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14 results on '"Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben)"'

1. A Chimeric TGA Repressor Slows Down Fruit Maturation and Ripening in Tomato

Author

Carine Ferrand, Christophe Rothan, Martine Lemaire-Chamley, Takayuki Tohge, Joana Jorly, Hiroshi Ezura, Erika Asamizu, Marilise Nogueira, Lázaro Eustáquio Pereira Peres, Paul D Fraser, Takuya Yoshida, Claude Koutouan, Alisdair R. Fernie, Julien Assali, Mohammad-Reza Hajirezaei, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, The University of Tokyo (UTokyo), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Royal Holloway [University of London] (RHUL), University of São Paulo (USP), Université de Tsukuba = University of Tsukuba, Ryukoku University, and Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben)

Subjects
Crops, Agricultural, 0106 biological sciences, Genotype, Physiology, [SDV]Life Sciences [q-bio], Repressor, Plant Science, tomato, Biology, Genes, Plant, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, chloroplast, ripening competency, Solanum lycopersicum, Gene Expression Regulation, Plant, bZIP, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription factor, Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, TOMATE, hormone regulation, Genetic Variation, food and beverages, Ripening, Cell Biology, General Medicine, Metabolism, biology.organism_classification, Cell biology, Chloroplast, Basic-Leucine Zipper Transcription Factors, chemistry, Fruit, développement du fruit, Mutation, Plant hormone, Salicylic acid, Systemic acquired resistance, 010606 plant biology & botany
Abstract

The bZIP transcription factor (TF) SlTGA2.2 was previously highlighted as a possible hub in a network regulating fruit growth and transition to ripening (maturation phase). It belongs to a clade of TFs well known for their involvement in the regulation of the salicylic acid–dependent systemic acquired resistance. To investigate if this TGA TF plays a role in tomato fruit growth and maturation, we took advantage of the fruit-specific SlPPC2 promoter (PPC2pro) to target the expression of a SlTGA2.2-SRDX chimeric repressor in a developmental window restricted to early fruit growth and maturation. Here, we show that this SlTGA2.2-SRDX repressor alters early fruit development and metabolism, including chloroplast number and structure, considerably extends the time necessary to reach the mature green stage and slows down fruit ripening. RNA sequencing and plant hormone analyses reveal that PPC2pro:SlTGA2.2-SRDX fruits are maintained in an immature stage as long as PPC2pro is active, through early modifications of plant hormonal signaling and down-regulation of MADS-RIN and NAC-NOR ripening regulators. Once PPC2pro becomes inactive and therefore SlTGA2.2-SRDX expression is reduced, ripening can proceed, albeit at a slower pace than normal. Altogether, this work emphasizes the developmental continuum between fruit growth, maturation and ripening and provides a useful tool to alter and study the molecular bases of tomato fruit transition to ripening.

Published
2021

2. Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation

Author

Amber Hartman Scholz, Jens Freitag, Christopher H. C. Lyal, Rodrigo Sara, Martha Lucia Cepeda, Ibon Cancio, Scarlett Sett, Andrew Lee Hufton, Yemisrach Abebaw, Kailash Bansal, Halima Benbouza, Hamadi Iddi Boga, Sylvain Brisse, Michael W. Bruford, Hayley Clissold, Guy Cochrane, Jonathan A. Coddington, Anne-Caroline Deletoille, Felipe García-Cardona, Michelle Hamer, Raquel Hurtado-Ortiz, Douglas W. Miano, David Nicholson, Guilherme Oliveira, Carlos Ospina Bravo, Fabian Rohden, Ole Seberg, Gernot Segelbacher, Yogesh Shouche, Alejandra Sierra, Ilene Karsch-Mizrachi, Jessica da Silva, Desiree M. Hautea, Manuela da Silva, Mutsuaki Suzuki, Kassahun Tesfaye, Christian Keambou Tiambo, Krystal A. Tolley, Rajeev Varshney, María Mercedes Zambrano, Jörg Overmann, European Commission, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), The Natural History Museum [London] (NHM), One Planet Solutions, Montpellier, Universidad de los Andes [Bogota] (UNIANDES), European Marine Biological Resource Centre (EMBRC-ERIC), Ethiopian Biotechnology Institute, Addis Ababa, National Academy of Agricultural Science and Global Plant Council, New Delhi, National Council of Scientific Research and Technologies (NCSRT), Algiers (NCSRT), Ministry of Agriculture, Livestock, Fisheries and Cooperatives, Nairobi, Institut Pasteur [Paris] (IP), Cardiff University, The Wellcome Trust Sanger Institute [Cambridge], European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Global Genome Initiative, Smithsonian National Museum of Natural History, Washington, DC, Alexander von Humboldt Biological Resources Research Institute, Bogota, South African National Biodiversity Institute, University of Nairobi (UoN), Instituto Tecnológico Vale [Belém, Brazil] (ITV), Ministry of the Environment and Sustainable Developmentment, University of Lethbridge, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Freiburg [Freiburg], National Centre for Cell Science [Pune, India] (NCCS), Mariano Galvez University, Guatemala City, National Center for Biotechnology Information (NCBI), University of Johannesburg [South Africa] (UJ), University of the Philippines Los Baños (UP Los Baños), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), National Institute of Genetics (NIG), Institute of Biotechnology [Vilnius], Life Science Center [Vilnius], Vilnius University [Vilnius]-Vilnius University [Vilnius], Centre for Tropical Livestock Genetics and Health [Edimburgh] (CTLGH), Murdoch University, Corporación CorpoGen, Bogota, Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], This work was funded by the German Federal Ministry of Education and Research (BMBF) WiLDSI 031B0862 (A.H.S., J.O., and J.F.) and Horizon Europe EVA-GLOBAL 871029 (A.H.S.). I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine, National Institutes of Health., European Project: 871029,H2020,H2020-INFRAIA-2019-1,EVA-GLOBAL(2020), and European Project: 01UU1602A/C

