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151. Combined QTL and Selective Sweep Mappings with Coding SNP Annotation andcis-eQTL Analysis RevealedPARK2andJAG2as New Candidate Genes for Adiposity Regulation

Author: Morgane Boutin, M. J. Duclos, Colette Désert, Elisabeth Le Bihan-Duval, Diane Esquerre, Yuna Blum, Sandrine Lagarrigue, Frédérique Pitel, Hervé Guillou, Pierre-François Roux, Etienne Mouisel, Brian W. Parks, Olivier Demeure, Sophie Leroux, Christophe Klopp, Anis Djari, Bertrand Servin, Aldons J. Lusis, Simon Boitard, Alexandra Montagner, Frédéric Lecerf, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université européenne de Bretagne - European University of Brittany (UEB), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Medecine/Division of Cardiology, University of California [Los Angeles] (UCLA), University of California-University of California, ToxAlim (ToxAlim), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), SIGENAE, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherches Avicoles (URA), Department of Human Genetics, Toxicologie Intégrative & Métabolisme (ToxAlim-TIM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] ( PEGASE ), Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Université européenne de Bretagne ( UEB ), Biologie Intégrative des Populations, École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS ), Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, University of California at Los Angeles [Los Angeles] ( UCLA ), Toxicologie Alimentaire ( UTA ), 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, UMR 1048 I2MC, Institut National de la Santé et de la Recherche Médicale, Unité de Biométrie et Intelligence Artificielle ( UBIA ), Institut National de la Recherche Agronomique ( INRA ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, GENOTOUL, Recherches Avicoles ( SRA ), 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), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), 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-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Toxicologie Alimentaire (UTA), 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 National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Recherches Avicoles (SRA), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of California (UC)-University of California (UC), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Candidate gene, QTL, [SDV]Life Sciences [q-bio], génomique fonctionnelle, métabolisme des lipides, Mice, selective sweeps, 0302 clinical medicine, Family-based QTL mapping, régulation, Genetics (clinical), Genetics, adiposity, 0303 health sciences, Genome, Chromosome Mapping, High-Throughput Nucleotide Sequencing, adiposité, cis-eQTLs, divergent lines, gène candidat, Jagged-2 Protein, JAG2, Adipose Tissue, White, Ubiquitin-Protein Ligases, Quantitative Trait Loci, poulet, Context (language use), annotation génomique, Myosins, Investigations, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Cell Line, 03 medical and health sciences, Gene mapping, séquençage à haut débit, Animals, Molecular Biology, Alleles, 030304 developmental biology, [ SDV ] Life Sciences [q-bio], Membrane Proteins, Molecular Sequence Annotation, Sequence Analysis, DNA, PARK2, détection de qtl, SNP annotation, Expression quantitative trait loci, Selective sweep, Chickens, 030217 neurology & neurosurgery
Abstract: Very few causal genes have been identified by quantitative trait loci (QTL) mapping because of the large size of QTL, and most of them were identified thanks to functional links already known with the targeted phenotype. Here, we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify potential causal genes underlying QTL identified in divergent line designs. As a model, we chose experimental chicken lines divergently selected for only one trait, the abdominal fat weight, in which several QTL were previously mapped. Using new haplotype-based statistics exploiting the very high SNP density generated through whole-genome resequencing, we found 129 significant selective sweeps. Most of the QTL colocalized with at least one sweep, which markedly narrowed candidate region size. Some of those sweeps contained only one gene, therefore making them strong positional causal candidates with no presupposed function. We then focused on two of these QTL/sweeps. The absence of nonsynonymous SNPs in their coding regions strongly suggests the existence of causal mutations acting in cis on their expression, confirmed by cis-eQTL identification using either allele-specific expression or genetic mapping analyses. Additional expression analyses of those two genes in the chicken and mice contrasted for adiposity reinforces their link with this phenotype. This study shows for the first time the interest of combining selective sweeps mapping, coding SNP annotation and cis-eQTL analyses for identifying causative genes for a complex trait, in the context of divergent lines selected for this specific trait. Moreover, it highlights two genes, JAG2 and PARK2, as new potential negative and positive key regulators of adiposity in chicken and mice.
Published: 2015

152. Histone posttranslational modifications rather than DNA methylation underlie gene reprogramming in pollination‐dependent and pollination‐independent fruit set in tomato.

Author: Hu, Guojian, Huang, Baowen, Wang, Keke, Frasse, Pierre, Maza, Elie, Djari, Anis, Benhamed, Moussa, Gallusci, Philippe, Li, Zhengguo, Zouine, Mohamed, and Bouzayen, Mondher
Subjects: POST-translational modification, EPIGENOMICS, DNA methylation, FRUIT, NUCLEOTIDE sequence, FRUIT processing
Abstract: Summary: Fruit formation comprises a series of developmental transitions among which the fruit set process is essential in determining crop yield. Yet, our understanding of the epigenetic landscape remodelling associated with the flower‐to‐fruit transition remains poor.We investigated the epigenetic and transcriptomic reprogramming underlying pollination‐dependent and auxin‐induced flower‐to‐fruit transitions in the tomato (Solanum lycopersicum) using combined genomewide transcriptomic profiling, global ChIP‐sequencing and whole genomic DNA bisulfite sequencing (WGBS).Variation in the expression of the overwhelming majority of genes was associated with change in histone mark distribution, whereas changes in DNA methylation concerned a minor fraction of differentially expressed genes. Reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone posttranslational modifications rather than DNA methylation are associated with the remodelling of the epigenetic landscape underpinning the flower‐to‐fruit transition.Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations. [ABSTRACT FROM AUTHOR]
Published: 2021
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153. TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks

Author: Mohammed Zouine, Abdelaziz Smouni, Mattieu Lauvernier, Julien Pirrello, Anis Djari, Pierre Frasse, Mondher Bouzayen, Elie Maza, Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Université Mohammed V-Rabat - UM5 (MOROCCO), Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Biotechnologie et Physiologie Végétales, Centre de recherche BioBio, Faculté des Sciences, Université Mohammed V de Rabat, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), and Institut National Polytechnique de Toulouse - INPT (FRANCE)
Subjects: 0106 biological sciences, 0301 basic medicine, Tomato, RNA-Seq, Database, Platform, Web tool, Gene expression, Data mining, analyse de données, Agronomie, data analysis, Value (computer science), Plant Science, Web Browser, tomato, Bioinformatics, computer.software_genre, 01 natural sciences, tomate, Solanum lycopersicum, Databases, Genetic, Cluster Analysis, 2. Zero hunger, Vegetal Biology, Identification (information), RNA, Plant, Biodiversité, User interface, Genome, Plant, expression génique, Biology, Set (abstract data type), 03 medical and health sciences, Data visualization, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cluster analysis, Internet, Sequence Analysis, RNA, business.industry, Web tools, plateforme informatique, Cell Biology, Pipeline (software), Visualization, 030104 developmental biology, séquence d'arn, visualisation de données, gene expression, business, computer, Biologie végétale, 010606 plant biology & botany
Abstract: The TomExpress platform was developed to provide the tomato research community with a browser and integrated web tools for public RNA-Seq data visualization and data mining. To avoid major biases that can result from the use of different mapping and statistical processing methods, RNA-Seq raw sequence data available in public databases were mapped de novo on a unique tomato reference genome sequence and post-processed using the same pipeline with accurate parameters. Following the calculation of the number of counts per gene in each RNA-Seq sample, a communal global normalization method was applied to all expression values. This unifies the whole set of expression data and makes them comparable. A database was designed where each expression value is associated with corresponding experimental annotations. Sample details were manually curated to be easily understandable by biologists. To make the data easily searchable, a user-friendly web interface was developed that provides versatile data mining web tools via on-the-fly generation of output graphics such as expression bar plots, comprehensive in planta representations and heatmaps of hierarchically clustered expression data. In addition, it allows for the identification of co-expressed genes and for the visualization of correlation networks of co-regulated gene groups. TomExpress provides one of the most complete free resources of publicly available tomato RNA-Seq data and allows for the immediate interrogation of transcriptional programs that regulate vegetative and reproductive development in tomato under diverse conditions. The design of the pipeline developed in this project enables easy updating of the database with newly published RNA-Seq data, thereby allowing for continuous enrichment of the resource.
Published: 2017

