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3. Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation.

Author

Roux, Pierre-François, Boitard, Simon, Blum, Yuna, Parks, Brian, Montagner, Alexandra, Mouisel, Etienne, Djari, Anis, Esquerré, Diane, Désert, Colette, Boutin, Morgane, Leroux, Sophie, Lecerf, Frédéric, Le Bihan-Duval, Elisabeth, Klopp, Christophe, Servin, Bertrand, Pitel, Frédérique, Duclos, Michel, Guillou, Hervé, Lusis, Aldons, Demeure, Olivier, and Lagarrigue, Sandrine

Subjects
JAG2, PARK2, QTL, adiposity, cis-eQTLs, divergent lines, selective sweeps, Adipose Tissue, White, Adiposity, Alleles, Animals, Cell Line, Chickens, Chromosome Mapping, Genome, High-Throughput Nucleotide Sequencing, Jagged-2 Protein, Membrane Proteins, Mice, Molecular Sequence Annotation, Myosins, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Sequence Analysis, DNA, Ubiquitin-Protein Ligases
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

8. Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaelle, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali San, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard-Van der Laan, Marie-Hélène, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Published
2019
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11. Survey of allele specific expression in bovine muscle

Author

Guillocheau, Gabriel M., El Hou, Abdelmajid, Meersseman, Cédric, Esquerré, Diane, Rebours, Emmanuelle, Letaief, Rabia, Simao, Morgane, Hypolite, Nicolas, Bourneuf, Emmanuelle, Bruneau, Nicolas, Vaiman, Anne, Vander Jagt, Christy J., Chamberlain, Amanda J., and Rocha, Dominique

Published
2019
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17. Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae

Author

Allais-Bonnet, Aurélie, Hintermann, Aurélie, Deloche, Marie-Christine, Cornette, Raphaël, Bardou, Philippe, Naval-Sanchez, Marina, Pinton, Alain, Haruda, Ashleigh, Grohs, Cécile, Zakany, Jozsef, Bigi, Daniele, Medugorac, Ivica, Putelat, Olivier, Greyvenstein, Ockert, Hadfield, Tracy, Jemaa, Slim Ben, Bunevski, Gjoko, Menzi, Fiona, Hirter, Nathalie, Paris, Julia M, Hedges, John, Palhiere, Isabelle, Rupp, Rachel, Lenstra, Johannes A, Gidney, Louisa, Lesur, Joséphine, Schafberg, Renate, Stache, Michael, Wandhammer, Marie-Dominique, Arbogast, Rose-Marie, Guintard, Claude, Blin, Amandine, Boukadiri, Abdelhak, Rivière, Julie, Esquerré, Diane, Donnadieu, Cécile, Danchin-Burge, Coralie, Reich, Coralie M, Riley, David G, van Marle-Koster, Este, Cockett, Noelle, Hayes, Benjamin J, Drögemüller, Cord, Kijas, James, Pailhoux, Eric, Tosser-Klopp, Gwenola, Duboule, Denis, Capitan, Aurélien, Allais-Bonnet, Aurélie, Hintermann, Aurélie, Deloche, Marie-Christine, Cornette, Raphaël, Bardou, Philippe, Naval-Sanchez, Marina, Pinton, Alain, Haruda, Ashleigh, Grohs, Cécile, Zakany, Jozsef, Bigi, Daniele, Medugorac, Ivica, Putelat, Olivier, Greyvenstein, Ockert, Hadfield, Tracy, Jemaa, Slim Ben, Bunevski, Gjoko, Menzi, Fiona, Hirter, Nathalie, Paris, Julia M, Hedges, John, Palhiere, Isabelle, Rupp, Rachel, Lenstra, Johannes A, Gidney, Louisa, Lesur, Joséphine, Schafberg, Renate, Stache, Michael, Wandhammer, Marie-Dominique, Arbogast, Rose-Marie, Guintard, Claude, Blin, Amandine, Boukadiri, Abdelhak, Rivière, Julie, Esquerré, Diane, Donnadieu, Cécile, Danchin-Burge, Coralie, Reich, Coralie M, Riley, David G, van Marle-Koster, Este, Cockett, Noelle, Hayes, Benjamin J, Drögemüller, Cord, Kijas, James, Pailhoux, Eric, Tosser-Klopp, Gwenola, Duboule, Denis, and Capitan, Aurélien

Published
2021

18. Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae

Author

Allais-Bonnet, Aurélie, primary, Hintermann, Aurélie, additional, Deloche, Marie-Christine, additional, Cornette, Raphaël, additional, Bardou, Philippe, additional, Naval-Sanchez, Marina, additional, Pinton, Alain, additional, Haruda, Ashleigh, additional, Grohs, Cécile, additional, Zakany, Jozsef, additional, Bigi, Daniele, additional, Medugorac, Ivica, additional, Putelat, Olivier, additional, Greyvenstein, Ockert, additional, Hadfield, Tracy, additional, Jemaa, Slim Ben, additional, Bunevski, Gjoko, additional, Menzi, Fiona, additional, Hirter, Nathalie, additional, Paris, Julia M, additional, Hedges, John, additional, Palhiere, Isabelle, additional, Rupp, Rachel, additional, Lenstra, Johannes A, additional, Gidney, Louisa, additional, Lesur, Joséphine, additional, Schafberg, Renate, additional, Stache, Michael, additional, Wandhammer, Marie-Dominique, additional, Arbogast, Rose-Marie, additional, Guintard, Claude, additional, Blin, Amandine, additional, Boukadiri, Abdelhak, additional, Rivière, Julie, additional, Esquerré, Diane, additional, Donnadieu, Cécile, additional, Danchin-Burge, Coralie, additional, Reich, Coralie M, additional, Riley, David G, additional, Marle-Koster, Este van, additional, Cockett, Noelle, additional, Hayes, Benjamin J, additional, Drögemüller, Cord, additional, Kijas, James, additional, Pailhoux, Eric, additional, Tosser-Klopp, Gwenola, additional, Duboule, Denis, additional, and Capitan, Aurélien, additional

