Author: "Magali SanCristobal" - Searchworks@Jio Institute Digital Library Search Results

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1. The structure of a gene co-expression network reveals biological functions underlying eQTLs.

Author: Nathalie Villa-Vialaneix, Laurence Liaubet, Thibault Laurent, Pierre Cherel, Adrien Gamot, and Magali SanCristobal
Subjects: Medicine, Science
Abstract: What are the commonalities between genes, whose expression level is partially controlled by eQTL, especially with regard to biological functions? Moreover, how are these genes related to a phenotype of interest? These issues are particularly difficult to address when the genome annotation is incomplete, as is the case for mammalian species. Moreover, the direct link between gene expression and a phenotype of interest may be weak, and thus difficult to handle. In this framework, the use of a co-expression network has proven useful: it is a robust approach for modeling a complex system of genetic regulations, and to infer knowledge for yet unknown genes. In this article, a case study was conducted with a mammalian species. It showed that the use of a co-expression network based on partial correlation, combined with a relevant clustering of nodes, leads to an enrichment of biological functions of around 83%. Moreover, the use of a spatial statistics approach allowed us to superimpose additional information related to a phenotype; this lead to highlighting specific genes or gene clusters that are related to the network structure and the phenotype. Three main results are worth noting: first, key genes were highlighted as a potential focus for forthcoming biological experiments; second, a set of biological functions, which support a list of genes under partial eQTL control, was set up by an overview of the global structure of the gene expression network; third, pH was found correlated with gene clusters, and then with related biological functions, as a result of a spatial analysis of the network topology.
Published: 2013
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2. Comparing the intestinal transcriptome of Meishan and Large White piglets during late fetal development reveals genes involved in glucose and lipid metabolism and immunity as valuable clues of intestinal maturity

Author: H. Quesnel, Laure Gress, Marie-Christine Père, Véronique Romé, Laurianne Canario, Laurence Liaubet, Gaëlle Boudry, Yannick Lippi, Ying Yao, Isabelle Le Huërou-Luron, Magali SanCristobal, Yvon Billon, Samir Dou, Valentin Voillet, Pierre Mormède, Nathalie Iannucelli, Maëva Jégou, Nutrition, Métabolismes et Cancer (NuMeCan), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM), Sichuan Agricultural University, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, ToxAlim (ToxAlim), Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UPS), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), This project received financial support from French National Agency of Research (PORCINET project, ANR-09-GENM005), Agrocampus Ouest (FRANCE), Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National de la Santé et de la Recherche Médicale - INSERM (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Sichuan Agriculture University - SICAU (CHINA), Université de Rennes 1 (FRANCE), Génétique, Physiologie et Systèmes d’Elevage - GenPhySE (Toulouse, France), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Transcriptomic impact of Xenobiotics (E23 TRiX), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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)-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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), PORCINET project, ANR-09-GENM005, The French National Research Agency, China Scholarship Council (CSC)-INRA joint PhD program, INRA GA and PHASE departments and the region Midi-Pyrénées, ANR-09-GENM-0005,PORCINET,Approche intégrée de la maturité des porcelets(2009), Institut National Polytechnique de Toulouse - INPT (FRANCE), 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), Génétique, Expérimentation et Système Innovants, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université 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)-Plateforme Génome & Transcriptome (GET), 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), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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)-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), (OATAO), Open Archive Toulouse Archive Ouverte, and Génomique et biotechnologies végétales - Approche intégrée de la maturité des porcelets - - PORCINET2009 - ANR-09-GENM-0005 - GENOM-BTV - VALID
Subjects: 0301 basic medicine, pig, Microarray, Swine, Transcriptome, Fetal Development, 0302 clinical medicine, Intestinal Mucosa, 2. Zero hunger, Genetics, [SDV.BDD.EO] Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Phenotype, Intestine, Intestines, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], PPARGC1A, microarray, Biotechnology, Research Article, Offspring, Biology, Carbohydrate metabolism, Andrology, Maturity, Lipid and glucose metabolism, Inflammation, Pig, 03 medical and health sciences, intestin, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Biologie animale, Animals, métabolisme du glucose, Fetus, métabolisme lipidique, Gene Expression Profiling, Immunity, Ripening, Lipid metabolism, maturité, Lipid Metabolism, 030104 developmental biology, Glucose, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, [SDV.BA.ZV] Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, 030217 neurology & neurosurgery, porc
Abstract: Background Maturity of intestinal functions is critical for neonatal health and survival, but comprehensive description of mechanisms underlying intestinal maturation that occur during late gestation still remain poorly characterized. The aim of this study was to investigate biological processes specifically involved in intestinal maturation by comparing fetal jejunal transcriptomes of two representative porcine breeds (Large White, LW; Meishan, MS) with contrasting neonatal vitality and maturity, at two key time points during late gestation (gestational days 90 and 110). MS and LW sows inseminated with mixed semen (from breed LW and MS) gave birth to both purebred and crossbred fetuses. We hypothesized that part of the differences in neonatal maturity between the two breeds results from distinct developmental profiles of the fetal intestine during late gestation. Reciprocal crossed fetuses were used to analyze the effect of parental genome. Transcriptomic data and 23 phenotypic variables known to be associated with maturity trait were integrated using multivariate analysis with expectation of identifying relevant genes-phenotypic variable relationships involved in intestinal maturation. Results A moderate maternal genotype effect, but no paternal genotype effect, was observed on offspring intestinal maturation. Four hundred and four differentially expressed probes, corresponding to 274 differentially expressed genes (DEGs), more specifically involved in the maturation process were further studied. In day 110-MS fetuses, Ingenuity® functional enrichment analysis revealed that 46% of DEGs were involved in glucose and lipid metabolism, cell proliferation, vasculogenesis and hormone synthesis compared to day 90-MS fetuses. Expression of genes involved in immune pathways including phagocytosis, inflammation and defense processes was changed in day 110-LW compared to day 90-LW fetuses (corresponding to 13% of DEGs). The transcriptional regulator PPARGC1A was predicted to be an important regulator of differentially expressed genes in MS. Fetal blood fructose level, intestinal lactase activity and villous height were the best predicted phenotypic variables with probes mostly involved in lipid metabolism, carbohydrate metabolism and cellular movement biological pathways. Conclusions Collectively, our findings indicate that the neonatal maturity of pig intestine may rely on functional development of glucose and lipid metabolisms, immune phagocyte differentiation and inflammatory pathways. This process may partially be governed by PPARGC1A. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4001-2) contains supplementary material, which is available to authorized users.
Published: 2017