154. Voltage stability assessment using the V-Q sensitivity and modal analyses methods

Author: Mohammed Adel Djari, Walid Rahmouni, and Lahouaria Benasla
Subjects: Coupling, 020209 energy, Modal analysis, 05 social sciences, Diagonal, Mathematical analysis, 02 engineering and technology, AC power, symbols.namesake, Modal, 0502 economics and business, Jacobian matrix and determinant, 0202 electrical engineering, electronic engineering, information engineering, symbols, Sensitivity (control systems), 050203 business & management, Eigenvalues and eigenvectors, Mathematics
Abstract: Voltage stability is an important factor, which needs to be taken into consideration in order to avoid voltage collapse. There are different methods used to study the voltage collapse phenomenon. In this paper, V-Q Sensitivity and Modal analyses methods are implemented on IEEE 14 bus system. Modal analysis method makes use the Jacobian matrix to determine the eigenvalues necessary to evaluate the voltage stability and V-Q Sensitivity method makes use of the diagonal elements of the inverse of reduced Jacobian matrix to a assess this stability. In this paper, our main objective is to apply V-Q Sensitivity and Modal analysis methods by analyzing the effect of neglecting the weak coupling between reactive power Q and voltage angle δ A comparison in terms of the weakest buses is made between the results obtained by taking into account the weak coupling between Q and δ, i.e., by considering the reduced Jacobian matrix and those obtained by neglecting this coupling.
Published: 2017

155. FLC based Gaussian membership functions tuned by PSO and GA for MPPT of photovoltaic system: A comparative study

Author: Abdelhamid Djari, Djamel Boukhetala, Noureddine Bouarroudj, Boualem Benlahbib, and Younes Rais
Subjects: Engineering, business.industry, 020209 energy, Gaussian, Principal (computer security), Photovoltaic system, Control engineering, 02 engineering and technology, Maximum power point tracking, Fuzzy logic controller, symbols.namesake, Control theory, 0202 electrical engineering, electronic engineering, information engineering, symbols, business
Abstract: This article focuses on two principal subjects. In the first, a Mamdani Fuzzy Logic Controller (FLC) based Gaussian membership functions is considered for the maximum power point tracking (MPPT) of a photovoltaic (PV) system.
Published: 2017

156. Tuning of decentralized fuzzy logic sliding mode controller using PSO algorithm for nonlinear Twin Rotor Mimo System

Author: Djamel Boukhetala, Noureddine Bouarroudj, Fares Boudjema, and Abdelhamid Djari
Subjects: 0209 industrial biotechnology, Engineering, Rotor (electric), business.industry, MIMO, Particle swarm optimization, 020206 networking & telecommunications, 02 engineering and technology, Sliding mode control, Fuzzy logic, law.invention, Nonlinear system, 020901 industrial engineering & automation, Control theory, law, 0202 electrical engineering, electronic engineering, information engineering, Trajectory, business
Abstract: This paper presents the optimization of a variable structure controller based on a decentralized fuzzy logic sliding mode (DFLSM) strategy for the control of the pitch and azimuth angles of a TRMS when coupling vertical and horizontal axes. Particle Swarm Optimization (PSO) algorithm is used to tune the DFLSMC parameters to ensure optimal performance in the closed loop, within a given cost function. Finally, simulation results show the effectiveness of the decentralized FLSMC-based PSO algorithm in the stabilization and trajectory tracking tests compared to a non-optimized DFLSMC.
Published: 2017

157. Genetic variability of the activity of bidirectional promoters : a pilot study in bovine muscle

Author: Abderrahman Maftah, Emmanuelle Rebours, Rabia Letaief, Gabriel Guillocheau, Véronique Léjard, Diane Esquerre, Christy J. Vander Jagt, Mekki Boussaha, Dominique Rocha, Gilles Renand, Anis Djari, Amanda J. Chamberlain, Cédric Meersseman, Daniel Petit, Christophe Klopp, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Génétique Moléculaire Animale (UGMA), Université de Limoges (UNILIM)-Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Dairy Futures Cooperat Res, Ctr, Bundoora, AgriBio, Dept Econ Dev Jobs Transport & Resources, Bundoora, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Unité de Génétique Moléculaire Animale (UMR GMA)
Subjects: Male, 0301 basic medicine, muscle, [SDV]Life Sciences [q-bio], Pilot Projects, Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, cattle genome, Genetic variation, genetic variability, Genetics, Animals, Genetic variability, Promoter Regions, Genetic, bidirectional promoter, Molecular Biology, Gene, Regulation of gene expression, Back Muscles, Gene Expression Profiling, Proteins, Promoter, General Medicine, Full Papers, Gene expression profiling, Editor's Choice, 030104 developmental biology, Gene Expression Regulation, Regulatory sequence, Cattle
Abstract: Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters. Combining bovine gene information and expression data obtained using RNA-Seq, we identified 120 putative bidirectional promoters active in bovine muscle. We experimentally validated in vitro 16 of these bidirectional promoters. Finally, using gene expression and whole-genome genotyping data, we explored the variability of the activity in muscle of the identified bidirectional promoters and discovered genetic variants affecting their activity. We found that the expression level of 77 genes is correlated with the activity of 12 bidirectional promoters. We also identified 57 single nucleotide polymorphisms associated with the activity of 5 bidirectional promoters. To our knowledge, our study is the first analysis in any species of the genetic variability of the activity of bidirectional promoters.
Published: 2017

158. A Computational Study on Fairness of the Tendermint Blockchain Protocol

Author: Önder Gürcan, Nicolas Lagaillardie, and Mohamed Aimen Djari
Subjects: blockchain, 021110 strategic, defence & security studies, Delegate, Computer science, Investment strategy, 0211 other engineering and technologies, fairness, 02 engineering and technology, Rational agent, simulation, Asset (computer security), Computer security, computer.software_genre, Validator, 0202 electrical engineering, electronic engineering, information engineering, tendermint, 020201 artificial intelligence & image processing, Set (psychology), computer, Protocol (object-oriented programming), Information Systems, Block (data storage)
Abstract: Fairness is a crucial property for blockchain systems since it affects the participation: the ones that find the system fair tend to stay or enter, the ones that find the system unfair tend to leave. While current literature mainly focuses on fairness for Bitcoin-like blockchains, little has been done to analyze Tendermint. Tendermint is a blockchain technology that uses a committee-based consensus algorithm, which finds an agreement among a set of block creators (called validators), even if some are malicious. Validators are regularly selected to the committee based on their investments. When a validator does not have enough asset to invest, it can increase it with the help of participants that delegate their assets to the validators (called delegators). In this paper, we implement the default Tendermint model and a Tendermint model for fairness in a multi-agent blockchain simulator where participants are modeled as rational agents who enter or leave the system based on their utility values. We conducted experiments for both models where agents have different investment strategies and with various numbers of delegators. In the light of our experimental evaluation, we observed that while, for both models, the fairness decreases and the system shrinks in the absence of delegators, the fairness increases, and the system expands for the second model in the presence of delegators.
Published: 2019

159. Synthesis of high silica zeolites using a combination of pyrrolidine and tetramethylammonium as template

Author: Djari Rima, Djafri Fatiha, and Dari Djamal
Subjects: Tetramethylammonium, Mas nmr spectroscopy, Polymers and Plastics, Metals and Alloys, Nucleation, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Pyrrolidine, High silica, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, law.invention, Biomaterials, chemistry.chemical_compound, Crystallography, chemistry, Molar ratio, law, Crystallization, 0210 nano-technology, Fluoride
Abstract: High silica ZSM-39 (MTN structure), ZSM-35 (FER structure) and ZSM-5(MFI structure) zeolites were successfully synthesized using pyrrolidine and tetramethylammonium as structure directing agents (SDAs), in absence of alkaline cation and fluoride medium. The effect of the relative amount of tetramethylammonium and pyrrolidine, and Si/Al molar ratio on the crystalline phases was investigated. All structures could be synthesized using pyrrolidine as solely SDA. On the other hand, when a mixed template system being used, the crystallization was accelerated by a factor of 2 times, TMA+ would then play a generally beneficial but structurally non-specific role in the crystallization spicily for FER and MFI zeolites. The obtained products were characterized by XRD, 13C solid-state CP MAS NMR, TGA and SEM techniques. The XRD patterns confirmed the formation of pure zeolites with high crystallinity.13C CP MAS NMR spectroscopy confirmed the incorporation of pyrrolidine and tetramethylammonium in the structure of Al-ZSM-5 and Al-ZSM-35 zeolites. These two kinds of SDAs played a cooperative role in the crystallization of these zeolites. The role of pyrrolidine was to provide the initial nucleation and tetramethylammonium to provide both space-filling and basicity capacities.
Published: 2018

