni, Vasilis Kokkoris, Miranda M. Hart, Daniel Rosa, Rebecca C. Tyson, Jimmy Garnier, Department of Mathematics, University of British Columbia, Kelowna, BC, Laboratoire de Mathématiques (LAMA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Department of Biology, University of British Columbia, Canada, Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Department of mathematics, and University of British Columbia, Kelowna
Subjects: 0106 biological sciences, Statistics and Probability, Carbon Sequestration, productivity, carbon sink strength, mutualism, synergy, Biology, 010603 evolutionary biology, 01 natural sciences, Plant Roots, General Biochemistry, Genetics and Molecular Biology, Soil, Nutrient, Mycorrhizae, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], Ecosystem, Biomass, multiple mutualist effects (MMEs), Restoration ecology, nutrient exchange, Soil Microbiology, agriculture, 2. Zero hunger, Mutualism (biology), [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Biomass (ecology), General Immunology and Microbiology, Applied Mathematics, fungi, Fungi, Carbon sink, food and beverages, General Medicine, 15. Life on land, Carbon, Arbuscular mycorrhizal fungi (AMF), Agronomy, Productivity (ecology), 13. Climate action, Modeling and Simulation, Sink (computing), General Agricultural and Biological Sciences, inoculum, 010606 plant biology & botany
Abstract: International audience; Arbuscular mycorrhizal (AM) fungi play a key role in determining ecosystem functionality. Understanding how diversity in the fungal community affects plant productivity is therefore an important question in ecology. Current research has focused on understanding the role of functional complementarity in the fungal community when the host plant faces multiple stress factors. Fewer studies, however, have investigated how variation in traits affecting nutrient exchange can impact the plant growth dynamics, even in the absence of environmental stressors. Combining experimental data and a mathematical model based on ordinary differential equations, we investigate the role played by carbon sink strength on plant productivity. We simulate and measure plant growth over time when the plant is associated with two fungal isolates with different carbon sink strength, and when the plant is in pairwise association with each of the isolates alone. Overall, our theoretical as well as our experimental results show that co-inoculation with fungi with different carbon sink strength can induce positive non-additive effects (or synergistic effects) in plant productivity. Fungi with high carbon sink strength are able to quickly establish a fungal community and increase the nutrient supply to the plant, with a consequent positive impact on plant growth rate. On the other side, fungi with low carbon sink strength inflict lower carbon costs to the host plant, and support maximal plant productivity once plant biomass is large. As AM fungi are widely used as organic fertilizers worldwide, our findings have important implications for restoration ecology and agricultural management.
Published: 2021
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26. Modelling interference between vectors of non-persistently transmitted plant viruses to identify effective control strategies

Author: Marta Zaffaroni, Loup Rimbaud, Ludovic Mailleret, Nik J. Cunniffe, Daniele Bevacqua, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Pathologie Végétale (PV), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Biological control of artificial ecosystems (BIOCORE), 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'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Sciences (Cambridge, UK), University of Cambridge [UK] (CAM), PACA (Provence-Alpes-Côtes d’Azur) region, INRAE Agroècosystèmes department, Bourse Perdiguier (Avignon Université), Université Nice Sophia Antipolis (... - 2019) (UNS), Zaffaroni, Marta [0000-0002-2951-8626], Rimbaud, Loup [0000-0002-8098-9984], Mailleret, Ludovic [0000-0001-7019-8401], Cunniffe, Nik J [0000-0002-3533-8672], Bevacqua, Daniele [0000-0002-3341-1696], Apollo - University of Cambridge Repository, Cunniffe, Nik [0000-0002-3533-8672], Cunniffe, Nik J. [0000-0002-3533-8672], and The PhD grant to M.Z. was funded by the PACA (Provence-Alpes-Côtes d’Azur) region and INRAE Agroècosistèmes department. M.Z. also thanks Avignon Université for the Bourse Perdiguier, which supported her temporary stay at the University of Cambridge during which much of this work was done.
Subjects: 0106 biological sciences, Epidemiology, Pesticide application, Plant Science, FOS: Health sciences, Disease Vectors, 01 natural sciences, Plant Viruses, Roguing, Medical Conditions, 2.2 Factors relating to the physical environment, Vector (molecular biology), Biology (General), 2. Zero hunger, 2 Aetiology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Ecology, plant pathology, Eukaryota, food and beverages, Agriculture, Plant disease, 3108 Plant Biology, 3. Good health, Insects, Infectious Diseases, Computational Theory and Mathematics, Modeling and Simulation, Viral disease, Viral Vectors, Agrochemicals, Infection, Research Article, Crops, Agricultural, Arthropoda, Infectious Disease Control, QH301-705.5, 30 Agricultural, Veterinary and Food Sciences, epidemiological model, Biology, 010603 evolutionary biology, Microbiology, Insect Control, Infectious Disease Epidemiology, Vector Biology, Cellular and Molecular Neuroscience, 03 medical and health sciences, Disease management (agriculture), Plant virus, Virology, Genetics, Animals, Pesticides, Disease Eradication, Fertilizers, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Plant Diseases, Medicine and health sciences, Biology and life sciences, Host (biology), business.industry, fungi, Organisms, 15. Life on land, Invertebrates, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Biotechnology, Insect Vectors, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Species Interactions, aphid, Aphids, Pest Control, business, Zoology, Entomology, Viral Transmission and Infection, 010606 plant biology & botany, 31 Biological Sciences
Abstract: Aphids are the primary vector of plant viruses. Transient aphids, which probe several plants per day, are considered to be the principal vectors of non-persistently transmitted (NPT) viruses. However, resident aphids, which can complete their life cycle on a single host and are affected by agronomic practices, can transmit NPT viruses as well. Moreover, they can interfere both directly and indirectly with transient aphids, eventually shaping plant disease dynamics. By means of an epidemiological model, originally accounting for ecological principles and agronomic practices, we explore the consequences of fertilization and irrigation, pesticide deployment and roguing of infected plants on the spread of viral diseases in crops. Our results indicate that the spread of NPT viruses can be i) both reduced or increased by fertilization and irrigation, depending on whether the interference is direct or indirect; ii) counter-intuitively increased by pesticide application and iii) reduced by roguing infected plants. We show that a better understanding of vectors’ interactions would enhance our understanding of disease transmission, supporting the development of disease management strategies., Author summary A range of both experimental and theoretical studies show that the behaviour and population dynamics of insects depend strongly upon interactions with other insect species. These interactions have the potential to greatly affect the dynamics of insect-vectored plant disease, as transmission of viruses is intimately dependent on the local density of vectors, as well as how they select and move between potential host plants. Surprisingly, the effects of interaction between vector species on epidemics remains little studied and even worse understood, probably because experimentation is costly and difficult. Here, we present a model which permits us to investigate the effect of interaction between a virus, two vector species and the host plant on the spread of viral disease in crops. In this study, our model is used to explore the consequences of common agronomic practices on epidemics. Our study highlights the importance of exploring vectors’ interactions to enhance the understanding of disease transmission, supporting the development of disease management strategies.
Published: 2021
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27. High variation in hydraulic efficiency but not xylem safety between roots and branches in four temperate broad‐leaved tree species

