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1. Capulavirus and Grablovirus: two new genera in the family Geminiviridae

Author: Jesús Navas-Castillo, F. Murilo Zerbini, Rob W. Briddon, Enrique Moriones, Ali M. Idris, Philippe Roumagnac, Darren P. Martin, Arvind Varsani, Rafael F. Rivera-Bustamante, Marc Fuchs, The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, Arizona State University [Tempe] (ASU), Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, New York State Agricultural Experiment Station, Cornell University [New York], Instituto de Hortofruticultura Subtropical y Mediterranea 'La Mayora' (IHSM), Universidad de Málaga [Málaga] = University of Málaga [Málaga]-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), School of Plant Sciences [Tucson], University of Arizona, National Institute for Biotechnology and Genetic Engineering (NIBGE), Unidad Irapuato, Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Departemente de Fitopatologia/Bioagro, Universidade Federal de Viçosa (UFC), Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Cornell University, Instituto de Hortofruticultura Subtropical y Mediterranea ‘‘La Mayora’’, Consejo Superior de Investigaciones Cientıificas (IHSM-UMA-CSIC), Universidad de Málaga [Málaga], School of Plant Sciences, University, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0301 basic medicine, Phylogénie, Identification, Citrus, Virologie, Eragrovirus, viruses, Topocuvirus, Euphorbia, Turncurtovirus, Curtovirus, Alfalfa leaf, Phylogeny, genre (taxon), Species demarcation criterion, food and beverages, General Medicine, Pairwise identity, 3. Good health, Latent virus, Vecteur de maladie, geminiviridae, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Species demarcation, Espèce nouvelle, Medicago sativa, food.ingredient, Aphis craccivora, Biology, Phaseolus vulgaris, 03 medical and health sciences, Mastrevirus, food, Spissistilus festinus, Virology, Botany, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Geminiviridae, Géminivirus, H20 - Maladies des plantes, Plant Diseases, Begomovirus, fungi, Virus des végétaux, Taxonomie, biology.organism_classification, Insect Vectors, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 030104 developmental biology, Vitis vinifera, Aphids, Becurtovirus, maladie virale, Morus
Abstract: Geminiviruses are plant-infecting single-stranded DNA viruses that occur in most parts of the world. Currently, there are seven genera within the family Geminiviridae (Becurtovirus, Begomovirus, Curtovirus, Eragrovirus, Mastrevirus, Topocuvirus and Turncurtovirus). The rate of discovery of new geminiviruses has increased significantly over the last decade as a result of new molecular tools and approaches (rolling-circle amplification and deep sequencing) that allow for high-throughput workflows. Here, we report the establishment of two new genera: Capulavirus, with four new species (Alfalfa leaf curl virus, Euphorbia caput-medusae latent virus, French bean severe leaf curl virus and Plantago lanceolata latent virus), and Grablovirus, with one new species (Grapevine red blotch virus). The aphid species Aphis craccivora has been shown to be a vector for Alfalfa leaf curl virus, and the treehopper species Spissistilus festinus is the likely vector of Grapevine red blotch virus. In addition, two highly divergent groups of viruses found infecting citrus and mulberry plants have been assigned to the new species Citrus chlorotic dwarf associated virus and Mulberry mosaic dwarf associated virus, respectively. These species have been left unassigned to a genus by the ICTV because their particle morphology and insect vectors are unknown.
Published: 2017
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2. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Author: Lukas A. Mueller, T. P. Robbins, Gonzalo H. Villarino, Trude Schwarzacher, Julia Weiss, Eva Nouri, Natalia Dudareva, Jan Zethof, Kevin M. Davies, Michiel Vandenbussche, Xiaodan Lv, Marcel Bucher, Philipp Franken, Nunzio D’Agostino, Massimo Delledonne, Mélanie K. Rich, Neil S. Mattson, Eric Lyons, Patrice Morel, Mattijs Bliek, Jennifer D. Hintzsche, Ronald Koes, Mitrick A. Johns, Laurie Grandont, Susan L. Urbanus, M. Eric Schranz, Qinzhou Qi, Michael C. Schatz, Enrico Martinoia, Laure Bapaume, Robert C. Schuurink, Aureliano Bombarely, Didier Reinhardt, Rémy Bruggmann, Katja R. Richert-Pöggeler, Mario Pezzotti, Maaike R. Boersma, Michel Moser, J. S. Heslop-Harrison, Uwe Druege, Diwa Malla, Kitty Vijverberg, Lorenzo Borghi, Ryan M. Warner, Haibao Tang, Avichai Moshe Amrad, Kees Spelt, Thomas L. Sims, Valentina Passeri, Francesca Quattrocchio, Manzhu Bao, Joëlle K. Muhlemann, Marcos Egea-Cortines, Cornelius S. Barry, Zhen Yue, Noe Fernandez-Pozo, Cris Kuhlemeier, Plant Physiology (SILS, FNWI), Plant Development & (Epi)Genetics (SILS, FNWI), Department of Horticulture, University of Wisconsin-Madison, Institute of Plant Sciences, University of Bern, Huazhong Agricultural University, Department of Biology, Northern Arizona University [Flagstaff], University of Amsterdam [Amsterdam] (UvA), Universität Zürich [Zürich] = University of Zurich (UZH), Universität Bern- University of Bern [Bern], Partenaires INRAE, University of Cologne, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Plant & Food Research, Leibniz Institute of Vegetable and Ornamental Crops, Leibniz Association, Purdue University, Universidad Politécnica de Cartagena, Dipartimento di Biotecnologie, University of Verona (UNIVR), Boyce Thompson Institute [Ithaca], Wageningen University and Research Centre (WUR), Department of Genetics [Leicester], University of Leicester, Department of Biological Sciences, The Open University [Milton Keynes] (OU), Northern University, Beijing Genomics Institute [Shenzhen] (BGI), School of Plant Sciences, iPlant Collaborative, University of Arizona, Cornell University [New York], Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants, University of Nottingham, UK (UON), Cold Spring Harbor Laboratory (CSHL), School of Plant Sciences, Radboud university [Nijmegen], Institute of Plant Science, NWO-ALW grant 022.001.018 820.02.015, Marie Curie Independent Fellowship, Swiss NSF grant 31003A_159493 31003A_135778, NCCR Plant Survival, NWO-TOP grant 854.11.006, Borsa di Studio Lanzi per Genetica Agraria, Accademia dei Lincei, CNRS ATIP-AVENIR award, Deutsche Forschungsgemeinschaft grant DR411/2-1, Bombarely, Aureliano, Moser, Michel, Amrad, Avichai, Bao, Manzhu, Bapaume, Laure, Barry, Cornelius S., Bliek, Mattij, Boersma, Maaike R., Borghi, Lorenzo, Bruggmann, Rémy, Bucher, Marcel, D'Agostino, Nunzio, Davies, Kevin, Druege, Uwe, Dudareva, Natalia, Egea-Cortines, Marco, Delledonne, Massimo, Fernandez-Pozo, Noe, Franken, Philipp, Grandont, Laurie, Heslop-Harrison, J. S., Hintzsche, Jennifer, Johns, Mitrick, Koes, Ronald, Lv, Xiaodan, Lyons, Eric, Malla, Diwa, Martinoia, Enrico, Mattson, Neil S., Morel, Patrice, Mueller, Lukas A., Muhlemann, Joëlle, Nouri, Eva, Passeri, Valentina, Pezzotti, Mario, Qi, Qinzhou, Reinhardt, Didier, Rich, Melanie, Richert-Pöggeler, Katja R., Robbins, Tim P., Schatz, Michael C., Schranz, M. Eric, Schuurink, Robert C., Schwarzacher, Trude, Spelt, Kee, Tang, Haibao, Urbanus, Susan L., Vandenbussche, Michiel, Vijverberg, Kitty, Villarino, Gonzalo H., Warner, Ryan M., Weiss, Julia, Yue, Zhen, Zethof, Jan, Quattrocchio, Francesca, Sims, Thomas L., Kuhlemeier, Cris, Huazhong Agricultural University [Wuhan] (HZAU), Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria = Council for Agricultural Research and Economics (CREA), Purdue University [West Lafayette], Università degli studi di Verona = University of Verona (UNIVR), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and Radboud University [Nijmegen]
Subjects: 0106 biological sciences, 0301 basic medicine, Animal Ecology and Physiology, Plant Science, 580 Plants (Botany), Plant Genetics, 01 natural sciences, Petunia, Genome, Petunia axillaris, NUMBER, Plant evolution, SYNTHASE, Genetics, biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Biosystematiek, Life Sciences & Biomedicine, Solanaceae, Genome, Plant, Evolution, Genetics, Plant evolution, Plant sciences, EXPRESSION, DATABASE, Evolution, SEQUENCE, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Genetic model, Life Science, Gene, SUPPRESSION, Whole genome sequencing, Science & Technology, Plant Sciences, 15. Life on land, biology.organism_classification, GENE, 030104 developmental biology, POLLINATOR ATTRACTION, TRANSPOSABLE ELEMENTS, Biosystematics, Hybridization, Genetic, EPS, Plant sciences, GENERATION, 010606 plant biology & botany
Abstract: Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.
Published: 2016
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3. Updated phylogenetic and systematics of the Acrapex albivena Hampson, 1910 and A. stygiata (Hampson, 1910) species groups (Lepidoptera, Noctuidae, Noctuinae, Apameini, Sesamiina), with the description of nine new species from the Afrotropics

Author: Muluken Goftishu, Bruno Le Ru, Yoseph Assefa, Claire Capdevielle-Dulac, George Ong’amo, D. E. Conlong, Gael J. Kergoat, Gilson Chipabika, Beatrice Pallangyo, Jérôme Barbut, Boaz K. Musyoka, Mohamedi Njaku, International Centre of Insect Physiology and Ecology (ICIPE), Université Paris-Sud - Paris 11 (UP11), UMR 247, Institut de Recherche pour le Développement (IRD [France-Ouest]), Biocontrol Programme, School of Plant Sciences, University of Arizona, University of Swaziland, Zambia Agriculture Research Institute, Partenaires INRAE, University of KwaZulu-Natal (UKZN), South African Sugarcane Research Institute, University of Nairobi (UoN), Département Systématique et Évolution, Muséum national d'Histoire naturelle (MNHN), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, Systematics, Acrapex, Zoology, Biology, Apameini, 010603 evolutionary biology, 01 natural sciences, molecular phylogenetics, Lepidoptera genitalia, taxonomy, 03 medical and health sciences, systematics, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, [SDV.BA]Life Sciences [q-bio]/Animal biology, biology.organism_classification, Noctuinae, host plants, Insect Science, Molecular phylogenetics, Noctuidae, Taxonomy (biology), Afrotropics
Abstract: International audience; The genus Acrapex Hampson, 1891 (Lepidoptera, Noctuidae, Noctuinae, Apameini, Sesamiina) constitutes a speciose group of noctuid stemborers mostly distributed in the Afrotropics. In this study nine new Acrapex species are described: Acrapex abyssinica n. sp., Acrapex dabaga n. sp., Acrapex jansei n. sp., Acrapex kifanya n. sp., Acrapex lusinga n. sp., Acrapex ngwenya n. sp., Acrapex njombea n. sp., Acrapex vetiveria n. sp. and Acrapex zima n. sp. All species are assigned to the A. albivena group with the exception of A. lusinga which is assigned to the A. stygiata group. We also provide supplemental descriptions for two previously described species of the A. albivena group, A. punctosa Berio, 1973 and A. sysciodes Berio, 1973, and for one species belonging to the A. stygiata group: A. brunneella Le Ru, 2014. Host plants of three species are recorded; A. brunneella and Acrapex jansei were reared on Cymbopogon pospischilii (K.Schum.) C.E.Hubb and A. vetiveria on Chrysopogon zizanioides (L.). We also conducted molecular phylogenetic analyses (using both Bayesian inference and maximum likelihood) on a multi-marker (four mitochondrial and two nuclear genes) molecular dataset encompassing 138 specimens (including 98 specimens from the A. albivena group and 23 specimens from the A. stygiata group) from 48 stemborer species. The results of the corresponding analyses support the monophyly of the two groups of interest and the species status of all newly described taxa, except for A. lusinga that was not sequenced. The phylogenetic analyses also unravel several evolutionary lineages whose precise status is pending because their DNA was extracted from larval stages.; Actualisation des connaissances de la phylogénie et de la systématique des groupes d’espèces Acrapex albivena Hampson, 1910 et A. stygiata (Hampson, 1910) (Lepidoptera, Noctuidae, Noctuinae, Apameini, Sesamiina), avec la description de neuf nouvelles espèces de la région Afrotropicale. Le genre Acrapex Hampson, 1891 (Lepidoptera, Noctuidae, Noctuinae, Apameini, Sesamiina) est un groupe diversifié de noctuelles foreuses, majoritairement distribué dans la région Afrotropicale. Dans cette étude neuf espèces nouvelles sont décrites : Acrapex abyssinica n. sp., Acrapex dabaga n. sp., Acrapex jansei n. sp., Acrapex kifanya n. sp., A. lusinga n. sp., Acrapex ngwenya n. sp., Acrapex njombea n. sp., Acrapex vetiveria n. sp. et Acrapex zima n. sp. Toutes ces espèces sont assignées au groupe d’espèce A. albivena à l’exception d’A. lusinga qui est assignée au groupe d’espèce A. stygiata. Nous fournissons également des descriptions supplémentaires pour deux espèces, A. punctosa Berio, 1973 et A. sysciodes, Berio 1973, précedemment décrites dans le groupe A. albivena ainsi que pour A. brunneella Le Ru, 2014, une espèce qui appartient au groupe A. stygiata. Les plantes-hôtes de trois espèces sont répertoriées ; Acrapex brunneella et A. jansei ont été élevées sur Cymbopogon pospischilii (K. Schum.) C. E. Hubb et A. vetiveria sur Chrysopogon zizanioides (L.). Nous avons également réalisé des analyses de reconstruction phylogénétique (utilisant à la fois l’inférence Bayésienne et le maximum de vraisemblance) sur un jeu de données moléculaires multi-marqueurs (quatre gènes mitochondriaux et deux gènes nucléaires) comprenant 138 specimens (incluant 98 specimens du groupe A. albivena et 23 specimens du groupe A. stygiata) de 48 espèces de foreurs. Les résultats de ces analyses soutiennent à la fois l’hypothèse de monophylie des deux groupes d’intérêt et le statut d’espèces des taxa nouvellement décris, à l’exception d’A. lusinga qui n’a pas été séquencé. Les analyses phylogénétiques révèlent également l’existence de plusieurs lignées évolutives distinctes dont le statut reste à définir car leur ADN a été extrait de stades larvaires
Published: 2019
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4. Sublethal Endpoints in Non-target Organism Testing for Insect-Active GE Crops

Author: Jörg Romeis, John L. Teem, Marina Mühl, Richard L. Hellmich, Judith K. Brown, Xuguo Zhou, Thais B. Rodrigues, Rachel L. Melnick, Ana María Vélez, Fernando Hercos Valicente, Martin G. Edwards, Andrew Roberts, Steven L Levine, Chad J. Boeckman, Andrew Roberts, Agriculture and Food Systems Institute, Washington, DC, Martin G. Edwards, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, Ana M. Vélez, Department of Entomology, University of Nebraska-Lincoln, Richard L. Hellmich, USDA, Corn Insects and Crop Genetics Research Unit, Ames., Xuguo Zhou, Department of Entomology, University of Kentucky, Lexington, KY, Thais B. Rodrigues, Greenlight Biosciences, Inc., Medford, MA, Rachel L. Melnick, Agriculture and Food Systems Institute, Washington, DC, Steven L. Levine, Bayer Crop Science, Chesterfield, MO, Chad J. Boeckman, Corteva Agriscience, Marina Mühl, Ministerio de Agricultura, Ganadería y Pesca, Dirección de Biotecnología, Buenos Aires, Jörg Romeis, Research Division Agroecology and Environment, Agroscope, Zurich, John L. Teem, Agriculture and Food Systems Institute, Washington, DC, FERNANDO HERCOS VALICENTE, CNPMS, and Judith K. Brown, School of Plant Sciences, The University of Arizona, Tucson
Subjects: 0301 basic medicine, Histology, media_common.quotation_subject, lcsh:Biotechnology, Biomedical Engineering, environmental risk assessment, Bioengineering, Review, 02 engineering and technology, Insect, sublethal endpoints, Melhoramento Genético Vegetal, Biology, Bt Cry, Parâmetros subletais, 03 medical and health sciences, Bacillus thuringiensis, lcsh:TP248.13-248.65, Mode of action, non-target organisms, Organism, Environmental risk assessment, media_common, Non target organism, 2. Zero hunger, business.industry, Genetically engineered, GE plants, fungi, Bioengineering and Biotechnology, Controle Biológico, 021001 nanoscience & nanotechnology, biology.organism_classification, Organismos não-alvo, Biotechnology, 030104 developmental biology, RNAi, Inseto, Planta Transgênica, 0210 nano-technology, business, Planta geneticamente modificada
Abstract: Historically, genetically engineered (GE) plants that have incorporated genes conferring insect protection have primarily used Cry proteins derived from Bacillus thuringiensis (Bt) to achieve their insecticidal phenotype. As a result, regulators have developed a level of familiarity and confidence in reviewing plants incorporating these insecticidal proteins. However, new technologies have been developed that produce GE plants that incorporate pest protection by triggering an RNA interference (RNAi) response or proteins other than Bt Cry proteins. These technologies have new modes of action. Although the overall assessment paradigm for GE plants is robust, there are ongoing discussions about the appropriate tests and measurement endpoints needed to inform non-target arthropod assessment for technologies that have a different mode of action than the Bt Cry proteins. As a result, increasing attention is being paid to the use of sublethal endpoints and their value for environmental risk assessment (ERA). This review focuses on the current status and history of sublethal endpoint use in insect-active GE crops, and evaluates the future use of sublethal endpoints for new and emerging technologies. It builds upon presentations made at the Workshop on Sublethal Endpoints for Non-target Organism Testing for Non-Bt GE Crops (Washington DC, USA, 4â??5 March 2019), and the discussions of government, academic and industry scientists convened for the purpose of reviewing the progress and status of sublethal endpoint testing in non-target organisms. Made available in DSpace on 2020-07-01T11:10:59Z (GMT). No. of bitstreams: 1 Sublethal-endpoints.pdf: 658109 bytes, checksum: b99f655b21f3494483d1a135eca41cfa (MD5) Previous issue date: 2020
Published: 2020
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5. Species richness effects on grassland recovery from drought depend on community productivity in a multisite experiment

