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1. Driving gut microbiota enterotypes through host genetics

Author: Catherine Larzul, Jordi Estellé, Marion Borey, Fany Blanc, Gaëtan Lemonnier, Yvon Billon, Mamadou Gabou Thiam, Benoît Quinquis, Nathalie Galleron, Deborah Jardet, Jérôme Lecardonnel, Florian Plaza Oñate, and Claire Rogel-Gaillard
Subjects: Gut microbiota, Genetics, Genetic selection, Enterotype, Holobiont, Metagenomics, Microbial ecology, QR100-130
Abstract: Abstract Background Population stratification based on interindividual variability in gut microbiota composition has revealed the existence of several ecotypes named enterotypes in humans and various animal species. Enterotypes are often associated with environmental factors including diet, but knowledge of the role of host genetics remains scarce. Moreover, enterotypes harbor functionalities likely associated with varying abilities and susceptibilities of their host. Previously, we showed that under controlled conditions, 60-day-old pig populations consistently split into two enterotypes with either Prevotella and Mitsuokella (PM enterotype) or Ruminococcus and Treponema (RT enterotype) as keystone taxa. Here, our aim was to rely on pig as a model to study the influence of host genetics to assemble enterotypes, and to provide clues on enterotype functional differences and their links with growth traits. Results We established two pig lines contrasted for abundances of the genera pairs specifying each enterotype at 60 days of age and assessed them for fecal microbiota composition and growth throughout three consecutive generations. Response to selection across three generations revealed, per line, an increase in the prevalence of the selected enterotype and in the average relative abundances of directly and indirectly selected bacterial genera. The PM enterotype was found less diverse than the RT enterotype but more efficient for piglet growth during the post-weaning period. Shotgun metagenomics revealed differentially abundant bacterial species between the two enterotypes. By using the KEGG Orthology database, we show that functions related to starch degradation and polysaccharide metabolism are enriched in the PM enterotype, whereas functions related to general nucleoside transport and peptide/nickel transport are enriched in the RT enterotype. Our results also suggest that the PM and RT enterotypes might differ in the metabolism of valine, leucin, and isoleucine, favoring their biosynthesis and degradation, respectively. Conclusion We experimentally demonstrated that enterotypes are functional ecosystems that can be selected as a whole by exerting pressure on the host genetics. We also highlight that holobionts should be considered as units of selection in breeding programs. These results pave the way for a holistic use of host genetics, microbiota diversity, and enterotype functionalities to understand holobiont shaping and adaptation. Video Abstract
Published: 2024
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2. The 3D nuclear conformation of the major histocompatibility complex changes upon cell activation both in porcine and human macrophages

Author: Florence Mompart, Alain Kamgoué, Yvette Lahbib-Mansais, David Robelin, Agnès Bonnet, Claire Rogel-Gaillard, Silvia Kocanova, and Martine Yerle-Bouissou
Subjects: Nuclear architecture, Gene expression, Major histocompatibility complex, Macrophage, LPS/IFNγ activation, 3D-FISH, Cytology, QH573-671
Abstract: Abstract Background The crucial role of the major histocompatibility complex (MHC) for the immune response to infectious diseases is well-known, but no information is available on the 3D nuclear organization of this gene-dense region in immune cells, whereas nuclear architecture is known to play an essential role on genome function regulation. We analyzed the spatial arrangement of the three MHC regions (class I, III and II) in macrophages using 3D-FISH. Since this complex presents major differences in humans and pigs with, notably, the presence of the centromere between class III and class II regions in pigs, the analysis was implemented in both species to determine the impact of this organization on the 3D conformation of the MHC. The expression level of the three genes selected to represent each MHC region was assessed by quantitative real-time PCR. Resting and lipopolysaccharide (LPS)-activated states were investigated to ascertain whether a response to a pathogen modifies their expression level and their 3D organization. Results While the three MHC regions occupy an intermediate radial position in porcine macrophages, the class I region was clearly more peripheral in humans. The BAC center-to-center distances allowed us to propose a 3D nuclear organization of the MHC in each species. LPS/IFNγ activation induces a significant decompaction of the chromatin between class I and class III regions in pigs and between class I and class II regions in humans. We detected a strong overexpression of TNFα (class III region) in both species. Moreover, a single nucleus analysis revealed that the two alleles can have either the same or a different compaction pattern. In addition, macrophage activation leads to an increase in alleles that present a decompacted pattern in humans and pigs. Conclusions The data presented demonstrate that: (i) the MHC harbors a different 3D organization in humans and pigs; (ii) LPS/IFNγ activation induces chromatin decompaction, but it is not the same area affected in the two species. These findings were supported by the application of an original computation method based on the geometrical distribution of the three target genes. Finally, the position of the centromere inside the swine MHC could influence chromatin reorganization during the activation process.
Published: 2021
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3. Links between fecal microbiota and the response to vaccination against influenza A virus in pigs

Author: Marion Borey, Fany Blanc, Gaëtan Lemonnier, Jean-Jacques Leplat, Deborah Jardet, Marie-Noëlle Rossignol, Laure Ravon, Yvon Billon, Maria Bernard, Jordi Estellé, and Claire Rogel-Gaillard
Subjects: Immunologic diseases. Allergy, RC581-607, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract: Abstract This study describes the associations between fecal microbiota and vaccine response variability in pigs, using 98 piglets vaccinated against the influenza A virus at 28 days of age (D28) with a booster at D49. Immune response to the vaccine is measured at D49, D56, D63, and D146 by serum levels of IAV-specific IgG and assays of hemagglutination inhibition (HAI). Analysis of the pre-vaccination microbiota characterized by 16S rRNA gene sequencing of fecal DNA reveals a higher vaccine response in piglets with a richer microbiota, and shows that 23 operational taxonomic units (OTUs) are differentially abundant between high and low IAV-specific IgG producers at D63. A stronger immune response is linked with OTUs assigned to the genus Prevotella and family Muribaculaceae, and a weaker response is linked with OTUs assigned to the genera Helicobacter and Escherichia-Shigella. A set of 81 OTUs accurately predicts IAV-specific IgG and HAI titer levels at all time points, highlighting early and late associations between pre-vaccination fecal microbiota composition and immune response to the vaccine.
Published: 2021
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4. Influence of genetics and the pre-vaccination blood transcriptome on the variability of antibody levels after vaccination against Mycoplasma hyopneumoniae in pigs

Author: Fany Blanc, Tatiana Maroilley, Manuel Revilla, Gaëtan Lemonnier, Jean-Jacques Leplat, Yvon Billon, Laure Ravon, Olivier Bouchez, Jean-Pierre Bidanel, Bertrand Bed’Hom, Marie-Hélène Pinard-van der Laan, Jordi Estellé, and Claire Rogel-Gaillard
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background The impact of individual genetic and genomic variations on immune responses is an emerging lever investigated in vaccination strategies. In our study, we used genetic and pre-vaccination blood transcriptomic data to study vaccine effectiveness in pigs. Results A cohort of 182 Large White pigs was vaccinated against Mycoplasma hyopneumoniae (M. hyo) at weaning (28 days of age), with a booster 21 days later. Vaccine response was assessed by measuring seric M. hyo antibodies (Ab) at 0 (vaccination day), 21 (booster day), 28, 35, and 118 days post-vaccination (dpv). Inter-individual variability of M. hyo Ab levels was observed at all time points and the corresponding heritabilities ranged from 0.46 to 0.57. Ab persistence was higher in females than in males. Genome-wide association studies with a 658 K SNP panel revealed two genomic regions associated with variations of M. hyo Ab levels at 21 dpv at positions where immunity-related genes have been mapped, DAB2IP on chromosome 1, and ASAP1, CYRIB and GSDMC on chromosome 4. We studied covariations of Ab responses with the pre-vaccination blood transcriptome obtained by RNA-Seq for a subset of 82 pigs. Weighted gene correlation network and differential expression analyses between pigs that differed in Ab responses highlighted biological functions that were enriched in heme biosynthesis and platelet activation for low response at 21 dpv, innate antiviral immunity and dendritic cells for high response at 28 and 35 dpv, and cell adhesion and extracellular matrix for high response at 118 dpv. Sparse partial least squares discriminant analysis identified 101 genes that efficiently predicted divergent responders at all time points. We found weak negative correlations of M. hyo Ab levels with body weight traits, which revealed a trade-off that needs to be further explored. Conclusions We confirmed the influence of the host genetics on vaccine effectiveness to M. hyo and provided evidence that the pre-vaccination blood transcriptome co-varies with the Ab response. Our results highlight that both genetic markers and blood biomarkers could be used as potential predictors of vaccine response levels and more studies are required to assess whether they can be exploited in breeding programs.
Published: 2021
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5. Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets

Author: Francesca Romana Massacci, Mustapha Berri, Gaetan Lemonnier, Elodie Guettier, Fany Blanc, Deborah Jardet, Marie Noelle Rossignol, Marie-José Mercat, Joël Doré, Patricia Lepage, Claire Rogel-Gaillard, and Jordi Estellé
Subjects: Piglet, Gut microbiota, Age, Weaning, Diversity, F. Prausnitzii, Veterinary medicine, SF600-1100, Microbiology, QR1-502
Abstract: Abstract Background In pig production systems, weaning is a crucial period characterized by nutritional, environmental, and social stresses. Piglets transition from a milk-based diet to a solid, more complex plant-based diet, and their gut physiology must adapt accordingly. It is well established that piglets weaned later display improved health, better wean-to-finish growth performance, and lower mortality rates. The aim of this study was to evaluate the impact of weaning age on fecal microbiota diversity and composition in piglets. Forty-eight Large White piglets were divided into 4 groups of 12 animals that were weaned at different ages: 14 days (early weaning), 21 days (a common weaning age in intensive pig farming), 28 days (idem), and 42 days (late weaning). Microbiota composition was assessed in each group by sequencing the 16S rRNA gene using fecal samples taken on the day of weaning, 7 days later, and at 60 days of age. Results In each group, there were significant differences in fecal microbiota composition before and after weaning (p
Published: 2020
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6. Quelle science pour les élevages de demain ? Une réflexion prospective conduite à l’INRA

Author: Jean-Louis PEYRAUD, Joël AUBIN, Marc BARBIER, René BAUMONT, Cécile BERRI, Jean-Pierre BIDANEL, Christine CITTI, Corinne COTINOT, Christian DUCROT, Pierre DUPRAZ, Philippe FAVERDIN, Nicolas FRIGGENS, Sabine HOUOT, Marie-Odile NOZIÈRES-PETIT, Claire ROGEL-GAILLARD, and Véronique SANTÉ-LHOUTELLIER
Subjects: Animal culture, SF1-1100, Aquaculture. Fisheries. Angling, SH1-691
Abstract: L’ambition de l’Atelier de Réflexion Prospective sur l’élevage a été de repenser la place, les rôles de l’élevage et en quoi il doit se transformer pour contribuer pleinement au développement de systèmes agri-alimentaires plus durables ainsi que d’identifier des thématiques de recherches interdisciplinaires permettant d’explorer des fronts de science ou méthodologiques porteurs d’avenir pour lever les verrous de connaissances. La réflexion a été animée par un groupe de 15 chercheurs et en a mobilisé une centaine. À partir d’une analyse du contexte et des drivers d’évolution des systèmes nous proposons un nouveau cadre conceptuel et des voies de progrès pour penser l’élevage de demain. L’élevage doit s’inscrire dans le cadre de systèmes agri-alimentaires circulaires dans lesquels il doit contribuer, au-delà d’une efficience accrue des moyens de production, à la préservation de la qualité des ressources et à la production d’une alimentation à un prix abordable. Il faut repenser les systèmes pour qu’ils soient climato-intelligents et répondent aux enjeux de santé et du bien-être des animaux et des Hommes ; repenser les liens entre élevage, production végétale et territoire pour maximiser les recyclages et repenser les liens entre élevage, transformation et consommation des produits de l’élevage. Les innovations doivent être basées sur les principes de l’agroécologie complétés par ceux de l’économie circulaire et par la mobilisation des leviers des (bio)technologies et de l’innovation organisationnelle. Le texte décrit quatre grandes priorités scientifiques avec leurs enjeux de recherche et produit des recommandations pour un plan d’action.
Published: 2019
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7. Discovery of Predictors of Mycoplasma hyopneumoniae Vaccine Response Efficiency in Pigs: 16S rRNA Gene Fecal Microbiota Analysis

Author: Peris M. Munyaka, Fany Blanc, Jordi Estellé, Gaëtan Lemonnier, Jean-Jacques Leplat, Marie-Noëlle Rossignol, Déborah Jardet, Graham Plastow, Yvon Billon, Benjamin P. Willing, and Claire Rogel-Gaillard
Subjects: vaccination, microbiota, pig, prediction, Mycoplasma hyopneumoniae, Biology (General), QH301-705.5
Abstract: The gut microbiota comprises a large and diverse community of bacteria that play a significant role in swine health. Indeed, there is a tight association between the enteric immune system and the overall composition and richness of the microbiota, which is key in the induction, training and function of the host immunity, and may therefore, influence the immune response to vaccination. Using vaccination against Mycoplasma hyopneumoniae (M. hyo) as a model, we investigated the potential of early-life gut microbiota in predicting vaccine response and explored the post-vaccination dynamics of fecal microbiota at later time points. At 28 days of age (0 days post-vaccination; dpv), healthy piglets were vaccinated, and a booster vaccine was administered at 21 dpv. Blood samples were collected at 0, 21, 28, 35, and 118 dpv to measure M. hyo-specific IgG levels. Fecal samples for 16S rRNA gene amplicon sequencing were collected at 0, 21, 35, and 118 dpv. The results showed variability in antibody response among individual pigs, whilst pre-vaccination operational taxonomic units (OTUs) primarily belonging to Prevotella, [Prevotella], Anaerovibrio, and Sutterella appeared to best-predict vaccine response. Microbiota composition did not differ between the vaccinated and non-vaccinated pigs at post-vaccination time points, but the time effect was significant irrespective of the animals’ vaccination status. Our study provides insight into the role of pre-vaccination gut microbiota composition in vaccine response and emphasizes the importance of studies on full metagenomes and microbial metabolites aimed at deciphering the role of specific bacteria and bacterial genes in the modulation of vaccine response.
Published: 2020
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8. Extensive expression differences along porcine small intestine evidenced by transcriptome sequencing.

Author: Núria Mach, Mustapha Berri, Diane Esquerré, Claire Chevaleyre, Gaëtan Lemonnier, Yvon Billon, Patricia Lepage, Isabelle P Oswald, Joël Doré, Claire Rogel-Gaillard, and Jordi Estellé
Subjects: Medicine, Science
Abstract: The aim of this study was to analyse gene expression along the small intestine (duodenum, jejunum, ileum) and in the ileal Peyer's patches in four young pigs with no clinical signs of disease by transcriptome sequencing. Multidimensional scaling evidenced that samples clustered by tissue type rather than by individual, thus prefiguring a relevant scenario to draw tissue-specific gene expression profiles. Accordingly, 1,349 genes were found differentially expressed between duodenum and jejunum, and up to 3,455 genes between duodenum and ileum. Additionally, a considerable number of differentially expressed genes were found by comparing duodenum (7,027 genes), jejunum (6,122 genes), and ileum (6,991 genes) with ileal Peyer's patches tissue. Functional analyses revealed that most of the significant differentially expressed genes along small intestinal tissues were involved in the regulation of general biological processes such as cell development, signalling, growth and proliferation, death and survival or cell function and maintenance. These results suggest that the intrinsic large turnover of intestinal tissues would have local specificities at duodenum, ileum and jejunum. In addition, in concordance with their biological function, enteric innate immune pathways were overrepresented in ileal Peyer's patches. The reported data provide an expression map of the cell pathway variation in the different small intestinal tissues. Furthermore, expression levels measured in healthy individuals could help to understand changes in gene expression that occur in dysbiosis or pathological states.
Published: 2014
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9. Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA) as a model region.