Published
2021
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19. Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 to Determine the Number and Topology of Horns in Bovidae

Author

Allais-Bonnet, Aurélie, primary, Hintermann, Aurélie, additional, Deloche, Marie-Christine, additional, Cornette, Raphaël, additional, Bardou, Philippe, additional, Naval-Sanchez, Marina, additional, Pinton, Alain, additional, Haruda, Ashleigh, additional, Grohs, Cécile, additional, Zakany, Jozsef, additional, Bigi, Daniele, additional, Medugorac, Ivica, additional, Putelat, Olivier, additional, Greyvenstein, Ockert, additional, Hadfield, Tracy, additional, Ben Jemaa, Slim, additional, Bunevski, Gjoko, additional, Menzi, Fiona, additional, Hirter, Nathalie, additional, Paris, Julia M., additional, Hedges, John, additional, Palhiere, Isabelle, additional, Rupp, Rachel, additional, Lenstra, Johannes A., additional, Gidney, Louisa, additional, Lesur, Joséphine, additional, Schafberg, Renate, additional, Stache, Michael, additional, Wandhammer, Marie-Dominique, additional, Arbogast, Rose-Marie, additional, Guintard, Claude, additional, Blin, Amandine, additional, Boukadiri, Abdelhak, additional, Riviere, Julie, additional, Esquerré, Diane, additional, Donnadieu, Cécile, additional, Danchin-Burge, Coralie, additional, Reich, Coralie M, additional, Riley, David, additional, van Marle-Koster, Este, additional, Cockett, Noelle, additional, Hayes, Benjamin J., additional, Drögemüller, Cord, additional, Kijas, James, additional, Pailhoux, Eric, additional, Tosser-Klopp, Gwenola, additional, Duboule, Denis, additional, and Capitan, Aurélien, additional

Published
2020
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20. Layers response to suboptimal diet through phenotypic and transcriptomic changes in four tissues

Author

Jehl, Frédéric, Brenet, M., Rau, Andrea, Désert, Colette, Boutin, Morgane, Leroux, Sophie, Esquerré, Diane, Klopp, Christophe, Gourichon, David, Collin, Anne, Pitel, Frédérique, Zerjal, Tatiana, 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, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Pôle d'Expérimentation Avicole de Tours (UE PEAT), Biologie des Oiseaux et Aviculture (BOA), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), European Project: 633531,H2020,H2020-SFS-2014-2,Feed-a-Gene(2015), 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), 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, and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT]
Abstract

International audience; Poultry meat and eggs are major sources of nutrients in human alimentation. The long production career of layers expose them to numerous stressors. Understanding the adaptive mechanisms is crucial to select robust animals and meet the needs of a growing human population. In this context, we compared the effects of a 15%-energy-reduced diet (LE) vs. a commercial diet (CT) in two feed-efficiency-diverging chicken lines. We first studied the effects of the LE on performances (egg mass, feed intake [FI], body weight) and body energy reserves, before investigating the molecular mechanisms at work by studying the adipose tissue, blood, hypothalamus and liver transcriptomes. The absence of differences in egg production between diets, combined to the increase in feed intake and the decrease in body weight in LE suggest an adaptation to the diet through an increase in energy input and a mobilization of body energy reserves. The birds reacted similarly to the diet in both lines, as shown by the absence of significant line×diet interactions. At the transcriptomic level, no interactions were detected. The increase in FI did not affect the liver, neither did the mobilization of body reserves for the adipose tissue. In blood, the differentially expressed genes were related to amino-acids, monosaccharides and steroid metabolisms. In the hypothalamus, the fatty acids metabolism and endocannabinoid signaling pathways were affected. We propose a mechanism involving endocannabinoids that could explain the increase in FI and therefore part of the adaptation to the low-energy diet. Work funded by ANR-13-ADAP-0014 and H2020-Feed-a-Gene projects.

Published
2019

22. MOESM1 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Raphaelle Momal-Leisenring, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Marie-Hélène Pinard-Van Der Laan, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Abstract

Additional file 1 Additional file 1: Supplementary figures (S1-S26) and tables (S1-S15).

Published
2019
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23. Additional file 5: of RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed

Author

Hérault, Frédéric, Houée-Bigot, Magalie, Baéza, Elisabeth, Bouchez, Olivier, Esquerré, Diane, Klopp, Christophe, and Diot, Christian

Subjects
body regions, nervous system, fungi
Abstract

Clusters of enriched GO terms associated to differentially expressed genes defined by semantic similarity. (PDF 2017 kb)

Published
2019
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24. Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout

Author

Boussaha Mekki, Guyomard René, Cabau Cédric, Esquerré Diane, and Quillet Edwige

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background There is considerable interest in developing high-throughput genotyping with single nucleotide polymorphisms (SNPs) for the identification of genes affecting important ecological or economical traits. SNPs are evenly distributed throughout the genome and are likely to be functionally relevant. In rainbow trout, in silico screening of EST databases represents an attractive approach for de novo SNP identification. Nevertheless, EST sequencing errors and assembly of EST paralogous sequences can lead to the identification of false positive SNPs which renders the reliability of EST-derived SNPs relatively low. Further validation of EST-derived SNPs is therefore required. The objective of this work was to assess the quality of and to validate a large number of rainbow trout EST-derived SNPs. Results A panel of 1,152 EST-derived SNPs was selected from the INRA Sigenae SNP database and was genotyped in standard and double haploid individuals from several populations using the Illumina GoldenGate BeadXpress assay. High-quality genotyping data were obtained for 958 SNPs representing a genotyping success rate of 83.2 %, out of which, 350 SNPs (36.5 %) were polymorphic in at least one population and were designated as true SNPs. They also proved to be a potential tool to investigate genetic diversity of the species, as the set of SNP successfully sorted individuals into three main groups using STRUCTURE software. Functional annotations revealed 28 non-synonymous SNPs, out of which four substitutions were predicted to affect protein functions. A subset of 223 true SNPs were polymorphic in the two INRA mapping reference families and were integrated into the INRA microsatellite-based linkage map. Conclusions Our results represent the first study of EST-derived SNPs validation in rainbow trout, a species whose genome sequences is not yet available. We designed several specific filters in order to improve the genotyping yield. Nevertheless, our selection criteria should be further improved in order to reduce the observed high rate of false positive SNPs which results from the occurrence of whole genome duplications.

Published
2012
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25. Analysis of whole genome sequence data on a tropical admixed cattle breed, the Creole cattle of Guadeloupe

Author

Adam, Gabrièle, Esquerré, Diane, Bouchez, Olivier, Bardou, Philippe, Klopp, Christophe, Naves, Michel, Unité de Recherches Zootechniques (URZ), Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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-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), 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), 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), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), 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), and 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)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2018

27. Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response

Author

Esquerré Diane, Lecardonnel Jérome, Flori Laurence, Gao Yu, Hu Zhi-Liang, Teillaud Angélique, Lemonnier Gaëtan, Lefèvre Francois, Oswald Isabelle P, and Rogel-Gaillard Claire

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Designing sustainable animal production systems that better balance productivity and resistance to disease is a major concern. In order to address questions related to immunity and resistance to disease in pig, it is necessary to increase knowledge on its immune system and to produce efficient tools dedicated to this species. Results A long-oligonucleotide-based chip referred to as SLA-RI/NRSP8-13K was produced by combining a generic set with a newly designed SLA-RI set that targets all annotated loci of the pig major histocompatibility complex (MHC) region (SLA complex) in both orientations as well as immunity genes outside the SLA complex. The chip was used to study the immune response of pigs following stimulation of porcine peripheral blood mononuclear cells (PBMCs) with lipopolysaccharide (LPS) or a mixture of phorbol myristate acetate (PMA) and ionomycin for 24 hours. Transcriptome analysis revealed that ten times more genes were differentially expressed after PMA/ionomycin stimulation than after LPS stimulation. LPS stimulation induced a general inflammation response with over-expression of SAA1, pro-inflammatory chemokines IL8, CCL2, CXCL5, CXCL3, CXCL2 and CCL8 as well as genes related to oxidative processes (SOD2) and calcium pathways (S100A9 and S100A12). PMA/ionomycin stimulation induced a stronger up-regulation of T cell activation than of B cell activation with dominance toward a Th1 response, including IL2, CD69 and TNFRSF9 (tumor necrosis factor receptor superfamily, member 9) genes. In addition, a very intense repression of THBS1 (thrombospondin 1) was observed. Repression of MHC class I genes was observed after PMA/ionomycin stimulation despite an up-regulation of the gene cascade involved in peptide processing. Repression of MHC class II genes was observed after both stimulations. Our results provide preliminary data suggesting that antisense transcripts mapping to the SLA complex may have a role during immune response. Conclusion The SLA-RI/NRSP8-13K chip was found to accurately decipher two distinct immune response activations of PBMCs indicating that it constitutes a valuable tool to further study immunity and resistance to disease in pig. The transcriptome analysis revealed specific and common features of the immune responses depending on the stimulation agent that increase knowledge on pig immunity.

Published
2010
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28. Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis

Author

Esquerré Diane, Ricordel Marie-Jo, Montfort Jérôme, Goupil Anne-Sophie, Lareyre Jean-Jacques, Rolland Antoine D, Hugot Karine, Houlgatte Rémi, Chalmel Fréderic, and Le Gac Florence

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Spermatogenesis is a late developmental process that involves a coordinated expression program in germ cells and a permanent communication between the testicular somatic cells and the germ-line. Current knowledge regarding molecular factors driving male germ cell proliferation and differentiation in vertebrates is still limited and mainly based on existing data from rodents and human. Fish with a marked reproductive cycle and a germ cell development in synchronous cysts have proven to be choice models to study precise stages of the spermatogenetic development and the germ cell-somatic cell communication network. In this study we used 9K cDNA microarrays to investigate the expression profiles underlying testis maturation during the male reproductive cycle of the trout, Oncorhynchus mykiss. Results Using total testis samples at various developmental stages and isolated spermatogonia, spermatocytes and spermatids, 3379 differentially expressed trout cDNAs were identified and their gene activation or repression patterns throughout the reproductive cycle were reported. We also performed a tissue-profiling analysis and highlighted many genes for which expression signals were restricted to the testes or gonads from both sexes. The search for orthologous genes in genome-sequenced fish species and the use of their mammalian orthologs allowed us to provide accurate annotations for trout cDNAs. The analysis of the GeneOntology terms therefore validated and broadened our interpretation of expression clusters by highlighting enriched functions that are consistent with known sequential events during male gametogenesis. Furthermore, we compared expression profiles of trout and mouse orthologs and identified a complement of genes for which expression during spermatogenesis was maintained throughout evolution. Conclusion A comprehensive study of gene expression and associated functions during testis maturation and germ cell differentiation in the rainbow trout is presented. The study identifies new pathways involved during spermatogonia self-renewal or rapid proliferation, meiosis and gamete differentiation, in fish and potentially in all vertebrates. It also provides the necessary basis to further investigate the hormonal and molecular networks that trigger puberty and annual testicular recrudescence in seasonally breeding species.