Author: Giandiego Campetella, Iva Apostolova, Michaela Zeiter, Sándor Bartha, Carl Beierkuhnlein, Pauline Hernandez, Ivan Nijs, Jürgen Dengler, Catherine Picon-Cochard, Julia Walter, Desislava Sopotlieva, Emin Uğurlu, Sigi Berwaers, Andreas Stampfli, Michael Bahn, Philipp von Gillhaussen, Camilla Wellstein, Hans J. De Boeck, Behlül Güler, Juergen Kreyling, Yasin Altan, Marcelo Sternberg, Anke Jentsch, Mohammed Abu Sayed Arfin Khan, Juliette M. G. Bloor, Johannes Ransijn, Nikolay Velev, Uğurlu, Emin, Experimental Plant Ecology, Ernst-Moritz-Arndt University Greifswald, Greifswald, D-17487, Germany, Plant Ecology, BayCEER, University of Bayreuth, Bayreuth, 95440, Germany, German Centre for Integrative Biodiversity Research (iDiv), Leipzig, 04103, Germany, Landscape Ecology, University of Hohenheim, Stuttgart, 70599, Germany, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria, Forest Engineering, Faculty of Forestry, Bursa Technical University, 152 Evler Str., No:2/10, Yildirim, Bursa, 16330, Turkey, Disturbance Ecology, BayCEER, University of Bayreuth, Bayreuth, 95440, Germany, Grassland Ecosystem Research, UMR0874 INRA, VetAgroSup, Clermont-Ferrand, 63000, France, Plants and Ecosystems, Department of Biology, University of Antwerp, Wilrijk, 2610, Belgium, Department of Biology, Faculty of Science & Letters, Manisa Celal Bayar University, Şehit İlhan Varank Campus, Yunusemre, Manisa, 45040, Turkey, Biogeography, BayCEER, University of Bayreuth, Bayreuth, 95440, Germany, Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh, School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, CH-3052, Switzerland, Institute of Plant Sciences, University of Bern, Bern, CH-3013, Switzerland, Faculty of Science and Technology, Free University of Bozen, Bozen, I-39100, Italy, School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel, School of Biosciences and Veterinary Medicine, Plant Diversity and Ecosystems Management unit, University of Camerino, Camerino, Italy, Institute of Ecology and Botany, MTA Centre for Ecological Research, Vácrátót, H-2163, Hungary, School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia, Institute of Ecology, University of Innsbruck, Innsbruck, A-6020, Austria, Universität Greifswald - University of Greifswald, University of Bayreuth, University of Hohenheim, Bulgarian Academy of Sciences (BAS), Bursa Technical University, Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), University of Antwerp (UA), Department of Biology, Bern University of Applied Sciences (BFH), Free University of Bozen-Bolzano, Tel Aviv University (TAU), Università degli Studi di Camerino = University of Camerino (UNICAM), MTA Centre for Ecological Research, Leopold Franzens Universität Innsbruck - University of Innsbruck, European Project: 266546,EC:FP7:ENV,FP7-ERANET-2010-RTD,BIODIVERSA2(2010), Tel Aviv University [Tel Aviv], University of Camerino, and University of Innsbruck
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Asynchrony, Climate Change, Biodiversity, Insurance hypothesis, Biology, 010603 evolutionary biology, 01 natural sciences, Diversity-stability relationship, résilience, insurance hypothesis, Species Specificity, Temperate climate, Ecosystem, Biomass, 577: Ökologie, coordinated distributed experiment, resilience, Plant Physiological Phenomena, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, 2. Zero hunger, Biomass (ecology), Resilience, Resistance (ecology), Coordinated distributed experiment, Ecology, fungi, diversity-stability relationship, food and beverages, Extreme event ecology, extreme event ecology, 15. Life on land, Grassland, Droughts, Chemistry, Productivity (ecology), Disturbance (ecology), 13. Climate action, événement écologique extrème, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Sopotlieva, Desislava/0000-0002-9281-7039; Guler, Behlul/0000-0003-2638-4340; Velev, Nikolay/0000-0001-6812-3670; De Boeck, Hans/0000-0003-2180-8837; Kreyling, Juergen/0000-0001-8489-7289; Bahn, Michael/0000-0001-7482-9776; Dengler, Jurgen/0000-0003-3221-660X; Nijs, Ivan/0000-0003-3111-680X; Wellstein, Camilla/0000-0001-6994-274X; Apostolova, Iva/0000-0002-2701-175X; Stampfli, Andreas/0000-0002-5517-1363; Picon-Cochard, Catherine/0000-0001-7728-8936; Bloor, Juliette M.G./0000-0002-8668-1323; Arfin Khan, Mohammed Abu Sayed/0000-0001-6275-7023; Campetella, Giandiego/0000-0001-6126-522X WOS:000413145900006 PubMed ID: 28941071 Biodiversity can buffer ecosystem functioning against extreme climatic events, but few experiments have explicitly tested this. Here, we present the first multisite biodiversityxdrought manipulation experiment to examine drought resistance and recovery at five temperate and Mediterranean grassland sites. Aboveground biomass production declined by 30% due to experimental drought (standardised local extremity by rainfall exclusion for 72-98 consecutive days). Species richness did not affect resistance but promoted recovery. Recovery was only positively affected by species richness in low-productive communities, with most diverse communities even showing overcompensation. This positive diversity effect could be linked to asynchrony of species responses. Our results suggest that a more context-dependent view considering the nature of the climatic disturbance as well as the productivity of the studied system will help identify under which circumstances biodiversity promotes drought resistance or recovery. Stability of biomass production can generally be expected to decrease with biodiversity loss and climate change. ERA-Net BiodivERsA [01LC1201]; Belgian Federal Science Policy Office (BELSPO)Belgian Federal Science Policy Office; German Federal Ministry of Education and Research (BMBF)Federal Ministry of Education & Research (BMBF); Bulgarian Science Found; Ministere de l'Ecologie, du Developpement durable et de l'Energie (France) This work is part of the project SIGNAL which is funded by the ERA-Net BiodivERsA (http://www.biodiversa.org; Funding ID 01LC1201), with the national funders Belgian Federal Science Policy Office (BELSPO), German Federal Ministry of Education and Research (BMBF), Bulgarian Science Found and Ministere de l'Ecologie, du Developpement durable et de l'Energie (France) as part of the 2011-2012 BiodivERsA call for research proposals. For site FR, we thank P. Pichon, A. Salcedo, J. Pottier, M.E. Lefranc, M. Michaux, A. Vernay and G. Zannin for help during the course of the experiment. We thank three anonymous referees for insightful and constructive comments on an earlier version of this manuscript.
Published: 2017
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6. Multitarget Immunohistochemistry for Confocal and Super-resolution Imaging of Plant Cell Wall Polysaccharides

Author: Methieu Rivière, Raymond Wightman, Kalina T. Haas, Alexis Peaucelle, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Faculty of Life Sciences, School of Plant Sciences and Food Security, Tel Aviv University [Tel Aviv]-Tel Aviv University [Tel Aviv], Microscopy Core Facility, Sainsbury Laboratory, University of Cambridge [UK] (CAM)-University of Cambridge [UK] (CAM), and French National Research Agency (ANR)ANR-17-CE13-0007EU through the award of an AgreenSkills+ fellowship 201310Saclay Plant Sciences-SPS ANR17-EUR-0007Gatsby Charitable Foundation IJPBs Plant Observatory technological platforms
Subjects: 0106 biological sciences, Chemical imaging, Microscope, Strategy and Management, Confocal, 3D dSTORM nanoscopy, 01 natural sciences, Industrial and Manufacturing Engineering, law.invention, 03 medical and health sciences, Immunolabeling, law, Microscopy, Morphogenesis, Methods Article, Plant cell wall, Super-resolution microscopy, 030304 developmental biology, 0303 health sciences, Mechanical Engineering, Resolution (electron density), Metals and Alloys, STED microscopy, Immunohistochemistry, Biophysics, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Cell wall polysaccharides, 010606 plant biology & botany
Abstract: International audience; The plant cell wall (PCW) is a pecto-cellulosic extracellular matrix that envelopes the plant cell. By integrating extra-and intra-cellular cues, PCW mediates a plethora of essential physiological functions. Notably, it permits controlled and oriented tissue growth by tuning its local mechano-chemical properties. To refine our knowledge of these essential properties of PCW, we need an appropriate tool for the accurate observation of the native (in muro) structure of the cell wall components. The label-free techniques, such as AFM, EM, FTIR, and Raman microscopy, are used; however, they either do not have the chemical or spatial resolution. Immunolabeling with electron microscopy allows observation of the cell wall nanostructure, however, it is mostly limited to single and, less frequently, multiple labeling. Immunohistochemistry (IHC) is a versatile tool to analyze the distribution and localization of multiple biomolecules in the tissue. The subcellular resolution of chemical changes in the cell wall component can be observed with standard diffraction-limited optical microscopy. Furthermore, novel chemical imaging tools such as multicolor 3D dSTORM (Three-dimensional, direct Stochastic Optical Reconstruction Microscopy) nanoscopy makes it possible to resolve the native structure of the cell wall polymers with nanometer precision and in three dimensions.Here we present a protocol for preparing multi-target immunostaining of the PCW components taking as example Arabidopsis thaliana, Star fruit (Averrhoa carambola), and Maize thin tissue sections. This protocol is compatible with the standard confocal microscope, dSTORM nanoscope, and can also be implemented for other optical nanoscopy such as STED (Stimulated Emission Depletion Microscopy). The protocol can be adapted for any other subcellular compartments, plasma membrane, cytoplasmic, and intracellular organelles.
Published: 2020
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7. Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination

Author: Corinne Blugeon, Damarys Loew, Moussa Benhamed, Christophe Bailly, Fredy Barneche, Clara Bourbousse, Nicole Chaumont, Martin Rougée, Sophie Lemoine, David Latrasse, Chris Bowler, Anne-Flore Deton-Cabanillas, Gérald Zabulon, Anne-Sophie Fiorucci, Ammara Mohammad, Bérangère Lombard, Elodie Layat, Lorenzo Concia, Soon Kap Kim, David Stroebel, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement (LBD), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement [Paris] (LBD), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Curie [Paris], Agence Nationale pour la Recherche (ANR) [ANR-11-JSV2-003-01], Investissements d'Avenir program, ANR [ANR-10-LABX-54 MEMOLIFE, ANR-10-IDEX-0001-02 PSL], Universite Paris-Sud Doctoral School in Plant Sciences, Region Ile-de-France, Fondation pour la Recherche Medicale, 'Investissements d'Avenir' program [ANR-10-INBS-09], Fiorucci, Anne-Sophie, Bourbousse, Clara, Barneche, Fredy, Institut de biologie de l'ENS Paris (IBENS), 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), Laboratoire de Biologie du Développement [IBPS] (LBD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), GenomiqueENS (Genomique ENS), 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)-Département de Biologie - ENS Paris, Gestionnaire, HAL Sorbonne Université 5, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - 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), and 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)
Subjects: lcsh:QH426-470, [SDV]Life Sciences [q-bio], Protein subunit, Saccharomyces cerevisiae, Arabidopsis, Histones, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Histone H2B, Monoubiquitination, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, lcsh:QH301-705.5, Gene, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, Research, Ubiquitination, biology.organism_classification, Arabidopsis/metabolism, Histone Methyltransferases/metabolism, Histones/metabolism, Cell biology, [SDV] Life Sciences [q-bio], lcsh:Genetics, lcsh:Biology (General), Histone methyltransferase, Histone Methyltransferases, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], H3K4me3, 030217 neurology & neurosurgery
Abstract: Background The functional determinants of H3K4me3, their potential dependency on histone H2B monoubiquitination, and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in Saccharomyces cerevisiae, where a single SET1 protein catalyzes H3K4me3 as part of COMPlex of proteins ASsociated with Set1 (COMPASS), in Arabidopsis thaliana, this activity involves multiple histone methyltransferases. Among these, the plant-specific SET DOMAIN GROUP 2 (SDG2) has a prominent role. Results We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. We show that S2Lb co-purifies with the AtCOMPASS core subunit WDR5, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. However, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2, or H3K4me3, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Conclusions Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been co-opted by the plant-specific SDG2 histone methyltransferase and mediates H3K4me3 deposition through an H2B monoubiquitination-independent pathway in Arabidopsis. Electronic supplementary material The online version of this article (10.1186/s13059-019-1705-4) contains supplementary material, which is available to authorized users.
Published: 2019
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8. A Spatiotemporal DNA endoploidy map of the arabidopsis root Reveals roles for the endocycle in root development and stress adaptation

Author: Fan Xu, Ran Lu, Rahul Bhosale, Richard S. Smith, Robert P. Kumpf, Ilse Vercauteren, Anna Kremer, David W. Galbraith, John C. Larkin, Herman Höfte, Fabiola Cuevas, Tom Beeckman, Thomas Eekhout, Veronique Storme, Lieven De Veylder, Georgina M. Lambert, Riet De Rycke, Gert Van Isterdael, Moritz K. Nowack, Zhubing Hu, Veronique Boudolf, Steven Maere, Flanders Institute for Biotechnology, Department of plant Biotechnology and Bioinformatics, University of Gent, Bioinformatics institute Ghent, Universiteit Gent = Ghent University [Belgium] (UGENT), University of Nottingham, UK (UON), Henan Normal University, School of Plant Sciences, University of Arizona, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), Department of Biological Sciences, Louisiana State University (LSU), Newton International and OMICS@vibMarie Curie COFUND fellowship, National Science Foundation [IOS 1146620, DBI-052163], CSC fellowship, ANR project 'Pectosign', LabEx Saclay Plant Sciences-SPS [ANR-10-LABX-0040-SPS], Research Foundation Flanders [G.002911N], Interuniversity Attraction Poles Programme [IUAP P7/29], and Belgian Science Policy Office
Subjects: 0301 basic medicine, dependent kinase inhibitors, DNA, Plant, o-acetylation, Somatic cell, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, Plant Roots, endoreduplication, Polyploidy, Transcriptome, 03 medical and health sciences, Spatio-Temporal Analysis, Gene Expression Regulation, Plant, Stress, Physiological, Transcription (biology), Plant Cells, Gene expression, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Endoreduplication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, thaliana, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Gene, Research Articles, transcription factor, Cell Size, biology, Cell growth, Gene Expression Profiling, Reproducibility of Results, Cell Biology, hair initiation, 15. Life on land, duf231 domain, Plants, Genetically Modified, biology.organism_classification, Adaptation, Physiological, gene-expression, Cell biology, 030104 developmental biology, fruit-growth, cell-size
Abstract: International audience; Somatic polyploidy caused by endoreplication is observed in arthropods, molluscs, and vertebrates but is especially prominent in higher plants, where it has been postulated to be essential for cell growth and fate maintenance. However, a comprehensive understanding of the physiological significance of plant endopolyploidy has remained elusive. Here, we modeled and experimentally verified a high-resolution DNA endoploidy map of the developing Arabidopsis thaliana root, revealing a remarkable spatiotemporal control of DNA endoploidy levels across tissues. Fitting of a simplified model to publicly available data sets profiling root gene expression under various environmental stress conditions suggested that this root endoploidy patterning may be stress-responsive. Furthermore, cellular and transcriptomic analyses revealed that inhibition of endoreplication onset alters the nuclear-to-cellular volume ratio and the expression of cell wall-modifying genes, in correlation with the appearance of cell structural changes. Our data indicate that endopolyploidy might serve to coordinate cell expansion with structural stability and that spatiotemporal endoreplication pattern changes may buffer for stress conditions, which may explain the widespread occurrence of the endocycle in plant species growing in extreme or variable environments.
Published: 2018
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9. Re-establishment of Spodoptera teferii Laporte in Rougeot (Lepidoptera: Noctuidae, Noctuinae), with an updated molecular phylogeny for the genus Spodoptera Guenee

Author: Claire Capdevielle-Dulac, Gael J. Kergoat, Muluken Goftishu, Bruno Le Ru, Jérôme Barbut, Muséum national d'Histoire naturelle (MNHN), School of Plant Sciences, University of Arizona, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national 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), IRD, project IMPACT_PHYTO - Division for Plant Health and Environment (SPE) of INRA, and International Centre of Insect Physiology and Ecology (ICIPE)
Subjects: 0106 biological sciences, 0301 basic medicine, molecular species, Afrotropical region, Spodoptera, 010603 evolutionary biology, 01 natural sciences, Lepidoptera genitalia, molecular phylogenetics, 03 medical and health sciences, taxonomy, Botany, Ecology, Evolution, Behavior and Systematics, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, fungi, delimitation, molecular species delimitation, 15. Life on land, biology.organism_classification, Noctuinae, 030104 developmental biology, Insect Science, Molecular phylogenetics, Noctuidae, Taxonomy (biology)
Abstract: International audience; The genus Spodoptera Guenee (Lepidoptera: Noctuidae, Noctuinae) is a group of economic importance which encompasses several major pests of crops worldwide. Although this genus has been the focus of many studies, the status of several Spodoptera species is still unstable, especially in the light of recent molecular analyses. In 2015 five Spodoptera specimens collected in Ethiopia were first identified as S. apertura (Walker). However, preliminary studies suggested that these specimens belong to a distinct species, S. teferii Laporte in Rougeot, which has been previously synonymized with S. apertura. In this study, on the basis of morphological and molecular evidence, we re-establish the species status of S. teferii. We provide a supplemental description of S. teferii male and the first description of S. teferii female. We also conducted several molecular analyses. First, we reconstructed an updated phylogeny for the genus based on a multilocus dataset (four mitochondrial and three nuclear gene fragments) including S. teferii and 28 of the 31 currently recognized Spodoptera species; the results of phylogenetic analyses support the hypothesis that S. teferii is more closely related to the clade encompassing S. littoralis (Boisduval), S. litura (Fabricius), S. pectinicornis (Hampson) and S. picta (Guerin-Meneville) than to S. apertura. Second, we carried out molecular species delimitation analyses on a 683-specimen dataset that also clearly support the status of S. teferii as a species distinct to S. apertura.
Published: 2018
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10. The Hot Serial Cereal Experiment for modeling wheat response to temperature: Field experiments and AgMIP-Wheat multi-model simulations