Subjects
Conservation of Natural Resources, Multidisciplinary, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, General Physics and Astronomy, General Chemistry, Biodiversity, General Biochemistry, Genetics and Molecular Biology
Abstract

Open access to sequence data is a cornerstone of biology and biodiversity research, but has created tension under the United Nations Convention on Biological Diversity (CBD). Policy decisions could compromise research and development, unless a practical multilateral solution is implemented. This workwas funded by the German Federal Ministry of Education and Research (BMBF) WiLDSI 031B0862 (A.H.S., J.O., and J.F.) and Horizon Europe EVA-GLOBAL 871029 (A.H.S.). I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine, National Institutes of Health.

Published
2022
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3. Polymorphism in the short arm of 1R rye chromosomes in wheat lines with 1RS.1BL translocation and 1R(1B) substitution from different sources

Author

M. K. Toporash, A. Börner, Pierre Sourdille, I. I. Motsnyy, S. V. Chebotar, Odessa National I.I.Mechnikov University, National Center of Seed and Cultivar Investigations, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Génétique Diversité et Ecophysiologie des Céréales (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
2. Zero hunger, 0106 biological sciences, 0301 basic medicine, Genetics, 1RS.1BL translocation, [SDV]Life Sciences [q-bio], food and beverages, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Chromosomal translocation, General Medicine, Biology, 01 natural sciences, polymorphism, microsatellites markers, 03 medical and health sciences, 030104 developmental biology, PCR analysis, Polymorphism (materials science), [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 010606 plant biology & botany
Abstract

Aim. The short arm of 1R rye (Secale cereale L.) chromosome is widely used in the breeding of bread wheat (Triticum aestivum L.), in particular 1RS.1BL, to introsgress genes of resistance to leaf (Lr26), stem (Sr31), striped (Yr9) rusts, as well as powdery mildew (Pm8); 1RS.1AL carries Gb2/Gb6 resistance genes to the wheat aphid (Schizaphis graminum Rondani), powdery mildew (Pm17), and the Cmc4 resistance gene to the Aceria tosichella Koifer mite, which is a vector for spreading of wheat mosaic virus. The aim of the research is to reveal molecular genetic polymorphisms of short arm rye 1RS chromosomes of different origins in bread wheat lines with 1RS.1BL translocation or 1R(1B) substitution from different sources. Methods. Genetic polymorphism of lines was analyzed by using PCR with a number of rye and wheat microsatellite markers. Results. It was shown that the CWXs line has a recombinant 1RS arm that contains the chromosomes parts of 1RS of the parental lines H242/97-2 and H273/97, due to crossover event, which led to the recombination of marked loci. Conclusions. Molecular genetic polymorphism has been reviled in 1RS.1BL translocations and 1R substituted rye chromosomes of different origins in H242/97-2, CWXs, H273/97, PavonMA1, Salmon lines, as there are different alleles present at loci: Xscm9, Xtsm422, Xgwm752, Xgwm18, Taglgap. Keywords: polymorphism, 1RS.1BL translocation, PCR analysis, microsatellites markers.