3. Accounting for Linkage Disequilibrium in genome scans for selection without individual genotypes: the local score approach

Author: Patrice Dehais, María Inés Fariello, Olivier Bouchez, Frédérique Pitel, Simon Boitard, Julien Recoquillay, Thomas Faraut, Cécile Arnould, Sophie Leroux, David Robelin, Sabine Mercier, Magali SanCristobal, Christine Leterrier, David Gourichon, Gerald Salin, 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 de Mathématiques de Toulouse UMR5219 (IMT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), UFR SES, Département de Mathématique-Informatique, Université Toulouse Le Mirail (Toulouse 2) (UTM), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, Plateforme SIGENAE, Pôle d'Expérimentation Avicole de Tours (PEAT), Dynamiques Forestières dans l'Espace Rural (DYNAFOR), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), French Agence Nationale de la Recherche (SNP-BB project, ANR-009-GENM-008) (DéLiSus project, ANR-07-GANI-001), The Région Midi-Pyrénées, Département de Génétique Animale of Institut National de la Recherche Agronomique, Agencia Nacional de Investigacion e Innovacion (grant PD NAC 2013 1 10964), Universidad de la Republica, Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), 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), Unité de Recherches Avicoles (URA), 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 (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), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Pôle d'Expérimentation Avicole de Tours (UE PEAT), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), ANR-09-GENM-0008,SNP-BB,Recherche de QTL par marquage SNP pour des caractères de comportement social et de production chez l'oiseau(2009), 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), 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), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, UMR 5219, Institut de Mathématiques, Université de Toulouse, Université Toulouse Le Mirail (Toulouse 2) ( UTM ), 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]-Université de Tours-Centre National de la Recherche Scientifique ( CNRS ), Recherches Avicoles ( SRA ), Institut National de la Recherche Agronomique ( INRA ), Pôle d'Expérimentation Avicole de Tours ( PEAT ), Dynamiques Forestières dans l'Espace Rural ( DYNAFOR ), Institut National Polytechnique [Toulouse] ( INP ) -Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Supérieure Agronomique de Toulouse, 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], Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), 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), Hubbard SAS, Partenaires INRAE, Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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 Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT)
Subjects: 0301 basic medicine, Linkage disequilibrium, haplotype, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Genotype, Genome-wide association study, Accounting, Biology, Genome, Polymorphism, Single Nucleotide, selection signatures, Linkage Disequilibrium, 03 medical and health sciences, ngs, Genomic Segment, Genetics, Animals, Computer Simulation, analyse génomique, [ SDV.OT ] Life Sciences [q-bio]/Other [q-bio.OT], Selection, Genetic, Association mapping, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Genetic association, Models, Genetic, business.industry, local score, génome, Haplotype, quail, scintigraphie, 030104 developmental biology, Haplotypes, scintiscanning, pool sequencing, génotype, business, simulation informatique
Abstract: Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans increases detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium in genome scans for selection, cumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a selection signal. Using computer simulations, we demonstrate that this approach detects selection with higher power than several state-of-the-art single marker, windowing or haplotype-based approaches. We illustrate this on two benchmark data sets including individual genotypes, for which we obtain similar results with the local score and one haplotype-based approach. Finally, we apply the local score approach to Pool-Seq data obtained from a divergent selection experiment on behavior in quail, and obtain precise and biologically coherent selection signals: while competing methods fail to highlight any clear selection signature, our method detects several regions involving genes known to act on social responsiveness or autistic traits. Although we focus here on the detection of positive selection from multiple population data, the local score approach is general and can be applied to other genome scans for selection or other genome-wide analyses such as GWAS.
Published: 2017