Author: Torben Lübbe, Laurent J. Lamarque, Sylvain Delzon, José M. Torres Ruiz, Régis Burlett, Christoph Leuschner, Bernhard Schuldt, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Georg-August-University [Göttingen], University of Würzburg = Universität Würzburg, German Research Foundation (DFG) - DFG GRK 1086Bordeaux International Post-Doctoral Program - UB101 CR1024-R s/CR 1024-6M, ANR-10-LABX-0045,COTE,COntinental To coastal Ecosystems: evolution, adaptability and governance(2010), ANR-10-EQPX-0016,XYLOFOREST,Plateforme d'Innovation ' Forêt-Bois-Fibre-Biomasse du Futur '(2010), European Project: FP7-339728, and Georg-August-University = Georg-August-Universität Göttingen
Subjects: 0106 biological sciences, 0303 health sciences, vulnerability curve, food and beverages, 15. Life on land, wood density, 01 natural sciences, 03 medical and health sciences, ddc:570, embolism resistance, wood anatomy, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, hydraulic architecture, vessel tapering, flow path, Ecology, Evolution, Behavior and Systematics, hydraulic conductivity, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; 1. Xylem hydraulic safety and efficiency are key traits determining tree fitness in a warmer and drier world. While numerous plant hydraulic studies have focused on branches, our understanding of root hydraulic functioning remains limited, although roots control water uptake, influence stomatal regulation and have commonly been considered as the most vulnerable organ along the hydraulic pathway.2. We investigated 11 traits related to xylem safety and efficiency along the hydraulic pathway in four temperate broad-leaved tree species.3. Continuous vessel tapering from coarse roots to stems and branches caused considerable reduction in hydraulic efficiency. Wood density was always lowest in roots, but did not decline linearly along the flow path. In contrast, xylem embolism resistance (P-50) did not differ significantly between roots and branches, except for one species. The limited variation in xylem safety between organs did not adequately reflect the corresponding reductions in vessel diameter (by similar to 70%) and hydraulic efficiency (by similar to 85%). Although we did not observe any trade-off between xylem safety and specific conductivity, vessel diameter, vessel lumen fraction and wood density were related to embolism resistance, both across and partly within organs.4. We conclude that coarse roots are not highly vulnerable to xylem embolism as commonly believed, indicating that hydraulic failure during soil drying might be restricted to fine roots. A free Plain Language Summary can be found within the Supporting Information of this article.
Published: 2021
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28. Potassium Use Efficiency of Plants

Author: Ivica Djalovic, Philippe Hinsinger, Philip J. White, Michael J. Bell, Zed Rengel, The James Hutton Institute, University of Queensland [Brisbane], Institute of Field and Vegetable Crops [Novi Sad], Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), The University of Western Australia (UWA), Murrell T.S., Mikkelsen R.L., Sulewski G., Norton R., Thompson M.L., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Potassium uptake, Potassium, Root function, chemistry.chemical_element, Context (language use), Root system, Biology, engineering.material, Photosynthesis, Intraspecific variation, Root exudates, 01 natural sciences, Crop, 03 medical and health sciences, Yield (wine), [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, 2. Zero hunger, Potassium remobilization, 0303 health sciences, Rhizosphere, 15. Life on land, Agronomy, chemistry, Interspecific variation, engineering, Fertilizer, 010606 plant biology & botany
Abstract: There are many terms used to define aspects of potassium (K) use efficiency of plants. The terms used most frequently in an agricultural context are (1) agronomic K use efficiency (KUE), which is defined as yield per unit K available to a crop and is numerically equal to the product of (2) the K uptake efficiency (KUpE) of the crop, which is defined as crop K content per unit K available and (3) its K utilization efficiency (KUtE), which is defined as yield per unit crop K content. There is considerable genetic variation between and within plant species in KUE, KUpE, and KUtE. Root systems of genotypes with greatest KUpE often have an ability (1) to exploit the soil volume effectively, (2) to manipulate the rhizosphere to release nonexchangeable K from soil, and (3) to take up K at low rhizosphere K concentrations. Genotypes with greatest KUtE have the ability (1) to redistribute K from older to younger tissues to maintain growth and photosynthesis and (2) to reduce vacuolar K concentration, while maintaining an appropriate K concentration in metabolically active subcellular compartments, either by anatomical adaptation or by greater substitution of K with other solutes in the vacuole. Genetic variation in traits related to KUpE and KUtE might be exploited in breeding crop genotypes that require less K fertilizer. This could reduce fertilizer costs, protect the environment, and slow the exhaustion of nonrenewable resources.
Published: 2021
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29. Rhizosphere Processes and Root Traits Determining the Acquisition of Soil Potassium

Author: John L. Kovar, Philip J. White, Philippe Hinsinger, Michael J. Bell, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Queensland [Brisbane], USDA-ARS : Agricultural Research Service, The James Hutton Institute, King Saud University [Riyadh] (KSU), Murrell T.S., Mikkelsen R.L., Sulewski G., Norton R., Thompson M.L., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Mobility Root hair, Root length, Bioavailability, Potassium, chemistry.chemical_element, Root hair, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, 01 natural sciences, Acidification, Diffusion, Depletion, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Organic matter, Dissolution, Subsoil, 2. Zero hunger, chemistry.chemical_classification, Rhizosphere, Chemistry, fungi, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, Agronomy, Rooting depth, Soil water, 040103 agronomy & agriculture, Exudation, 0401 agriculture, forestry, and fisheries, Clay minerals, 010606 plant biology & botany
Abstract: Plants acquire K+ ions from the soil solution, and this small and dynamic pool needs to be quickly replenished via desorption of surface-adsorbed K from clay minerals and organic matter, by release of interlayer K from micaceous clay minerals and micas, or structural K from feldspars. Because of these chemical interactions with soil solid phases, solution K+ concentration is kept low and its mobility is restricted. In response, plants have evolved efficient strategies of root foraging. Root traits related to root system architecture (root angle and branching), root length and growth, together with root hairs and mycorrhiza-related traits help to determine the capacity of plants to cope with the poor mobility of soil K. Rooting depth is also important, given the potentially significant contribution of subsoil K in many soils. Root-induced depletion of K+ shifts the exchange equilibria, enhancing desorption of K, as well as the release of nonexchangeable, interlayer K from minerals in the rhizosphere. Both these pools can be bioavailable if plant roots can take up significant amounts of K at low concentrations in the soil solution (in the micromolar range). In addition, roots can significantly acidify their environment or release large amounts of organic compounds (exudates). These two processes ultimately promote the dissolution of micas and feldspars in the rhizosphere, contributing to the mining strategy evolved by plants. There are thus several root or rhizosphere-related traits (morphological, physiological, or biochemical) that determine the acquisition of K by crop species and genotypes.
Published: 2021
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30. Genetic architecture and genomic prediction accuracy of apple quantitative traits across environments

Author: Christian Dujak, Beat Keller, Maria José Aranzana, Andrea Knauf, Marijn Rymenants, Annemarie Auwerkerken, François Laurens, Nadia Sanin, Michaela Jung, Helene Muranty, Frédérique Didelot, Mariusz Lewandowski, Andrea Patocchi, Walter Guerra, Bruno Studer, Morgane Roth, Mehdi Al-Rifai, Carolina Font i Forcada, Breeding Research Group, Institute of Agrifood Research and Technology (IRTA), Centre for Research in Agricultural Genomics (CRAG), Better3Fruit N.V., Research Centre Laimburg, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The National Institute of Horticultural Research, Unité Horticole (HORTI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich
Subjects: 0106 biological sciences, 0303 health sciences, Multivariate statistics, fungi, Univariate, Genome-wide association study, Computational biology, Biology, Quantitative trait locus, biochemical phenomena, metabolism, and nutrition, equipment and supplies, 01 natural sciences, complex mixtures, Genetic architecture, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Genotype, Trait, bacteria, Predictive modelling, 030304 developmental biology, 010606 plant biology & botany
Abstract: Implementation of genomic tools is desirable to increase the efficiency of apple breeding. The apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic prediction accuracy, and studying genotype by environment interactions (G×E). Here we show contrasting genetic architecture and genomic prediction accuracies for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic prediction accuracies of 0.18–0.88 were estimated using single-environment univariate, single-environment multivariate, multi-environment univariate, and multi-environment multivariate models. The G×E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.
Published: 2021