Published
2019

4. The native acyltransferase-coding genes DGA1 and DGA2 affect lipid accumulation in Blastobotrys raffinosifermentans differently when overexpressed

Author

Cécile Neuvéglise, Daniel Ruben Akiola Sanya, Djamila Onésime, Gotthard Kunze, Anne-Marie Crutz-Le Coq, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and DS received PhD funding from the IsDB (Islamic Development Bank).

Subjects
Blastobotrys raffinosifermentans, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Lipid accumulation, Biology, Arxula, Applied Microbiology and Biotechnology, Microbiology, DGAT, 03 medical and health sciences, Amino Acid Sequence, Diacylglycerol O-Acyltransferase, Gene, 030304 developmental biology, Diacylglycerol kinase, 2. Zero hunger, 0303 health sciences, Strain (chemistry), 030306 microbiology, Fatty Acids, lipid production, General Medicine, Lipid Metabolism, Yeast, Biochemistry, Acyltransferases, Acyltransferase, Saccharomycetales, diacylglycerol acyltransferase, Microorganisms, Genetically-Modified, triacylglycerol
Abstract

Blastobotrys raffinosifermentans is an ascomycetous yeast with biotechnological applications, recently shown to be an oleaginous yeast accumulating lipids under nitrogen limitation. Diacylglycerol acyltransferases (DGATs) act in the lipid storage pathway, in the last step of triacylglycerol biosynthesis. Two DGAT families are widespread in eukaryotes. We first checked that B. raffinosifermentans strain LS3 possessed both types of DGAT, and we then overexpressed the native DGAT-encoding genes, DGA1 and DGA2, separately or together. DGA2 (from the DGAT1 family) overexpression was sufficient to increase lipid content significantly in LS3, to up to 26.5% of dry cell weight (DCW), 1.6 times the lipid content of the parental strain (16.90% of DCW) in glucose medium under nitrogen limitation. By contrast, DGA1 (of the DGAT2 type) overexpression led to a large increase (up to 140-fold) in the amount of the corresponding transcript, but had no effect on overall lipid content relative to the parental strain. Analysis of the expression of the native genes over time in the parental strain revealed that DGA2 transcript levels quadrupled between 8 and 24 h in the N-limited lipogenic medium, whereas DGA1 transcript levels remained stable. This survey highlights the predominant role of the DGAT1 family in lipid accumulation and demonstrates the suitability of B. raffinosifermentans for engineering for lipid production.

Published
2020

5. The Arabidopsis condensin CAP-D subunits arrange interphase chromatin

Author

Andrea Bräutigam, Celia Municio, Michiel Van Bel, Veit Schubert, Wojciech Antosz, Frederik Coppens, Ignacio Eguinoa, Klaus D. Grasser, Andreas Houben, Etienne Kornobis, Inna Lermontova, Katarzyna Zelkowska, Astrid Bruckmann, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), University of Regensburg, Biomics (plateforme technologique), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Mendel Centre for Plant Genomics and Proteomics [Brno, Czech Republic], Masaryk University [Brno] (MUNI)-CEITEC - Central European Institute of Technology [Brno, Czech Republic], and The work was supported by a Marie Curie Initial Training Network fellowship (FP7-PEOPLE-2013-ITN, CHIP-ET). The A. Bruckmann and KDG laboratories were supported by the German Research Foundation through grant SFB960. IL was supported by European Regional Development ‘Fund-Project MSCAfellow@MUNI’ (no. CZ.02.2.69/0.0/0.0/17_050/0008496).

Subjects
0106 biological sciences, 0301 basic medicine, chromosomes, Euchromatin, Arabidopsis thaliana, Physiology, Heterochromatin, Condensin, Arabidopsis, Plant Science, macromolecular substances, 01 natural sciences, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Condensin complex, Animals, Interphase, Adenosine Triphosphatases, biology, Chemistry, condensin, Biology and Life Sciences, biology.organism_classification, Chromatin, Cell biology, DNA-Binding Proteins, SMC proteins, 030104 developmental biology, Histone, Multiprotein Complexes, biology.protein, 010606 plant biology & botany, chromatin organization, interphase nuclei
Abstract

