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1. Common microgeographical selection patterns revealed in four European conifers

Author

Ivan Scotti, Hadrien Lalagüe, Sylvie Oddou‐Muratorio, Caroline Scotti‐Saintagne, Rose Ruiz Daniels, Delphine Grivet, François Lefevre, Philippe Cubry, Bruno Fady, Santiago C. González‐Martínez, Anne Roig, Isabelle Lesur‐Kupin, Francesca Bagnoli, Vanina Guerin, Christophe Plomion, Philippe Rozenberg, Giovanni G. Vendramin, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Edinburgh, Instituto Nacional de Investigación Agropecuaria (INIA), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), CREAF - Centre for Ecological Research and Applied Forestries, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), 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), Ministere de l'Ecologie, du Developpement Durable et de l'Energie10-MCGOT-GICC-8-CVS-139, ANR-12-ADAP-0007,FLAG,Génétique écologique des arbres forestiers : interactions entre flux de gènes et variabilité environnementale dans la détermination de l'adaptation locale et du potentiel d'adaptation(2012), European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), Agence Nationale de la Recherche (France), European Commission, Ministère de l'Écologie, du Développement durable et de l'Énergie (France), Scotti, Ivan, Oddou-Muratorio, Sylvie, Scotti-Saintagne, Caroline, Ruiz Daniels, Rose, Grivet, Delphine, Lefevre, François, Cubry, Philippe {0000-0003-1561-8949], Fady, Bruno, Lesur-Kupin, Isabelle, Bagnoli, Francesca {0000-0001-6909-0006], Plomion, Christophe, Rozenberg, Philippe, Vendramin, Giovanni G., and Hadrien Lalagüe

Subjects
forests, adaptive divergence, plants, [SDE]Environmental Sciences, Genetics, natural selection, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Ecology, Evolution, Behavior and Systematics, local adaptation
Abstract

19 Pág., Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions., Agence Nationale de la Recherche, Grant/ Award Number: FLAG project (ANR-12- ADAP-0007-01); European Commission, Grant/Award Number: TOPWOOD project (MSCA-RISE-2014-645654- TOPWOOD) and grant agreement No. 676876 (GenTree); Ministère de l'Écologie, du Développement Durable et de l'Énergie, Grant/Award Number: GRAAL project (10-MCGOT-GICC-8-CVS-139)

Published
2023
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2. The GenTree Leaf Collection: Inter‐ and intraspecific leaf variation in seven forest tree species in Europe

Author

Jérémy Marchon, Alan Gray, Sebastian Richter, Christophe Plomion, René Graf, Francesca Bagnoli, Elisabet Martínez-Sancho, Volker Schneck, Frédéric Bernier, Vladimir L. Semerikov, Henry Bignalet, José Alberto Ramírez-Valiente, Ioannis Ganopoulos, Felix Gugerli, Agathe Hurel, Geir Ostreng, Sandro Morganti, Santiago C. González-Martínez, David López-Quiroga, Luc Puzos, William Brunetto, Raquel Benavides, Damien Bouic, Olivier Ambrosio, Filippos A. Aravanopoulos, Mirko Liesebach, Cristina C. Bastias, Veronique Jorge, Outi Savolainen, Stephen Cavers, Célia Michotey, Bernard Dokhelar, Mehdi Pringarbe, Enja Hollenbach, Camilla Avanzi, Silvio Schueler, José M. García del Barrio, Annie Raffin, Bruno Fady, Anna-Maria Farsakoglou, Olivier Gilg, Pascal Milesi, Sonja T. Kujala, Nicolas Mariotte, Florian Knutzen, Nicolas Cheval, F. J. Auñón, Céline Lalanne, Marc Villar, Catherine Bastien, Katri Kärkkäinen, Nicolas Poinot, Fernando Del Caño, Jan-Philipp Kappner, Florence Jean, Birte Pakull, Tanja Pyhäjärvi, Jørn Henrik Sønstebø, Rémi Dourthe, Ermioni Malliarou, Ivan Scotti, Timo Kumpula, Mariaceleste Labriola, Silvia Matesanz, Bernard Issehuth, Martin Lascoux, Jean Thevenet, Christian Rellstab, Marianne Correard, Ricardo Alía, Johannes Lambertz, Anne Eskild Nilsen, Eva Cremer, Christoph Hartleitner, Darius Danusevičius, Lars Opgenoorth, Fernando Valladares, Arnaud Jouineau, Ana M. Cabanillas‐Saldaña, José Climent, Audrey Albet, Jurata Buchovska, Benjamin Dauphin, Sergio San Segundo, Ilaria Spanu, Antonio Mas, Johan Westin, Eduardo Notivol, Juan J. Robledo-Arnuncio, Andrea Piotti, Evangelos Barbas, Robert Kesälahti, Andreas Fera, Mari Mette Tollefsrud, Helge Meischner, Grégoire Le Provost, Eduardo Ballesteros, Tor Myking, Bárbara Carvalho, Jean-Luc Denou, Katrin Heer, Giovanni G. Vendramin, Evangelia V. Avramidou, Norbert Turion, Patrick Fonti, Delphine Grivet, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), 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, 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), UK Centre for Ecology & Hydrology, Natural Environment Research Council (NERC), Unité expérimentale Forêt Pierroton (UEFP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Forest Ecology and Genetics, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Ecologie des Forêts Méditerranéennes (URFM), Aristotle University of Thessaloniki, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), 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), Vytautas Magnus University - Vytauto Didziojo Universitetas (VDU), Gobierno de Aragon, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), Bavarian Office for Forest Seeding and Planting, Partenaires INRAE, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Austrian Research Centre for Forests (BFW), Institute of Plant Breeding and Genetic Resources, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), LIECO GmbH & Co KG, Philipps Universität Marburg = Philipps University of Marburg, Natural Resources Institute Finland (LUKE), University of Oulu, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Thunen Institute of Forest Ecosystems, Thünen Institute, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Universidad Rey Juan Carlos [Madrid] (URJC), Unité de Recherche Génomique Info (URGI), Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), Skogforsk - Swedish Forestry Research Institute, Horizon 2020. Grant Numbers: 676876, 4540-143AP, 6, 0032 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazil), European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Comunidad de Madrid, State Secretariat for Education, Research and Innovation (Switzerland), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Museo Nacional de Ciencias Naturales (CSIC), 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), Consiglio Nazionale delle Ricerche (CNR), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigacion Y Tecnologia Agroalimentaria de Aragon, Philipps Universität Marburg, Norwegian Institute of Bioeconomy Research (NIBIO), and Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA)

Subjects
0106 biological sciences, Specific leaf area, Population, Phenotypic variation, 010603 evolutionary biology, 01 natural sciences, Ecology and Environment, Leaf functional traits, tree species, Fagus sylvatica, leaf functional traits, Leaf economics spectrum, Leaf size, education, intraspecific variability, Ecology, Evolution, Behavior and Systematics, Global and Planetary Change, education.field_of_study, Ecology, biology, leaf economics spectrum, 010604 marine biology & hydrobiology, Intraspecific variability, Botany, phenotypic variation, Botanik, Interspecific competition, 15. Life on land, biology.organism_classification, Forest genetic resources, Quercus petraea, Sample collection, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, European forests, Tree species
Abstract

[Motivation] Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes., [Main types of variable contained] We chose morphological and chemical characters linked to trade-offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope 13C and 15N in leaves., [Spatial location and grain] We surveyed between 18 and 22 populations per species, 141 in total, across Europe., [Time period] Leaf sampling took place between 2016 and 2017., [Major taxa and level of measurement] We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea., [Software format] The data files are in ASCII text, tab delimited, not compressed., All authors acknowledge support from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 676876 (Project GenTree). Laboratory work was also supported by other projects: COMEDIAS (CGL2017- 83170-R, Spanish Ministry of Science, Innovation and Universities), REMEDINAL IV (TE-CM S2018/EMT-4338, Project of the Autonomous Community of Madrid, Spain), SPONFOREST (BIODIVERSA-3, PCIN-2016-055), and International Laboratory of Global Change (LINCGlobal 4540-143AP). The Swiss contribution was supported by the Swiss Secretariat for Education, Research and Innovation (SERI) under contract no. 6.0032. BC was funded by a Scholarship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazil).