Published
2009
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29. Changes induced by dietary energy intake and divergent selection for muscle fat content in rainbow trout (Oncorhynchus mykiss), assessed by transcriptome and proteome analysis of the liver

Author

Lefèvre Florence, SanCristobal Magali, Esquerré Diane, Borthaire Maïena, Paboeuf Gilles, Kolditz Catherine-Ines, and Médale Françoise

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Growing interest is turned to fat storage levels and allocation within body compartments, due to their impact on human health and quality properties of farm animals. Energy intake and genetic background are major determinants of fattening in most animals, including humans. Previous studies have evidenced that fat deposition depends upon balance between various metabolic pathways. Using divergent selection, we obtained rainbow trout with differences in fat allocation between visceral adipose tissue and muscle, and no change in overall body fat content. Transcriptome and proteome analysis were applied to characterize the molecular changes occurring between these two lines when fed a low or a high energy diet. We focused on the liver, center of intermediary metabolism and the main site for lipogenesis in fish, as in humans and most avian species. Results The proteome and transcriptome analyses provided concordant results. The main changes induced by the dietary treatment were observed in lipid metabolism. The level of transcripts and proteins involved in intracellular lipid transport, fatty acid biosynthesis and anti-oxidant metabolism were lower with the lipid rich diet. In addition, genes and proteins involved in amino-acid catabolism and proteolysis were also under expressed with this diet. The major changes related to the selection effect were observed in levels of transcripts and proteins involved in amino-acid catabolism and proteolysis that were higher in the fat muscle line than in the lean muscle line. Conclusion The present study led to the identification of novel genes and proteins that responded to long term feeding with a high energy/high fat diet. Although muscle was the direct target, the selection procedure applied significantly affected hepatic metabolism, particularly protein and amino acid derivative metabolism. Interestingly, the selection procedure and the dietary treatment used to increase muscle fat content exerted opposite effects on the expression of the liver genes and proteins, with little interaction between the two factors. Some of the molecules we identified could be used as markers to prevent excess muscle fat accumulation.

Published
2008
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30. Dynamic gene expression in fish muscle during recovery growth induced by a fasting-refeeding schedule

Author

Esquerré Diane, Le Cam Aurélie, Rallière Cécile, Montfort Jerome, Rescan Pierre-Yves, and Hugot Karine

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Recovery growth is a phase of rapid growth that is triggered by adequate refeeding of animals following a period of weight loss caused by starvation. In this study, to obtain more information on the system-wide integration of recovery growth in muscle, we undertook a time-course analysis of transcript expression in trout subjected to a food deprivation-refeeding sequence. For this purpose complex targets produced from muscle of trout fasted for one month and from muscle of trout fasted for one month and then refed for 4, 7, 11 and 36 days were hybridized to cDNA microarrays containing 9023 clones. Results Significance analysis of microarrays (SAM) and temporal expression profiling led to the segregation of differentially expressed genes into four major clusters. One cluster comprising 1020 genes with high expression in muscle from fasted animals included a large set of genes involved in protein catabolism. A second cluster that included approximately 550 genes with transient induction 4 to 11 days post-refeeding was dominated by genes involved in transcription, ribosomal biogenesis, translation, chaperone activity, mitochondrial production of ATP and cell division. A third cluster that contained 480 genes that were up-regulated 7 to 36 days post-refeeding was enriched with genes involved in reticulum and Golgi dynamics and with genes indicative of myofiber and muscle remodelling such as genes encoding sarcomeric proteins and matrix compounds. Finally, a fourth cluster of 200 genes overexpressed only in 36-day refed trout muscle contained genes with function in carbohydrate metabolism and lipid biosynthesis. Remarkably, among the genes induced were several transcriptional regulators which might be important for the gene-specific transcriptional adaptations that underlie muscle recovery. Conclusion Our study is the first demonstration of a coordinated expression of functionally related genes during muscle recovery growth. Furthermore, the generation of a useful database of novel genes associated with muscle recovery growth will allow further investigations on particular genes, pathways or cellular process involved in muscle growth and regeneration.

Published
2007
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31. MOESM3 of Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions

Author

Fraslin, Clémence, Dechamp, Nicolas, Bernard, Maria, Krieg, Francine, Hervet, Caroline, Guyomard, René, Esquerré, Diane, Barbieri, Johanna, Kuchly, Claire, Duchaud, Eric, Boudinot, Pierre, Rochat, Tatiana, Jean-François Bernardet, and Quillet, Edwige

Abstract

Additional file 3: Figure S2. Evolution of the rate of hererozygosity along chromosomes (mean values for the 24 individuals with an overall rate of heterozygosity higher than 1%). Description: Metacentric chromosomes (a): under the hypothesis of spontaneous retention of the second polar body during meiosis, the rate of heterozygosity is expected to be lower around the centromere (—) than in telomeric regions (- - - -). Acrocentric chromosomes (b): under the hypothesis of spontaneous retention of the second polar body during meiosis, the rate of heterozygosity is expected to increase along the chromosome from the centromeric region to the telomere. Data are illustrated for 15 chromosomes.