Author: Roberto C. Izaurralde, Jakarat Anothai, Andrew J. Challinor, Reimund P. Rötter, Jørgen E. Olesen, Curtis D. Jones, Bing Liu, T. Palosuo, Peter J. Thorburn, Kurt Christian Kersebaum, Mohamed Jabloun, Iwan Supit, Frank Ewert, Mikhail A. Semenov, Margarita Garcia-Vila, Claudio O. Stöckle, Benjamin Dumont, Belay T. Kassie, Jordi Doltra, Christian Biernath, Dominique Ripoche, Giacomo De Sanctis, Enli Wang, Elias Fereres, Bruce A. Kimball, Thilo Streck, Gerard W. Wall, L. A. Hunt, Pierre Stratonovitch, Fulu Tao, Jeffrey W. White, Christoph Müller, Bruno Basso, Senthold Asseng, Katharina Waha, Ann-Kristin Koehler, Andrea Maiorano, Ehsan Eyshi Rezaei, Eckart Priesack, Soora Naresh Kumar, Claas Nendel, Gerrit Hoogenboom, Davide Cammarano, David B. Lobell, Joost Wolf, Pierre Martre, Pramod K. Aggarwal, Garry O'Leary, Zhigan Zhao, Michael J. Ottman, Sebastian Gayler, Yan Zhu, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Agricultural Research Service / US Arid Land Agricultural Research Center, United States Department of Agriculture, The School of Plant Sciences, University of Arizona, Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Consultative Group on International Agricultural Research (CGIAR), AgWeatherNet Program, Washington State University (WSU), Department of Geological Sciences and W. K. Kellogg Biological Station, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, German Research Center for Environmental Health - Helmholtz Center München (GmbH), University of Leeds, GMO Unit, European Food Safety Authority = Autorité européenne de sécurité des aliments, Catabrian Agricultural Research and Training Center (CIFA), Universidad de Córdoba [Cordoba], Instituto de Agricultura Sostenible - Institute for Sustainable Agriculture (IAS CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Soil Science and Land Evaluation, University of Hohenheim, Department of Plant Agriculture, University of Guelph, Department of Geographical Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, Texas A and M AgriLife Research, Texas A&M University System, Department of Agroecology, Aarhus University [Aarhus], Leibniz Association, Potsdam Institute for Climate Impact Research (PIK), Indian Agricultural Research Institute (IARI), National Engineering and Technology Center for Information Agriculture, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricutural University, Department of Environmental Earth System Science and Center on Food Security and the Environment, Stanford University, Landscape & Water Sciences, Department of Environment of Victoria, Natural Resources Institute Finland (LUKE), Agroclim (AGROCLIM), Institut National de la Recherche Agronomique (INRA), Computational and Systems Biology Department, Rothamsted Research, Biological Systems Engineering, PPS and WSG &CALM, Wageningen University and Research [Wageningen] (WUR), Institute of geographical sciences and natural resources research, Chinese Academy of Sciences [Changchun Branch] (CAS), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), College of Agronomy and Biotechnology, and Southwest University
Subjects: Simulations, 0106 biological sciences, Irrigation, 010504 meteorology & atmospheric sciences, Water en Voedsel, Wheat, Field experimental data, Heat stress, Crop model simulations, AgMIP, Hot Serial Cereal, 01 natural sciences, donnée expérimentale, Crop, blé, température, Life Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Relative humidity, Cultivar, 0105 earth and related environmental sciences, 2. Zero hunger, WIMEK, Water and Food, Vegetal Biology, Global warming, Sowing, essai en plein champ, food and beverages, série climatique, Modélisation et simulation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Agronomy, Plant Production Systems, 13. Climate action, Plantaardige Productiesystemen, Modeling and Simulation, Frost, Weather data, Environmental science, Water Systems and Global Change, stress hydrique, Biologie végétale, modèle de production, 010606 plant biology & botany
Abstract: The data set reported here includes the part of a Hot Serial Cereal Experiment (HSC) experiment recently used in the AgMIP-Wheat project to analyze the uncertainty of 30 wheat models and quantify their response to temperature. The HSC experiment was conducted in an open-field in a semiarid environment in the southwest USA. The data reported herewith include one hard red spring wheat cultivar (Yecora Rojo) sown approximately every six weeks from December to August for a two-year period for a total of 11 planting dates out of the 15 of the entire HSC experiment. The treatments were chosen to avoid any effect of frost on grain yields. On late fall, winter and early spring plantings temperature free-air controlled enhancement (T-FACE) apparatus utilizing infrared heaters with supplemental irrigation were used to increase air temperature by 1.3°C/2.7°C (day/night) with conditions equivalent to raising air temperature at constant relative humidity (i.e. as expected with global warming) during the whole crop growth cycle. Experimental data include local daily weather data, soil characteristics and initial conditions, detailed crop measurements taken at three growth stages during the growth cycle, and cultivar information. Simulations include both daily in-season and end-of-season results from 30 wheat models. Data access via doi 10.7910/DVN/M9ZT0F
Published: 2018
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11. The uncertainty of crop yield projections is reduced by improved temperature response functions

Author: Alex C. Ruane, Peter J. Thorburn, Mikhail A. Semenov, Joost Wolf, Claudio O. Stöckle, Pramod K. Aggarwal, Gerard W. Wall, Margarita Garcia-Vila, Matthew P. Reynolds, Eckart Priesack, Jørgen E. Olesen, Enli Wang, Bruce A. Kimball, Jordi Doltra, Iurii Shcherbak, Ehsan Eyshi Rezaei, Jeffrey W. White, Leilei Liu, L. A. Hunt, Senthold Asseng, Frank Ewert, Yan Zhu, Fulu Tao, Christoph Müller, Daniel Wallach, Christian Biernath, Davide Cammarano, Mohamed Jabloun, Zhigan Zhao, Michael J. Ottman, Pierre Martre, Sebastian Gayler, Garry O'Leary, Zhimin Wang, Jakarat Anothai, Elias Fereres, Claas Nendel, Bruno Basso, Thilo Streck, Curtis D. Jones, Andrea Maiorano, Phillip D. Alderman, Andrew J. Challinor, Reimund P. Rötter, Taru Palosuo, Iwan Supit, Katharina Waha, Giacomo De Sanctis, Kurt Christian Kersebaum, Soora Naresh Kumar, Gerrit Hoogenboom, Dominique Ripoche, Pierre Stratonovitch, Ann-Kristin Koehler, Roberto C. Izaurralde, Commonwealth Scientific and Industrial Research Organisation (Australia), Chinese Academy of Sciences, China Scholarship Council, Ministry of Education of the People's Republic of China, Institut National de la Recherche Agronomique (France), European Commission, International Food Policy Research Institute (US), CGIAR (France), Department of Agriculture (US), Federal Ministry of Education and Research (Germany), Deutsche Gesellschaft für Internationale Zusammenarbeit, Danish Council for Strategic Research, Federal Ministry of Food and Agriculture (Germany), Finnish Ministry of Agriculture and Forestry, National Natural Science Foundation of China, Helmholtz Association, Grains Research and Development Corporation (Australia), Texas AgriLife Research, Texas A&M University, National Institute of Food and Agriculture (US), CSIRO, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), College of Agronomy and Biotechnology, Southwest University, Institute of Crop Science and Resource Conservation, Division of Plant Nutrition-University of Bonn, Institute of Landscape Systems Analysis, Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Department of Crop Sciences, University of Goettingen, Centre of Biodiversity and Sustainable Land Use (CBL), United States Department of Agriculture - Agricultural Research Service, The School of Plant Sciences, University of Arizona, Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Washington State University (WSU), Department of Earth and Environmental Sciences and W.K. Kellogg Biological Station, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Institute of Biochemical Plant Pathology (BIOP), German Research Center for Environmental Health - Helmholtz Center München (GmbH), Agricultural and Biological Engineering Department, Purdue University [West Lafayette], Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, GMO Unit, European Food Safety Authority = Autorité européenne de sécurité des aliments, Cantabrian Agricultural Research and Training Centre, Dep. Agronomia, University of Córdoba [Córdoba], Spanish National Research Council (CSIC), Institute of Soil Science and Land Evaluation, University of Hohenheim, Department of Plant Agriculture, University of Guelph, Department of Geographical Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, Texas A&M AgriLife Research and Extension Center, Texas A&M University System, Department of Agroecology, Aarhus University [Aarhus], National Engineering and Technology Center for Information Agriculture, Nanjing Agricutural University, Potsdam Institute for Climate Impact Research (PIK), Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute (IARI), Department of Economic Development, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Natural Resources Institute Finland, Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, UE Agroclim (UE AGROCLIM), Institut National de la Recherche Agronomique (INRA), NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), Computational and Systems Biology Department, Rothamsted Research, Biological Systems Engineering, University of Wisconsin-Madison, PPS and WSG &CALM, Wageningen University and Research Center (WUR), Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences [Beijing] (CAS), Agriculture and Food, Universidad de La Rioja (UR), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, China Agricultural University, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), China Agricultural University (CAU), Institute of Crop Science and Resource Conservation [Bonn], Georg-August-University [Göttingen], Arid-Land Agricultural Research Center, Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), University of Leeds, European Food Safety Authority (EFSA), Catabrian Agricultural Research and Training Center (CIFA), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), AgWeatherNet Program, Texas A and M AgriLife Research, Jiangsu Collaborative Innovation Center for Modern Crop Production, Landscape and Water Sciences, Natural Resources Institute Finland (LUKE), Agroclim (AGROCLIM), Wageningen University and Research [Wageningen] (WUR), Chinese Academy of Agricultural Sciences (CAAS), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Écophysiologie des Plantes sous Stress environnementaux ( LEPSE ), Institut National de la Recherche Agronomique ( INRA ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Leibniz Centre for Agricultural Landscape Research, International Maize and Wheat Improvement Center ( CIMMYT ), CGIAR Research Program on Climate Change, Agriculture and Food Security ( CCAFS ), Washington State University ( WSU ), Michigan State University, Institute of Biochemical Plant Pathology ( BIOP ), Institute for Climate and Atmospheric Science, School of Earth and Environment, European Food Safety Authority, Spanish National Research Council ( CSIC ), Texas A and M University ( TAMU ), Potsdam Institute for Climate Impact Research ( PIK ), Centre for Environment Science and Climate Resilient Agriculture ( CESCRA ), Indian Agricultural Research Institute ( IARI ), Department of Economic Development, Jobs, Transport and Resources ( DEDJTR ), University of Bonn (Rheinische Friedrich-Wilhelms), UE Agroclim ( UE AGROCLIM ), Institut National de la Recherche Agronomique ( INRA ), NASA Goddard Institute for Space Studies ( GISS ), NASA Goddard Space Flight Center ( GSFC ), University of Wisconsin-Madison [Madison], Wageningen University and Research Center ( WUR ), Chinese Academy of Sciences [Beijing] ( CAS ), Universidad de La Rioja ( UR ), University of Bonn-Division of Plant Nutrition, 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), USDA-ARS : Agricultural Research Service, Consultative Group on International Agricultural Research [CGIAR]-Consultative Group on International Agricultural Research [CGIAR], Natural resources institute Finland, Georg-August-University = Georg-August-Universität Göttingen, Universidad de Córdoba = University of Córdoba [Córdoba], Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), and Université de Toulouse (UT)-Université de Toulouse (UT)
Subjects: Crops, Agricultural, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Yield (finance), Water en Voedsel, Growing season, Climate change, klim, Plant Science, Agricultural engineering, Models, Biological, 01 natural sciences, [SHS]Humanities and Social Sciences, Crop, Life Science, Computer Simulation, Productivity, 0105 earth and related environmental sciences, 2. Zero hunger, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, WIMEK, Water and Food, Food security, business.industry, Crop yield, Temperature, Agriculture, 04 agricultural and veterinary sciences, 15. Life on land, Climate Resilience, Agronomy, Klimaatbestendigheid, 13. Climate action, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Water Systems and Global Change, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract: Increasing the accuracy of crop productivity estimates is a key element in planning adaptation strategies to ensure global food security under climate change. Process-based crop models are effective means to project climate impact on crop yield, but have large uncertainty in yield simulations. Here, we show that variations in the mathematical functions currently used to simulate temperature responses of physiological processes in 29 wheat models account for >50% of uncertainty in simulated grain yields for mean growing season temperatures from 14 °C to 33 °C. We derived a set of new temperature response functions that when substituted in four wheat models reduced the error in grain yield simulations across seven global sites with different temperature regimes by 19% to 50% (42% average). We anticipate the improved temperature responses to be a key step to improve modelling of crops under rising temperature and climate change, leading to higher skill of crop yield projections., E.W. acknowledges support from the CSIRO project ‘Enhanced modelling of genotype by environment interactions’ and the project ‘Advancing crop yield while reducing the use of water and nitrogen’ jointly funded by CSIRO and the Chinese Academy of Sciences (CAS). Z.Z. received a scholarship from the China Scholarship Council through the CSIRO and the Chinese Ministry of Education PhD Research Program. P.M., A.M. and D.R. acknowledge support from the FACCE JPI MACSUR project (031A103B) through the metaprogram Adaptation of Agriculture and Forests to Climate Change (AAFCC) of the French National Institute for Agricultural Research (INRA). A.M. received the support of the EU in the framework of the Marie-Curie FP7 COFUND People Programme, through the award of an AgreenSkills fellowship under grant agreement No. PCOFUND-GA-2010-267196. S.A. and D.C. acknowledge support provided by the International Food Policy Research Institute (IFPRI), CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), the CGIAR Research Program on Wheat and the Wheat Initiative. C.S. was funded through USDA National Institute for Food and Agriculture award 32011-68002-30191. C.M. received financial support from the KULUNDA project (01LL0905 L) and the FACCE MACSUR project (031A103B) funded through the German Federal Ministry of Education and Research (BMBF). F.E. received support from the FACCE MACSUR project (031A103B) funded through the German Federal Ministry of Education and Research (2812ERA115) and E.E.R. was funded through the German Federal Ministry of Economic Cooperation and Development (Project: PARI). M.J. and J.E.O. were funded through the FACCE MACSUR project by the Danish Strategic Research Council. K.C.K. and C.N. were funded by the FACCE MACSUR project through the German Federal Ministry of Food and Agriculture (BMEL). F.T., T.P. and R.P.R. received financial support from the FACCE MACSUR project funded through the Finnish Ministry of Agriculture and Forestry (MMM); F.T. was also funded through the National Natural Science Foundation of China (No. 41071030). C.B. was funded through the Helmholtz project ‘REKLIM-Regional Climate Change: Causes and Effects’ Topic 9: ‘Climate Change and Air Quality’. M.P.R. and PD.A. received funding from the CGIAR Research Program on Climate Change, Agriculture, and Food Security (CCAFS). G.O'L. was funded through the Australian Grains Research and Development Corporation and the Department of Economic Development, Jobs, Transport and Resources Victoria, Australia. R.C.I. was funded by Texas AgriLife Research, Texas A&M University. B.B. was funded by USDA-NIFA Grant No: 2015-68007-23133.
Published: 2017
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12. Similar estimates of temperature impacts on global wheat yield by three independent methods

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

Author: Maiorano, Andrea, Martre, Pierre, Asseng, S., Ewert, F., Müller, C., Rötter, R. P., Ruane, A. C., Semenov, M. A., Wallach, Daniel, Wang, E., Alderman, P. D., Kassie, B. T., Biernath, C., Basso, B., Cammarano, D., Challinor, A. J., Doltra, J., Dumont, B., Gayler, S., Kersebaum, Kimball, B. A., Koehler, A. K., Liu, L., O'Leary, G., Olesen, J. E., Ottman, Michael J., Priesack, E., Reynolds, M. P., Eyshi Rezaei, E., Stratonovitch, P., Streck, T., Thorburn, P., Waha, K., Wall, G. W., White, J. W., Zhao, Z., Zhu, Y., Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Florida [Gainesville] (UF), INRES, Rheinische Friedrich-Wilhelms-Universität Bonn, Potsdam Institute for Climate Impact Research (PIK), Natural Resources Institute Finland (LUKE), NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), Computational and Systems Biology Department, Rothamsted Research, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Agriculture, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), German Research Center for Environmental Health - Helmholtz Center München (GmbH), Michigan State University [East Lansing], Michigan State University System, University of Leeds, International Center for Tropical Agriculture, Catabrian Agricultural Research and Training Center (CIFA), Department of Geological Sciences and W. K. Kellogg Biological Station, Michigan State University System-Michigan State University System, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), ARS/ALARC, United States Department of Agriculture, Nanjing Agricultural University, Landscape & Water Sciences, Department of Environment of Victoria, Department of Agroecology, Aarhus University [Aarhus], The School of Plant Sciences, University of Arizona, Institute of Soil Science and Land Evaluation, University of Hohenheim, and Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research, Leibniz Association (ZALF). DEU.
Subjects: Vegetal Biology, comparaison de modèles, Modélisation et simulation, modèle de simulation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, incertitude, blé, Modeling and Simulation, température, modèle phénologique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biologie végétale, modèle de production, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2016

