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1,988 results on '"Institute of Experimental Botany"'

1. The regulation of intrinsic signaling in Brassica napus defending against Leptosphaeria maculans

Author: Stasolla, Claudio (Plant Science), Li, Genyi (Plant Science), Belmonte, Mark (Biological Sciences), Burkertová, Lenka (Institute of Experimental Botany of the Czech Academy of Sciences), Fernando, W. G. Dilantha (Plant Science), Yang, Cunchun, Stasolla, Claudio (Plant Science), Li, Genyi (Plant Science), Belmonte, Mark (Biological Sciences), Burkertová, Lenka (Institute of Experimental Botany of the Czech Academy of Sciences), Fernando, W. G. Dilantha (Plant Science), and Yang, Cunchun
Abstract: Plants are able to trigger multiple signaling pathways to cope with pathogenic invasion. Hypersensitive response (HR), one of the effective mechanisms, is triggered by the interaction between pathogenic Avr effectors from the pathogen and plant R proteins (also known as gene-for-gene interaction). Plant tissues induce distinct activities when they have, or have no HR, and those differences may help scientists to find out the crucial factors in efficient defense against plant pathogens. The general objective of this Ph.D. thesis is based on that background and applied on the studies of Brassica napus – Leptosphaeria maculans pathosystem. Three cultivars of B. napus (Westar, Surpass400 and 01-23-2-1) were inoculated by two L. maculans isolates (HCRT75 8-1 and HCRT77 7-2) to cause three distinct levels of severity: susceptible, intermediate and resistant. Expression studies (by RT-qPCR), histochemical assays (such as trypan blue staining) were applied on the cotyledons of those cultivars to search the differences in defense response from those cultivars (with distinct severities). Histochemical assays transcriptional analysis suggested that the intermediate and resistant genotypes (i.e. Surpass400 and 01-23-2-1) displayed earlier H2O2 accumulation and cell death on the cotyledons. and activation of the genes related to salicylic acid (SA) and ROS (as early as 3 and 5 dpi). The results indicated that the early activation of SA/ROS signaling is one of the crucial components for B. napus to defend against L. maculans. Environmental factors are essential components for plant growth/development; therefore, it is reasonable that the environmental changes are able to alter the actions in plant defense. The third part of this study was to explore the association between temperature and HR resistance. Lesion measurements suggested that high incubation temperature resulted in larger lesion size. RT – qPCR results reflected the distinct expression levels of putative temperature –
Published: 2021

2. Diphenylurea-derived cytokinin oxidase/dehydrogenase inhibitors for biotechnology and agriculture

Author: Zdeněk Wimmer, David Zalabák, Nino Murvanidze, Pierre Briozzo, David Kopečný, Martina Kopečná, Stefaan Werbrouck, Solange Moréra, Jaroslav Nisler, Zuzana Pěkná, Radoslav Koprna, Nuria De Diego, Miroslav Strnad, Radka Končitíková, Libor Havlíček, Lukáš Spíchal, University of Chemistry and Technology Prague (UCT Prague), Palacky University Olomouc, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Faculty of Bioscience Engineering [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT), Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Universiteit Gent = Ghent University (UGENT), Grant Agency of the Czech Republic 18-07563S, ERDF from the Ministry of Education, Youth and Sports, Czech Republic CZ.02.1.01/0.0/0.0/16_019/000 0827CZ.02.2.69/0.0/0.0/16_027/0008482, Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Faculty of Science, Department of Biochemistry, Grant Agency of the Czech Republic18-07563S, ERDF from the Ministry of Education, Youth and Sports, Czech RepublicCZ.02.1.01/0.0/0.0/16_019/000 0827, and CZ.02.2.69/0.0/0.0/16_027/0008482
Subjects: 0106 biological sciences, BIOCHEMICAL-CHARACTERIZATION, Cytokinins, Rapeseed, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Dehydrogenase, Plant Science, THIDIAZURON, 01 natural sciences, CKX inhibitor, stress, chemistry.chemical_compound, Arabidopsis thaliana, ZEA-MAYS, 2. Zero hunger, 0303 health sciences, Oxidase test, biology, Chemistry, food and beverages, Agriculture, Cytokinin, Plant hormone, Oxidoreductases, biotechnology, EXPRESSION, crystal structure, Plant tissue culture, OXIDASE, cytokinin, 03 medical and health sciences, DEHYDROGENASE, 030304 developmental biology, diphenylurea, PURIFICATION, business.industry, fungi, Biology and Life Sciences, yield, biology.organism_classification, Biotechnology, ARABIDOPSIS-THALIANA, plant tissue culture, business, SEED YIELD, MAIZE, cytokinin oxidase/dehydrogenase, 010606 plant biology & botany
Abstract: Increasing crop productivity is our major challenge if we are to meet global needs for food, fodder and fuel. Controlling the content of the plant hormone cytokinin is a method of improving plant productivity. Cytokinin oxidase/dehydrogenase (CKO/CKX) is a major target in this regard because it degrades cytokinins. Here, we describe the synthesis and biological activities of new CKX inhibitors derived mainly from diphenylurea. They were tested on four CKX isoforms from maize and Arabidopsis, where the best compounds showed IC50 values in the 10–8 M concentration range. The binding mode of the most efficient inhibitors was characterized from high-resolution crystal complexed structures. Although these compounds do not possess intrinsic cytokinin activity, we have demonstrated their tremendous potential for use in the plant tissue culture industry as well as in agriculture. We have identified a key substance, compound 19, which not only increases stress resistance and seed yield in Arabidopsis, but also improves the yield of wheat, barley and rapeseed grains under field conditions. Our findings reveal that modulation of cytokinin levels via CKX inhibition can positively affect plant growth, development and yield, and prove that CKX inhibitors can be an attractive target in plant biotechnology and agriculture.
Published: 2020

3. Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

Author: Helena Toegelová, Hana Šimková, Andrew G. Sharpe, Benoit Darrier, Adam M. Dimech, Jan Šafář, Nathan S. Watson-Haigh, Pierre Sourdille, Zeev Frenkel, Matthew J. Hayden, Frédéric Choulet, Johan Nyström-Persson, Iwgsc, Dangqun Cui, Gabriel Keeble-Gagnère, Matthias Pfeifer, Sébastien Boisvert, Angéla Juhász, Jaroslav Doležel, Francisco Câmara, Simone Rochfort, Matthew Tinning, Colin Cavanagh, Kerrie Forrest, Paul Eckermann, Delphine Fleury, Ute Baumann, Aurélien Bernard, Ming-Cheng Luo, B. Emma Huang, Jen Taylor, Rudi Appels, Dal-Hoe Koo, Zhengang Ru, David Konkin, Raj K. Pasam, Philippe Rigault, Michael Abrouk, Don Isdale, Abraham B. Korol, Marc-Alexandre Nolin, Josquin Tibbits, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, GYDLE, Center for Organismal Studies, Heidelberg University, Institute of Evolution, University of Haifa [Haifa], CSIRO Plant Industrie, Desert Agriculture Initiati, King Abdullah University of Science and Technology (KAUST), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Global Institute of Food Security, University of Saskatchewan [Saskatoon] (U of S), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), School of Agriculture, Food and Wine, University of Adelaide, Veterinary and Agriculture, Murdoch University, Plant Genetics and Bioinformatics, Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC)-University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, GYB Akihabara, Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Australian Genome Research Facility, National Research Council of Canada, Henan Agricultural University, Australian Government Department of Industry, Innovation, Science, Research and Tertiary Education ACSRF00542, BioPlatforms Australia (BPA), Grains Research Development Corporation UMU00037, CSIRO Plant Industry, Australia, Agriculture Victoria Research, National Science Foundation (NSF) grant 1338897, INB ('Instituto National de Bioinformatica') Project (ISCIII - FEDER) PT13/0001/0021, Czech Ministry of Education Youth and Sports (National Program of Sustainability) LO1204, University of Saskatchewan, UC Davis Plant Sciences, University of Heidelberg, Institute of Experimental Botany (IEB), Czech Academy of Sciences [Prague] (ASCR), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Universitat Pompeu Fabra [Barcelona], and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: 0106 biological sciences, 0301 basic medicine, Chromosomes, Artificial, Bacterial, Optical Phenomena, 01 natural sciences, Genome, Megabase-scale integration, 570 Life sciences, wheat, chromosome, lcsh:QH301-705.5, Paired-end tag, Triticum, 2. Zero hunger, 0303 health sciences, Vegetal Biology, Physical Chromosome Mapping, Agriculture, Wheat Sequence Finishing, Megabase-scale Integration, Optical/physical Maps Grain Quality, Yield, restriction map, Seeds, Wheat sequence finishing, Genome, Plant, carte physique, lcsh:QH426-470, Centromere, Genomics, Computational biology, Biology, Chromosomes, Plant, DNA sequencing, 03 medical and health sciences, blé, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Optical/physical maps Grain quality, 030304 developmental biology, Whole genome sequencing, Bacterial artificial chromosome, génome, Research, Chromosome, Fructans, lcsh:Genetics, 030104 developmental biology, lcsh:Biology (General), Human genome, Biologie végétale, 010606 plant biology & botany, Reference genome
Abstract: GK-G, PR, JT contributed equally to experimental design, data analysis andinterpretation/writing of manuscript;, RP, MH, KF, RA genome analyses andinterpretation; ZF, AK data analysis and physical map construction; EH, CC, JTMAGIC map construction; MA rice-wheat phylogenomic; AS, DK, mate-pairlibraries; PS. BD, FC, PL, Chinese Spring x Renan molecular genetic map andannotation of genome sequence; NW-H, UB, PE, DF, AJ analysis of genespace and QTL, SB, M-AN, development of Bionano alignments and tools; JD,HŠ, JŠ, HT, flow sorting of chromosomes, BAC library construction andBionano maps; M-CL fingerprinting of BAC library; FC, MP gene annotation;DC, ZR, AK58 genome assembly, JN-P, genome assembly; DI in-housesoftware development; IWGSC, genome assembly network, D-HK, CENH3antibody cytology; RA, planning of experiments and writing of manuscript.All authors have read and approved the final manuscript.; Background: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.Results: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.Conclusions: Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
Published: 2018

4. Recognition of Elicitors in Grapevine: From MAMP and DAMP Perception to Induced Resistance

Author: Marie-Claire Héloir, Marielle Adrian, Daphnée Brulé, Justine Claverie, Sylvain Cordelier, Xavier Daire, Stéphan Dorey, Adrien Gauthier, Christelle Lemaître-Guillier, Jonathan Negrel, Lucie Trdá, Sophie Trouvelot, Elodie Vandelle, Benoit Poinssot, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Résistance Induite et Bioprotection des Plantes - EA 4707 (RIBP), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche Vigne et Vins de Champagne Stress et Environnement - EA 4707 (URVVC), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie (PMEBBCE), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Institute of Experimental Botany ASCR, Poinssot, Benoît, Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), ANRFrench National Research Agency (ANR), FederEuropean Union (EU), Regional Council of Bourgogne Franche-ComteRegion Bourgogne-Franche-Comte, Bureau Interprofessionnel des Vins de Bourgogne, and MESRI (Ministere de l'Enseignement Superieur, de la Recherche et de l'Innovation)
Subjects: 0106 biological sciences, 0301 basic medicine, Damp, Vitis vinifera, innate immunity, defense responses, Pattern Recognition Receptor (PRR), MicrobeAssociated Molecular Pattern (MAMP), Damage-Associated Molecular Pattern (DAMP), Induced Resistance (IR), [SDV]Life Sciences [q-bio], MicrobeAssociated Molecular Pattern (MAMP), Context (language use), Plant Science, Review, Biology, lcsh:Plant culture, 01 natural sciences, Cell wall, 03 medical and health sciences, Microbe-Associated Molecular Pattern (MAMP), Plant defense against herbivory, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, MAMP, innate immunity, Damage-Associated Molecular Pattern (DAMP), ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Innate immune system, fungi, defense responses, induced resistance (IR), damage-associated molecular pattern (damp), microbe-associated molecular pattern (mamp), pattern recognition receptor (prr), vitis vinifera, Pattern recognition receptor, food and beverages, Induced Resistance (IR), Elicitor, Cell biology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 030104 developmental biology, Vitis vinifera, Pattern Recognition Receptor (PRR), 010606 plant biology & botany
Abstract: International audience; In a context of a sustainable viticulture, the implementation of innovative eco-friendly strategies, such as elicitor-triggered immunity, requires a deep knowledge of the molecular mechanisms underlying grapevine defense activation, from pathogen perception to resistance induction. During plant-pathogen interaction, the first step of plant defense activation is ensured by the recognition of microbe-associated molecular patterns, which are elicitors directly derived from pathogenic or beneficial microbes. Vitis vinifera, like other plants, can perceive elicitors of different nature, including proteins, amphiphilic glycolipid, and lipopeptide molecules as well as polysaccharides, thanks to their cognate pattern recognition receptors, the discovery of which recently began in this plant species. Furthermore, damage-associated molecular patterns are another class of elicitors perceived by V. vinifera as an invader's hallmark. They are mainly polysaccharides derived from the plant cell wall and are generally released through the activity of cell wall-degrading enzymes secreted by microbes. Elicitor perception and subsequent activation of grapevine immunity end in some cases in efficient grapevine resistance against pathogens. Using complementary approaches, several molecular markers have been identified as hallmarks of this induced resistance stage. This review thus focuses on the recognition of elicitors by Vitis vinifera describing the molecular mechanisms triggered from the elicitor perception to the activation of immune responses. Finally, we discuss the fact that the link between elicitation and induced resistance is not so obvious and that the formulation of resistance inducers remains a key step before their application in vineyards.
Published: 2019

5. The genome of cowpea ( Vigna unguiculata [L.] Walp.)

Author: Samuel Hokin, Steven B. Cannon, Tingting Zhu, Jansen R. P. Santos, Sassoum Lo, Jerome Verdier, María Muñoz-Amatriaín, Shengqiang Shu, Qihua Liang, Timothy J. Close, Abid Hasan, Arsenio Ndeve, Steve Wanamaker, Jaroslav Doležel, Hind Alhakami, Andrew Farmer, Alan H. Schulman, Philip A. Roberts, Stefano Lonardi, Jan Vrána, Jaakko Tanskanen, Rachid Ounit, Ming-Cheng Luo, Department of Engineering Science [Oxford], Institute of Biomedical Engineering [Oxford] (IBME), University of Oxford [Oxford]-University of Oxford [Oxford], Laboratoire Matériaux et Durabilité des constructions (LMDC), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre of the Region Haná for Biotechnical and Agricultural Research, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), University of California [Riverside] (UCR), University of California, United States Department of Energy, Natural Resources Institute Finland (LUKE), University of California [Davis] (UC Davis), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), National center for genome resources (NCGR), USDA-ARS : Agricultural Research Service, NSF IOS-1543963 ('Advancing the Cowpea Genome for Food Security'), NSF IIS-1526742('Algorithms for Genome Assembly of Ultra-Deep Sequencing Data') and NSF IIS-1814359 ('Improving de novoGenome Assembly using Optical Maps'). Estimation of the genome size was supported by the Czech Ministry of Education, Youth and Sports (award LO1204 from the National Program of Sustainability I). The analysis of gene families was provided through by in-kind contributions from the USDA Agricultural Research Service, project 5030-21000-069-00-D, while the repetitive elements analysis was supported by the Academy of Finland 'Papugeno' (Decision 298314)., Institute of Biotechnology, Viikki Plant Science Centre (ViPS), University of Oxford-University of Oxford, Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, analyse chromosomique, carte génétique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, genome annotation, legumes, Plant Biology, next‐generation sequencing, Vigna unguiculata, chromosomal inversion, cowpea, genome evolution, genome size, next-generation sequencing, Phaseolus vulgaris, repetitive elements, Retrotransposon, Plant Science, ANNOTATION, 01 natural sciences, Genome, Vigna, Genome Size, ComputingMilieux_MISCELLANEOUS, Phaseolus, 2. Zero hunger, Genetics, 0303 health sciences, Vegetal Biology, 1184 Genetics, developmental biology, physiology, Chromosome Mapping, food and beverages, Genome project, Agricultural sciences, ALIGNMENT, virus de la mosaïque du vigna, 1181 Ecology, evolutionary biology, Bio-informatique, Sequence Analysis, Genome, Plant, Biotechnology, Resource, Genome evolution, AFLP, DNA, Plant, Retroelements, Bioinformatics, Plant Biology & Botany, Biotechnologies, NUCLEAR-DNA CONTENT, Biology, Genes, Plant, Synteny, SEQUENCE, Chromosomes, Plant, Chromosomes, analyse de génome, 03 medical and health sciences, domestication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Striga spp, ALGORITHM, Gene, Genome size, 030304 developmental biology, Whole genome sequencing, Peas, Sequence Analysis, DNA, Plant, DNA, Cell Biology, 15. Life on land, biology.organism_classification, EVOLUTION, SIZE, 030104 developmental biology, Genes, MUTANTS, Biochemistry and Cell Biology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Biologie végétale, Sciences agricoles, RESISTANCE, 010606 plant biology & botany
Abstract: Summary Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub‐Saharan Africa, that is resilient to hot and drought‐prone environments. An assembly of the single‐haplotype inbred genome of cowpea IT97K‐499‐35 was developed by exploiting the synergies between single‐molecule real‐time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination‐poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high‐recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS‐LRR and the SAUR‐like auxin superfamilies compared with other warm‐season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented., Significance Statement State‐of‐the‐art technologies and assembly methods were used to generate a reference genome sequence of cowpea, a drought‐resilient crop on which millions of people in sub‐Saharan Africa depend as a source of protein. This sequence facilitated the identification of: repetitive elements and gene families expanded in cowpea compared with other closely related legumes; a large and apparently rare chromosomal inversion; and an interesting candidate gene that is associated with several domestication‐related traits.
Published: 2019