4. Differentially expressed genes and gene networks involved in pig ovarian follicular atresia

Author: Magali SanCristobal, Agnès Bonnet, Julien Sarry, Elena Terenina, Danielle Monniaux, Philippe Monget, Florence Gondret, Florence Vignoles, Gwenola Tosser-Klopp, Christèle Robert-Granié, Stéphane Fabre, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), INPT-ENSAT - INPT-ENVT, UMR 1388 GenPhySE Génétique Physiologie et Systèmes d'Elevage. Centre de recherche Toulouse, 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, French Agence Nationale de la Recherche GENOVUL project (ANR-05-GANI-001-01), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and 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: 0301 basic medicine, pig, Candidate gene, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Physiology, Granulosa cell, Sus scrofa, Down-Regulation, Apoptosis, atresia, Biology, atresie folliculaire, 03 medical and health sciences, Ovarian Follicle, folliculogenesis, Genetics, medicine, Animals, Cluster Analysis, Gene Regulatory Networks, porcin, Ovarian follicle, genes, upstream regulators, Gene Expression Profiling, Follicular atresia, gène, ovaire, biomarkers, medicine.disease, Up-Regulation, Cell biology, Gene expression profiling, INHBB, Gene Ontology, 030104 developmental biology, medicine.anatomical_structure, Atresia, gene expression, Female, ovary, Folliculogenesis, follicular atresia, Autre (Sciences du Vivant), Signal Transduction
Abstract: Ovarian folliculogenesis corresponds to the development of follicles leading to either ovulation or degeneration, this latter process being called atresia. Even if atresia involves apoptosis, its mechanism is not well-understood. The objective of this project was to analyse global gene expression in pig granulosa cells of ovarian follicles during atresia. The transcriptome analysis was performed using 9216 cDNAs microarray to identify gene networks and candidate genes involved in pig ovarian follicular atresia. One thousand six hundred and eighty four significantly regulated genes were differentially regulated between small healthy follicles and small atretic follicles. Among them, two hundred and eighty seven genes had a fold-change higher than 2 between the two follicle groups. Eleven genes (DKK3, GADD45A, CAMTA2, CCDC80, DAPK2, ECSIT, MSMB, NUPR1, RUNX2, SAMD4A, and ZNF628) having a fold-change higher than 5 between groups could likely serve as markers of follicular atresia. Moreover, automatic confrontation of deregulated genes with literature data enlightened 93 genes as regulatory candidates of pig granulosa cell atresia. Among these genes known to be inhibitors of apoptosis, stimulators of apoptosis or tumor suppressors INHBB, HNF4, CLU, different interleukins (IL5, IL24), TNF-associated receptor (TNFR1), and cytochrome-c oxidase (COX) were suggested as playing an important role in porcine atresia. Present study also enlists key upstream regulators in follicle atresia based on our results and on a literature review. The novel gene candidates and gene networks identified in the current study lead to a better understanding of the molecular regulation of ovarian follicular atresia.
Published: 2017