Author: Marie-Laure Endale Ahanda, Eric R Fritz, Jordi Estellé, Zhi-Liang Hu, Ole Madsen, Martien A M Groenen, Dario Beraldi, Ronan Kapetanovic, David A Hume, Robert R R Rowland, Joan K Lunney, Claire Rogel-Gaillard, James M Reecy, and Elisabetta Giuffra
Subjects: Medicine, Science
Abstract: THE SLA (swine leukocyte antigen, MHC: SLA) genes are the most important determinants of immune, infectious disease and vaccine response in pigs; several genetic associations with immunity and swine production traits have been reported. However, most of the current knowledge on SLA is limited to gene coding regions. MicroRNAs (miRNAs) are small molecules that post-transcriptionally regulate the expression of a large number of protein-coding genes in metazoans, and are suggested to play important roles in fine-tuning immune mechanisms and disease responses. Polymorphisms in either miRNAs or their gene targets may have a significant impact on gene expression by abolishing, weakening or creating miRNA target sites, possibly leading to phenotypic variation. We explored the impact of variants in the 3'-UTR miRNA target sites of genes within the whole SLA region. The combined predictions by TargetScan, PACMIT and TargetSpy, based on different biological parameters, empowered the identification of miRNA target sites and the discovery of polymorphic miRNA target sites (poly-miRTSs). Predictions for three SLA genes characterized by a different range of sequence variation provided proof of principle for the analysis of poly-miRTSs from a total of 144 M RNA-Seq reads collected from different porcine tissues. Twenty-four novel SNPs were predicted to affect miRNA-binding sites in 19 genes of the SLA region. Seven of these genes (SLA-1, SLA-6, SLA-DQA, SLA-DQB1, SLA-DOA, SLA-DOB and TAP1) are linked to antigen processing and presentation functions, which is reminiscent of associations with disease traits reported for altered miRNA binding to MHC genes in humans. An inverse correlation in expression levels was demonstrated between miRNAs and co-expressed SLA targets by exploiting a published dataset (RNA-Seq and small RNA-Seq) of three porcine tissues. Our results support the resource value of RNA-Seq collections to identify SNPs that may lead to altered miRNA regulation patterns.
Published: 2012
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10. Co-expression of host and viral microRNAs in porcine dendritic cells infected by the pseudorabies virus.

Author: Anna Anselmo, Laurence Flori, Florence Jaffrezic, Teresa Rutigliano, Maria Cecere, Naima Cortes-Perez, François Lefèvre, Claire Rogel-Gaillard, and Elisabetta Giuffra
Subjects: Medicine, Science
Abstract: MicroRNAs are small non-coding RNAs approximately 22 nt long that modulate gene expression in animals and plants. It has been recently demonstrated that herpesviruses encode miRNAs to control the post-transcriptional regulation of expression from their own genomes and possibly that of their host, thus adding an additional layer of complexity to the physiological cross-talk between host and pathogen. The present study focussed on the interactions between porcine dendritic cells (DCs) and the Pseudorabies virus (PRV), an alpha-herpesvirus causing Aujeszky's disease in pigs. A catalogue of porcine and viral miRNAs, expressed eight hours post-infection, was established by deep sequencing. An average of 2 million reads per sample with a size of 21-24 nucleotides was obtained from six libraries representing three biological replicates of infected and mock-infected DCs. Almost 95% of reads mapped to the draft pig genome sequence and pig miRNAs previously annotated in dedicated databases were detected by sequence alignment. In silico prediction allowed the identification of unknown porcine as well as of five miRNAs transcribed by the Large Latency Transcript (LLT) of PRV. The gene target prediction of the viral miRNAs and the Ingenuity Pathway Analysis of differentially expressed pig miRNAs were conducted to contextualize the identified small RNA molecules and functionally characterize their involvement in the post-transcriptional regulation of gene expression. The results support a role for PRV miRNAs in the maintenance of the host cell latency state through the down-regulation of immediate-early viral genes which is similar to other herpesviruses. The differentially expressed swine miRNAs identified a unique network of target genes with highly significant functions in the development and function of the nervous system and in infectious mechanisms, suggesting that the modulation of both host and viral miRNAs is necessary for the establishment of PRV latency.
Published: 2011
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11. Immunity traits in pigs: substantial genetic variation and limited covariation.

Author: Laurence Flori, Yu Gao, Denis Laloë, Gaëtan Lemonnier, Jean-Jacques Leplat, Angélique Teillaud, Anne-Marie Cossalter, Joëlle Laffitte, Philippe Pinton, Christiane de Vaureix, Marcel Bouffaud, Marie-José Mercat, François Lefèvre, Isabelle P Oswald, Jean-Pierre Bidanel, and Claire Rogel-Gaillard
Subjects: Medicine, Science
Abstract: BACKGROUND: Increasing robustness via improvement of resistance to pathogens is a major selection objective in livestock breeding. As resistance traits are difficult or impossible to measure directly, potential indirect criteria are measures of immune traits (ITs). Our underlying hypothesis is that levels of ITs with no focus on specific pathogens define an individual's immunocompetence and thus predict response to pathogens in general. Since variation in ITs depends on genetic, environmental and probably epigenetic factors, our aim was to estimate the relative importance of genetics. In this report, we present a large genetic survey of innate and adaptive ITs in pig families bred in the same environment. METHODOLOGY/PRINCIPAL FINDINGS: Fifty four ITs were studied on 443 Large White pigs vaccinated against Mycoplasma hyopneumoniae and analyzed by combining a principal component analysis (PCA) and genetic parameter estimation. ITs include specific and non specific antibodies, seric inflammatory proteins, cell subsets by hemogram and flow cytometry, ex vivo production of cytokines (IFNα, TNFα, IL6, IL8, IL12, IFNγ, IL2, IL4, IL10), phagocytosis and lymphocyte proliferation. While six ITs had heritabilities that were weak or not significantly different from zero, 18 and 30 ITs had moderate (0.10.4) heritability values, respectively. Phenotypic and genetic correlations between ITs were weak except for a few traits that mostly include cell subsets. PCA revealed no cluster of innate or adaptive ITs. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that variation in many innate and adaptive ITs is genetically controlled in swine, as already reported for a smaller number of traits by other laboratories. A limited redundancy of the traits was also observed confirming the high degree of complementarity between innate and adaptive ITs. Our data provide a genetic framework for choosing ITs to be included as selection criteria in multitrait selection programmes that aim to improve both production and health traits.
Published: 2011
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12. Importance of the Major Histocompatibility Complex (Swine Leukocyte Antigen) in Swine Health and Biomedical Research

Author: C. S. Ho, M. Tector, Asako Ando, Joan K. Lunney, Sabine E. Hammer, M. Charles, Claire Rogel-Gaillard, A. J. Tector, Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine [Vienna] (Vetmeduni), Gift of Hope Organ & Tissu e Donor Network, Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris Saclay (COMUE), Department of Surgery Birmingham, University of Alabama at Birmingham (UAB), Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, USDA-ARS : Agricultural Research Service, Lunney, Joan, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Agricultural Research Service
Subjects: 0301 basic medicine, Swine, [SDV]Life Sciences [q-bio], Xenotransplantation, medicine.medical_treatment, Sus scrofa, Antigen presentation, Transplants, 030230 surgery, Biology, Major histocompatibility complex, 03 medical and health sciences, 0302 clinical medicine, Antigen, Genetics, medicine, Animals, Gene, Swine Diseases, allogeneic, Chromosome 7 (human), General Veterinary, xenogeneic, Histocompatibility Antigens Class I, fungi, Haplotype, SLA polymorphism, Transplantation, 030104 developmental biology, swine leukocyte antigen, vaccine responses, Gene Expression Regulation, Models, Animal, biology.protein, Animal Science and Zoology, Biotechnology
Abstract: In pigs, the major histocompatibility complex (MHC), or swine leukocyte antigen (SLA) complex, maps to Sus scrofa chromosome 7. It consists of three regions, the class I and class III regions mapping to 7p1.1 and the class II region mapping to 7q1.1. The swine MHC is divided by the centromere, which is unique among mammals studied to date. The SLA complexspans between 2.4 and 2.7 Mb, depending on haplotype, and encodes approximately 150 loci, with at least 120 genes predicted to be functional. Here we update the whole SLA complex based on the Sscrofa11.1 build and annotate the organization for all recognized SLA genes and their allelic sequences. We present SLA nomenclature and typing methods and discuss the expression of SLA proteins, as well as their role in antigen presentation and immune, disease, and vaccine responses. Finally, we explore the role of SLA genes in transplantation and xenotransplantation and their importance in swine biomedical models.
Published: 2020
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13. Host genotype and amoxicillin administration affect the incidence of diarrhoea and faecal microbiota of weaned piglets during a natural multiresistant ETEC infection

Author: Silvia Tofani, Claudio Forte, Gaetan Lemonnier, Adrien Castinel, Claudia Bevilacqua, Claire Rogel-Gaillard, Chiara Francesca Magistrali, Lucia Marchi, Giovanni Pezzotti, Carmela Lovito, Diana Luise, Micol Bertocchi, Serenella Orsini, Paolo Trevisi, Fany Blanc, Jordi Estellé, Michele Tentellini, Francesca Romana Massacci, Francesca Romana Massacci,| Silvia Tofani, Claudio Forte, Micol Bertocchi, Carmela Lovito, Serenella Orsini, Michele Tentellini, Lucia Marchi, Gaetan Lemonnier, Diana Luise, Fany Blanc, Adrien Castinel, Claudia Bevilacqua, Claire Rogel‐Gaillard, Giovanni Pezzotti, Jordi Estellé, Paolo Trevisi, Chiara Francesca Magistrali, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Partenaires INRAE, Department of Agricultural and Food Sciences, University of Bologna, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ministry of Health, ItalyIZSUM RC 006/2016INRA (Animal Genetics division)France Genomique National infrastructureANR-10INBS-09Department of Agricultural and Food Sciences (DISTAL) of Bologna University (Italy), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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: Antibiotic resistance, Swine, [SDV]Life Sciences [q-bio], Antibiotics, Gut flora, medicine.disease_cause, Feces, fluids and secretions, Food Animals, Oral administration, Enterotoxigenic Escherichia coli, Genotype, Escherichia coli Infections, 0303 health sciences, biology, Microbiota, Bacterial, Antibiotic resistance, Escherichia coli, FUT1, gut microbiota, MUC4, swine, General Medicine, Single Nucleotide, 3. Good health, medicine.drug, DNA, Bacterial, Diarrhea, medicine.drug_class, FUT1, Weaning, Polymorphism, Single Nucleotide, digestive system, Microbiology, 03 medical and health sciences, medicine, Escherichia coli, Animals, Polymorphism, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, gut microbiota, 030306 microbiology, Amoxicillin, DNA, biology.organism_classification, bacterial infections and mycoses, MUC4, swine, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Animal Science and Zoology
Abstract: International audience; Enterotoxigenic Escherichia coli (ETEC) is the aetiological agent of postweaning diarrhoea (PWD) in piglets. The SNPs located on the Mucine 4 (MUC4) and Fucosyltransferase 1 (FUT1) genes have been associated with the susceptibility to ETEC F4 and ETEC F18, respectively. The interplay between the MUC4 and FUT1 genotypes to ETEC infection and the use of amoxicillin in modifying the intestinal microbiota during a natural infection by multiresistant ETEC strains have never been investigated. The aim of this study was to evaluate the effects of the MUC4 and FUT1 genotypes and the administration of amoxicillin through different routes on the presence of diarrhoea and the faecal microbiota composition in piglets naturally infected with ETEC. Seventy-one piglets were divided into three groups: two groups differing by amoxicillin administration routes-parenteral (P) or oral (O) and a control group without antibiotics (C). Faecal scores, body weight, presence of ETEC F4 and F18 were investigated 4 days after the arrival in the facility (T0), at the end of the amoxicillin administration (T1) and after the withdrawal period (T2). The faecal bacteria composition was assessed by sequencing the 16S rRNA gene. We described that MUC4 and FUT1 genotypes were associated with the presence of ETEC F4 and ETEC F18. The faecal microbiota was influenced by the MUC4 genotypes at T0. We found the oral administration to be associated with the presence of diarrhoea at T1 and T2. Furthermore, the exposure to amoxicillin resulted in significant alterations of the faecal microbiota. Overall, MUC4 and FUT1 were confirmed as genetic markers for the susceptibility to ETEC infections in pigs. Moreover, our data highlight that group amoxicillin treatment may produce adverse outcomes on pig health in course of multiresistant ETEC infection. Therefore, alternative control measures able to maintain a healthy faecal microbiota in weaners are recommended.
Published: 2020
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14. Immunogenetics in the rabbit

Author: Rose G. Mage and Claire Rogel-Gaillard
Published: 2021
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15. Discovery of Predictors of Mycoplasma hyopneumoniae Vaccine Response Efficiency in Pigs: 16S rRNA Gene Fecal Microbiota Analysis

Author: Deborah Jardet, Yvon Billon, Gaetan Lemonnier, Claire Rogel-Gaillard, Benjamin P. Willing, Jean-Jacques Leplat, Fany Blanc, Jordi Estellé, Peris M. Munyaka, Graham Plastow, Marie-Noelle Rossignol, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Alberta, Unité Expérimentale Elevages Porcins Innovants (GenESI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Genome Canada 2014LSARP_8202, Canada Research Chairs, Stollery Children's Hospital Foundation through the Women and Children's Health Research Institute (WCHRI) Postdoctoral Fellowship, European Project: 633184,H2020,H2020-SFS-2014-2,SAPHIR(2015), and Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, Microbiology (medical), pig, 030106 microbiology, Booster dose, Gut flora, Sutterella, Microbiology, digestive system, Article, 03 medical and health sciences, Immune system, fluids and secretions, Mycoplasma hyopneumoniae, Virology, Prevotella, microbiota, lcsh:QH301-705.5, Feces, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, biology, prediction, biology.organism_classification, vaccination, 3. Good health, Vaccination, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, lcsh:Biology (General), [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, [SDV.IMM]Life Sciences [q-bio]/Immunology
Abstract: The gut microbiota comprises a large and diverse community of bacteria that play a significant role in swine health. Indeed, there is a tight association between the enteric immune system and the overall composition and richness of the microbiota, which is key in the induction, training and function of the host immunity, and may therefore, influence the immune response to vaccination. Using vaccination against Mycoplasma hyopneumoniae (M. hyo) as a model, we investigated the potential of early-life gut microbiota in predicting vaccine response and explored the post-vaccination dynamics of fecal microbiota at later time points. At 28 days of age (0 days post-vaccination, dpv), healthy piglets were vaccinated, and a booster vaccine was administered at 21 dpv. Blood samples were collected at 0, 21, 28, 35, and 118 dpv to measure M. hyo-specific IgG levels. Fecal samples for 16S rRNA gene amplicon sequencing were collected at 0, 21, 35, and 118 dpv. The results showed variability in antibody response among individual pigs, whilst pre-vaccination operational taxonomic units (OTUs) primarily belonging to Prevotella, [Prevotella], Anaerovibrio, and Sutterella appeared to best-predict vaccine response. Microbiota composition did not differ between the vaccinated and non-vaccinated pigs at post-vaccination time points, but the time effect was significant irrespective of the animals&rsquo, vaccination status. Our study provides insight into the role of pre-vaccination gut microbiota composition in vaccine response and emphasizes the importance of studies on full metagenomes and microbial metabolites aimed at deciphering the role of specific bacteria and bacterial genes in the modulation of vaccine response.
Published: 2020
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16. Review: divergent selection for residual feed intake in the growing pig