14. Inter-comparison of wheat models to identify knowledge gaps and improve process modeling

Author: Wang, E., Martre, Pierre, Asseng, S., Ewert, F., Zhao, Z., Maiorano, Andrea, Rotter, R. P., Kimball, B. A., Ottman, Michael J., Wall, G. W., White, J. W., Aggarwal, P. K., Alderman, P. D., Anothai, J., Basso, B., Biernath, C., Cammarano, D., Challinor, A. J., De Sanctis, Giacomo, Doltra, J., Fereres, E., Garcia-Vila, M., Gayler, S., Hoogenboom, G., Hunt, L. A., Izaurralde, R. C., Jabloun, M., Jones, C. D., Kersebaum, K.C., Koehler, A. K., Müller, C., Liu, L., Kumar Naresh, S., Nendel, C., O'Leary, G., Olesen, J. E., Palosuo, T., Priesack, E., Reynolds, M. P., Eyshi Rezaei, E., Ripoche, Dominique, Ruane, A. C., Semenov, M. A., Shcherbak, I., Stöckle, C., Stratonovitch, P., Streck, T., Supit, I., Tao, F., Thorburn, P., Waha, K., Wallach, Daniel, Wolf, J., Zhu, Y., Agriculture, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Florida [Gainesville] (UF), INRES, Rheinische Friedrich-Wilhelms-Universität Bonn, Natural Resources Institute Finland (LUKE), ARS/ALARC, United States Department of Agriculture, The School of Plant Sciences, University of Arizona, CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), AgWeatherNet Program, Washington State University (WSU), Michigan State University [East Lansing], Michigan State University System, German Research Center for Environmental Health - Helmholtz Center München (GmbH), University of Leeds, International Center for Tropical Agriculture, Agroclim (AGROCLIM), Institut National de la Recherche Agronomique (INRA), Catabrian Agricultural Research and Training Center (CIFA), Universidad de Córdoba [Cordoba], IAS, Princeton University, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Department of Plant Agriculture, University of Guelph, Department of Geographical Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, Texas A and M AgriLife Research, Texas A&M University System, Department of Agroecology, Aarhus University [Aarhus], Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Potsdam Institute for Climate Impact Research (PIK), Nanjing Agricultural University, Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute (IARI), Landscape & Water Sciences, Department of Environment of Victoria, NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), Computational and Systems Biology Department, Rothamsted Research, Institute of Soil Science and Land Evaluation, University of Hohenheim, Wageningen University and Research Centre (WUR), Institute of geographical sciences and natural resources research, Chinese Academy of Sciences [Changchun Branch] (CAS), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research, Leibniz Association (ZALF). DEU.
Subjects: blé, Modeling and Simulation, comparaison de modèles, température, modèle phénologique, Modélisation et simulation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, ComputingMilieux_MISCELLANEOUS, modèle de production, incertitude
Abstract: International audience
Published: 2016

15. Identification and genetic diversity of two invasive Pissodes spp. Germar (Coleoptera: Curculionidae) in their introduced range in the southern hemisphere

Author: Mesfin Wondafrash, Jiri Foit, Bernard Slippers, Géraldine Roux, Jeffrey R. Garnas, Brett Phillip Hurley, David W. Langor, University of Pretoria [South Africa], School of Plant Sciences, University of Arizona, Unité de recherche Zoologie Forestière (URZF), Institut National de la Recherche Agronomique (INRA), Université d'Orléans (UO), Mendel University in Brno (MENDELU), and Natural Resources Canada (NRCan)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Fusarium circinatum, mitochondrial DNA, Biology, 01 natural sciences, law.invention, 03 medical and health sciences, forest, Pissodes, law, Quarantine, Southern Hemisphere, Ecology, Evolution, Behavior and Systematics, Deodar Weevil, Genetic diversity, Ecology, Banded Pine Weevil, morphometric analysis, Weevil, population structure, genetic diversity, Bark Weevils, biology.organism_classification, 010602 entomology, 030104 developmental biology, Northern Pine Weevil, Curculionidae, Genetic structure, invasive forest insects
Abstract: International audience; During the first half of the twentieth century, two accidental cases of introduction of Pissodes weevils were recorded from the southern hemisphere. The weevils in South Africa were identified as the deodar weevil (Pissodes nemorensis) and those in South America as the small banded pine weevil (Pissodes castaneus). Wide distribution of the two species in their invasive range, general difficulty in identifying some Pissodes spp., and the varying feeding and breeding behaviours of the species in South Africa has necessitated better evidence of species identity and genetic diversity of both species and population structure of the species in South Africa. Barcoding and the Jerry-to-Pat region of the COI gene were investigated. Morphometric data of the South African species was analysed. Our results confirmed the introduction of only one Pissodes species of North American origin to South Africa. However, this species is not P. nemorensis, but an unrecognized species of the P. strobi complex or a hybrid between P. strobi and P. nemorensis. Only P. castaneus, of European origin, was identified from South America. We identified ten mitochondrial DNA haplotypes from South Africa with evidence of moderate genetic structure among geographic populations. Terminal leader and bole-feeding weevils did not differ at the COI locus. A single haplotype was identified from populations of P. castaneus in South America. Results of the present study will have implications on quarantine, research and management of these insect species.
Published: 2016
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16. Data access for the 1,000 Plants (1KP) project

Author: Carl J. Rothfels, Eric K. Wafula, Tandy Warnow, Matthew A. Gitzendanner, Jonathan Shaw, Jim Leebens-Mack, Regina S. Baucom, Juan Carlos Villarreal, J. G. Burleigh, Xiao Sun, Xiaolei Wu, Tao Chen, Toni M. Kutchan, Ram Samudrala, Pamela S. Soltis, Gane Ka-Shu Wong, Michael K. Deyholos, Naim Matasci, Sean W. Graham, Jun Wang, Lisa DeGironimo, Nicholas W. Miles, Joshua P. Der, Sarah Mathews, Megan Rolf, Brad R. Ruhfel, Eric J. Carpenter, Béatrice Roure, Barbara Surek, Dennis W. Stevenson, Claude W. dePamphilis, Ling-Hong Hung, Lisa Pokorny, Saravanaraj Ayyampalayam, Zhijian Tian, Nam Nguyen, Yong Zhang, Michael Melkonian, Zhixiang Yan, Hervé Philippe, Douglas E. Soltis, Siavash Mirarab, Michael S. Barker, Norman J. Wickett, School of Plant Sciences, iPlant Collaborative, University of Arizona, University of Washington [Seattle], Beijing Genomics Institute [Shenzhen] (BGI), University of Alberta, Chicago Botanic Garden, Northwestern University [Evanston], University of Texas at Austin [Austin], University of Georgia [USA], University of Florida [Gainesville] (UF), Pennsylvania State University (Penn State), Penn State System, Université de Montréal (UdeM), Station d’Ecologie Expérimentale du CNRS à Moulis (SEEM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Eastern Kentucky University, Florida Museum of Natural History [Gainesville], University of British Columbia (UBC), Harvard University [Cambridge], Universität zu Köln, Duke University [Durham], Real Jardín Botánico (RJB–CSIC), New York Botanical Garden (NYBG), University of Munich (LMU Munich), Chinese Academy of Sciences [Beijing] (CAS), Donald Danforth Plant Science Center, University of Michigan [Ann Arbor], and University of Michigan System
Subjects: 0106 biological sciences, Computer science, Interactions, Health Informatics, Review, Viridiplantae, computer.software_genre, 01 natural sciences, Transcriptomes, 03 medical and health sciences, Upload, Phylogenomics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Pathways, Clade, 030304 developmental biology, 0303 health sciences, biology, Biodiversity, 15. Life on land, biology.organism_classification, Data science, Computer Science Applications, Visualization, Data access, Scalable system, Plant species, Data mining, computer, 010606 plant biology & botany
Abstract: International audience; The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.
Published: 2014
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17. Early allopolyploid evolution in the post-Neolithic[i] Brassica napus[/i] oilseed genome

Author: Patrick Wincker, Pascal Bento, Sahana Manoli, Agnieszka A. Golicz, G. Deniot, Shengyi Liu, Christine Sidebottom, Chu Shin Koh, Ian Bancroft, Christian Daviaud, David C. Tack, Rod J. Snowdon, Jörg Tost, Guangyi Fan, Hui Guo, Smahane Chalabi, Boulos Chalhoub, Xinfa Wang, Harry Belcram, Aurélie Chauveau, Gilles Lassalle, Jean-Marc Aury, Tae-Ho Lee, Houda Chelaifa, Jinling Meng, Christopher D. Town, Haibao Tang, Zhongsong Liu, Julien Chiquet, Andrew G. Sharpe, Salman Alamery, Chunyun Guan, Mathieu Charles, Qiong Hu, Xiyin Wang, Xiaowu Wang, Jianxin Ma, Régine Delourme, Mei Guan, Eric Lyons, Chaobo Tong, Margot Correa, Adriana Alberti, Keith L. Adams, Patrick P. Edger, Marie-Christine Le Paslier, Yunhai Lu, Corinne Da Silva, Christophe Battail, Andrew H. Paterson, Isabelle Le Clainche, Benjamin Noel, Jérémy Just, Jacqueline Batley, Jinxiong Shen, Fengming Sun, Kamel Jabbari, Karine Labadie, Michel Renard, Maria Bernard, Birgit Samans, Aurélie Canaguier, Isobel A. P. Parkin, Yong Pyo Lim, Vinh Ha Dinh Thi, Victor Renault, Meixia Zhao, David Edwards, Graham J.W. King, Nicolas Schnel, Dominique Brunel, Cyril Falentin, Reece Tollenaere, Aurélie Bérard, Yongming Zhou, Dominique Arnaud, Imen Mestiri, Philippe E. Bayer, Chuchuan Fan, Wei Hua, J. Chris Pires, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture-Chinese Academy of Agricultural Sciences (CAAS), Agriculture and Agri-Food (AAFC), J. Craig Venter Institute [La Jolla, USA] (JCVI), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University (FAFU), University of Georgia [USA], School of Life Sciences, Center of Genomics and Computational Biology, Hebei United University, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Research Center for Biosystems, Land Use and Nutrition, Department of Plant Breeding, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, National Research Council of Canada (NRC), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Centre National de Genotypage, Plant Genome Mapping Laboratory, Laboratoire épigénétique et environnement, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Cologne Center for Genomics, University of Cologne, Department of Agronomy, Purdue University [West Lafayette], Department of Plant and Microbial Biology, University of California (UC), Department of Botany [Vancouver] (UBC Botany), University of British Columbia (UBC), National Key Laboratory of Crop Genetic Improvement [China], Huazhong Agricultural University [Wuhan] (HZAU), Beijing Genome Institute, Fondation Jean Dausset - Centre d’Étude du Polymorphisme Humain, College of Agronomy, Hunan Agricultural University [Changsha], Department of Horticulture, Molecular Genetics and Genomics Laboratory, Chungnam National University (CNU), School of Plant Sciences, iPlant Collaborative, University of Arizona, Department of Biology, University of York [York, UK], Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS), Division of Biological Sciences, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Southern Cross Plant Science, Southern Cross University (SCU), School of Plant Biology, The University of Western Australia (UWA), Laboratory for Epigenetics and Environment, Agriculture and Agri-Food [Ottawa] (AAFC), Laboratoire de Mathématiques et Modélisation d'Evry, Justus-Liebig-Universität Gießen (JLU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of California, Huazhong Agricultural University, Euralis Semences, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), BIOGEMMA, Unité de Recherches Zootechniques (URZ), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Limagrain, J. Craig Venter Institute, Fujian Agriculture and Forestry University, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Botany, University of Missouri [Columbia], Southern Cross University, Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), UMR 1165 Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique ( INRA ) -Université d'Evry Val d'Essonne, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ministry of Agriculture-Chinese Academy of Agricultural Sciences ( CAAS ), Agriculture and Agri-Food [Ottawa] ( AAFC ), University of Georgia, Laboratoire de Mathématiques et Modélisation d'Evry ( LaMME ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -ENSIIE-Centre National de la Recherche Scientifique ( CNRS ), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Justus Liebig University Giessen, Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, National Research Council of Canada ( NRC ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), University of British Columbia ( UBC ), National Key Laboratory of Crop Genetic Improvement, Chungnam National University, Institute of Vegetables and Flowers ( IVF ), Chinese Academy of Agricultural Sciences ( CAAS ), University of Missouri ( Saisissez le sigle en majuscules sans points ), The University of Western Australia ( UWA ), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, plant genome, [SDV]Life Sciences [q-bio], Brassica, rapeseed, Biology, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, 03 medical and health sciences, chemistry.chemical_compound, Gene duplication, genetics, Epigenetics, Domestication, Gene, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, [ SDV ] Life Sciences [q-bio], molecular evolution, Brassica napus, chromosome duplication, food and beverages, plant seed, biology.organism_classification, chemistry, Glucosinolate, Seeds, cytology, Genome, Plant, 010606 plant biology & botany
Abstract: Oilseed rape (Brassica napus L.) was formed ∼7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content.We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement., Erratum published in Vol 345, no. 6202 September 2014 DOI: 10.1126/science.1260782
Published: 2014
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18. Draft Genome Sequences of a Phylogenetically Diverse Suite of Pseudomonas syringae Strains from Multiple Source Populations

Author: Caroline Guilbaud, David Sands, Scott Yourstone, David A. Baltrus, Corbin D. Jones, Jeffrey L. Dangl, Cindy E. Morris, Abigail L. Lind, Baltrus, David A, School of Plant Sciences, University of Arizona, Department of Biology, Northern Arizona University [Flagstaff], Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Department Plant Sciences and Plant Pathology [Bozeman], Montana State University (MSU), Carolina Center for Genome Sciences, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), Howard Hughes Medical Institute, University of California, Unité de Pathologie Végétale (PV), and Howard Hughes Medical Institute (HHMI)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, bactérie phytopathogène, Genetics, Biodiversité et Ecologie, pseudomonas syringae, séquençage du génome complet, Outbreak, Biology, phytopathogenic bacteria, Crop species, Multiple source, Genome, Agricultural sciences, Biodiversity and Ecology, bactérie saprophyte, Botany, Pseudomonas syringae, Prokaryotes, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Molecular Biology, Sciences agricoles, relation habitat population
Abstract: Here, we report the draft genome sequences for 7 phylogenetically diverse isolates of Pseudomonas syringae , obtained from numerous environmental sources and geographically proximate crop species. Overall, these sequences provide a wealth of information about the differences (or lack thereof) between isolates from disease outbreaks and those from other sources.
Published: 2014
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19. The Amborella Genome and the Evolution of Flowering Plants

Author: Albert, Va, Barbazuk, Wb, Depamphilis, Cw, Der, Jp, Leebens Mack, J, Ma, H, Palmer, Jd, Rounsley, S, Sankoff, D, Schuster, Sc, Soltis, De, Soltis, Ps, Wessler, Sr, Wing, Ra, Ammiraju, Js, Chamala, S, Chanderbali, As, Determann, R, Ralph, P, Talag, J, Tomsho, L, Walts, B, Wanke, S, Chang, Th, Lan, T, Arikit, S, Axtell, Mj, Ayyampalayam, S, Burnette JM 3rd, DE PAOLI, Emanuele, Estill, Jc, Farrell, Np, Harkess, A, Jiao, Y, Liu, K, Mei, W, Meyers, Bc, Shahid, S, Wafula, E, Zhai, J, Zhang, X, Carretero Paulet, L, Lyons, E, Tang, H, Zheng, C, Altman, Ns, Chen, F, Chen, Jq, Chiang, V, De Paoli, E, Fogliani, B, Guo, C, Harholt, J, Job, C, Job, D, Kim, S, Kong, H, Li, G, Li, L, Liu, J, Park, J, Qi, X, Rajjou, L, Burtet Sarramegna, V, Sederoff, R, Sun, Yh, Ulvskov, P, Villegente, M, Xue, Jy, Yeh, Tf, Yu, X, Acosta, Jj, Bruenn, Ra, de Kochko, A, Herrera Estrella LR, Ibarra Laclette, E, Kirst, M, Pissis, Sp, Poncet, V, Tomsho, L., Department of Biological Sciences, University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY)-State University of New York (SUNY), Department of Biology, University of Florida [Gainesville], University of Florida Genetics Institute, Huck Institutes of the Life Sciences [University Park], Intercollege Plant Biology Graduate Program, Pennsylvania State University (Penn State), Penn State System-Penn State System, Center for Comparative Genomics and Bioinformatics, Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA, Université Paris Diderot - Paris 7 (UPD7), Department of Plant Biology [Athens], University of Georgia [USA], Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA, Penn State Univ, Dept Biol, University Pk, PA 16802 USA, Fudan Univ, Sch Life Sci, State Key Lab Genet Engn, Shanghai 200433, Peoples R China, Fudan Univ, Inst Genet, Inst Plant Biol, Ctr Evolutionary Biol,Inst Biomed Sci, Shanghai 200433, Peoples R China, Indiana Univ, Dept Biol, Bloomington, IN 47405 USA, Univ Arizona, Inst Collaborat Res BIO5, Tucson, AZ 85721 USA, Dow AgroSci, Indianapolis, IN 46268 USA, Univ Arizona, Sch Biol Sci, Tucson, AZ 85721 USA, Department of Mathematics and Statistics, University of Ottawa [Ottawa] (uOttawa), Singapore Ctr Environm Life Sci Engn, Singapore, Singapore, Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA, Florida Museum of Natural History, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UCR), University of California-University of California, Univ Arizona, Arizona Genom Inst, Tucson, AZ 85721 USA, Atlanta Bot Garden, Atlanta, GA 30309 USA, Univ Florida, Dept Biol, Gainesville, FL 32611 USA, Tech Univ Dresden, Inst Bot, D-01062 Dresden, Germany, SUNY Buffalo, Dept Biol Sci, Buffalo, NY 14260 USA, Chongqing Univ Sci & Technol, Dept Biol, Chongqing 4000042, Peoples R China, Univ Delaware, Delaware Biotechnol Inst, Newark, DE 19711 USA, Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA, Univ Udine, Dipartimento Sci Agr & Ambientali, I-33100 Udine, Italy, Penn State Univ, Intercoll Plant Biol Grad Program, University Pk, PA 16802 USA, Univ Arizona, iPlant Collaborat, Tucson, AZ 85721 USA, J Craig Venter Inst, Rockville, MD 20850 USA, Univ Ottawa, Dept Math & Stat, Ottawa, ON K1N 6N5, Canada, Penn State Univ, Dept Stat, University Pk, PA 16802 USA, Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA, Nanjing Univ, Sch Life Sci, Nanjing 210093, Jiangsu, Peoples R China, N Carolina State Univ, Dept Forestry & Environm Resources, Raleigh, NC 27695 USA, Institut Agronomique Néo-Calédonien (IAC), Univ New Caledonia, Lab Insulaire Vivant & Environm, Noumea 98851, New Caledonia, Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China, Univ Copenhagen, Dept Plant & Environm Sci, DK-1871 Frederiksberg C, Denmark, Univ Claude Bernard Lyon, Inst Natl Sci Appl Bayer CropSci Joint Lab UMR524, CNRS, Bayer CropSci, F-69263 Lyon 9, France, Sungshin Womens Univ, Basic Sci Res Inst, Seoul 142732, South Korea, Sungshin Womens Univ, Sch Biol Sci & Chem, Seoul 142732, South Korea, Zhejiang Univ, Coll Life Sci, Lab Systemat & Evolutionary Bot & Biodivers, Hangzhou 310058, Zhejiang, Peoples R China, Zhejiang Univ, Coll Life Sci, Key Lab Conservat Biol Endangered Wildlife, Minist Educ, Hangzhou 310058, Zhejiang, Peoples R China, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Natl Chung Hsing Univ, Dept Forestry, Taichung 40227, Taiwan, Natl Taiwan Univ, Sch Forestry & Resource Conservat, Taipei 10617, Taiwan, Univ Florida, Sch Forest Resources & Conservat, Gainesville, FL 32611 USA, Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Lab Nacl Genom Biodiversidad, Irapuato 36821, Mexico, Univ Florida, Genet Inst, Gainesville, FL 32610 USA, Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA, Heidelberg Inst Theoret Studies, Sci Comp Grp, D-69118 Heidelberg, Germany, NSF Plant Genome Research Program [0922742], NSF, University of Florida [Gainesville] (UF), University of Florida Genetics Institute (UFGI), Center for Comparative Genomics and Bioinformatics (CCBB), Department of Biology [PennState], State Key Laboratory of Genetic Engineering, Fudan University [Shanghai], Institute of Plant Biology [Shanghai], Department of Biology [Bloomington], Indiana University [Bloomington], Indiana University System-Indiana University System, BIO5 - Institute for Collaborative Bioresearch, University of Arizona, Dow AgroSciences LLC, School of Plant Sciences [Tucson], Department of Mathematics and Statistics [Ottawa], University of Ottawa [Ottawa], Singapore Centre for Environmental Life Sciences Engineering [Singapore] (SCELSE), Nanyang Technological University [Singapour], Department of Biochemistry and Molecular Biology [PennState], Arizona Genomics Institute [Tucson], Atlanta Botanical Garden, Department of Biology [Gainesville] (UF|Biology), Institut für Botanik [Dresden], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Department of Biological Sciences [Buffalo], Department of Biology [Chongqing], Chongqing University of Science & Technology, Plant Genome Mapping Laboratory (PGML), Dipartimento di Scienze Agrarie e Ambientali (DiSA), Università degli Studi di Udine - University of Udine [Italie], iPlant Collaborative, J. Craig Venter Institute, Department of Statistics [PennState], Department of Plant Sciences [Knoxville], The University of Tennessee [Knoxville], School of Life Sciences [Nanjing] (SLiS), Nanjing University (NJU), Department of Forestry and Environmental Resources [Raleigh] (FER), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Université de la Nouvelle-Calédonie (UNC), State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany [Beijing] (IB-CAS), Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS), Department of Plant and Environmental Sciences [Frederiksberg], University of Copenhagen = Københavns Universitet (KU), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Génomique fonctionnelle des champignons pathogènes des plantes (FungiPath), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Basic Science Research Institute [Seoul], Sungshin Women's University, School of Biological Sciences and Chemistry [Seoul], Laboratory of Systematic & Evolutionary Botany and Biodiversity, Zhejiang University, Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Department of Forestry [Taichung], National Chung Hsing University (NCHU), School of Forestry and Resource Conservation [Taiwan], National Taïwan University (NTU), School of Forest Resources and Conservation [Gainesville] (UF|IFAS|FFGS), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Department of Plant and Microbial Biology [Berkeley], University of California [Berkeley], Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Florida Museum of Natural History [Gainesville], Heidelberg Institute for Theoretical Studies (HITS ), 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]), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0106 biological sciences, Most recent common ancestor, Genetics, Transposable element, 0303 health sciences, education.field_of_study, Multidisciplinary, Lineage (evolution), [SDV]Life Sciences [q-bio], Population, fungi, food and beverages, Biology, 01 natural sciences, Genome, 03 medical and health sciences, Gene duplication, Gene family, education, Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract: Shaping Plant Evolution Amborella trichopoda is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by Adams ). To validate and assemble the sequence, Chamala et al. (p. 1516 ) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The Amborella Genome Project (p. 10.1126/science.1241089 ) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and Rice et al. (p. 1468 ) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae.
Published: 2013
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20. GABA Accumulation Causes Cell Elongation Defects and a Decrease in Expression of Genes Encoding Secreted and Cell Wall-Related Proteins in Arabidopsis thaliana