31. Tracking down coupled innovations supporting agroecological vegetable crop protection to foster sustainability transition of agrifood systems

Author: Boulestreau, Yann, Peyras, Claire-Lise, Casagrande, Marion, Navarrete, Mireille, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME), and Institut Technique de l'Agriculture Biologique (ITAB)
Subjects: 2. Zero hunger, 0106 biological sciences, agroecology, design, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, agrifood system, 04 agricultural and veterinary sciences, 01 natural sciences, sociotechnical levers, niche, coupled innovation, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Animal Science and Zoology, Agronomy and Crop Science, ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany
Abstract: International audience
Published: 2021

32. Root membrane ubiquitinome under short-term osmotic stress

Author: Nathalie Berger, Vincent Demolombe, Sonia Hem, Valérie Rofidal, Laura Steinmann, Gabriel Krouk, Amandine Crabos, Philippe Nacry, Lionel Verdoucq, Véronique Santoni, Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Proteomics, 0106 biological sciences, Proteome, [SDV]Life Sciences [q-bio], Arabidopsis, aquaporin, mass spectrometry, osmotic stress, ubiquitination, Plant Roots, 01 natural sciences, Catalysis, Inorganic Chemistry, 03 medical and health sciences, Osmotic Pressure, ddc:570, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy, 030304 developmental biology, 0303 health sciences, Ubiquitin, Lysine, Organic Chemistry, Membrane Proteins, General Medicine, Ubiquitinated Proteins, Computer Science Applications, Protein Processing, Post-Translational, 010606 plant biology & botany
Abstract: Osmotic stress can be detrimental to plants, whose survival relies heavily on proteomic plasticity. Protein ubiquitination is a central post-translational modification in osmotic mediated stress. Plants use the ubiquitin (Ub) proteasome system to modulate protein content, and a role for Ub in mediating endocytosis and trafficking plant plasma membrane proteins has recently emerged. In this study, we used the K-ε-GG antibody enrichment method integrated with high-resolution mass spectrometry to compile a list of 719 ubiquitinated lysine (K-Ub) residues from 450 Arabidopsis root membrane proteins (58% of which are transmembrane proteins), thereby adding to the database of ubiquitinated substrates in plants. Although no Ub motifs could be identified, the presence of acidic residues close to K-Ub was revealed. Our ubiquitinome analysis pointed to a broad role of ubiquitination in the internalization and sorting of cargo proteins. Moreover, the simultaneous proteome and ubiquitinome quantification showed that ubiquitination is mostly not involved in membrane protein degradation in response to short osmotic treatment, but putatively in protein internalization as described for the aquaporin PIP2;1. Our in silico analysis of ubiquitinated proteins shows that two E2 Ub ligases, UBC32 and UBC34, putatively target membrane proteins under osmotic stress. Finally, we revealed a positive role for UBC32 and UBC34 in primary root growth under osmotic stress.
Published: 2021

33. Multiplex CRISPR/Cas9 editing of the long‐chain acyl‐CoA synthetase family in the diatom Phaeodactylum tricornutum reveals that mitochondrial ptACSL3 is involved in the synthesis of storage lipids

Author: Xiahui Hao, Wenchao Chen, Alberto Amato, Juliette Jouhet, Eric Maréchal, Daniel Moog, Hanhua Hu, Hu Jin, Lingjie You, Fenghong Huang, Mark Moosburner, Andrew E. Allen, Yangmin Gong, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops, LIPID, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Laboratory for Cell Biology, Philipps-University Marburg, Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California, J. Craig Venter Institute [La Jolla, USA] (JCVI), National Natural Science Foundation of China (41776175 and 31961133008), Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2013-OCRI), 2021 CEA-CAS bilateral program, Institut Carnot 3BCAR, Grants from the United States Department of Energy Genomics Science program, US National Science Foundation, NSF-MCB-1818390, Gordon and Betty Moore Foundation GBMF3828, ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), Scripps Institution of Oceanography (SIO - UC San Diego), and University of California (UC)-University of California (UC)
Subjects: 0106 biological sciences, Diatoms, 0303 health sciences, Physiology, Fatty Acids, Multiplexed CRISPR/Cas9, Plant Science, Fatty acid, Long-chain acyl-CoA synthetase, 01 natural sciences, Phaeodactylum tricornutum, Triacylglycerol, Mitochondria, 03 medical and health sciences, Coenzyme A Ligases, Coenzyme A, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, CRISPR-Cas Systems, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Long-chain acyl-CoA synthetases (LACSs) play diverse and fundamentally important roles in lipid metabolism. While their functions have been well-established in bacteria, yeast and plants, the mechanisms by which LACS isozymes regulate lipid metabolism in unicellular oil-producing microalgae, including the diatom Phaeodactylum tricornutum, remain largely unknown. In P. tricornutum, a family of five genes (ptACSL1~5) encodes LACS activities. We generated single lacs knockout/knockdown mutants using multiplexed CRISPR/Cas9 method, and determined their substrate specificities towards different fatty acids (FAs) and subcellular localizations. ptACSL3 is localized in the mitochondria and its disruption led to compromised growth and reduced triacylglycerol (TAG) content when cells were bubbled with air. The ptACSL3 mutants showed altered FA profiles in two galactoglycerolipids and phosphatidylcholine (PC) with significantly reduced distribution of 16:0 and 16:1. ptACSL5 is localized in the peroxisome and its knockdown resulted in reduced growth rate and altered molecular species of PC and TAG, indicating a role in controlling the composition of acyl-CoAs for lipid synthesis. Our work demonstrates the potential of generating gene knockout mutants with the mutation of large fragment deletion using multiplexed CRISPR/Cas9 and provides insight into the functions of LACS isozymes in lipid metabolism in the oleaginous microalgae.
Published: 2021
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34. Stomatal responses in grapevine become increasingly more tolerant to low water potentials throughout the growing season

Author: Astrid Forneck, Alberto Calderan, Hervé Cochard, Enrico Peterlunger, Gregory A. Gambetta, Uri Hochberg, Paolo Sivilotti, Jose Carlos Herrera, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Università degli Studi di Udine - University of Udine [Italie], Università degli studi di Trieste = University of Trieste, 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 de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), and University of Trieste
Subjects: 0106 biological sciences, Pressure-volume curves, Stomatal conductance, Osmosis, anisohydric, isohydric, Drought tolerance, Turgor pressure, Growing season, Plant Science, Biology, 01 natural sciences, 03 medical and health sciences, water stress, Osmotic Pressure, vine hydraulics, Genetics, Osmotic pressure, Vitis, Cultivar, Plant Physiological Phenomena, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, fungi, Water, food and beverages, osmotic adjustment, Cell Biology, 15. Life on land, Adaptation, Physiological, Droughts, Plant Leaves, Horticulture, Vitis vinifera, drought acclimation, pressure-volume curves, stomatal conductance, 13. Climate action, Osmolyte, Plant Stomata, [SDE]Environmental Sciences, Seasons, 010606 plant biology & botany
Abstract: International audience; The leaf of a deciduous species completes its life cycle in a few months. During leaf maturation, osmolyte accumulation leads to a significant reduction of the turgor loss point (psi(TLP)), a known marker for stomatal closure. Here we exposed two grapevine cultivars to drought at three different times during the growing season to explore if the seasonal decrease in leaf psi(TLP) influences the stomatal response to drought. The results showed a significant seasonal shift in the response of stomatal conductance to stem water potential (g(s)similar to psi(stem)), demonstrating that grapevines become increasingly tolerant to low psi(stem) as the season progresses in coordination with the decrease in psi(TLP). We also used the SurEau hydraulic model to demonstrate a direct link between osmotic adjustment and the plasticity of g(s)similar to psi(stem). To understand the possible advantages of g(s)similar to psi(stem) plasticity, we incorporated a seasonally dynamic leaf osmotic potential into the model that simulated stomatal conductance under several water availabilities and climatic scenarios. The model demonstrated that a seasonally dynamic stomatal closure threshold results in trade-offs: it reduces the time to turgor loss under sustained long-term drought, but increases overall gas exchange particularly under seasonal shifts in temperature and stochastic water availability. A projected hotter future is expected to lower the increase in gas exchange that plants gain from the seasonal shift in g(s)similar to psi(stem). These findings show that accounting for dynamic stomatal regulation is critical for understanding drought tolerance.
Published: 2021
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35. Bioproduction of Anticancer Podophyllotoxin and Related Aryltretralin-Lignans in Hairy Root Cultures of Linum flavum L