Published
2021
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3. 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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4. The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species

Author

Opgenoorth, Lars, Dauphin, Benjamin, Benavides, Raquel, Heer, Katrin, Alizoti, Paraskevi, Martínez-Sancho, Elisabet, Alía, Ricardo, Ambrosio, Olivier, Audrey, Albet, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia, Bagnoli, Francesca, Barbas, Evangelos, Bastias, Cristina C, Bastien, Catherine, Ballesteros, Eduardo, Beffa, Giorgia, Bernier, Frédéric, Bignalet, Henri, Bodineau, Guillaume, Bouic, Damien, Brodbeck, Sabine, Brunetto, William, Buchovska, Jurata, Buy, Melanie, Cabanillas-Saldaña, Ana M, Carvalho, Bárbara, Cheval, Nicolas, Climent, José M, Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Del Caño, Fernando, Denou, Jean-Luc, Di Gerardi, Nicolas, Dokhelar, Bernard, Ducousso, Alexis, Nilsen, Anne Eskild, Farsakoglou, Anna-Maria, Fonti, Patrick, Ganopoulos, Ioannis, García Del Barrio, José M, Gilg, Olivier, González-Martínez, Santiago C, Graf, René, Gray, Alan, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Hollenbach, Enja, Hurel, Agathe, Issehut, Bernard, Jean, Florence, Jorge, Veronique, Jouineau, Arnaud, Kappner, Jan-Philipp, Kärkkäinen, Katri, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T, Kumpula, Timo A, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Lascoux, Martin, Lejeune, Vincent, Le-Provost, Gregoire, Levillain, Joseph, Liesebach, Mirko, López-Quiroga, David, Meier, Benjamin, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Mas, Antonio, Matesanz, Silvia, Meischner, Helge, Michotey, Célia, Milesi, Pascal, Morganti, Sandro, Nievergelt, Daniel, Notivol, Eduardo, Østreng, Geir, Pakull, Birte, Perry, Annika, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez-Valiente, José A, Rellstab, Christian, Remi, Dourthe, Richter, Sebastian, Robledo-Arnuncio, Juan J, San Segundo, Sergio, Savolainen, Outi, Schueler, Silvio, Schneck, Volker, Scotti, Ivan, Semerikov, Vladimir, Slámová, Lenka, Sønstebø, Jørn Henrik, Spanu, Ilaria, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Vendramin, Giovanni Giuseppe, Villar, Marc, von Arx, Georg, Westin, Johan, Fady, Bruno, Myking, Tor, Valladares, Fernando, Aravanopoulos, Filippos A, Cavers, Stephen, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Philipps Universität Marburg = Philipps University of Marburg, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Aristotle University of Thessaloniki, Department of Forest Ecology and Genetics, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité expérimentale Forêt Pierroton (UEFP), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), 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, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biologie 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), Génétique et Biomasse Forestières ORléans (GBFOR), Vytautas Magnus University - Vytauto Didziojo Universitetas (VDU), Unité de Recherche Génomique Info (URGI), Gobierno de Aragon, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), Bavarian Office for Forest Seeding and Planting, Partenaires INRAE, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), UK Centre for Ecology & Hydrology, Natural Environment Research Council (NERC), LIECO GmbH & Co KG, Natural Resources Institute Finland (LUKE), University of Oulu, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Thunen Institute of Forest Ecosystems, Thünen Institute, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Universidad Rey Juan Carlos [Madrid] (URJC), Austrian Research Centre for Forests (BFW), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), Skogforsk - Swedish Forestry Research Institute, Swiss Secretariat for Education, Research and Innovation (SERI) 6.0032, European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), Philipps Universität Marburg, Museo Nacional de Ciencias Naturales (CSIC), Consiglio Nazionale delle Ricerche (CNR), 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), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigacion Y Tecnologia Agroalimentaria de Aragon, Norwegian Institute of Bioeconomy Research (NIBIO), and Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA)

Subjects
crown size, fruit number, Skogsvetenskap, bark thickness, AcademicSubjects/SCI02254, DBH, Forest Science, soil depth, forking index, Botany, Pinus sylvestris, Botanik, Forests, Data Note, stem straightness, Ecology and Environment, Trees, regeneration, branch angle, Fagus, AcademicSubjects/SCI00960, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Picea, height
Abstract

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients. Conclusion: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.

Published
2021
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5. In-depth study to decipher mechanisms underlying Arabidopsis thaliana tolerance to metal(loid) soil contamination in association with biochar and/or bacteria

Author

Andrea Scaloni, Gabriella Sferra, Domenico Morabito, Sylvain Bourgerie, Giovanni Renzone, Gabriella S. Scippa, Dalila Trupiano, Melissa Simiele, Manhattan Lebrun, Università degli Studi del Molise (Unimol), 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), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), and Consiglio Nazionale delle Ricerche (CNR)

Subjects
0106 biological sciences, 0301 basic medicine, Bioinformatics, Microorganism, Plant Science, 01 natural sciences, 03 medical and health sciences, Bacillus isolates, Nutrient, Arabidopsis, Proteomics analysis, Biochar, Arabidopsis thaliana, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, biology, Chemistry, fungi, food and beverages, biology.organism_classification, Soil contamination, 030104 developmental biology, Lead, 13. Climate action, Environmental chemistry, Bacillus sp, [SDE]Environmental Sciences, Agronomy and Crop Science, Bacteria, 010606 plant biology & botany
Abstract

International audience; Metal(loid)s are toxic to animal life, human health and plants; therefore, their removal from polluted areas is imperative in order to minimize their impact on the ecosystems. The use of plant-amendment-microorganism synergy is a promising option, but not yet fully explored, to manage lands contaminated with metal(loid)s. However, molecular factors and mechanisms underlying this interaction are almost unknown. The aim of the present study was to evaluate the effects of amendments and bacteria, both alone and in combination, on Arabidopsis thaliana grown on arsenic and lead polluted soils. To accomplish this aim, a pot experiment was performed testing the effect of biochar and/or autochthonous metal(loid) resistant Bacillus isolates on physicochemical soil properties and on plant growth and metal(loid) uptake/intake. Furthermore, bioinformatics-assisted proteomics was used to understand common and specific mechanisms regulating plant growth and metal(loid) tolerance in tested conditions. Results showed that biochar and/or Bacillus induced significant and positive effects on soil properties, increasing pH, C-tot, N-tot and P-tot concentrations and decreasing nutrients (N-av and P-av), As and Pb availability. Plant growth was also enhanced by addition of biochar and/or bacterial inoculum, reaching the maximum when biochar and microorganism were combined. The deciphering of molecular mechanisms revealed that combination of biochar and bacterial inoculation mitigate Arabidopsis growth and defense tradeoff, and underline the great potential of plant-biochar-inoculum synergic application in more effective and large scale-up phytostabilizing systems.

Published
2021
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6. Species–area relationship and small-island effect of vascular plant diversity in a young volcanic archipelago

Author

Daniel Pavon, Alfonso La Rosa, José María Fernández-Palacios, Piero Zannini, Frédéric Médail, Alessandro Chiarucci, Pietro Lo Cascio, Salvatore Pasta, Riccardo Guarino, Chiarucci A., Guarino R., Pasta S., Rosa A.L., Cascio P.L., Medail F., Pavon D., Fernandez-Palacios J.M., Zannini P., Chiarucci, Alessandro, Guarino, Riccardo, Pasta, Salvatore, Rosa, Alfonso La, Cascio, Pietro Lo, Médail, Frédéric, Pavon, Daniel, Fernández‐Palacios, José María, Zannini, Piero, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Università degli studi di Palermo - University of Palermo, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Cooperativa Silene, Palermo, Italy, Associazione 'Nesos', Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Universidad de La Laguna [Tenerife - SP] (ULL), BIOME Lab, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy, Univ Palermo, STEBICEF, Palermo, Italy, Consiglio Nazionale delle Ricerche (CNR), and Island Ecology and Biogeography Group, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), La Laguna, Spain

Subjects
0106 biological sciences, Mediterranean climate, Vascular plant, 010504 meteorology & atmospheric sciences, Insular biogeography, media_common.quotation_subject, Biodiversity, biodiversity, island biogeography, Mediterranean, species richness, species–area relationships, vascular flora, Mediterranean, 010603 evolutionary biology, 01 natural sciences, 14. Life underwater, species– area relationships, species richne, species richness, Ecology, Evolution, Behavior and Systematics, species–area relationship, 0105 earth and related environmental sciences, media_common, biodiversity, vascular flora, geography, geography.geographical_feature_category, Ecology, biology, island biogeography, 15. Life on land, biology.organism_classification, Volcano, Archipelago, [SDE]Environmental Sciences, Settore BIO/03 - Botanica Ambientale E Applicata, Species richness, geographic locations, Diversity (politics)
Abstract

International audience; Aims: Aeolian islands form an active volcanic archipelago. By using updated vascular plant checklists for islands and islets, we tested four hypotheses: (i) Island speciesarea relationship (ISAR) of alien species has lower c-and higher z-values than native species, (ii) islands with active volcanoes have lower species richness than expected for native and alien species, (iii) ISAR of native species shows lower c-and higher z-values than ISARs of Mediterranean land bridge archipelagos and (iv) species richness of smaller islets is independent of area.Location: Aeolian Archipelago, Mediterranean Basin.Taxon: Vascular plants, identified and named according to the Flora of Italy (Pignatti et al., 2017– 2019).Methods: Checklists of native and alien plant species were obtained for eight islands and 24 islets. ISARs were fitted by the Arrhenius power function (S = c ⋅ Az) and used to test the first two hypotheses. The third hypothesis was tested by comparing ISAR of Aeolian Archipelago to those from other central and eastern Mediterranean archipelagos. The fourth hypothesis was tested by fitting models defining the presence and limit of the small- island effect.Results: The checklists included 894 species — 749 native and 145 alien. ISARs fitted well for native and alien species and resulted in typical values of c and z parameters. The first and second hypotheses were supported by model fitting. The third hypothesis was not confirmed by the comparison of the ISAR of the Aeolian Archipelago with other archipelagos. The small- island effect predicted by the fourth hypothesis was supported using S versus LogA for both native and alien species, while for native species it was supported also using the log transformation of the Arrhenius model.Main conclusions: We reported a first comprehensive analysis of plant species richness in the unique Aeolian Archipelago, verifying typical ISARs, no peculiarity with respect to land bridge archipelagos and a somewhat unclear signal for the small- island effect.