160. Les mutations activatrices de la PKA altèrent les fonctions exocrines et endocrines de l’ovaire : exemple d’un modèle murin de complexe de Carney

Author: Roumeau, S., primary, Sahut-Barnola, I., additional, Djari, C., additional, Tauveron, I., additional, Val, P., additional, Martinez, A., additional, and Lefrançois-Martinez, A.M., additional
Published: 2018
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161. Contribution des compartiments sertoliens et leydigiens à la tumorigenèse testiculaire dépendante de la signalisation PKA

Author: Djari, C., primary, Sahut-Barnola, I., additional, Septier, A., additional, Guillou, F., additional, Swain, A., additional, Lefebvre, H., additional, Stratakis, C., additional, Plotton, I., additional, Val, P., additional, Martinez, A., additional, and Lefrançois-Martinez, A.M., additional
Published: 2018
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162. Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA ‐Seq data normalization and interpretation

Author: Pirrello, Julien, primary, Deluche, Cynthia, additional, Frangne, Nathalie, additional, Gévaudant, Frédéric, additional, Maza, Elie, additional, Djari, Anis, additional, Bourge, Mickaël, additional, Renaudin, Jean‐Pierre, additional, Brown, Spencer, additional, Bowler, Chris, additional, Zouine, Mohamed, additional, Chevalier, Christian, additional, and Gonzalez, Nathalie, additional
Published: 2018
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163. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

Author: Christophe Klopp, Julien Bobe, Frédéric Escudié, Anis Djari, Yann Guiguen, Cédric Cabau, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), ANR-10-GENM-017, PhyloFish, ANR10-INBS-09-08, France Génomique, École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), ANR-10-GENM-0017,PhyloFish,Analyse phylogénomique des duplications géniques chez les poissons téléostéens: une approche par RNA-Seq(2010), and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
Subjects: 0301 basic medicine, quality assessment, Bioinformatics, De novo transcriptome assembly, lcsh:Medicine, computational science, de novo assembly, compaction, correction, genomic, bioinformatic, Sequence assembly, RNA-Seq, Computational biology, Biology, 010501 environmental sciences, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Transcriptome, 03 medical and health sciences, Software, Expression analysis, bioinformatique, 0105 earth and related environmental sciences, Genetics, 030102 biochemistry & molecular biology, Contig, Reference genome sequence, business.industry, General Neuroscience, lcsh:R, assemblage bioinformatique, General Medicine, séquençage du génome, 030104 developmental biology, Bio-informatique, RNA-seq, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], General Agricultural and Biological Sciences, business, transcriptome, expression des gènes
Abstract: Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.
Published: 2016

164. Compacting and correcting Trinity and Oases RNA-Seq

Author: Cédric, Cabau, Frédéric, Escudié, Anis, Djari, Yann, Guiguen, Julien, Bobe, and Christophe, Klopp
Subjects: Bioinformatics, De novo assembly, Compaction, Computational Biology, Correction, Genomics, RNA-Seq, Computational Science, Quality assessment
Abstract: Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.
Published: 2016

165. Les mutations activatrices de la PKA altèrent les fonctions exocrines et endocrines de l’ovaire : exemple d’un modèle murin de complexe de Carney

Author: Antoine Martinez, Igor Tauveron, Isabelle Sahut-Barnola, Cyril Djari, S. Roumeau, Pierre Val, and Anne-Marie Lefrançois-Martinez
Subjects: 0301 basic medicine, 03 medical and health sciences, 030104 developmental biology, Endocrinology, Endocrinology, Diabetes and Metabolism, General Medicine
Abstract: Objectif Le complexe de Carney se caracterise par une neoplasie endocrinienne multiple et des tumeurs des tissus conjonctifs. Les lesions ovariennes toucheraient 14 % des patientes mais restent mal connues du fait de la rarete de la pathologie. L’objectif de cette etude est de caracteriser les anomalies ovariennes structurelles et fonctionnelles dans un modele murin de complexe de Carney. Methodes Une inactivation du gene PRKAR1A dans les gonades des souris « AdKO2,0 » a ete realisee par l’approche Cre/Lox et reproduit les anomalies moleculaires (hyperactivation de la proteine-kinase A, PKA) a l’origine des atteintes du complexe de Carney. Nous avons etudie les ovaires de souris AdKO2,0 et temoins de 14 jours, 1 et 2 mois : dosages hormonaux, histologie, immunohistochimie et RTqPCR. Resultats Les souris AdKO2,0 sont steriles, presentent des kystes et des tumeurs solides ovariennes, une hyper-testosteronemie d’origine ovarienne, et une dysfonction de la folliculogenese : atresie folliculaire precoce majeure, diminution prematuree de la reserve folliculaire, absence de corps jaune. A 2 mois nous constatons une hyperplasie du stroma ovarien composee de cellules steroidogeniques exprimant CYP 17, expliquant l’hyperproduction des androgenes, mais aussi CYP 21, enzyme caracteristique de la steroidogenese surrenalienne. Nous observons des structures ovariennes issues de follicules, contenant des cellules FOXL2 negatives et SOX 9 positives temoignant d’un potentiel plastique des cellules de la granulosa vers des cellules pseudo-sertoliennes. Conclusions Nos resultats confirment l’importance de la signalisation PKA dans le maintien de l’identite cellulaire et les fonctions ovariennes et incitent a depister les atteintes ovariennes au cours du complexe de Carney.
Published: 2018

166. Douleurs abdominales aiguës

Author: A. Zrig, A. Laribi, M.H. Ben Romdhane, F. Djari, and F. Mounir
Subjects: business.industry, Medicine, Radiology, Nuclear Medicine and imaging, business
Published: 2008

167. Voltage stability assessment using the V-Q sensitivity and modal analyses methods

Author: Djari, Mohammed Adel, primary, Benasla, Lahouaria, additional, and Rahmouni, Walid, additional
Published: 2017
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168. Tuning of decentralized fuzzy logic sliding mode controller using PSO algorithm for nonlinear Twin Rotor Mimo System

Author: Bouarroudj, Noureddine, primary, Djari, Abdelhamid, additional, Boukhetala, Djamel, additional, and Boudjema, Fares, additional
Published: 2017
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169. Fractional order sliding mode control with pole-placement for non-linear systems with uncertain disturbances

Author: Abdelhamid, Djari, primary, Noureddine, Bouarroudj, additional, Feliu-Batlle, Vicente, additional, Djamel, Boukhetala, additional, and Bodjema, Fares, additional
Published: 2017
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170. FLC based Gaussian membership functions tuned by PSO and GA for MPPT of photovoltaic system: A comparative study

Author: Bouarroudj, Noureddine, primary, Boukhetala, Djamel, additional, Djari, Abdelhamid, additional, Rais, Younes, additional, and Benlahbib, Boualem, additional
Published: 2017
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171. Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle

Author: Meersseman, Cédric, primary, Letaief, Rabia, additional, Léjard, Véronique, additional, Rebours, Emmanuelle, additional, Guillocheau, Gabriel, additional, Esquerré, Diane, additional, Djari, Anis, additional, Chamberlain, Amanda, additional, Vander Jagt, Christy, additional, Klopp, Christophe, additional, Boussaha, Mekki, additional, Renand, Gilles, additional, Maftah, Abderrahman, additional, Petit, Daniel, additional, and Rocha, Dominique, additional
Published: 2017
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172. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

Author: Cabau, Cédric, primary, Escudié, Frédéric, additional, Djari, Anis, additional, Guiguen, Yann, additional, Bobe, Julien, additional, and Klopp, Christophe, additional
Published: 2017
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173. Expanding Duplication of Free Fatty Acid Receptor-2 (GPR43) Genes in the Chicken Genome