Author: Avninder S. Bhambra, Duangjai Tungmunnithum, Atul Kabra, Cyrielle Corbin, Sara Mikac, Lucija Markulin, Samantha Drouet, Eric Lainé, Sullivan Renouard, Bilal Haider Abassi, Christophe Hano, Elisabeth Fuss, Randolph R.J. Arroo, Reza Kiani, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk (UG), University of Zagreb, Mahidol University [Bangkok], University of Tehran, I.K. Gujral Punjab Technical University, Kapurthala, India, Quaid-i-Azam University (QAU), Chimie et Biologie des Membranes et des Nanoobjets (CBMN), École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), De Montfort University [Leicester, United Kingdom] (DMU), Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, 72076, Tübingen, Germany, and University of Tübingen
Subjects: 0106 biological sciences, Lignan, [SDV]Life Sciences [q-bio], 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Hairy root, Linum flavum, medicine, heterocyclic compounds, Etoposide, 030304 developmental biology, Podophyllotoxin, 2. Zero hunger, 0303 health sciences, Traditional medicine, biology, Chemistry, Hairy roots, biology.organism_classification, Bioproduction, Anticancer, 010606 plant biology & botany, medicine.drug
Abstract: International audience; Podophyllotoxin (PPT) is the unique natural precursor of Etoposide, a topoisomerase II inhibitor drug, used in more than a dozen anticancer chemotherapy treatments. Etoposide is appearing on the list of essential medicines of the World Health Organization. PPT is still exclusively extracted from the rhizome of Podophyllum species, its main natural source. The supply of Podophyllum hexandrum plants is limited, since the occurrence of these plant species is scarce, collection is destructive, and the plants need a long regeneration period. As a consequence, this species is now endangered and listed on Appendix II of the Convention on International Trading of Endangered Species. Chemical synthesis of PPT is difficult due to the presence of four contiguous chiral centers and the presence of a base sensitive trans-lactone moiety. Alternatives are being actively searched, but so far, no wild plants have been described with similar PPT production capacity as compared to Podophyllum. However, several plants producing PPT or other related aryltetralin lignans (ATL) have been identified in recent decades, including the Linaceae. Given its high lignan accumulation capacity, Linum flavum is considered a promising alternative source of PPT and other related ATL. However, unlike the common flax L. usitatissimum, L. flavum has a low agricultural potential (e.g., slow growth and dehiscence of fruits). Therefore, in vitro cultures of plant cells and/or tissues provide an interesting alternative to whole L. flavum plants for the production of these valuable ATL. In particular, L. flavum hairy roots (HRs) accumulate high levels of ATL and it is also possible to further increase this ATL accumulation by the selection of the best genotype, optimization of cultures media and conditions and choice of carbon sources, use of plant growth regulators, elicitor treatments, or precursors’ addition. To date, the ATL accumulation levels can still be perceived insufficient for L. flavum HRs before being used as a commercially viable biotechnological production system. To reach this goal, a better knowledge of the mechanisms that regulate the metabolic flux of intermediates in the different branches of the ATL metabolic pathway will be an important prerequisite to direct the biosynthesis toward the production of a high amount of the desired PPT. In the future, metabolic engineering aiming at constructing the PPT pathway in a heterologous host is very appealing, but for that approach in-depth knowledge of the biosynthetic pathway toward PPT and other related ATL is necessary.
Published: 2021
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36. Nitrogen dynamics and fertilisation use efficiency: carry‐over effect of crop limitation

Author: T. Verdenal, J.E. Spangenberg, Á. Dienes‐Nagy, V. Zufferey, J.‐L. Spring, O. Viret, C. van Leeuwen, Agroscope, Institute of Earth Surface Dynamics [Lausanne], Université de Lausanne (UNIL), Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), and 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)
Subjects: 0106 biological sciences, 2. Zero hunger, amino acids, fungi, food and beverages, 04 agricultural and veterinary sciences, reserve mobilisation, 15. Life on land, Horticulture, 15N isotope labelling, 15 N isotope labelling, yield, 01 natural sciences, nitrogen use efficiency, 040501 horticulture, nitrogen use efciency, [SDE]Environmental Sciences, 0405 other agricultural sciences, 010606 plant biology & botany, foliar urea
Abstract: International audience; Background and Aims Knowing the impact of cultural practices on nitrogen (N) dynamics in perennial crops is critical to promote N use efficiency. This study focused on the impact of crop regulation on the plant N dynamics, on the fruit N composition, and on the N fertilisation use efficiency. Methods and Results A large crop load gradient was set in a homogeneous plot of the grape cultivar Chasselas. Fertilisation in the form of N-15-labelled foliar urea allowed the measurement of N uptake and partitioning among plant fractions. Dry mass, carbon, and N dynamics were assessed over two consecutive seasons. Crop regulation did not affect grape N concentration at harvest. Both N uptake and root N mobilisation were reduced in response to crop regulation. Fertilisation efficiency was higher under high-yield conditions in terms of N uptake and grape N accumulation. The carry-over effects of crop regulation in the following year were highlighted. Conclusions Crop regulation strongly affects the overall plant N cycle, that is, uptake, distribution and release. Crop regulation improves must sugar concentration at harvest, while N concentration remained unchanged. The efficiency of N fertilisation varies greatly with crop load, which limits the interest of fertilisation under low-yield conditions. Significance of the Study These results contribute to the development of accurate nutrition models and sustainable cultural practices.
Published: 2021
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37. Genome-wide and comparative phylogenetic analysis of senescence-associated NAC transcription factors in sunflower (Helianthus annuus)