Published
2021
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7. Biological control of invasive stink bugs: review of global state and future prospects

Author

Gonzalo A. Avila, Guillaume Martel, Raul Alberto Laumann, Gabriele Rondoni, Cesar Rodriguez-Saona, Barbara I. P. Barratt, Michael Rostás, Fernanda Cingolani, Eric Conti, Kim A. Hoelmer, Stefano Colazza, René Sforza, Eric Wajnberg, Luciana Tavella, Salvatore Guarino, Lara Maistrello, Ezio Peri, Pio Federico Roversi, Conti E., Avila G., Barratt B., Cingolani F., Colazza S., Guarino S., Hoelmer K., Laumann R.A., Maistrello L., Martel G., Peri E., Rodriguez-Saona C., Rondoni G., Rostas M., Roversi P.F., Sforza R.F.H., Tavella L., Wajnberg E., Dept. of Pharmaceutical Sciences, University of Perugia, The New Zealand Institute for Plant & Food Research Limited [Auckland] (Plant & Food Research), Better Border Biosecurity (B3), Partenaires INRAE, Centro de Estudios Parasitologicos y de Vectores [La Plata] (CEPAVE), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional de la Plata [Argentine] (UNLP)-Comisión de Investigaciones Científicas [Buenos Aires] (CIC), Università degli studi di Palermo - University of Palermo, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), USDA-ARS : Agricultural Research Service, Embrapa Recursos Genéticos e Biotecnologia [Brasília], Università degli Studi di Modena e Reggio Emilia (UNIMORE), 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), European Biological Control Laboratory (EBCL), United States Department of Agriculture (USDA), Rutgers University System (Rutgers), Georg-August-University [Göttingen], Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Università degli studi di Torino (UNITO), HExapode, PHysiologie, AssISTance et Objets de Service (HEPHAISTOS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 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), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia (UNIMORE), Georg-August-University = Georg-August-Universität Göttingen, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria = Council for Agricultural Research and Economics (CREA), Università degli studi di Torino = University of Turin (UNITO), and Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
0106 biological sciences, Integrated pest management, Biological pest control, Tachinidae, pre-emptive classical biological control, landscape management, 010603 evolutionary biology, 01 natural sciences, invasive species, Hemiptera, Encyrtidae, invasive specie, Pentatomidae, biocontrol, biocontrol chemical ecology Hemiptera invasive species landscape management pre‐emptive classical biological control semiochemicals parasitoid Pentatomidae risk assessment Tachinidae Scelionidae, parasitoid, Ecology, Evolution, Behavior and Systematics, Bagrada hilaris, biology, semiochemicals, business.industry, Ecology, Pest control, chemical ecology, preemptive classical biological control, risk assessment, semiochemical, biocontrol, chemical ecology, Hemiptera, invasive species, landscape management, preemptive classical biological control, semiochemicals, parasitoid, Pentatomidae, risk assessment, Tachinidae, Scelionidae, biology.organism_classification, 010602 entomology, Settore AGR/11 - Entomologia Generale E Applicata, 13. Climate action, Insect Science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Scelionidae, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Invasive stink bugs (Hemiptera: Pentatomidae) are responsible for high economic losses to agricul-ture on a global scale. The most important species, dating from recent to old invasions, includeBagrada hilaris (Burmeister), Halyomorpha halys (Stal), Piezodorus guildinii (Westwood), Nezara vir-idula (L.), and Murgantia histrionica (Hahn). Bagrada hilaris, H. halys,andN. viridula are nowalmost globally distributed. Biological control of these pests faces a complex set of challenges thatmust be addressed to maintain pest populations below the economic injury level. Several case studiesof classical and conservation biological control of invasive stink bugs are reported here. The mostcommon parasitoids in their geographical area of origin are egg parasitoids (Hymenoptera: Scelion-idae, Encyrtidae, and Eupelmidae). Additionally, native parasitoids of adult stink bugs (Diptera:Tachinidae) have in some cases adapted to the novel hosts in the invaded area and native predatorsare known to prey on the various instars. Improving the efficacy of biocontrol agents is possiblethrough conservation biological control techniques and exploitation of their chemical ecology.Moreover, integration of biological control with other techniques, such as behavioural manipulationof adult stink bugs and plant resistance, may be a sustainable pest control method within organicfarming and integrated pest management programs. However, additional field studies are needed toverify the efficacy of these novel methods and transfer them from research to application.

Published
2021
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8. Are physicochemical properties shaping the allergenic potency of plant allergens?

Author

Laura Martín-Pedraza, Colette Larré, Thomas Holzhauser, Pedro M. Rodrigues, Daniel Lozano-Ojalvo, Karin Hoffmann-Sommergruber, Sara Benedé, Isabel Mafra, Gabriel Mazzucchelli, Tanja Cirkovic-Velickovic, Annette Kuehn, Cristian Piras, Joana Costa, Denise Schrama, Eva Gelencser, Kitty C.M. Verhoeckx, Cristina Bueno-Díaz, Roberta Lupi, Linda Monaci, Araceli Díaz-Perales, Julia Klueber, Caterina Villa, Simona L. Bavaro, Elena Molina, Paola Roncada, European Commission, Fundação para a Ciência e a Tecnologia (Portugal), Ministry of Education, Science and Technological Development (Serbia), Ministério da Ciência, Tecnologia e Ensino Superior (Portugal), Fonds National de la Recherche Luxembourg, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidade do Porto, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), Teagasc Food Research Centre, Food Chemistry and Technology department, Moorepark, Fermoy, Country Cork, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), European Cooperation in Science and Technology (COST) Office, European Cooperation in Science and Technology (COST) : FA1402, Portuguese Foundation for Science and Technology, European Commission : UIDB 50006/2020, projects AlleRiskAssess, PTDC/BAA-AGR/31720/2017, NORTE-01-0145-FEDER-00001, FCT - POPH-QREN, PD/BD/114576/2016, Ministry of Education, Science and Technological Development of the Republic of Serbia : OI172024, Portuguese Foundation for Science and Technology European Commission : UIDB/04326/2020, and 16-02-01-FMP0014.Luxembourg National Research FundPRIDE/11012546/NEXTIMMUNEPersonalised Medicine Consortium (PMC), Luxembourg PMC/2017/02

Subjects
Allergy, LIPID TRANSFER PROTEIN, PRU P 3, Food processing, Protein family, [SDV]Life Sciences [q-bio], Plant allergens, Clinical manifestation, Computational biology, Protein aggregation, Biology, PEANUT ALLERGENS, 03 medical and health sciences, Mice, 0302 clinical medicine, medicine, Medicine and Health Sciences, Immunology and Allergy, Potency, Animals, Humans, ARA H 1, SEED STORAGE PROTEINS, Matrix effect, ComputingMilieux_MISCELLANEOUS, Plant Proteins, 2. Zero hunger, 030203 arthritis & rheumatology, ALPHA-AMYLASE INHIBITOR, General Medicine, IN-VITRO DIGESTION, Allergens, COMPONENT-RESOLVED DIAGNOSIS, medicine.disease, 3. Good health, EXERCISE-INDUCED ANAPHYLAXIS, Animal allergens, WHEAT GLUTEN PROTEINS, Protein families, Plant protein, Allergenicity, Pollen, Food Hypersensitivity, 030215 immunology
Abstract