Author: Pascal Froment, Philippe Monget, Sophie Leroux, Isabelle Callebaut, Camille Meslin, Florence Gondret, Christophe Klopp, Sandrine Lagarrigue, Edith Guilbert, Colette Désert, Frédérique Pitel, Pascal G.P. Martin, Anis Djari, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Université Francois Rabelais [Tours], Institut Francais du Cheval et de l’Equitation, UMR 1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage, Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Institut National de la Recherche Agronomique (INRA)-Génétique animale (G.A.)-Physiologie Animale et Systèmes d'Elevage (PHASE), Institut National de la Recherche Agronomique (INRA), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC), INRA, INRA, BIA, Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Unité de recherche Pharmacologie-Toxicologie (UPT), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation [Saumur], Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique (CNRS), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), ANT FATINTEGER - ANR EpiBird, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), 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 Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Nonsynonymous substitution, Male, animal structures, Swine, [SDV]Life Sciences [q-bio], chicken, poulet, génomique fonctionnelle, FFAR, Biology, métabolisme des lipides, Genome, Receptors, G-Protein-Coupled, Avian Proteins, Evolution, Molecular, 03 medical and health sciences, régulation, positive selection, Gene Duplication, Gene duplication, evolution, Genetics, Animals, Tissue Distribution, Gene conversion, Copy-number variation, acide gras libre, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, gene conversion, 0402 animal and dairy science, 04 agricultural and veterinary sciences, 040201 dairy & animal science, genomic DNA, adiposité, duplication, Multigene Family, Female, Synonymous substitution, récepteur, Chickens, Research Article
Abstract: International audience; Free fatty acid receptors (FFAR) belong to a family of five G-protein coupled receptors that are involved in the regulation of lipidmetabolism, so that their loss of function increases the risk of obesity. The aim of this study was to determine the expansion of genesencoding paralogs of FFAR2 in the chicken, considered as amodel organism for developmental biology and biomedical research. Byestimating the gene copy number using quantitative polymerase chain reaction, genomic DNA resequencing, and RNA sequencingdata, we showed the existence of 23 ±1.5 genes encoding FFAR2 paralogs in the chicken genome. The FFAR2 paralogs shared anidentity from 87.2%up to 99%. Extensive gene conversion was responsible for this high degree of sequence similarities betweenthese genes, and this concerned especially the four amino acids known to be critical for ligand binding. Moreover, elevated nonsynonymous/synonymous substitutionratios onsomeamino acids withinor inclose-vicinity of the ligand-bindinggroove suggest thatpositive selectionmay have reduced the effective rate of gene conversion in this region, thus contributing to diversify the function ofsome FFAR2 paralogs. All the FFAR2 paralogs were located on a microchromosome in a same linkage group. FFAR2 genes wereexpressed in different tissues and cells such as spleen, peripheral blood mononuclear cells, abdominal adipose tissue, intestine, andlung, with the highest rate of expression in testis. Further investigations are needed to determine whether these chicken-specificevents along evolution are the consequence of domestication and may play a role in regulating lipid metabolism in this species.
Published: 2015

174. La combinaison de cartographie de signatures de sélection, de re-séquençage de génomes et d'analyses d'expression révèle PARK2 et JAG2 comme nouveaux genes candidats régulant l'adiposité

Author: Roux, Pierre-François, Boitard, Simon, Blum, Anne, Parks, Brian, Montagner, Alexandra, Mouisel, Etienne, Djari, Anis, Esquerre, Diane, Désert, Colette, Boutin, Morgane, Leroux, Sophie, Lecerf, Frédéric, Duval, Elisabeth, Klopp, Christophe, Servin, Bertrand, Pitel, Frederique, Duclos, Michel, Guillou, Hervé, Lusis, Aldons J., Demeure, Olivier, Lagarrigue, Sandrine, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Université européenne de Bretagne - European University of Brittany (UEB), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Department of Medecine, University of California [Los Angeles] (UCLA), University of California-University of California, Toxicologie Alimentaire (UTA), 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, UMR 1048 IMPC, Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, SIGENAE, Institut National de la Recherche Agronomique (INRA), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de Recherches Avicoles (URA), Department of Medicine, Department of Human Genetics, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), GENOTOUL, Recherches Avicoles (SRA), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of California (UC)-University of California (UC), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ProdInra, Archive Ouverte, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] ( PEGASE ), Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Université européenne de Bretagne ( UEB ), Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS ), University of California at Los Angeles [Los Angeles] ( UCLA ), Toxicologie Alimentaire ( UTA ), 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 National de la Santé et de la Recherche Médicale, GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Institut National de la Recherche Agronomique ( INRA ), and Recherches Avicoles ( SRA )
Subjects: [SDV] Life Sciences [q-bio], re-séquencage de génomes, adiposité, [ SDV ] Life Sciences [q-bio], signature de sélection, [SDV]Life Sciences [q-bio], expression, annotation des SNP
Abstract: Very few causal genes have been identified by quantitative trait loci (QTLs) mapping because of the large size ofQTLs, and most of them were identified thanks to functional links already known with the targeted phenotype.Here we propose to combine selection signature detection, SNP annotation, and expression analyses to identifycausal genes underlying QTLs. As a model, we chose experimental chicken lines divergently selected for onlyone trait, the abdominal fat weight, in which several QTLs were previously mapped. Using a new haplotypebasedstatistics exploiting the very high SNP density generated through whole genome re-sequencing, we found129 significant selective sweeps. Most of the QTLs co-localized with at least one sweep, which markedlynarrowed candidate region size. Some of those sweeps contained only one gene, therefore making them strongpositional causal candidates with no presupposed function. We then focused on two of these QTLs/sweeps. Theabsence of non-synonymous SNP in their coding regions strongly suggests the existence of causal mutationsacting in cis on their expression, confirmed for one of both. Additional expression analyses on those two genesin the divergent chicken lines and in genetically diverse mice contrasted for adiposity confirm their link with thisphenotype. This study shows for the first time the interest of using selective sweeps combined with SNPs andexpression analyses in divergent lines selected for a specific trait for identifying causative genes and highlightstwo genes, JAG2 and PARK2, as new potential negative and positive key regulators of adiposity in chicken andmice., Très peu de gènes responsables de la variation de caractères quantitatifs ont été identifiés par les méthodes decartographie de QTLs (Quantitative Trait Loci) en raison de la grande taille de ces régions. La plupart des gènesidentifiés jusqu’alors l’ont été en raison d'un lien fonctionnel déjà connu avec le phénotype ciblé. Cette étudepropose de combiner des approches de détection de QTLs et de signatures de sélection, d’annotation de SNPs, etd’analyses d'expression pour faciliter l’identification des gènes causaux sous-jacents aux régions QTLs.L’étude a été menée sur des lignées expérimentales de poulets sélectionnées de façon divergente pour un seulcaractère complexe, le poids de gras abdominal, et pour lesquelles plusieurs QTLs ont déjà été cartographiés. Enutilisant une nouvelle approche statistique exploitant des densités très élevées de SNPs et basée sur lesfréquences haplotypiques, nous avons identifié 129 signatures de sélection. La plupart des QTLs co-localisentavec au moins une signature de sélection ; cette co-localisation réduit alors considérablement la taille de cesrégions QTLs. Certaines de ces régions ne contiennent plus qu’un seul gène, faisant de ces derniers de sérieuxcandidats sans aucun a priori fonctionnel. Nous nous sommes ensuite focalisés sur deux de ces régions QTLsparticulièrement réduites en taille. L'absence de SNP non-synonyme dans les régions codantes suggère fortementl'existence de mutations causales agissant en cis sur l’expression des gènes associés à ces régions. L’analyse del'expression de ces gènes dans les lignées divergentes de poulets mais aussi dans des modèles murinsgénétiquement contrastés pour l’adiposité confirme leur liaison avec le phénotype d’intérêt. Cette étude montrepour la première fois l'intérêt de combiner des approches basées sur la détection de traces de sélection,l’annotation de SNPs et l’analyse d'expression dans des lignées divergentes sélectionnées pour un caractèrespécifique et met en évidence deux nouveaux gènes JAG2 et PARK2 comme de potentiels régulateurs clés,négatif et positif respectivement, de l'adiposité chez le poulet et la souris.
Published: 2015

175. Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates

Author: Sandrine Lagarrigue, David Gourichon, Diane Esquerre, Sophie Leroux, Frédérique Pitel, Stéphane Fabre, Pierre-François Roux, Christophe Klopp, Anis Djari, Patrice Dehais, Laure Fresard, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), SIGENAE, Pôle d'Expérimentation Avicole de Tours (UE PEAT), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], and Pôle d'Expérimentation Avicole de Tours (PEAT)
Subjects: Genome evolution, human transcriptome, Sequence analysis, [SDV]Life Sciences [q-bio], lcsh:Medicine, Sequence alignment, Chick Embryo, Computational biology, Biology, DNA sequencing, dna sequence, b messenger-rna, widespread rna, accurate identification, gaba (a) receptor, seq data, adenosine, evolution, Evolution, Molecular, Transcription (biology), Animals, lcsh:Science, Genetics, Genome, Multidisciplinary, Sequence Analysis, RNA, lcsh:R, Intron, Computational Biology, High-Throughput Nucleotide Sequencing, RNA, DNA, Sequence Analysis, DNA, RNA editing, lcsh:Q, RNA Editing, Chickens, Research Article
Abstract: RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation sequencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome.
Published: 2015