Author: Bengoa Luoni, Sofia A., Cenci, Alberto, Moschen, Sebastian, Nicosia, Salvador, Radonic, Laura M., Sabio, Julia, Garcia, Langlade, Nicolas B., Vile, Denis, Rovere, Cecilia Vazquez, Fernandez, Paula, Instituto Nacional de Tecnología Agropecuaria (INTA), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INTA PE 1131022, 1131043, ANPCyT Préstamo BID PICT 2012–0390, PICT 2014–0175, PIP CONICET PIP 11220120100262CO, Marie Curie IRSES Project DEANN (PIRSES-GA-2013-612583), CONICET, SUNRISE and Heliagen Project, and ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011)
Subjects: 0106 biological sciences, Leaves, Arabidopsis thaliana, Arabidopsis, QH426-470, Senescence, 01 natural sciences, 03 medical and health sciences, Leaf senescence, Factores de Transcripción, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Girasol, Phylogeny, 030304 developmental biology, Plant Proteins, 2. Zero hunger, 0303 health sciences, Leaf Senescence, Research, High throughput phenotyping, Correction, food and beverages, Helianthus annuus, Phylogenetic Analysis, 15. Life on land, HaNAC001, Genética, Plant Senescence, Plant Leaves, Sunflower, Análisis Filogenético, NAC transcriptions factors, Avejentamiento, Hojas, Helianthus, TP248.13-248.65, 010606 plant biology & botany, Biotechnology, Transcription Factors
Abstract: Background: Leaf senescence delay impacts positively in grain yield by maintaining the photosynthetic area during the reproductive stage and during grain filling. Therefore a comprehensive understanding of the gene families associated with leaf senescence is essential. NAC transcription factors (TF) form a large plant-specific gene family involved in regulating development, senescence, and responses to biotic and abiotic stresses. The main goal of this work was to identify sunflower NAC TF (HaNAC) and their association with senescence, studying their orthologous to understand possible functional relationships between genes of different species. Results: To clarify the orthologous relationships, we used an in-depth comparative study of four divergent taxa, in dicots and monocots, with completely sequenced genomes (Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa). These orthologous groups provide a curated resource for large scale protein sequence annotation of NAC TF. From the 151 HaNAC genes detected in the latest version of the sunflower genome, 50 genes were associated with senescence traits. These genes showed significant differential expression in two contrasting lines according to an RNAseq assay. An assessment of overexpressing the Arabidopsis line for HaNAC001 (a gene of the same orthologous group of Arabidopsis thaliana ORE1) revealed that this line displayed a significantly higher number of senescent leaves and a pronounced change in development rate. Conclusions: This finding suggests HaNAC001 as an interesting candidate to explore the molecular regulation of senescence in sunflower. Instituto de Biotecnología Fil: Bengoa Luoni, Sofia Ailin. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Cenci, Alberto. Bioversity International; Francia Fil: Moschen, Sebastian Nicolás. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina. Fil: Nicosia, Salvador. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Radonic, Laura Mabel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Sabio Y Garcia, Julia Veronica. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Langlade, Nicolas B. Université de Toulouse. LIPM-INRA-CNRS; Francia Fil: Langlade, Nicolas B. Université de Montpellier. LEPSE; Francia Fil: Vazquez Rovere, Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Fernandez, Paula Del Carmen. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina.
Published: 2021
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38. Annual intercropping suppresses weeds: A meta-analysis

Author: Lammert Bastiaans, Wopke van der Werf, David Makowski, Niels P. R. Anten, Chunfeng Gu, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wageningen University and Research [Wageningen] (WUR), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, Centre International de Recherche sur l'Environnement et le Développement (CIRED), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École des hautes études en sciences sociales (EHESS)-AgroParisTech-École des Ponts ParisTech (ENPC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), China Scholarship Council201708330239, European Project: 727217,ReMIX(2017), and Mathématiques et Informatique Appliquées (MIA Paris-Saclay)
Subjects: 0106 biological sciences, Cash crop, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Cash crops, Biology, [STAT.OT]Statistics [stat]/Other Statistics [stat.ML], 01 natural sciences, Crop, Legume, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Biomass (ecology), [STAT.AP]Statistics [stat]/Applications [stat.AP], Ecology, business.industry, Intercropping, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, PE&RC, Meta-analysis, Agronomy, Agriculture, 040103 agronomy & agriculture, Centre for Crop Systems Analysis, 0401 agriculture, forestry, and fisheries, Animal Science and Zoology, Weeds, Arable land, Weed, business, Crop and Weed Ecology, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience Intercropping has been advocated as an environmentally benign method to suppress weeds in agriculture. However, it is not evident from the literature what size of weed suppressive effect is achieved on average by intercropping, and how species choice and crop management affect this effect. We conducted a global metaanalysis of published data to quantify the effect of intercropping on weed biomass in annual arable intercrops grown for their final product. We searched the literature to identify all papers reporting usable experimental data and extracted 339 data records from 39 publications containing data from 76 independent experiments. Two metrics of weed suppression were defined to assess the weed suppressive effect of intercropping: the ratio of observed weed biomass in an intercrop to weed biomass in the less weed suppressive sole crop (Rweak), and the ratio of weed biomass in the intercrop to weed biomass in the more weed suppressive sole crop (Rstrong). On average, weed biomass in the intercrop was substantially and significantly (58%) lower (Rweak = 0.42) than in the less suppressive sole crop. No significant difference was found between weed biomass in the intercrop and weed biomass in the more weed suppressive sole crop, even though weed biomass tended to be slightly larger in the intercrop than in the more weed suppressive sole crop (Rstrong = 1.08). Findings were consistent across different groups of species combinations, such as maize/legume and small-grain cereal/legume intercrops. Intercrops with an additive design had stronger weed suppression than intercrops with a replacement design. In the latter, a mixed arrangement gave stronger weed suppression than a row design, while spatial arrangement did not affect weed suppressive ability in additive designs. No significant effects on weed biomass were found of simultaneous vs. relay intercropping, and of nitrogen fertilizer input. The Rweak decreased significantly with the land equivalent ratio in additive intercrops but not in replacement intercrops, while Rstrong was unrelated to LER in both designs. The results confirm that intercropping is generally a useful approach for suppressing weeds in annual crop cultivation. Further work is needed to disentangle the contributions of species density, species traits and mixing ratio to weed suppression in intercropping.
Published: 2021
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39. A ménage à trois: salicylic acid, growth inhibition, and immunity

Author: Igor Pokotylo, Michael Hodges, Volodymyr Kravets, Eric Ruelland, Institut of Bioorganic Chemistry and Petrochemistry of NASU, National Academy of Sciences of Ukraine (NASU), 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 Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génie Enzymatique et Cellulaire (GEC), Université de Technologie de Compiègne (UTC)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), GEC UTC (GEC UTC), Université de Technologie de Compiègne (UTC)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Compiègne (UTC)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), and 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)
Subjects: 0106 biological sciences, 0303 health sciences, [SDV]Life Sciences [q-bio], Plant Science, 01 natural sciences, 03 medical and health sciences, Plant Growth Regulators, Gene Expression Regulation, Plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Immunity, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Salicylic Acid, ComputingMilieux_MISCELLANEOUS, Plant Diseases, 030304 developmental biology, 010606 plant biology & botany
Abstract: Salicylic acid (SA) is a plant hormone almost exclusively associated with the promotion of immunity. It is also known that SA has a negative impact on plant growth, yet only limited efforts have been dedicated to explain this facet of SA action. In this review, we focus on SA-related reduced growth and discuss whether it is a regulated process and if the role of SA in immunity imperatively comes with growth suppression. We highlight molecular targets of SA that interfere with growth and describe scenarios where SA can improve plant immunity without a growth penalty.
Published: 2021
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40. Rubisco catalytic adaptation is mostly driven by photosynthetic conditions – Not by phylogenetic constraints

Author: Guillaume Tcherkez, Graham D. Farquhar, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Research School of Biology [Canberra, Australia], Australian National University (ANU), and University of Angers, the Region Pays de la Loire and Angers Loire Metropole via the grant Connect Talent Isoseed.
Subjects: inorganic chemicals, 0106 biological sciences, Rubisco, Physiology, Evolution, Ribulose-Bisphosphate Carboxylase, Trade-off, Plant Science, Biology, Photosynthesis, 01 natural sciences, Catalysis, 03 medical and health sciences, Magnoliopsida, Carboxylation, Oxygenation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Phylogeny, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, fungi, RuBisCO, Inheritance (genetic algorithm), food and beverages, Carbon Dioxide, Kinetics, Evolutionary biology, biology.protein, Adaptation, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; The prevalence of phylogenetic constraints in Rubisco evolution has been emphasised recently by (Bouvier et al., 2021), who argued that phylogenetic inheritance limits Rubisco adaptation much more than the biochemical trade-off between specificity, CO2 affinity and turn-over. In this Opinion, we have critically examined how a phylogenetic signal can be computed with Rubisco kinetic properties and phylogenetic trees, and we arrive at a different conclusion. In particular, Rubisco's adaptation is partly driven by C-4 vs. C-3 photosynthetic conditions in Angiosperms, apparent phylogenetic signals being mostly due to either homoplasy, computation artefacts or the use of nearly identical sister species. While phylogenetic inheritance of an ancestral enzyme form probably has some role in Rubisco's adaptation landscape, it is a minor player, at least compared to microenvironmental conditions such as CO2 and O-2 concentrations.
Published: 2021
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41. Development of a low cost open-source ultrasonic device for plant height measurements