Published
2018
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32. Gut microbiota composition of Turopolje pigs in outdoor production and acorn supplementation

Author

Estellé, Jordi, Massacci, Francesca Romana, Esquerré, Diane, Jardet, Deborah, Lemonnier, Gaetan, Óvilo, Cristina, Čandek-Potokar, Marjeta, Salajpal, Krešimir, Karolyi, Danijel, and EAAP

Subjects
Turopolje pig, outdoor production, acorn, gut microbiota
Abstract

The Turopolje pig is a local porcine breed originating from Croatia characterised by its rusticity and adaptation to the traditional outdoor farming system linked to local oak forests. While this once-widespread breed was almost completely replaced by industrial breeds in the second half of the 20th century, there is growing interest on promoting its production in the framework of sustainable porcine production. The objective of our study was to characterise the gut microbiota composition in 24 Turopolje pigs raised outdoor by using a conventional feed and a conventional feed supplemented with acorns. The gut microbiota composition of all pigs was determined by re-sequencing the bacterial 16S gene in an Illumina MiSeq. Bioinformatics analyses were performed by using Qiime’s open-reference OTU calling subsampled method following author’s recommendations. NMDS and PERMANOVA analyses performed by using the Vegan R package showed significant effects of diet, showing that the acorn supplementation has a relevant impact on gut microbiota, notably by reducing richness and diversity. This result was confirmed in differential abundance analysis that showed that 152 out of 1466 OTUs were significantly different between the two groups. Interestingly, the predicted microbiota metabolic functions that were differentially abundant involved fatty acid and amino-acid metabolisms. Funded by European Union’s H2020 RIA program (Grant agreement No 634476).

Published
2018

33. Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kévin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, CRISCI, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, González, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaëlle, Mompart, Florence, Quéré, Pascale, Robelin, David, San Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard - Van Der Laan, Marie-Helene, Klopp, Christophe, Tixier-Boichard, Michele, ACLOQUE, Hervé, Lagarrigue, Sandrine, Giuffra, Elisabetta, 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), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), iRCM, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 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, 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 de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Livestock, Hi-C, [SDV]Life Sciences [q-bio], Functional annotation, [INFO]Computer Science [cs], ATAC-seq, RNA-seq, [MATH]Mathematics [math]
Abstract

Article publié dans BMC Biology. Disponible ici : https://prodinra.inra.fr/record/491694; Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aims at profiling the landscape of transcription (RNA-seq) and chromatin accessibility and conformation (ATAC-seq and Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Standardized protocols were applied to produce transcriptome and chromatin datasets for the four species. RNA-seq assays allowed to considerably extend the available catalog of protein-coding and non-coding transcripts. Gene expression profiles were consistent with known metabolic/immune functions and revealed differentially expressed transcripts with unknown function, including new lncRNAs in syntenic regions. The majority of ATAC-seq peaks of chromatin accessibility mapped to putative regulatory regions, with an enrichment of predicted transcription factor binding sites in differentially accessible peaks. Hi-C provided the first set of genome-wide maps of three-dimensional interactions across livestock and showed consistency with results from gene expression and chromatin accessibility in topological compartments of the genomes. We report the first multi-species and multi-assay genome annotation results obtained by a FAANG pilot project. The global consistency between gene expression and chromatin structure data in these four livestock species adds up to previous findings in model animals. Overall, these results emphasize the value of FAANG for the research on domesticated animals and strengthen the importance of future meta-analyses of the reference datasets being generated by this community on different species.

Published
2018
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34. Progressive ataxia of Charolais cattle highlights a role of KIF1C in sustainable myelination

Author

Duchesne, Amandine, primary, Vaiman, Anne, additional, Frah, Magali, additional, Floriot, Sandrine, additional, Legoueix-Rodriguez, Sabrina, additional, Desmazières, Anne, additional, Fritz, Sébastien, additional, Beauvallet, Christian, additional, Albaric, Olivier, additional, Venot, Eric, additional, Bertaud, Maud, additional, Saintilan, Romain, additional, Guatteo, Raphaël, additional, Esquerré, Diane, additional, Branchu, Julien, additional, Fleming, Anaïs, additional, Brice, Alexis, additional, Darios, Frédéric, additional, Vilotte, Jean-Luc, additional, Stevanin, Giovanni, additional, Boichard, Didier, additional, and El Hachimi, Khalid Hamid, additional

Published
2018
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35. Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species

Author

Foissac, Sylvain, primary, Djebali, Sarah, additional, Munyard, Kylie, additional, Vialaneix, Nathalie, additional, Rau, Andrea, additional, Muret, Kevin, additional, Esquerré, Diane, additional, Zytnicki, Matthias, additional, Derrien, Thomas, additional, Bardou, Philippe, additional, Blanc, Fany, additional, Cabau, Cèdric, additional, Crisci, Elisa, additional, Dhorne-Pollet, Sophie, additional, Drouet, Françoise, additional, Faraut, Thomas, additional, Gonzalez, Ignacio, additional, Goubil, Adeline, additional, Lacroix-Lamandé, Sonia, additional, Laurent, Fabrice, additional, Marthey, Sylvain, additional, Marti-Marimon, Maria, additional, Momal-Leisenring, Raphaelle, additional, Mompart, Florence, additional, Quéré, Pascale, additional, Robelin, David, additional, Cristobal, Magali San, additional, Tosser-Klopp, Gwenola, additional, Vincent-Naulleau, Silvia, additional, Fabre, Stéphane, additional, der Laan, Marie-Hélène Pinard-Van, additional, Klopp, Christophe, additional, Tixier-Boichard, Michelè, additional, Acloque, Hervé, additional, Lagarrigue, Sandrine, additional, and Giuffra, Elisabetta, additional