Author: Emily P. Updegraff, Ravishankar Palanivelu, Carole Deleu, Alain Bouchereau, Agnès Yu, Daphne Preuss, Hugues Renault, Jean-Pierre Renou, Abdelhak El Amrani, Amélioration des Plantes et Biotechnologies Végétales (APBV), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), School of Plant Sciences, University of Arizona, University of Arizona, Department of Molecular Genetics and Cell Biology, Chicago, University of Chicago, Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Ministère de l'Enseignement Supérieur et de la Recherche, Howard Hughes Medical Institute, the United States Department of Energy, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), College of Agriculture & Life Sciences [University of Arizona], Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Interactions cellulaires et moléculaires (ICM), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-IFR140-Université de Rennes 1 (UR1), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: 0106 biological sciences, Arabidopsis thaliana, Physiology, [SDV]Life Sciences [q-bio], Cell, Mutant, Arabidopsis, Plant Science, Pollen Tube, Microarray, 01 natural sciences, Plant Roots, GABA, Gene Expression Regulation, Plant, Gene expression, Spectroscopy, Fourier Transform Infrared, gamma-Aminobutyric Acid, Oligonucleotide Array Sequence Analysis, Regulation of gene expression, Genetics, 0303 health sciences, biology, Cell wall, General Medicine, Darkness, Hypocotyl, Cell biology, medicine.anatomical_structure, Phenotype, Plant Shoots, medicine.drug, Secretory pathway, Genes, Plant, Cell elongation, gamma-Aminobutyric acid, 03 medical and health sciences, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Microarray analysis techniques, Arabidopsis Proteins, Gene Expression Profiling, Regular Papers, Cell Biology, biology.organism_classification, Plant Leaves, nervous system, Seedlings, Mutation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: International audience; GABA (γ-aminobutyric acid), a non-protein amino acid, is a signaling factor in many organisms. In plants, GABA is known to accumulate under a variety of stresses. However, the consequence of GABA accumulation, especially in vegetative tissues, remains poorly understood. Moreover, gene expression changes as a consequence of GABA accumulation in plants are largely unknown. The pop2 mutant, which is defective in GABA catabolism and accumulates GABA, is a good model to examine the effects of GABA accumulation on plant development. Here, we show that the pop2 mutants have pollen tube elongation defects in the transmitting tract of pistils. Additionally, we observed growth inhibition of primary root and dark-grown hypocotyl, at least in part due to cell elongation defects, upon exposure to exogenous GABA. Microarray analysis of pop2-1 seedlings grown in GABA-supplemented medium revealed that 60% of genes whose expression decreased encode secreted proteins. Besides, functional classification of genes with decreased expression in the pop2-1 mutant showed that cell wall-related genes were significantly enriched in the microarray data set, consistent with the cell elongation defects observed in pop2 mutants. Our study identifies cell elongation defects caused by GABA accumulation in both reproductive and vegetative tissues. Additionally, our results show that genes that encode secreted and cell wall-related proteins may mediate some of the effects of GABA accumulation. The potential function of GABA as a growth control factor under stressful conditions is discussed.
Published: 2011
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21. Canopy temperature for simulation of heat stress in irrigated wheat in a semi-arid environment: A multi-model comparison

Author: Michael J. Ottman, Jørgen E. Olesen, Ehsan Eyshi Rezaei, Mikhail A. Semenov, Giacomo De Sanctis, Bruce A. Kimball, Frank Ewert, Pierre Martre, Gerard W. Wall, Jordi Doltra, Jeffrey W. White, Heidi Webber, Belay T. Kassie, Senthold Asseng, Andrea Maiorano, Dominique Ripoche, Pierre Stratonovitch, Robert F. Grant, Rheinische Friedrich-Wilhelms-Universität Bonn, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Arid-Land Agricultural Research Center, School of Plant Sciences, University of Arizona, JRC Institute for Energy and Transport (IET), European Commission - Joint Research Centre [Petten], Cantabrian Agricultural Research and Training Centre, University of Alberta, Department of Agroecology, Aarhus University [Aarhus], Agroclim (AGROCLIM), Institut National de la Recherche Agronomique (INRA), Computational and Systems Biology Department, Rothamsted Research, German Science Foundation EW 119/5-1 /FACCE JPI MACSUR 031A103B, European Project: 267196, Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), Agricultural & Biological Engineering Department, University of Florida [Gainesville], and UE Agroclim (UE AGROCLIM)
Subjects: Canopy, stress thermique, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Yield (engineering), ble tendre, 010504 meteorology & atmospheric sciences, comparaison de modèles, Energy balance, Soil Science, Grain filling, Canopy temperature, Atmospheric sciences, 01 natural sciences, heat stress, high temperature, Crop model comparison, crop model comparison, Atmospheric instability, climat semi aride, condition environnementale, 0105 earth and related environmental sciences, semi arid climate, 2. Zero hunger, 04 agricultural and veterinary sciences, Arid, canopy temperature, Heat stress, Agronomy, soft wheat, 13. Climate action, Semi-arid climate, Wheat, 040103 agronomy & agriculture, rendement agricole, 0401 agriculture, forestry, and fisheries, Environmental science, haute température, Agronomy and Crop Science, modèle multifactoriel
Abstract: Even brief periods of high temperatures occurring around flowering and during grain filling can severely reduce grain yield in cereals. Recently, ecophysiological and crop models have begun to represent such phenomena. Most models use air temperature (T-air) in their heat stress responses despite evidence that crop canopy temperature (T-c) better explains grain yield losses. T-c can deviate significantly from T-air based on climatic factors and the crop water status. The broad objective of this study was to evaluate whether simulation of T-c improves the ability of crop models to simulate heat stress impacts on wheat under irrigated conditions. Nine process-based models, each using one of three broad approaches (empirical, EMP; energy balance assuming neutral atmospheric stability, EBN; and energy balance correcting for the atmospheric stability conditions, EBSC) to simulate To simulated grain yield under a range of temperature conditions. The models varied widely in their ability to reproduce the measured T-c with the commonly used EBN models performing much worse than either EMP or EBSC. Use of T-c to account for heat stress effects did improve simulations compared to using only T-air to a relatively minor extent, but the models that additionally use T-c on various other processes as well did not have better yield simulations. Models that simulated yield well under heat stress had varying skill in simulating T-c For example, the EBN models had very poor simulations of T-c but performed very well in simulating grain yield. These results highlight the need to more systematically understand and model heat stress events in wheat.
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22. Rising temperatures reduce global wheat production

Author: Margarita Garcia-Vila, L. A. Hunt, Jørgen E. Olesen, P. V. V. Prasad, Pierre Martre, Katharina Waha, Curtis D. Jones, Pramod K. Aggarwal, Yan Zhu, Phillip D. Alderman, Christian Biernath, Fulu Tao, Bruno Basso, Davide Cammarano, Christoph Müller, Eckart Priesack, Taru Palosuo, Mohamed Jabloun, Thilo Streck, Zhigan Zhao, Jordi Doltra, Roberto C. Izaurralde, Alex C. Ruane, Andrew J. Challinor, Michael J. Ottman, Jeffrey W. White, Garry O'Leary, Reimund P. Rötter, David B. Lobell, Sebastian Gayler, Gerard W. Wall, G. De Sanctis, Matthew P. Reynolds, Senthold Asseng, Iurii Shcherbak, Peter J. Thorburn, Enli Wang, Bruce A. Kimball, Daniel Wallach, Mikhail A. Semenov, Claudio O. Stöckle, Claas Nendel, Jakarat Anothai, Ehsan Eyshi Rezaei, Pierre Stratonovitch, Ann-Kristin Koehler, Joost Wolf, Kurt Christian Kersebaum, Gerrit Hoogenboom, Frank Ewert, Iwan Supit, S. Naresh Kumar, Elias Fereres, NASA's Goddard Space Flight Center, Columbia University, University of Florida, Department of Agriculture (US), Oregon State University, International Maize and Wheat Improvement Center, University of Agriculture Faisalabad, Shahid Beheshti University, ARVALIS, International Food Policy Research Institute (US), Federal Ministry of Education and Research (Germany), German Research Foundation, Danish Council for Strategic Research, Federal Ministry of Food and Agriculture (Germany), Finnish Ministry of Agriculture and Forestry, National Natural Science Foundation of China, CGIAR (France), Grains Research and Development Corporation (Australia), Department of Environment and Primary Industries (Australia), Texas AgriLife Research, Texas A&M University, Commonwealth Scientific and Industrial Research Organisation (Australia), Chinese Academy of Sciences, Department of Agricultural and Biological Engineering [Gainesville] (UF|ABE), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Plant Production Research, Agrifood Research Finland, Stanford University, Agricultural Research Service / US Arid Land Agricultural Research Center, United States Department of Agriculture, The School of Plant Sciences, University of Arizona, International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Department of Agronomy, Purdue University [West Lafayette], CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Washington State University (WSU), Department of geological sciences, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, W. K. Kellogg Biological Station (KBS), Institute of Soil Ecology, Helmholtz-Zentrum München (HZM), CGIAR-ESSP Program on Climate Change,Agriculture and Food Security, International Center for Tropical Agriculture, University of Leeds, Agroclim (AGROCLIM), Institut National de la Recherche Agronomique (INRA), Catabrian Agricultural Research and Training Center (CIFA), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Córdoba [Cordoba], WESS-Water and Earth System Science Competence Cluster, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Biological Systems Engineering, Department of Plant Agriculture, University of Guelph, Department of Geographical Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, Texas A&M University System, Department of Agroecology, Aarhus University [Aarhus], Institute of Landscape System Analysis, Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Potsdam Institute for Climate Impact Research (PIK), Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute (IARI), Institute of landscape systems analysis, Department of Environment and Primary Industries, NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), Computational and Systems Biology Department, Rothamsted Research, Department of Geological Sciences, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Computational and Systems Biology, John Innes Centre [Norwich], Institute of Soil Science and Land Evaluation, University of Hohenheim, Plant Production Systems and Earth System Science, Wageningen University and Research [Wageningen] (WUR), Institute of geographical sciences and natural resources research, Chinese Academy of Sciences [Changchun Branch] (CAS), Agriculture Flagship, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Department of Agronomy and Biotechnology, China Agricultural University (CAU), Nanjing Agricultural University, International Food Policy Research Institute (IFPRI), USDA National Institute for Food and Agriculture [32011-68002-30191], KULUNDA [01LL0905L], FACCE MACSUR project through the German FederalMinistry of Education and Research (BMBF) [031A103B, 2812ERA115], German Science Foundation [EW119/5-1], FACCEMACSUR project by the Danish Strategic Research Council, FACCE MACSUR project through the German Federal Ministry of Food and Agriculture (BMEL), FACCE MACSUR project funded through the Finnish Ministry of Agriculture and Forestry, National Natural Science Foundation of China [41071030], Helmholtz project 'REKLIM-Regional Climate Change: Causes and Effects' Topic 9: 'Climate Change and Air Quality', CGIAR Research Program on Climate Change, Agriculture, and Food Security (CCAFS), Australian Grains Research and Development Corporation, Department of Environment and Primary Industries Victoria, Australia, Texas AgriLife Research, Texas AM University, CSIRO, Chinese Academy of Sciences (CAS), Helmholtz Zentrum München = German Research Center for Environmental Health, Universidad de Córdoba = University of Córdoba [Córdoba], Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), Institute of geographical sciences and natural resources research [CAS] (IGSNRR), Chinese Academy of Sciences [Beijing] (CAS), Université de Toulouse (UT)-Université de Toulouse (UT), and Nanjing Agricultural University (NAU)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Yield (finance), Growing season, Climate change, Environmental Science (miscellaneous), Atmospheric sciences, 01 natural sciences, [SHS]Humanities and Social Sciences, Crop, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Production (economics), 0105 earth and related environmental sciences, 2. Zero hunger, business.industry, Global warming, Simulation modeling, 15. Life on land, Agronomy, 13. Climate action, Agriculture, [SDE]Environmental Sciences, Environmental science, business, Social Sciences (miscellaneous), 010606 plant biology & botany
Abstract: Asseng, S. et al., Crop models are essential tools for assessing the threat of climate change to local and global food production1. Present models used to predict wheat grain yield are highly uncertain when simulating how crops respond to temperature2. Here we systematically tested 30 different wheat crop models of the Agricultural Model Intercomparison and Improvement Project against field experiments in which growing season mean temperatures ranged from 15 °C to 32 °C, including experiments with artificial heating. Many models simulated yields well, but were less accurate at higher temperatures. The model ensemble median was consistently more accurate in simulating the crop temperature response than any single model, regardless of the input information used. Extrapolating the model ensemble temperature response indicates that warming is already slowing yield gains at a majority of wheat-growing locations. Global wheat production is estimated to fall by 6% for each °C of further temperature increase and become more variable over space and time., We thank the Agricultural Model Intercomparison and Improvement Project and its leaders C. Rosenzweig from NASA Goddard Institute for Space Studies and Columbia University (USA), J. Jones from University of Florida (USA), J. Hatfield from United States Department of Agriculture (USA) and J. Antle from Oregon State University (USA) for support. We also thank M. Lopez from CIMMYT (Turkey), M. Usman Bashir from University of Agriculture, Faisalabad (Pakistan), S. Soufizadeh from Shahid Beheshti University (Iran), and J. Lorgeou and J-C. Deswarte from ARVALIS—Institut du Végétal (France) for assistance with selecting key locations and quantifying regional crop cultivars, anthesis and maturity dates and R. Raymundo for assistance with GIS. S.A. and D.C. received financial support from the International Food Policy Research Institute (IFPRI). C.S. was funded through USDA National Institute for Food and Agriculture award 32011-68002-30191. C.M. received financial support from the KULUNDA project (01LL0905L) and the FACCE MACSUR project (031A103B) funded through the German Federal Ministry of Education and Research (BMBF). F.E. received support from the FACCE MACSUR project (031A103B) funded through the German Federal Ministry of Education and Research (2812ERA115) and E.E.R. was funded through the German Science Foundation (project EW 119/5-1). M.J. and J.E.O. were funded through the FACCE MACSUR project by the Danish Strategic Research Council. K.C.K. and C.N. were funded by the FACCE MACSUR project through the German Federal Ministry of Food and Agriculture (BMEL). F.T., T.P. and R.P.R. received financial support from FACCE MACSUR project funded through the Finnish Ministry of Agriculture and Forestry (MMM); F.T. was also funded through National Natural Science Foundation of China (No. 41071030). C.B. was funded through the Helmholtz project ‘REKLIM—Regional Climate Change: Causes and Effects’ Topic 9: ‘Climate Change and Air Quality’. M.P.R. and P.D.A. received funding from the CGIAR Research Program on Climate Change, Agriculture, and Food Security (CCAFS). G.O’L. was funded through the Australian Grains Research and Development Corporation and the Department of Environment and Primary Industries Victoria, Australia. R.C.I. was funded by Texas AgriLife Research, Texas A&M University. E.W. and Z.Z. were funded by CSIRO and the Chinese Academy of Sciences (CAS) through the research project ‘Advancing crop yield while reducing the use of water and nitrogen’ and by the CSIRO-MoE PhD Research Program.
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23. A new phylogenetic framework for the genus Kalanchoe (Crassulaceae) and implications for infrageneric classification.