Author: Germain Montazeaud, Simon Moinard, A. Ducanchez, Christophe Langrume, Guilhem Brunel, Cédric Goby, Bruno Tisseyre, 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), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), 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), 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 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, Département d'écologie et évolution [Lausanne] (DEE), Université de Lausanne = University of Lausanne (UNIL), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and G.M. benefitted from a PhD grant from the Ministère de l’Enseignement Supérieur, de la Recherche et de l’Innovation.
Subjects: 0106 biological sciences, Open-source, Backscatter, Agriculture (General), Field experiment, Ultrasonic device, Agricultural industries, Crop species, 01 natural sciences, S1-972, Semi-automated measurement, [SDV.SA.STA]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of agriculture, Range (statistics), [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], ComputingMilieux_MISCELLANEOUS, Remote sensing, HD9000-9495, Low cost, 04 agricultural and veterinary sciences, Plant height, Open source, Phenotyping, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Ultrasonic sensor, Precision agriculture, 010606 plant biology & botany
Abstract: Plant height is commonly used to characterize crops in various domains such as plant breeding or precision farming. Despite significant advances in sensing technologies, plant height is still very often measured manually in many research applications where high-throughput alternatives are not always suitable. Here, we have developed a low cost, open-source ultrasonic device for semi-automated plant height measurements in small- to medium-scale applications. The main innovation compared to previous developments is the combination of a low-cost ultrasonic sensor and a plastic backscatter plate to improve plant tip detection. We compared the device to the manual method under controlled laboratory conditions and in a field experiment with 26 sorghum (Sorghum bicolor) inbred lines. The accuracy of the device was close to 1 cm in controlled conditions and 2 cm in the field, and the bias was close to 0 in both cases. In the field, measurements were 42% faster when compared with the classical ruler, and sensor-based values were strongly correlated with ruler-based values (R² = 0.9965). Overall, the device allows significant time savings while maintaining very high accuracy compared to the manual method. Its low cost (∼75 €) and compact design make it suitable for a wide range of applications, either for crop species, natural species, or model organisms. We encourage such implementations by providing all code and materials in free and open access.
Published: 2021
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42. The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

Author: Gabriela Castellanos-Morales, Erika Aguirre-Planter, Yocelyn T. Gutiérrez-Guerrero, Rafael Lira-Saade, Guillermo Sánchez-de la Vega, Josué Barrera-Redondo, Luis E. Eguiarte, Jonás A. Aguirre-Liguori, Xitlali Aguirre-Dugua, Maud I. Tenaillon, Instituto de Ecologia, Universidad Nacional Autónoma de México (UNAM), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), and AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Cucurbita argyrosperma, Plant domestication, Population genetics, Introgression, Plant Science, Horticulture, Subspecies, 01 natural sciences, Biochemistry, Article, Gene flow, 03 medical and health sciences, Genetics, Cucurbita, Domestication, 1234567890(), 2. Zero hunger, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], food and beverages, Genomics, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], humanities, 030104 developmental biology, Evolutionary biology, Cucurbita moschata, Gourd, 010606 plant biology & botany, Biotechnology
Abstract: Despite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.
Published: 2021
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43. UV-C mediated accumulation of pharmacologically significant phytochemicals under light regimes in in vitro culture of Fagonia indica (L.)

Author: Bilal Haider Abbasi, Christophe Hano, Samantha Drouet, Muhammad Nadeem, Taimoor Khan, Razia Khurshid, Quaid-i-Azam University (QAU), Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), and Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Antioxidant, Light, DPPH, Ultraviolet Rays, medicine.medical_treatment, Science, [SDV]Life Sciences [q-bio], Phytochemicals, In Vitro Techniques, 01 natural sciences, Biochemistry, Antioxidants, Article, 03 medical and health sciences, chemistry.chemical_compound, Plant Cells, medicine, Food science, Isorhamnetin, Multidisciplinary, ABTS, food and beverages, 030104 developmental biology, chemistry, Callus, Apigenin, Medicine, Myricetin, Kaempferol, Zygophyllaceae, Plant sciences, 010606 plant biology & botany, Biotechnology
Abstract: Fagonia indica (L.) is an important medicinal plant with multitude of therapeutic potentials. Such application has been attributed to the presence of various pharmacological important phytochemicals. However, the inadequate biosynthesis of such metabolites in intact plants has hampered scalable production. Thus, herein, we have established an in vitro based elicitation strategy to enhance such metabolites in callus culture of F. indica. Cultures were exposed to various doses of UV radiation (UV-C) and grown in different photoperiod regimes and their impact was evaluated on biomass accumulation, biosynthesis of phytochemicals along antioxidant expression. Cultures grown under photoperiod (16L/8D h) after exposure to UV-C (5.4 kJ/m2) accumulated optimal biomass (438.3 g/L FW; 16.4 g/L DW), phenolics contents (TPC: 11.8 μgGAE/mg) and flavonoids contents (TFC: 4.05 μgQE/mg). Similarly, HPLC quantification revealed that total production (6.967 μg/mg DW) of phytochemicals wherein kaempferol (1.377 μg/mg DW), apigenin (1.057 μg/mg DW), myricetin (1.022 μg/mg DW) and isorhamnetin (1.022 μg/mg DW) were recorded highly accumulated compounds in cultures at UV-C (5.4 kJ/m2) dose than other UV-C radiations and light regimes.. The antioxidants activities examined as DPPH (92.8%), FRAP (182.3 µM TEAC) and ABTS (489.1 µM TEAC) were also recorded highly expressed by cultures under photoperiod after treatment with UV-C dose 5.4 kJ/m2. Moreover, same cultures also expressed maximum % inhibition towards phospholipase A2 (sPLA2: 35.8%), lipoxygenase (15-LOX: 43.3%) and cyclooxygenases (COX-1: 55.3% and COX-2: 39.9%) with 1.0-, 1.3-, 1.3- and 2.8-fold increased levels as compared with control, respectively. Hence, findings suggest that light and UV can synergistically improve the metabolism of F. indica and could be used to produce such valuable metabolites on commercial scale.
Published: 2021
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44. Overlapping roles of spliceosomal components SF3B1 and PHF5A in rice splicing regulation