International audience; Condensins are best known for their role in shaping chromosomes. Other functions such as organizing interphase chromatin and transcriptional control have been reported in yeasts and animals, but little is known about their function in plants. To elucidate the specific composition of condensin complexes and the expression of CAP-D2 (condensin I) and CAP-D3 (condensin II), we performed biochemical analyses in Arabidopsis. The role of CAP-D3 in interphase chromatin organization and function was evaluated using cytogenetic and transcriptome analysis in cap-d3 T-DNA insertion mutants. CAP-D2 and CAP-D3 are highly expressed in mitotically active tissues. In silico and pulldown experiments indicate that both CAP-D proteins interact with the other condensin I and II subunits. In cap-d3 mutants, an association of heterochromatic sequences occurs, but the nuclear size and the general histone and DNA methylation patterns remain unchanged. Also, CAP-D3 influences the expression of genes affecting the response to water, chemicals, and stress. The expression and composition of the condensin complexes in Arabidopsis are similar to those in other higher eukaryotes. We propose a model for the CAP-D3 function during interphase in which CAP-D3 localizes in euchromatin loops to stiffen them and consequently separates centromeric regions and 45S rDNA repeats.

Published
2020

6. Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops

Author

Evangelia V. Avramidou, Stéphane Maury, Philippe Gallusci, Efi Sarri, Federico Martinelli, Eleni M. Abraham, Maria Gerakari, Eleni Tani, Na'ama Segal, Chiara Vergata, Mateo Gašparović, Valya Vassileva, Pilar S. Testillano, Glória Pinto, Eirini Kaiserli, Vasileios Fotopoulos, Miroslav Baránek, Hans Hoenicka, Erna Karalija, Dragana Miladinović, Aliki Kapazoglou, Velimir Mladenov, Manuela Nagel, European Cooperation in Science and Technology, Mladenov, Velimir, Fotopoulos, Vasileios, Kaiserli, Eirini, Karalija, Erna, Maury, Stéphane, Baránek, Miroslav, Segal, Na’ama, Testillano, P. S., Vassileva, Valya, Pinto, Glória, Nagel, Manuela, Hoenicka, Hans, Miladinovic, Dragana, Gallusci, Philippe, Vergata, Chiara, Kapazoglou, Aliki, Abraham, Eleni, Tani, Eleni, Sarri, Efi, Avramidou, Evangelia V., Gašparović, Mateo, Martinelli, Federico, Mladenov, Velimir [0000-0002-2182-6579], Fotopoulos, Vasileios [0000-0003-1205-2070], Kaiserli, Eirini [0000-0003-1517-4591], Karalija, Erna [0000-0001-7262-0645], Maury, Stéphane [0000-0003-0481-0847], Baránek, Miroslav [0000-0002-1583-3588], Segal, Na’ama [0000-0002-4133-6411, Testillano, P. S. [0000-0003-4509-7646], Vassileva, Valya [0000-0002-9055-8002], Pinto, Glória [0000-0001-7735-5131], Nagel, Manuela [0000-0003-0396-0333], Hoenicka, Hans [0000-0001-7226-3772], Miladinovic, Dragana [0000-0001-9555-9162], Gallusci, Philippe [0000-0003-1163-8299], Vergata, Chiara [0000-0003-2727-7977], Kapazoglou, Aliki [0000-0002-7584-5994], Abraham, Eleni [0000-0003-4032-5830], Tani, Eleni [0000-0001-6178-0459], Sarri, Efi [0000-0003-4816-2167], Avramidou, Evangelia V. [0000-0002-5932-1189], Gašparović, Mateo [0000-0003-2345-7882], Martinelli, Federico [0000-0002-8502-767X], University of Novi Sad, Cyprus University of Technology, University of Glasgow, University of Sarajevo, UNIVERZITET U SARAJEVU, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mendel University in Brno (MENDELU), National Center for Mariculture, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Bulgarian Academy of Sciences (BAS), Universidade de Aveiro, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Thünen Institute of Forest Genetics, Institute of Field and Vegetable Crops [Novi Sad], Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute for Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organisation 'DEMETER', Aristotle University of Thessaloniki, Agricultural University of Athens, and University of Zagreb

Subjects
Epigenomics, 0106 biological sciences, 0301 basic medicine, Acclimatization, Inheritance Patterns, Review, 01 natural sciences, Epigenesis, Genetic, Biotic stress, Gene Expression Regulation, Plant, Biology (General), Stress memory, Spectroscopy, 2. Zero hunger, Agricultural Sciences, Epigenetic, food and beverages, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Adaptation, Physiological, Computer Science Applications, Chemistry, Identification (biology), abiotic stress, biotic stress, epigenetic, methodology, stress memory, transgenerational memory, Crops, Agricultural, QH301-705.5, Biology, Catalysis, Inorganic Chemistry, 03 medical and health sciences, Transgenerational epigenetics, Stress, Physiological, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Epigenetics, Physical and Theoretical Chemistry, QD1-999, Molecular Biology, Abiotic stress, fungi, Organic Chemistry, Methodology, Agriculture Forestry and Fisheries, Transgenerational memory, DNA Methylation, Plant Breeding, 030104 developmental biology, 13. Climate action, Evolutionary biology, Alphabet, Adaptation, 010606 plant biology & botany
Abstract

20 p.-3 fig., Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics, This finalization of the review was funded by COST Action CA19125—EPIgenetic mechanisms of Crop Adaptation to Climate cHange.