Author: Marie-Christine Meunier-Salaün, Florence Gondret, Claire Rogel-Gaillard, L. Lefaucheur, Yvon Billon, Bénédicte Lebret, Jean Noblet, Elodie Merlot, J. van Milgen, J. Faure, Pierre Mormède, Philippe Gatellier, Juliette Riquet, Hélène Gilbert, Annie Vincent, Isabelle Louveau, N. Le Floc’h, Etienne Labussière, Ludovic Brossard, David Renaudeau, Lucile Montagne, 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], UE 1372 Génétique, Expérimentation et Système Innovants, 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)-Génétique, Expérimentation et Système Innovants (GenESI), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), ANR PigFeed, FatInteger, 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, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique, Expérimentation et Système Innovants (GenESI), 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), AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, efficience digestive, pig, consommation alimentaire résiduelle, Swine, Protein metabolism, qualité de la viande, robustness, Review Article, chemistry.chemical_compound, Nutrient, Lactation, feed efficiency, genetics, sélection divergente, media_common, Animal biology, 2. Zero hunger, comportement alimentaire, [SDV.BA]Life Sciences [q-bio]/Animal biology, Reproduction, 04 agricultural and veterinary sciences, Animal culture, medicine.anatomical_structure, Phenotype, Alimentation et Nutrition, Body Composition, biomarker, efficience alimentaire, impact environnemental, divergent selection, Digestion, biomarqueur, media_common.quotation_subject, residual feed intake, Selection, Genetics, selection, Biology, food habits, paramètre génétique, Feed conversion ratio, environmental impact, SF1-1100, 03 medical and health sciences, Animal science, Biologie animale, medicine, Food and Nutrition, Animals, métabolisme, Selection (genetic algorithm), Animal fat, 0402 animal and dairy science, Nutritional Requirements, 040201 dairy & animal science, robustesse, Animal Feed, Diet, Red Meat, 030104 developmental biology, chemistry, Animal Science and Zoology, genetic variance, Breeding and Genetics, Residual feed intake, Energy Metabolism, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, porc
Abstract: To view supplementary material for this article, please visit https:/doi.org/10.1017/S175173111600286X; This review summarizes the results from the INRA (Institut National de la Recherche Agronomique) divergent selection experiment on residual feed intake (RFI) in growing Large White pigs during nine generations of selection. It discusses the remaining challenges and perspectives for the improvement of feed efficiency in growing pigs. The impacts on growing pigs raised under standard conditions and in alternative situations such as heat stress, inflammatory challenges or lactation have been studied. After nine generations of selection, the divergent selection for RFI led to highly significant ( P
Published: 2017
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17. Towards the quantitative characterization of piglets' robustness to weaning: A modelling approach

Author: Manuel Revilla, Laure Ravon, N. Le Floc’h, Claire Rogel-Gaillard, L.-P. Broudiscou, Fany Blanc, Jordi Estellé, Yvon Billon, Gaetan Lemonnier, Rafael Muñoz-Tamayo, Marie-José Mercat, Nicolas Friggens, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona [Barcelona] (UAB), Modélisation Systémique Appliquée aux Ruminants (MoSAR), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Génétique, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), Institut du Porc (IFIP), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Live weight, robustness, Biology, modelling, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Time windows, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Statistics, Weaning, Robustness (economics), resilience, 030304 developmental biology, 0303 health sciences, precision farming, weaning, 0402 animal and dairy science, Large white, 04 agricultural and veterinary sciences, Transition time, 040201 dairy & animal science, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Concordance correlation coefficient, Livestock farming, 13. Climate action, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, piglet
Abstract: Weaning is a critical transition phase in swine production in which piglets must cope with different stressors that may affect their health. During this period, the prophylactic use of antibiotics is still frequent to limit piglet morbidity, which raises both economic and public health concerns such as the appearance of antimicrobial-resistant microbes. With the interest of developing tools for assisting health and management decisions around weaning, it is key to provide robustness indexes that inform on the animals capacity to endure the challenges associated to weaning. This work aimed at developing a modelling approach for facilitating the quantification of piglet resilience to weaning. We monitored 325 Large White pigs weaned at 28 days of age and further housed and fed conventionally during the post-weaning period without antibiotic administration. Body weight and diarrhoea scores were recorded before and after weaning, and blood was sampled at weaning and one week later for collecting haematological data. We constructed a dynamic model based on the Gompertz-Makeham law to describe live weight trajectories during the first 75 days after weaning following the rationale that the animal response is partitioned in two time windows (a perturbation and a recovery window). Model calibration was performed for each animal. Our results show that the transition time between the two time windows, as well as the weight trajectories are characteristic for each individual. The model captured the weight dynamics of animals at different degrees of perturbation, with an average coefficient of determination of 0.99, and a concordance correlation coefficient of 0.99. The utility of the model is that it provides biological parameters that inform on the amplitude and length of perturbation, and the rate of animal recovery. Our rationale is that the dynamics of weight inform on the capability of the animal to cope with the weaning disturbance. Indeed, there were significant correlations between model parameters and individual diarrhoea scores and haematological traits. Overall, the parameters of our model can be useful for constructing weaning robustness indexes by using exclusively the growth curves. We foresee that this modelling approach will provide a step forward in the quantitative characterization of robustness.ImplicationsThe quantitative characterization of animal robustness at weaning is a key step for management strategies to improve health and welfare. This characterization is also instrumental for the further design of selection strategies for productivity and robustness. Within a precision livestock farming optic, this study develops a mathematical modelling approach to describe the body weight of piglets from weaning with the rationale that weight trajectories provide central information to quantify the capability of the animal to cope with the weaning disturbance.
Published: 2019

18. Transcription from a gene desert in a melanoma porcine model

Author: Emmanuelle Bourneuf, Per Wahlberg, Jordi Estellé, Jérôme Lecardonnel, A. Blin, Sylvain Marthey, Francoise Créchet, F. Tessiot, Claire Rogel-Gaillard, Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Acquisition et Analyse de Données pour l'Histoire naturelle (2AD), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de radiobiologie et d'étude du génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay, Laboratoire Composant pour l'Energie (LCE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), La Ligue Nationale Contre le Cancer (Genetic Epidemiology) PRE09/FD, Institut National du Cancer (INCA) France PL-Bio 5982, French Atomic Energy Commission, INRA (Institut National de la Recherche Agronomique), INRA program 'Jeunes Docteurs', Ligue nationale contre le cancer, ANR-08-GENM-0032,CapSeqAn,Capture de Séquences sur microarrays pour séquençage ciblé de régions d'intérêt : développement sur des études pilotes en génomique Animale(2008), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Skin Neoplasms, Swine, [SDV]Life Sciences [q-bio], Sus scrofa, Locus (genetics), Biology, 01 natural sciences, Polymorphism, Single Nucleotide, Genetic determinism, Association, 03 medical and health sciences, Repeated elements, Genetics, medicine, SNP, Animals, Humans, Molecular Biology, Gene, Melanoma, Pig, [SDV.GEN]Life Sciences [q-bio]/Genetics, Tiling array, [SDV.BA]Life Sciences [q-bio]/Animal biology, Gene Expression Profiling, Chromosome Mapping, General Medicine, medicine.disease, Melanoma model, Chromosomes, Mammalian, Human genetics, Gene Expression Regulation, Neoplastic, Disease Models, Animal, 030104 developmental biology, Long Interspersed Nucleotide Elements, Cutaneous melanoma, Disease Progression, Female, Gene desert, 010606 plant biology & botany
Abstract: International audience; The genetic mechanisms underlying cutaneous melanoma onset and progression need to be further understood to improve patients' care. Several studies have focused on the genetic determinism of melanoma development in the MeLiM pig, a biomedical model of cutaneous melanoma. The objective of this study was to better describe the influence of a particular genomic region on melanoma progression in the MeliM model. Indeed, a large region of theSus scrofachromosome 1 has been identified by linkage and association analyses, but the causal mechanisms have remained elusive. To deepen the analysis of this candidate region, a dedicated SNP panel was used to fine map the locus, downsizing the interval to less than 2 Mb, in a genomic region located within a large gene desert. Transcription from this locus was addressed using a tiling array strategy and further validated by RT-PCR in a large panel of tissues. Overall, the gene desert showed an extensive transcriptional landscape, notably dominated by repeated element transcription in tumor and fetal tissues. The transcription of LINE-1 and PERVs has been confirmed in skin and tumor samples from MeLiM pigs. In conclusion, although this study still does not identify a candidate mutation for melanoma occurrence or progression, it highlights a potential role of repeated element transcriptional activity in the MeLiM model.
Published: 2019
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19. Integrative analysis of blood and gut microbiota data suggests a non-alcoholic fatty liver disease (NAFLD)-related disorder in French SLA

Author: Marco, Moroldo, Peris Mumbi, Munyaka, Jérôme, Lecardonnel, Gaëtan, Lemonnier, Eric, Venturi, Claire, Chevaleyre, Isabelle P, Oswald, Jordi, Estellé, and Claire, Rogel-Gaillard
Subjects: Feces, Phenotype, Non-alcoholic Fatty Liver Disease, Swine, Molecular biology, Gene Expression Profiling, Animals, Swine, Miniature, Gene expression, Metagenomics, Zoology, Article, Gastrointestinal Microbiome
Abstract: Minipigs are a group of small-sized swine lines, which show a broad range of phenotype variation and which often tend to be obese. The SLAdd (DD) minipig line was created by the NIH and selected as homozygous at the SLA locus. It was brought to France more than 30 years ago and maintained inbred ever since. In this report, we characterized the physiological status of a herd of French DD pigs by measuring intermediate phenotypes from blood and faeces and by using Large White (LW) pigs as controls. Three datasets were produced, i.e. complete blood counts (CBCs), microarray-based blood transcriptome, and faecal microbiota obtained by 16S rRNA sequencing. CBCs and expression profiles suggested a non-alcoholic fatty liver disease (NAFLD)-related pathology associated to comorbid cardiac diseases. The characterization of 16S sequencing data was less straightforward, suggesting only a potential weak link to obesity. The integration of the datasets identified several fine-scale associations between CBCs, gene expression, and faecal microbiota composition. NAFLD is a common cause of chronic liver disease in Western countries and is linked to obesity, type 2 diabetes mellitus and cardiac pathologies. Here we show that the French DD herd is potentially affected by this syndrome.
Published: 2019

20. Science for tomorrow's livestock farming: A forward thinking conducted at INRA

Author: Sabine Houot, Véronique Santé-Lhoutellier, Jean-Louis Peyraud, René Baumont, Claire Rogel-Gaillard, Christian Ducrot, Philippe Faverdin, Marie-Odile Nozières-Petit, Marc Barbier, Jean Pierre Bidanel, Nicolas Friggens, Joël Aubin, Pierre Dupraz, Corinne Cotinot, Cécile Berri, Christine Citti, Direction Scientifique Agriculture, Institut National de la Recherche Agronomique (INRA), Sol Agro et hydrosystème Spatialisation (SAS), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire Interdisciplinaire Sciences, Innovations, Sociétés (LISIS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Est Marne-la-Vallée (UPEM)-ESIEE Paris-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), 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, 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), Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Structures et Marché Agricoles, Ressources et Territoires (SMART), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Modélisation Systémique Appliquée aux Ruminants (MoSAR), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), Université Paris Saclay (COMUE), Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Qualité des Produits Animaux (QuaPA), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Biologie des Oiseaux et Aviculture (BOA), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Biologie du Développement et Reproduction (BDR), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Structures et Marché Agricoles, Ressources et Territoires (SMART-LERECO), Laboratoire d'Études et de Recherches en Economie (LERECO CEDRAN), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 2. Zero hunger, interdisciplinarité, business.industry, Circular economy, media_common.quotation_subject, [SDV]Life Sciences [q-bio], 0402 animal and dairy science, Factors of production, 04 agricultural and veterinary sciences, 15. Life on land, 040201 dairy & animal science, innovation, 12. Responsible consumption, Futures studies, élevage durable, Livestock farming, Conceptual framework, 13. Climate action, Action plan, Livestock, recherche, business, Welfare, Environmental planning, media_common
Abstract: The ambition of the foresight on livestock farming was to rethink the place, the roles of livestock and how it should be transformed to fully contribute to the development of more sustainable agri-food systems. It was also to identify cross-disciplinary research themes that explore promising fronts of science or methodologies to solve knowledge locks. The foresight was managed by a group of 15 researchers and mobilized a hundred researchers. Based on an analysis of the context and the drivers for the evolution of the systems, we propose a new conceptual framework to think about innovations. Livestock farming must be part of circular agri-food systems in which it must contribute, beyond an increased efficiency of production factors, to the preservation of the quality of the resources and to the production of a food at an affordable price. Systems need to be rethought to be climate-smart and to respond to the health and welfare challenges of animals and people, rethink the linkages between livestock, crop production and territories to maximize recycling and rethink livestock linkages, processing and consumption of livestock products. Innovations should be based on the principles of agro-ecology supplemented by those of the circular economy and mobilizing levers of (bio) technologies and organizational innovation. The text describes 4 major scientific priorities with their research issues and produces recommendations for an action plan., L’ambition de l’Atelier de Réflexion Prospective sur l’élevage a été de repenser la place, les rôles de l’élevage et en quoi il doit se transformer pour contribuer pleinement au développement de systèmes agri-alimentaires plus durables ainsi que d’identifier des thématiques de recherches interdisciplinaires permettant d’explorer des fronts de science ou méthodologiques porteurs d’avenir pour lever les verrous de connaissances. La réflexion a été animée par un groupe de 15 chercheurs et en a mobilisé une centaine. À partir d’une analyse du contexte et des drivers d’évolution des systèmes nous proposons un nouveau cadre conceptuel et des voies de progrès pour penser l’élevage de demain. L’élevage doit s’inscrire dans le cadre de systèmes agri-alimentaires circulaires dans lesquels il doit contribuer, au-delà d’une efficience accrue des moyens de production, à la préservation de la qualité des ressources et à la production d’une alimentation à un prix abordable. Il faut repenser les systèmes pour qu’ils soient climato-intelligents et répondent aux enjeux de santé et du bien-être des animaux et des Hommes ; repenser les liens entre élevage, production végétale et territoire pour maximiser les recyclages et repenser les liens entre élevage, transformation et consommation des produits de l’élevage. Les innovations doivent être basées sur les principes de l’agroécologie complétés par ceux de l’économie circulaire et par la mobilisation des leviers des (bio)technologies et de l’innovation organisationnelle. Le texte décrit quatre grandes priorités scientifiques avec leurs enjeux de recherche et produit des recommandations pour un plan d’action.
Published: 2019
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21. Systems immunology approaches to decipher individual variability of immune capacity: application to the pig species

Author: Claire Rogel Gaillard, Tatiana Maroilley, Fany BLANC, Jordi Estellé, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Université Paris Saclay (COmUE)
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

22. How to predict that some animals respond better to vaccination than others: application to vaccination against Mycoplasma hyopneumoniae in pigs?