This review searched for published evidence that could explain how different physicochemical properties impact on the allergenicity of food proteins and if their effects would follow specific patterns among distinct protein families. Owing to the amount and complexity of the collected information, this literature overview was divided in two articles, the current one dedicated to protein families of plant allergens and a second one focused on animal allergens. Our extensive analysis of the available literature revealed that physicochemical characteristics had consistent effects on protein allergenicity for allergens belonging to the same protein family. For example, protein aggregation contributes to increased allergenicity of 2S albumins, while for legumins and cereal prolamins, the same phenomenon leads to a reduction. Molecular stability, related to structural resistance to heat and proteolysis, was identified as the most common feature promoting plant protein allergenicity, although it fails to explain the potency of some unstable allergens (e.g. pollen-related food allergens). Furthermore, data on physicochemical characteristics translating into clinical effects are limited, mainly because most studies are focused on in vitro IgE binding. Clinical data assessing how these parameters affect the development and clinical manifestation of allergies is minimal, with only few reports evaluating the sensitising capacity of modified proteins (addressing different physicochemical properties) in murine allergy models. In vivo testing of modified pure proteins by SPT or DBPCFC is scarce. At this stage, a systematic approach to link the physicochemical properties with clinical plant allergenicity in real-life scenarios is still missing., The authors highly appreciate the support from the European Cooperation in Science and Technology (COST) Office. This article is based upon work from COST Action FA1402, supported by COST (www.cost.eu). This work was also supported by Fundação para a Ciência e Tecnologia under the Partnership Agreement UIDB 50006/2020 and by the projects AlleRiskAssess - PTDC/BAA-AGR/31720/2017 and NORTE-01-0145-FEDER-00001. C.V. is grateful to FCT grants (PD/BD/114576/2016) financed by POPH-QREN (subsidised by FSE and MCTES). T.C.V. is grateful to the Ministry of Education, Science and Technological Development of the Republic of Serbia through grant number OI172024. P.M.R. and D.S. are grateful to FCT through project UIDB/04326/2020 and Mar2020 16–02-01-FMP-0014 – ‘ALLYFISH’. J.K. and A.K. acknowledge the PRIDE program grant (PRIDE/11012546/NEXTIMMUNE) by the Fonds National de la Recherche (FNR), Luxembourg and a translational grant (APSIS, PMC/2017/02) by the Personalised Medicine Consortium (PMC), Luxembourg.

Published
2021
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9. Spatial patterns of genus-level phylogenetic endemism in the tree flora of Mediterranean Europe

Author

Anne-Christine Monnet, Francesca Bagnoli, Arndt Hampe, Frédéric Médail, Panayotis Dimopoulos, Giovanni G. Vendramin, Toni Nikolić, Gianni Baccheta, Agathe Leriche, Marwan Cheikh Albassatneh, Bruno Fady, Juan Arroyo, Loic Ponger, Marcial Escudero, Universidad de Sevilla. Departamento de Biología Vegetal y Ecología, Aix-Marseille University, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Biology and Ecology, University of Seville, Università degli Studi di Cagliari = University of Cagliari (UniCa), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), University of Patras [Patras], Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Division of Botany [Zagreb], Department of Biology [Zagreb], Faculty of Science [Zagreb], University of Zagreb-University of Zagreb-Faculty of Science [Zagreb], University of Zagreb-University of Zagreb, Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-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 Life and Environmental Sciences, Botany Division, University of Cagliari, Cagliari, Italy, Department of Biology, Laboratory of Botany, University of Patras, Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), and University of Patras

Subjects
0106 biological sciences, Mediterranean climate, Nonmetric Multidimensional Scaling, Biodiversity, Context (language use), Conservation, Relative environmental turnover, 010603 evolutionary biology, 01 natural sciences, Mediterranean Basin, Phylogenetic diversity, relative environmental turnover, phylogenetic endemism, Phylogenetic endemism, Endemism, Ecology, Evolution, Behavior and Systematics, Phylogenetic tree, Ecology, 010604 marine biology & hydrobiology, conservation, Euro-Mediterranean vascular flora, 15. Life on land, Geography, 13. Climate action, [SDE]Environmental Sciences, Spatial ecology, phylogenetic diversity
Abstract

Aim: The Mediterranean Basin is a major hotspot of plant biodiversity, including forest trees. Over the past centuries, Mediterranean forests have been fragmented and over-exploited, to which the threats of climate change are now added. Our aim is to better understand patterns and processes of tree biodiversity in the Mediterranean and to provide indicators complementing the traditional approaches to biodiversity conservation based on species counts and occurrences, using georeferenced phylogenetic diversity and endemism analyses in a spatial ecological context. Location: Mediterranean Europe. Methods: Using a dated phylogeny of the 64 Euro-Mediterranean tree genera, we calculated phylogenetic diversity for all 50 × 50 km2 grid cells spanning Mediterranean Europe (n = 643) and compared values with those obtained for genus-level taxonomic diversity. Then, we tested the relative influence of geography, past and present climate, and soil on tree diversity (phylogenetic or taxonomic) and its geographical turnover. Geographical patterns of phylogenetic endemism were inferred using the Categorical Analyses of Neo- and Paleo-Endemism (CANAPE) methodology. Results: We showed that phylogenetic and taxonomic diversity within and among cells are correlated and influenced by soil parameters as well as current, Holocene and Late Glacial Maximum climate. Southern Spain, Cyprus and some Aegean islands contained areas of disproportionately high phylogenetic diversity and a concentration of phylogenetic paleo-endemics, while phylogenetic neo-endemism was high in eastern Sicily. Mixed phylogenetic endemism regions were detected in southern Spain and Portugal, in the Balkans and in Crete. Main conclusions: Our phylogenetic approach provides relevant indicators for better protecting forests of the Mediterranean, encompassing past and present evolutionary processes and factors. We consider areas that show a concentration of evolutionary history manifested by high phylogenetic endemism as high priority targets for the conservation of the European tree flora. Aix-Marseille University ANR-11-LABX-0061

Published
2021
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10. Plantes vasculaires nouvelles ou rares pour la Tunisie présentes sur les îles (Galite, Zembra, Kuriat, Monastir, Kerkennah, Kneiss, Djerba)

Author

Mohamed Chaieb, Médail Frédéric, Errol Véla, Gianniantonio Domina, Ridha El Mokni, Salvatore Pasta, Matthieu Charrier, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), FloraConsult, 82 chemin du Grand Jas, 13 580 La Fare les Oliviers, France., Faculté des Sciences de Sfax, Université de Sfax - University of Sfax, Department of Agriculture, Food and Forest Sciences, University of Palermo, Université de Monastir, Laboratoire de Botanique, Cryptogamie et Biologie végéta-le, Département de Sciences pharmaceutiques 'A', Faculté de Pharmacie deMonastir, avenue Avicenne, 5000-Monastir, Tunisie., Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), 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), Université de Montpellier (UM), Università degli studi di Palermo - University of Palermo, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Medail F., Charrier M., Chaieb M., Domina G., El Mokni R., Pasta S., and Vela E.

Subjects
0106 biological sciences, Biodiversity, North africa, Plant Science, rare plants, Bellis perennis, 010603 evolutionary biology, 01 natural sciences, Biogeography, Coastal flora, Endemism, Rare plants, Small Mediterranean islands, Galium, Moraea, 14. Life underwater, biogeography, biology, Ecology, Settore BIO/02 - Botanica Sistematica, coastal flora, Asplenium balearicum, 15. Life on land, biology.organism_classification, Geography, Taxon, endemism, Settore BIO/03 - Botanica Ambientale E Applicata, [SDE]Environmental Sciences, small Mediterranean islands, 010606 plant biology & botany
Abstract

International audience; Vascular plants new or rare for Tunisia occurring on the islands (Galite, Zembra, Kuriat, Monastir, Kerkennah, Kneiss, Djerba).-This study concerns the indigenous vascular plants newly reported for Tunisia and discovered on the islands during some field trips performed since 2014. Five native taxa are new to Tunisia: Bellis perennis, Carthamus creticus, Moraea mediterranea, Asplenium balearicum and Galium minutulum, the latter two also being new to North Africa. Information on 24 rare or poorly known taxa, most often of great biogeographical interest, is given, too. Most of these were discovered on the islands of the eastern coast (Kuriat, Monastir, Kerkennah, Kneiss, Djerba), but also on the northern islands of Zembra and La Galite. The new chorological data underline the first-rate conservation importance of these islands and islets for the preservation of the overall coastal biodiversity of Tunisia.