176. Genome-wide study of structural variants in bovine Holstein, Montbéliarde and Normande dairy breeds

Author: Alain Pinton, Frédéric Escudié, Maria Bernard, Anis Djari, Alain Roulet, Mekki Boussaha, Franck Samson, Diane Esquerre, Cécile Grohs, Johanna Barbieri, Sébastien Fritz, Rabia Letaief, Christophe Klopp, Gerald Salin, Didier Boichard, Dominique Rocha, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), Unité Mathématique, Informatique et Génome (MIG), ANR-Apisgene Cartoseq, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], and Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale
Subjects: bovin, Genotype, variants structuraux, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Genomic Structural Variation, lcsh:Medicine, Single-nucleotide polymorphism, Genome-wide association study, Quantitative trait locus, Biology, Genome, Structural variation, Animals, Copy-number variation, lcsh:Science, 2. Zero hunger, Genetics, Multidisciplinary, génome, lcsh:R, Dairying, Bovine genome, lcsh:Q, Cattle, Animals, Inbred Strains, Genome-Wide Association Study, Research Article
Abstract: High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest.
Published: 2015

177. علاقة بعض الأساليب المعرفية بصعوبات القراءة

Author: Djari Bachir
Published: 2015
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178. The BioMart community portal: An innovative alternative to large, centralized data repositories

Author: Smedley, D, Haider, S, Durinck, S, Pandini, L, Provero, P, Allen, J, Arnaiz, O, Awedh, MH, Baldock, R, Barbiera, G, Bardou, P, Beck, T, Blake, A, Bonierbale, M, Brookes, AJ, Bucci, G, Buetti, I, Burge, S, Cabau, C, Carlson, JW, Chelala, C, Chrysostomou, C, Cittaro, D, Collin, O, Cordova, R, Cutts, RJ, Dassi, E, Di Genova, A, Djari, A, Esposito, A, Estrella, H, Eyras, E, Fernandez-Banet, J, Forbes, S, Free, RC, Fujisawa, T, Gadaleta, E, Garcia-Manteiga, JM, Goodstein, D, Gray, K, Guerra-Assunção, JA, Haggarty, B, Han, DJ, Han, BW, Harris, T, Harshbarger, J, Hastings, RK, Hayes, RD, Hoede, C, Hu, S, Hu, ZL, Hutchins, L, Kan, Z, Kawaji, H, Keliet, A, Kerhornou, A, Kim, S, Kinsella, R, Klopp, C, Kong, L, Lawson, D, Lazarevic, D, Lee, JH, Letellier, T, Li, CY, Lio, P, Liu, CJ, Luo, J, Maass, A, Mariette, J, Maurel, T, Merella, S, Mohamed, AM, Moreews, F, Nabihoudine, I, Ndegwa, N, Noirot, C, Perez-Llamas, C, Primig, M, Quattrone, A, Quesneville, H, Rambaldi, D, Reecy, J, Riba, M, Rosanoff, S, Saddiq, AA, Salas, E, Sallou, O, Shepherd, R, Simon, R, and Sperling, L
Abstract: © 2015 The Author(s). The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
Published: 2015

179. The BioMart community portal: an innovative alternative to large, centralized data repositories

Author: Byung Woo Han, Jose Manuel Garcia-Manteiga, Alejandro Maass, Jayson Harshbarger, Daniel M. Staines, Zhengyan Kan, Davide Rambaldi, Dong Jin Han, Richard Baldock, Ji Hyun Lee, Merideth Bonierbale, Hadi Quesneville, Anthony Esposito, Thomas Letellier, Jun Wang, Steven Rosanoff, Céline Noirot, Richard D. Hayes, Sarah W. Burge, Anthony J. Brookes, Gabriele Bucci, Giulia Barbiera, Elia Stupka, Olivier Arnaiz, Thomas Maurel, Shen Hu, Olivier Sallou, Emanuela Gadaleta, Jérôme Mariette, Rosalind J. Cutts, Joseph W. Carlson, Damian Smedley, Robert C. Free, James E. Allen, Simon A. Forbes, Kevin R. Stone, Jie Luo, Andrew Blake, Chu Jun Liu, Takatomo Fujisawa, Jon W. Teague, Cristian Perez-Llamas, Rebecca Shepherd, Julio Fernandez-Banet, Raul Cordova, David Goodstein, Shi Jian Zhang, Ken Youens-Clark, Cédric Cabau, José Afonso Guerra-Assunção, Iwan Buetti, Stefania Merella, Delphine Steinbach, Linda Sperling, Robert K. Hastings, Abu Z. Dayem Ullah, Claude Chelala, Erik Dassi, Eduardo Eyras, Sunghoon Kim, Kristian Gray, Dejan Lazarevic, Luca Pandini, Azza M. Mohamed, Doreen Ware, William Spooner, Alex Di Genova, Daniel Lawson, Alessandro Quattrone, Davide Cittaro, Heather Estrella, Rhoda Kinsella, Chuan-Yun Li, Christophe Klopp, Aminah Keliet, Michela Riba, Zhi-Liang Hu, Hideya Kawaji, Arnaud Kerhornou, James M. Reecy, Tim Beck, Charalambos Chrysostomou, François Moreews, Nelson Ndegwa, Arek Kasprzyk, Michael Primig, Claire Hoede, Ibounyamine Nabihoudine, Amonida Zadissa, Paolo Provero, Reinhard Simon, Todd W. Harris, Bernard Haggarty, Lucie N. Hutchins, Marie Wong-Erasmus, Philippe Bardou, Elisa Salas, Lei Kong, Anis Djari, Syed Haider, Steffen Durinck, Mohammad Awedh, Pietro Liò, Amna A. Saddiq, Olivier Collin, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Computer Laboratory [Cambridge], University of Cambridge [UK] (CAM), Genentech, Inc., Genentech, Inc. [San Francisco], San Raffaele Scientific Institute, Vita-Salute San Raffaele University and Center for Translational Genomics and Bioinformatics, Genetics, Biology and Biochemistry, Molecular Biotechnology Centre, Centre de génétique moléculaire (CGM), Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), King Abdulaziz University, MRC Human Genetics Unit, University of Edinburgh-Western General Hospital, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Department of Genetics [Leicester], University of Leicester, Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Medical Research Counc, International Potato Center, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Centre for Molecular Oncology and Imaging, Centre for Molecular Oncology and Imaging, Barts Cancer Institute, Plateforme bioinformatique GenOuest [Rennes], Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Plateforme Génomique Santé Biogenouest®-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec, University of Trento [Trento], University of Chile [Santiago], Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Pfizer Oncology, Institució Catalana de Recerca i Estudis Avançats (ICREA), Cancer Genome Project, The Wellcome Trust Sanger Institute [Cambridge], Kasuza DNA Research Institute, Seoul National University [Seoul] (SNU), Cold Spring Harbor Laboratory (CSHL), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), School of Dentistry and Dental Research Institute [UCLA], University of California [Los Angeles] (UCLA), University of California-University of California, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University (ISU), Mouse Genomic Informatics Group (MGI), The Jackson Laboratory, Unité de Recherche Génomique Info (URGI), Center for Bioinformatics [Pekin], Peking University [Beijing], Division of Industrial Ecology (KTH), Royal Institute of Technology [Stockholm] (KTH ), Institute of Molecular Medicine, Universidad de Santiago de Chile [Santiago] (USACH), Centro de Regulación Génica (CRG), Pontificia Universidad Católica de Chile (UC)-Universidad Andrés Bello [Santiago] (UNAB)-Universidad de Santiago de Chile [Santiago] (USACH), Centre de Modélisation Mathématique / Centro de Modelamiento Matemático (CMM), Centre National de la Recherche Scientifique (CNRS), Unité Mathématiques et Informatique Appliquées de Toulouse (MIAT), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Mathématiques et Informatique Appliquées Toulouse, Universitat Pompeu Fabra [Barcelona], Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Animal Science, Eagle Genomics Ltd, Eagle Genomics, State Key Laboratory of Lithospheric Evolution (SKL), Institute of Geology and Geophysics [Beijing] (IGG), Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS), University of the Chinese Academy of Sciences, Ontario Institute for Cancer Research [Canada] (OICR), Ontario Institute for Cancer Research, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, International Potato Center [Lima] (CIP), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Universidad de Chile = University of Chile [Santiago] (UCHILE), The Jackson Laboratory [Bar Harbor] (JAX), Center for Bioinformatics [Peking], Pontificia Universidad Católica de Chile (UC)-Universidad Andrés Bello [Santiago] (UNAB), 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), Universitat Pompeu Fabra [Barcelona] (UPF), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), University of California (UC)-University of California (UC), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Jonchère, Laurent, CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Lio, Pietro [0000-0002-0540-5053], and Apollo - University of Cambridge Repository
Subjects: Proteomics, Interface (Java), Data management, [SDV]Life Sciences [q-bio], génomique fonctionnelle, Biology, Ontology (information science), computer.software_genre, World Wide Web, Genomics, Humans, Internet, Neoplasms, Database Management Systems, Genetics, cancer, Web Server issue, protéomique, ontologie, ComputingMilieux_MISCELLANEOUS, base de données, business.industry, Toolbox, [SDV] Life Sciences [q-bio], espèce modèle, Scalability, The Internet, Web service, business, Host (network), computer
Abstract: International audience; The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
Published: 2015