Author: Fany BLANC, Jordi Estellé, Gaëan Lemonnier, Jean-Jacques Leplat, Yvon Billon, Olivier Bouchez, Marie-Noelle Rossignol, Jean Pierre Bidanel, Claire Rogel Gaillard, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Génétique, Expérimentation et Système Innovants (GenESI), 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), 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), 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)-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), BBSRC Pirbright Institute. GBR., European Project: 633184,H2020,H2020-SFS-2014-2,SAPHIR(2015), Université Toulouse III - Paul Sabatier (UT3), 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)-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 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)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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 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)
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], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

23. Characterization of whole blood transcriptome and early-life fecal microbiota in high and low responder pigs before, and after vaccination for Mycoplasma hyopneumoniae

Author: Claire Rogel-Gaillard, Janelle M Fouhse, Benjamin P. Willing, Paul Stothard, Peris M. Munyaka, Jamie Wilkinson, Arun Kommadath, Jordi Estellé, Graham Plastow, Natalie E. Diether, Department of Agricultural, Food and Nutritional Science, University of Alberta, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Alberta Agriculture and Forestry project 2014F034R, Genome Canada (2014 Genome Canada LSARP - Application of Genomics to Improve Disease Resilience and Sustainability in Pork Production), and Canada Research Chairs Program
Subjects: pig, Swine, [SDV]Life Sciences [q-bio], Booster dose, Biology, Feces, 03 medical and health sciences, 0302 clinical medicine, Immune system, Mycoplasma hyopneumoniae, 030225 pediatrics, Prevotella, microbiota, Animals, 030212 general & internal medicine, 2. Zero hunger, [SDV.GEN]Life Sciences [q-bio]/Genetics, General Veterinary, General Immunology and Microbiology, Gene Expression Profiling, Public Health, Environmental and Occupational Health, Antibody titer, prediction, Pneumonia of Swine, Mycoplasmal, biology.organism_classification, vaccination, Gastrointestinal Microbiome, 3. Good health, Vaccination, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Infectious Diseases, Bacterial Vaccines, Immunology, biology.protein, Molecular Medicine, Antibody, transcriptome
Abstract: International audience; We investigated gene expression patterns in whole blood and fecal microbiota profile as potential predictors of immune response to vaccination, using healthy M. hyopneumoniae infection free piglets (n = 120). Eighty piglets received a dose of prophylactic antibiotics during the first two days of life, whereas the remaining 40 did not. Blood samples for RNA-Seq analysis were collected on experimental Day 0 (D0; 28 days of age) just prior to vaccination, D2, and D6 post-vaccination. A booster vaccine was given at D24. Fecal samples for microbial 16SrRNA sequencing were collected at 7 days of age, and at D0 and D35 post-vaccination. Pigs were ranked based on the levels of M. hyopneumoniae-specific antibodies in serum samples collected at D35, and groups of 'high' (HR) and 'low' (LR) responder pigs (n = 15 each) were selected. Prophylactic antibiotics did not influence antibody titer levels and differential expression analysis did not reveal differences between HR and LR at any time-point (FDR > 0.05); however, based on functional annotation with Ingenuity Pathway Analysis, D2 post-vaccination, HR pigs were enriched for biological terms relating to increased activation of immune cells. In contrast, the immune activation decreased in HR, 6 days post-vaccination. No significant differences were observed prior to vaccination (D0). Two days post-vaccination, multivariate analysis revealed that ADAM8, PROSER3, B4GALNT1, MAP7D1, SPP1, HTRA4, and ENO3 genes were the most promising potential biomarkers. At D0, OTUs annotated to Prevotella, CF21, Bacteroidales and S24-7 were more abundant in HR, whereas Fibrobacter, Paraprevotella, Anaerovibrio, [Prevotella], YRC22, and Helicobacter positively correlated with the antibody titer as well as MYL1, SPP1, and ENO3 genes. Our study integrates gene differential expression and gut microbiota to predict vaccine response in pigs. The results indicate that post-vaccination gene-expression and early-life gut microbiota profile could potentially predict vaccine response in pigs, and inform a direction for future research.
Published: 2019
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24. Integrating blood transcriptome and immunity traits to identify markers of immune capacity in pigs

Author: Tatiana Maroilley, Fany BLANC, Gaetan Lemonnier, Jerôme Lecardonnel, Jean Pierre Bidanel, Andrea Rau, Yvon Billon, Marie-José Mercat, Jordi Estelle Fabrellas, Claire Rogel Gaillard, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Génétique, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), Institut du Porc (IFIP), and European Federation of Animal Science (EAAP). INT.
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], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2018

25. Impact of weaning age on the gut microbiota composition in piglets

Author: Francesca Massacci, El Mostafa Berri, Gaetan Lemonnier, Deborah Jardet, Fany BLANC, Manuel Revilla Sanchez, Marie-José Mercat, Joel Dore, Patricia Lepage, Claire Rogel Gaillard, Jordi Estelle Fabrellas, Pigletbiota Anr Consortium, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Département Santé Animale (DEPT SA), Institut National de la Recherche Agronomique (INRA), Modélisation Systémique Appliquée aux Ruminants (MoSAR), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut du Porc (IFIP), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Projet ANR-14-CE18-0004 PIGLETBIOTA, and European Federation of Animal Science (EAAP). INT.
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], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2018
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26. Individual genetic variability of vaccine responses in pigs

Author: Fany BLANC, Tatiana Maroilley, Gaetan Lemonnier, Jean Jacques Leplat, Edwige Bouguyon, Yvon Billon, Jean Pierre Bidanel, Bertrand Bed'Hom, Jordi Estelle Fabrellas, Claire Rogel-Gaillard, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Génétique, Expérimentation et Système Innovants (GenESI), and European Project: 633184,H2020,H2020-SFS-2014-2,SAPHIR(2015)
Subjects: [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology
Abstract: National audience; The impact of host genetic variation in shaping innate and adaptive immune responses is an emerging lever to consider in new vaccination strategies. This issue has been addressed by the H2020-funded SAPHIR project by studying the genetic control of responses to vaccines against Mycoplasma hyopneumoniae (M. hyo) or Influenza A Virus (IAV) in pigs. Large White pigs housed in a conventional facility (48 families produced in five batches) were vaccinated at weaning (around 28 days of age), which was followed with a booster vaccination three weeks later. Overall, 182 and 98 piglets were vaccinated against M. hyo or IAV, respectively, and 64 non-vaccinated piglets were included as shared controls for the two vaccine experiments. The humoral vaccine response was measured by following the dynamics of seric M. hyo- or IAV-specific IgG, prior vaccination on the vaccine day, every week during five weeks post-vaccination, and before slaughtering at 21 weeks-of-age. In addition, haemagglutination inihibition (HAI) assays were performed for IAV-vaccinated pigs. Our results showed a wide range of individual variability. One week after the booster vaccination, M. hyo IgG levels (relative to a positive control) ranged from 0.36 to 2.15 (mean=1.34, coefficient of variation=21.2%) and IAV-specific IgG levels ranged from 10.3 to 128.5 µg/mL (mean=33.41 µg/mL, coefficient of variation=69.6%). For IAV-vaccinated animals, HAI titers ranged from 40 to 2560 (geometric mean=343.7). Interestingly, females exhibited a significantly higher humoral immune response to vaccination compared to males for the two vaccines. Heritability of specific antibody response variation could be estimated for animals vaccinated against M. hyo (h2=0.34 one week after the booster vaccination), showing a moderate genetic control. Ongoing genome wide association studies (GWAS) have revealed few candidate genomic regions found associated with the individual variability of vaccine responses to M. hyo or IAV that need to be further investigated.
Published: 2018

27. Inferring the evolution of the major histocompatibility complex of wild pigs and peccaries using hybridisation DNA capture-based sequencing

Author: Marco Moroldo, Sylvain Marthey, Núria Mach, Amanda Y. Chong, Claire Rogel-Gaillard, Simon Y. W. Ho, Carol Lee, Jérôme Lecardonnel, Per Wahlberg, Jaime Gongora, Alvaro Perdomo-Sabogal, Jordi Estellé, University of Sydney, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), University of Hohenheim, Earlham Institute, Sydney School of Veterinary Science at the University of Sydney, and French National Research Agency PSC-08-GENO-CapSeqAn
Subjects: 0301 basic medicine, Swine, [SDV]Life Sciences [q-bio], Immunology, Antigen presentation, DNA sequence capture, Genes, MHC Class I, Major histocompatibility complex, Genome, Evolution, Molecular, Major Histocompatibility Complex, 03 medical and health sciences, Genetics, peccaries, Gene family, Animals, Gene, Phylogeny, Artiodactyla, [SDV.GEN]Life Sciences [q-bio]/Genetics, Comparative Genomic Hybridization, biology, Phylogenetic tree, Base Sequence, pigs, adaptive immunity, Sequence Analysis, DNA, Biological Evolution, Histocompatibility, Domestic pig, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Evolutionary biology, biology.protein
Abstract: International audience; The major histocompatibility complex (MHC) is a key genomic model region for understanding the evolution of gene families and the co-evolution between host and pathogen. To date, MHC studies have mostly focused on species from major vertebrate lineages. The evolution of MHC classical (Ia) and non-classical (Ib) genes in pigs has attracted interest because of their antigen presentation roles as part of the adaptive immune system. The pig family Suidae comprises over 18 extant species (mostly wild), but only the domestic pig has been extensively sequenced and annotated. To address this, we used a DNA-capture approach, with probes designed from the domestic pig genome, to generate MHC data for 11 wild species of pigs and their closest living family, Tayassuidae. The approach showed good efficiency for wild pigs (~80% reads mapped, ~87× coverage), compared to tayassuids (~12% reads mapped, ~4× coverage). We retrieved 145 MHC loci across both families. Phylogenetic analyses show that the class Ia and Ib genes underwent multiple duplications and diversifications before suids and tayassuids diverged from their common ancestor. The histocompatibility genes mostly form orthologous groups and there is genetic differentiation for most of these genes between Eurasian and sub-Saharan African wild pigs. Tests of selection showed that the peptide-binding region of class Ib genes was under positive selection. These findings contribute to better understanding of the evolutionary history of the MHC, specifically, the class I genes, and provide useful data for investigating the immune response of wild populations against pathogens.
Published: 2018
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28. Early-life establishment of the swine gut microbiome and impact on host phenotypes

Author: Yvon Billon, Catherine Denis, Núria Mach, Florence Levenez, Gaetan Lemonnier, Jean-Jacques Leplat, Claire Rogel-Gaillard, Claire Chevaleyre, Patricia Lepage, Jordi Estellé, Joël Doré, and Mustapha Berri
Subjects: 2. Zero hunger, Immunoglobulin A, 0303 health sciences, biology, 030306 microbiology, Firmicutes, Gastrointestinal Microbiome, Bacteroidetes, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), Microbiology, 03 medical and health sciences, fluids and secretions, Prevotella, biology.protein, Microbiome, Bacteroides, Ecology, Evolution, Behavior and Systematics, Feces, 030304 developmental biology
Abstract: Early bacterial colonization and succession within the gastrointestinal tract has been suggested to be crucial in the establishment of specific microbiota composition and the shaping of host phenotype. Here, the composition and dynamics of faecal microbiomes were studied for 31 healthy piglets across five age strata (days 14, 36, 48, 60 and 70 after birth) together with their mothers. Faecal microbiome composition was assessed by 16S rRNA gene 454-pyrosequencing. Bacteroidetes and Firmicutes were the predominant phyla present at each age. For all piglets, luminal secretory IgA concentration was measured at day 70, and body weight was recorded until day 70. The microbiota of suckling piglets was mainly represented by Bacteroides, Oscillibacter, Escherichia/Shigella, Lactobacillus and unclassified Ruminococcaceae genera. This pattern contrasted with that of Acetivibrio, Dialister, Oribacterium, Succinivibrio and Prevotella genera, which appeared increased after weaning. Lactobacillus fermentum might be vertically transferred via breast milk or faeces. The microbiota composition coevolved with their hosts towards two different clusters after weaning, primarily distinguished by unclassified Ruminococcaceae and Prevotella abundances. Prevotella was positively correlated with luminal secretory IgA concentrations, and body weight. Our study opens up new possibilities for health and feed efficiency manipulation via genetic selection and nutrition in the agricultural domain.
Published: 2015
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29. Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis

Author: Diane Esquerre, Tatiana Maroilley, Gaetan Lemonnier, Jérôme Lecardonnel, Claire Rogel-Gaillard, Marie-José Mercat, Yuliaxis Ramayo-Caldas, Jordi Estellé, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), 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, Institut du Porc (IFIP), ANR SUSFLORA, ANR IMMOPIG, AAP DGA IMMUNOME, Maroilley, Tatiana, and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Male, eGWAS, lcsh:QH426-470, Swine, lcsh:Biotechnology, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Genome-wide association study, Single-nucleotide polymorphism, RNA-Seq, Biology, eQTL, Polymorphism, Single Nucleotide, Allele-Specific Expression, Transcriptome, 03 medical and health sciences, lcsh:TP248.13-248.65, Histocompatibility Antigens, Genetics, Animals, [INFO]Computer Science [cs], Gene Regulatory Networks, Gene, Alleles, 2. Zero hunger, [SDV.GEN]Life Sciences [q-bio]/Genetics, Pig, Genetic architecture, lcsh:Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Blood, Gene Expression Regulation, Expression quantitative trait loci, RNA, blood, pig, transcriptome, allele-specific expression, Female, DNA microarray, Biomarkers, Biotechnology, Genome-Wide Association Study, Research Article
Abstract: Background Efforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual’s health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity. The objective of this work was to study the genetic architecture of variation in gene expression in the blood of healthy young pigs using two approaches: an expression genome-wide association study (eGWAS) and allele-specific expression (ASE) analysis. Results The blood transcriptomes of 60-day-old Large White pigs were analyzed by expression microarrays for eGWAS (242 animals) and by RNA-Seq for ASE analysis (38 animals). Using eGWAS, the expression levels of 1901 genes were found to be associated with expression quantitative trait loci (eQTLs). We recovered 2839 local and 1752 distant associations (Single Nucleotide Polymorphism or SNP located less or more than 1 Mb from expression probe, respectively). ASE analyses confirmed the extensive cis-regulation of gene transcription in blood, and revealed allelic imbalance in 2286 SNPs, which affected 763 genes. eQTLs and ASE-genes were widely distributed on all chromosomes. By analyzing mutually overlapping eGWAS results, we were able to describe putative regulatory networks, which were further refined using ASE data. At the functional level, genes with genetically controlled expression that were detected by eGWAS and/or ASE analyses were significantly enriched in biological processes related to RNA processing and immune function. Indeed, numerous distant and local regulatory relationships were detected within the major histocompatibility complex region on chromosome 7, revealing ASE for most class I and II genes. Conclusions This study represents, to the best of our knowledge, the first genome-wide map of the genetic control of gene expression in porcine peripheral blood. These results represent an interesting resource for the identification of genetic markers and blood biomarkers associated with variations in immunity traits in pigs, as well as any other complex traits for which blood is an appropriate surrogate tissue. Electronic supplementary material The online version of this article (10.1186/s12864-017-4354-6) contains supplementary material, which is available to authorized users.
Published: 2017
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30. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Author: Jeremy A. Johnson, Guillaume Queney, Sarah Young, G. Bolet, Frank W. Albert, Anqi Xiong, Gerli Pielberg, Rose G. Mage, Leif Andersson, Samuel Boucher, Alvaro Martinez Barrio, Shady Younis, Carl-Johan Rubin, Nima Rafati, Kerstin Lindblad-Toh, Magali Ruffier, Eric S. Lander, Sandra Afonso, Bronwen Aken, Shumaila Sayyab, Federica Di Palma, Miguel Carneiro, Claire Rogel-Gaillard, Jessica Alföldi, Karin Forsberg-Nilsson, Jeffrey M. Good, Nuno Ferrand, Steve Searle, Rita Campos, Jean L. Chang, Luca Fontanesi, Daniel Barrell, Rafael Villafuerte, Hernán A. Burbano, Joel M. Alves, Ze Peng, Hervé Garreau, David I. Heiman, Véronique Duranthon, Jason Turner-Maier, Centro de Investigaçao em Biodiversidade e Recursos Genéticos, Science of Life Laboratory Uppsala - Department of Medical Biochemistry and Microbiology, Uppsala University, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Vertebrate and Health Genomics, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Department of Human Genetics, University of California, Science of Life Laboratory Uppsala - Department of Medical Biochemistry and Microbioology, Department of Animal Bredding and Genetics, Swedish University of Agricultural Sciences (SLU), Department of Animal Production, Université Ain Shams, The Wellcome Trust Sanger Institute [Cambridge], University of Cambridge [UK] (CAM), 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, Labovet Conseil, Max-Planck-Gesellschaft, Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Department of Agricultural and Food Sciences - Division of Animal Sciences, Alma Mater Studiorum University of Bologna (UNIBO), Laboratory of Immunology, National Institute of Allergy and Infectious Deseases (NIAID), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Antagene - Animal Genomics Laboratory, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Spanish National Research Council (CSIC), Science for Life Laboratory - Department of Immunology , Genetics and Pathology, Science for Life Laboratory - Department of Immunology, Genetics and Pathology, Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, U54 HG003067 NHGRI NIH HHS, WT095908 Wellcome Trust, WT098051 Wellcome Trust, Carneiro, Miguel, Rubin, Carl-Johan, Palma, Federica Di, Albert, Frank W., Alföldi, Jessica, Barrio, Alvaro Martinez, Pielberg, Gerli, Rafati, Nima, Sayyab, Shumaila, Turner-Maier, Jason, Younis, Shady, Afonso, Sandra, Aken, Bronwen, Alves, Joel M., Barrell, Daniel, Bolet, Gerard, Boucher, Samuel, Burbano, Hernán A., Campos, Rita, Chang, Jean L., Duranthon, Veronique, Fontanesi, Luca, Garreau, Herve, Heiman, David, Johnson, Jeremy, Mage, Rose G., Peng, Ze, Queney, Guillaume, Rogel-Gaillard, Claire, Ruffier, Magali, Searle, Steve, Villafuerte, Rafael, Xiong, Anqi, Young, Sarah, Forsberg-Nilsson, Karin, Good, Jeffrey M., Lander, Eric S., Ferrand, Nuno, Lindblad-Toh, Kerstin, Andersson, Leif, Max Planck Institute for Evolutionary Anthropology, Department of Animal Breeding and Genetics, 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], Biologie du Développement et Reproduction (BDR), and Institut National de la Recherche Agronomique (INRA)
Subjects: Molecular Sequence Data, Animals, Wild, Single-nucleotide polymorphism, Rabbit, Breeding, Biology, Polymorphism, Single Nucleotide, Genome, Article, Evolution, Molecular, Gene Frequency, Animals, Selection, Genetic, Allele, Domestication, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Gene, Allele frequency, Genetics, Multidisciplinary, Base Sequence, Behavior, Animal, Animal, Medicine (all), Sequence Analysis, DNA, Phenotype, Genetic Loci, Animals, Domestic, Rabbits, Reference genome
Abstract: Rabbits softly swept to domestication When people domesticate animals, they select for tameness and tolerance of humans. What else do they look for? To identify the selective pressures that led to rabbit domestication, Carneiro et al. sequenced a domestic rabbit genome and compared it to that of its wild brethren (see the Perspective by Lohmueller). Domestication did not involve a single gene changing, but rather many gene alleles changing in frequency between tame and domestic rabbits, known as a soft selective sweep. Many of these alleles have changes that may affect brain development, supporting the idea that tameness involves changes at multiple loci. Science , this issue p. 1074 ; see also p. 1000
Published: 2014
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31. Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20

Author: Richa Agarwala, E. Michael Gertz, Amélie Bonnet-Garnier, Hélène Hayes, Rose G. Mage, Alejandro A. Schäffer, Claire Rogel-Gaillard, National Center for Biotechnology Information, National Institutes of Health, Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratory of Immunology, NIAID, Biologie du développement et reproduction (BDR), and Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)
Subjects: Male, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Immunoglobulin gene, Chromosomes, Artificial, Bacterial, Immunology, Immunoglobulin Variable Region, rabbit, Immunoglobulins, Locus (genetics), Biology, Genome, Article, Immunoglobulin kappa-Chains, 03 medical and health sciences, 0302 clinical medicine, Immunoglobulin lambda-Chains, Genetics, Animals, Humans, Gene conversion, Immunoglobulin Allotypes, heavy chain, fluorescence in situ hybridization, Gene, In Situ Hybridization, Fluorescence, 030304 developmental biology, Synteny, ligh chain, 0303 health sciences, Chromosome Mapping, Computational Biology, Reproducibility of Results, Chromosomes, Mammalian, immunoglobulin gene, chromosome 20, Female, Rabbits, Chromosome 20, Immunoglobulin Heavy Chains, Chromosome 21, 030215 immunology
Abstract: We report on the analyses of genes encoding immunoglobulin heavy and light chains in the rabbit 6.51× whole genome assembly. This OryCun2.0 assembly confirms previous mapping of the duplicated IGK1 and IGK2 loci to chromosome 2 and the IGL lambda light chain locus to chromosome 21. The most frequently rearranged and expressed IGHV1 that is closest to IG DH and IGHJ genes encodes rabbit VHa allotypes. The partially inbred Thorbecke strain rabbit used for whole-genome sequencing was homozygous at the IGK but heterozygous with the IGHV1a1 allele in one of 79 IGHV-containing unplaced scaffolds and IGHV1a2, IGHM, IGHG, and IGHE sequences in another. Some IGKV, IGLV, and IGHA genes are also in other unplaced scaffolds. By fluorescence in situ hybridization, we assigned the previously unmapped IGH locus to the q-telomeric region of rabbit chromosome 20. An approximately 3-Mb segment of human chromosome 14 including IGH genes predicted to map to this telomeric region based on synteny analysis could not be located on assembled chromosome 20. Unplaced scaffold chrUn0053 contains some of the genes that comparative mapping predicts to be missing. We identified discrepancies between previous targeted studies and the OryCun2.0 assembly and some new BAC clones with IGH sequences that can guide other studies to further sequence and improve the OryCun2.0 assembly. Complete knowledge of gene sequences encoding variable regions of rabbit heavy, kappa, and lambda chains will lead to better understanding of how and why rabbits produce antibodies of high specificity and affinity through gene conversion and somatic hypermutation.
Published: 2013
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32. Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits

Author: Claire Rogel-Gaillard, Jean-Jacques Leplat, Mustapha Berri, Yvon Billon, Florence Levenez, Yuliaxis Ramayo-Caldas, Núria Mach, Jordi Estellé, Joël Doré, Patricia Lepage, Gaetan Lemonnier, Catherine Denis, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), DSV-IRCM-LREG, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génétique, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: 0301 basic medicine, Operational taxonomic unit, Swine, Short Communication, Gut flora, Microbiology, digestive system, 03 medical and health sciences, Feces, Microbial ecology, Phylogenetics, RNA, Ribosomal, 16S, Prevotella, Animals, Cluster Analysis, Humans, Ecology, Evolution, Behavior and Systematics, Phylogeny, 2. Zero hunger, biology, Bacteria, Ecology, Ruminococcus, [SDV.BA]Life Sciences [q-bio]/Animal biology, biology.organism_classification, Biota, Gastrointestinal Microbiome, 030104 developmental biology, Environmental biotechnology, Evolutionary biology, Enterotype
Abstract: International audience; The ecological interactions within the gut microbial communities are complex and far from being fully understood. Here we report the first study that aims at defining the interaction network of the gut microbiota in pigs and comparing it with the enterotype-like clustering analysis. Fecal microbiota of 518 healthy piglets was characterized by 16S ribosomal RNA gene sequencing. Two networks were constructed at the genus and operational taxonomic unit levels. Within-network interactions mirrored the human gut microbiota relationships, with a strong co-exclusion between Prevotella and Ruminococcus genera, and were consistent with the two enterotype-like clusters identified in the pig microbiota. Remarkably, the cluster classification of the individuals was significantly associated with the body weight at 60 days of age (P=0.005) and average daily gain (P=0.027). To the best of our knowledge, this is the first study to provide an integrated overview of the porcine gut microbiota that suggests a conservation of the ecological community interactions and functional architecture between humans and pig. Moreover, we show that the microbial ecosystems and porcine growth traits are linked, which allows us to foresee that the enterotype concept may have an important role in the animal production industry.The ISME Journal advance online publication, 13 May 2016; doi:10.1038/ismej.2016.77.
Published: 2016
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33. A reference gene catalogue of the pig gut microbiome

Author: Lise Madsen, Claire Rogel-Gaillard, Suisha Liang, Emmanuelle Maguin, Junhua Li, Zhongkui Xia, Jordi Estellé, Stanislav D Ehrlich, Liu Chuan, Qiang Feng, Pia Kiilerich, Anni Øyan Pedersen, Yuliaxis Ramayo-Caldas, Xin Liu, Huijue Jia, Liang Xiao, Nicolas Pons, Xun Xu, Niels Jørgen Kjeldsen, Jun Wang, Joël Doré, Edi Prifti, Karsten Kristiansen, BGI Shenzhen, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratory of Genomics and Molecular Biomedicine, Department of Biology, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Pig Research Centre, Danish Agriculture and Food Council, Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), MetaGenoPolis, Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, King‘s College London, National Institute of Nutrition and Seafood Research (NIFES), Microbiota Interaction with Human and Animal (MIHA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Beijing Genomics Institute [Shenzhen] (BGI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Kristiansen, Karsten, Rogel-Gaillard, Claire, Wang, Jun, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), INRA metaprogramme Meta-omics of Microbial Ecosystems (MEM), Animal Genetics Division of INRA, and Biology Department of the University of Copenhagen
Subjects: 0301 basic medicine, Microbiology (medical), medicine.drug_class, [SDV]Life Sciences [q-bio], 030106 microbiology, Immunology, Antibiotics, Gut flora, Applied Microbiology and Biotechnology, Microbiology, Genome, 03 medical and health sciences, Antibiotic resistance, Genetics, medicine, Gene, 2. Zero hunger, biology, business.industry, Host (biology), Cell Biology, biology.organism_classification, 030104 developmental biology, Metagenomics, Livestock, business
Abstract: International audience; The pig is a major species for livestock production and is also extensively used as the preferred model species for analyses of a wide range of human physiological functions and diseases1. The importance of the gut microbiota in complementing the physiology and genome of the host is now well recognized2. Knowledge of the functional interplay between the gut microbiota and host physiology in humans has been advanced by the human gut reference catalogue3,4. Thus, establishment of a comprehensive pig gut microbiome gene reference catalogue constitutes a logical continuation of the recently published pig genome5. By deep metagenome sequencing of faecal DNA from 287 pigs, we identified 7.7 million non-redundant genes representing 719 metagenomic species. Of the functional pathways found in the human catalogue, 96% are present in the pig catalogue, supporting the potential use of pigs for biomedical research. We show that sex, age and host genetics are likely to influence the pig gut microbiome. Analysis of the prevalence of antibiotic resistance genes demonstrated the effect of eliminating antibiotics from animal diets and thereby reducing the risk of spreading antibiotic resistance associated with farming systems.
Published: 2016
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34. Analyses of pig genomes provide insight to porcine demography and evolution