Author: Ayman Eid, Martin Crespi, Anireddy S. N. Reddy, Jérémie Bazin, Magdy M. Mahfouz, Sahar Alshareef, Moussa Benhamed, Haroon Butt, Laboratory for Genome Engineering and Synthetic Biology, King Abdullah University of Science and Technology (KAUST), 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), Department of Biology and Program in Cell and Molecular Biology, Colorado State University [Fort Collins] (CSU), King Abdullah University of Science & Technology, 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, Spliceosome, retention, Plant molecular biology, RNA splicing, intron, QH301-705.5, [SDV]Life Sciences [q-bio], Mutant, Medicine (miscellaneous), Biology, insights, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, target, 03 medical and health sciences, Gene Expression Regulation, Plant, snRNP, Abiotic Stress Responses, Biology (General), Gene, Plant Proteins, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, molecular Architecture, tolerance, lsm2-8 Complex, fungi, Wild type, Intron, RNA-Binding Proteins, food and beverages, Oryza, Directed evolution, proteins, Cell biology, networks, Spliceosomes, RNA Splicing Factors, General Agricultural and Biological Sciences, 010606 plant biology & botany
Abstract: The SF3B complex, a multiprotein component of the U2 snRNP of the spliceosome, plays a crucial role in recognizing branch point sequence and facilitates spliceosome assembly and activation. Several chemicals that bind SF3B1 and PHF5A subunits of the SF3B complex inhibit splicing. We recently generated a splicing inhibitor-resistant SF3B1 mutant named SF3B1 GEX1A RESISTANT 4 (SGR4) using CRISPR-mediated directed evolution, whereas splicing inhibitor-resistant mutant of PHF5A (Overexpression-PHF5A GEX1A Resistance, OGR) was generated by expressing an engineered version PHF5A-Y36C. Global analysis of splicing in wild type and these two mutants revealed the role of SF3B1 and PHF5A in splicing regulation. This analysis uncovered a set of genes whose intron retention is regulated by both proteins. Further analysis of these retained introns revealed that they are shorter, have a higher GC content, and contain shorter and weaker polypyrimidine tracts. Furthermore, splicing inhibition increased seedlings sensitivity to salt stress, consistent with emerging roles of splicing regulation in stress responses. In summary, we uncovered the functions of two members of the plant branch point recognition complex. The novel strategies described here should be broadly applicable in elucidating functions of splicing regulators, especially in studying the functions of redundant paralogs in plants., Butt et al. used CRISPR-mediated directed evolution to generate rice mutants for the spliceosome components SF3B1 and PHF5A. They demonstrate that these mutants have different levels of sensitivity to salt treatments and suggest that the strategies they employed can be used in the future to study functions of redundant paralogs in plants.
Published: 2021
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45. Radiative transfer modeling in structurally complex stands: towards a better understanding of parametrization

Author: Mathieu Jonard, François De Coligny, Vincent Gauthray-Guyénet, Gauthier Ligot, Benoît Courbaud, Louis de Wergifosse, Nicolas Beudez, Frédéric André, Université Catholique de Louvain = Catholic University of Louvain (UCL), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, symbols.namesake, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Heterogeneous forests, Parametrization (atmospheric modeling), Statistical physics, 0105 earth and related environmental sciences, Bayesian optimization, Light interception, Ecology, Radiative transfer modeling, Crown asymmetry, Beer-Lambert, Beer–Lambert law, Forestry, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Porous envelope, symbols, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: International audience; Abstract• Key messageThe best options to parametrize a radiative transfer model change according to the response variable used for fitting. To predict transmitted radiation, the turbid medium approach performs much better than the porous envelop, especially when accounting for the intra-specific variations in leaf area density but crown shape has limited effects. When fitting with tree growth data, the porous envelop approach combined with the more complex crown shape provides better results. When using a joint optimization with both variables, the better options are the turbid medium and the more detailed approach for describing crown shape and leaf area density.• ContextSolar radiation transfer is a key process of tree growth dynamics in forest.• AimsDetermining the best options to parametrize a forest radiative transfer model in heterogeneous oak and beech stands from Belgium.• MethodsCalibration and evaluation of a forest radiative transfer module coupled to a spatially explicit tree growth model were repeated for different configuration options (i.e., turbid medium vs porous envelope to calculate light interception by trees, crown shapes of contrasting complexity to account for their asymmetry) and response variables used for fitting (transmitted radiation and/or tree growth data).• ResultsThe turbid medium outperformed the porous envelope approach. The more complex crown shapes enabling to account for crown asymmetry improved performances when including growth data in the calibration.• ConclusionOur results provide insights on the options to select when parametrizing a forest radiative 3D-crown transfer model depending on the research or application objectives.
Published: 2021
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46. Pip shape echoes grapevine domestication history

Author: Vincent Bonhomme, Sarah Ivorra, Clémence Pagnoux, Cécile Marchal, Thierry Lacombe, Isabel Figueiral, Allowen Evin, David Maghradze, Hervé Pomarèdes, Thierry Pastor, Roberto Bacilieri, Laurent Bouby, Jean-Frédéric Terral, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Domaine expérimental de Vassal (MONTP DOM VASSAL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INRAP Méditerranée, National Wine Agency of Georgia, École française d'Athènes (EfA), ANR-16-CE27-0013,VINICULTURE,Vignes et vins en France du Néolithique au Moyen Age. Approche intégrée en archéosciences(2016), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), 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), Institut national de recherches archéologiques préventives (Inrap), Archéologie des Sociétés Méditerranéennes (ASM), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Amélioration Génétique et Adaptation des Plantes méditerranéennes et Tropicales Corse - Antenne Corse (AGAP-Corse), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-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] : UR226, 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 Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Wine, 0303 health sciences, Multidisciplinary, Plant domestication, Science, [SDV]Life Sciences [q-bio], 01 natural sciences, Wine grape, Archaeology, Late iron age, Article, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Plant evolution, Geography, [SDE]Environmental Sciences, Medicine, Viticulture, Domestication, 030304 developmental biology, 010606 plant biology & botany
Abstract: The pip, as the most common grapevine archaeological remain, is extensively used to document past viticulture dynamics. This paper uses state of the art morphological analyses to analyse the largest reference collection of modern pips to date, representative of the present-day diversity of the domesticated grapevine from Western Eurasia. We tested for a costructure between the form of the modern pips and the: destination use (table/wine), geographical origins, and populational labels obtained through two molecular approaches. Significant structuring is demonstrated for each of these cofactors and for the first time it is possible to infer properties of varieties without going through the parallel with modern varieties. These results provide a unique tool that can be applied to archaeological pips in order to reconstruct the spatio-temporal dynamics of grape diversity on a large scale and to better understand viticulture history. The models obtained were then used to infer the affiliations with archaeobotanical remains recovered in Mas de Vignoles XIV (Nîmes, France). The results show a twofold shift between the Late Iron Age and the Middle Ages, from table to wine grape varieties and from eastern to western origins which correlates with previous palaeogenomic results.
Published: 2021
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47. Investigating the links between management practices and economic performances of smallholders' oil palm plots. A case study in Jambi province, Indonesia