6. Molecular framework for TIR1/AFB-Aux/IAA-dependent auxin sensing controlling adventitious rooting in Arabidopsis

Author: Emilie Cavel, Ondřej Novák, Zahra Raneshan, Rozenn Le Hir, Laurent Gutierrez, François Jobert, Irene Perrone, Salma Chaabouni, Alok Ranjan, Catherine Bellini, László Bakó, Abdellah Lakehal, Daniel Ioan Pacurar, Umea Plant Science Centre, Department of Plant Physiology, Umeå University, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris Saclay (COmUE), Shahid Bahonar University, Partenaires INRAE, Laboratory of Growth Regulators [Univ Palacký] (LGR), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Centre de ressources régionales en biologie moléculaire (CRRBM) (CRRBM), and Université de Picardie Jules Verne (UPJV)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Repressor, adventitious roots, 01 natural sciences, 03 medical and health sciences, Auxin, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, heterocyclic compounds, Jasmonate, Transcription factor, 030304 developmental biology, chemistry.chemical_classification, Regulation of gene expression, 0303 health sciences, biology, AuxIAA, fungi, food and beverages, biology.organism_classification, jasmonate, Cell biology, chemistry, TIR1/AFB, 010606 plant biology & botany
Abstract: In Arabidopsis thaliana, canonical auxin-dependent gene regulation is mediated by 23 transcription factors from the AUXIN RESPONSE FACTOR (ARF) family, most of which interact with 29 auxin/indole acetic acid (Aux/IAA) repressors, themselves forming, in the presence of auxin, coreceptor complexes with one of six TRANSPORT INHIBITOR1/AUXIN-SIGNALLING F-BOX PROTEINS (TIR1/AFB). Different combinations of co-receptors drive specific sensing outputs, allowing auxin to control a myriad of processes. Considerable efforts have been made to discern the temporal and spatial specificity of auxin action. However, owing to a lack of obvious phenotype in single loss-of-function mutants in Aux/IAA genes, most genetic studies have relied on gain-of-function mutants, which are highly pleiotropic. In this article, we describe a molecular framework for the role of several members of the auxin sensing machinery. Using loss-of-function mutants, we demonstrate that TIR1 and AFB2 are positive regulators, whereas IAA6, IAA9 and IAA17 are negative regulators of adventitious root (AR) formation. The three Aux/IAA proteins interact with ARF6 and/or ARF8, which we have previously shown to be positive regulators of AR formation upstream of jasmonate, and likely repress their activity. Our data also suggest a dual role for TIR1 in the control of JA biosynthesis and conjugation, as revealed by upregulation of several JA biosynthesis genes in the tir1-1 mutant. In conclusion, we propose that in the presence of auxin, TIR1 and AFB2 form specific sensing complexes with IAA6, IAA9 and/or IAA17 that modulate JA homeostasis to control AR initiation.
Published: 2019
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7. Transient Gene Expression as a Tool to Monitor and Manipulate the Levels of Acidic Phospholipids in Plant Cells

Author: Juraj Sekereš, Přemysl Pejchar, Martin Potocký, Lise C. Noack, Yvon Jaillais, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS 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), Institute of Experimental Botany, Czech Academy of Sciences [Prague] (ASCR), Charles University [Prague], Fatima Cvrčková, Viktor Žárský, 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 of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Charles University [Prague] (CU), and École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0106 biological sciences, 0301 basic medicine, Cell, phospholipid-binding domains, 01 natural sciences, transient expression, 03 medical and health sciences, chemistry.chemical_compound, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Nicotiana benthamiana, Phosphatidylinositol, Microscopy, Nicotiana tabacum, Peripheral membrane protein, Phosphatidic acid, Phosphatidylserine, phosphoinositides, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Plant cell, pollen tube, Cell biology, 030104 developmental biology, Membrane, medicine.anatomical_structure, chemistry, Second messenger system, lipids (amino acids, peptides, and proteins), 010606 plant biology & botany
Abstract: International audience; Anionic phospholipids represent only minor fraction of cell membranes lipids but they are critically important for many membrane-related processes, including membrane identity, charge, shape, the generation of second messengers and the recruitment of peripheral proteins. The main anionic phospholipids of the plasma membrane are phosphoinositides phosphatidylinositol 4-phosphate (PI4P), phosphatidylinositol 4,5-bisphosphate (PI4,5P 2), phosphatidylserine (PS), and phosphatidic acid (PA). Recent insights in the understanding of the nature of protein-phospholipid interactions enabled the design of genetically-encoded fluorescent molecular probes that can interact with various phospholipids in a specific manner allowing their imaging in live cells. Here, we describe the use of transiently transformed plant cells to study phospholipid-dependent membrane recruitment.
Published: 2019

8. Interplay between phosphoinositides and actin cytoskeleton in the regulation of immunity related responses in Arabidopsis thaliana seedlings

Author: Oksana Iakovenko, Daniela Kocourková, Hana Leontovyčová, Eric Ruelland, Jan Martinec, Pavel Klouček, Petr Marsik, Martin Janda, Romana Pospíchalová, Tetiana Kalachova, Olga Valentová, Lenka Burketová, Institute of Experimental Botany, Czech Academy of Sciences [Prague] (ASCR), Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Czech University of Life Sciences Prague, University of Chemistry and Technology Prague (UCT Prague), Charles University [Prague], Ludwig-Maximilians-Universität München (LMU), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Czech University of Life Sciences Prague (CZU), and Charles University [Prague] (CU)
Subjects: 0106 biological sciences, 0301 basic medicine, Cytochalasin E, salicylic acid, Mutant, latrunculin B, Plant Science, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Arabidopsis thaliana, Phosphatidylinositol, phosphatidylinositol-4-kinase, Ecology, Evolution, Behavior and Systematics, Actin, biology, Callose, Wild type, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Actin cytoskeleton, biology.organism_classification, Cell biology, 030104 developmental biology, chemistry, Agronomy and Crop Science, 010606 plant biology & botany, callose
Abstract: International audience; Actin cytoskeleton is indispensable for plant cell integrity. Besides, increasing evidences illustrate its crucial role in plant responses to environment, including defence against pathogens. Recently, we have demonstrated that pre-treatment with actin disrupting drugs latrunculin B (latB) and cytochalasin E can enhance plant resistance against bacterial and fungal pathogens via activation of salicylic acid (SA) pathway. Here, we show that actin depolymerization in Arabidopsis thaliana seedlings not only triggers SA biosynthesis by ICS1, but also induces callose deposition via callose synthase PMR4. This effect is SA-independent since still present in mutants that do not accumulate SA. LatB also triggers the expression of several defence related genes. We could distinguish genes, induced in a SA-dependent manner (PR1, WRKY38, ICS1) and those that are SA-independent (PR2, PAD4, BAP1). As actin cytoskeleton is tightly connected with membrane trafficking, we assayed the effect of latB on mutant plants invalidated in phosphatidylinositol 4-kinase beta1 and beta2 (PI4Kβ1β2). Deficiency in PI4Kβ1β2 enhanced latB-triggered actin filaments depolymerisation. Yet, it did not lead to a stronger callose deposition or SA biosynthesis in response to latB. Surprisingly, introduction of NahG construct or pad4 mutation in pi4kß1ß2 background had much lower effect on SA induction and SA-dependent gene expression changes than in wild type. We can thus conclude that actin disruption itself triggers immune-like responses: there is an induction of SA via PAD4 coupled to ICS1; it leads to the induction of PR1 and WRKY38, and this requires a functional PI4Kβ1β2 to be properly regulated. However, an alternative, SA-independent, pathway also exists that leads to the enhanced expression of PR2 and to callose accumulation.
Published: 2019

9. Accessing a russian wheat aphid resistance gene in bread wheat by long-read technologies

Author: Nora L. V. Lapitan, Petr Novák, Kateřina Holušová, Helena Toegelová, David Kopecký, Zuzana Tulpová, Jaroslav Doležel, Frank B. Peairs, Mira Mazáčová, Philippe Leroy, Hana Šimková, Jan Vrána, Jiří Macas, Adam J. Lukaszewski, Inst. of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Bureau for Food Security, United States Agency for International Development, Dep. of Bioagricultural Sciences and Pest Management, Colorado State University [Fort Collins] (CSU), Biology Centre, Institute of Plant Molecular Biology [Branišovská] (IPMB / BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Dep. of Botany and Plant Sciences, Univ. of California, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Grant Agency of the Czech Republic P501/12/2554, Czech Ministry of Education, Youth and Sports (National Program of Sustainability I) LO1204, Czech Academy of Sciences RVO60077344, Centre of the Region Hana for Biotechnological and Agricultural Research, Colorado State Univ., Czech Academy of Sciences, Institute of Plant Molecular Biology, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Palacky University Olomouc-Palacky University Olomouc, and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Plant Biology, Plant Science, 01 natural sciences, Genome, Triticum, Disease Resistance, 2. Zero hunger, Genetics, biology, Chromosome Mapping, food and beverages, gène de résistance, puceron russe du blé, HIV/AIDS, Russian wheat aphid, Functional genomics, Sequence Analysis, Biotechnology, Genetic Markers, Crop and Pasture Production, DNA, Plant, lcsh:QH426-470, Locus (genetics), Genomics, lcsh:Plant culture, Genes, Plant, DNA sequencing, Chromosomes, Plant, Chromosomes, 03 medical and health sciences, Gene mapping, resistance gene, Animals, lcsh:SB1-1110, Plant Diseases, Bacterial artificial chromosome, Sequence Analysis, DNA, Plant, DNA, biology.organism_classification, lcsh:Genetics, 030104 developmental biology, Genes, Aphids, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: This is an open access article distributed under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-ncnd/4.0/)PublicationType:FULL_TEXT;; Russian wheat aphid (RWA) (Diuraphis noxia Kurdjumov) is a serious invasive pest of small-grain cereals and many grass species. An efficient strategy to defy aphid attacks is to identify sources of natural resistance and transfer resistance genes into susceptible crop cultivars. Revealing the genes helps understand plant defense mechanisms and engineer plants with durable resistance to the pest. To date, more than 15 RWA resistance genes have been identified in wheat (Triticum aestivum L.) but none of them has been cloned. Previously, we genetically mapped the RWA resistance gene Dn2401 into an interval of 0.83 cM on the short arm of chromosome 7D and spanned it with five bacterial artificial chromosome (BAC) clones. Here, we used a targeted strategy combining traditional approaches toward gene cloning (genetic mapping and sequencing of BAC clones) with novel technologies, including optical mapping and long-read nanopore sequencing. The latter, with reads spanning the entire length of a BAC insert, enabled us to assemble the whole region, a task that was not achievable with short reads. Long-read optical mapping validated the DNA sequence in the interval and revealed a difference in the locus organization between resistant and susceptible genotypes. The complete and accurate sequence of the Dn2401 region facilitated the identification of new markers and precise annotation of the interval, revealing six high-confidence genes. Identification of Epoxide hydrolase 2 as the most likely Dn2401 candidate opens an avenue for its validation through functional genomics approaches.
Published: 2019

10. Cytokinins Are Initial Targets of Light in the Control of Bud Outgrowth

Author: Soulaiman Sakr, Tiffanie Girault, Ondřej Novák, Thomas Péron, Alain Vian, Aleš Pěnčík, Nathalie Leduc, François Barbier, Hanaé Roman, Jérémy Lothier, José Le Gourrierec, Nathalie Brouard, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, School Biology Science, Royal Holloway [University of London] (RHUL), Queensland Alliance Agr & Food Innovat, University of Queensland [Brisbane], Laboratory of Growth Regulators, Palacky University and Institute of Experimental Botany ASCR, Department of Chemical Biology and Genetics, Palacky University, Institute of Experimental Botany, Centre of the Region Hana' for Biotechnological and Agricultural Research, Angers Loire Metropole France, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratory of Growth Regulators [Univ Palacký] (LGR), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Palacky University Olomouc, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: 0106 biological sciences, 0301 basic medicine, Cell division, Physiology, [SDV]Life Sciences [q-bio], lateral buds, Strigolactone, arabidopsis-thaliana, Plant Science, Biology, 01 natural sciences, apical dominance, 03 medical and health sciences, Auxin, Genetics, Psychological repression, meristem activity, chemistry.chemical_classification, Regulation of gene expression, cell-cycle regulation, oryza-sativa l, plant-responses, rosa sp, Meristem, pea axillary buds, Cell biology, 030104 developmental biology, chemistry, Biochemistry, Darkness, Signal transduction, acts downstream, 010606 plant biology & botany
Abstract: Bud outgrowth is controlled by environmental and endogenous factors. Through the use of the photosynthesis inhibitor norflurazon and of masking experiments, evidence is given here that light acts mainly as a morphogenic signal in the triggering of bud outgrowth and that initial steps in the light signaling pathway involve cytokinins (CKs). Indeed, in rose (Rosa hybrida), inhibition of bud outgrowth by darkness is suppressed solely by the application of CKs. In contrast, application of sugars has a limited effect. Exposure of plants to white light (WL) induces a rapid (after 3-6 h of WL exposure) up-regulation of CK synthesis (RhIPT3 and RhIPT5), of CK activation (RhLOG8), and of CK putative transporter RhPUP5 genes and to the repression of the CK degradation RhCKX1 gene in the node. This leads to the accumulation of CKs in the node within 6 h and in the bud at 24 h and to the triggering of bud outgrowth. Molecular analysis of genes involved in major mechanisms of bud outgrowth (strigolactone signaling [RwMAX2], metabolism and transport of auxin [RhPIN1, RhYUC1, and RhTAR1], regulation of sugar sink strength [RhVI, RhSUSY, RhSUC2, and RhSWEET10], and cell division and expansion [RhEXP and RhPCNA]) reveal that, when supplied in darkness, CKs up-regulate their expression as rapidly and as intensely as WL. Additionally, up-regulation of CKs by WL promotes xylem flux toward the bud, as evidenced by Methylene Blue accumulation in the bud after CK treatment in the dark. Altogether, these results suggest that CKs are initial components of the light signaling pathway that controls the initiation of bud outgrowth.
Published: 2016

11. Genomic imprinting mediates dosage compensation in a young plant XY system.: An article peer-reviewed and recommended by Peer Community In Evolutionary Biology (PCI Evol Biol)