Published
2018
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36. Bovine and murine models highlight novel roles for SLC25A46 in mitochondrial dynamics and metabolism, with implications for human and animal health

Author

Duchesne, Amandine, Vaiman, Anne, Castille, Johan, Beauvallet, Christian, Gaignard, Pauline, Floriot, Sandrine, Rodriguez, Sabrina, Vilotte, Marthe, Boulanger, Laurent, Passet, Bruno, Albaric, Olivier, Guillaume, François, Boukadiri, Abdelhak, Richard, Laurence, Bertaud, Maud, Timsit, Edouard, Guatteo, Raphaël, Jaffrézic, Florence, Calvel, Pierre, Helary, Louise, Mahla, Rachid, Esquerré, Diane, Péchoux, Christine, Liuu, Sophie, Vallat, Jean-Michel, Boichard, Didier, Slama, Abdelhamid, Vilotte, Jean-Luc, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Hôpital Bicêtre, Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Bicêtre, Toulouse White Biotechnology (TWB), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Centre de référence national neuropathies périphériques rares [CHU Limoges], CHU Limoges, University of Calgary, Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de la Recherche Agronomique (INRA), Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), 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, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), ANR APIS-GENE Bovano ANR-14-CE19-0011, Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), 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 Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Bicêtre, Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]

Subjects
Proteomics, bovin, Protein Extraction, [SDV]Life Sciences [q-bio], Artificial Gene Amplification and Extension, souris, Biochemistry, Polymerase Chain Reaction, Mitochondrial Dynamics, Phosphate Transport Proteins, Energy-Producing Organelles, Protein Metabolism, Mammals, Extraction Techniques, Animal Models, Ruminants, Mitochondrial DNA, Mitochondria, Nucleic acids, Phenotype, Experimental Organism Systems, Vertebrates, Cellular Structures and Organelles, anomalie veau tourneur, gène SLC25A46, Research Article, mice, lcsh:QH426-470, Forms of DNA, Mouse Models, Bioenergetics, Research and Analysis Methods, Mitochondrial Proteins, Polyneuropathies, Model Organisms, Bovines, Genetics, Animals, Humans, Molecular Biology Techniques, Molecular Biology, Organisms, Biology and Life Sciences, Cell Biology, DNA, lcsh:Genetics, Metabolism, Amino Acid Substitution, Amniotes, Mutation, Cattle, Mitochondrial Membrane, anomalie génétique
Abstract

Neuropathies are neurodegenerative diseases affecting humans and other mammals. Many genetic causes have been identified so far, including mutations of genes encoding proteins involved in mitochondrial dynamics. Recently, the “Turning calves syndrome”, a novel sensorimotor polyneuropathy was described in the French Rouge-des-Prés cattle breed. In the present study, we determined that this hereditary disease resulted from a single nucleotide substitution in SLC25A46, a gene encoding a protein of the mitochondrial carrier family. This mutation caused an apparent damaging amino-acid substitution. To better understand the function of this protein, we knocked out the Slc25a46 gene in a mouse model. This alteration affected not only the nervous system but also altered general metabolism, resulting in premature mortality. Based on optic microscopy examination, electron microscopy and on biochemical, metabolic and proteomic analyses, we showed that the Slc25a46 disruption caused a fusion/fission imbalance and an abnormal mitochondrial architecture that disturbed mitochondrial metabolism. These data extended the range of phenotypes associated with Slc25a46 dysfunction. Moreover, this Slc25a46 knock-out mouse model should be useful to further elucidate the role of SLC25A46 in mitochondrial dynamics., Author summary Mitochondria are essential organelles, the site of numerous biochemical reactions, with a critical role in delivering energy to cells, particularly in the nervous system. Consequently, disrupted mitochondrial function often results in neurodegenerative diseases, in humans and in other mammals. Herein, we determined that the “Turning calves syndrome”, a new hereditary sensorimotor polyneuropathy in the French Rouge-des-Prés cattle breed was due to a single substitution in SLC25A46, a gene encoding a protein of the mitochondrial carrier family. We created a mouse knock-out model and determined that disruption of this gene dramatically disturbed mitochondrial dynamics in various organs that resulted in altered metabolism and early death, indirectly confirming the gene identification in cattle. Moreover, our novel findings extended the range of phenotypes associated with polymorphisms of this gene and help to elucidate the role of SLC25A46 in mitochondrial function.

Published
2017
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37. MOESM1 of Long noncoding RNA repertoire in chicken liver and adipose tissue

Author

Kévin Muret, Klopp, Christophe, Wucher, Valentin, Esquerré, Diane, Legeai, Fabrice, Lecerf, Frédéric, Désert, Colette, Boutin, Morgane, Jehl, Frédéric, Acloque, Hervé, Giuffra, Elisabetta, Djebali, Sarah, Foissac, Sylvain, Derrien, Thomas, and Lagarrigue, Sandrine

Abstract

Additional file 1: Fig. S1. Global Jaccard index for our RNA-Seq data calculated with various threshold values using the R software HTSfilter [32]. This figure shows on the left, count data for long noncoding RNAs; and on the right, count data for protein-coding genes. Count data were normalized by TMM methods [81]. For each type of gene, the data-based threshold corresponds to the red cross and red dotted line. For the long noncoding genes (left), the curve shape of the Jaccard index (that gives a threshold—at the maximum of the curve—equal to one read) is not consistent with the expected index curve shape, in contrast to the protein-coding genes (right) that behave correctly, with a maximum of approximately 32 reads.