Author: Ronan Kapetanovic, Patrice Dehais, Zhi-Qiang Du, Loretta Auvil, Ricardo H. Ramirez-Gonzalez, Kyung-Tai Lee, Patrick Chardon, Hiroyuki Kanamori, Gary A. Rohrer, Jianguo Zhang, Celine Chen, Simon D. M. White, Guojie Zhang, Jian Wang, Hyeonju Ahn, Ole Madsen, Miguel Pérez-Enciso, Richard Clark, Bruce R. Southey, Yasuhiro Takeuchi, Bronwen Aken, Bo Thomsen, Frank Panitz, Katie E. Fowler, Peter F. Stadler, Jennifer Harrow, Takeya Morozumi, Ryan Cheng, Christian Bendixen, Laurent A. F. Frantz, Yogesh Paudel, Sara Botti, Kellye Eversole, Jaebum Kim, Jian Ma, Matthew Jones, Jan Gorodkin, Zhi-Liang Hu, John C. Schwartz, Suneel Kumar Onteru, Tae-Hun Kim, Fioravante De Sapio, Nizar Drou, Stephen M. J. Searle, Wan Sheng Liu, Yingrui Li, Yao Lu, Thomas Faraut, Richard P. M. A. Crooijmans, Joan K. Lunney, Göran O. Sperber, Bert Dibbits, Denis Milan, Richard M. Leggett, Boris Capitanu, Xun Xu, Bertrand Servin, Megan Bystrom, Carol Scott, Kyle M. Schachtschneider, Bouabid Badaoui, Harris A. Lewin, Mirte Bosse, Sang-Haeng Choi, Yongming Sang, Jane Rogers, Patric Jern, Kerstin Howe, Sean Humphray, Henrik Hornshøj, Martien A. M. Groenen, Jerzy Jurka, James M. Reecy, Frank Blecha, Darren K. Griffin, Susan Fairley, Jonas Blomberg, Claire Rogel-Gaillard, Eung-Woo Park, Jonathan V. Sweedler, Hong-Seog Park, Stuart McLaren, Denise Carvalho-Silva, Christopher K. Tuggle, Géraldine Pascal, Rashmi Wali, Mario Caccamo, Katherine M. Mann, Lawrence B. Schook, C M Clee, James G. R. Gilbert, Christian Anthon, Merete Fredholm, Chankyu Park, Harry D. Dawson, Craig W. Beattie, Elisabetta Giuffra, Zhan Bujie, Kyu-Won Kim, Toby Hunt, Jae-Hwan Kim, Daniel Berman, Shuhong Zhao, Hakim Tafer, Jin-Tae Jeon, Sandra L. Rodriguez-Zas, Hendrik-Jan Megens, Linda Scobie, Jie Zhang, Alan Archibald, Joshua G. Schraiber, Jitendra Narayan, Alexander Hayward, Lucy Matthews, Lauretta A. Rund, Jane E. Loveland, Peixiang Ni, Denis M. Larkin, Song-Jung Oh, Dinh Truong Nguyen, Kyooyeol Lee, Lars Bolund, João Fadista, William Chow, Jun Wang, Hirohide Uenishi, Shengting Li, Eric Fritz, Heebal Kim, Geoffrey J. Faulkner, Martine Yerle, Michael P. Murtaugh, Max F. Rothschild, Carol Churcher, Greger Larson, Anna Anselmo, Laboratoire de radiobiologie et d'étude du génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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 de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), The Genome Analysis Centre (TGAC), Parco Tecnologico Padano, CERSA, Department of Clinical Genetics, Odense University Hospital, The Wellcome Trust Sanger Institute [Cambridge], Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de la Recherche Agronomique (INRA), Faculty of Life Sciences, Division of Genetics and Bioinformatics, Faculty of Life Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory [Hong Kong], The University of Hong Kong (HKU), Beijing Genomics Institute [Shenzhen] (BGI), Department of Biochemistry, University of Nijmegen, The Netherlands, University of Nijmegen, Molecular Carcinogenesis [Sutton], Institute of cancer research, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), 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), Université de Tours (UT), Canadian Light Source Inc., University of Saskatchewan [Saskatoon] (U of S), Department of Mechanical Engineering, University of Auckland, University of Auckland [Auckland], ANR-07-GANI-0001,DELISUS,An integrated study of the haplotypic variability at the whole genome level on animals finely phenotyped from French porcine populations(2007), European Project: LSHB-CT-2006-037377, European Project: 249894,EC:FP7:ERC,ERC-2009-AdG,SELSWEEP(2010), European Project: 38710,SABRE, European Project: 222664,EC:FP7:KBBE,FP7-KBBE-2007-2A,QUANTOMICS(2009), European Commission, European Research Council, Biotechnology and Biological Sciences Research Council (UK), Wellcome Trust, 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, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), 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), Université de Tours, Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Sainsbury Laboratory Cambridge, 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA), and 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)
Subjects: pig, Evolution, receptor, Molecular Sequence Data, Population Dynamics, Sus scrofa, sus-scrofa, Locus (genetics), Genomics, Biology, Animal Breeding and Genomics, Genome, Article, genomic, taste, 03 medical and health sciences, Phylogenetics, evolution, Genetics, Animals, animal, Fokkerij en Genomica, Domestication, gene, Gene, Phylogeny, Demography, 030304 developmental biology, 0303 health sciences, locus, variants, Multidisciplinary, Phylogenetic tree, [SDV.BA]Life Sciences [q-bio]/Animal biology, 0402 animal and dairy science, 04 agricultural and veterinary sciences, sequence, 040201 dairy & animal science, Models, Animal, WIAS, genetic, Selective sweep, complex
Abstract: For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model., The research leading to these results has received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 249894 (SelSweep)
Published: 2012
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35. Transcription specificity of the class Ib genes SLA-6, SLA-7 and SLA-8 of the swine major histocompatibility complex and comparison with class Ia genes

Author: Claire Rogel-Gaillard, Z. Bősze, Laurence Flori, Silvia Vincent-Naulleau, Emmanuelle Bourneuf, S. Kusza, R. Hu, Gaetan Lemonnier, Yu Gao, and Angélique Teillaud
Subjects: 0303 health sciences, biology, Lipopolysaccharide, fungi, Pseudorabies, General Medicine, biology.organism_classification, Major histocompatibility complex, Molecular biology, Peripheral blood mononuclear cell, Virus, 3. Good health, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, chemistry, Transcription (biology), Ionomycin, Genetics, biology.protein, Animal Science and Zoology, Gene, 030304 developmental biology, 030215 immunology
Abstract: Our aim was to analyse the transcription levels of the three non-classical class Ib genes SLA-6, SLA-7 and SLA-8 of the swine major histocompatibility complex in various tissues and conditions and to compare them to the transcription levels of classical class Ia genes. Twenty-five adult tissues from two pig breeds, pig renal PK15 cells infected with the Pseudorabies virus, and peripheral blood mononuclear cells (PBMCs) stimulated by lipopolysaccharide or a mixture of phorbol myristate acetate and ionomycin were included in our study. Relative transcription was quantified by quantitative real-time PCR. On average, in adult tissues and PBMCs and compared to SLA-6, the transcription level of SLA-Ia genes was 100-1000 times higher, the level of SLA-8 was 10-20 times higher, and that of SLA-7 was five times higher. Thus, SLA-8 is the most transcribed SLA-Ib gene, followed by the SLA-7 and SLA-6 genes. The highest transcription levels of SLA-Ib transcripts were found in the lymphoid organs, followed by the lung and the digestive tract. The tissue variability of expression levels was widest for the SLA-6 gene, with a 1:32 ratio between the lowest and highest levels in contrast to a 1:12 ratio for the SLA-7 and SLA-8 genes and a 1:16 ratio for the SLA-Ia genes. During PK-15 infection and PBMC stimulation, SLA-Ia and SLA-8 genes were downregulated, whereas SLA-6 and SLA-7 were upregulated, downregulated or not significantly modified. Our overall results confirm the tissue-wide transcription of the three SLA-Ib genes and suggest that they have complementary roles.
Published: 2011
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36. Centimorgan-Range One-Step Mapping of Fertility Traits Using Interspecific Recombinant Congenic Mice

Author: Ahmad Oulmouden, Xavier Montagutelli, Paul Laissue, Catherine Serres, Claire Rogel-Gaillard, David L'Hôte, and Daniel Vaiman
Subjects: Male, Mus spretus, media_common.quotation_subject, Quantitative Trait Loci, Congenic, Fertility, Investigations, Quantitative trait locus, Mice, Mice, Congenic, 03 medical and health sciences, Centimorgan, 0302 clinical medicine, Gene mapping, Genetics, Animals, Gene, Infertility, Male, 030304 developmental biology, media_common, 0303 health sciences, biology, Chromosome Mapping, biology.organism_classification, Phenotype, 030217 neurology & neurosurgery
Abstract: In mammals, male fertility is a quantitative feature determined by numerous genes. Until now, several wide chromosomal regions involved in fertility have been defined by genetic mapping approaches; unfortunately, the underlying genes are very difficult to identify. Here, 53 interspecific recombinant congenic mouse strains (IRCSs) bearing 1–2% SEG/Pas (Mus spretus) genomic fragments disseminated in a C57Bl/6J (Mus domesticus) background were used to systematically analyze male fertility parameters. One of the most prominent advantages of this model is the possibility of analyzing stable phenotypes in living animals. Here, we demonstrate the possibility in one-step fine mapping for several fertility traits. Focusing on strains harboring a unique spretus fragment, we could unambiguously localize two testis and one prostate weight-regulating QTL (Ltw1, Ltw2, and Lpw1), four QTL controlling the sperm nucleus shape (Sh1, Sh2, Sh3, and Sh4), and one QTL influencing sperm survival (Dss1). In several cases, the spretus DNA fragment was small enough to propose sound candidates. For instance, Spata1, Capza, and Tuba7 are very strong candidates for influencing the shape of the sperm head. Identifying new genes implied in mammalian fertility pathways is a necessary prerequisite for clarifying their molecular grounds and for proposing diagnostic tools for masculine infertilities.
Published: 2007
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37. Pattern recognition receptors in the gut: analysis of their expression along the intestinal tract and the crypt/villus axis

Author: Pascal Gourbeyre, Isabelle P. Oswald, Joëlle Laffitte, Philippe Pinton, Claire Rogel-Gaillard, Yannick Lippi, François Meurens, Silvia Vincent-Naulleau, Mustapha Berri, 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, UR Infectiologie animale et Santé publique ( UR IASP ), Institut National de la Recherche Agronomique ( INRA ), Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan [Saskatoon] ( U of S ), Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, DSV, IRCM, SREIT, Laboratoire de Radiobiologie et Etude du Génome, Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), 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, UR Infectiologie animale et Santé publique (UR IASP), Institut National de la Recherche Agronomique (INRA), University of Saskatchewan [Saskatoon] (U of S), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 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, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Transcriptomic impact of Xenobiotics (E23 TRiX), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biosynthèse & Toxicité des Mycotoxines (ToxAlim-BioToMyc), Institut National de la Recherche Agronomique (INRA)-Université de Tours, 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)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), 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), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: pig, Pathology, medicine.medical_specialty, Physiology, [SDV]Life Sciences [q-bio], Crypt, Ileum, Biology, Gut flora, digestive system, Jejunum, RIG-I, 03 medical and health sciences, 0302 clinical medicine, Physiology (medical), TLR, medicine, RIG‐I, Mesenteric lymph nodes, NOD, 030304 developmental biology, Original Research, 0303 health sciences, Lamina propria, [ SDV ] Life Sciences [q-bio], Immune system, small intestine, digestive, oral, and skin physiology, biology.organism_classification, Small intestine, medicine.anatomical_structure, Duodenum, 030215 immunology
Abstract: Pattern recognition receptors (PRRs) play a critical role in the detection of microorganisms and the induction of inflammatory and immune responses. Using PCR and Western-blot analysis, this study investigated the differential expression in the intestine of 14 PRRs and nine associated cytokines. Thirty-two pigs were used to determine the expression of these markers (1) along the proximal/distal axis of the small intestine (duodenum, jejunum, and ileum) and (2) between the intestinal segments and their respective lymphoid organs (Peyer's patches [PP] and mesenteric lymph nodes [MLN]). Six additional animals were used to quantify the expression of these genes along the crypt/villus axis of jejunum, using microdissected samples. Most genes showed increased expression (1) in the distal than in the proximal parts of the small intestine (TLR3, 5, RIG-I, IL-1β, IL-8, and IFN-γ); (2) in lymphoid organs (TLR1, 2, 6, 9, 10, IL-10, TNF-α), especially the MLN (TLR4, 7, 8, NOD1, NOD2, NALP3, IFN-α, IL-6, IL-12, and TGF-β), than in intestinal segments. The analysis along the crypt/villus identified: (1) genes with higher expression in lamina propria (TLR1, 2, 4, 9, NOD1, NOD2, IL-1β, IL-10, TGF-β, TNF-α) and (2) genes with higher expression in the villus (TLR3, 5, 6, RIG-I, IL-6). These results highlight the differential expression of PRRs and cytokines along the proximal/distal and the crypt/villus axis of the intestine, contributing to a fine analysis of the complex functional architecture of the small intestine and should be related to the gut microbiota.
Published: 2015
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38. Genome-wide immunity studies in the rabbit: transcriptome variations in peripheral blood mononuclear cells after in vitro stimulation by LPS or PMA-Ionomycin

Author: Claire Rogel-Gaillard, Marco Moroldo, Jason Turner-Maier, Jordi Estellé, Gaetan Lemonnier, Barbara Schmaltz-Panneau, Thierry Gidenne, Jérôme Lecardonnel, Véronique Duranthon, Isabelle P. Oswald, Vincent Jacquier, Rogel-Gaillard, Claire, 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 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], Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], 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, 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, École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Biosynthèse & Toxicité des Mycotoxines (ToxAlim-BioToMyc), 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), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Biologie du Développement et Reproduction ( BDR ), Institut National de la Recherche Agronomique ( INRA ), Broad Institute of Harvard and MIT, Toxicologie Alimentaire ( UTA ), and 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
Subjects: Interleukin 2, Lipopolysaccharides, LPS, Microarray, Lipopolysaccharide, [SDV]Life Sciences [q-bio], Rabbit, Biology, Peripheral blood mononuclear cell, Transcriptome, chemistry.chemical_compound, Immune system, In vitro stimulation, Genetics, medicine, Animals, Immune response, Interleukin 4, Genome, [ SDV ] Life Sciences [q-bio], Ionomycin, Immunity, hemic and immune systems, PMA-Ionomycin, Molecular biology, 3. Good health, chemistry, Peripheral blood mononuclear cells, Immunology, Leukocytes, Mononuclear, Cytokines, Tetradecanoylphorbol Acetate, Rabbits, Biotechnology, medicine.drug, Research Article
Abstract: Background Our purpose was to obtain genome-wide expression data for the rabbit species on the responses of peripheral blood mononuclear cells (PBMCs) after in vitro stimulation by lipopolysaccharide (LPS) or phorbol myristate acetate (PMA) and ionomycin. This transcriptome profiling was carried out using microarrays enriched with immunity-related genes, and annotated with the most recent data available for the rabbit genome. Results The LPS affected 15 to 20 times fewer genes than PMA-Ionomycin after both 4 hours (T4) and 24 hours (T24), of in vitro stimulation, in comparison with mock-stimulated PBMCs. LPS induced an inflammatory response as shown by a significant up-regulation of IL12A and CXCL11 at T4, followed by an increased transcription of IL6, IL1B, IL1A, IL36, IL37, TNF, and CCL4 at T24. Surprisingly, we could not find an up-regulation of IL8 either at T4 or at T24, and detected a down-regulation of DEFB1 and BPI at T24. A concerted up-regulation of SAA1, S100A12 and F3 was found upon stimulation by LPS. PMA-Ionomycin induced a very early expression of Th1, Th2, Treg, and Th17 responses by PBMCs at T4. The Th1 response increased at T24 as shown by the increase of the transcription of IFNG and by contrast to other cytokines which significantly decreased from T4 to T24 (IL2, IL4, IL10, IL13, IL17A, CD69) by comparison to mock-stimulation. The granulocyte-macrophage colony-stimulating factor (CSF2) was by far the most over-expressed gene at both T4 and T24 by comparison to mock-stimulated cells, confirming a major impact of PMA-Ionomycin on cell growth and proliferation. A significant down-regulation of IL16 was observed at T4 and T24, in agreement with a role of IL16 in PBMC apoptosis. Conclusions We report new data on the responses of PBMCs to LPS and PMA-Ionomycin in the rabbit species, thus enlarging the set of mammalian species for which such reports exist. The availability of the rabbit genome assembly together with high throughput genomic tools should pave the way for more intense genomic studies for this species, which is known to be a very relevant biomedical model in immunology and physiology. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1218-9) contains supplementary material, which is available to authorized users.
Published: 2015
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39. Expanded comparative mapping between man and rabbit and detection of a new conserved segment between HSA22 and OCU4