Published
2021

7. BrAPI-an application programming interface for plant breeding applications

Author

Guilhem Sempere, Patrick König, Bruno Costa, Jan Erik Backlund, Jack Elendil B. Lagare, Viana C. Calaminos, Jeremy D. Edwards, Gordon Stephen, Omar Eduardo Benites-Alfaro, Pierre Carceller, Martin Basterrechea Salido, David LeBauer, Maikel P. H. Verouden, Guillaume Cornut, Nicolas Morales, Philip Glaser, David Marshall, Evangelia Papoutsoglou, Cyril Pommier, Guillaume Bauchet, Valentin Guignon, Kelly R. Robbins, Iain Milne, David A. Lyon, Pascal Neveu, Brian Pearce, Chaitanya Sarma, Qi Sun, Nahuel Soldevilla, Sebastian Raubach, Peter Selby, Clarysabel Tovar, Grzegorz Uszynski, Rafael Abbeloos, Reinhard Simon, Paul Shaw, Marie-Angélique Laporte, Mathieu Rouard, Star Yanxin Gao, Naymesh Mistry, Puthick Hok, Uwe Scholz, Trevor W. Rife, Ricardo H. Ramirez-Gonzalez, Dave Matthews, Mehmood Ghaffar, Pierre Larmande, Matthias Lange, Andrzej Kilian, Clayton Birkett, Ivan Perez-Masias, Angel Manica Raquel, Abhishek Rathore, Lukas A. Mueller, Richard Finkers, Wren, Jonathan, Flanders Institute for Biotechnology, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Boyce Thompson Institute [Ithaca], International Potato Center, USDA-ARS : Agricultural Research Service, International Rice Research Institute [Philippines] (IRRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Instituto de Biologia Experimental e Tecnológica (IBET), Wageningen University and Research Centre (WUR), Cornell University [New York], CGIAR, Diversity Arrays Technology Pty Ltd (DArT P/L), Institut de Recherche pour le Développement (IRD), University of Arizona, The James Hutton Institute, LeafNode Technology, Partenaires INRAE, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT), Kansas State University, Leafnode Technolog, Biometris, Gates Foundation, Bioversity International, Federal Ministry of Education & Research (BMBF) : FKZ 031A536A, 031B0190A, Boyce Thompson Institute for Plant Research CGIAR Research Program on Roots, Tubers and Bananas, Cornell University Excellence in Breeding Platform, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and John Innes Centre

Subjects
0106 biological sciences, Germplasm, programme informatique, Computer science, [SDV]Life Sciences [q-bio], Data management, computer.software_genre, 01 natural sciences, Biochemistry, F30 - Génétique et amélioration des plantes, User-Computer Interface, Software, Laboratorium voor Plantenveredeling, [MATH]Mathematics [math], 0303 health sciences, Application programming interface, U10 - Informatique, mathématiques et statistiques, Genomics, Original Papers, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, Web service, sélection végétale, Statistics and Probability, Technology and Engineering, Databases and Ontologies, génomique, 03 medical and health sciences, Bioinformatique, application informatique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Life Science, [INFO]Computer Science [cs], Plant breeding, Genotyping, Molecular Biology, 030304 developmental biology, business.industry, Biology and Life Sciences, Amélioration des plantes, Data science, Plant Breeding, business, computer, 010606 plant biology & botany
Abstract

Motivation Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. Availability and implementation More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.