5. Depicting gene co-expression networks underlying eQTLs

Author: Magali SanCristobal, Laurence Liaubet, Nathalie Villa-Vialaneix, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Haja N. Kadarmideen
Subjects: 0303 health sciences, [STAT.AP]Statistics [stat]/Applications [stat.AP], [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Computer science, [SDV]Life Sciences [q-bio], Inference, Computational biology, Network theory, 01 natural sciences, Phenotype, Expression (mathematics), 010104 statistics & probability, 03 medical and health sciences, Betweenness centrality, Expression quantitative trait loci, Graphical model, 0101 mathematics, Gene, 030304 developmental biology
Abstract: International audience; Deciphering the biological mechanisms underlying a list of genes whose expression is under partial genetic control (i.e., having at least one eQTL) may not be as easy as for a list of differential genes. Indeed, no specific phenotype (e.g., health or production phenotype) is linked to the list of transcripts under study. There is a need to find a coherent biological interpretation of a list of genes under (partial) genetic control. We propose a pipeline using appropriate statistical tools to build a co-expression network from the list of genes, then to finely depict the network structure. Graphical models are relevant because they are based on partial correlations, closely linked with causal dependencies. Highly connected genes (hubs) and genes that are important for the global structure of the network (genes with high betweenness) are often biologically meaningful. Extracting modules of genes that are highly connected permits a significant enrichment in one biological function for each module, thus linking statistical results with biological significance. This approach has been previously used on a pig eQTL dataset (Villa-Vialaneix et al. 2013) and was proven to be highly relevant. Throughout the present chapter, we define statistical notions linked with network theory, and apply them on a reduced dataset of genes with eQTL that were found in the pig species to illustrate the basics of network inference and mining.
Published: 2016

6. Genetic characterization of the Blonde d’Aquitaine cattle breed using microsatellite markers and relationship with three other French cattle populations

Author: Dominique Rocha, Magali SanCristobal, Christine Bertrand, Y. Amigues, and Simon Boitard
Subjects: 2. Zero hunger, 0303 health sciences, Genetic diversity, Animal breeding, 0402 animal and dairy science, food and beverages, Zoology, 04 agricultural and veterinary sciences, General Medicine, Biology, 040201 dairy & animal science, Breed, Genetic differentiation, 03 medical and health sciences, Animal science, Food Animals, Microsatellite, Blonde d'Aquitaine, Animal Science and Zoology, 030304 developmental biology
Abstract: This study was conducted to evaluate the genetic diversity of Blonde d'Aquitaine, a well-muscled native French beef breed, and to understand the relationships between Blonde d'Aquitaine, Limousin and Salers. We also compared these three beef breeds to the Holstein dairy breed. For this purpose, a set of 16 microsatellite markers were investigated. The obtained results show that Blonde d'Aquitaine has a high level of genetic diversity. Our study shows also that the French beef breeds have genetic differentiation among them, with approximately 9% of the total variation owing to breed differences. Our results show also that Blonde d'Aquitaine and Salers populations are genetically more similar to each other than to the Limousin.
Published: 2011