Author: Claire Rogel-Gaillard, M. Perrocheau, S Chadi-Taourit, Céline Chantry-Darmon, M. Bertaud, Hélène Hayes, Céline Urien, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Unité de recherche Génétique Biochimique et Cytogénétique (LGBC), Laboratoire de radiobiologie et d'étude du génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: Genetic Markers, Chromosomes, Artificial, Bacterial, carte génétique, Quantitative Trait Loci, Computational biology, Biology, ENCODE, Polymerase Chain Reaction, Genome, 03 medical and health sciences, Gene mapping, Genetics, Animals, Chromosomes, Human, Humans, lapin, Molecular Biology, Gene, In Situ Hybridization, Fluorescence, Genetics (clinical), 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Gene map, 030305 genetics & heredity, Chromosome Mapping, Genome project, génétique comparée, Chromosomes, Mammalian, homme, Human genome, Rabbits, Chromosome 22
Abstract: International audience; Rabbit, a domestic species exploited both in animal production and medical research has only recently begun to be included in gene mapping projects, in particular by the French National Institute of Agronomics. By 2002, less than 60 genes had been precisely localised on rabbit chromosomes, which led us to start a large-scale project on gene mapping in rabbit with the publication of 133 gene localisations in 2003 (Chantry-Darmon et al., 2003). Here, we report the localisation of 102 new genes resulting in good coverage of the rabbit genome and an eight-fold enrichment of the gene map. In addition, we have detected a new conserved segment between rabbit chromosome 4q15.3 and part of human chromosome 22 and thus improved the comparative map with the human genome.
Published: 2005
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40. P4052 The Swine Leukocyte Antigen (SLA) nomenclature system of the International Society for Animal Genetics (ISAG) and the International Union of Immunological Societies (IUIS): Update 2016

Author: Asako Ando, S. Ho, Junsung Lee, Douglas M. Smith, Claire Rogel-Gaillard, Lawrence B. Schook, Joan K. Lunney, and Sabine E. Hammer
Subjects: Animal Genetics, Swine leukocyte antigen, Immunology, Genetics, Animal Science and Zoology, General Medicine, Biology, Nomenclature, Food Science
Published: 2016
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41. Mapping of Rabbit Microsatellite Markers Using Chromosome-Specific Libraries

Author: Ron Korstanje, L.F.M. van Zutphen, S.A. Versteeg, A.A. Bosma, H.A. van Lith, G. F. Gillissen, Claire Rogel-Gaillard, and B.A. van Oost
Subjects: Genetic Markers, 0106 biological sciences, medicine.medical_specialty, Coat, Genetic Linkage, [SDV]Life Sciences [q-bio], Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genetic linkage, Molecular genetics, Genetics, medicine, Animals, Allele, Molecular Biology, Gene, Genetics (clinical), Gene Library, 030304 developmental biology, 0303 health sciences, Chromosome Mapping, RABBITS, GENETIC MAPS, Genetic marker, Cytogenetic Analysis, Labrador Retriever, Microsatellite, Microsatellite Repeats, Biotechnology
Abstract: The domestic dog exhibits a variety of coat colors that encompass a wide range of variation among different breeds. Very little is known about the molecular biology of dog pigmentation; current understanding is based mostly on traditional breeding experiments, which in some cases have suggested genetic interactions that are different from those reported in other mammals. We have examined the molecular genetics of dominant black, a uniform coat color characteristic of black Labrador retrievers or Newfoundlands that has been proposed to be caused by either variation in the melanocortin-1 receptor gene (Mc1r) or by variation in the Agouti gene (A). We identified several coding polymorphisms within Mc1r and several simple sequence repeat polymorphisms closely linked to A, and examined their inheritance in a Labrador retriever 3 greyhound cross that segregates dominant black. No single Mc1r allele was found consistently in animals carrying dominant black, and neither Mc1r nor A cosegregated with dominant black. These results refine our understanding of mammalian coat color inheritance and suggest that dominant black coat color in dogs is caused by a gene not previously implicated in pigment type switching.
Published: 2003
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42. Characterization of Chromosomally Assigned Replication-Competent Gamma Porcine Endogenous Retroviruses Derived from a Large White Pig and Expression in Human Cells

Author: Patrick Chardon, Marcus Niebert, Ralf R. Tönjes, Claire Rogel-Gaillard, Laboratoire de radiobiologie et d'étude du génome (LREG), Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)
Subjects: pig, Chromosomes, Artificial, Bacterial, Swine, [SDV]Life Sciences [q-bio], Virus Integration, Molecular Sequence Data, Immunology, men, Endogenous retrovirus, Genome, Viral, 030230 surgery, Biology, Virus Replication, Microbiology, Cell Line, 03 medical and health sciences, 0302 clinical medicine, Proviruses, endogenous retrovirus, Virology, molecular genetic, Animals, Humans, Cloning, Molecular, gène expression, 030304 developmental biology, Swine Diseases, Chromosome 7 (human), 0303 health sciences, Bacterial artificial chromosome, Genome, Base Sequence, Endogenous Retroviruses, Chromosome Mapping, Sequence Analysis, DNA, Provirus, Molecular biology, Long terminal repeat, Virus-Cell Interactions, 3. Good health, Transplantation, Viral replication, Chromosome 3, Insect Science, HeLa Cells
Abstract: Vertically transmitted endogenous retroviruses pose an infectious risk in the course of pig-to-human transplantation of cells, tissues, and organs. Two classes of polytropic type C porcine endogenous retroviruses (PERV) productively infect human cells in vitro. The cloning and characterization of replication-competent PERV-B sequences from infected human cells (F. Czauderna, N. Fischer, K. Boller, R. Kurth, and R. R. Tönjes, J. Virol. 74:4028-4038, 2000) as well as the cloning of functional PERV-A and -B sequences from porcine cell line PK15 (U. Krach, N. Fischer, F. Czauderna, and R. R. Tönjes, J. Virol. 75:5465-5472, 2001) have been previously described. Here we report the isolation of four full-length proviral sequences from a porcine bacterial artificial chromosome (BAC) library that comprises chromosomally assigned PERV. Clones Bac-PERV-A(130A12) and Bac-PERV-A(151B10) map to pig chromosome 1 and demonstrate close homology to PK15-PERV-A(58) in env and to PERV-MSL in long terminal repeat (LTR), gag , and pro/pol sequences. Clone Bac-PERV-A(463H12) is located on pig chromosome 3 and demonstrates close homology to PK15-PERV-A(58) in env and to 293-PERV-B(43) in LTR, gag , and pro/pol (Czauderna et al.; R. R. Tönjes, F. Czauderna, N. Fischer, U. Krach, K. Boller, P. Chardon, C. Rogel-Gailard, M. Niebert, G. Scheef, A. Werner, and R. Kurth, Transplant Proc. 32:1158-1161, 2000). Clone Bac-PERV-B(192B9) is located on pig chromosome 7 in the swine leukocyte antigen region and is highly homologous with but distinct from the previously described functional clone 293-PERV-B(43) and bears the number of repeats initially observed in the LTRs of clone 293-PERV-A(42) (Czauderna et al.; Krach et al.). Clones Bac-PERV-A(130A12), Bac-PERV-A(151B10), and Bac-PERV-A(463H12) were replication competent upon transfection into susceptible 293 and HeLa cells. Bac-PERV-B(192B9), however, bears two stop codons in pro/pol preventing this clone from being replication competent in some individual pigs, but initial screenings indicate that this provirus might be intact in others. The data suggest that the porcine genome harbors a limited number of infectious PERV sequences, allowing for specific screening in different pig breeds.
Published: 2002
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43. P116 Major update to the swine leukocyte antigen (SLA) nomenclature system of the international society for animal genetics (ISAG) and the international union of immunological societies (IUIS)

Author: Joan K. Lunney, Jun Heon Lee, Sabine E. Hammer, Asako Ando, Sam Ho, Claire Rogel-Gaillard, and Lawrence B. Schook
Subjects: Genetics, biology, Sequence database, fungi, Immunology, Haplotype, General Medicine, Human leukocyte antigen, Major histocompatibility complex, Transplantation, biology.protein, Immunology and Allergy, TAP2, Allele, Nomenclature
Abstract: Aim The Swine Leukocyte Antigen (SLA) system is among the most well characterized major histocompatibility complex (MHC) systems in non-human animal species. Methods The ISAG/IUIS SLA Nomenclature Committee was established 15 years ago with primary objectives to: (1) validate newly identified SLA sequences according to the guidelines established for maintaining high quality standards of the accepted sequences; (2) assign appropriate nomenclatures for new alleles as they are validated; and (3) serve as a curator of the IPD-MHC SLA Sequence Database ( www.ebi.ac.uk/ipd/mhc/group/SLA ), which is the repository for all recognized SLA genes, their allelic sequences and haplotypes. The newly released and improved IPD-MHC Database version 2.0 has incorporated the latest sequence updates, provide new tools that enhance database queries and improve the submission process (Maccari et al., Nucleic Acids Res 2017; 45(D1):D860–D864). Results The SLA Nomenclature Committee met at the 2016 ISAG meeting and made some major revisions to the allele naming system. The Committee decided to retire the provisional alphanumerical naming system for unconfirmed alleles and re-designate each allele an official number, adopting the HLA Nomenclature System with colons as field separators (e.g. SLA-1∗01rh28 → SLA-1∗01:03). Phylogeny will remain the primary approach for assigning SLA-1, −2, −3, DRA, DRB1, DQA and DQB1 alleles into allele groups with similar sequence motifs, while alleles of SLA-5, −6, −7, −8, −12, DMA, DMB, DOA, DOB1, DRB2, DRB3, DRB4, DRB5 are designated sequentially as they are discovered. Naming convention for alleles of other loci (SLA-4, −9, −11, DQB2, DOB2, DYB, MIC1, MIC2, TAP1, TAP2) is to be determined as sequences accumulate. There are currently 223 class I, 214 class II, 2 SLA-related and 2 non-SLA alleles officially designated. There are also 61 class I (SLA-1-3-2) and 49 class II (DRB1-DQB1) haplotypes designated at allele level resolution. Conclusions This systematic nomenclature for SLA genes is critical to the understanding of the architecture and polymorphism of the SLA system and their role in swine diseases, vaccine development and allo- or xeno-responses in transplantation research.
Published: 2017
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44. Extensive Expression Differences along Porcine Small Intestine Evidenced by Transcriptome Sequencing

Author: Gaetan Lemonnier, Claire Chevaleyre, Patricia Lepage, Diane Esquerre, Mustapha Berri, Isabelle P. Oswald, Núria Mach, Yvon Billon, Jordi Estellé, Claire Rogel-Gaillard, Joël Doré, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours, 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, Génétique, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), Biosynthèse & Toxicité des Mycotoxines (ToxAlim-BioToMyc), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), UR Infectiologie animale et Santé publique (UR IASP), Ecole Nationale Vétérinaire de Toulouse (ENVT), UE 1372 Génétique, Expérimentation et Système Innovants, 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)-Génétique, Expérimentation et Système Innovants (GenESI), 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, Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, UR Infectiologie animale et Santé publique ( UR IASP ), Institut National de la Recherche Agronomique ( INRA ), Laboratoire de Génétique Cellulaire ( LGC ), Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Vétérinaire de Toulouse, Institut National de la Recherche Agronomique ( INRA ) -Génétique animale ( G.A. ) -Physiologie Animale et Systèmes d'Elevage ( PHASE ) -Génétique, Expérimentation et Système Innovants ( GenESI ), MICrobiologie de l'ALImentation au Service de la Santé humaine ( MICALIS ), 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, and Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT)
Subjects: Male, appareil intestinal, Anatomy and Physiology, Swine, [SDV]Life Sciences [q-bio], Gene Expression, Veterinary Anatomy and Physiology, duodenum, Genetic Networks, Global Health, Transcriptomes, Jejunum, Transcriptome, Peyer's Patches, 0302 clinical medicine, Gene expression, Intestine, Small, Cluster Analysis, Animal Management, Animal biology, Regulation of gene expression, 0303 health sciences, Multidisciplinary, analyse statistique, Gene Ontologies, digestive, oral, and skin physiology, Genomics, medicine.anatomical_structure, Veterinary Informatics, 030220 oncology & carcinogenesis, Medicine, Small Intestine, Algorithms, expression des gènes, Research Article, Signal Transduction, Science, Immunology, Ileum, Gastroenterology and Hepatology, Biology, digestive system, Molecular Genetics, 03 medical and health sciences, Genome Analysis Tools, Biologie animale, medicine, Genetics, Animals, Gene Regulation, jejunum, Gene Networks, 030304 developmental biology, Inflammation, Models, Statistical, [ SDV ] Life Sciences [q-bio], Sequence Analysis, RNA, Gene Expression Profiling, Computational Biology, Molecular biology, Small intestine, étude transcriptomique, ileon, Gene expression profiling, Gene Expression Regulation, Immune System, Duodenum, Veterinary Science, Gene Function, Biomarkers, Software, porc
Abstract: The aim of this study was to analyse gene expression along the small intestine (duodenum, jejunum, ileum) and in the ileal Peyer's patches in four young pigs with no clinical signs of disease by transcriptome sequencing. Multidimensional scaling evidenced that samples clustered by tissue type rather than by individual, thus prefiguring a relevant scenario to draw tissue-specific gene expression profiles. Accordingly, 1,349 genes were found differentially expressed between duodenum and jejunum, and up to 3,455 genes between duodenum and ileum. Additionally, a considerable number of differentially expressed genes were found by comparing duodenum (7,027 genes), jejunum (6,122 genes), and ileum (6,991 genes) with ileal Peyer's patches tissue. Functional analyses revealed that most of the significant differentially expressed genes along small intestinal tissues were involved in the regulation of general biological processes such as cell development, signalling, growth and proliferation, death and survival or cell function and maintenance. These results suggest that the intrinsic large turnover of intestinal tissues would have local specificities at duodenum, ileum and jejunum. In addition, in concordance with their biological function, enteric innate immune pathways were overrepresented in ileal Peyer's patches. The reported data provide an expression map of the cell pathway variation in the different small intestinal tissues. Furthermore, expression levels measured in healthy individuals could help to understand changes in gene expression that occur in dysbiosis or pathological states.
Published: 2014
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45. Le microbiote intestinal : un compartiment biologique à explorer chez les animaux d’élevage

Author: Claire Rogel-Gaillard
Subjects: Animal breeding, General Veterinary, biology, business.industry, Ecology, Host (biology), gut microbiota, phenotyping, livestock species, breeding goals, Zoology, Context (language use), Gut flora, biology.organism_classification, Cultivable bacteria, digestive system, Gut Epithelium, microbiote intestinal, phénotypage, animaux d’élevage, objectifs de sélection, Livestock, business, Bacteria
Abstract: The microbiota of the gastro-intestinal tract : a biological compartment to explore in livestock species In a perspective of safe, competitive and sustainable animal breeding systems, deepening animal phenotyping and defining new breeding goals are identified as major concerns. The intestine hosts a microbial ecosystem referred to as the gut microbiota. The gut epithelium, at the interface between the host and the microbiota, plays fundamental roles in nutrient absorption, local and systemic immune functions, as well as adaptive functions. The onset of high throughput sequencing methods have paved the way toward an unprecedented characterization of the microbiota by producing data on the non cultivable bacteria set. In livestock species, the scientific and technological context is in place to study the gut microbiota at both phylogenetic (bacteria diversity) and functional levels, and analyze the impact on shaping the host phenotype., L’élaboration de systèmes productifs et durables en élevage est une priorité. Dans ce contexte, il convient d’élargir le champ du phénotypage et d’identifier des leviers d’action. L’intestin héberge une communauté microbienne appelée microbiote intestinal. La muqueuse intestinale, à l’interface entre l’hôte et son microbiote, assure des fonctions vitales dans l’absorption des nutriments, dans l’équilibre immunitaire à la fois local et systémique, et dans la dynamique adaptative au cours de la vie. L’avènement de méthodes de séquençage à haut débit permet aujourd’hui de caractériser le microbiote intestinal avec une précision encore jamais atteinte, fournissant des données sur la portion bactérienne non cultivable. Chez les animaux d’élevage, le contexte scientifique et technologique est favorable pour mettre en place des projets qui croisent des informations individuelles liées au microbiote intestinal (diversité, écologie fonctionnelle) et à l’hôte (génétique, caractères zootechniques et cliniques, statut immunitaire), afin d’aborder de manière intégrée les nouveaux caractères à mesurer et améliorer., Rogel-Gaillard Claire. Le microbiote intestinal : un compartiment biologique à explorer chez les animaux d’élevage . In: Bulletin de l'Académie Vétérinaire de France tome 167 n°2, 2014. pp. 131-136.
Published: 2014

46. Intégrer la caractérisation du microbiote digestif dans le phénotypage de l’animal de rente : vers un nouvel outil de maîtrise de la santé en élevage ?