Published
2018

8. Novel loci and a role for nitric oxide for seed dormancy and preharvest sprouting in barley

Author

Ahmad M. Alqudah, Marlène Bailly, Loïc Rajjou, Manuela Nagel, Gabriele Matzig, Ilse Kranner, Andreas Börner, Sibylle Pistrick, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), and University of Innsbruck

Subjects
0106 biological sciences, 0301 basic medicine, hordeum vulgare, Physiology, [SDV]Life Sciences [q-bio], Germination, Plant Science, Biology, Genes, Plant, Nitric Oxide, 01 natural sciences, 03 medical and health sciences, Anthesis, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, 2. Zero hunger, after-ripening, Arabidopsis Proteins, Seed dormancy, food and beverages, Hordeum, Plant Dormancy, Horticulture, 030104 developmental biology, Dormancy, Preharvest, Gibberellin, Hordeum vulgare, 010606 plant biology & botany, Sprouting, Genome-Wide Association Study
Abstract

International audience; Barley is used for food and feed, and brewing. Nondormant seeds are required for malting, but the lack of dormancy can lead to preharvest sprouting (PHS), which is also undesired. Here, we report several new loci that modulate barley seed dormancy and PHS. Using genome-wide association mapping of 184 spring barley genotypes, we identified four new, highly significant associations on chromosomes 1H, 3H, and 5H previously not associated with barley seed dormancy or PHS. A total of 71 responsible genes were found mostly related to flowering time and hormone signalling. A homolog of the well-known Arabidopsis Delay of Germination 1 (DOG1) gene was annotated on the barley chromosome 3H. Unexpectedly, DOG1 appears to play only a minor role in barley seed dormancy. However, the gibberellin oxidase gene HvGA20ox1 contributed to dormancy alleviation, and another seven important loci changed significantly during after-ripening. Furthermore, nitric oxide release correlated negatively with dormancy and shared 27 associations. Origin and growth environment affected seed dormancy and PHS more than did agronomic traits. Days to anthesis and maturity were shorter when seeds were produced under drier conditions, seeds were less dormant, and PHS increased, with a heritability of 0.57-0.80. The results are expected to be useful for crop improvement.

Published
2018

9. Immersive Analytics: An Introduction

Author

Tim Dwyer, Wolfgang Stuerzlinger, Karsten Klein, Kim Marriott, Bruce H. Thomas, Tobias Isenberg, Nathalie Henry Riche, Falk Schreiber, Monash University [Clayton], Analysis and Visualization (AVIZ), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), The University of Sydney, Microsoft Research [Redmond], Microsoft Corporation [Redmond, Wash.], Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Department of Computer Science and Engineering [York], York University [Toronto], Centre Européen de Réalité Virtuelle (CERV), École Nationale d'Ingénieurs de Brest (ENIB), Dwyer, Tim, Marriott, Kim, Isenberg, Tobias, Klein, Karsten, Riche, Nathalie, Schreiber, Falk, Stuerzlinger, Wolfgang, Thomas, Bruce H., and University of South Australia [Adelaide]

Subjects
Computer science, 05 social sciences, ComputingMilieux_PERSONALCOMPUTING, [SCCO.COMP]Cognitive science/Computer science, Multi-sensory, 020207 software engineering, 02 engineering and technology, Research initiative, Data science, Immersive analytics, Multi sensory, Data analytics, 2D and 3D, ComputerApplications_MISCELLANEOUS, 0202 electrical engineering, electronic engineering, information engineering, 0501 psychology and cognitive sciences, Decision making, 050107 human factors, ComputingMethodologies_COMPUTERGRAPHICS
Abstract

International audience; Immersive Analytics is a new research initiative that aims to remove barriers between people, their data and the tools they use for analysis and decision making. Here we clarify the aims of immersive analytics research, its opportunities and historical context, as well as providing a broad research agenda for the field. In addition, we review how the term immersion has been used to refer to both technological and psychological immersion, both of which are central to immersive analytics research.

Published
2018

10. In-flight photometry extraction of PLATO targets

Author

Juan Cabrera, N. Kutrowski, Martin Pertenais, A. Monsky, Carsten Paproth, Anko Börner, R. Samadi, F. Fialho, A. Santerne, V. Marchiori, Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centro de Astrofísica da Universidade do Porto (CAUP), Universidade do Porto, Deutsches Zentrum für Luft- und Raumfahrt [Berlin] (DLR), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and Institut de Radioprotection et de Sûreté Nucléaire (IRSN)

Subjects
Extrasolare Planeten und Atmosphären, planets and satellites: detection, FOS: Physical sciences, Context (language use), Astrophysics, 01 natural sciences, Asteroseismology, methods: numerical, Photometry (optics), techniques: photometric, Apparent magnitude, Planet, 0103 physical sciences, Instrumentation and Methods for Astrophysics (astro-ph.IM), 010303 astronomy & astrophysics, Institut für Optische Sensorsysteme, Earth and Planetary Astrophysics (astro-ph.EP), Physics, 010308 nuclear & particles physics, zodiacal dust, Astrophysics::Instrumentation and Methods for Astrophysics, Astronomy and Astrophysics, Planetary system, Exoplanet, instrumentation: photometers, Space and Planetary Science, Astrophysics::Earth and Planetary Astrophysics, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Astrophysics - Instrumentation and Methods for Astrophysics, Circumstellar habitable zone, catalogs, Astrophysics - Earth and Planetary Astrophysics
Abstract