7. Genetic variability, structure and assignment of Spanish and French pig populations based on a large sampling

Author: Armand Sánchez, J. Tibau, Claude Chevalet, M. J. Mercat, Simon Boitard, Magali SanCristobal, and J. C. Meriaux
Subjects: Genetics, 0303 health sciences, Genetic diversity, education.field_of_study, Population, 0402 animal and dairy science, 04 agricultural and veterinary sciences, General Medicine, Biology, 040201 dairy & animal science, Breed, 03 medical and health sciences, Evolutionary biology, Genetic variation, Microsatellite, Animal Science and Zoology, Genetic variability, Allele, education, Purebred, 030304 developmental biology
Abstract: Summary The Spanish and French pig populations share the common practice of quasi systematic paternity control of pure breed and composite line males. Ten microsatellite markers are in common between Spain and France controls, among the 17 markers used in France and the 13 used in Spain. After the adjustment of allele sizes, it is possible to merge the two datasets and to obtain a set of 5791 animals, including the vast majority of the males in the Duroc, Landrace, Large White and Pietrain French and Spanish breeds. Twelve French composite lines are also available. The genetic diversity analysis of these pig populations is presented, as well as the assignment of an individual to its breed. The effects of heterogeneous sampling across time and of relatedness among animals are also assessed. Consistent with the results of the previous studies, we found that different populations from the same breed clearly clustered together. In addition, all populations of this study, whether purebred or composite, are quite well differentiated from the other ones. As a result, we note that the 10 microsatellites commonly used for paternity control ensure a powerful detection of the breed of origin, with the power of detection being 95–99%. The detection of the exact population within breed is more difficult, but the power exceeds 70% for most of the populations. Practical implications include, for instance, the detection of outlier animals, crosses and admixture events.
Published: 2010

8. A muscle transcriptome analysis identifies positional candidate genes for a complex trait in pig

Author: Denis Milan, J. Rallières, Laurence Liaubet, J. Glénisson, Magali SanCristobal, François Hatey, Valérie Lobjois, Katia Feve, P. Le Roy, P. Cherel, 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, France Hybrides, Génétique Animale (GARen), 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)-Ecole Nationale Supérieure Agronomique de Rennes, and ProdInra, Migration
Subjects: pig, Meat, Transcription, Genetic, Swine, Gene Expression, [SDV.GEN] Life Sciences [q-bio]/Genetics, Biology, Quantitative trait locus, Genome, quantitative trait, Transcriptome, 03 medical and health sciences, Meat tenderness, positional candidate gene, Muscular Diseases, Species Specificity, Gene expression, Genetics, medicine, Animals, skeletal muscle, Muscle, Skeletal, Gene, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, cDNA microarray, 2. Zero hunger, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Cell Cycle, 0402 animal and dairy science, 04 agricultural and veterinary sciences, General Medicine, 040201 dairy & animal science, Tenderness, tenderness, Animal Science and Zoology, Stress, Mechanical, medicine.symptom, DNA microarray, Energy Metabolism
Abstract: International audience; Muscle tenderness is an important complex trait for meat quality and thus for genetic improvement through animal breeding. However, the physiological or genetic control of tenderness development in muscle is still poorly understood. In this work, using transcriptome analysis, we found a relationship between gene expression variability and tenderness. Muscle (longissimus dorsi) samples from 30 F2 pigs were characterized by Warner–Bratzler Shear Force (WBSF) on cooked meat as a measurement of muscle tenderness. Gene expression levels were measured using microarrays for 17 muscle samples selected to represent a range of WBSF values. Using a linear regression model, we determined that samples with WBSF values above 30 N could be effectively analysed for genes exhibiting a significant association of their expression level on shear force (false discovery rate
Published: 2008