Author: Christine Martin, Claire Rogel-Gaillard, N. Le Floc’h, P. Quéré, Florence Phocas, Diego P. Morgavi, Fanny Calenge, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), UR Infectiologie animale et Santé publique (UR IASP), Institut National de la Recherche Agronomique (INRA), UMR 1282 ISP, Université Francois Rabelais [Tours], Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, 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), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Florence Phocas, Institut National de la Recherche Agronomique (INRA)-Université de Tours, Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] ( PEGASE ), Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, UR Infectiologie animale et Santé publique ( UR IASP ), and Institut National de la Recherche Agronomique ( INRA )
Subjects: 2. Zero hunger, Gynecology, 0303 health sciences, medicine.medical_specialty, [ SDV ] Life Sciences [q-bio], 030306 microbiology, système immunitaire, santé animale, Gastrointestinal microbiota, [SDV]Life Sciences [q-bio], régulation du metabolisme, Biology, élevage, 03 medical and health sciences, Human health, microbiote, appareil digestif, medicine, séquençage à haut débit, pathologie digestive, système nerveux, variabilité inter individuelle, 030304 developmental biology, développement
Abstract: Le microbiote digestif est un symbionte dont on a démontré l’implication essentielle dans la régulation de la physiologie de l’hôte qui l’héberge pour la digestion, le métabolisme et l’immunité. Ce microbiote a en particulier un rôle majeur, et jusqu’ici sous-estimé, sur la santé de son hôte et participe à son adaptabilité à des environnements changeants. Les technologies de séquençage à haut débit devraient faciliter l’inclusion de cet écosystème complexe dans le phénotypage des animaux d’élevage. Il faut pour ce faire prendre en compte sa composition, sa diversité, sa stabilité au cours du temps et ses variations selon différents facteurs comme le génotype de l’hôte, l’alimentation et les conditions d’élevage. Ces connaissances devraient permettre de définir les propriétés d’un microbiote digestif « normal » associé à une bonne santé, d’en préciser les dysfonctionnements et de comprendre leurs répercussions sur l’état de santé de l’animal. Cela conduira à identifier des marqueurs de diagnostic et de pronostic de ces dysfonctionnements, fournissant des moyens de contrôle nouveaux de la santé en élevage, appréhendée en terme d’optimisation des rendements de production, de résistance aux maladies et de maintien du bien-être. A terme, le contrôle du microbiote digestif par l’alimentation, la génétique ou les pratiques d’élevage permettra de favoriser l’adaptation des animaux à leur environnement d’élevage en améliorant leur robustesse, de limiter l’utilisation d’antibiotiques et de préserver la sécurité sanitaire des aliments en évitant le développement de bactéries pathogènes pour l’Homme. L’ampleur des données à générer et à analyser pour les différentes espèces d’intérêt reste le défi à relever., The gastrointestinal microbiota is a symbiont deeply involved in the physiology of its host through the regulation of digestion, metabolism and immunity and consequently in the host adaptability to changing environments. In particular, the role of the gastrointestinal microbiota in maintaining host health is important and has been under-estimated until now. It is an inherent component of the animal that should be described when phenotyping animals. The rapid development of high throughput sequencing technologies facilitates the description of this complex ecosystem in livestock species. For each animal species, its description should include the measure of its composition, diversity and stability over time and the measure of its variability according to different factors such as genotype, nutrition and breeding conditions. This knowledge should allow defining the properties of a ‘normal’ gastrointestinal microbiota associated with health, identifying the microbiota dysfunctions and understanding their consequences on host physiology. It will lead to the identification of diagnostic and prognostic markers for gastrointestinal dysbiosis thus furnishing new tools for promoting health. Finally, the manipulation of the gastrointestinal microbiota will constitute a way to better adapt animals to their environment by improving their robustness, limit the use of antibiotics and improve food safety by preventing the development of bacteria threatening human health. Due to the high quantity of data to be acquired and analyzed, achieving these objectives for each species of interest remains a challenge.
Published: 2014

47. Analysis of melanoma-related microRNAs expression during the spontaneous regression of cutaneous melanomas in MeLiM pigs

Author: Chia-ying Chu, Chia-Yu Chu, Emmanuelle Bourneuf, Fabienne Le Provost, Michael Baco, Silvia Vincent-Naulleau, Claire Rogel-Gaillard, Stephan Bouet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, CEA, DSV, IRCM, SREIT, Laboratoire de Radiobiologie et d'Etude du génome, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute of Zoology, College of Life Science, National Taiwan University [Taiwan] (NTU), Center for Systems Biology, and Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine
Subjects: Skin Neoplasms, Swine, Melanoma, [SDV]Life Sciences [q-bio], Dermatology, Biology, medicine.disease, Bioinformatics, General Biochemistry, Genetics and Molecular Biology, Gene Expression Regulation, Neoplastic, MicroRNAs, Oncology, microRNA, Gene expression, Cutaneous melanoma, medicine, Cancer research, Animals, RNA, Neoplasm, Gene
Abstract: Treatment of advanced cutaneous melanoma is still challenging and new data on melanoma biology are required. MicroRNAs (miRNAs) represent an emerging field in melanoma understanding. These small regulators of gene expression, involved in melanoma development and progression (Da cruz et al., 2012), showed promising results as biomarkers (Nair et al., 2012). As each miRNA could regulate multiple protein-coding genes and conversely, one gene could be targeted by different miRNAs (Bartel et al., 2009), the dysregulation of miRNAs could significantly impact various pathways and cells behavior.
Published: 2014
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48. A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality

Author: Claire Rogel-Gaillard, Denis Milan, Nathalie Iannuccelli, Thierry Tribout, Patrice Dehais, Bertrand Servin, Hélène Gilbert, Nelly Muller, Jean Pierre Bidanel, Marie-José Mercat, Marie Pierre Sanchez, A.M.M. Tenghe, Marcel Bouffaud, Maria Pilar Del Schneider, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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 expérimentale de testage de porcs, Institut National de la Recherche Agronomique (INRA), Pôle génétique, Institut du Porc (IFIP), French National Agency for Research (ANR, Paris) [ANR-07-GANI-001, ANR-06-GANI-008], BIOPORC (ADN, Nucleus and Gene + breeding organizations), AgroParisTech-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), UE 0450 Unité Expérimentale de Testage de Porcs, Institut National de la Recherche Agronomique (INRA)-Génétique animale (G.A.)-Unité Expérimentale de Testage de Porcs (UETP), and Institut du Porc
Subjects: Male, Meat, Genotype, [SDV]Life Sciences [q-bio], Population, Quantitative Trait Loci, Sus scrofa, Single-nucleotide polymorphism, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Family-based QTL mapping, Genetics, Animals, Genetics(clinical), education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetic association, 2. Zero hunger, 0303 health sciences, education.field_of_study, Autosome, Genome, Research, Haplotype, 0402 animal and dairy science, food and beverages, 04 agricultural and veterinary sciences, General Medicine, 040201 dairy & animal science, Phenotype, Haplotypes, Body Composition, Microsatellite, Animal Science and Zoology, Genome-Wide Association Study
Abstract: Background: Numerous quantitative trait loci (QTL) have been detected in pigs over the past 20 years using microsatellite markers. However, due to the low density of these markers, the accuracy of QTL location has generally been poor. Since 2009, the dense genome coverage provided by the Illumina PorcineSNP60 BeadChip has made it possible to more accurately map QTL using genome-wide association studies (GWAS). Our objective was to perform high-density GWAS in order to identify genomic regions and corresponding haplotypes associated with production traits in a French Large White population of pigs. Methods: Animals (385 Large White pigs from 106 sires) were genotyped using the PorcineSNP60 BeadChip and evaluated for 19 traits related to feed intake, growth, carcass composition and meat quality. Of the 64 432 SNPs on the chip, 44 412 were used for GWAS with an animal mixed model that included a regression coefficient for the tested SNPs and a genomic kinship matrix. SNP haplotype effects in QTL regions were then tested for association with phenotypes following phase reconstruction based on the Sscrofa10.2 pig genome assembly. Results: Twenty-three QTL regions were identified on autosomes and their effects ranged from 0.25 to 0.75 phenotypic standard deviation units for feed intake and feed efficiency (four QTL), carcass (12 QTL) and meat quality traits (seven QTL). The 10 most significant QTL regions had effects on carcass (chromosomes 7, 10, 16, 17 and 18) and meat quality traits (two regions on chromosome 1 and one region on chromosomes 8, 9 and 13). Thirteen of the 23 QTL regions had not been previously described. A haplotype block of 183 kb on chromosome 1 (six SNPs) was identified and displayed three distinct haplotypes with significant (0.0001 < P < 0.03) associations with all evaluated meat quality traits. Conclusions: GWAS analyses with the PorcineSNP60 BeadChip enabled the detection of 23 QTL regions that affect feed consumption, carcass and meat quality traits in a LW population, of which 13 were novel QTL. The proportionally larger number of QTL found for meat quality traits suggests a specific opportunity for improving these traits in the pig by genomic selection.
Published: 2014
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49. The rabbit as an experimental and production animal: from genomics to proteomics

Author: Claire Rogel-Gaillard, André M. Almeida, Ingrid Miller, Luca Fontanesi, Domenico Spina, Inst Med Biochem, University of Veterinary Medicine [Vienna] (Vetmeduni), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Inst Pharmaceut Sci, King‘s College London, Dept Agr & Food Sci, Div Anim Sci, Alma Mater Studiorum University of Bologna (UNIBO), Instituto de Investigação Científica Tropical (IICT), Inst Tecnol Quim & Biol, Instituto de Biologia Experimental e Tecnológica (IBET), Ctr Anim Hlth Res, CIISA Interdisciplinary, European Science Foundation through COST action - Proteomics in Farm Animals [FA-1002], European Science Foundation through COST action - RGB-Net: a Collaborative European Network on Rabbit Genome Biology [TD-1101], Fundacao para a Ciencia e a Tecnologia (Lisboa, Portugal) [SFRH/BPD/90916/2012], Fundacao para a Ciencia e a Tecnologia (Lisboa, Portugal) through Ciencia Research contract, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Instituto de Biologia Experimental e Tecnológica, Miller, Ingrid, Rogel-Gaillard, Claire, Spina, Domenico, Fontanesi, Luca, and de Almeida, André M.
Subjects: [SDV]Life Sciences [q-bio], rabbit, review, Genomics, Computational biology, Biology, Bioinformatics, Proteomics, Biochemistry, proteomics, genomics, Animals, Animal species, Muscle, Skeletal, Molecular Biology, Medicine (all), Proteomic, Rabbit (nuclear engineering), Cell Biology, General Medicine, Oryctolagus cuniculu, Antibody production, Blood Circulation, Models, Animal, Genomic, Rabbits
Abstract: The rabbit ([i]Oryctolagus cuniculus[/i]) is an important animal species widely used for biomedical research purposes, meat production and as a pet animal. There are numerous biomedical and scientific applications that include important areas such as antibody production, muscle, eye and circulatory physiology. The use of proteomics has been limited when considering this species. The aim of this article is to provide a review on applications of proteomics to the rabbit species, including those that are most relevant and where rabbit is a key species: muscle and circulatory system physiology.
Published: 2014
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50. Cloning, transcription and chromosomal localization of the porcine whey acidic protein gene and its expression in HC11 cell line

Author: Martine Yerle, Corinne Delville-Giraud, Sylvie Rival, Claire Rogel-Gaillard, Joe Attal, Louis-Marie Houdebine, Pascale Laffont, Unité biologie du développement et biotechnologie, École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Unité de recherche Génétique Biochimique et Cytogénétique (LGBC), 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 de radiobiologie et d'étude du génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), and Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: Transcription, Genetic, Swine, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Gene Expression, Biology, Cell Line, Mice, 03 medical and health sciences, Exon, Mammary Glands, Animal, Plasmid, Sequence Homology, Nucleic Acid, Complementary DNA, Genetics, Animals, Lactation, Coding region, Amino Acid Sequence, Cloning, Molecular, Gene, In Situ Hybridization, Fluorescence, 030304 developmental biology, 0303 health sciences, Bacterial artificial chromosome, Base Sequence, 030302 biochemistry & molecular biology, Chromosome Mapping, DNA, Sequence Analysis, DNA, General Medicine, BIOLOGIE MOLECULAIRE, Milk Proteins, Molecular biology, Chromosome Banding, LIGNE CELLULAIRE, Genes, Regulatory sequence, biology.protein, RNA, Rabbits, Whey Acidic Protein
Abstract: The whey acidic protein (WAP) is the major whey protein of rodent, rabbit and camel. Recently, it was identified in the milk of swine ( Simpson et al., 1998 . J. Mol. Endocrinol. 20, 27–35). In this paper, the cloning of the pig WAP cDNA and of bacterial artificial chromosome (BAC) construct containing the entire porcine WAP gene is reported. The comparison of the coding sequence of the pig WAP gene to rodent or lagomorph WAP sequence already published demonstrated that only exon sequences are partially conserved. The porcine WAP gene was localized on the subtelomeric region of the chromosome 18. The estimation of the expression of the swine WAP gene in the mammary gland from lactating animals revealed a high level of expression. In order to compare the expression level of the porcine WAP gene from the large genomic fragment which contained 70 kb downstream and 50 kb upstream the pig WAP gene or the smaller one (1 kb downstream and 2.4 kb upstream), these two genomic fragments were transfected in HC11 cell line. The BAC construct was expressed 15 times higher than the plasmid when reported to the integrated copy number. This report suggests that the HC11 cell line is a useful tool to identify the regulatory sequences of milk protein genes.
Published: 2001
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