Author: Nicklaus Zemp, Raquel Tavares, Radim Cegan, Jan Vrána, Aline Muyle, Franck Picard, Alex Widmer, Roman Hobza, Cécile Fruchard, Gabriel A. B. Marais, Clothilde Deschamps, Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Genetic Diversity Center [ETH Zurich] (GDC), Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)-Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Institute of Biophysics of the Czech Academy of Sciences, Brno, Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany of the ASCR, Pôle Rhône-Alpin de BioInformatique [Lyon] (PRABI), Université de Lyon-Université de Lyon, Statistique en grande dimension pour la génomique, Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS 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), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institute of Genomics and Integrative Biology, Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS), Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Institute of Integrative Biology (IBZ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], and École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Plant Science, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Chromosomes, Plant, X-inactivation, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Genomic Imprinting, 03 medical and health sciences, Downregulation and upregulation, Gene Expression Regulation, Plant, Dosage Compensation, Genetic, Silene latifolia, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Imprinting (psychology), Silene, Animal species, Gene, X chromosome, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Sex Chromosomes, Dosage compensation, Autosome, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], XY sex-determination system, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 030104 developmental biology, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genomic imprinting, 010606 plant biology & botany
Abstract: This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100044).Sex chromosomes have repeatedly evolved from a pair of autosomes1. Consequently, X and Y chromosomes initially have similar gene content, but ongoing Y degeneration leads to reduced Y gene expression and eventual Y gene loss. The resulting imbalance in gene expression between Y genes and the rest of the genome is expected to reduce male fitness, especially when protein networks have components from both autosomes and sex chromosomes. A diverse set of dosage compensating mechanisms that alleviates these negative effects has been described in animals2–4. However, the early steps in the evolution of dosage compensation remain unknown and dosage compensation is poorly understood in plants5. Here we show a novel dosage compensation mechanism in the evolutionarily young XY sex determination system of the plant Silene latifolia. Genomic imprinting results in higher expression from the maternal X chromosome in both males and females. This compensates for reduced Y expression in males but results in X overexpression in females and may be detrimental. It could represent a transient early stage in the evolution of dosage compensation. Our finding has striking resemblance to the first stage proposed by Ohno for the evolution of X inactivation in mammals.
Published: 2018

12. Interaction between systemic nitrogen signaling and hormones, in arabidopsis

Author: Ruffel, Sandrine, Poitout, Arthur, Crabos, Amandine, Petřík, Ivan, Novák, Ondrej, Krouk, Gabriel, Lacombe, Benoît, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Hormones, Nutriments et Développement (HoNuDe) (HONUDE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS, Laboratory of Growth Regulators, Faculty of Science of Palacký University, Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc, Faculty of Science [Univ Palacký], Palacky University Olomouc, Laboratory of Growth Regulators [Univ Palacký] (LGR), Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), and Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)
Subjects: système racinaire, cytokinine, [SDV]Life Sciences [q-bio], zéatine, fungi, root systems, food and beverages, glutamate, zeatin, cytokinin, arabidopsis, adaptation au milieu, absorption azotée, absorption de substances nutritives, glutamine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, adaptation to the environment
Abstract: International audience; Rapid adjustment of plant physiology and development to external fluctuations is critical for sessile organism, giving a singular interest to network signaling controlling these mechanisms. Among many adaptation processes, root plasticity is primordial to optimize nutrient acquisition but relies on a complex network integrating local and systemic (root shoot) signaling. Indeed, locally, plants invest resource in soil area where nutrients are available and systemically they adjust nutrient acquisition to the whole plant demand.Our main goal is to decipher systemic signaling underlying the perception of nitrate heterogeneous provision, in Arabidopsis. Using the split-root system, in which physically isolated root systems of the same plant were challenged with different environments, we previously demonstrated that cytokinin biosynthesis constitutes one critical component of root-shoot-root communication. By combining the use of cytokinin mutants with hormone measurements, transcriptomic analysis, nitrate uptake assays, and root growth measurements, we show that root to shoot trans-zeatin (tZ) translocation is likely crucial for long distance signaling controlling rapid sentinel gene regulation and long-term functional acclimation to heterogeneous nitrate supply. Interestingly, shoot transcriptome profiling revealed that glutamate/glutamine metabolism is likely a target of tZ root-to-shoot translocation, prompting an interesting hypothesis regarding shoot-to-root communication. Finally, this study also highlights tZ-independent pathways triggered by variation into nitrogen supply.
Published: 2018

13. Positional cloning of Ph2, a gene impacting homoeologous pairing in polyploid bread wheat Triticum aestivum L

Author: Serra, Heidi, Svacina, Radim, Sourdille, Pierre, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institute of Experimental Botany, Czech Academy of Sciences [Prague] (ASCR), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and ProdInra, Archive Ouverte
Subjects: [SDV] Life Sciences [q-bio], clonage positionnel, blé, wheat, gène, [SDV]Life Sciences [q-bio], digestive, oral, and skin physiology, food and beverages, triticum aestivum, genes
Abstract: Positional cloning of Ph2, a gene impacting homoeologous pairing in polyploid bread wheat Triticum aestivum L.. 5. annual AgreenSkills+ meeting
Published: 2018

14. Root Responses to Heterogeneous Nitrate Availability are Mediated by trans-Zeatin in Arabidopsis Shoots

Author: Ivan Petřík, Benoît Lacombe, Arthur Poitout, Ondrej Novak, Amandine Crabos, Sandrine Ruffel, Gabriel Krouk, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc, Czech Academy of Sciences [Prague] (CAS), Faculty of Science [Univ Palacký], Palacky University Olomouc, Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Hormones, Nutriments et Développement (HoNuDe) (HONUDE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre of the Region Haná for Biotechnological and Agricultural Research, Laboratory of Growth Regulators, Institute of Experimental Botany CAS, Faculty of Science of Palacký University, Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Equipe Hormones, Nutriments et Développement (HoNuDe) ( HONUDE ), and Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro )
Subjects: 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Mutant, 01 natural sciences, Genome, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, adaptation au milieu, absorption azotée, nitrate, Arabidopsis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, adaptation to the environment, 030304 developmental biology, 0303 health sciences, biology, food and beverages, biology.organism_classification, induction de racine, Reverse genetics, Cell biology, arabidopsis, chemistry, Shoot, Cytokinin, Zeatin, 010606 plant biology & botany
Abstract: Plants are subjected to variable nitrogen (N) availability including frequent spatial nitrate (NO3-) heterogeneity in soil. Thus, plants constantly adapt their genome expression and root physiology in order to optimize N acquisition from this heterogeneous source. These adaptations rely on a complex and long-distance root-shoot-root signaling network that is still largely unknown. Here, we used a combination of reverse genetics, transcriptomic analysis, NO3- uptake experiments and hormone profiling under conditions of homogeneous or heterogeneous NO3- availability to characterize the systemic signaling involved. We demonstrate the important role of the trans-zeatin form of cytokinin (CK) in shoots, in particular using a mutant altered for ABCG14-mediated trans-zeatin-translocation from the root to the shoot, in mediating: (i) rapid long distance N-demand signaling and (ii) long term functional adaptations to heterogeneous NO3- supply, including changes in NO3- transport capacity and root growth modifications. We also provide insights into the potential CK-dependent and independent shoot-to-root signals involved in root adaptation to heterogeneous N availability.
Published: 2018

15. Responses to Systemic Nitrogen Signaling in Arabidopsis Roots Involve trans-Zeatin in Shoots

Author: Amandine Crabos, Ondrej Novak, Gabriel Krouk, Ivan Petřík, Sandrine Ruffel, Arthur Poitout, Benoît Lacombe, Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Equipe Hormones, Nutriments et Développement (HoNuDe) ( HONUDE ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS, Laboratory of Growth Regulators, Faculty of Science of Palacký University, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc, Faculty of Science [Univ Palacký], Palacky University Olomouc, Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Hormones, Nutriments et Développement (HoNuDe) (HONUDE), and Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, transport de nitrate, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Mutant, Plant Science, Biology, 01 natural sciences, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, absorption azotée, Arabidopsis, Gene expression, cytokine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Regulation of gene expression, interaction sol racine, fungi, food and beverages, Cell Biology, biology.organism_classification, Cell biology, arabidopsis, croissance racinaire, 030104 developmental biology, chemistry, Cytokinin, Signal transduction, Zeatin, 010606 plant biology & botany
Abstract: Plants face temporal and spatial variation in nitrogen (N) availability. This includes heterogeneity in soil nitrate (NO3-) content. To overcome these constraints, plants modify their gene expression and physiological processes to optimize N acquisition. This plasticity relies on a complex long-distance root-shoot-root signaling network that remains poorly understood. We previously showed that cytokinin (CK) biosynthesis is required to trigger systemic N signaling. Here, we performed split-root experiments and used a combination of CK-related mutant analyses, hormone profiling, transcriptomic analysis, NO3- uptake assays, and root growth measurements to gain insight into systemic N signaling in Arabidopsis thaliana. By comparing wild-type plants and mutants affected in CK biosynthesis and ABCG14-dependent root-to-shoot translocation of CK, we revealed an important role for active trans-Zeatin (tZ) in systemic N signaling. Both rapid sentinel gene regulation and long-term functional acclimation to heterogeneous NO3- supply, including NO3- transport and root growth regulation, are likely mediated by the integration of tZ content in shoots. Furthermore, shoot transcriptome profiling revealed that glutamate/glutamine metabolism is likely a target of tZ root-to-shoot translocation, prompting an interesting hypothesis regarding shoot-to-root communication. Finally, this study highlights tZ-independent pathways regulating gene expression in shoots as well as NO3- uptake activity in response to total N-deprivation.
Published: 2018

16. A Combinatorial Lipid Code Shapes the Electrostatic Landscape of Plant Endomembranes

Author: Thomas Stanislas, Laetitia Fouillen, Alenka Čopič, Mathilde Laetitia Audrey Simon, Patrick Moreau, Lise C. Noack, Matthieu Pierre Platre, Vincent Bayle, Lilly Maneta-Peyret, Laia Armengot, Marie-Cécile Caillaud, Mehdi Doumane, Yvon Jaillais, Martin Potocký, Přemysl Pejchar, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS 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), Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Czech Academy of Sciences [Prague] (ASCR), Institute of Experimental Botany, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Czech Academy of Sciences [Prague] (CAS), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), ERC under FP 3363360-APPL, French Ministry of Higher Education, Czech Science Foundation 17-27477S, ANR-16-CE13-0021,INTERPLAY,Role des phosphoinositides pendant la cytokinèse chez les plantes(2016), and European Project: 615739,EC:FP7:ERC,ERC-2013-CoG,MECHANODEVO(2014)
Subjects: 0301 basic medicine, 0106 biological sciences, [SDV]Life Sciences [q-bio], Endocytic cycle, Static Electricity, Membrane biology, Arabidopsis, Phosphatidic Acids, Phosphatidylserines, Biology, Endocytosis, 01 natural sciences, Plant Roots, General Biochemistry, Genetics and Molecular Biology, Cell membrane, 03 medical and health sciences, chemistry.chemical_compound, Phosphatidylinositol Phosphates, Static electricity, Organelle, medicine, Compartment (development), Molecular Biology, 030304 developmental biology, Organelles, 0303 health sciences, Arabidopsis Proteins, Cell Membrane, Cell Biology, Phosphatidylserine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Electrostatics, Cytosol, 030104 developmental biology, medicine.anatomical_structure, Membrane, chemistry, Biophysics, Intracellular, Developmental Biology, 010606 plant biology & botany, Signal Transduction
Abstract: Membrane surface charge is critical for the transient, yet specific recruitment of proteins with polybasic regions to certain organelles. In all eukaryotes, the plasma membrane (PM) is the most electronegative compartment of the cell, which specifies its identity. As such, membrane electrostatics is a central parameter in signaling, intracellular trafficking and polarity. Here, we explore which are the lipids that control membrane electrostatics using plants as a model. We show that phosphatidic acidic (PA), phosphatidylserine (PS) and phosphatidylinositol-4-phosphate (PI4P) are separately required to generate the electrostatic signature of the plant PM. In addition, we reveal the existence of an electrostatic territory that is organized as a gradient along the endocytic pathway and is controlled by PS/PI4P combination. Altogether, we propose that combinatorial lipid composition of the cytosolic leaflet of cellular organelles not only defines the plant electrostatic territory but also distinguishes different compartments within this territory by specifying their varying surface charges.
Published: 2018

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

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

18. Physical Map of the Short Arm of Bread Wheat Chromosome 3D

Author: Thomas Letellier, Kateřina Holušová, Federica Cattonaro, Benoit Darrier, Etienne Paux, Hana Šimková, Jaroslav Doležel, Michael Alaux, Jan Šafář, Barbora Balcárková, Jan Bartoš, Hélène Bergès, Jan Vrána, Zeev Frenkel, Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Institute of Evolution, Department of Evolutionary and Environmental Biology, University of Haifa [Haifa], Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Istituto di Genomica Applicata, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Czech Science Foundation 13-08786S, Ministry of Education, Youth and Sports of the Czech Republic (National Program of Sustainability I) LO1204, National Grid Infrastructure MetaCentrum LM2010005, Institute of Experimental Botany, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0301 basic medicine, Chromosomes, Artificial, Bacterial, lcsh:QH426-470, [SDV]Life Sciences [q-bio], Plant Science, Biology, lcsh:Plant culture, 01 natural sciences, Genome, Polymorphism, Single Nucleotide, DNA sequencing, Chromosomes, Plant, Polyploidy, clonage de gènes, 03 medical and health sciences, Genetics, lcsh:SB1-1110, triticum aestivum, Cloning, Molecular, Gene, Triticum, 2. Zero hunger, Bacterial artificial chromosome, Contig, carte chromosomique, séquence génomique, Chromosome, Chromosome Mapping, food and beverages, lcsh:Genetics, 030104 developmental biology, Chromosome Arm, blé panifiable, Agronomy and Crop Science, 010606 plant biology & botany, Reference genome
Abstract: Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning. It comprises 869 contigs with a cumulative length of 274.5 Mbp and represents 85.5% of the estimated chromosome arm size. Eighty-six Mbp of survey sequences from chromosome arm 3DS were assigned in silico to physical map contigs via next-generation sequencing of bacterial artificial chromosome pools, thus providing a high-density framework for physical map ordering along the chromosome arm. About 60% of the physical map was anchored in this single experiment. Finally, 1393 high-confidence genes were anchored to the physical map. Comparisons of gene space of the chromosome arm 3DS with genomes of closely related species [Brachypodium distachyon (L.) P. Beauv., rice (Oryza sativa L.), and sorghum [Sorghum bicolor (L.) Moench] and homeologous wheat chromosomes provided information about gene movement on the chromosome arm.
Published: 2017

19. Development of deletion lines for physical mapping of Ph2 gene in bread wheat

Author: Svacina, Radim, Bartos, Jan, Karafiatova, Miroslava, Sourdille, Pierre, Endo, Takashi R., Dolezel, Jaroslav, Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Institut National de la Recherche Agronomique (INRA), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Faculty of Agriculture, University of Bengkulu, ProdInra, Archive Ouverte, Institute of Experimental Botany ASCR, and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: Proceedings: Book of abstracts, ISBN: 978-3-900932-48-0Poster 35, p. 193; Development of deletion lines for physical mapping of Ph2 gene in bread wheat. 13. Int. Wheat Genet. Symp
Published: 2017

20. Stability of genome composition and recombination between homoeologous chromosomes in Festulolium (Festuca x Lolium) cultivars