180. Comparison of whole-genome (13X) and capture (87X) resequencing methods for SNP and genotype callings

Author: Jordi Estellé, Pierre-François Roux, Olivier Demeure, Sandrine Lagarrigue, Sylvain Marthey, Christophe Klopp, Marco Moroldo, Anis Djari, Diane Esquerre, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Université européenne de Bretagne - European University of Brittany (UEB), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: genotype calling, Genotype, Genotyping Techniques, Single-nucleotide polymorphism, Biology, Genome, Polymorphism, Single Nucleotide, DNA sequencing, Deep sequencing, sequencing depth, single nucleotide polymorphism, Genetics, SNP, Animals, Genotyping, [SDV.BA]Life Sciences [q-bio]/Animal biology, SNP calling, High-Throughput Nucleotide Sequencing, General Medicine, Sequence Analysis, DNA, SNP genotyping, Animal Science and Zoology, next-generation sequencing, Chickens
Abstract: The number of polymorphisms identified with next-generation sequencing approaches depends directly on the sequencing depth and therefore on the experimental cost. Although higher levels of depth ensure more sensitive and more specific SNP calls, economic constraints limit the increase of depth for whole-genome resequencing (WGS). For this reason, capture resequencing is used for studies focusing on only some specific regions of the genome. However, several biases in capture resequencing are known to have a negative impact on the sensitivity of SNP detection. Within this framework, the aim of this study was to compare the accuracy of WGS and capture resequencing on SNP detection and genotype calling, which differ in terms of both sequencing depth and biases. Indeed, we have evaluated the SNP calling and genotyping accuracy in a WGS dataset (13X) and in a capture resequencing dataset (87X) performed on 11 individuals. The percentage of SNPs not identified due to a sevenfold sequencing depth decrease was estimated at 7.8% using a down-sampling procedure on the capture sequencing dataset. A comparison of the 87X capture sequencing dataset with the WGS dataset revealed that capture-related biases were leading with the loss of 5.2% of SNPs detected with WGS. Nevertheless, when considering the SNPs detected by both approaches, capture sequencing appears to achieve far better SNP genotyping, with about 4.4% of the WGS genotypes that can be considered as erroneous and even 10% focusing on heterozygous genotypes. In conclusion, WGS and capture deep sequencing can be considered equivalent strategies for SNP detection, as the rate of SNPs not identified because of a low sequencing depth in the former is quite similar to SNPs missed because of method biases of the latter. On the other hand, capture deep sequencing clearly appears more adapted for studies requiring great accuracy in genotyping.
Published: 2014

181. Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events

Author: Frédérique Pitel, Sandrine Lagarrigue, David Gourichon, Patrice Dehais, Christophe Klopp, Laure Fresard, Anis Djari, Stéphane Fabre, Sophie Leroux, Diane Esquerre, and Pierre-François Roux
Subjects: Genetics, 0303 health sciences, Intron, RNA, Genomics, Computational biology, Biology, Genome, DNA sequencing, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Transcription (biology), RNA editing, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: RNA editing corresponds to a post-transcriptional nucleotide change in the RNA sequence, creating an alternative nucleotide, not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is more and more described in mammals, notably since the availability of next generation sequencing technologies allowing a whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken are still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, to understand to what extent this phenomenon is conserved in vertebrates. We performed RNA and DNA sequencing from 8 embryos. Being aware of common pitfalls inherent to sequence analyses leading to false positive discovery, we stringently filtered our datasets and found less than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual editing level increase with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, and provide support of an absence of non A-to-I events from the chicken transcriptome.
Published: 2014
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182. Rapid discovery of mutations responsible for sporadic dominant genetic defects in livestock using genome sequence data: enhancing the value of farm animals as model species

Author: Capitan, Aurelien, Michot, Pauline, Guillaume, François, Grohs, Cecile, Djari, Anis, Fritz, Sebastien, Barbey, Sarah, Otz, Pauline, Bourneuf, Emmanuelle, Esquerre, Diane, Gallard, Yves, Klopp, Christophe, Boichard, Didier, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Institut National de la Recherche Agronomique (INRA), Domaine Expérimental du Pin (DEP), DSV/iRCM/SREIT/LREG, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), ANR Apisgene Cartoseq, Unité de Biométrie et Intelligence Artificielle (UBIA), Domaine expérimental animal du Pin (SEA), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale, and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]
Subjects: bovin, [SDV]Life Sciences [q-bio], anomalie génétique
Abstract: absent
Published: 2014

183. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

Author: Daetwyler, Hans D, Capitan, Aurélien, Pausch, Hubert, Stothard, Paul, van Binsbergen, Rianne, Brøndum, Rasmus Froberg, Liao, Xiaoping, Djari, Anis, Rodriguez, Sabrina C, Grohs, Cécile, Jung, Simone, Esquerré, Diane, Bouchez, Olivier, Gollnick, Nicole S, Rossignol, Marie-Noëlle, Klopp, Christophe, Rocha, Dominique, Fritz, Sébastien, Eggen, André, Bowman, Phil J, Coote, David, Chamberlain, Amanda J, VanTassell, Curt P, Hulsegge, Ina, Goddard, Mike E, Guldbrandtsen, Bernt, Lund, Mogens Sandø, Veerkamp, Roel F, Boichard, Didier A, Fries, Ruedi, and Hayes, Ben J
Abstract: The 1000 bull genomes project supports the goal of accelerating the rates of genetic gain in domestic cattle while at the same time considering animal health and welfare by providing the annotated sequence variants and genotypes of key ancestor bulls. In the first phase of the 1000 bull genomes project, we sequenced the whole genomes of 234 cattle to an average of 8.3-fold coverage. This sequencing includes data for 129 individuals from the global Holstein-Friesian population, 43 individuals from the Fleckvieh breed and 15 individuals from the Jersey breed. We identified a total of 28.3 million variants, with an average of 1.44 heterozygous sites per kilobase for each individual. We demonstrate the use of this database in identifying a recessive mutation underlying embryonic death and a dominant mutation underlying lethal chrondrodysplasia. We also performed genome-wide association studies for milk production and curly coat, using imputed sequence variants, and identified variants associated with these traits in cattle
Published: 2014

184. Combining Genetics Mapping, Selective Sweeps, Genome Re-Requencing and Allele Specific Expression Reveals Several Serious Causative Genes for QTL Regions

Author: Pierre-François Roux, Simon Boitard, Anis Djari, Diane Esquerre, Colette Désert, Morgane Boutin, Sylvain Marthey, Frédéric Lecerf, Elisabeth Duval, Christophe Klopp, Bertrand Servin, Frederique Pitel, Michel DUCLOS, Marco Moroldo, Olivier Demeure, Sandrine Lagarrigue, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Recherches Avicoles (SRA), 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), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]
Subjects: volaille, [SDV]Life Sciences [q-bio], séquençage, education, sélection divergente, identification de gènes, allèle spécifique, expression des gènes
Abstract: Workshop : Poultry; absent
Published: 2014

185. Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events

Author: Frésard, Laure, Leroux, Sophie, Roux, Pierre-François, Klopp, Christophe, Fabre, Stéphane, Esquerre, Diane, Dehais, Patrice, Djari, Anis, Gourichon, David, Lagarrigue, Sandrine, and Pitel, Frederique
Subjects: poulet, édition des arn
Abstract: RNA editing corresponds to a post-transcriptional nucleotide change in the RNA sequence, creating an alternative nucleotide, not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is more and more described in mammals, notably since the availability of next generation sequencing technologies allowing a whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken are still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, to understand to what extent this phenomenon is conserved in vertebrates. We performed RNA and DNA sequencing from 8 embryos. Being aware of common pitfalls inherent to sequence analyses leading to false positive discovery, we stringently filtered our datasets and found less than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual editing level increase with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, and provide support of an absence of non A-to-I events from the chicken transcriptome.
Published: 2014

186. Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing

Author: Diane Esquerre, Coline Billerey, Dominique Rocha, Mekki Boussaha, Daniel Gautheret, Emmanuelle Rebours, Anis Djari, Cédric Meersseman, Christophe Klopp, Rocha, Dominique, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), INRA Animal Genetics Department (BovRNA-Seq project), Agence Nationale de la Recherche [ANR-05-GANI-005, ANR-05-GANI-017-01, ANR-11-INSB-0013], APIS GENE [01-2005-QualviGenA-02], Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Génétique Cellulaire, and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT)
Subjects: RNA-Seq, Biology, Quantitative trait locus, 03 medical and health sciences, 0302 clinical medicine, Genetics, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, 030304 developmental biology, 2. Zero hunger, Regulation of gene expression, 0303 health sciences, Gene Expression Profiling, Muscles, Computational Biology, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Long non-coding RNA, Gene expression profiling, Bovine genome, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Gene Expression Regulation, 030220 oncology & carcinogenesis, Muscle, Cattle, RNA, Long Noncoding, DNA microarray, Beef, Transcriptome, Biotechnology, Research Article
Abstract: Background The advent of large-scale gene expression technologies has helped to reveal in eukaryotic cells, the existence of thousands of non-coding transcripts, whose function and significance remain mostly poorly understood. Among these non-coding transcripts, long non-coding RNAs (lncRNAs) are the least well-studied but are emerging as key regulators of diverse cellular processes. In the present study, we performed a survey in bovine Longissimus thoraci of lincRNAs (long intergenic non-coding RNAs not overlapping protein-coding transcripts). To our knowledge, this represents the first such study in bovine muscle. Results To identify lincRNAs, we used paired-end RNA sequencing (RNA-Seq) to explore the transcriptomes of Longissimus thoraci from nine Limousin bull calves. Approximately 14–45 million paired-end reads were obtained per library. A total of 30,548 different transcripts were identified. Using a computational pipeline, we defined a stringent set of 584 different lincRNAs with 418 lincRNAs found in all nine muscle samples. Bovine lincRNAs share characteristics seen in their mammalian counterparts: relatively short transcript and gene lengths, low exon number and significantly lower expression, compared to protein-encoding genes. As for the first time, our study identified lincRNAs from nine different samples from the same tissue, it is possible to analyse the inter-individual variability of the gene expression level of the identified lincRNAs. Interestingly, there was a significant difference when we compared the expression variation of the 418 lincRNAs with the 10,775 known selected protein-encoding genes found in all muscle samples. In addition, we found 2,083 pairs of lincRNA/protein-encoding genes showing a highly significant correlated expression. Fourteen lincRNAs were selected and 13 were validated by RT-PCR. Some of the lincRNAs expressed in muscle are located within quantitative trait loci for meat quality traits. Conclusions Our study provides a glimpse into the lincRNA content of bovine muscle and will facilitate future experimental studies to unravel the function of these molecules. It may prove useful to elucidate their effect on mechanisms underlying the genetic variability of meat quality traits. This catalog will complement the list of lincRNAs already discovered in cattle and therefore will help to better annotate the bovine genome. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-499) contains supplementary material, which is available to authorized users.
Published: 2014

187. Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events

Author: FRESARD , Laure, Leroux , Sophie, Roux , Pierre-François, Klopp , Christophe, Fabre , Stéphane, Esquerre , Diane, Dehais , Patrice, Djari , Anis, Gourichon , David, Lagarrigue , Sandrine, Pitel , Frederique, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, Pôle d'Expérimentation Avicole de Tours (PEAT), auto-saisine, Absent, École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, 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), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Pôle d'Expérimentation Avicole de Tours (UE PEAT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] ( PEGASE ), Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Unité de Biométrie et Intelligence Artificielle ( UBIA ), Institut National de la Recherche Agronomique ( INRA ), and Pôle d'Expérimentation Avicole de Tours ( PEAT )
Subjects: [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: RNA editing corresponds to a post-transcriptional nucleotide change in the RNA sequence, creating an alternative nucleotide, not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is more and more described in mammals, notably since the availability of next generation sequencing technologies allowing a whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken are still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, to understand to what extent this phenomenon is conserved in vertebrates. We performed RNA and DNA sequencing from 8 embryos. Being aware of common pitfalls inherent to sequence analyses leading to false positive discovery, we stringently filtered our datasets and found less than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual editing level increase with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, and provide support of an absence of non A-to-I events from the chicken transcriptome.
Published: 2014

188. Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken

Author: Anis Djari, Diane Esquerre, Colette Désert, Sandrine Lagarrigue, Christophe Klopp, Morgane Boutin, Olivier Demeure, Pierre-François Roux, Demeure, Olivier, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université européenne de Bretagne - European University of Brittany (UEB), SIGENAE, Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], 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), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: Candidate gene, Heredity, Genetic Linkage, [SDV]Life Sciences [q-bio], génomique fonctionnelle, lcsh:Medicine, tissu adipeux, 0302 clinical medicine, INDEL Mutation, Genome Sequencing, lcsh:Science, Adiposity, Genetics, 0303 health sciences, Multidisciplinary, Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, Genome project, Genomics, Genetic Mapping, Linkage Analysis, annotation fonctionnelle, Research Article, cartographie de qtl, Genotype, Quantitative Trait Loci, poulet, Single-nucleotide polymorphism, Quantitative trait locus, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genetic linkage, Animals, Obesity, Indel, Molecular Biology Techniques, Sequencing Techniques, Gene, Molecular Biology, Genetic Association Studies, 030304 developmental biology, Evolutionary Biology, Population Biology, High Throughput Sequencing, lcsh:R, Biology and Life Sciences, Computational Biology, Molecular Sequence Annotation, Genome Analysis, Genetic Polymorphism, lcsh:Q, Chickens, 030217 neurology & neurosurgery, Population Genetics
Abstract: In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments.
Published: 2014

189. RNAbrowse: RNA-Seq de novo assembly results browser

Author: Christophe Klopp, Anis Djari, Philippe Bardou, Cédric Cabau, Jérôme Mariette, Céline Noirot, Claire Hoede, Ibounyamine Nabihoudine, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Plateforme Bio-Informatique - Génotoul, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Plateforme SIGENAE
Subjects: Computer science, [SDV]Life Sciences [q-bio], Sequence assembly, lcsh:Medicine, RNA-Seq, 010501 environmental sciences, Bioinformatics, computer.software_genre, 01 natural sciences, Computer Applications, Transcriptome, User-Computer Interface, [MATH]Mathematics [math], lcsh:Science, 0303 health sciences, Multidisciplinary, Contig, Programming language, Software Engineering, Genome project, Genomics, Web-Based Applications, RNA extraction, Transcriptome Analysis, Research Article, Computer and Information Sciences, Sequence analysis, Gene prediction, Sequence alignment, 03 medical and health sciences, Genetics, Humans, [INFO]Computer Science [cs], 030304 developmental biology, 0105 earth and related environmental sciences, Internet, Sequence Assembly Tools, Software Tools, Sequence Analysis, RNA, Gene Expression Profiling, lcsh:R, RNA, Biology and Life Sciences, Computational Biology, Genome Analysis, Gene expression profiling, lcsh:Q, Genome Expression Analysis, computer, Software
Abstract: International audience; Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse.
Published: 2014

190. Un modèle génétique murin pour l’exploration moléculaire et cellulaire des tumorigenèses testiculaires du complexe de Carney

Author: Djari, C., primary, Barnola, I., additional, Dumontet, T., additional, Felicia, L., additional, Septier, A., additional, Val, P., additional, Martinez, A., additional, and Lefrançois-Martinez, A.-M., additional
Published: 2016
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191. Multi Pass Optimization of Cutting Conditions by Using the Genetic Algorithms

Author: Djenane, Mohamed, primary, Djari, Derradji, additional, Benbouta, Rachid, additional, and Assas, Mekki, additional
Published: 2016
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192. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