Published
2020
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11. Author Correction: The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Guillaume Bodineau, Johan Westin, Juan J. Robledo-Arnuncio, Katrin Heer, Cristina C. Bastias, Georg von Arx, Francesca Bagnoli, Fernando Valladares, Bruno Fady, Frédéric Bernier, Christophe Plomion, Kurt Ramskogler, Mehdi Pringarbe, Grégoire Le-Provost, Felix Gugerli, José M. García del Barrio, Vladimir L. Semerikov, Filippos A. Aravanopoulos, Sandro Morganti, Florian Knutzen, Florence Courdier, Tanja Pyhäjärvi, Tor Myking, Bárbara Carvalho, Marc Villar, Catherine Bastien, Katri Kärkkäinen, Olivier Gilg, Pascal Milesi, Christian Rellstab, Mariaceleste Labriola, Lenka Slámová, Mirko Liesebach, Claudio Grefen, Sonja T. Kujala, Outi Savolainen, Stephen Cavers, Dominique Veisse, Birte Pakull, Norbert Turion, Christoph Hartleitner, José Alberto Ramírez-Valiente, Silvio Schueler, Marlène Lefebvre, Ermioni Malliarou, Annie Raffin, Silvia Matesanz, Marianne Correard, Giovanni G. Vendramin, Camilla Avanzi, Eduardo Notivol, Anna-Maria Farsakoglou, Agathe Hurel, Ricardo Alía, Arnaud Jouineau, Alan Gray, Ilaria Spanu, Raquel Benavides, Jean Thevenet, Elisabet Martínez-Sancho, Darius Danusevičius, Lars Opgenoorth, Célia Michotey, Benjamin Dauphin, Santiago C. González-Martínez, Patrick Fonti, Jean-Paul Charpentier, Vincent Lejeune, José Climent, Martin Lascoux, Nicolas Mariotte, Andrea Piotti, Evangelos Barbas, Mari Mette Tollefsrud, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Philipps Universität Marburg, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (CSIC), Bavarian Office for Forest Seeding and Planting, Partenaires INRAE, Centre for Ecology and Hydrology (CEH), Natural Environment Research Council (NERC), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Forest Ecology and Genetics, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Aristotle University of Thessaloniki, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), 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), Unité expérimentale Forêt Pierroton (UEFP), Génétique et Biomasse Forestières ORléans (GBFOR), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), Vytautas Magnus University - Vytauto Didziojo Universitetas (VDU), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), LIECO GmbH & Co KG, Natural Resources Institute Finland (LUKE), Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Thunen Institute of Forest Ecosystems, Thünen Institute, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Universidad Rey Juan Carlos [Madrid] (URJC), Unité de Recherche Génomique Info (URGI), Norwegian Institute of Bioeconomy Research (NIBIO), Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA), University of Oulu, Austrian Research Centre for Forests (BFW), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), and Skogforsk - Swedish Forestry Research Institute

Subjects
0106 biological sciences, Statistics and Probability, Data Descriptor, Climate Change, Forests, Library and Information Sciences, 010603 evolutionary biology, 01 natural sciences, Trees, Education, Quercus, Dendrochronology, Fagus, Picea, lcsh:Science, Author Correction, Betula, Forestry, 15. Life on land, Pinus, Wood, Computer Science Applications, Europe, Geography, Populus, lcsh:Q, Forest ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Statistics, Probability and Uncertainty, Tree species, 010606 plant biology & botany, Information Systems
Abstract

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios., Measurement(s)growth ring • wood densityTechnology Type(s)measuring table • calculationFactor Type(s)tree speciesSample Characteristic - OrganismBetula pendula • Fagus sylvatica • Picea abies • Populus nigra • Pinus pinaster • Pinus sylvestris • Quercus petraeaSample Characteristic - LocationEurope Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11294993

Published
2020
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12. Genetic Mapping of the Incompatibility Locus in Olive and Development of a Linked Sequence-Tagged Site Marker

Author

Roberto Mariotti, Alice Fornasiero, Soraya Mousavi, Nicolò G.M. Cultrera, Federico Brizioli, Saverio Pandolfi, Valentina Passeri, Martina Rossi, Gabriele Magris, Simone Scalabrin, Davide Scaglione, Gabriele Di Gaspero, Pierre Saumitou-Laprade, Philippe Vernet, Fiammetta Alagna, Michele Morgante, Luciana Baldoni, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), Institute of Biosciences and Bioressources (IBBR), University of Amsterdam [Amsterdam] (UvA), Institute of Applied Genomics [Udine] (IGA), Institute of Applied Genomics, Applied Genomics Institute (IGA), Université de Lille, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Mariotti, R., Fornasiero, A., Mousavi, S., Cultrera, N. G. M., Brizioli, F., Pandolfi, S., Passeri, V., Rossi, M., Magris, G., Scalabrin, S., Scaglione, D., Di Gaspero, G., Saumitou-Laprade, P., Vernet, P., Alagna, F., Morgante, M., Baldoni, L., National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Population, Single-nucleotide polymorphism, Locus (genetics), Plant Science, [object Object], Biology, lcsh:Plant culture, 01 natural sciences, self-incompatibility, functional markers, Loss of heterozygosity, Sequence-tagged site, 03 medical and health sciences, symbols.namesake, Gene mapping, lcsh:SB1-1110, genetic map, education, Olea europaea, double digest restriction associated deoxyribonucleic acid sequencing, Original Research, 2. Zero hunger, Genetics, education.field_of_study, Haplotype, 15. Life on land, 030104 developmental biology, Mendelian inheritance, symbols, 010606 plant biology & botany
Abstract

International audience; The genetic control of self-incompatibility (SI) has been recently disclosed in olive. Intervarietal crossing confirmed the presence of only two incompatibility groups (G1 and G2), suggesting a simple Mendelian inheritance of the trait. A double digest restriction associated DNA (ddRAD) sequencing of a biparental population segregating for incompatibility groups has been performed and high-density linkage maps were constructed in order to map the SI locus and identify gene candidates and linked markers. The progeny consisted of a full-sib family of 229 individuals derived from the cross ‘Leccino’ (G1) × ‘Dolce Agogia’ (G2) varieties, segregating 1:1 (G1:G2), in accordance with a diallelic self-incompatibility (DSI) model. A total of 16,743 single nucleotide polymorphisms was identified, 7,006 in the female parent ‘Leccino’ and 9,737 in the male parent ‘Dolce Agogia.’ Each parental map consisted of 23 linkage groups and showed an unusual large size (5,680 cM in ‘Leccino’ and 3,538 cM in ‘Dolce Agogia’). Recombination was decreased across all linkage groups in pollen mother cells of ‘Dolce Agogia,’ the parent with higher heterozygosity, compared to megaspore mother cells of ‘Leccino,’ in a context of a species that showed exceptionally high recombination rates. A subset of 109 adult plants was assigned to either incompatibility group by a stigma test and the diallelic self-incompatibility (DSI) locus was mapped to an interval of 5.4 cM on linkage group 18. This region spanned a size of approximately 300 Kb in the olive genome assembly. We developed a sequence-tagged site marker in the DSI locus and identified five haplotypes in 57 cultivars with known incompatibility group assignment. A combination of two single-nucleotide polymorphisms (SNPs) was sufficient to predict G1 or G2 phenotypes in olive cultivars, enabling early marker-assisted selection of compatible genotypes and allowing for a rapid screening of inter-compatibility among cultivars in order to guarantee effective fertilization and increase olive production. The construction of high-density linkage maps has led to the development of the first functional marker in olive and provided positional candidate genes in the SI locus.

Published
2020
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13. A draft genome of sweet cherry ( Prunus avium L.) reveals genome‐wide and local effects of domestication

Author

Michele Morgante, Ioannis Ganopoulos, Filippos A. Aravanopoulos, Gabriella Sonnante, Sara Pinosio, Michele Vidotto, Andrea Zuccolo, Fabio Marroni, Amy Iezzoni, Gabriele Magris, Giovanni G. Vendramin, Nicola Vitulo, Stéphanie Mariette, Marino Palasciano, Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), Università degli Studi di Udine - University of Udine [Italie], Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP), University of Verona (UNIVR), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Aristotle University of Thessaloniki, Hellenic Agricultural Organization Demeter (HAO Demeter), Università degli Studi di Bari Aldo Moro, Institute of Applied Genomics [Udine] (IGA), Institute of Applied Genomics, Michigan State University [East Lansing], and Michigan State University System

Subjects
0106 biological sciences, 0301 basic medicine, Candidate gene, Plant Science, DNA, Satellite, Biology, Prunus avium, Genes, Plant, 01 natural sciences, Genome, Chromosomes, Plant, Gene flow, 03 medical and health sciences, Prunus, domestication, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, Gene, 2. Zero hunger, Genetic diversity, genome structure and evolution, Resistance (ecology), Chromosome Mapping, Genetic Variation, food and beverages, Cell Biology, genetic diversity, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, Genetics, Population, 030104 developmental biology, Evolutionary biology, genome assembly, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Plant, 010606 plant biology & botany
Abstract

Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety "Big Star*" and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome-wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.