The ESA PLATO space mission is devoted to unveiling and characterizing new extrasolar planets and their host stars. This mission will encompass a very large field of view, granting it the potential to survey up to one million stars depending on the final observation strategy. The telemetry budget of the spacecraft cannot handle transmitting individual images for such a huge stellar sample at the right cadence, so the development of an appropriate strategy to perform on-board data reduction is mandatory. We employ aperture photometry to produce stellar light curves in flight. Our aim is thus to find the mask model that optimizes the scientific performance of the reduced data. We considered three distinct aperture models: binary mask, weighted Gaussian mask, and weighted gradient mask giving lowest noise-to-signal ratio, computed through a novel direct method. An innovative criterion was adopted for choosing between different mask models. We designated as optimal the model providing the best compromise between sensitivity to detect true and false planet transits. We determined the optimal model based on simulated noise-to-signal ratio and frequency of threshold crossing events. Our results show that, although the binary mask statistically presents a few percent higher noise-to-signal ratio compared to weighted masks, both strategies have very similar efficiency in detecting legitimate planet transits. When it comes to avoiding spurious signals from contaminant stars however the binary mask statistically collects considerably less contaminant flux than weighted masks, thereby allowing the former to deliver up to $\sim$30\% less false transit signatures at $7.1\sigma$. Our proposed approach for choosing apertures has been proven to be decisive for the determination of a mask model capable to provide near maximum planet yield and substantially reduced occurrence of false positives., Comment: 20 pages, 22 figures, Astronomy & Astrophysics (accepted)

Published
2019

11. Nitrite–nitric oxide control of mitochondrial respiration at the frontier of anoxia

Author

Ljudmilla Borisjuk, David Macherel, Marie-Hélène Avelange-Macherel, Abdelilah Benamar, H. Ahmed Mostefai, Gilles Curien, Ramaroson Andriantsitohaina, Hardy Rolletschek, Physiologie Moléculaire des Semences (PMS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-Institut National d'Horticulture, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Biologie Neurovasculaire Intégrée (BNVI), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Institut für Pflanzengenetik und Kulturpflanzenforschung, 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 National d'Horticulture-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), 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)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
0106 biological sciences, Bioenergetics, Nitrite, Cell Respiration, Biophysics, plant, Mitochondrion, bioenergetics, 01 natural sciences, Biochemistry, mathematical analysis, Nitric oxide, 03 medical and health sciences, chemistry.chemical_compound, Oxygen homeostasis, Respiration, Animals, Cytochrome c oxidase, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Nitrites, Pisum sativum, 030304 developmental biology, 0303 health sciences, biology, hypoxia, Electron Spin Resonance Spectroscopy, Peas, anoxia, Cell Biology, Plants, Cell biology, Oxygen, mitochondria, chemistry, germination, Coenzyme Q – cytochrome c reductase, Seeds, Mammalia, biology.protein, Oxidation-Reduction, seed, respiration, 010606 plant biology & botany
Abstract

International audience; Actively respiring animal and plant tissues experience hypoxia because of mitochondrial O(2) consumption. Controlling oxygen balance is a critical issue that involves in mammals hypoxia-inducible factor (HIF) mediated transcriptional regulation, cytochrome oxidase (COX) subunit adjustment and nitric oxide (NO) as a mediator in vasodilatation and oxygen homeostasis. In plants, NO, mainly derived from nitrite, is also an important signalling molecule. We describe here a mechanism by which mitochondrial respiration is adjusted to prevent a tissue to reach anoxia. During pea seed germination, the internal atmosphere was strongly hypoxic due to very active mitochondrial respiration. There was no sign of fermentation, suggesting a down-regulation of O(2) consumption near anoxia. Mitochondria were found to finely regulate their surrounding O(2) level through a nitrite-dependent NO production, which was ascertained using electron paramagnetic resonance (EPR) spin trapping of NO within membranes. At low O(2), nitrite is reduced into NO, likely at complex III, and in turn reversibly inhibits COX, provoking a rise to a higher steady state level of oxygen. Since NO can be re-oxidized into nitrite chemically or by COX, a nitrite-NO pool is maintained, preventing mitochondrial anoxia. Such an evolutionarily conserved mechanism should have an important role for oxygen homeostasis in tissues undergoing hypoxia.