Author: Rodewald SE, Klein DP, Shtein R, Smith GF, Joyce E, Morales Briones DF, Bernhard S, Letsara R, Mertes H, Hühn P, and Kadereit G
Abstract: Background and Aims: Kalanchoe is a diverse genus in the Crassulaceae, with centres of diversity in Madagascar and sub-Saharan Africa. The genus is known for its popularity in horticulture, its use as a model system for research on CAM photosynthesis and vegetative reproduction, its high invasive potential, and its use in traditional medicine. The genus-rank circumscription and infrageneric classification of Kalanchoe have been the subject of debate for centuries, especially regarding the status and rank of what is now treated as K. subg. Bryophyllum and K. subg. Kitchingia. We aim to generate a densely sampled phylogeny of Kalanchoe s.l. and evaluate the current infrageneric classification system., Methods: We inferred a phylogenetic tree for Kalanchoe using a ddRAD sequencing approach, covering 70% of taxa and four out of five subgenera currently recognised in the genus., Key Results: We recovered four well-supported clades, partially corresponding to the current subgeneric classification. Kalanchoe subg. Calophygia resolves as sister to the rest of the genus. The relationships among the three remaining clades, however, receive less support. The predominantly mainland African K. subg. Kalanchoe forms a strongly supported clade that resolves as sister to K. subg. Bryophyllum. These two clades are together sister to a clade containing mainly species from K. subg. Kitchingia and K. sect. Pubescentes., Conclusions: The current subgeneric classification of Kalanchoe is partially backed up by our phylogenetic tree but requires further refinement. The tree topology suggests a Malagasy origin of the genus and one dispersal event to the African mainland, with subsequent dispersal from continental Africa to the Arabian Peninsula and Southeast Asia. The formation of bulbils on the leaf margin is restricted to a larger clade within K. subg. Bryophyllum and thus only evolved once. Our tree provides a framework for further taxonomic, evolutionary, and physiological research on the genus., (© The Author(s) 2025. Published by Oxford University Press on behalf of the Annals of Botany Company.)
Published: 2025
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24. Deciphering the core shunt mechanism in Arabidopsis cuticular wax biosynthesis and its role in plant environmental adaptation.

Author: Li S, Zhang X, Huang H, Yin M, Jenks MA, Kosma DK, Yang P, Yang X, Zhao H, and Lü S
Abstract: Plant cuticular waxes serve as highly responsive adaptations to variable environments 1-7 . Aliphatic waxes consist of very-long-chain (VLC) compounds produced from 1-alcohol- or alkane-forming pathways 5,8 . The existing variation in 1-alcohols and alkanes across Arabidopsis accessions revealed that 1-alcohol amounts are negatively correlated with aridity factors, whereas alkanes display the opposite behaviour. How carbon resources are allocated between the 1-alcohol and alkane pathways responding to environmental stimuli is still largely unknown. Here, in Arabidopsis, we report a novel 1-alcohol biosynthesis pathway in which VLC acyl-CoAs are first reduced to aldehydes by CER3 and then converted into 1-alcohols via a newly identified putative aldehyde reductase SOH1. CER3, previously shown to interact with CER1 in alkane synthesis, is identified to interact with SOH1 as well, channelling wax precursors into either alcohol- or alkane-forming pathways, and the directional shunting of these precursors is tightly regulated by the SOH1-CER3-CER1 module in response to environmental conditions., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s), under exclusive licence to Springer Nature Limited.)
Published: 2025
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25. The Plant Ionome as a Functional Trait: Variation across Bioclimatic Regions and Functional Groups.

Author: Katz O, Moura RF, Gruntman M, and Sternberg M
Subjects: Plants metabolism, Climate, Strontium metabolism, Ions metabolism, Poaceae genetics, Poaceae metabolism, Poaceae physiology, Mediterranean Region, Spectrometry, X-Ray Emission, Calcium metabolism, Fabaceae metabolism, Fabaceae genetics, Fabaceae physiology, Soil chemistry
Abstract: Plant chemical composition is a trait gaining increasing importance in plant ecology. However, there is limited research on the patterns and drivers of its variation among different plant functional groups and bioclimatic regions. We conducted an analysis of ionomes utilising X-ray fluorescence on 83 plant species from four distinct functional groups (grasses, legumes, forbs and woody species); we marked plots across 15 sites located in both the desert and Mediterranean bioclimatic regions. The primary factors influencing variations in ionomes are predominantly attributed to bioclimatic factors rather than soil composition. Across all functional groups, plants from the Mediterranean region are characterised by greater association with calcium, whereas desert plants exhibit a higher affinity for strontium (Sr), suggesting its potential role in drought tolerance. Among functional groups, grasses uniquely exhibit distinct ionomic features, primarily due to their higher silicon (Si) concentrations. Plant species' affinities for certain elements and their interactions are likely driven by physiological constraints, whereas variations within a functional group are mostly driven by environmental conditions. We conclude that interactions among elements form physiological phenotypes shaped by natural selection under large-scale environmental variability, making plant ionome composition an important plant functional trait., (© 2025 Scandinavian Plant Physiology Society.)
Published: 2025
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26. The roles of florivory and herbivory in maintaining intra-population flower colour variation in Anemone coronaria.

Author: Saabna N, Keasar T, and Sapir Y
Subjects: Animals, Plant Leaves physiology, Color, Flowers physiology, Herbivory physiology, Pollination physiology, Anemone physiology, Pigmentation physiology
Abstract: Most flowering plants are colour monomorphic, while within-population flower colour variation is rare. Multiple selection agents on flower colour, each favouring a different colour morph, may drive such uncommon polymorphisms. We tested the role of biotic antagonistic interactions in maintaining flower colour variation in Anemone coronaria (Ranunculaceae), in colour-polymorphic populations comprised of red, purple, and white flowers. We estimated the extent of leaf herbivory and petal florivory in each flower colour morph in three populations over two flowering seasons. We categorized types of damage to four groups of herbivores and estimated the plant maternal fitness. We tested pollinator response to different levels (0-30%) of simulated florivory in experimental flower arrays. Leaf and petal damage did not differ between white- and purple-flowering plants. Red-flowering plants had higher leaf damage than white-flowering plants and higher petal damage than purple-flowering plants. Nevertheless, all colour morphs had similar fitness. Red flowers exhibited more petal scratches (attributed to glaphyrid beetles), but fewer petal bites (attributed to caterpillars or grasshoppers), than white and purple flowers. Experimentally induced florivory did not reduce visits by potential pollinators in any colour morph. Glaphyrid beetles are the major pollinators of red anemone flowers, suggesting that their service to red flowers as mutualists (pollinators) should be weighed against their disservice as antagonists (florivores). A balance between pollination service and petal scratch damage of red flowers, both mediated by Glaphyird beetles, may equalize fitness between the red and the purple/white colour morphs, contributing to colour polymorphism., (© 2024 The Author(s). Plant Biology published by John Wiley & Sons Ltd on behalf of German Society for Plant Sciences, Royal Botanical Society of the Netherlands.)
Published: 2025
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27. Investigating the mechanism of chloroplast singlet oxygen signaling in the Arabidopsis thaliana accelerated cell death 2 mutant.

Author: Lemke MD, Abate AN, and Woodson JD
Subjects: Photosynthesis genetics, Arabidopsis genetics, Arabidopsis metabolism, Singlet Oxygen metabolism, Chloroplasts metabolism, Arabidopsis Proteins metabolism, Arabidopsis Proteins genetics, Signal Transduction genetics, Mutation genetics
Abstract: As sessile organisms, plants have evolved complex signaling mechanisms to sense stress and acclimate. This includes the use of reactive oxygen species (ROS) generated during dysfunctional photosynthesis to initiate signaling. One such ROS, singlet oxygen ( 1 O 2 ), can trigger retrograde signaling, chloroplast degradation, and programmed cell death. However, the signaling mechanisms are largely unknown. Several proteins (e.g. PUB4, OXI1, EX1) are proposed to play signaling roles across three Arabidopsis thaliana mutants that conditionally accumulate chloroplast 1 O 2 ( fluorescent in blue light ( flu ), chlorina 1 ( ch1 ), and plastid ferrochelatase 2 ( fc2 )). We previously demonstrated that these mutants reveal at least two chloroplast 1 O 2 signaling pathways (represented by flu and fc2 / ch1 ). Here, we test if the 1 O 2 -accumulating lesion mimic mutant, accelerated cell death 2 ( acd2 ), also utilizes these pathways. The pub4-6 allele delayed lesion formation in acd2 and restored photosynthetic efficiency and biomass. Conversely, an oxi1 mutation had no measurable effect on these phenotypes. acd2 mutants were not sensitive to excess light (EL) stress, yet pub4-6 and oxi1 both conferred EL tolerance within the acd2 background, suggesting that EL-induced 1 O 2 signaling pathways are independent from spontaneous lesion formation. Thus, 1 O 2 signaling in acd2 may represent a third (partially overlapping) pathway to control cellular degradation.
Published: 2024
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28. Response of sorghum genotypes to anthracnose (Colletotrichum sublineolum) resistance under field conditions in eastern Ethiopia.

Author: Aragaw G and Terefe H
Subjects: Ethiopia, Sorghum microbiology, Sorghum genetics, Plant Diseases microbiology, Plant Diseases genetics, Genotype, Disease Resistance genetics, Colletotrichum pathogenicity
Abstract: Sorghum anthracnose is one of the major diseases that have negative impacts on sorghum production in Ethiopia. This study was conducted to evaluate the resistance response of sorghum genotypes against sorghum anthracnose and to determine yield performances of sorghum genotypes under field conditions in two consecutive cropping years. Forty-nine sorghum genotypes were tested for their reactions to anthracnose in the East and West Hararghe Zones, East Ethiopia, during the 2017 and 2018 main cropping seasons. The design of the experiment was laid out in triple lattice square design with three replications. Anthracnose severity was assessed on 16 randomly selected and pre-tagged sorghum plants in the middle two rows of each plot. The eight subsequent times of severity assessments were used to evaluate the response of the genotypes to sorghum anthracnose. The ranges of the mean severity of anthracnose in 2017 and 2018 were 35 to 91% and 38 to 93%, respectively. In 2017 and 2018, the area under disease progress curve varied from 1744 to 3865% of days and from 2354 to 4908% of days, respectively. During the two growing seasons, the genotype ETSL 101469 displayed the highest anthracnose severity, followed by BTX-623. In both experimental years, anthracnose had very strong negative relationships with grain yield and thousand seed weight. The current study demonstrated how Ethiopian sorghum genotypes affect anthracnose development in the field conditions. Throughout the two experimental years, the sorghum genotypes ETSL 100335, ETSL 100395, ETSL 10474, ETSL 100523, ETSL 100498, ETSL 100989, ETSL 100597, and ETSL 101000 continuously exhibited lower disease levels than the other genotypes. Therefore, it is advised to use these genotypes as alternate sources of sorghum anthracnose resistance. Nonetheless, further research across location is necessary to validate their anthracnose resistance in a variety of agro-ecologies., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Aragaw, Terefe. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Published: 2024
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29. Streamlining Global Germplasm Exchange: Integrating Scientific Rigor and Common Sense to Exclude Phantom Agents from Regulation.

Author: Tzanetakis IE, Aknadibossian V, Špak J, Constable F, Harper SJ, Hammond J, Candresse T, Folimonova SY, Freitas-Astúa J, Fuchs M, Jelkmann W, Maliogka VI, Marais A, Martin RR, Mollov D, Vidalakis G, Aboughanem-Sabanadzovic N, Al Rwahnih M, Alabi OJ, Alioto D, Atanda HY, Bagi F, Baranwal VK, Barbosa C, Bar-Joseph M, Batista Le Riverend L, Belien T, Benítez-Galeano MJ, Bennypaul H, Bertaccini A, Bester R, Blouin AG, Blystad DR, Botermans M, Bozan O, Brakta A, Brans Y, Bulajić A, Caglayan K, Catara A, Choueiri E, Cieślińska M, Cook G, Cui W, da Graça J, Davino S, Delmiglio C, Dewdney MM, Di Serio F, Diaz-Lara A, Digiaro M, Djelouah K, Dong YF, Donovan N, Druciarek TZ, Duran-Vila N, Elçi E, Esquivel-Fariña A, Fall ML, Fan XD, Figueroa J, Fiore N, Fowkes AR, Fox A, Fránová J, Fuchs R, Gaafar YZA, García ML, Ghosh D, Girardi E, Glasa M, Gomez Talquenca S, Gratz A, Gritsenko D, Hajeri S, Hajizadeh M, Hamborg Z, Ho T, Holeva M, Holkar SK, Horner M, Hurtado-Gonzales OP, Ippolito A, Isac V, Iwanami T, Jofre-Y-Garfias AE, Jordan R, Katis N, Koloniuk I, Konings H, Križanac I, Krueger R, Kyrychenko A, Laranjeira F, Lavagi-Craddock I, Levy A, Licciardello G, Lu QY, MacFarlane SA, Marcone C, Maree HJ, Margaria P, Martić A, Massart S, Mathioudakis MM, Matić S, Mavric Plesko I, Meekes ETM, Mehle N, Melzer MJ, Meng B, Menzel W, Miljanić V, Minafra A, Minutolo M, Mitra A, Moreno P, Navarro L, Navarro B, Nerva L, Okić A, Olmos A, Önelge N, Osundahunsi B, Palacios MF, Pallas V, Panno S, Perez-Egusquiza Z, Poudel-Ward B, Radišek S, Ramos-González PL, Ramteke P, Ranabhat NB, Rivarez MPS, Rivas F, Roenhorst A, Roy A, Ruiz-García AB, Sabanadzovic S, Šafářová D, Saldarelli P, Salem N, Sanahuja Solsona G, Schoen R, Sharma SK, Shilts T, Sierra-Mejia A, Singh S, Skelton A, Škorić D, Stainton D, Štajner N, Starović M, Stuchi E, Svoboda P, Tahzima R, Tang J, Tessitori M, Thermoz JP, Thompson E, Thompson J, Trebicki P, Turina M, Ulubas Serce C, Umble J, Valiunas D, Varallyay E, Varma A, Varveri C, Vásquez-Gutiérrez U, Vazquez-Iglesias I, Veerakone S, Villamor DE, Vives MC, Vončina D, Wang J, Westenberg M, Wetzel T, Winter S, Wright G, Wulff NA, Xu WX, Yokomi R, Zhou C, Zikeli K, and Zindović J
Abstract: This collaborative work by over 180 researchers from 40+ countries addresses the challenges posed by "phantom agents"-putative pathogenic agents named in literature without supporting data on their existence. Those agents remain on regulatory lists, creating barriers in trade and plant certification. Historically identified based solely on symptoms, these agents lack isolates or sequence data, making reliable detection or risk assessment impossible. After reviewing over 120 such agents across 10 key plant genera, we recommend their removal from regulatory lists and call for revised standards aligned with modern diagnostics. This effort seeks to streamline germplasm exchange, benefiting global agriculture by removing the constraints imposed by phantoms., Competing Interests: The author(s) declare no conflict of interest.
Published: 2024
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30. First report of foliar blight of castor bean caused by Alternaria ricini in Sinaloa, Mexico.