Published
2020
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14. Contribution of genetic resources to grain storage protein composition and wheat quality

Author

Michela Janni, Patricia Giraldo, Kunpu Zhang, Gérard Branlard, B. Wentzel, Tatsuya M. Ikeda, Maryke Labuschagne, Gilberto Igrejas, Daowen Wang, Zhonghu He, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidad Politécnica de Madrid (UPM), Chinese Academy of Agricultural Sciences (CAAS), International Maize and Wheat Improvement Center [Beijing] (CIMMYT), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Trás-os-Montes and Alto Douro [Portugal] (UTAD), National Agriculture and Food Research Organization (NARO), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), University of the Free State [South Africa], College of Agronomy-State Key Laboratory of Wheat and Maize Crop Science [Zhengzhou], Henan Agricultural University, Agricultural Research Council – Small Grain (ARC-SG), Gilberto Igrejas, Tatsuya M. Ikeda, Carlos Guzmán, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), and University of the Free State [South Africa] (UFS)

Subjects
0106 biological sciences, Polymers, Glutenin, [SDV]Life Sciences [q-bio], Wheat flour, Triticum aestivum, Context (language use), Technological tests, 01 natural sciences, Gliadin, 03 medical and health sciences, Storage protein, Alleles, 030304 developmental biology, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, Genetic diversity, biology, business.industry, food and beverages, Durum wheat quality, Grain hardness, Gluten, Biotechnology, genetic resources, chemistry, Triticum durum, biology.protein, business, Protein quality, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 010606 plant biology & botany
Abstract

The technological quality of wheat flour is defined by a range of dough characteristics relevant to the breadmaking processes and practices of individual countries and for particular products. The influence of storage protein diversity on wheat quality has been widely documented in the last three decades. The present chapter focuses on several aspects of wheat quality that merit more attention. The huge genetic diversity of wheat storage proteins means that all the possible allelic combinations and their interactions are too numerous to be tested in terms of their influence on the major quality parameters. However it is still relevant to describe the variation in rheological and viscoelastic properties of gluten in relation to its component proteins, glutenin and gliadin. Although gluten plays a major role in determining the properties of dough, the abundance of the two major storage protein fractions does not solely explain the observed variation in those properties. We therefore examine the influence of some genetic factors, including those affecting the protein composition, on the variation in the glutenin polymer sizes. Some examples will be given to illustrate how end-use quality can be improved by taking advantage of the available genetic resources in parallel with molecular genome analyses with the dual aim of widening the scope of characteristics that can be harnessed in breeding and ensuring consistent wheat quality in changing agro-climatic situations. The known alleles of the major genes are highlighted in the context of the challenges that the research community is facing regarding wheat allele nomenclature, exchange of gene bank material and the numerous quality attributes of interest. Finally, important research objectives are proposed for breeding future wheats with grain protein quality and technological properties tailored for different food products.

Published
2020
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15. Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis

Author

Rosa Paparo, Clara Conicella, Pasquale Termolino, Riccardo Aiese Cigliano, Matthieu Falque, Gaetana Cremona, Olivier C. Martin, Federica Consiglio, Antoine G. H. Ederveen, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), 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), Universitat Autònoma de Barcelona (UAB), and Radboud university [Nijmegen]

Subjects
0106 biological sciences, 0301 basic medicine, Heterozygote, [SDV]Life Sciences [q-bio], Arabidopsis, crossing over, Plant Science, Chromosomal rearrangement, Biology, Genes, Plant, Interference (genetic), Polymorphism, Single Nucleotide, 01 natural sciences, Chromosomes, Plant, Chromosomal crossover, 03 medical and health sciences, Meiosis, chromosome rearrangement, Genetics, Homologous chromosome, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, meiosis, Crossing Over, Genetic, Chromosomal inversion, Recombination, Genetic, Chromosome Mapping, Chromosome, Original Articles, Cell Biology, crossover interference, Chiasma, recombination, 030104 developmental biology, Chromosome Inversion, Pollen, Original Article, interchromosomal effect, Genome, Plant, 010606 plant biology & botany
Abstract

Summary During meiosis, recombination ensures allelic exchanges through crossovers (COs) between the homologous chromosomes. Advances in our understanding of the rules of COs have come from studies of mutations including structural chromosomal rearrangements that, when heterozygous, are known to impair COs in various organisms. In this work, we investigate the effect of a large heterozygous pericentric inversion on male and female recombination in Arabidopsis. The inversion was discovered in the Atmcc1 mutant background and was characterized through genetic and next‐generation sequencing analysis. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the mutant and the wild type, both crossed with Landsberg erecta, were analyzed genome‐wide by 143 single‐nucleotide polymorphisms. The negative impact of inversion became evident in terms of CO loss in the rearranged chromosome in both male and female meiosis. No single‐CO event was detected within the inversion, consistent with a post‐meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F1 plants confirmed that COs were reduced in male meiosis in the chromosome with inversion. Crossover suppression on the rearranged chromosome is associated with a significant increase of COs in the other chromosomes, thereby maintaining unchanged the number of COs per cell. The CO pattern observed in our study is consistent with the interchromosomal (IC) effect as first described in Drosophila. In contrast to male meiosis, in female meiosis no IC effect is visible. This may be related to the greater strength of interference that constrains the CO number in excess of the minimum value imposed by CO assurance in Arabidopsis female meiosis., Significance Statement This work provides further information into the poorly described phenomenon of the interchromosomal (IC) effect in plants. Indeed, the few studies on this phenomenon in maize date back to the 1960s and 1970s and have low resolution, being limited to a few specific regions and genetic markers. In this paper we underscore the significance for plant scientists of the IC effect during meiosis and provide more detailed data and analyses.

Published
2019
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16. Certainties and uncertainties about the life cycle of the Périgord black truffle (Tuber melanosporum Vittad.)

Author

Christophe Robin, Claude Murat, Aurélie Deveau, Francesco Paolocci, Beatrice Belfiori, Andrea Rubini, Claudia Riccioni, Bernd Zeller, Emila Akroume, François Le Tacon, Herminia De la Varga, Francis Martin, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), Laboratoire Agronomie et Environnement (LAE), Unité de recherche Biogéochimie des Ecosystèmes Forestiers (BEF), Institut National de la Recherche Agronomique (INRA), ANR (ANR-09-STRA-10-02, ANR-11-LABX-0002-01), SYSTRUF programme, and Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, 0301 basic medicine, Black truffle, Mating type, [SDV]Life Sciences [q-bio], media_common.quotation_subject, Male and female gametes, Model system, Fungus, 01 natural sciences, Competition (biology), [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 03 medical and health sciences, type sexuel, champignon comestible, tuber melanosporum, reproduction sexuée, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, media_common, Competition, Ecology, biology, hétérothallisme, Forestry, champignon ectomycorhizien, 15. Life on land, biology.organism_classification, Sexual reproduction, Ascocarp, 030104 developmental biology, cycle de vie, competititon, Tuber melanosporum, 010606 plant biology & botany
Abstract

International audience; Key message Several aspects of the life cycle of the Périgord black truffle have been elucidated only recently, while others remain either controversial or unstudied. In this paper, we present a revised life cycle of this fungus and highlight key aspects that have yet to be addressed or require further understanding.• ContextThe hypogeous sporophores of several Tuber species, renowned for their aromatic and gustatory qualities, are widely commercialized. One of the most valuable species is Tuber melanosporum Vittad., the Périgord black truffle also known as “the black diamond”. However, many aspects of T. melanosporum life cycle remain unsolved.• AimsIn this work, we examine past and recent findings on the life cycle of T. melanosporum, currently regarded as a model system for Tuber species, with the view of highlighting aspects of its life cycle which remain unsolved.• ResultsSeveral aspects of its life cycle have recently been elucidated (i.e. characterization of two mating type genes, heterothallism, prevalence of sexual reproduction on vegetative propagation, exclusion of one mating type by its opposite on ectomycorrhizas, dependency of ascocarps on their host for carbon allocation), while others remain unaddressed.• ConclusionNumerous additional aspects of the T. melanosporum life cycle remain unsolved, such as exclusion or competition mechanisms between ectomycorrhizal mating types, factors involved in ascocarp initiation, the nature of the connection linking ascocarps and mycorrhizas and atmospheric nitrogen fixation.