Published
2017
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38. Identification of a t(3;4)(p1.3;q1.5) translocation breakpoint in pigs using somatic cell hybrid mapping and high-resolution mate-pair sequencing

Author

Fève, Katia, Foissac, Sylvain, Pinton, Alain, Mompart, Florence, Esquerré, Diane, Faraut, Thomas, Yerle, Martine, Riquet, Juliette, 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Swine, reciprocal translocation, lcsh:Medicine, population, Artificial Gene Amplification and Extension, Polymerase Chain Reaction, Translocation, Genetic, Database and Informatics Methods, ADAMTS Proteins, chromosome, lcsh:Science, hybridization, Mammals, Chromosome Biology, Eukaryota, Chromosome Mapping, High-Throughput Nucleotide Sequencing, Genomics, Chromosomal Aberrations, BAC cloning, adamtsl4, Vertebrates, Sequence Analysis, Autre (Sciences du Vivant), Research Article, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], isolated ectopia lentis, mutation, gene, cytogenetic, biogenesis, Bioinformatics, Research and Analysis Methods, Vector cloning, Genetics, Animals, Molecular Biology Techniques, Molecular Biology, Sequence Assembly Tools, Models, Genetic, Gene Mapping, lcsh:R, Organisms, Biology and Life Sciences, Computational Biology, Cell Biology, Genome Analysis, Chromosomes, Mammalian, Chromosomal Translocations, Amniotes, lcsh:Q, Sequence Alignment, Cloning
Abstract

International audience; Reciprocal translocations are the most frequently occurring constitutional structural rear-rangements in mammalian genomes. In phenotypically normal pigs, an incidence of 1/200 is estimated for such rearrangements. Even if constitutional translocations do not necessarily induce defects and diseases, they are responsible for significant economic losses in domestic animals due to reproduction failures. Over the last 30 years, advances in molecular and cytogenetic technologies have led to major improvements in the resolution of the characterization of translocation events. Characterization of translocation breakpoints helps to decipher the mechanisms that lead to such rearrangements and the functions of the genes that are involved in the translocation. Here, we describe the fine characterization of a reciprocal translocation t(3;4)(p1.3;q1.5) detected in a pig line. The breakpoint was identified at the base-pair level using a positional cloning and chromosome walking strategy in somatic cell hybrids that were generated from an animal that carries this translocation. We show that this translocation occurs within the ADAMTSL4 gene and results in a loss of expression in homozygous carriers. In addition, by taking this translocation as a model, we used a whole-genome next-generation mate-pair sequencing approach on pooled individuals to evaluate this strategy for high-throughput screening of structural rearrangements.

Published
2017
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39. MOESM2 of Identification of copy number variation in French dairy and beef breeds using next-generation sequencing

Author

Letaief, Rabia, Rebours, Emmanuelle, Grohs, Cécile, Meersseman, Cédric, Fritz, Sébastien, Trouilh, Lidwine, Esquerré, Diane, Barbieri, Johanna, Klopp, Christophe, Philippe, Romain, Blanquet, Véronique, Boichard, Didier, Rocha, Dominique, and Mekki Boussaha

Subjects
ComputerSystemsOrganization_COMPUTER-COMMUNICATIONNETWORKS
Abstract

Additional file 2. CGH protocol. In this document, a detailed CGH protocol is provided.

Published
2017
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40. Characterization of 3D genomic interactions in fetal pig muscle

Author

Marti Marimon, Maria Eugenia, Acloque, Hervé, Zytnicki, Matthias, Robelin, David, Djebali Quelen, Sarah, Villa-Vialaneix, Nathalie, Madsen, Ole, Lahbib Mansais, Yvette, Esquerré, Diane, Mompart, Florence, Yerle-Bouissou, Martine, Groenen, Martien, Foissac, Sylvain, Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Wageningen University & Research - WUR (NETHERLANDS), 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), Wageningen University and Research [Wageningen] (WUR), Dynamiques Forestières dans l'Espace Rural (DYNAFOR), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), 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], Wageningen University and Research Center (WUR), 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
Hi-C, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, Biologie animale, Biologie du développement, Nuclear architecture, Fetal development, Pig muscle, nuclear architecture, fetal development, pig muscle, CTCF, [SDV.BDD]Life Sciences [q-bio]/Development Biology
Abstract

Genome sequence alone is not sufficient to explain the overall coordination of nuclear activity in a particular tissue. The nuclear organisation and genomic long-range intra- and inter-chromosomal interactions play an important role in the regulation of gene expression and the activation of tissue- specific gene networks. Here we present an overview of the pig genome architecture in muscle at two late developmental stages. The muscle maturation process occurs between the 90th day and the end of gestation (114 days), a key period for survival at birth. To characterise this period we profiled chromatin interactions genome-wide with in situ Hi-C (High Throughput Chromosome Conformation Capture) in muscle samples collected at 90 and 110 days of gestation, specific moments where a drastic change in gene expression has been reported. About 200 million read pairs per library were generated (3 replicates per condition). This allowed: (a) the design of an experimental Hi-C protocol optimized for frozen fetal tissues, (b) the first Hi-C contact heatmaps in fetal porcine muscle cells, and (c) to profile Topologically Associated Domains (TADs) defined as genomic domains with high levels of chromatin interactions. Using the new assembly version Sus scrofa v11, we could map 82% of the Hi-C reads on the reference genome. After filtering, 49% of valid read pairs were used to infer the genomic interactions in both developmental stages. In addition, ChIP-seq experiments were performed to map the binding of the structural protein CTCF, known to regulate genome structure by promoting interactions between genes and distal enhancers. The Hi-C and ChIP-seq data were analysed in combination with the results of a previous transcriptome analysis, focusing on the hun-dreds of genes that were reported as differentially expressed during muscle maturation. We will report the observed general differences between both developmental stages in terms of transcription and structure.