Author: Kopecky, David, Simonikova, Denisa, Ghesquière, Marc, Dolezel, Jaroslav, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany ASCR, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de la Recherche Agronomique (INRA), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), and Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)
Subjects: Festuca, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, potentiel de rendement, fungi, food and beverages, genomic in situ hybridization, Lolium x Festuca, Aneuploidy, festulolium, Chromosomes, Plant, grass hybrids, homoeologous recombination, fétuque, Lolium, tolérance au stress abiotique, outbreeding, raygrass, Homologous Recombination, Genome, Plant, composition génomique, genome composition, outcrossing (method)
Abstract: Festulolium are hybrids between fescue (Festuca) and ryegrass (Lolium) species and combine high seed yield of ryegrasses with abiotic stress tolerance of fescues. Chromosomes of Festuca and Lolium present in Festulolium freely pair and recombine, which results in highly variable progeny where every single plant has a unique chromosome constitution. Thus, the stability of the genomic composition in Festulolium cultivars is an important issue. In this work, we used in situ hybridization to examine the genomic composition (understood as the proportion of parental genomes present) over 3 consecutive generations of propagation via outcrossing (the first one being the generation used for cultivar registration) of 3 Festulolium cultivars. Our analysis revealed that the genome composition largely differs among the plants from individual cultivars but appears to be relatively stable over the generations. A gradual shift in the genome composition towards Lolium observed in the early generations of hybrids appears to reach a plateau where the proportions of parental genomes become stabilized. Nevertheless, the pro-portion remains unbalanced to a certain extent ( always in favor of the Lolium genome) in each cultivar. Our observations indicate a possibility to modulate genomic composition in hybrids by breeders' selection without a compromise on stability.
Published: 2017

21. Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes

Author: Catherine Feuillet, Raphael Flores, Tzion Fahima, Marco Maccaferri, Delphine Steinbach, Hadi Quesneville, Silvio Salvi, Umar Masood Quraishi, Jérôme Salse, Jaroslav Doležel, Michael Alaux, Beat Keller, Caroline Pont, Hikmet Budak, Séverine Foucrier, Sébastien Guizard, Florent Murat, Yannick Bidet, University of Zurich, Salse, Jérôme, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Plateforme GINA, Université de Clermont, Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Departement of Evolutionary and Environmental Biology, University of Haifa [Haifa], Faculty of Engineering and Natural Sciences, Sabanci University [Istanbul], Institut de Biologie des Plantes, Universität Zürich [Zürich] = University of Zurich (UZH), DiSTA- Agronomia, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), DiSTA-Agronomia, INRA (Genetique et Amelioration des Plantes' reference: 'Appel d'Offre AIP Bioressources'), Auvergne region (Pole de competitivite: Cereales Vallee reference: programme 'Semences de Demain'), Agence Nationale de la Recherche (Programs ANRjc-PaleoCereal) [ANR-09-JCJC-0058-01], Agence Nationale de la Recherche (programme ANR Blanc-PAGE) [ANR-2011-BSV6-00801], European 7th Framework Programme (programme 'TRITICEAE GENOME') [FP7-212019], Institute of Experimental Botany, Universität Zürich [Zürich] (UZH), Università di Bologna [Bologna] (UNIBO), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Caroline Pont, Florent Murat, Sébastien Guizard, Raphael Flore, Séverine Foucrier, Yannick Bidet, Umar Masood Quraishi, Michael Alaux, Jaroslav Doležel, Tzion Fahima, Hikmet Budak, Beat Keller, Silvio Salvi, Marco Maccaferri, Delphine Steinbach, Catherine Feuillet, Hadi Quesneville, and Jérôme Salse
Subjects: 0106 biological sciences, ble tendre, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Plant Science, 580 Plants (Botany), 01 natural sciences, paléogène, 1307 Cell Biology, 10126 Department of Plant and Microbial Biology, partitioning, 1110 Plant Science, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, Conserved Sequence, Triticum, Genes, Dominant, 2. Zero hunger, Genetics, 0303 health sciences, paleogenomic, conserved orthologous set, food and beverages, Genomics, Gene conservation, gène dominant, Genome, Plant, Recombination, Autre (Sciences du Vivant), Genetic Markers, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], DNA, Plant, SNP, Biotechnologies, Plasticity, Biology, dominance, Models, Biological, Polymorphism, Single Nucleotide, Synteny, Chromosomes, Plant, Evolution, Molecular, Polyploidy, 03 medical and health sciences, 1311 Genetics, COS, Gene, 030304 developmental biology, Single nucleotide polymorphisms, Sequence Analysis, DNA, Cell Biology, paleogenomics, évolution chromosomique, 010606 plant biology & botany
Abstract: édition online; Bread wheat derives from a grass ancestor structured in 7 protochromosomes followed by a paleotetraploidization to reach a 12 chromosomes intermediate and a neohexaploidization (involving subgenomes A, B and D) event that finally shaped the 21 modern chromosomes. Insights into wheat syntenome in sequencing COS (Conserved Orthologous Set) genes unravelled differences in genomic structure (such as gene conservation and diversity) and genetical landscape (such as recombination pattern) between ancestral as well as recent duplicated blocks. Contrasted evolutionary plasticity is observed where the B subgenome appears more sensitive (i.e. plastic) in contrast to A as dominant (i.e. stable) in response to the neotetraploidization and D subgenome as supradominant (i.e. pivotal) in response to the neohexaploidization event. Finally, the wheat syntenome, delivered through a public web interface PlantSyntenyViewer at http://urgi.versailles.inra.fr/synteny-wheat, can be considered as a guide for accelerated dissection of major agronomical traits in wheat. This article is protected by copyright. All rights reserved.
Published: 2013

22. Pea Genomics : What Else ?

Author: Aubert, Gregoire, Madoui, Mohammed-Amin, Kreplak, Jonathan, Tayeh, Nadim, Labadie, Karine, Klein, Anthony, Falque, Matthieu, Batley, Jacqueline, Pichon, Jean-Philippe, Cruaud, Corinne, Le Paslier, Marie-Christine, Leveugle, Magalie, Lichtenzveig, Judith, Edwards, Dave, Warkentin, Tom, Coyne, Clarice, Dolezel, Jaroslav, Wincker, Patrick, Burstin, Judith, Agroécologie [Dijon], Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Institut de Génomique, Génoscope, Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), The Samuel Roberts Noble Foundation, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), School of Plant Biology, The University of Western Australia ( UWA ), Biogemma, Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), Curtin University [Perth], Planning and Transport Research Centre ( PATREC ), Plant Sciences, University of Cambridge [UK] ( CAM ), USDA-ARS, Institute of Experimental Botany ASCR, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, 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), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), The University of Western Australia (UWA), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Planning and Transport Research Centre (PATREC), University of Cambridge [UK] (CAM), USDA-ARS : Agricultural Research Service, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), American Society of Agronomy (ASA). USA., 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, Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), and ProdInra, Archive Ouverte
Subjects: [SDV] Life Sciences [q-bio], [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], food and beverages
Abstract: BAP GEAPSIBAPGEAPSI; Legume use in arable rotations provides several significant ecological services that can help to meet the challenge of delivering high quality food in an environmentally sustainable manner. Among legumes, pea has long been a model species for geneticists. But despite its major role in the discovery of the laws of genetics by Mendel, the keys to decipher the impressive phenotypic diversity of the species have been lacking until recently. Under the impetus of large national and international programs, and driven by innovations in informatics and biotechnology, useful genomic resources are now available in pea. High precision mapping of the pea genome, an atlas of the expression of its genes in many tissues, and the ongoing sequencing of its genome are valuable tools for dissecting the genetic determinism of traits of interest and ultimately select new varieties more effectively for these traits. In order to develop novel pea varieties and optimize seed yield and quality regularity in the context of pesticide reduction and climate change, different complementary approaches are used: (i) develop genomic selection programs based on naturally occurring variability, (ii) enhance gene discovery through comparative mapping, and (iii) create innovative plant architecture ideotypes by screening mutations and symbiotic biological regulations. Thanks to the high conservation of synteny, that is to say, the order of genes on the genome, between peas and other legumes species, knowledge gained on peas will be useful to accelerate progress in the species’ close relatives such as fava beans.
Published: 2016

23. Towards the genome sequence of pea : a tribute to Mendel

Author: Madoui , Mohammed-Amin, Labadie , K., Kreplak , Jonathan, Aubert , Gregoire, d'Agata , Léo, Capal , P., Fournier , Carine, KOUGBEADJO , Ayité, Vrana , J., Gali , K., Taran , B., Belser , C., Le Paslier , Marie-Christine, McGee , Rebecca, Edwards , D., Batley , J., Bendahmane , Abdelhafid, Berges , Helene, Barbe , V., Tayeh , Nadim, Klein , Anthony, Lichtenzveig , Judith, Aury , J-M., Coyne , C.J., Warkentin , T., Dolezel , J., Wincker , P., Burstin , Judith, 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), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan [Saskatoon] (U of S), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Grain Legume Genetics Physiology Research, USDA-ARS : Agricultural Research Service, The University of Western Australia (UWA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), 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), Centre National de Ressources Génomiques Végétales (CNRGV), Molecular Biology, Bioinformatics, Evolutionary Biology, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), Western Region Plant Introduction Station, Legume Society., 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, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institute of Experimental Botany ASCR, 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), 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), Génoscope, Institut de Génomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), University of Saskatchewan [Saskatoon] ( U of S ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), USDA-ARS, University of Western Australia, UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), Centre National de Ressources Génomiques Végétales ( CNRGV ), and Planning and Transport Research Centre ( PATREC ) -Planning and Transport Research Centre ( PATREC )
Subjects: pea, genome, sequence, [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], food and beverages
Abstract: BAP GEAPSI BAP GEAPSIBAPGEAPSI; Pea (Pisum sativum L.) was the original model organism for Mendel´s discovery of the laws of inheritance and kept this model status until the advent of molecular biology at the end of the 20th century. Pea is also one of the world’s oldest domesticated crops. It is currently the third most widely grown pulse crop, as its seeds serve as a protein-rich food for humans and livestock alike. While several legume species genome's draft sequences have been produced, progress in pea genomics has lagged behind largely as a consequence of its complex and large genome size. The pea genome is large (ca 4.45 Gb), probably resulting from recent expansion of retrotransposons followed by sequence diversification. The Pea Genome International Project has undertaken several complementary strategies in order to produce a high-quality draft sequence of the species. We will present how this draft sequence opens the way to renew strategies in pea breeding.
Published: 2016

24. What is the best way to maintain embryogenic capacity of embryogenic lines initiated from Douglas-fir immature embryos?

Author: Florian Gautier, Kateřina Eliášová, Cathie Reeves, Leopoldo Sanchez Rodriguez, Caroline Teyssier, Jean-François Trontin, Claire Le Mette, Martin Vágner, Guy Costa, Catherine Hargreaves, Marie-Anne Lelu-Walter, Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Institut National de la Recherche Agronomique (INRA), Laboratoire de chimie des substances naturelles, Université Cadi Ayyad [Marrakech] (UCA), Institute of Experimental Botany ASCR, Scion, Institut Technologique Forêt Cellulose Bois-Construction Ameublement (FCBA), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), and Institut Technologique Forêt Cellulose Bois-construction Ameublement (FCBA)
Subjects: non-embryogenic cells, multiplication, morphologie, morphology, cytology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, somatic embryogenesis, pseudotsuga menziesii, masse embryonnaire, embryogénèse somatique, cytologie, embryonal masses
Abstract: Douglas-fir (Pseudotsuga menziesii (Mirb) Franco) is a native conifer from the Pacific North-West of the US and Canada, and is one of the most important timber species used in the world. Douglas-fir is highly productive in a range of climatic conditions and has valuable wood properties (quality) as well as a strong tolerance to diseases and insects. In Europe, Douglas-fir is a major species for reforestation with increasing demand for its wood. Adaptation of new varieties to climate change and associated stresses is one challenging question for ongoing breeding programs. Efficient selection and vegetative propagation of improved varieties are key issues to maintain productivity in plantation forestry (Lelu-Walter et al. 2013), however, as in many other conifers, early maturation is preventing clonal forestry through conventional multiplication methods in Douglas-fir (Bastien et al. 2013). Somatic embryogenesis from immature seeds, coupled with cryopreservation, is a promising retroactive clonal propagation system of selected trees. This technology has been developed for an increasing number of conifer species (Klimaszewska et al. 2016). Excluding patents, there are only a few published studies on Douglas-fir somatic embryogenesis (Durzan and Gupta 1987; Pullman et al. 2005, 2009). One recurrent problem is the sustainable multiplication of initiated embryogenic material, i.e., embryonal masses (EMs). Yellowish, non-embryogenic cells (NEC), which are interspersed with EM, is frequently observed during this process. In this work, we describe EM morphology and cytology (light and confocal microscopy) of different embryogenic lines. A suggested method to reduce the formation of NEC and sustain EM proliferation is presented.
Published: 2016

25. Leptosphaeria maculans effector AvrLm4-7 affects SA- and ET-signalling and H2O2 accumulation in Brassica napus

Author: Nováková, Miroslava, Šašek, Vladimír, Trdá, Lucie, Krutinová, Hana, Mongin, Thomas, Valentová, Olga, Balesdent, Marie-Helene, Rouxel, Thierry, Burketová, Lenka, Institute of Experimental Botany ASCR, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Charles University, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Czech Science Foundation (GA13-26798S), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), and Charles University [Prague] (CU)
Subjects: effector, salicylic acid, [SDV]Life Sciences [q-bio], Brassica napus, ethylene, food and beverages, ROS, AvrLm4-7, Leptosphaeria
Abstract: To achieve host colonization, successful pathogens need to overcome plant basal defences. For this, (hemi) biotrophic pathogens secrete effectors that interfere with a range of physiological processes of the host plant. AvrLm4-7 is one of the cloned effectors from the hemibiotrophic fungus Leptosphaeria maculans ‘brassicaceae’ infecting mainly oilseed rape (Brassica napus). Although its mode of action is still unknown, AvrLm4-7 is strongly involved in L. maculans virulence. Here, we investigated the effect of AvrLm4-7 on plant defence responses in a susceptible cultivar of B. napus. Using two isogenic L. maculans isolates differing in the presence of a functional AvrLm4-7 allele [absence (‘a4a7’) and presence (‘A4A7’) of the allele], the plant hormone concentrations, defence-related gene transcription and reactive oxygen species (ROS) accumulation were analysed in infected B. napus cotyledons. Various components of the plant immune system were affected. Infection with the ‘A4A7’ isolate caused suppression of salicylic acid- and ethylene-dependent signalling, the pathways regulating an effective defence against L. maculans infection. Furthermore, ROS accumulation was decreased in cotyledons infected with the ‘A4A7’ isolate. Treatment with an antioxidant agent, ascorbic acid, increased the aggressiveness of the ‘a4a7’ L. maculans isolate, but not that of the ‘A4A7’ isolate. Together, our results suggest that the increased aggressiveness of the ‘A4A7’ L. maculans isolate could be caused by defects in ROSdependent defence and/or linked to suppressed SA and ET signalling. This is the first study to provide insights into the manipulation of B. napus defence responses by an effector of L. maculans.
Published: 2016

26. Artificial selection of rhizosphere microbial communities associated with plant resistance to leaf pathogens

Author: Puga-Freitas, Ruben, Burketová, Lenka, Kalachova, Tetiana, Monard, Cécile, LERCH, Thomas, BLOUIN, Manuel, Ruelland, Eric, Dijon (Kevin Oudard), Institut Agro, Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), 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), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-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), Université de Rennes (UNIV-RENNES)-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), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), 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), Institut d'écologie et des sciences de l'environnement de Paris (IEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Institute of Experimental Botany ASCR, Institute of Experimental Botany of the ASCR, 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), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), 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), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], education, fungi, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, health care economics and organizations
Abstract: International audience; Artificial selection of rhizosphere microbial communities associated with plant resistance to leaf pathogens
Published: 2016

27. Cytokinin metabolism in maize: Novel evidence of cytokinin abundance, interconversions and formation of a new trans-zeatin metabolic product with a weak anticytokinin activity