Author: Olivas-Peraza NG, Nguyen AE, Rodriguez BA, Zizzo KJ, Pryor BM, and Félix-Gastélum R
Abstract: Castor bean (Ricinus communis) is cultivated agriculturally for oil and ornamentally for its bright foliage and seed. Ornamental castor bean has naturalized in many areas of the world, including the state of Sinaloa, Mexico, where it is not planted commercially. In a survey conducted in 2019 in Sinaloa, wild castor bean was found widely affected by a foliar blight with symptoms similar to Alternaria ricini previously described in the United States (Stevenson 1945) and in the state of Chiapas, Mexico (López-Guillén et al. 2015). Sampling was conducted from February to April along roadsides and irrigation canals at 10 sites that were 10-12 km apart. Symptoms consisted of dark lesions < 2 cm dia with occasional concentric rings and coalescing with age. Incidence of disease among sites ranged from 20 to 60%. The severity of disease was greater in the lower canopy where the foliage area diseased (FAD) ranged from 15 to 35%. Ten symptomatic leaves were collected from each site and leaf fragments were plated on potato dextrose agar (PDA) using standard microbiological techniques for fungal recovery. Isolates of long-beaked Alternaria were recovered from 60 to 70% of fragments from each site and representative isolates (1/site) were selected for further studies. Isolates were transferred to Petri dishes containing PDA for characterization of the colony and V8 juice agar (V8A) for examination of the conidia (Simmons 2007). On PDA, colonies were dark olive brown, cottony, subsurface microsclerotia production abundant, and no production of pigments in the medium. On V8A, conidia were produced singly, darkly pigmented, and broadly ellipsoidal. The length and width of mature conidia ranged 70 to 100 µm (avg 88 µm) and 17 to 26 µm (avg 22 µm), respectively, with 2 to 4 transepta and 1 to 3 longisepta. The apical beak length ranged 10 to 125 um (avg 72 µm). Morphological characteristics were consistent with those of A. ricini from commercial castor bean (Simmons 2007). DNA was extracted from each isolate and the GAPDH and calmodulin genes were sequenced using protocol previously described (Lawrence et al. 2013). For each locus, sequences were identical among fungal isolates and representative sequences were deposited in GenBank (accessions OQ868796 and OQ868803, respectively). When compared to the NCBI database by BLASTn, the sequences had 100% identities to A. ricini GAPDH JQ646331 (576/576 bp) and A. ricini calmodulin JQ646230 (772/772 bp). To confirm pathogenicity of recovered Alternaria, all ten isolates were tested on the commercial castor bean cultivar Chinatan in two independent greenhouse trials. Seed was sown one per pot and four plants per isolate were tested. Spore solutions were prepared from V8A plates and spore densities were adjusted to 4 x 104 conidia/ml. At 4 to 5 leaves stage, plants were sprayed with spore solution until runoff, placed in clear polyethylene bags for 48 hr. After 14 dpi, the percentage of FAD ranged from 19 to 80% with significant differences among fungal isolates. Control plants sprayed with water remained healthy. To fulfill Koch´s postulates, the fungus was re-isolated from representative inoculated plants and its identity was confirmed using morphological characteristics. This is the first report of A. ricini causing foliar blight of castor bean in the state of Sinaloa, Mexico. Strategies for managing inoculum from wild castor bean should be developed in advance of increasing commercial castor production in Sinaloa.
Published: 2024
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31. Genetic Diversity, Association, and Path Coefficient Analyses of Sorghum [ Sorghum bicolor (L.) Monech] Genotypes.

Author: Gebre W, Mekbib F, Tirfessa A, and Bekele A
Abstract: For sustainable genetic improvement of crops like sorghum, assessing genetic variability and knowing the nature and extent of the association between grain yield and yield-related traits is a prerequisite. However, there needs to be sufficient information about the genetic variability study as well as yield-related trait correlation and path coefficient analysis for sorghum accessions, especially those from southern Ethiopia. Hence, this field experiment assessed genetic variability, determined the nature and extent of phenotypic-genetic correlation, and analyzed the path coefficients among 17 quantitative traits. A total of 225 sorghum genotypes were tested using a simple lattice design with two replications at the Jinka Agricultural Research Center during the 2021 cropping season. Based on the analysis of variance, most traits showed highly significant (P 0.001) differences, suggesting genetic diversity between the genotypes. High estimates of GCV and PCV were noted for leaf width (3924.50% and 3924.50%), while the lowest GCV and PCV estimates were obtained for days to flowering and days to maturity. High heritability coupled with high GAM estimates was recorded for plant height, leaf number, leaf length, leaf width, and leaf area. The magnitudes of genotypic correlations were higher than those of phenotypic correlations for most of the studied traits, implying that the traits under study were genetically controlled. Grain yield was positively and significantly correlated with most of the traits at phenotypic and genotypic levels, indicating the presence of a strong inherent association between grain yield and other traits. Phenotypic path coefficient analysis showed that grain filling period and biomass yield exerted a high positive direct effect on grain yield. Genotypic path coefficient analysis revealed that biomass yield, grain filling period, leaf width, and days to flowering had a relatively high positive direct effect on grain yield. However, days to maturity, plant height, leaf number, leaf area, yield per panicle, straw weight, and harvest index exerted a negative direct effect on grain yield. Almost for all the studied traits, genotypic direct and indirect effects were higher than the phenotypic direct and indirect effects, indicating that the studied traits had a genetically inherited relationship with grain yield. Grain yield in sorghum can be improved through indirect selection for traits such as plant height, leaf number, leaf length, leaf width, and biomass yield. In general, the observed variability and the information obtained from this study can be used for the genetic enhancement of sorghum thereby developing high-yielding varieties., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2024 Wedajo Gebre et al.)
Published: 2024
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32. Identifying climatic drivers of forage quantity and quality in Mediterranean rangelands using remote sensing.

Author: Adar S, Paz-Kagan T, Argaman E, Dubinin MV, and Sternberg M
Subjects: Israel, Grassland, Animals, Ecosystem, Biomass, Satellite Imagery, Climate Change, Remote Sensing Technology, Environmental Monitoring methods
Abstract: Rangelands are dynamic ecosystems shaped by fluctuations in precipitation, temperature, and grazing intensity. Accurate assessment of forage availability is critical for optimizing land use, preventing overgrazing, and mitigating degradation, especially under future climate change scenarios. This study employed a multi-scale approach to monitor pasture using Sentinel-2 satellite imagery, calibrated with ground truth measurements, and enhanced with drone-derived vegetation cover estimates. The research was conducted in a Mediterranean grassland ecosystem under varying grazing intensities in northeastern Israel. A time series of Sentinel-2 images from 2018 to 2023 was analyzed to monitor five vegetation growth cycles. We evaluated how climate variables, such as temperature, rainfall, and vapor pressure deficit (VPD), impacted forage availability and nutritional quality. Over the past three decades, significant climatological trends showed increasing temperatures and more concentrated winter rainfall. Correlation analysis between field data and Sentinel-2 imagery demonstrated strong agreement (R 2 = 0.73 for biomass and 0.72 for forage quality), validating the effectiveness of this integrated remote sensing approach. Moderate grazing reduced forage quantity but improved its quality, while extreme weather events, including drought and heatwaves, negatively impacted forage biomass and quality. Key meteorological indices, including the Standardized Precipitation-Evapotranspiration Index (SPEI) and the Simple Daily Intensity Index (SDII), were found to influence forage quantity, indicating that drought stress and concentrated rainfall events reduced biomass production. Higher values of daily temperature range and vapor pressure deficit adversely impacted forage quality. This study highlights the importance of adaptive management strategies to mitigate the projected reductions in forage quantity and quality due to climate change. The methodologies developed offer novel insights into improving ecological monitoring for sustainable rangeland management under changing climatic conditions., Competing Interests: Declaration of competing interest The authors declare that there is no conflict of interest regarding the publication of this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)
Published: 2024
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33. A data-integrative modeling approach accurately characterizes the effects of mutations on Arabidopsis lipid metabolism.

Author: Correa Córdoba S, Burgos A, Cuadros-Inostroza Á, Xu K, Brotman Y, and Nikoloski Z
Abstract: Collections of insertional mutants have been instrumental for characterizing the functional relevance of genes in different model organisms, including Arabidopsis (Arabidopsis thaliana). However, mutations may often result in subtle phenotypes, rendering it difficult to pinpoint the function of a knocked-out gene. Here, we present a data-integrative modeling approach that enables predicting the effects of mutations on metabolic traits and plant growth. To test the approach, we gathered lipidomics data and physiological read-outs for a set of 64 Arabidopsis lines with mutations in lipid metabolism. Use of flux sums as a proxy for metabolite concentrations allowed us to integrate the relative abundance of lipids and facilitated accurate predictions of growth and biochemical phenotype in approximately 73% and 76% of the mutants, respectively, for which phenotypic data were available. Likewise, we showed that this approach can pinpoint alterations in metabolic pathways related to silent mutations. Therefore, our study paves the way for coupling model-driven characterization of mutant lines from different mutagenesis approaches with metabolomic technologies, as well as for validating knowledge structured in large-scale metabolic networks of plants and other species., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)
Published: 2024
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34. Metagenome-assembled genomes of freshwater Hyphomicrobium sp. G-191 and Methylophilus sp. enriched from Cedar Swamp, Woods Hole, MA.

Author: Huang Y, Schomer R, Reyes MJR, Costa K, Parales RE, Whitaker R, and Dawson SC
Abstract: Hyphomicrobium are facultative denitrifying anaerobes capable of using one-carbon compounds as a sole carbon source. Hyphomicrobium sp. G-191 was enriched from Cedar Swamp, Woods Hole, Massachusetts, using a selective medium for methanol-utilizing bacteria. We present two draft metagenome-assembled genomes (MAGs) of a Hyphomicrobium and a Methylophilus species., Competing Interests: The authors declare no conflict of interest.
Published: 2024
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35. Phylogenetic Analysis of 590 Species Reveals Distinct Evolutionary Patterns of Intron-Exon Gene Structures Across Eukaryotic Lineages.

Author: Glick L, Castiglione S, Loewenthal G, Raia P, Pupko T, and Mayrose I
Subjects: Animals, Introns, Phylogeny, Exons, Evolution, Molecular, Eukaryota genetics
Abstract: Introns are highly prevalent in most eukaryotic genomes. Despite the accumulating evidence for benefits conferred by the possession of introns, their specific roles and functions, as well as the processes shaping their evolution, are still only partially understood. Here, we explore the evolution of the eukaryotic intron-exon gene structure by focusing on several key features such as the intron length, the number of introns, and the intron-to-exon length ratio in protein-coding genes. We utilize whole-genome data from 590 species covering the main eukaryotic taxonomic groups and analyze them within a statistical phylogenetic framework. We found that the basic gene structure differs markedly among the main eukaryotic groups, with animals, and particularly chordates, displaying intron-rich genes, compared with plants and fungi. Reconstruction of gene structure evolution suggests that these differences evolved prior to the divergence of the main phyla and have remained mostly conserved within groups. We revisit the previously reported association between the genome size and the mean intron length and report that this association differs considerably among phyla. Analyzing a large and diverse dataset of species with whole-genome information while applying advanced modeling techniques allowed us to obtain a global evolutionary perspective. Our findings may indicate that introns play different molecular and evolutionary roles in different organisms., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
Published: 2024
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36. Influence of Alectra vogelii inoculation and phosphorus fertilizer application on phenology, yield components and grain yield of bambara groundnut genotypes.

Author: Musango R, Tana T, Mabasa S, Gasura E, Pasipanodya JT, Mandumbu R, and Tauro TP
Abstract: In sub-Saharan Africa, the parasitic Alectra vogelii is seriously threatening Bambara groundnuts, farmers to suffer yield losses of up to 100 %. The objective of this study was to determine the effects of phosphorus (P) application and Alectra vogelii inoculation on Bambara groundnut genotypes for growth and reproductive phrase. The experiment was conducted in 2020 at the Henderson Research Station in Mazowe, Zimbabwe in a 2 × 2 × 26 factorial design with 26 genotypes arranged in a completely randomized design (CRD) with four replications, two P rates (0 and 20 kg ha- 1 ) and two levels of inoculation (with and without Alectra vogelii ). Half of the perforated black plastic bags were inoculated with Alectra vogelii seeds. The results showed a significant (p < 0.001) interaction between P application and Alectra vogelii inoculation, leading to decreased Alectra vogelii counts after 109 days, days to maturity, days to flowering, and chlorophyll content. There was a significant (p < 0.001) interaction between Bambara groundnut genotypes and Alectra -inoculation on number of pods, pod weight, number of seeds, and grain yield. Alectra vogelii parasitism significantly (p < 0.001) decreased number of pods, pod weight, number of seeds, and grain yield across all groundnut genotypes. G2, G23, G24, and G25 genotypes exhibited tolerance to Alectra vogelii , with grain yield per plant of 4.82, 6.12, 5.65, and 5.34 g, respectively, outperforming other genotypes. It was found that the combination of 20 kg P ha -1 with Alectra -resistant genotypes improved Bambara groundnut productivity., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier Ltd.)
Published: 2024
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37. Eco-phylogenetic study of Trebouxia in southern Africa reveals interbiome connectivity and potential endemism in a green algal lichen photobiont.

Author: Medeiros ID, Ibáñez A, Arnold AE, Hedderson TA, Miadlikowska J, Flakus A, Carbone I, LaGreca S, Magain N, Mazur E, Castillo RV, Geml J, Kaup M, Maggs-Kölling G, Oita S, Sathiya Seelan JS, Terlova E, Hom EFY, Lewis LA, and Lutzoni F
Subjects: South Africa, Biodiversity, Chlorophyta genetics, Chlorophyta microbiology, Symbiosis, Namibia, Africa, Southern, Chlorophyceae genetics, Chlorophyceae physiology, Lichens microbiology, Lichens physiology, Phylogeny
Abstract: Premise: Southern Africa is a biodiversity hotspot rich in endemic plants and lichen-forming fungi. However, species-level data about lichen photobionts in this region are minimal. We focused on Trebouxia (Chlorophyta), the most common lichen photobiont, to understand how southern African species fit into the global biodiversity of this genus and are distributed across biomes and mycobiont partners., Methods: We sequenced Trebouxia nuclear ribosomal ITS and rbcL of 139 lichen thalli from diverse biomes in South Africa and Namibia. Global Trebouxia phylogenies incorporating these new data were inferred with a maximum likelihood approach. Trebouxia biodiversity, biogeography, and mycobiont-photobiont associations were assessed in phylogenetic and ecological network frameworks., Results: An estimated 43 putative Trebouxia species were found across the region, including seven potentially endemic species. Only five clades represent formally described species: T. arboricola s.l. (A13), T. cf. cretacea (A01), T. incrustata (A06), T. lynniae (A39), and T. maresiae (A46). Potential endemic species were not significantly associated with the Greater Cape Floristic Region or desert. Trebouxia species occurred frequently across multiple biomes. Annual precipitation, but not precipitation seasonality, was significant in explaining variation in Trebouxia communities. Consistent with other studies of lichen photobionts, the Trebouxia-mycobiont network had an anti-nested structure., Conclusions: Depending on the metric used, ca. 20-30% of global Trebouxia biodiversity occurs in southern Africa, including many species yet to be described. With a classification scheme for Trebouxia now well established, tree-based approaches are preferable over "barcode gap" methods for delimiting new species., (© 2024 Botanical Society of America.)
Published: 2024
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38. Transcript profiling of plastid ferrochelatase two mutants reveals that chloroplast singlet oxygen signals lead to global changes in RNA profiles and are mediated by Plant U-Box 4.

Author: Rai S, Lemke MD, Arias AM, Gomez Mendez MF, Dehesh K, and Woodson JD
Abstract: Background: In response to environmental stresses, chloroplasts generate reactive oxygen species, including singlet oxygen ( 1 O 2 ), an excited state of oxygen that regulates chloroplast-to-nucleus (retrograde) signaling, chloroplast turnover, and programmed cell death (PCD). Yet, the central signaling mechanisms and downstream responses remain poorly understood. The Arabidopsis thaliana plastid ferrochelatase two ( fc2 ) mutant conditionally accumulates 1 O 2 and Plant U-Box 4 (PUB4), a cytoplasmic E3 ubiquitin ligase, is involved in propagating 1 O 2 signals for chloroplast turnover and cellular degradation. Thus, the fc2 and fc2 pub4 mutants are useful genetic tools to elucidate these signaling pathways. Previous studies have focused on the role of 1 O 2 in promoting cellular degradation in fc2 mutants, but its impact on retrograde signaling from mature chloroplasts (the major site of 1 O 2 production) is poorly understood., Results: To gain mechanistic insights into 1 O 2 signaling pathways, we compared transcriptomes of adult wt, fc2 , and fc2 pub4 plants. The accumulation of 1 O 2 in fc2 plants broadly repressed genes involved in chloroplast function and photosynthesis, while inducing genes and transcription factors involved in abiotic and biotic stress, the biosynthesis of jasmonic acid (JA) and salicylic acid (SA), microautophagy, and senescence. Elevated JA and SA levels were observed in 1 O 2 -stressed fc2 plants. pub4 reversed most of this 1 O 2 -induced gene expression and reduced the JA content in fc2 plants. The pub4 mutation also blocked JA-induced senescence pathways in the dark. However , fc2 pub4 plants maintained constitutively elevated levels of SA even in the absence of bulk 1 O 2 accumulation., Conclusions: Together, this work demonstrates that in fc2 plants, 1 O 2 leads to a robust retrograde signal that may protect cells by downregulating photosynthesis and ROS production while simultaneously mounting a stress response involving SA and JA. The induction of microautophagy and senescence pathways indicate that 1 O 2 -induced cellular degradation is a genetic response to this stress, and the bulk of this transcriptional response is modulated by the PUB4 protein. However, the effect of pub4 on hormone synthesis and signaling is complex and indicates that an intricate interplay of SA and JA are involved in promoting stress responses and programmed cell death during photo-oxidative damage.
Published: 2024
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39. Enhanced pollen tube performance at high temperature contributes to thermotolerant fruit and seed production in tomato.

Author: Ouonkap SVY, Palaniappan M, Pryze K, Jong E, Foteh Ali M, Styler B, Althiab Almasaud R, Harkey AF, Reid RW, Loraine AE, Smith SE, Pease JB, Muday GK, Palanivelu R, and Johnson MA
Subjects: Solanum lycopersicum growth & development, Solanum lycopersicum physiology, Pollen Tube growth & development, Pollen Tube physiology, Thermotolerance, Fruit growth & development, Seeds growth & development, Seeds physiology, Hot Temperature
Abstract: Rising temperature extremes during critical reproductive periods threaten the yield of major grain and fruit crops. Flowering plant reproduction depends on the ability of pollen grains to generate a pollen tube, which elongates through the pistil to deliver sperm cells to female gametes for double fertilization. We used tomato as a model fruit crop to determine how high temperature affects the pollen tube growth phase, taking advantage of cultivars noted for fruit production in exceptionally hot growing seasons. We found that exposure to high temperature solely during the pollen tube growth phase limits fruit biomass and seed set more significantly in thermosensitive cultivars than in thermotolerant cultivars. Importantly, we found that pollen tubes from the thermotolerant Tamaulipas cultivar have enhanced growth in vivo and in vitro under high temperature. Analysis of the pollen tube transcriptome's response to high temperature allowed us to define two response modes (enhanced induction of stress responses and higher basal levels of growth pathways repressed by heat stress) associated with reproductive thermotolerance. Importantly, we define key components of the pollen tube stress response, identifying enhanced reactive oxygen species (ROS) homeostasis and pollen tube callose synthesis and deposition as important components of reproductive thermotolerance in Tamaulipas. Our work identifies the pollen tube growth phase as a viable target to enhance reproductive thermotolerance and delineates key pathways that are altered in crop varieties capable of fruiting under high-temperature conditions., Competing Interests: Declaration of interests R.P. is the editor-in-chief of Plant Reproduction., (Copyright © 2024 Elsevier Inc. All rights reserved.)
Published: 2024
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40. PP2C phosphatase Pic6 suppresses MAPK activation and disease resistance in tomato.