9. Longitudinal Analysis of Gene Expression in Porcine Skeletal Muscle After Post-Injection Local Injury

Author: Pierre-Louis Toutain, François Hatey, Pierre J. Ferré, Magali SanCristobal, Agnès Bonnet, Gwenola Tosser-Klopp, Laurence Liaubet, Didier Concordet, Emmanuelle Uro-Coste, Hervé P. Lefebvre, Physiologie et Toxicologie Expérimentales, 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 Génétique Cellulaire (LGC), Régulations cellulaires: lipidoses et atherosclerose, IFR 31 Louis Bugnard (IFR 31), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Simon, Marie Francoise, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), and Régulations cellulaires: lipidoses et atherosclerose.
Subjects: Male, Pathology, Time Factors, MESH: Thymosin, Swine, [SDV]Life Sciences [q-bio], Muscle Proteins, MESH: Collagen Type I, Pharmaceutical Science, Post injection, MESH: Down-Regulation, MESH: Collagen, MESH: Fibronectins, Gene expression, MESH: Up-Regulation, Osteonectin, MESH: Animals, Pharmacology (medical), MESH: Swine, Oligonucleotide Array Sequence Analysis, MESH: Muscle, Skeletal, 0303 health sciences, 030302 biochemistry & molecular biology, MESH: Injections, Intramuscular, Pathophysiology, Up-Regulation, [SDV] Life Sciences [q-bio], medicine.anatomical_structure, Matrix Metalloproteinase 2, Molecular Medicine, Collagen, MESH: Osteonectin, Intramuscular injection, MESH: ras Proteins, Biotechnology, medicine.medical_specialty, Down-Regulation, Biology, Injections, Intramuscular, Collagen Type I, MESH: Gene Expression Profiling, MESH: Muscle Proteins, 03 medical and health sciences, medicine, Animals, Muscle, Skeletal, Pathological, 030304 developmental biology, Pharmacology, Gene Expression Profiling, MESH: Time Factors, Organic Chemistry, Skeletal muscle, MESH: Male, Fibronectins, Collagen Type I, alpha 1 Chain, Thymosin, MESH: Matrix Metalloproteinase 2, Gene expression profiling, MESH: Oligonucleotide Array Sequence Analysis, Time course, ras Proteins
Abstract: International audience; PURPOSE: The purpose of this study is to describe the time course of gene expression in a skeletal muscle local injury induced by an intramuscular (IM) injection, and to compare the dynamics of gene expression with pathological events. MATERIALS AND METHODS: Ten piglets received 4 IM injections of propylene glycol in the longissimus dorsi muscles 6 h, 2, 7, and 21 days before euthanasia, where control and injected muscle sites were sampled for RNA isolation and microscopic examination. The hybridization of nylon cDNA microarrays was carried out with radioactive probes obtained from the muscle RNA. RESULTS: 153 genes were found under- or over-expressed at least once among the investigated time-conditions. The eight most discriminant genes were also identified: Two genes (GTP-binding protein RAD and Ankyrin repeat domain protein) were over-expressed at 6 h and six genes between 2 and 21 days (Osteonectin, Fibronectin, Matrix metalloproteinase-2, Collagen alpha 1(I) chain, Collagen alpha 2(I) chain, and Thymosin beta-4). Necrosis, inflammation and regeneration were observed through both the dynamics of gene expression profiles and through the microscopic examinations. CONCLUSION: Our data demonstrate that several pathways are involved in post-injection muscle injury, and that necrosis, inflammation and regeneration are not sequential but occur in parallel.
Published: 2007

10. Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

Author: Denis Milan, Thomas Faraut, Lidwine Trouilh, Thierry Tribout, Magali SanCristobal, Christine Lascor, Laurence Liaubet, Florian Rohart, Pascal G.P. Martin, Marcel Bouffaud, Marie-José Mercat, Yannick Lippi, 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 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), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), 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, BioPorc, Institut du Porc, École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité expérimentale de testage de porcs, Institut National de la Recherche Agronomique (INRA), 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), 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), 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), Institut du Porc (IFIP), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Institut National de la Recherche Agronomique ( INRA ) -Génétique animale ( G.A. ) -Unité Expérimentale de Testage de Porcs ( UETP ), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés ( LISBP ), Institut National de la Recherche Agronomique ( INRA ) -Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Toxicologie Alimentaire ( UTA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Plateforme Génome & Transcriptome (GET), 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)-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), and 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)-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: Male, Swine, vitamin-d, [SDV]Life Sciences [q-bio], Sus scrofa, selection, pattern, european pig breed, gene expression, skeletal muscle, population transcriptomic, evolution, domestication, mechanism, Biology, Breeding, Transcriptome, medicine, Genetics, Animals, Muscle, Skeletal, Gene, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, Regulation of gene expression, [ SDV ] Life Sciences [q-bio], Gene Expression Profiling, Skeletal muscle, Actin cytoskeleton, Breed, Gene expression profiling, medicine.anatomical_structure, Gene Expression Regulation, Female, DNA microarray, Signal Transduction, Research Article, Biotechnology
Abstract: Background Among transcriptomic studies, those comparing species or populations can increase our understanding of the impact of the evolutionary forces on the differentiation of populations. A particular situation is the one of short evolution time with breeds of a domesticated species that underwent strong selective pressures. In this study, the gene expression diversity across five pig breeds has been explored in muscle. Samples came from: 24 Duroc, 33 Landrace, 41 Large White dam line, 10 Large White sire line and 39 Piétrain. From these animals, 147 muscle samples obtained at slaughter were analyzed using the porcine Agilent 44 K v1 microarray. Results A total of 12,358 genes were identified as expressed in muscle after normalization and 1,703 genes were declared differential for at least one breed (FDR
Published: 2015