Author: Filip Kokáš, Jitka Frébortová, Marek Zatloukal, David Kopečný, Petr Galuszka, Dana Tarkowská, Pierre Briozzo, Václav Motyka, David Zalabák, Tomáš Hluska, Petre I. Dobrev, Ondřej Plíhal, Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacky University Olomouc, Laboratory of Hormonal Regulations in Plants [Prague] (EB / CAS), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Department of Metabolomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Czech Science Foundation 16-14649S 14-12355S National Program for Sustainability LO1204, Palacky University, Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, and Czech Academy of Sciences [Prague] (ASCR)
Subjects: 0106 biological sciences, 0301 basic medicine, BIOCHEMICAL-CHARACTERIZATION, Cytokinins, Glycosylation, Metabolite, [SDV]Life Sciences [q-bio], Plant Science, 01 natural sciences, chemistry.chemical_compound, Tissue culture, Plant Growth Regulators, Gene Expression Regulation, Plant, Kernels, Pollination, Plant Proteins, chemistry.chemical_classification, KERNEL DEVELOPMENT, biology, General Medicine, ABSCISIC-ACID, O-GLUCOSYLATION, Biochemistry, Cytokinin, Seeds, Zeatin, Oxidoreductases, ENDOGENOUS CYTOKININS, Zea mays, ATP/ADP ISOPENTENYLTRANSFERASES, 03 medical and health sciences, Biosynthesis, Oxidoreductase, Zea mays L, Glycosyltransferase, Genetics, BIOSYNTHESIS, CIS-ZEATIN, trans-zeatin, Terpenes, Glycosyltransferases, GENE, 030104 developmental biology, Metabolism, chemistry, Seedlings, Anticytokinin, biology.protein, ARABIDOPSIS-THALIANA, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: Cytokinins (CKs) are an important group of phytohormones. Their tightly regulated and balanced levels are essential for proper cell division and plant organ development. Here we report precise quantification of CK metabolites and other phytohormones in maize reproductive organs in the course of pollination and kernel maturation. A novel enzymatic activity dependent on NADP(+) converting trans-zeatin (tZ) to 6-(3-methylpyrrol-1-yl)purine (MPP) was detected. MPP shows weak anticytokinin properties and inhibition of CK dehydrogenases due to their ability to bind to an active site in the opposite orientation than substrates. Although the physiological significance of tZ side-chain cyclization is not anticipated as the MPP occurrence in maize tissue is very low, properties of the novel CK metabolite indicate its potential for utilization in plant in vitro tissue culture. Furthermore, feeding experiments with different isoprenoid CKs revealed distinct preferences in glycosylation of tZ and cis-zeatin (cZ). While tZ is preferentially glucosylated at the N9 position, cZ forms mainly O-glucosides. Since O-glucosides, in contrast to N9-glucosides, are resistant to irreversible cleavage catalyzed by CK dehydrogenases, the observed preference of maize CK glycosyltransferases to O-glycosylate zeatin in the cis-position might be a reason why cZ derivatives are over-accumulated in different maize tissues and organs.
Published: 2016

28. Arabidopsis capping protein senses cellular phosphatidic acid levels and transduces these into changes in actin cytoskeleton dynamics

Author: Roman Pleskot, Martin Potocký, Jessica L. Henty-Ridilla, Laurent Blanchoin, Christopher J. Staiger, Jiejie Li, Department of Biological Sciences [Lafayette IN], Purdue University [West Lafayette], Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Biological Sciences and Bindley Bioscience Center, Institute of Experimental Botany, Czech Academy of Sciences [Prague] (ASCR), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Arabidopsis thaliana, capping protein, Actin Capping Proteins, Arabidopsis, Arp2/3 complex, Phosphatidic Acids, plant, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Plant Science, macromolecular substances, actin-binding protein, 01 natural sciences, actin dynamics, 03 medical and health sciences, Actin-binding protein, Cytoskeleton, phospholipids, 030304 developmental biology, 0303 health sciences, biology, Arabidopsis Proteins, Actin remodeling, cytoskeleton, actin binding protein, biology.organism_classification, Actin cytoskeleton, Cell biology, Addendum, Actin Cytoskeleton, Profilin, biology.protein, MDia1, actin, signal transduction, 010606 plant biology & botany
Abstract: Addendum to: J Li, JL Henty-Ridilla, S Huang, X Wang, L Blanchoin, CJ Staiger. Capping protein modulates the dynamic behavior of actin filaments in response to phosphatidic acid in Arabidopsis.. Plant Cell 2012; 24:; International audience; Plants respond rapidly and precisely to a broad spectrum of developmental, biotic and abiotic cues. In many instances, signaling cascades involved in transducing this information result in changes to the cellular architecture and cytoskeletal rearrangements. Based originally on paradigms for animal cell signaling, phospholipids have received increased scrutiny as key intermediates for transmitting information to the actin cytoskeleton. Significantly, a wealth of biochemical data for plant actin-binding proteins (ABPs) demonstrates that many of these interact with phosphoinositide lipids in vitro. Moreover, phosphatidic acid (PA) has been identified not only as an abundant structural lipid in plants, but also as an intermediary in developmental and stress signaling pathways that lead to altered actin organization. Several years ago, the heterodimeric capping protein (CP) from Arabidopsis was demonstrated to bind PA and is negatively regulated by this lipid in vitro. Whether this form of regulation occurs in cells, however, remained a mystery. A new study, that combines live-cell imaging of cytoskeletal dynamics with reverse-genetic analyses in Arabidopsis, provides compelling new evidence that CP is inhibited from binding filament ends in the presence of PA in vivo. This allows rapid actin polymerization and increases in filament abundance following stimulation and could be one key factor in the physiological responses of plant cells to environmental stimuli.
Published: 2012

29. Nitrate-Regulated Auxin Transport by NRT1.1 Defines a Mechanism for Nutrient Sensing in Plants

Author: Eva Benková, Alain Gojon, Katerina Malinska, Karin Ljung, Klára Hoyerová, Francine Perrine-Walker, Emmanuelle Mounier, Philippe Nacry, Gabriel Krouk, Eva Zazímalová, Agnieszka Bielach, Sarah Leon, Benoît Lacombe, Pascal Tillard, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Flanders Institute for Biotechnology, Ghent University [Belgium] (UGENT)-Department of Plant Systems Biology, Institute of Experimental Botany, Czech Academy of Sciences [Prague] (ASCR), Umea Plant Science Center, Swedish University of Agricultural Sciences (SLU)-Department of Forest Genetics and Plant Physiology, Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Universiteit Gent = Ghent University [Belgium] (UGENT)-Department of Plant Systems Biology, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Umea Plant Science Center (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), and Travail soutenu par la Fondation Agropolis (projet 07024) et par le CNRS (projet PEPS INSB)
Subjects: 0106 biological sciences, Xenopus, pathways, Arabidopsis, DEVBIO, Plant Roots, 01 natural sciences, chemistry.chemical_compound, Nitrate, Gene Expression Regulation, Plant, functional-characterization, Arabidopsis thaliana, Cells, Cultured, chemistry.chemical_classification, 0303 health sciences, biology, food and beverages, Plant physiology, efflux, Chemoreceptor Cells, Cell biology, Biochemistry, SIGNALING, Periplasmic Binding Proteins, Female, Signal Transduction, PROTEINS, root-system architecture, growth, Biological Transport, Active, arabidopsis-thaliana, Nutrient sensing, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Auxin, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, gene, Molecular Biology, 030304 developmental biology, Nitrates, Indoleacetic Acids, Tumor Suppressor Proteins, fungi, Lateral root, Cell Biology, biology.organism_classification, chl1, chemistry, Food, Mutation, Oocytes, Basipetal auxin transport, 010606 plant biology & botany, Developmental Biology
Abstract: Travail soutenu par la Fondation Agropolis (projet 07024) et par le CNRS (projet PEPS INSB).; International audience; Nitrate is both a nitrogen source for higher plants and a signal molecule regulating their development. In Arabidopsis, the NRT1.1 nitrate transporter is crucial for nitrate signaling governing root growth, and has been proposed to act as a nitrate sensor. However, the sensing mechanism is unknown. Herein we show that NRT1.1 not only transports nitrate but also facilitates uptake of the phytohormone auxin. Moreover, nitrate inhibits NRT1.1-dependent auxin uptake, suggesting that transduction of nitrate signal by NRT1.1 is associated with a modification of auxin transport. Among other effects, auxin stimulates lateral root development. Mutation of NRT1.1 enhances both auxin accumulation in lateral roots and growth of these roots at low, but not high, nitrate concentration. Thus, we propose that NRT1.1 represses lateral root growth at low nitrate availability by promoting basipetal auxin transport out of these roots. This defines a mechanism connecting nutrient and hormone signaling during organ development.
Published: 2010

30. Construction de bibliothèques de chromosomes artificiels de bactérie (BAC) de bananier (Musa acuminata et Musa balbisiana)

Author: Xavier Sabau, Pietro Piffanelli, Jaroslav Dolezel, Jan Safar, Alberto Duarte Vilarinhos, Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Padano, Partenaires INRAE, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, Cytom., Inst. Exp. Bot., Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Pietro Piffanelli, CIRAD-BIOS/Parco Tecnologico Padano, Alberto Duarte Vilarinhos, CNPMF, Jan Safar, Institute of Experimental Botany, Xavier Sabau, CIRAD-BIOS, and Jaroslav Dolezel, Institute of Experimental Botany.
Subjects: 0106 biological sciences, ADN, Method, Musa acuminata, 01 natural sciences, F30 - Génétique et amélioration des plantes, Genetic map, Musa balbisiana, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Marqueur génétique, 2. Zero hunger, 0303 health sciences, CARTE GENETIQUE, METHODS, Locus des caractères quantitatifs, Méthodologie, Musa sp, METHODE, CARTOGRAPHIE GENETIQUE, Horticulture, Biology, Chromosome, ELECTROPHORESIS, 03 medical and health sciences, Botany, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Genetic marker, 030304 developmental biology, Génie génétique, Bacterial artificial chromosome, Génome, BANANIER, Virus des végétaux, DNA, biology.organism_classification, Molecular biology, GENETIC MARKERS, Électrophorèse, GENETIC MAPS, electrophoresis, Carte génétique, Agronomy and Crop Science, 010606 plant biology & botany, Food Science
Abstract: Correspondance: pietro.piffanelli@tecnoparco.org; International audience; Introduction. This protocol applies to the characterization of genome structure and evolution of M. acuminata and M. balbisiana genomes; construction of physical maps around markers of interest and QTLs; comparative genomic studies with other monocot species; and study of banana streak virus (BSV) integration patterns in banana nuclear genomes. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. This part describes the required materials, and the protocols for isolation and lysis of banana nuclei; high-molecular-weight (HMW) DNA Hind III digestion and pulsed-field gel electrophoresis (PFGE) analysis; large-scale HMW DNA Hind III digestion and ligation to the pINDIGOBAC–5 vector; and analysis of recombinant BAC clones. It mentions the main problems which can occur. Results. The described protocols will enable the efficient construction of BAC libraries from Musa species. These libraries can be used to construct physical maps and select specific genomic regions to be sequenced.; Introduction. Le protocole s'applique à la caractérisation de la structure du génome et à l'évolution des génomes de M. acuminata et de M. balbisiana ; à la construction de cartes physiques autour des marqueurs d'intérêt et des QTLs ; aux études de génomique comparative avec d'autre espèce de monocotylédones ; à l’étude des modèles d'intégration du virus BSV dans les génomes nucléaires de la banane. Le principe, les principaux avantages, le matériel végétal utilisé, le temps nécessaire et les résultats attendus sont présentés. Matériel et méthodes. Cette partie décrit le matériel de laboratoire nécessaire, et les protocoles permettant l'isolement et la lyse des noyaux de cellules de bananier ; la digestion Hind III de ADN à haut poids moléculaire (HPM) et l’analyse électrophorèse sur gels à champ pulsé ; la digestion Hind III à grande échelle de ADN à HPM et ligation au vecteur pINDIGOBAC-5 ; l’analyse des clones recombinants de BAC. Elle mentionne les principaux problèmes pouvant se poser. Résultats. Les protocoles présentés permettent de construire des bibliothèques de BAC à partir d'espèces du genre Musa. Ces bibliothèques peuvent être utilisées pour construire des cartes physiques et sélectionner des régions du génome à séquencer.
Published: 2008

31. A Conserved Cytochrome P450 Evolved in Seed Plants Regulates Flower Maturation

Author: Benoît Boachon, Hugues Renault, Patrick Achard, Valérie Demais, Zhenhua Liu, Stéphanie Pateyron, Véronique Brunaud, Raquel Tavares, Fan Gong, Mathieu Erhardt, Danièle Werck-Reichhart, Raphaël Lugan, Peter Hedden, Toshiyuki Ohnishi, Ales Pencik, Jérôme Mutterer, Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Plateforme d'Imagerie In Vitro, Université Louis Pasteur - Strasbourg I-Institut Fédératif de Recherche 37 des Neurosciences, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), 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), Unité Mathématique Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Laboratory of Growth Regulators [Univ Palacký] (LGR), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), China Scholarship Council, Region Alsace, Agence Nationale pour la Recherche via the PHENOWALL ANR-10-BLAN-1528, Freiburg Institute for Advanced Studies (FRIAS), University of Strasbourg Institute for Advanced Study (USIAS), Ministry of Education, Youth and Sport of the Czech Republic LO1204, European Fund for Regional Development, 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), Laboratory of Growth Regulators, Palacky University and Institute of Experimental Botany ASCR, and Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)
Subjects: [SDV]Life Sciences [q-bio], gibberellins, Stamen, Arabidopsis, Flowers, Plant Science, chemistry.chemical_compound, Anthesis, Cytochrome P-450 Enzyme System, Gene Expression Regulation, Plant, flower development, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Jasmonate, volatile compounds, Molecular Biology, Conserved Sequence, Phylogeny, Genetics, Tapetum, biology, Arabidopsis Proteins, Jasmonic acid, fungi, Gene Expression Regulation, Developmental, food and beverages, negative selection, phylogenomics, Plants, biology.organism_classification, jasmonate, Cell biology, chemistry, Seeds, Petal
Abstract: International audience; Global inspection of plant genomes identifies genes maintained in low copies across taxa and under strong purifying selection, which are likely to have essential functions. Based on this rationale, we investigated the function of the low-duplicated CYP715 cytochrome P450 gene family that appeared early in seed plants and evolved under strong negative selection. Arabidopsis CYP715A1 showed a restricted tissue-specific expression in the tapetum of flower buds and in the anther filaments upon anthesis. cyp715a1 insertion lines showed a strong defect in petal development, and transient alteration of pollen intine deposition. Comparative expression analysis revealed the downregulated expression of genes involved in pollen development, cell wall biogenesis, hormone homeostasis, and floral sesquiterpene biosynthesis, especially TPS21 and several key genes regulating floral development such as MYB21, MYB24, and MYC2. Accordingly, floral sesquiterpene emission was suppressed in the cyp715a1 mutants. Flower hormone profiling, in addition, indicated a modification of gibberellin homeostasis and a strong disturbance of the turnover of jasmonic acid derivatives. Petal growth was partially restored by the active gibberellin GA3 or the functional analog of jasmonoyl-isoleucine, coronatine. CYP715 appears to function as a key regulator of flower maturation, synchronizing petal expansion and volatile emission. It is thus expected to be an important determinant of flower-insect interaction.
Published: 2015