Author: Cabau, Cédric, primary, Escudié, Frédéric, additional, Djari, Anis, additional, Guiguen, Yann, additional, Bobe, Julien, additional, and Klopp, Christophe, additional
Published: 2016
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193. The Extent of mRNA Editing Is Limited in Chicken Liver and Adipose, but Impacted by Tissular Context, Genotype, Age, and Feeding as Exemplified with a Conserved Edited Site in COG3

Author: Roux, Pierre-François, primary, Frésard, Laure, additional, Boutin, Morgane, additional, Leroux, Sophie, additional, Klopp, Christophe, additional, Djari, Anis, additional, Esquerré, Diane, additional, Martin, Pascal G P, additional, Zerjal, Tatiana, additional, Gourichon, David, additional, Pitel, Frédérique, additional, and Lagarrigue, Sandrine, additional
Published: 2016
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194. Design of fractional-order PID controller (FOPID) for a class of fractional-order MIMO systems using a particle swarm optimization (PSO) approach

Author: A. Djari, Abdesselem Boulkroune, and Toufik Bouden
Subjects: Mathematical optimization, Optimization problem, Flocking (behavior), Control theory, Computation, MathematicsofComputing_NUMERICALANALYSIS, PID controller, Particle swarm optimization, Multi-swarm optimization, Evolutionary computation, Mathematics, Mimo systems
Abstract: This paper deals with the tuning of conventional PID and fractional-order PID (FOPID) controllers by using a particle swarm optimization (PSO) algorithm, for a class of fractional-order MIMO systems. This algorithm is motivated from the organism behavior of fish schooling and bird flocking, and involves the social psychology principles in socio-cognition human agents and evolutionary computations. It has a good numerical convergence for solving optimization problem. To illustrate the validity of the PSO-based FOPID and PID controllers, some simulation results are given. In addition, a comparative study between those optimized controllers is carried out.
Published: 2013

195. Selective sweeps using hapFLK combined with genome re-sequencing data reveals strong candidate mutations in QTL regions in divergent chicken lines

Author: Roux, Pierre-François, Boitard, Simon, DJARI, Anis, Esquerre, Diane, Marthey, Sylvain, Désert, Colette, Lecerf, Frédéric, Duval, Elisabeth, Martin, Pascal G.P., Klopp, Christophe, Moroldo, Marco, Servin, Bertrand, Demeure, Olivier, Lagarrigue, Sandrine, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), Unité de recherche Pharmacologie-Toxicologie (UPT), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Recherches Avicoles (URA), and World's Poultry Science Association (WPSA). INT.
Subjects: [SDV]Life Sciences [q-bio]
Abstract: Session 1: Genomics and contemporary resources and methodologies; In the context of genome wide re-sequencing using NGS technologies, we analyzed selective sweeps in two divergent chicken lines selected for abdominal fat weight (AF). We applied a new statistic, hapFLK, to analyze the 9.4 M of SNP observed for the whole genome of 20 chickens. This genome scan revealed 129 significant selective sweeps with a size of 86 kb that contained 839 SNP and 2.2 genes, on average. These selective sweeps colocalize with different QTL responsible for abdominal fat and muscle weight, and drastically reduce their size. We then performed three complementary analyses for positional genes in these regions: 1) analysis of their biological functions to select functional candidate genes; 2) analysis in different tissues of their differential expression between both lines to argue in favor of a candidate mutation in regulatory or coding regions; 3) analysis of their polymorphism from DNA-seq and RNA-seq data to identify candidate mutations. The combination of these approaches reveals several strong candidate genes and mutations associated with the traits of interest.
Published: 2013

196. Using NGS data to characterize genetics of meet-type and egg-type chicken lines

Author: Roux, Pierre-François, Lecerf, Frédéric, Djari, Anis, Esquerre, Diane, Marthey, Sylvain, Zerjal, Tatiana, Le Bihan-Duval, Elisabeth, Klopp, Christophe, Moroldo, Marco, Estelle, Jordi, Désert, Colette, Bed'Hom, Bertrand, Tixier Boichard, Michèle, Demeure, Olivier, Lagarrigue, Sandrine, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Recherches Avicoles (URA), Génétique Physiologie et Systèmes d'Elevage, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, analyse de génome, adiposité, sélection génétique, caractérisation génomique, poulet, efficience alimentaire
Abstract: Session 25. Free communications - molecular genetics; absent
Published: 2013

197. Identification of candidate polymorphism in a QTL region by combining eQTL mapping with NGS data

Author: Roux, Pierre-François, Blum, Yuna, Désert, Colette, Djari, Anis, Esquerre, Diane, Le Bihan-Duval, Elisabeth, Bed'Hom, Bertrand, Le Roy, Pascale, Lecerf, Frédéric, Moroldo, Marco, Marthey, Sylvain, Klopp, Christophe, Lagarrigue, Sandrine, Demeure, Olivier, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Recherches Avicoles (URA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage, Recherches Avicoles (SRA), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, cartographie de qtl, adiposité, poulet, approche génomique
Abstract: Session 25. Free communications - molecular genetics; absent
Published: 2013

198. Concordance analysis: from QTL to candidate causative mutations

Author: VAN DEN BERG, Irene, Fritz, Sebastien, Djari, Anis, Esquerre, Diane, Klopp, Christophe, Rocha, Dominique, Boichard, Didier, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), SIGENAE Bioinformatics Team, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), GeT Genomics Facility, ANR-Apisgene Cartoseq ANR-10-GENM-0018, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: bovin, qtl, [SDV]Life Sciences [q-bio], séquence d'ADN
Abstract: absent
Published: 2013

199. Concordance analysis:from QTL to candidate causative mutations

Author: van den Berg, Irene, Fritz, S, Djari, A, Rodriguez, S C, Esquerre, D, Klopp, C, Rochar, D, and Lund, Mogens Sandø
Published: 2013

200. Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Author: Aurélien Capitan, Michel Fouchet, Stefan Krebs, Alexander Graf, Mekki Boussaha, Laura Salas-Cortes, Gunnfríður Elín Hreiðarsdóttir, Bernard Weiss, Dominique Thépot, Pierre Roy, Aurélia Baur, Olivier Catros, Marie-Noelle Rossignol, Sébastien Fritz, Helmut Blum, Yves Gallard, Sophie Rothammer, André Eggen, Cécile Grohs, L. Journaux, Emilie Cobo, Daniel Le Bourhis, Claire Ponsart, Aurélie Allais-Bonnet, Eric Pailhoux, Dominique Dozias, Laetitia Clément, Eric Venot, Este Van Marle-Koster, Christophe Klopp, Per Wahlberg, Carine Bernard-Capel, Ingolf Russ, Florence Phocas, Dominique Rocha, Patrick Reversé, Maëlle Pannetier, Jean-Luc Marchand, Marie-Noëlle Fouilloux, Brigitte Marquant-Leguienne, Anis Djari, Sarah Barbey, Diane Esquerre, Ivica Medugorac, Doris Seichter, Stephan Bouet, Pascal Soulas, Chris Hoze, Didier Boichard, Biologie du développement et reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-Universität München (LMU), Laboratory for Functional Genome Analysis, Gene Center, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), Department of Animal & Wildlife Sciences, University of Pretoria [South Africa], Domaine expérimental animal du Pin (SEA), This project was funded by Apis Gène 'Hornout' and Institut National de la Recherche Agronomique-DGA 'Interpolled' and 'Hornaseq' grants., Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biologie du Développement et Reproduction (BDR), Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, corne, Anatomy and Physiology, Veterinary Anatomy and Physiology, Receptors, G-Protein-Coupled, bovidae, 0302 clinical medicine, Gene expression, Morphogenesis, Basic Helix-Loop-Helix Transcription Factors, Animal Breeding, Animal Management, Skin, Horns, Genetics, 0303 health sciences, Multidisciplinary, Goats, Chromosome Mapping, Gene Expression Regulation, Developmental, Agriculture, Forkhead Transcription Factors, Phenotype, phénotype, ontogénèse, Autosomal Dominant, 030220 oncology & carcinogenesis, Medicine, Research Article, Genotype, Science, Genomics, Locus (genetics), Biology, OLIG2, 03 medical and health sciences, Animals, Allele, Alleles, 030304 developmental biology, Growth Control, Clinical Genetics, Sheep, Haplotype, Genetic Variation, Body Plan Organization, Animal Skin Anatomy, Mutation, Ectopic expression, Veterinary Science, Cattle, Animal Genetics, Developmental Biology
Abstract: Chantier qualité GA; Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae.
Published: 2013

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