Published
2016
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17. Gene mapping in tomato

Author

Silvana Grandillo, Mathilde Causse, Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Institut National de la Recherche Agronomique (INRA), Research Division Portici, Institute of Bioscience and BioResources (CNR-IBBR), Institute of Biosciences and Bioressources (IBBR), National Research Council (CNR), Génétique et Amélioration des Fruits et Légumes (GAFL), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), Mathilde Causse, Jim Giovannoni, Mondher Bouzayen, and Mohamed Zouine

Subjects
0106 biological sciences, 0301 basic medicine, genetical analysis, Plant growth, carte génétique, Positional cloning, mutation génétique, Resistance, Computational biology, Biology, tomato, 01 natural sciences, Genome, qualité du fruit, 03 medical and health sciences, tomate, Gene mapping, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, Whole genome sequencing, Fruit quality, food and beverages, séquence du génome, 030104 developmental biology, espèce modèle, Identification (biology), genetic mapping, indice de résistance, Recombination, Mutations, analyse génétique, 010606 plant biology & botany
Abstract

Tomato is a model species for genetic analyses since a long time. Many mutations controlled by a single gene were discovered and the underlying genes were mapped first on the tomato genetic map. Most of these genes are involved in fruit colour and shape, in plant growth and architecture and in disease resistances. With the construction of high-density molecular genetic maps, many genes were located on the genome and subsequently several of them were fine-mapped and further identified by positional cloning. Today with the availability of the tomato genome sequence these genes are physically located on the genome and the identification of new ones is being considerably accelerated. The alignment of the physical and genetic maps allowed the identification of hot spots of recombination and of large regions where recombination is almost suppressed, whatever the progeny studied. The impact of this heterogeneity in recombination is discussed.

Published
2016
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18. Evolution-based approach needed for the conservation and silviculture of peripheral forest tree populations

Author

Hojka Kraigher, Hassan Sbay, Urs Mühlethaler, Marjana Westergren, Srdjan Stojnic, Fulvio Ducci, Annika Perry, Maria Carolina Varela, Bruno Fady, Matti Rousi, Colin T. Kelleher, Filippos A. Aravanopoulos, Csaba Mátyás, Sanja Perić, Abdelhamid Khaldi, Giovanni G. Vendramin, Paraskevi Alizoti, Magda Bou Dagher Kharrat, Branislav Cvjetković, Tzvetan Zlatanov, Ivaylo Tsvetkov, Martina Tijardović, Koen Kramer, Gerhard Huber, Piero Belletti, Georg von Wühlisch, Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Faculty of Agriculture, Forest Science & Natural Environment, Aristotle University of Thessaloniki, Institute of Environmental and Earth Sciences [Sopron] (NRRC), University of West Hungary [Sopron], Institute of Forest Genetics, Johann Heinrich von Thünen Institut, Slovenian Forestry Institute, DISAFA Agricultural Genetics, University of Turin, Faculty of Forestry, University of Banja Luka, Forestry Research Centre, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Bavarian Institute for Forest Seeding and Planting, DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Institut National de Recherche en Génie Rural Eaux et Forêts (INRGREF), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Institution de la Recherche et de l'Enseignement Supérieur Agricoles [Tunis] (IRESA), Faculty of Science, Laboratoire Caractérisation Génomique des Plantes, Université Saint-Joseph de Beyrouth (USJ), Green World Research, Vegetation, Forest, and Landscape Ecology, ALTERRA, Wageningen University and Research [Wageningen] (WUR), Haute école des sciences agronomiques, forestières et alimentaires (HAFL), Croatian Forest Research Institute, Centre for Ecology and Hydrology, Natural resources institute Finland, Université Mohammed V de Rabat, Institute of Lowland Forestry and Environment, University of Novi Sad, Forest Research Institute, Instituto Nacional de Investigação Agrária e Veterinária = National Institute for Agrarian and Veterinary Research [Oeiras, Portugal] (INIAV), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), COST Action FP1202 ‘‘Strengthening conservation: a key issue for adaptation of marginal/peripheral populations of forest trees to climate change in Europe (MaP-FGR)', projects AMTools (ANR-11-AGRO-005-04) and ERA-NET BiodivERsA 2011– 2012 ‘‘TipTree' (ANR-12-EBID-0003), National Research Institute of Rural Engineering, Water and Forests (INRGREF), Université de Carthage - University of Carthage, Wageningen University and Research Centre [Wageningen] (WUR), Natural Resources Institute Finland, Instituto Nacional de Investigação Agrária e Veterinária (INIAV), Institute of Biosciences and Bioresources (IBBR), and Consiglio Nazionale delle Ricerche [Roma] (CNR)

Subjects
0106 biological sciences, Range (biology), Ecology (disciplines), Bos- en Landschapsecologie, Forest management, forest tree genetics, forest management, Climate change, Context (language use), Conservation, Management, Monitoring, Policy and Law, 010603 evolutionary biology, 01 natural sciences, Ecology and Environment, Geographic distribution range, Geographic distribution range, Forest tree genetics, Ecology, Climate change, Forest management, Conservation, Forest and Landscape Ecology, Vegetatie, Nature and Landscape Conservation, Local adaptation, Vegetation, Natural selection, Ecology, business.industry, geographic distribution range, ecology, climate change, conservation, Environmental resource management, Forest tree genetics, Forestry, 15. Life on land, PE&RC, Geography, Sustainability, Vegetatie, Bos- en Landschapsecologie, Vegetation, Forest and Landscape Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 010606 plant biology & botany
Abstract

The fate of peripheral forest tree populations is of particular interest in the context of climate change. These populations may concurrently be those where the most significant evolutionary changes will occur; those most facing increasing extinction risk; the source of migrants for the colonization of new areas at leading edges; or the source of genetic novelty for reinforcing standing genetic variation in various parts of the range. Deciding which strategy to implement for conserving and sustainably using the genetic resources of peripheral forest tree populations is a challenge. Here, we review the genetic and ecological processes acting on different types of peripheral populations and indicate why these processes may be of general interest for adapting forests and forest management to climate change. We particularly focus on peripheral populations at the rear edge of species distributions where environmental challenges are or will become most acute. We argue that peripheral forest tree populations are “natural laboratories” for resolving priority research questions such as how the complex interaction between demographic processes and natural selection shape local adaptation; and whether genetic adaptation will be sufficient to allow the long-term persistence of species within their current distribution. Peripheral populations are key assets for adaptive forestry which need specific measures for their preservation. The traditionally opposing views which may exist between conservation planning and sustainable forestry need to be reconciled and harmonized for managing peripheral populations. Based on existing knowledge, we suggest approaches and principles which may be used for the management and conservation of these distinctive and valuable populations, to maintain active genetic and ecological processes that have sustained them over time.

Published
2016
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19. Local adaptation in european firs assessed through extensive sampling across altitudinal gradients in southern Europe

Author

Dragos Postolache, Louise Brousseau, Martin Lascoux, Bruno Fady, Peter Zhelev, Thomas Källman, Andrea Piotti, Sascha Liepelt, Andreas D. Drouzas, Cristina Leonarduzzi, Giovanni G. Vendramin, Anna M. Roschanski, Flaviu Popescu, Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Institute of Biosciences and Bioresources (IBBR), Consiglio Nazionale delle Ricerche [Roma] (CNR), Scuola Superiore Sant’Anna, National Institute of Forest Research and Development, Institutul de Cercetari si Amenajari Silvice (ICAS), Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, School of Biology, Aristotle University of Thessaloniki, Institute of Biosciences and BioResources (IBBR, Faculty of Biology, Conservation Biology, University of Giessen and Marburg Lung Center (UGMLC), Leibniz Institute of Plant Genetics and Crop Plant Research, University of Forestry (UF), Funding was provided by the ERAnet BiodivERsA project ‘LinkTree’ (ANR-08-Biodiversa- 006-06), the ERAnet BiodivERsA project 'TipTree' (ANR-12-EBID-0003) and COST Action FP 1202. GGV was also supported by a grant by the Italian MIUR project ‘Biodiversitalia’ (RBAP10A2T4), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), and Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)

Subjects
0106 biological sciences, 0301 basic medicine, arbre forestier, Heredity, Climate, Biodiversité et Ecologie, lcsh:Medicine, Population genetics, Forests, europe du sud, Mechanical Treatment of Specimens, 01 natural sciences, Trees, Evolutionsbiologi, abies cephalonica, Gene Frequency, Natural Selection, Homogenizing, lcsh:Science, phenotypic and genetic divergence, Milieux et Changements globaux, abies alba, Expressed Sequence Tags, Adaptive traits, Multidisciplinary, Natural selection, Geography, Ecology, Altitude, Simulation and Modeling, Sampling (statistics), Adaptation, Physiological, Terrestrial Environments, Genetic Mapping, Phenotype, Abies, Research Article, Evolutionary Processes, DNA, Plant, Genotype, Local adaptation, [SDE.MCG]Environmental Sciences/Global Changes, Variant Genotypes, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, 010603 evolutionary biology, Ecosystems, Biodiversity and Ecology, 03 medical and health sciences, Evolutionary Adaptation, Genetic variation, Genetics, Computer Simulation, modélisation, Evolutionary Biology, Population Biology, lcsh:R, Ecology and Environmental Sciences, Genetic Variation, Biology and Life Sciences, Bayes Theorem, 15. Life on land, Genetic divergence, 030104 developmental biology, Specimen Preparation and Treatment, Genetic Loci, lcsh:Q, adaptation au changement climatique, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Population Genetics
Abstract

Background: Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales. Methods: A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical 'within-site' approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM). Results: HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species' southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches. Conclusion: Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales.