32. New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

Author: Catherine Feuillet, Miroslav Valárik, Bernardo J. Clavijo, Ingrid Garbus, Jeroslav Doležel, Maximo Rivarola, G. Tranquilli, Marcelo Helguera, Leonardo Sebastián Vanzetti, Mario Caccamo, Norma Paniego, Mihaela Martis, Viviana Echenique, Klaus F. X. Mayer, Hana Šimková, Phillippe Leroy, Sergio Alberto González, Estación Experimental Agropecuaria Marcos Juáre, Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), The Genome Analysis Centre (TGAC), MIPS/IBIS, Helmholtz-Zentrum München (HZM), Estación Experimental Agropecuaria Marcos Juárez, Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Centro de Recursos Naturales Renovables de la Zona Semiárida [Bahía Blanca] (CERZOS), Universidad Nacional del Sur [Argentina] (UNS)-Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Universidad Nacional del Sur [Argentina] (UNS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Norwich Research Park, (TGAC), Centro de Investigación de Recursos Naturales (CIRN), CONICET (International Cooperation Grant) D456, AEBIO 245001.711.732 902 PNBIO 1131041.43 PNCYO 1127041, Universidad Nacional del Sur (PGI-TIR) CSU-142/14, Agencia Espanola de Cooperacion Internacional y Desarrollo AECID-A1/041041/11, Czech Science Foundation P501/12/G090, National Program of Sustainability I LO1204, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Helmholtz Zentrum München = German Research Center for Environmental Health, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Sur [Argentina] (UNS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Cromosoma 4 D, Gene annotation, Virtual gene order, Plant Science, 01 natural sciences, Genome, Chromosome 4d Survey Sequence, Gene Annotation, Gene Content, Synteny, Triticum Aestivum, Virtual Gene Order, Gene Order, Triticum, Expressed Sequence Tags, 2. Zero hunger, Genetics, 0303 health sciences, Expressed sequence tag, virtual gene order, biology, Contig, synteny, Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, General Medicine, Gene content, SNP, single nucleotide polymorphism, dN/dS, non-synonymous-to-synonymous substitutions, EST, expressed sequence tag, ISBP, insertion site-based polymorphism, Biotecnología Agrícola y Biotecnología Alimentaria, Os, Oryza sativa – rice, Orthologous Gene, Chromosome 4D survey sequence, LMP, long mate pair, Molecular Sequence Data, gene content, Biotecnología Agropecuaria, Triticum aestivum, CDS, coding DNA sequences, Trigo, IWGSC, International Wheat Genome Sequencing Consortium, Bd, Brachypodium distachyon, Chromosomes, Chromosomes, Plant, Article, 03 medical and health sciences, chromosome 4D survey sequence, SE, single end, Aegilops tauschii, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Sb, Sorghum bicolor – sorghum, Cromosomas, NGS, next generation sequencing, Sequence Analysis, DNA, biology.organism_classification, gene annotation, Chromosome 4, Genes, CIENCIAS AGRÍCOLAS, MDA, multiple displacement amplification, SSR, single sequence repeat, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: Highlights • Survey sequence of T. aestivum chromosome 4D was obtained by pyrosequencing. • Near 5700 genes were predicted on 4D chromosome, ∼2200 on 4DS and ∼3500 on 4DL. • A 4D virtual gene order based on synteny with orthologous gene loci is proposed. • Among group 4, higher collinearity exists between 4D and 4B as compared to 4A. • Complementary data to that provided by IWGSC is presented, available at NCBI., Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223 Mb) and scaffolds (65 Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34 Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.
Published: 2015

33. Multiple mechanisms of nitrate sensing by Arabidopsis nitrate transceptor NRT1.1

Author: Sophie Léran, Emmanuel Guiderdoni, Gabriel Krouk, Benoît Lacombe, Eva Zažímalová, Martin Kubeš, Donaldo Meynard, Marjorie Pervent, Klára Hoyerová, Francois Brun, Philippe Nacry, Alain Gojon, Eléonore Bouguyon, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institute of Experimental Botany, Czech Academy of Sciences [Prague] (ASCR), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-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), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), and Czech Academy of Sciences [Prague] (CAS)
Subjects: [SDV]Life Sciences [q-bio], Nitrogen assimilation, Arabidopsis, Phénotype, Plant Science, Nitrate, medicine.disease_cause, F30 - Génétique et amélioration des plantes, chemistry.chemical_compound, Gene expression, Expression des gènes, Phosphorylation, Absorption de substances nutritives, Mutation, biology, Physiologie végétale, Biochemistry, transports auxin, Développement biologique, roots, regulation nitrate, F60 - Physiologie et biochimie végétale, Récepteurs, Downregulation and upregulation, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Croissance, Gene, Membrane cellulaire, Lateral root, nitrate transceptor, Biologie moléculaire, biology.organism_classification, F61 - Physiologie végétale - Nutrition, chemistry, Adsorption, Protéine végétale, Racine
Abstract: Supplementary information : http://www.nature.com/article-assets/npg/nplants/2015/nplants201515/extref/nplants201515-s1.pdf Voir communiqué de presse http://presse.inra.fr/Ressources/Communiques-de-presse/Les-strategies-des-plantes-pour-optimiser-l-utilisation-des-nitrates; International audience; In Arabidopsis the plasma membrane nitrate transceptor (transporter/receptor) NRT1.1 governs many physiological and developmental responses to nitrate. Alongside facilitating nitrate uptake, NRT1.1 regulates the expression levels of many nitrate assimilation pathway genes, modulates root system architecture, relieves seed dormancy and protects plants from ammonium toxicity. Here, we assess the functional and phenotypic consequences of point mutations in two key residues of NRT1.1 (P492 and T101). We show that the point mutations differentially affect several of the NRT1.1-dependent responses to nitrate, namely the repression of lateral root development at low nitrate concentrations, and the short-term upregulation of the nitrate-uptake gene NRT2.1, and its longer-term downregulation, at high nitrate concentrations. We also show that these mutations have differential effects on genome-wide gene expression. Our findings indicate that NRT1.1 activates four separate signalling mechanisms, which have independent structural bases in the protein. In particular, we present evidence to suggest that the phosphorylated and non-phosphorylated forms of NRT1.1 at T101 have distinct signalling functions, and that the nitrate-dependent regulation of root development depends on the phosphorylated form. Our findings add to the evidence that NRT1.1 is able to trigger independent signalling pathways in Arabidopsis in response to different environmental conditions.
Published: 2015

34. High-throughput physical map anchoring via BAC-pool sequencing

Author: Kateřina Cviková, Klaus F. X. Mayer, Jaroslav Doležel, Federica Cattonaro, Jan Bartoš, Michael Alaux, Nils Stein, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Istituto di Genomica Applicata, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Leibniz Institute of Plant Genetics and Crop Plant Research, Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Czech Science Foundation [13-08786S], Ministry of Education, Youth and Sports (from the National Program of Sustainability I) [LO1204], National Grid Infrastructure MetaCentrum [LM2010005], and Bartoš, Jan
Subjects: 0106 biological sciences, TILLING, Chromosomes, Artificial, Bacterial, Contig anchoring, [SDV]Life Sciences [q-bio], Plant Science, 01 natural sciences, Genome, Chromosomes, Plant, DNA sequencing, 03 medical and health sciences, Next generation sequencing, Aegilops tauschii, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Synteny, 2. Zero hunger, Genetics, 0303 health sciences, Massive parallel sequencing, Contig, biology, Physical map, Shotgun sequencing, Methodology Article, Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, Plants, biology.organism_classification, 010606 plant biology & botany
Abstract: Background Physical maps created from large insert DNA libraries, typically cloned in BAC vector, are valuable resources for map-based cloning and de novo genome sequencing. The maps are most useful if contigs of overlapping DNA clones are anchored to chromosome(s), and ordered along them using molecular markers. Here we present a novel approach for anchoring physical maps, based on sequencing three-dimensional pools of BAC clones from minimum tilling path. Results We used physical map of wheat chromosome arm 3DS to validate the method with two different DNA sequence datasets. The first comprised 567 genes ordered along the chromosome arm based on syntenic relationship of wheat with the sequenced genomes of Brachypodium, rice and sorghum. The second dataset consisted of 7,136 SNP-containing sequences, which were mapped genetically in Aegilops tauschii, the donor of the wheat D genome. Mapping of sequence reads from individual BAC pools to the first and the second datasets enabled unambiguous anchoring 447 and 311 3DS-specific sequences, respectively, or 758 in total. Conclusions We demonstrate the utility of the novel approach for BAC contig anchoring based on mass parallel sequencing of three-dimensional pools prepared from minimum tilling path of physical map. The existing genetic markers as well as any other DNA sequence could be mapped to BAC clones in a single in silico experiment. The approach reduces significantly the cost and time needed for anchoring and is applicable to any genomic project involving the construction of anchored physical map. Electronic supplementary material The online version of this article (doi:10.1186/s12870-015-0429-1) contains supplementary material, which is available to authorized users.
Published: 2015

35. A manipulation of carotenoid metabolism influence biomass partitioning and fitness in tomato

Author: Jianing Mi, Jose G. Vallarino, Ivan Petřík, Ondřej Novák, Sandra M. Correa, Monika Chodasiewicz, Michel Havaux, Manuel Rodriguez-Concepcion, Salim Al-Babili, Alisdair R. Fernie, Aleksandra Skirycz, Juan C. Moreno, King Abdullah University of Science and Technology (KAUST), Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Max-Planck-Gesellschaft, Laboratory of Growth Regulators [Univ Palacký] (LGR), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Plant Environmental Physiology and Stress Signaling (PEPSS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), and Instituto de Biología Molecular y Celular de Plantas
Subjects: Abiotic stress tolerance, [SDV]Life Sciences [q-bio], fungi, Biomass and yield, food and beverages, Bioengineering, Metabolites and lipids, Carotenoids, Applied Microbiology and Biotechnology, Biosynthetic Pathways, Solanum lycopersicum, Stress, Physiological, Apocarotenoids, Metabolic engineering, Phytohormones, Biomass, Biotechnology
Abstract: Improving yield, nutritional value and tolerance to abiotic stress are major targets of current breeding and biotechnological approaches that aim at increasing crop production and ensuring food security. Metabolic engineering of carotenoids, the precursor of vitamin-A and plant hormones that regulate plant growth and response to adverse growth conditions, has been mainly focusing on provitamin A biofortification or the production of high-value carotenoids. Here, we show that the introduction of a single gene of the carotenoid biosynthetic pathway in different tomato cultivars induced profound metabolic alterations in carotenoid, apocarotenoid and phytohormones pathways. Alterations in isoprenoid- (abscisic acid, gibberellins, cytokinins) and non-isoprenoid (auxin and jasmonic acid) derived hormones together with enhanced xanthophyll content influenced biomass partitioning and abiotic stress tolerance (high light, salt, and drought), and it caused an up to 77% fruit yield increase and enhanced fruit's provitamin A content. In addition, metabolic and hormonal changes led to accumulation of key primary metabolites (e.g. osmoprotectants and antiaging agents) contributing with enhanced abiotic stress tolerance and fruit shelf life. Our findings pave the way for developing a new generation of crops that combine high productivity and increased nutritional value with the capability to cope with climate change-related environmental challenges.
Published: 2022

36. BRASSINOSTEROID INSENSITIVE1 internalization can occur independent of ligand binding

Author: Lucas Alves Neubus Claus, Derui Liu, Ulrich Hohmann, Nemanja Vukašinović, Roman Pleskot, Jing Liu, Alexei Schiffner, Yvon Jaillais, Guang Wu, Sebastian Wolf, Daniël Van Damme, Michael Hothorn, Eugenia Russinova, Universiteit Gent = Ghent University (UGENT), Shandong Agricultural University (SDAU), VIB [Belgium], Université de Genève = University of Geneva (UNIGE), Austrian Academy of Sciences (OeAW), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Shaanxi Normal University (SNNU), Universitätsklinikum Tübingen - University Hospital of Tübingen, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), and École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: PERCEPTION, ligand-binding, RECEPTOR, Physiology, PROTEINS, ENDOCYTOSIS, Biology and Life Sciences, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, DEGRADATION, EXTRACELLULAR DOMAIN, BRI1, brassinosteroids, non-canonical, [SDE]Environmental Sciences, Genetics, KINASE, endocytosis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, TRAFFICKING
Abstract: The brassinosteroid (BR) hormone and its plasma membrane (PM) receptor BR INSENSITIVE1 (BRI1) are one of the best-studied receptor–ligand pairs for understanding the interplay between receptor endocytosis and signaling in plants. BR signaling is mainly determined by the PM pool of BRI1, whereas BRI1 endocytosis ensures signal attenuation. As BRs are ubiquitously distributed in the plant, the tools available to study the BRI1 function without interference from endogenous BRs are limited. Here, we designed a BR binding-deficient Arabidopsis (Arabidopsis thaliana) mutant based on protein sequence-structure analysis and homology modeling of members of the BRI1 family. This tool allowed us to re-examine the BRI1 endocytosis and signal attenuation model. We showed that despite impaired phosphorylation and ubiquitination, BR binding-deficient BRI1 internalizes similarly to the wild type form. Our data indicate that BRI1 internalization relies on different endocytic machineries. In addition, the BR binding-deficient mutant provides opportunities to study non-canonical ligand-independent BRI1 functions.
Published: 2023

37. Early molecular events involved in Pinus pinaster Ait. somatic embryo development under reduced water availability: transcriptomic and proteomic analyses

Author: Leila Belal-Bessai, Kateřina Eliášová, Nathalie Boizot, Philippe Label, Jean-François Trontin, Alexandre Morel, Caroline Teyssier, Claire Le Metté, Martine Beaufour, Luc Harvengt, Isabelle Reymond, Martine Cadene, Marie-Anne Lelu-Walter, Domenico Morabito, Françoise Corbineau, Martin Vágner, Bedřich Pešek, Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Institut National de la Recherche Agronomique (INRA), Pôle Biotechnologie et Sylviculture Avancée, Institut Technologique FCBA: Forêt, Cellulose, Bois-construction, Ameublement, Institute of Experimental Botany of the ASCR, Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Institut National de la Recherche Agronomique (INRA)-Université d'Orléans (UO), Sorbonne Universités, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut Technologique Forêt Cellulose Bois-construction Ameublement (FCBA), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Sorbonne Université (SU), Contrat Région Centre n°33639 'Embryome', Contrat Région Aquitaine n°09012579-045 'Embryo2011', Contrat de coopération Barrande, Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Frapart, Isabelle, and Lelu-Walter, Marie-Anne
Subjects: Plant Somatic Embryogenesis Techniques, Proteomics, early embryogènesis, animal structures, Somatic embryogenesis, Physiology, Somatic cell, [SDV]Life Sciences [q-bio], Biotechnologies, Plant Science, disponibilité en eau, Biology, Transcriptome, chemistry.chemical_compound, Genetics, protéome, Abscisic acid, Glycoproteins, Plant Proteins, Gel electrophoresis, Vegetal Biology, pinus pinaster, maturation, Water, Cell Biology, General Medicine, embryogénèse somatique, Pinus, Gellan gum, [SDV] Life Sciences [q-bio], réponse adaptative, chemistry, Biochemistry, analyse multiéchelle, Seeds, Proteome, stress hydrique, efficience d'utilisation de l'eau, Biologie végétale, Abscisic Acid
Abstract: International audience; Maritime pine somatic embryos (SEs) require a reduction in water availability (high gellan gum concentration in the maturation medium) to reach the cotyledonary stage. This key switch, reported specifically for pine species, is not yet well understood. To facilitate the use of somatic embryogenesis for mass propagation of conifers, we need a better understanding of embryo development. Comparison of both transcriptome (Illumina RNA sequencing) and proteome [two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis with mass spectrometry (MS) identification] of immature SEs, cultured on either high (9G) or low (4G) gellan gum concentration, was performed, together with analysis of water content, fresh and dry mass, endogenous abscisic acid (ABA; gas chromatography-MS), soluble sugars (high-pressure liquid chromatography), starch and confocal laser microscope observations. This multiscale, integrated analysis was used to unravel early molecular and physiological events involved in SE development. Under unfavorable conditions (4G), the glycolytic pathway was enhanced, possibly in relation to cell proliferation that may be antagonistic to SE development. Under favorable conditions (9G), SEs adapted to culture constraint by activating specific protective pathways, and ABA-mediated molecular and physiological responses promoting embryo development. Our results suggest that on 9G, germin-like protein and ubiquitin-protein ligase could be used as predictive markers of SE development, whereas protein phosphatase 2C could be a biomarker for culture adaptive responses. This is the first characterization of early molecular mechanisms involved in the development of pine SEs following an increase in gellan gum concentration in the maturation medium, and it is also the first report on somatic embryogenesis in conifers combining transcriptomic and proteomic datasets.
Published: 2014