Published
2017

41. Construction of whole genome interaction maps and study of correlation with gene expression level in fetal muscle cells

Author

Marti-Marimon, Maria, ACLOQUE, Hervé, Robelin, David, Zytnicki, Matthias, Djebali, Sarah, Lahbib Mansais, Yvette, Esquerré, Diane, Mompart, Florence, Yerle-Bouissou, Martine, Foissac, Sylvain, 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), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, correlation, [SDV]Life Sciences [q-bio], interaction, [INFO]Computer Science [cs], genetic, [MATH]Mathematics [math], genome, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

42. First microbial gene catalog and antibiotic resistome of rabbit gut microbiota established by metagenomic sequencing

Author

Achard, Caroline, RAMAYO CALDAS, Yuliaxis, Ghozlane, Amine, Almeida, Mathieu, Ballester, Maria, Boucher, Samuel, Chatellier, Stéphane, Chaubet, Adeline, Combes, Sylvie, Denis, Catherine, Dile, Benoit, Esquerré, Diane, Gabinaud, Beatrice, Le Normand, Bernadette, Pons, Nicolas, Ruppe, Etienne, Estellé, Jordi, Zemb, Olivier, 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, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Center for Bioinformatics and Computational Biology, University of Delaware [Newark], LABOVET Conseil, Réseau Cristal, Clinique Vétérinaire des Marchés de Bretagne, Genomic Research Laboratory, and Geneva University Hospital (HUG)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, microbiote, antibiotic, [SDV]Life Sciences [q-bio], rabbit, [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

43. First rabbit gut microbial gene catalog and metagenomic insights into the resistome : links with antibiotic use

Author

Achard, Caroline, RAMAYO CALDAS, Yuliaxis, Ghozlane, Amine, Almeida, Mathieu, Boucher, Samuel, Chatellier, Stéphane, Chaubet, Adeline, Combes, Sylvie, Denis, Catherine, Dile, Benoit, Esquerré, Diane, Gabinaud, Beatrice, Le Normand, Bernadette, Pons, Nicolas, Ruppe, Etienne, Estelle Fabrellas, Jordi, Zemb, Olivier, 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, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Center for Bioinformatics and Computational Biology, University of Delaware [Newark], LABOVET Conseil, Réseau Cristal, and Clinique Vétérinaire des Marchés de Bretagne

Subjects
resistance, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, antibiotic, [SDV]Life Sciences [q-bio], rabbit, microbiota, [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

44. A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly hair coat trait (Crd) in horse

Author

Morgenthaler, Caroline, primary, Diribarne, Mathieu, additional, Capitan, Aurélien, additional, Legendre, Rachel, additional, Saintilan, Romain, additional, Gilles, Maïlys, additional, Esquerré, Diane, additional, Juras, Rytis, additional, Khanshour, Anas, additional, Schibler, Laurent, additional, and Cothran, Gus, additional

Published
2017
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45. Identification of copy number variation in French dairy and beef breeds using next-generation sequencing

Author

Letaief, Rabia, primary, Rebours, Emmanuelle, additional, Grohs, Cécile, additional, Meersseman, Cédric, additional, Fritz, Sébastien, additional, Trouilh, Lidwine, additional, Esquerré, Diane, additional, Barbieri, Johanna, additional, Klopp, Christophe, additional, Philippe, Romain, additional, Blanquet, Véronique, additional, Boichard, Didier, additional, Rocha, Dominique, additional, and Boussaha, Mekki, additional

Published
2017
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46. The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology

Author

Mach, Núria, primary, Foury, Aline, additional, Kittelmann, Sandra, additional, Reigner, Fabrice, additional, Moroldo, Marco, additional, Ballester, Maria, additional, Esquerré, Diane, additional, Rivière, Julie, additional, Sallé, Guillaume, additional, Gérard, Philippe, additional, Moisan, Marie-Pierre, additional, and Lansade, Léa, additional

Published
2017
Full Text
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47. 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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48. 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

49. Long noncoding RNA repertoire in chicken liver and adipose tissue

Author

Muret, Kévin, primary, Klopp, Christophe, additional, Wucher, Valentin, additional, Esquerré, Diane, additional, Legeai, Fabrice, additional, Lecerf, Frédéric, additional, Désert, Colette, additional, Boutin, Morgane, additional, Jehl, Frédéric, additional, Acloque, Hervé, additional, Giuffra, Elisabetta, additional, Djebali, Sarah, additional, Foissac, Sylvain, additional, Derrien, Thomas, additional, and Lagarrigue, Sandrine, additional

Published
2017
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50. Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

Author

Boussaha, Mekki, primary, Michot, Pauline, additional, Letaief, Rabia, additional, Hozé, Chris, additional, Fritz, Sébastien, additional, Grohs, Cécile, additional, Esquerré, Diane, additional, Duchesne, Amandine, additional, Philippe, Romain, additional, Blanquet, Véronique, additional, Phocas, Florence, additional, Floriot, Sandrine, additional, Rocha, Dominique, additional, Klopp, Christophe, additional, Capitan, Aurélien, additional, and Boichard, Didier, additional

Published
2016
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