Published
2016
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20. Biosafety of Forest Transgenic Trees: Improving the Scientific Basis for Safe Tree Development and Implementation of EU Policy Directives

Author

Vettori, Cristina, Gallardo, Fernando, Häggman, Hely, Kazana, Vassiliki, Migliacci, Fabio, Pilate, Gilles, Fladung, Matthias, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), National Research Council (CNR), Universidad de Málaga [Málaga] = University of Málaga [Málaga], University of Oulu, Department of Forestry and Natural Environment Management, Technological Education Institute of Lamia, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Johann Heinrich von Thünen Institut, and Cost (European Cooperation in Science and Technology)

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract

FPS COST Action FP0905; International audience; This book provides up-to-date information on the environmental impact of transgenic trees on genetically modified tree (GMT) communication strategy. It is useful to public/private organisations as well as to private and public research bodies and universities worldwide since it reports on the global status of GMT research and policy. A high number of genetically modified trees (GMTs) with altered or novel characteristics have been produced in the last 15 years. However, their very low public acceptance is a basic problem in their commercialization. Breeders anticipate economic and ecological benefits, like reduced product costs and less pressure on native forests, while opponents fear risks, such as unintended spread of GMTs. But what is true? To answer this question, the COST Action FP0905 focused on key aspects related to GMTs: (a) biological characterization; (b) assessment of possible environmental impacts; (c) socio-economic implications and public acceptance/concerns; (d) providing science-based information to communicate with the public.

Published
2016
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21. Adapting through glacial cycles: insights from a long-lived tree (Taxus baccata)

Author

Santiago C. González-Martínez, Elisa Berganzo, Miquel Riba, Francesca Bagnoli, Giovanni G. Vendramin, Jacques-Louis de Beaulieu, Diana Krajmerová, Marta Dubreuil, Maria Mayol, Cristina Vettori, Ladislav Paule, Lucie Vincenot, Concetta Burgarella, Ivana Romšáková, Centre de Recerca Ecològica i Aplicacions Forestals, Univ. Autònoma de Barcelona (CREAF), université de Barcelone, Departamento de Sistemas y Recursos forestales, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institute of Biosciences and BioResources, Plant Genetics Institute, UOS Florence, Consiglio Nazionale delle Ricerche [Roma] (CNR), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), Consiglio Nazionale delle Ricerche (CNR), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institute of Biosciences and Bioresources (IBBR), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, demography, Physiology, Climate, Interglacial, Adaptation, Biological, Plant Science, 01 natural sciences, microsatellites, Ice Cover, Glacial period, 0303 health sciences, education.field_of_study, Ecology, DNA, Chloroplast, Approximate Bayesiancomputation (ABC), interglacial, Europe, Phylogeography, Genetic structure, Taxus, Approximate Bayesian computation, Demographic history, Environment-dependent selection, Climate Change, Population, Biology, 010603 evolutionary biology, Evolutionary hisory, environment-dependent selection, 03 medical and health sciences, Evolutionary history, Taxus baccata, education, Microsatellites, 030304 developmental biology, Demography, Genetic diversity, Environment_x0002_dependent seection, Genetic Variation, Microsatellite, 15. Life on land, Chloroplast DNA(cpDNA), Genetic divergence, chloroplast DNA (cpDNA), approximate Bayesian computation (ABC), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Quaternary, evolutionary history, Microsatellite Repeats
Abstract

Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long-lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation-by-distance) and selective (isolation-by-adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present-day patterns of genetic diversity. © 2015 New Phytologist Trust.

Published
2015
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22. Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq

Author

M. Bou Dagher-Kharrat, Giovanni G. Vendramin, Marie-Joe Karam, Sara Pinosio, François Lefèvre, Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), laboratoire de Caractérisation Génomique des Plantes, Université Saint-Joseph de Beyrouth (USJ), Applied Genomics Institute (IGA), Institute of Biosciences and Bioresources (IBBR), Consiglio Nazionale delle Ricerche [Roma] (CNR), This project was supported by the Agropolis Fondation (Montpellier, France) under the reference ID 'BIOFIS' 1001-001, Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), and Consiglio Nazionale delle Ricerche (CNR)

Subjects
0106 biological sciences, Genetic Markers, DNA, Plant, Molecular Sequence Data, SNP, Single-nucleotide polymorphism, Computational biology, Biology, 01 natural sciences, Genome, Polymorphism, Single Nucleotide, DNA sequencing, 03 medical and health sciences, chemistry.chemical_compound, Cedrus atlantica, next generation sequencing, RADseq, SSR, transcriptome, Molecular marker, Genetics, Genotyping, Cedrus, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Contig, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Restriction site, chemistry, Microsatellite, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Plant, 010606 plant biology & botany, Biotechnology
Abstract

We combined restriction site associated DNA sequencing (RADseq) using a hypomethylation-sensitive enzyme and messenger RNA sequencing (mRNAseq) to develop molecular markers for the 16 gigabase genome of[i] Cedrus atlantica[/i], a conifer tree species. With each method, Illumina(®) reads from one individual were used to generate de novo assemblies. SNPs from the RADseq data set were detected in a panel of one single individual and three pools of three individuals each. We developed a flexible script to estimate the ascertainment bias in SNP detection considering the pooling and sampling effects on the probability of not detecting an existing polymorphism. Gene Ontology (GO) and transposable element (TE) search analyses were applied to both data sets. The RADseq and the mRNAseq assemblies represented 0.1% and 0.6% of the genome, respectively. Genome complexity reduction resulted in 17% of the RADseq contigs potentially coding for proteins. This rate was doubled in the mRNAseq data set, suggesting that RADseq also explores noncoding low-repeat regions. The two methods gave very similar GO-slim profiles. As expected, the two assemblies were poor in TE-like sequences (

Published
2014
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23. The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum

Author

Alexis Sarazin, Hugues Richard, Alessandra Carbone, Alessandra Rogato, Angela Falciatore, Lionel Navarro, Soizic Cheminant Navarro, Wolfgang R. Hess, Björn Voss, Raphaël Champeimont, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Department of Biology, Genetics and Experimental Bioinformatics, University of Freiburg [Freiburg], Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Champeimont, Raphaël, Consiglio Nazionale delle Ricerche (CNR), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)

Subjects
Population, Genomics, Phaeodactylum tricornutum, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA, Small Nuclear, Genetics, Epigenetics, education, Gene, 030304 developmental biology, Epigenomics, Regulation of gene expression, Diatoms, 0303 health sciences, education.field_of_study, DNA methylation, Genome, biology, Small RNAs, Transposable Elements, Chromosome Mapping, Computational Biology, Molecular Sequence Annotation, Periodic small RNAs distribution, biology.organism_classification, tRNAs, Gene Expression Regulation, DNA Transposable Elements, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Nucleic Acid Conformation, RNA, Small Untranslated, 030217 neurology & neurosurgery, Research Article, U2 snRNA, Genome-Wide Association Study, Biotechnology
Abstract

Background Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA methylation and gene silencing activities. Yet, the biogenesis and regulatory function of small RNAs (sRNAs) remain ill defined in diatoms. Results Here we report the first comprehensive characterization of the sRNA landscape and its correlation with genomic and epigenomic information in Phaeodactylum tricornutum. The majority of sRNAs is 25 to 30 nt-long and maps to repetitive and silenced Transposable Elements marked by DNA methylation. A subset of this population also targets DNA methylated protein-coding genes, suggesting that gene body methylation might be sRNA-driven in diatoms. Remarkably, 25-30 nt sRNAs display a well-defined and unprecedented 180 nt-long periodic distribution at several highly methylated regions that awaits characterization. While canonical miRNAs are not detectable, other 21-25 nt sRNAs of unknown origin are highly expressed. Besides, non-coding RNAs with well-described function, namely tRNAs and U2 snRNA, constitute a major source of 21-25 nt sRNAs and likely play important roles under stressful environmental conditions. Conclusions P. tricornutum has evolved diversified sRNA pathways, likely implicated in the regulation of largely still uncharacterized genetic and epigenetic processes. These results uncover an unexpected complexity of diatom sRNA population and previously unappreciated features, providing new insights into the diversification of sRNA-based processes in eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-698) contains supplementary material, which is available to authorized users.

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