38. Genome interplay in the grain transcriptome of hexaploid bread wheat

Author: Pfeifer, Matthias, Kugler, Karl, Sandve, Simen, Zhan, Bujie, Rudi, Heidi, Hvidsten, Torgeir, Mayer, Klaus, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam, Sourdille, Pierre, Endo, Takashi, Kubaláková, Marie, Číhalíková, Jarmila, Dubská, Zdeňka, Vrána, Jan, Šperková, Romana, Šimková, Hana, Febrer, Melanie, Clissold, Leah, Mclay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K, Khurana, Jitendra, Akhunov, Eduard, Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, Spannagl, Manuel, Martis, Mihaela M, Mascher, Martin, Chapman, Jarrod, Poland, Jesse A, Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S, Muehlbauer, Gary J, Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Véronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Hélène, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Françoise, Couderc, Loïc, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikael, Keller, Beat, Praud, Sébastien, Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, Norwegian University of Life Sciences (NMBU), University of Norway, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Norwegian Research Council 199387, Deutsche Forschungsgemeinschaft (DFG) SFB924, German Federal Ministry of Education and Research (BMBF), European Commission's 7th Framework Program, Plant Genome and Systems Biology (PGSB), Helmholtz Zentrum München = German Research Center for Environmental Health, Centre for Integrative Genetics, Department of Chemistry, Biotechnology and Food Science, Eversole Associates, Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan [Saskatoon] (U of S), Bayer Crop Science, Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66506 USA, Partenaires INRAE, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Graduate School of Agriculture, Kyoto University, Kyoto, Japan, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Centre of the Region Haná for Biotechnological and Agricultural Research, Fraunhofer Institute for Intelligent Analysis and Information Systems (Fraunhofer IAIS), Fraunhofer (Fraunhofer-Gesellschaft), National Research Centre Plant Biotechnology, Dept Plant Pathol, Kansas State University, 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), Bayer Cropscience, Institute of Crop Sciences of CAAS [Beijing] (ICS CAAS), Chinese Academy of Agricultural Sciences (CAAS), National Institute of Agrobiological Sciences (NIAS), National Institute of Agrobiological Sciences, Natl Inst Agrobiol Sci, JST-CREST, Japan Science and Technology Agency, Global Institute of Food Security, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, The Sainsbury Laboratory [Norwich] (TSL), Genome Analysis Centre, John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), European Synchrotron Radiation Facility (ESRF), German Research Center for Environmental Health - Helmholtz Center München (GmbH), MIPS/IBIS, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), DOE Joint Genome Institute [Walnut Creek], United States Department of Energy, The James Hutton Institute, Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institute of Plant Biology, Universität Zürich [Zürich] = University of Zurich (UZH), Fac Engn & Nat Sci, Sabanci University [Istanbul], Genomics Research Centre, Consiglio per la Ricerca e Sperimentazione in Agricoltura, York University, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for Comparative Genomics, Murdoch University, CUBE Division of Computational Systems Biology, University of Vienna [Vienna], Department of Plant Pathology, Shizuoka University, Diversity Arrays Technology Pty Ltd (DArT P/L), Centre de Recherche de Chappes, BIOGEMMA, Research Council of Norway [199387], German Research Foundation (DFG) [SFB924], German Federal Ministry of Education and Research (BMBF), European Project: 283496,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2011-2,TRANSPLANT(2011), Helmholtz-Zentrum München (HZM), Univ Saskatchewan, Dept Plant Sci, Saskatoon, SK, Canada, University of California [Riverside] (UCR), University of California-University of California, 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, University of Saskatchewan, John Innes Centre, and University of Zurich
Subjects: MESH: Genome, Plant, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, [SDV]Life Sciences [q-bio], Gene Dosage, 01 natural sciences, Genome, MESH: Gene Dosage, Endosperm, Transcriptome, Gene Expression Regulation, Plant, Triticum, Cancer, Plant Proteins, International Wheat Genome Sequencing Consortium, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, MESH: Plant Proteins, food and beverages, alignment, Bread, MESH: Edible Grain, starchy endosperm, reveals, Genome, Plant, Biotechnology, profiles, General Science & Technology, Cereals, MESH: Triticum, Biology, Gene dosage, MESH: Endosperm, Polyploidy, MESH: Bread, 03 medical and health sciences, Polyploid, MESH: Polyploidy, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MD Multidisciplinary, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Gene Expression Regulation, Plant, Gene, Metabolic and endocrine, 030304 developmental biology, Whole genome sequencing, triticum, MESH: Transcriptome, Human Genome, Plant, Gene Expression Regulation, germination, gene expression, RNA, identification, Edible Grain, protein, 010606 plant biology & botany
Abstract: Allohexaploid bread wheat ( Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type–specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type– and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.
Published: 2014

39. Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

Author: Eva Hřibová, Angélique D'Hont, Patrick Wincker, Franc-Christophe Baurens, Arnaud Lemainque, Benjamin Noel, Corinne Cruaud, Jean-Marc Aury, Caroline Belser, Guillaume Martin, Jaroslav Doležel, Nabila Yahiaoui, Benjamin Istace, Karine Labadie, 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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), France GenomiqueANR-10-INBS-09-08, Center de cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), Agropolis Fondation1504-006, ERDF project 'Plants as a tool for sustainable global development'CZ.02.1.01/0.0/0.0/16_019/0000827, Genoscope, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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, QH301-705.5, [SDV]Life Sciences [q-bio], Medicine (miscellaneous), Computational biology, Genome informatics, Musa acuminata, 01 natural sciences, Genome, Chromosomes, Plant, Article, General Biochemistry, Genetics and Molecular Biology, F30 - Génétique et amélioration des plantes, génomique, Nanopores, 03 medical and health sciences, Gapless playback, Centromere, Biology (General), Gene, 030304 developmental biology, 0303 health sciences, Génome, biology, Contig, phytogénétique, food and beverages, Biotechnologie végétale, Musa, Genomics, Télomères, Telomere, biology.organism_classification, Nanopore Sequencing, Plant biotechnology, Nanopore sequencing, General Agricultural and Biological Sciences, Genome, Plant, 010606 plant biology & botany
Abstract: Long-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters. These technologies also make it possible to know the complete organization of chromosomes, which remained complicated before even when using genetic maps. However, generating a gapless and telomere-to-telomere assembly is still not trivial, and requires a combination of several technologies and the choice of suitable software. Here, we report a chromosome-scale assembly of a banana genome (Musa acuminata) generated using Oxford Nanopore long-reads. We generated a genome coverage of 177X from a single PromethION flowcell with near 17X with reads longer than 75 kbp. From the 11 chromosomes, 5 were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes., Belser, Baurens et al. report a chromosome-scale assembly of a banana genome (Musa acuminata) with five out of eleven chromosomes entirely reconstructed in a single contig from telomere to telomere. This work sheds light on the content of complex regions like centromeres or clusters of paralogous genes in the banana genome.
Published: 2021

40. Phosphoglycerolipids are master players in plant hormone signal transduction

Author: Alain Zachowski, Jan Martinec, Nabila Djafi, Martin Janda, Séverine Planchais, Lenka Burketová, Eric Ruelland, Olga Valentová, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Institute of Chemical Technology [Prague] (ICT), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Physiologie cellulaire et moléculaire des plantes (PCMP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Chemistry and Technology Prague (UCT Prague), Institute of Experimental Botany, Czech Academy of Sciences [Prague] (ASCR), and Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) )
Subjects: 0106 biological sciences, Cell signaling, G protein, Arabidopsis, Phosphatidic Acids, Glycerophospholipids, Plant Science, Signalling, 01 natural sciences, 03 medical and health sciences, Abscisic acid, Plant Growth Regulators, Gene Expression Regulation, Plant, Phosphatidic acid, Phosphoglycerolipids, Auxin, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Phospholipase, Plant Proteins, 030304 developmental biology, Lipid kinase, 0303 health sciences, NADPH oxidase, biology, Kinase, Phosphotransferases, General Medicine, Salicylic acid, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Cell biology, Metabolic pathway, Biochemistry, Phospholipases, biology.protein, Plant hormone, Signal transduction, Transcriptome, Agronomy and Crop Science, Signal Transduction, 010606 plant biology & botany
Abstract: International audience; Phosphoglycerolipids are essential structural constituents of membranes and some also have important cell signalling roles. In this review, we focus on phos-phoglycerolipids that are mediators in hormone signal transduction in plants. We first describe the structures of the main signalling phosphoglycerolipids and the metabolic pathways that generate them, namely the phospholi-pase and lipid kinase pathways. In silico analysis of Arabidopsis transcriptome data provides evidence that the genes encoding the enzymes of these pathways are trans-criptionally regulated in responses to hormones, suggesting some link with hormone signal transduction. The involvement of phosphoglycerolipid signalling in the early responses to abscisic acid, salicylic acid and auxins is then detailed. One of the most important signalling lipids in plants is phosphatidic acid. It can activate or inactivate protein kinases and/or protein phosphatases involved in hormone signalling. It can also activate NADPH oxidase leading to the production of reactive oxygen species. We will interrogate the mechanisms that allow the activation/ deactivation of the lipid pathways, in particular the roles of G proteins and calcium. Mediating lipids thus appear as master players of cell signalling, modulating, if not controlling , major transducing steps of hormone signals.
Published: 2013

41. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

Author: Frédéric Choulet, Hana Šimková, Catherine Feuillet, Zeev Frenkel, Sonia Vautrin, Simone Scalabrin, Arnaud Bellec, Hélène Bergès, Isabelle Bertin, Christel Laugier, Etienne Paux, Federica Cattonaro, Pierre Sourdille, Jan Šafář, Romain Philippe, Jaroslav Doležel, Mihaela Martis, Klaus F. X. Mayer, Federica Magni, Abraham B. Korol, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Centre of the Region Haná for Biotechnical and Agricultural Research, Institute of Experimental Botany of the ASCR, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa [Haifa], Applied Genomics Institute (IGA), Institute of Bioinformatics and Systems Biology, Munich Information Center for Protein Sequences, German Research Center for Environmental Health, European Community [FP7-212019], Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Helmholtz Zentrum München = German Research Center for Environmental Health, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), and Feuillet, Catherine
Subjects: 0106 biological sciences, Genetic Markers, Genome evolution, physical mapping, [SDV]Life Sciences [q-bio], blé hexaploïde, Quantitative Trait Loci, gene space, Genomics, Computational biology, syntenie, Biology, 01 natural sciences, Genome, DNA sequencing, Chromosomes, Plant, 03 medical and health sciences, evolution, Cloning, Molecular, Sorghum, Triticum, 030304 developmental biology, Synteny, 2. Zero hunger, Whole genome sequencing, Genetics, 0303 health sciences, Research, synteny, map-based cloning, Physical Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, Oryza, Genome project, sequencing, Biological Evolution, hexaploid wheat, grasses, Chromosome 1bl, Evolution, Gene Space, Grasses, Hexaploid Wheat, Map-based Cloning, Physical Mapping, Sequencing, chromosome 1BL, Genome, Plant, 010606 plant biology & botany, Brachypodium
Abstract: Background: As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. Results: Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. Conclusions: Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.
Published: 2013

42. Sucrose promotes the establishment of polarized auxin transport in axillary buds during outgrowth

Author: Barbier, François, Peron, Thomas, Perez-Garcia, Maria Dolores, BARRIERE, Quentin, Rolcik, Jakub, Le Gourrierec, José, Bertheloot, Jessica, Sakr, Soulaiman, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, AGROCAMPUS OUEST, Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Université d'Angers (UA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratory of Growth Regulators [Univ Palacký] (LGR), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: [SDV]Life Sciences [q-bio], fungi, food and beverages, heterocyclic compounds
Abstract: Sucrose promotes the establishment of polarized auxin transport in axillary buds during outgrowth. ECFG13 European conference on fungal genetic
Published: 2013

43. The plant non-specific phospholipase C gene family. Novel competitors in lipid signalling

Author: Zuzana Krčková, Jan Martinec, V. S. Kravets, Daniela Kocourková, Eric Ruelland, Igor Pokotylo, Přemysl Pejchar, Martin Potocký, Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine (NASU), Institute of Experimental Botany, Czech Academy of Sciences [Prague] (ASCR), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), and Czech Academy of Sciences [Prague] (CAS)
Subjects: 0106 biological sciences, MESH: Signal Transduction, Arabidopsis, 01 natural sciences, Biochemistry, 03 medical and health sciences, Phosphoinositide phospholipase C, Gene family, MESH: Arabidopsis, 030304 developmental biology, Diacylglycerol kinase, Plant Proteins, MESH: Lipid Metabolism, 0303 health sciences, Phospholipase C, biology, MESH: Plant Proteins, Abiotic stress, food and beverages, Lipid metabolism, Cell Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Lipid Metabolism, Cell biology, Plant protein, Multigene Family, Type C Phospholipases, MESH: Multigene Family, lipids (amino acids, peptides, and proteins), MESH: Type C Phospholipases, 010606 plant biology & botany, Signal Transduction
Abstract: International audience; Non-specific phospholipases C (NPCs) were discovered as a novel type of plant phospholipid-cleaving enzyme homologous to bacterial phosphatidylcholine-specific phospholipases C and responsible for lipid conversion during phosphate-limiting conditions. The six-gene family was established in Arabidopsis, and growing evidence suggests the involvement of two articles NPCs in biotic and abiotic stress responses as well as phytohormone actions. In addition, the diacylglycerol produced via NPCs is postulated to participate in membrane remodelling, general lipid metabolism and cross-talk with other phospholipid signalling systems in plants. This review summarises information concerning this new plant protein family and focusses on its sequence analysis, biochemical properties, cellular and tissue distribution and physiological functions. Possible modes of action are also discussed.
Published: 2013

44. Functional features of a single chromosome arm in wheat (1AL) determined from its structure

Author: Federica Cattonaro, Arnaud Bellec, Irena Jurman, Hélène Bergès, Stuart J. Lucas, Sonia Vautrin, Jaroslav Doležel, Hikmet Budak, Jan Šafář, Hana Šimková, Sabanci University, Partenaires INRAE, Istituto di Genomica Applicata, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc, European Community [FP7/2007-2013, FP7-212019], Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), and Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)
Subjects: 0106 biological sciences, Genetic Markers, Chromosomes, Artificial, Bacterial, RESOURCES, [SDV]Life Sciences [q-bio], ORGANIZATION, Biology, 01 natural sciences, Genome, Synteny, Chromosomes, Plant, 03 medical and health sciences, A genome, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cloning, Molecular, TRITICUM-AESTIVUM L, Gene, Triticum, 030304 developmental biology, Plant Proteins, 2. Zero hunger, Whole genome sequencing, Comparative genomics, 0303 health sciences, COMMON WHEAT, Polymorphism, Genetic, SEQUENCES, BAC end sequencing, Chromosome, food and beverages, Molecular Sequence Annotation, BREAD WHEAT, General Medicine, Genome project, Sequence Analysis, DNA, Marker design, EVOLUTION, YIELD, Chromosome Arm, Wheat, PLANT GENOMICS, HEXAPLOWHEAT, Genome, Plant, 010606 plant biology & botany, Microsatellite Repeats
Abstract: International audience; Bread wheat (Triticum aestivum L.) is one of the most important crops globally and a high priority for genetic improvement, but its large and complex genome has been seen as intractable to whole genome sequencing. Isolation of individual wheat chromosome arms has facilitated large-scale sequence analyses. However, so far there is no such survey of sequences from the A genome of wheat. Greater understanding of an A chromosome could facilitate wheat improvement and future sequencing of the entire genome. We have constructed BAC library from the long arm of T. aestivum chromosome 1A (1AL) and obtained BAC end sequences from 7,470 clones encompassing the arm. We obtained 13,445 (89.99%) useful sequences with a cumulative length of 7.57 Mb, representing 1.43% of 1AL and about 0.14% of the entire A genome. The GC content of the sequences was 44.7%, and 90% of the chromosome was estimated to comprise repeat sequences, while just over 1% encoded expressed genes. From the sequence data, we identified a large number of sites suitable for development of molecular markers (362 SSR and 6,948 ISBP) which will have utility for mapping this chromosome and for marker assisted breeding. From 44 putative ISBP markers tested 23 (52.3%) were found to be useful. The BAC end sequence data also enabled the identification of genes and syntenic blocks specific to chromosome 1AL, suggesting regions of particular functional interest and targets for future research.
Published: 2012