Published
2008
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12. Plant proteome analysis: A 2004–2006 update

Author

Andrea Matros, Jesús Jorrín, Michel Rossignol, Hans-Peter Mock, Ana M. Maldonado, Jean-Benoît Peltier, Unité de Recherche Protéomique (PROTEOMIQUE), Institut National de la Recherche Agronomique (INRA), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), and University of Córdoba [Córdoba]

Subjects
Proteomics, 0106 biological sciences, Proteome, [SDV]Life Sciences [q-bio], Arabidopsis, Computational biology, 01 natural sciences, Biochemistry, Mass Spectrometry, 03 medical and health sciences, Cell Wall, Stable isotope labeling by amino acids in cell culture, Protein Interaction Mapping, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, Electrophoresis, Gel, Two-Dimensional, Molecular Biology, Plant Proteins, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Oryza sativa, biology, food and beverages, Oryza, 15. Life on land, biology.organism_classification, Plant development, Plant species, Metaproteomics, Protein Processing, Post-Translational, Subcellular Fractions, 010606 plant biology & botany
Abstract

Since the appearance of the review entitled "Plant Proteome Analysis" in Proteomics in February 2004 (Cánovas, F. M., Dumas-Gaudot, E., Recorbert, G., Jorrín, J. et al., Proteomics 2004, 4, 285-298), about 200 original articles focusing on plant proteomics have been published. Although this represents less than 1% of the global proteomics output during this period, it nevertheless reflects an increase in activity over the period 1999-2004. These papers concern the proteome of at least 35 plant species but have concentrated mainly on thale cress (Arabidopsis thaliana) and rice (Oryza sativa). The scientific objectives have ranged from a proteomic analysis of organs, tissues, cell suspensions, or subcellular fractions to the study of plant development and response to various stresses. A number of contributions have covered PTMs and protein interactions. The dominant analytical platform has been 2-DE coupled to MS, but "second generation" techniques such as DIGE, multidimensional protein identification technology, isotope-coded affinity tags, and stable isotope labeling by amino acids in cell culture have begun to make an impact. This review aims to provide an update of the contribution of proteomics to plant biology during the period 2004-2006, and is divided into six sections: introduction, subcellular proteomes, plant development, responses to biotic and abiotic stresses, PTMs, and protein interactions. The conclusions summarize a view of the major pitfalls and challenges of plant proteomics.

Published
2006

13. bZIP transcription factors in Arabidopsis

Author

Marc Jakoby, Bernd Weisshaar, Wolfgang Dröge-Laser, Jesus Vicente-Carbajosa, Jens Tiedemann, Thomas Kroj, François Parcy, Max Planck Institute for Plant Breeding Research (MPIPZ), Albrecht-von-Haller-Institut, Laboratorio de Bioquimica y Biologia Molecular. Dept Biotecnologia - Centro de Biotecnologia y Genomica de Plantas, ETSIA Universidad Politecnica, Institut für Pflanzengenetik und Kulturpflanzenforschung, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Arabidopsis, Plant Science, MESH: Basic-Leucine Zipper Transcription Factors, 01 natural sciences, 03 medical and health sciences, Gene Expression Regulation, Plant, MESH: Zinc Fingers, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Arabidopsis, MESH: Gene Expression Regulation, Plant, 030304 developmental biology, Leucine Zippers, 0303 health sciences, MESH: G-Box Binding Factors, food and beverages, Zinc Fingers, MESH: Transcription Factors, MESH: Leucine Zippers, DNA-Binding Proteins, Basic-Leucine Zipper Transcription Factors, G-Box Binding Factors, Multigene Family, MESH: Multigene Family, MESH: DNA-Binding Proteins, Transcription Factors, 010606 plant biology & botany
Abstract

In plants, basic region/leucine zipper motif (bZIP) transcription factors regulate processes including pathogen defence, light and stress signalling, seed maturation and flower development. The Arabidopsis genome sequence contains 75 distinct members of the bZIP family, of which approximately 50 are not described in the literature. Using common domains, the AtbZIP family can be subdivided into ten groups. Here, we review the available data on bZIP functions in the context of subgroup membership and discuss the interacting proteins. This integration is essential for a complete functional characterization of bZIP transcription factors in plants, and to identify functional redundancies among AtbZIP factors.

Published
2002

14. 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

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