Author: Chakraborty J, Sobol G, Xia F, Zhang N, Martin GB, and Sessa G
Abstract: Type 2C protein phosphatases (PP2Cs) are essential for regulating plant immune responses to pathogens. Our study focuses on the tomato PP2C-immunity associated candidate 6 (Pic6), elucidating its role in negatively regulating pattern-triggered immunity (PTI) signaling pathways in tomato. Using reverse transcription quantitative polymerase chain reaction (RT-qPCR), we observed that treatment with microbe-associated molecular patterns (MAMPs)- flg22 and flgII-28-significantly increased Pic6 mRNA levels in wild-type (RG-PtoR) tomato plants. Pic6 features a conserved N-terminal kinase-interacting motif (KIM) and a C-terminal PP2C domain. We produced variants of Pic6 with mutations in these regions, demonstrating their involvements in negatively regulating tomato immunity. Agrobacterium -mediated transient overexpression of Pic6 resulted in enhanced growth of the bacterial pathogen Pseudomonas syringae pv. tomato ( Pst ) strain DC3000Δ hopQ1-1 compared to a YFP control. Additionally, Pic6 overexpression inhibited mitogen-activated protein kinase (MAPK) activation in response to flg22 and flgII-28 treatments. Importantly, Pic6 exhibited phosphatase activity and interacted with tomato Mkk1/Mkk2 proteins and dephosphorylated them in a KIM-dependent manner. Furthermore, we generated RG-pic6 loss-of-function mutants by CRISPR/Cas9, revealing that the absence of Pic6 heightened MAPK activity and increased resistance to Xanthomonas euvesicatoria strain 85-10 ( Xe 85-10) when compared with the wild-type (RG-PtoR) plants. Transcript analyses showed that after flg22/flgII-28 treatment, PTI-reporter genes NAC and osmotin were significantly upregulated in RG-pic6 mutants in comparison to the wild-type (RG-PtoR) plants. Overall, our findings indicate that Pic6 acts as a negative regulator of MAPK signaling and playing a pivotal role in modulating tomato immunity against bacterial pathogens.
Published: 2024
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41. A single NLR gene confers resistance to leaf and stripe rust in wheat.

Author: Sharma D, Avni R, Gutierrez-Gonzalez J, Kumar R, Sela H, Prusty MR, Shatil-Cohen A, Molnár I, Holušová K, Said M, Doležel J, Millet E, Khazan-Kost S, Landau U, Bethke G, Sharon O, Ezrati S, Ronen M, Maatuk O, Eilam T, Manisterski J, Ben-Yehuda P, Anikster Y, Matny O, Steffenson BJ, Mascher M, Brabham HJ, Moscou MJ, Liang Y, Yu G, Wulff BBH, Muehlbauer G, Minz-Dub A, and Sharon A
Subjects: Aegilops genetics, Aegilops microbiology, Plants, Genetically Modified genetics, Genes, Plant, Alleles, Triticum genetics, Triticum microbiology, Triticum immunology, Plant Diseases microbiology, Plant Diseases genetics, Plant Diseases immunology, Disease Resistance genetics, Puccinia pathogenicity, Basidiomycota pathogenicity, Basidiomycota physiology, NLR Proteins genetics, Phylogeny, Plant Proteins genetics, Plant Proteins metabolism, Plant Leaves microbiology, Plant Leaves genetics
Abstract: Nucleotide-binding leucine-rich repeat (NLR) disease resistance genes typically confer resistance against races of a single pathogen. Here, we report that Yr87/Lr85, an NLR gene from Aegilops sharonensis and Aegilops longissima, confers resistance against both P. striiformis tritici (Pst) and Puccinia triticina (Pt) that cause stripe and leaf rust, respectively. Yr87/Lr85 confers resistance against Pst and Pt in wheat introgression as well as transgenic lines. Comparative analysis of Yr87/Lr85 and the cloned Triticeae NLR disease resistance genes shows that Yr87/Lr85 contains two distinct LRR domains and that the gene is only found in Ae. sharonensis and Ae. longissima. Allele mining and phylogenetic analysis indicate multiple events of Yr87/Lr85 gene flow between the two species and presence/absence variation explaining the majority of resistance to wheat leaf rust in both species. The confinement of Yr87/Lr85 to Ae. sharonensis and Ae. longissima and the resistance in wheat against Pst and Pt highlight the potential of these species as valuable sources of disease resistance genes for wheat improvement., Competing Interests: Competing interests The authors declare the following competing interests: D.S., R.A., R.K, E.M., A.M-D., and A.S. are inventors on the US patent application 63/250,413 filed by Ramot (Tel Aviv University) and relating to the use of Yr87/Lr85 for leaf and stripe rust resistance in transgenic wheat. All other authors claim no competing interests., (© 2024. The Author(s).)
Published: 2024
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42. Effect of Mixed Manure and Inorganic Fertilizer on Phosphorus Adsorption and Desorption Characteristics of Vertisols in Haramaya District, Eastern Ethiopia.

Author: Teressa D, Kibret K, Dechasa N, and Wogi L
Abstract: Applying inorganic phosphorus fertilizer is less effective in increasing crop yields in tropical soils due to precipitation and adsorption reactions. However, research suggests that partial substitution of organic and inorganic fertilizers has shown to improve the efficiency of applied phosphorus fertilizer by reducing its adsorption and enhancing desorption due to their synergistic effects. This study aimed to investigate the impact of treating the soil with mixed manure (MM) rates and blended nitrogen, phosphorus, sulfur, and boron (NPSB) fertilizer on the soil's phosphorus adsorption and desorption characteristics. Results showed increased adsorbed phosphorus in all treatments, with increased added phosphorus (P) concentration from 100 to 500 mg kg -1 . However, the efficiency of adsorbed P decreased significantly as added P concentration rates increased from 100 to 400 mg·kg -1 in all treatments and then decreased as the added P concentration advanced to 500 mg·kg -1 . Moreover, in all treatments that received combined applications of MM and blended NPSB, both quantity and percentage of desorbed P showed a significant increase. The Freundlich adsorption coefficient and constant were also significantly reduced because of the combined application of MM and blended NPSB, compared to the control and their sole applications. Overall, the soil treated with a combined application of 15 t·ha -1 of MM with 100 kg·ha -1 of blended NPSB showed the highest reduction in the efficiency of adsorbed P, percentage of desorbed P, Freundlich adsorption capacity, and intensity by 8%, 37.5%, 60%, and 58%, respectively, as compared to the control. These findings indicate that the combined application of MM and blended NPSB can improve the P availability and uptake by maize by reducing its adsorption while increasing desorption characteristics. Finally, this experiment recommends further research on the long-term effects of MM and blended NPSB on P adsorption and desorption characteristics of vertisols., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2024 Dejene Teressa et al.)
Published: 2024
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43. A complete genome sequence of Pseudomonas amygdali pathovar lachrymans YM7902.

Author: Sweten A and Baltrus D
Abstract: Pseudomonas amygdali pathovar lachrymans YM7902 was originally isolated as a pathogen of cucumber in Japan. Here, we report a nearly complete genome sequence for this strain, assembled using a hybrid approach combining Illumina paired-end reads and longer reads sequenced using technology from Oxford Nanopore., Competing Interests: The authors declare no conflict of interest.
Published: 2024
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44. Modulation of Root Hydrotropism and Recovery From Drought by MIZ1-like Genes in Tomato.

Author: Wexler Y, Kiere Y, Sobol G, Nuriel R, Azoulay-Portal S, Cohen A, Toporik H, Pasmanik-Chor M, Finkler A, and Shkolnik D
Abstract: Drought limits crop performance worldwide. Plant roots' ability to grow toward moisture, termed hydrotropism, is considered one strategy for optimizing water recruitment from the growth medium. Based on the sequence of the hydrotropism-indispensable MIZ1 protein in Arabidopsis thaliana, we identify hydrotropism and drought-responsive genes in tomato. We utilized CRISPR/Cas9 genome-editing technology for targeted mutagenesis of three hydrotropism-associated loci (MIZ1-like) in tomato (Solanum lycopersicum). We show that the three tomato MIZ1-like genes are drought-responsive and two of them are hydrostimulation-responsive. Examination of the root hydrotropic response of triple and double mutants indicated the gene SlMIZ1-1 as indispensable for tomato root hydrotropism. Moreover, expression of the SlMIZ1-1 gene in the Arabidopsis miz1 mutant effectively complemented the lost MIZ1 functionality, including root hydrotropic bending and generation of hydrotropic Ca 2+ signals. Transcriptome analysis of hydrostimulated tomato root tips under control gravity and continuous clinorotation conditions was performed to identify gravitropism- and hydrotropism-responsive genes. This analysis suggested the involvement of ethylene and ABA signalling in modulating the interplay between hydrotropism and gravitropism. Unveiling the molecular mechanisms that underlie hydrotropism and drought response holds great potential for improving crop performance under limiting water availability due to global climate changes., (© 2024 The Author(s). Plant, Cell & Environment published by John Wiley & Sons Ltd.)
Published: 2024
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45. A strategy for identification and characterization of genic mutations using a temperature-sensitive chlorotic soybean mutant as an example.

Author: Hancock CN, Germany T, Redd P, Timmons J, Lipford J, Burns S, Cervantes-Perez SA, Libault M, Shen W, An YC, Kanizay L, Yerka M, and Parrott WA
Abstract: Screening a transposon-mutagenized soybean population led to the discovery of a recessively inherited chlorotic phenotype. This "y24" phenotype results in smaller stature, weaker stems, and a smaller root system. Genome sequencing identified 15 candidate genes with mutations likely to result in a loss of function. Amplicon sequencing of a segregating population was then used to narrow the list to a single candidate mutation, a single-base change in Glyma.07G102300 that disrupts splicing of the second intron. Single cell transcriptomic profiling indicates that this gene is expressed primarily in mesophyll cells, and RNA sequencing data indicate that it is upregulated in germinating seedlings by cold stress. Previous studies have shown that mutations to Os05g34040 , the rice ortholog of Glyma.07G102300 , produced a chlorotic phenotype that was more pronounced in cool temperatures. Growing soybean y24 mutants at lower temperatures also resulted in a more severe phenotype. In addition, transgenic expression of wild-type Glyma.07G102300 in the knockout mutant of the Arabidopsis ortholog At4930720 rescues the chlorotic phenotype, further supporting the hypothesis that the mutation in Glyma.07G102300 is causal of the y24 phenotype. The variant analysis strategy used to identify the genes underlying this phenotype provides a template for the study of other soybean mutants., Competing Interests: The authors have no conflict of interest to declare., (© 2024 The Author(s). Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley & Sons Ltd.)
Published: 2024
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46. Related type 2C protein phosphatases Pic3 and Pic12 negatively regulate immunity in tomato to Pseudomonas syringae.

Author: Xia F, Zhang N, Smith RE, Chakraborty J, Sobol G, Tang X, Fei Z, Sessa G, and Martin GB
Subjects: Gene Expression Regulation, Plant, Protein Phosphatase 2C genetics, Protein Phosphatase 2C metabolism, Nicotiana genetics, Nicotiana microbiology, Nicotiana immunology, Mutation genetics, Plant Leaves microbiology, Plant Leaves genetics, Plant Leaves immunology, Disease Resistance genetics, Pseudomonas syringae pathogenicity, Pseudomonas syringae physiology, Solanum lycopersicum microbiology, Solanum lycopersicum genetics, Solanum lycopersicum immunology, Plant Immunity genetics, Plant Diseases microbiology, Plant Diseases immunology, Plant Diseases genetics, Plant Proteins genetics, Plant Proteins metabolism
Abstract: Type 2C protein phosphatases (PP2Cs) constitute a large family in most plant species, but relatively few of them have been implicated in immunity. To identify and characterize PP2C phosphatases that affect tomato (Solanum lycopersicum) immunity, we generated loss-of-function mutations in 11 PP2C-encoding genes whose expression is altered in response to immune elicitors or pathogens. We report that 2 closely related PP2C phosphatases, PP2C immunity-associated candidate 3 (Pic3) and Pic12, are involved in regulating resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Loss-of-function mutations in Pic3 led to enhanced resistance to Pst in older but not younger leaves, whereas such mutations in Pic12 resulted in enhanced resistance in both older and younger leaves. Overexpression of Pic3 and Pic12 proteins in leaves of Nicotiana benthamiana inhibited resistance to Pst, and this effect was dependent on Pic3/12 phosphatase activity and an N-terminal palmitoylation motif associated with localization to the cell periphery. Pic3, but not Pic12, had a slight negative effect on flagellin-associated reactive oxygen species generation, although their involvement in the response to Pst appeared independent of flagellin. RNA-sequencing analysis of Rio Grande (RG)-PtoR wild-type plants and 2 independent RG-pic3 mutants revealed that the enhanced disease resistance in RG-pic3 older leaves is associated with increased transcript abundance of multiple defense-related genes. RG-pic3/RG-pic12 double-mutant plants exhibited stronger disease resistance than RG-pic3 or RG-pic12 single mutants. Together, our results reveal that Pic3 and Pic12 negatively regulate tomato immunity in an additive manner through flagellin-independent pathways., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)
Published: 2024
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47. Turning the page on front matter: Wishing Nan Eckardt a joyful retirement.

Author: Quatrano RS, Jorgensen RA, Martin C, Merchant SS, and Meyers BC
Abstract: Competing Interests: Conflict of interest statement. None declared.
Published: 2024
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48. In silico analysis of R2R3-MYB transcription factors in the basal eudicot model, Aquilegia coerulea .

Author: Phukela B, Leonard H, and Sapir Y
Abstract: R2R3-MYBs are an important group of transcription factors that regulate crucial developmental processes across the plant kingdom; yet no comprehensive analysis of the R2R3-MYBs in the early-diverging eudicot clade of Ranunculaceae has been conducted so far. In the present study, Aquilegia coerulea is chosen to understand the extent of conservation and divergence of R2R3-MYBs as a representative of the family by analysing the genomic distribution, organization, gene structure, physiochemical properties, protein architecture, evolution and possible mode of expansion. Genome-wide analysis showed the presence of 82 putative homologues classified into 21 subgroups, based on phylogenetic analysis of full-length protein sequences. The domain has remained largely conserved across all homologues with few differences from the characterized Arabidopsis thaliana R2R3-MYBs. The topology of the phylogenetic tree remains the same when full-length protein sequences are used, indicating that the evolution of R2R3-MYBs is driven by the domain region only. This is supported by the presence of similar structures of exon-intron and conserved motifs within the same subgroup. Furthermore, comparisons of the AqcoeR2R3-MYB members with monocots and core-eudicots revealed the evolutionary expansion of a few functional clades, such as A. thaliana R2R3-MYB subgroup 6 (SG6), the upstream regulatory factors of floral pigment biosynthesis and floral color. The reconstructed evolutionary history of SG6-like genes across angiosperms highlights the occurrence of independent duplication events in the genus Aquilegia . AqcoeR2R3-MYB genes are present in all seven chromosomes of A. coerulea , most of which result from local and segmental duplications. Selection analysis of these duplicated gene pairs indicates purifying selection except one, and the physiochemical analyses of R2R3-MYBs reveal differences among the MYBs signifying their functional diversification. This study paves the way for further investigation of paralogous copies and their probable role in the evolution of different floral traits in A. coerulea . It lays the foundation for functional genomic studies of R2R3-MYBs in the basal eudicots and facilitates comparative studies among angiosperms. The work also provides a framework for deciphering novel genetic regulatory pathways that govern the diversity of floral morphology., Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-04119-y., Competing Interests: Conflict of interestThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© The Author(s) 2024.)
Published: 2024
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49. Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean.

Author: Espina MJC, Lovell JT, Jenkins J, Shu S, Sreedasyam A, Jordan BD, Webber J, Boston L, Brůna T, Talag J, Goodstein D, Grimwood J, Stacey G, Cannon SB, Lorenz AJ, Schmutz J, and Stupar RM
Subjects: Chromosome Mapping, Molecular Sequence Annotation, Glycine max genetics, Genome, Plant genetics, Haplotypes, Chromosomes, Plant genetics
Abstract: Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48 387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (>20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the 'Williams' haplotype while the other two near-gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of 'Fiskeby III,' a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community., (© 2024 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)
Published: 2024
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50. Slow release of a synthetic auxin induces formation of adventitious roots in recalcitrant woody plants.

Author: Roth O, Yechezkel S, Serero O, Eliyahu A, Vints I, Tzeela P, Carignano A, Janacek DP, Peters V, Kessel A, Dwivedi V, Carmeli-Weissberg M, Shaya F, Faigenboim-Doron A, Ung KL, Pedersen BP, Riov J, Klavins E, Dawid C, Hammes UZ, Ben-Tal N, Napier R, Sadot E, and Weinstain R
Subjects: Eucalyptus growth & development, Eucalyptus drug effects, Eucalyptus metabolism, Plant Growth Regulators metabolism, Plant Growth Regulators pharmacology, Wood growth & development, Indoleacetic Acids metabolism, Plant Roots growth & development, Plant Roots metabolism, Plant Roots drug effects
Abstract: Clonal propagation of plants by induction of adventitious roots (ARs) from stem cuttings is a requisite step in breeding programs. A major barrier exists for propagating valuable plants that naturally have low capacity to form ARs. Due to the central role of auxin in organogenesis, indole-3-butyric acid is often used as part of commercial rooting mixtures, yet many recalcitrant plants do not form ARs in response to this treatment. Here we describe the synthesis and screening of a focused library of synthetic auxin conjugates in Eucalyptus grandis cuttings and identify 4-chlorophenoxyacetic acid-L-tryptophan-OMe as a competent enhancer of adventitious rooting in a number of recalcitrant woody plants, including apple and argan. Comprehensive metabolic and functional analyses reveal that this activity is engendered by prolonged auxin signaling due to initial fast uptake and slow release and clearance of the free auxin 4-chlorophenoxyacetic acid. This work highlights the utility of a slow-release strategy for bioactive compounds for more effective plant growth regulation., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Published: 2024
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