45. A 3,000-Loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat

Author: Camille Rustenholz, Sonia Vautrin, Christel Laugier, Federica Magni, Simone Scalabrin, Jaroslav Doležel, Frédéric Choulet, Hélène Bergès, Catherine Feuillet, Federica Cattonaro, Arnaud Bellec, Jan Šafář, Etienne Paux, Hana Šimková, Paux, Etienne, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institute of Experimental Botany, Centre of the Region Hana' for Biotechnological and Agricultural Research, Parco Scientifico e Tecnologico di Udine Luigi Danieli, Istituto di Genomica Applicata, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), This work was supported by the European Community's Seventh Framework Programme (FP7/2007-2013 under grant agreement no. FP7-212019), by the Institut National de la Recherche Agronomique (AIP 'ChromBle'), and by the Ministry of Education, Youth, and Sports of the Czech Republic and the European Regional Development Fund (Operational Programme Research and Development for Innovations no. CZ.1.05/2.1.00/01.0007). C. R. was financially supported by Region Auvergne., Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Physiology, caractère fonctionnel, gene space, Pair-rule gene, plant sciences, Locus (genetics), Plant Science, Biology, 01 natural sciences, 03 medical and health sciences, blé, Gene density, chromosome 3B, transcription map, Gene cluster, Genetics, Gene, 030304 developmental biology, 2. Zero hunger, Regulation of gene expression, 0303 health sciences, Gene map, carte chromosomique, food and beverages, Gene expression profiling, 010606 plant biology & botany
Abstract: To improve our understanding of the organization and regulation of the wheat (Triticum aestivum) gene space, we established a transcription map of a wheat chromosome (3B) by hybridizing a newly developed wheat expression microarray with bacterial artificial chromosome pools from a new version of the 3B physical map as well as with cDNA probes derived from 15 RNA samples. Mapping data for almost 3,000 genes showed that the gene space spans the whole chromosome 3B with a 2-fold increase of gene density toward the telomeres due to an increase in the number of genes in islands. Comparative analyses with rice (Oryza sativa) and Brachypodium distachyon revealed that these gene islands are composed mainly of genes likely originating from interchromosomal gene duplications. Gene Ontology and expression profile analyses for the 3,000 genes located along the chromosome revealed that the gene islands are enriched significantly in genes sharing the same function or expression profile, thereby suggesting that genes in islands acquired shared regulation during evolution. Only a small fraction of these clusters of cofunctional and coexpressed genes was conserved with rice and B. distachyon, indicating a recent origin. Finally, genes with the same expression profiles in remote islands (coregulation islands) were identified suggesting long-distance regulation of gene expression along the chromosomes in wheat.
Published: 2011

46. Unlocking the barley genome by chromosomal and comparative genomics

Author: Burkhard Steuernagel, Kazuhiro Sato, Marie Kubaláková, Takashi Endo, Hiroaki Sakai, Pete E. Hedley, Mihaela Martis, Jenny Morris, Heidrun Gundlach, Andreas Graner, Nils Stein, Matthias Platzer, Tsuyoshi Tanaka, Klaus F. X. Mayer, Jaroslav Dolezel, Jérôme Salse, Marius Felder, Florent Murat, Uwe Scholz, Robbie Waugh, Pavla Suchánková, Stefan Taudien, Takashi Matsumoto, Hui Liu, Thomas Nussbaumer, Hana Šimková, Takeshi Itoh, Stephan K. Roessner, Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Helmholtz-Zentrum München (HZM), Ctr Reg Hana Biotechnol & Agr Res, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Lab Plant Genet, Kyoto University [Kyoto], Tsukuba, Université de Tokyo,Faculté d'Agronomie, Inst Plant Sci & Resources, Kurashiki, Okayama University, Bundesministerium fur Bildung und Forschung [0314000], European Union commission [FP7-212019], Ministry of Education, Youth, and Sports of the Czech Republic, European Regional Development Fund [CZ.1.05/2.1.00/01.0007], Institute of Experimental Botany, Okayama University [Okayama], Helmholtz Zentrum München = German Research Center for Environmental Health, and Kyoto University
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, PSEUDO-RESPONSE-REGULATOR, Sequence analysis, FULL-LENGTH CDNAS, Large-Scale Biology Articles, Centromere, Plant Science, Biology, Genes, Plant, 01 natural sciences, Genome, Chromosomes, Plant, Evolution, Molecular, 03 medical and health sciences, TRITICUM-AESTIVUM L, Gene Order, ACETYL-COA CARBOXYLASE, GENE-EXPRESSION, POLYPLOWHEAT, 3-PHOSPHOGLYCERATE KINASE, PHYLOGENETIC ANALYSIS, HOMOEOLOGOUS GROUP-4, CEREAL GENOMICS, Gene, Triticum, 030304 developmental biology, 2. Zero hunger, Comparative genomics, Genetics, Gene Rearrangement, 0303 health sciences, Oryza sativa, Models, Genetic, Chromosome, food and beverages, Hordeum, Oryza, Cell Biology, Genomics, Sequence Analysis, DNA, biology.organism_classification, pseudo-response-regulator, acetyl-coa carboxylase, triticum-aestivum l, full-length cdnas, gene-expression, polyploid wheat, 3-phosphoglycerate kinase, phylogenetic analysis, homoeologous group-4, cereal genomics, Hordeum vulgare, Brachypodium distachyon, Genome, Plant, 010606 plant biology & botany
Abstract: L'article original est publié par The American Society of Plant Biologists; We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign; similar to 86% of the estimated; similar to 32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.
Published: 2011

47. Isolated chromosomes as a new and efficient source of DArT markers for the saturation of genetic maps

Author: Eric Huttner, Marie Kubaláková, Edie Paul, Pavla Suchánková, Catherine Feuillet, Peter Wenzl, Jaroslav Doležel, Jason Carling, Andrzej Kilian, Pierre Sourdille, Hana Šimková, Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany of the ASCR, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Czech Ministry of Education, Youth and Sports LC06004, and Grains Research and Development Corporation (GRDC) of Australia
Subjects: 0106 biological sciences, Genetic Markers, DNA, Plant, Genotype, Genetic Linkage, Biology, 01 natural sciences, Genome, Polymerase Chain Reaction, Chromosomes, Plant, 03 medical and health sciences, Gene mapping, Genetic linkage, Genetics, Genotyping, Triticum, 030304 developmental biology, DNA Primers, 2. Zero hunger, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Gene map, Diversity Arrays Technology, CARTE GENETIQUE, Chromosome, Chromosome Mapping, General Medicine, Agronomy and Crop Science, Chromosome 22, Genome, Plant, 010606 plant biology & botany, Biotechnology
Abstract: We describe how the diversity arrays technology (DArT) can be coupled with chromosome sorting to increase the density of genetic maps in specific genome regions. Chromosome 3B and the short arm of chromosome 1B (1BS) of wheat were isolated by flow cytometric sorting and used to develop chromosome- and chromosome arm-enriched genotyping arrays containing 2,688 3B clones and 384 1BS clones. Linkage analysis showed that 553 of the 711 polymorphic 3B-derived markers (78%) mapped to chromosome 3B, and 59 of the 68 polymorphic 1BS-derived markers (87%) mapped to chromosome 1BS, confirming the efficiency of the chromosome-sorting approach. To demonstrate the potential for saturation of genetic maps, we constructed a consensus map of chromosome 3B using 19 mapping populations, including some that were genotyped with the 3B-enriched array. The 3B-derived DArT markers doubled the number of genetic loci covered. The resulting consensus map, probably the densest genetic map of 3B available to this date, contains 939 markers (779 DArTs and 160 other markers) that segregate on 304 genetically distinct loci. Importantly, only 2,688 3B-derived clones (probes) had to be screened to obtain almost twice as many polymorphic 3B markers (510) as identified by screening approximately 70,000 whole genome-derived clones (269). Since an enriched DArT array can be developed from less than 5 ng of chromosomal DNA, a quantity which can be obtained within 1 h of sorting, this approach can be readily applied to any crop for which chromosome sorting is available.
Published: 2010

48. Structural and functional characterization of plant aminoaldehyde dehydrogenase from Pisum sativum with a broad specificity for natural and synthetic aminoaldehydes

Author: David Kopečný, Marek Šebela, Solange Moréra, Martina Tylichová, Jacques Snégaroff, Pierre Briozzo, René Lenobel, Faculty of Science, Department of Biochemistry, Palacky University, UPR3082 Laboratoire d'enzymologie et biochimie structurales (LEBS), Centre National de la Recherche Scientifique (CNRS), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institute of Experimental Botany, Laboratory of Growth Regulators, Palacky University Olomouc, Laboratoire d'enzymologie et biochimie structurales (LEBS), Laboratory of Growth Regulators [Univ Palacký] (LGR), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], and Palacky University Olomouc-Palacky University Olomouc
Subjects: 0106 biological sciences, Models, Molecular, Spectrometry, Mass, Electrospray Ionization, Stereochemistry, Dehydrogenase, Biology, Crystallography, X-Ray, 01 natural sciences, Cofactor, Substrate Specificity, betaine aldehyde dehydrogenase, 03 medical and health sciences, chemistry.chemical_compound, Betaine, Structural Biology, Oxidoreductase, Tandem Mass Spectrometry, Catalytic Domain, protein crystallography, Coenzyme binding, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Binding site, Molecular Biology, 030304 developmental biology, DNA Primers, chemistry.chemical_classification, NAD(+) complex, 0303 health sciences, Aldehydes, Binding Sites, Base Sequence, Peas, carnitine, NAD, Aldehyde Oxidoreductases, Recombinant Proteins, Protein Structure, Tertiary, Isoenzymes, Kinetics, chemistry, Biochemistry, aminoaldehyde dehydrogenase, biology.protein, Betaine-aldehyde dehydrogenase, NAD+ kinase, 010606 plant biology & botany
Abstract: Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; Aminoaldehyde dehydrogenases (AMADHs, EC 1.2.1.19) belong to the large aldehyde dehydrogenase (ALDH) superfamily, namely, the ALDH9 family. They oxidize polyamine-derived omega-aminoaldehydes to the corresponding omega-amino acids. Here, we report the first X-ray structures of plant AMADHs: two isoenzymes, PsAMADH1 and PsAMADH2, from Pisum sativum in complex with beta-nicotinamide adenine dinucleotide (NAD(+)) at 2.4 and 2.15 angstrom resolution, respectively. Both recombinant, proteins are dimeric and, similarly to other ALDHs, each monomer is composed of an oligomerization domain, a coenzyme binding domain and a catalytic domain. Each subunit binds NAD(+) as a coenzyme, contains a solvent-accessible C-terminal peroxisomal targeting signal (type 1) and a cation bound in the cavity close to the NAD(+) binding site. While the NAD(+) binding mode is classical for PsAMADH2, that for PsAMADH1 is unusual among ALDHs. A glycerol molecule occupies the substrate binding site and mimics a bound substrate. Structural analysis and substrate specificity study of both isoenzymes in combination with data published previously on other ALDH9 family members show that the established categorization of such enzymes into distinct groups based on substrate specificity is no more appropriate, because many of them seem capable of oxidizing a large spectrum of aminoaldehyde substrates. PsAMADH1 and PsAMADH2 can oxidize N,N,N-trimethyl-4-aminobutyraldehyde into gamma-butyrobetaine, which is the carnitine precursor in animal cells. This activity highly suggests that in addition to their contribution to the formation of compatible osmolytes such as glycine betaine, beta-alanine betaine and gamma-aminobutyric acid, AMADHs might participate in carnitine biosynthesis in plants.
Published: 2010

49. Far-red light inhibits germination through DELLA-dependent stimulation of ABA synthesis and ABI3 activity

Author: Veronika Turečková, Luis Lopez-Molina, Eric Lacombe, Urszula Piskurewicz, Département de Biologie Végétale, Université de Genève (UNIGE), Laboratory of Growth Regulators, Palacky University and Institute of Experimental Botany ASCR, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Growth Regulators [Univ Palacký] (LGR), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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, dormancy, Light, Abscisic Acid/biosynthesis, 01 natural sciences, Endosperm, abscisic acid, chemistry.chemical_compound, Basic Helix-Loop-Helix Transcription Factors, abscisic-acid biosynthesis, Abscisic acid, transcription factor, Basic Helix-Loop-Helix Transcription Factors/metabolism, 0303 health sciences, Phytochrome, plants, General Neuroscience, food and beverages, ddc:580, Biochemistry, Germination, Arabidopsis/radiation effects, Gibberellin, gibberellins, Germination/radiation effects, seed germination, Biology, pil5, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription Factors/metabolism, thaliana, gene, Molecular Biology, Transcription factor, 030304 developmental biology, phytochrome, General Immunology and Microbiology, Arabidopsis Proteins, Repressor Proteins/metabolism, ACL, fungi, Far-red, gibberellin, Repressor Proteins, arabidopsis, chemistry, Gene Expression Regulation, Arabidopsis Proteins/metabolism, Dormancy, DELLA, protein, 010606 plant biology & botany, Transcription Factors
Abstract: International audience; Under the canopy, far-red (FR) light represses seed germination by inactivating phytochrome photoreceptors. This elicits a decrease in gibberellins (GA) levels and an increase in abscisic acid (ABA) levels. GA promotes germination by enhancing the proteasome-mediated destruction of DELLA repressors. ABA prevents germination by stimulating the expression of ABI repressors. How phytochromes elicit changes in hormone levels or how GA- and ABA-dependent signals are coordinated to repress germination remains poorly understood. We show that repression of germination by FR light involves stabilized DELLA factors GAI, RGA and RGL2 that stimulate endogenous ABA synthesis. In turn, ABA blocks germination through the transcription factor ABI3. The role of PIL5, a basic helix-loop-helix transcription factor stimulating GAI and RGA expression, is significant, provided GA synthesis is high enough; otherwise, high GAI and RGA protein levels persist to block germination. Under white light, GAI and RGA driven by the RGL2 promoter can substitute for RGL2 to promote ABA synthesis and repress germination, consistent with the recent findings with RGL2. The three DELLA factors inhibit testa rupture whereas ABI3 blocks endosperm rupture.
Published: 2009

50. A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

Author: Kellye Eversole, Michel Bernard, Daryl Somers, Catherine Feuillet, Jaroslav Dolezel, Michael Alaux, Sonia Vautrin, Philippe Leroy, Monika Michalak, Abraham B. Korol, Hélène Bergès, Andrzej Kilian, Evans Lagudah, Etienne Paux, Frédéric Choulet, Hana Šimková, Wolfgang Spielmeyer, Rudi Appels, Cyrille Saintenac, Pierre Sourdille, Jan Safar, Shahryar F. Kianian, Jérôme Salse, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institute of Evolution, University of Haifa [Haifa], Department of Plant Sciences, North Dakota State University (NDSU), Plant Industry, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Cereal Research Centre, Agriculture and Agri-Food [Ottawa] (AAFC), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), International Wheat Genome Sequencing Consortium, Eversole Associates, Centre for Comparative Genomics, Murdoch University, Laboratory of Molecular Cytogenetics and Cytometry, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS)-Faculty of Science [Univ Palacký], Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Institute of Experimental Botany of the ASCR, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Agriculture and Agri-Food (AAFC)
Subjects: 0106 biological sciences, Chromosomes, Artificial, Bacterial, Population, BACTERIE, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Crop species, Physical Maps, 01 natural sciences, Genome, Chromosomes, Plant, Polyploidy, Contig Mapping, 03 medical and health sciences, Polyploid, education, Triticum, Gene Library, 030304 developmental biology, Expressed Sequence Tags, 2. Zero hunger, Genetics, Radiation Hybrid Mapping, 0303 health sciences, Bacterial artificial chromosome, education.field_of_study, Polymorphism, Genetic, Multidisciplinary, Contig, Chromosome, food and beverages, Oryza, Bread, Physical Chromosome Mapping, DNA Fingerprinting, GENOMIQUE, CHROMOSOME ARTIFICIEL, Genome, Plant, Microsatellite Repeats, 010606 plant biology & botany
Abstract: As the staple food for 35% of the world's population, wheat is one of the most important crop species. To date, sequence-based tools to accelerate wheat improvement are lacking. As part of the international effort to sequence the 17–billion–base-pair hexaploid bread wheat genome (2 n = 6 x = 42 chromosomes), we constructed a bacterial artificial chromosome (BAC)–based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases. A chromosome-specific BAC library was used to assemble 82% of the chromosome into 1036 contigs that were anchored with 1443 molecular markers, providing a major resource for genetic and genomic studies. This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach.
Published: 2008

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