Author: Eric Penot, Cécile Bessou, Alexis Thoumazeau, Jean Ollivier, Romane Mettauer, Puspita Demitria, Zulkifli Alamsyah, Hans Smit, Bénédicte Chambon, Victor Baron, Turinah, Agrosystèmes Biodiversifiés (UMR ABSys), 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), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Teknologi dan Sains Nahdlatul Ulama Pasuruan (ITSNU Pasuruan), Universitas Jambi, Partenaires INRAE, SNV Indonesia, Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), 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 Environnements et Sociétés (Cirad-ES), and This study was implemented under the framework of the 'Solidarity Sourcing Berbak Landscape' project funded by L'Oreal Company, through a trilateral partnership between L'Oreal, SNV and Cirad. The authors thank L'Oreal for support and Nisrine Zaaraoui, Alice Lemont and Stephanie Ringeissen for efficient project management.
Subjects: 0106 biological sciences, Trade-offs, Ex-plasma smallholders, F08 - Systèmes et modes de culture, [SDV]Life Sciences [q-bio], Performance de culture, 01 natural sciences, Gross margin, Agricultural science, parcelle, Elaeis guineensis, productivité agricole, 2. Zero hunger, 04 agricultural and veterinary sciences, Agricultural practices, Multi criteria analysis, Scale (social sciences), Oil palm, Profitability index, Context (language use), Economic performances, Petite exploitation agricole, pratique agricole, Palm oil, Management practices, business.industry, Économie agricole, Rentabilité, 15. Life on land, E20 - Organisation, administration et gestion des entreprises ou exploitations agricoles, Agriculture, Système d'exploitation agricole, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Système de culture, Animal Science and Zoology, business, Agronomy and Crop Science, 010606 plant biology & botany, Diversity (business)
Abstract: International audience; Highlights:• The diversity of oil palm smallholders management practice and their performances remain poorly known.• We aim to understand which farming systems optimize the economic performance of oil palm.• A first typology on agricultural practices revealed a gradient of intensification, a second on economic performances revealed an optimum.• Crossing the two typologies showed that intensive practices are not economically optimal.• The study recommends to adapt local recommendations using multicriteria approaches.Abstract:CONTEXT: Oil palm is widely cultivated in Indonesia and it is produced by various populations of smallholders. Among those, ex-plasma smallholders are characterized by the fact that they only start to manage their own plantations 5 to 10 years after those were initially planted and managed by a partner industrial company. Despite the large areas that are cultivated by ex-plasma smallholders, their diversity of practices and economic performances are poorly quantified.OBJECTIVE: The present study aims at investigating which smallholder farming systems optimize profitability at the plot scale.METHOD: We defined two typologies, one based on agricultural practices and the other based on economic performance, using multivariate statistical analysis. The typologies were crossed to understand the links between agricultural practices and economic performance at the plot level.RESULTS AND CONCLUSIONS: Our results showed that despite initial plot homogeneity during planting phase, ex-plasma smallholders can develop very diversified management practices. A gradient of intensification was observed from farmers implementing no fertilization or weeding management up to farmers following agroindustrial-like management. Economic performances at the plot level was found to be variable, with gross margins ranging from 1.1 to 26.9 M IDR.ha−1.yr−1 (eq. 66.4 to 1625.5€). We showed that the most intensive practices led to highest yields although these were not linked to the optimal economic plot performances. A trade-off based on input costs was revealed, as high fertilization practices did not seem economically optimal for smallholders.SIGNIFICANCE: The present study highlights the need to combine quantified agronomic assessments with economic analysis, to properly design recommendations to farmers.
Published: 2021
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48. Identification and distribution of novel badnaviral sequences integrated in the genome of cacao (Theobroma cacao)

Author: Emmanuelle Muller, Ihsan Ullah, Andrew Wetten, A. J. Daymond, Jim M. Dunwell, Joel Allainguillaume, Megan Richardson, 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), University of Reading (UOR), University of the West of England [Bristol] (UWE Bristol), Cocoa Research UK, University of the West of England, CIRAD, United States Department of Agriculture (USDA), ICQC, and Cocoa Research Association
Subjects: 0106 biological sciences, 0301 basic medicine, Indexage des virus des plantes, Informatics, Theobroma, Molecular biology, [SDV]Life Sciences [q-bio], 01 natural sciences, Genome, Sustainability & Climate Change, 2. Zero hunger, Genetics, Multidisciplinary, biology, Agriculture, Héritabilité génotypique, Africa, Western, Quarantine, symbols, Medicine, Identification (biology), Centre for Research in Biosciences, Cacao swollen-shoot virus, Genome, Plant, Biotechnology, Crops, Agricultural, Séquence nucléotidique, Evolution, Science, Article, Crop, 03 medical and health sciences, symbols.namesake, Multiplex polymerase chain reaction, Theobroma cacao, Badnavirus, Plant Diseases, H20 - Maladies des plantes, Cacao, Genetic Variation, biology.organism_classification, 030104 developmental biology, Food, Africa, Mendelian inheritance, Plant sciences, Multiplex Polymerase Chain Reaction, 010606 plant biology & botany
Abstract: Theobroma cacao is one of the most economically important tropical trees, being the source of chocolate. As part of an ongoing study to understand the diversity of the badnavirus complex, responsible for the cacao swollen shoot virus disease in West Africa, evidence was found recently of virus-like sequences in asymptomatic cacao plants. The present study exploited the wealth of genomic resources in this crop, and combined bioinformatic, molecular, and genetic approaches to report for the first time the presence of integrated badnaviral sequences in most of the cacao genetic groups. These sequences, which we propose to name eTcBV for endogenous T. cacao bacilliform virus, varied in type with each predominating in a specific genetic group. A diagnostic multiplex PCR method was developed to identify the homozygous or hemizygous condition of one specific insert, which was inherited as a single Mendelian trait. These data suggest that these integration events occurred before or during the species diversification in Central and South America, and prior to its cultivation in other regions. Such evidence of integrated sequences is relevant to the management of cacao quarantine facilities and may also aid novel methods to reduce the impact of such viruses in this crop.
Published: 2021
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49. Rhizobia use a pathogenic-like effector to hijack leguminous nodulation signalling

Author: Hien P. Nguyen, Takakazu Kaneko, Safirah Tasa Nerves Ratu, Shin Okazaki, Albin Teulet, Eric Giraud, Michiko Yasuda, Makoto Hayashi, Shusei Sato, Sachiko Masuda, Hiroki Miwa, Tokyo University of Agriculture and Technology (TUAT), 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)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Kyoto Sangyo University, RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), ANR-16-CE20-0013,SymEffectors,Système de sécrétion de type 3 pour la symbiose fixatrice d'azote(2016), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, 0301 basic medicine, Xanthomonas, Science, [SDV]Life Sciences [q-bio], Mutant, medicine.disease_cause, Plant Root Nodulation, Plant Roots, 01 natural sciences, Article, Type three secretion system, Rhizobia, Transcriptome, 03 medical and health sciences, Symbiosis, Gene Expression Regulation, Plant, medicine, Bradyrhizobium, Rhizobial symbiosis, Multidisciplinary, biology, Effector, fungi, food and beverages, Fabaceae, Pathogenic bacteria, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Xanthomonas campestris, Cell biology, 030104 developmental biology, Medicine, Soybeans, Root Nodules, Plant, Rhizobium, Signal Transduction, 010606 plant biology & botany
Abstract: Legume plants form a root-nodule symbiosis with rhizobia. This symbiosis establishment generally relies on rhizobium-produced Nod factors (NFs) and their perception by leguminous receptors (NFRs) that trigger nodulation. However, certain rhizobia hijack leguminous nodulation signalling via their type III secretion system, which functions in pathogenic bacteria to deliver effector proteins into host cells. Here, we report that rhizobia use pathogenic-like effectors to hijack legume nodulation signalling. The rhizobial effector Bel2-5 resembles the XopD effector of the plant pathogen Xanthomonas campestris and could induce nitrogen-fixing nodules on soybean nfr mutant. The soybean root transcriptome revealed that Bel2-5 induces expression of cytokinin-related genes, which are important for nodule organogenesis and represses ethylene- and defense-related genes that are deleterious to nodulation. Remarkably, Bel2-5 introduction into a strain unable to nodulate soybean mutant affected in NF perception conferred nodulation ability. Our findings show that rhizobia employ and have customized pathogenic effectors to promote leguminous nodulation signalling.
Published: 2021
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50. Absent daddy, but important father

Author: Thomas WIDIEZ, Nathanaël Jacquier, 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), ANR-19-CE20-0012,NOT-LIKE-DAD,Gynogenèse in vivo chez le maïs : nouvelles connaissances sur la double fécondation chez les plantes(2019), and École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0106 biological sciences, 0303 health sciences, Quantitative Biology - Subcellular Processes, fungi, food and beverages, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Plant Science, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], 01 natural sciences, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 03 medical and health sciences, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, FOS: Biological sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Subcellular Processes (q-bio.SC), [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Mixing maternal and paternal genomes is the base of plant sexual reproduction, but some so-called 'haploid inducer lines' lead to the formation of seeds bearing well-developed embryos with solely the maternal genome. A recent study adds a new piece to the puzzle of this enigmatic in planta haploid embryo induction process.
Published: 2021
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