11. How do introgression events shape the partitioning of diversity among breeds : A case study in sheep

Author: Coralie Danchin-Burge, Magali SanCristobal, Xavier Rognon, Yann Nédélec, Isabelle Palhiere, Grégoire Leroy, Etienne Verrier, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut de l'élevage (IDELE), 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 de l’Élevage, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: Genotyping Techniques, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Introgression, Biology, Selective breeding, domestication, conservation prioritie, Genetic variation, Genetics, Animals, Genetics(clinical), Selection, Genetic, Domestication, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Genetic diversity, Sheep, microsatellite marker, Genetic Variation, population structure, General Medicine, genetic diversity, United Kingdom, Reticulate evolution, Breed, cattle, reveals, Phylogeography, Evolutionary biology, Genetic structure, Animal Science and Zoology, France, Microsatellite Repeats, Selective Breeding, Research Article
Abstract: Background From domestication to the current pattern of differentiation, domestic species have been influenced by reticulate evolution with multiple events of migration, introgression, and isolation; this has resulted in a very large number of breeds. In order to manage these breeds and their genetic diversity, one must know the current genetic structure of the populations and the relationships among these. This paper presents the results of a genetic diversity analysis on an almost exhaustive sample of the sheep breeds reared in France. Molecular characterization was performed with a set of 21 microsatellite markers on a collection of 49 breeds that include five breed types: meat, hardy meat, dairy, high prolificacy and patrimonial breeds. Results Values of expected heterozygosity ranged from 0.48 to 0.76 depending on the breed, with specialized meat breeds exhibiting the lowest values. Neighbor-Net, multidimensional analysis or clustering approaches revealed a clear differentiation of the meat breeds compared to the other breed types. Moreover, the group that clustered meat breeds included all the breeds that originated from the United Kingdom (UK) and those that originated from crossbreeding between UK breeds and French local breeds. We also highlighted old genetic introgression events that were related to the diffusion of Merino rams to improve wool production. As a result of these introgression events, especially that regarding the UK breeds, the breeds that were clustered in the ‘meat type cluster’ exhibited the lowest contribution to total diversity. That means that similar allelic combinations could be observed in different breeds of this group. Conclusions The genetic differentiation pattern of the sheep breeds reared in France results from a combination of factors, i.e. geographical origin, historic gene flow, and breed use. The Merino influence is weaker than that of UK breeds, which is consistent with how sheep use changed radically at the end of 19th century when wool-producing animals (Merino-like) were replaced by meat-producing breeds. These results are highly relevant to monitor and manage the genetic diversity of sheep and can be used to set priorities in conservation programs when needed. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0131-7) contains supplementary material, which is available to authorized users.
Published: 2015

12. Genetic diversity in European pigs utilizing amplified fragment length polymorphism markers

Author: Guillaume Laval, P. Glodek, R. Cardellino, Alan Archibald, A.P. Rattink, Graham Plastow, Martien A. M. Groenen, Vincenzo Russo, M. Bagga, Henri C M Heuven, Amparo Martínez Martínez, J. Peleman, B. Brugmans, Juan Vicente Delgado, Chris Haley, R. Joosten, K. Hammond, L. Alderson, Maria Ramos, E. Fimland, Barbara Harlizius, J. N. Meyer, K. Siggens, Andy Law, Donato Matassino, Roberta Davoli, George C. Russell, Claude Chevalet, Gustavo Gandini, Y. Amigues, Magali SanCristobal, C. Désautés, David J. Milan, Jose Luis Vega-Pla, M.-Y. Boscher, M. G. M. van Schriek, ProdInra, Migration, San Cristobal M., Chevalet C., Peleman J., Heuven H., Brugmans B., Van Schriek M., Joosten R., Rattink A.P., Harlizius B., Groenen M.A.M., Amigues Y., Boscher M.-Y, Russel G., Law A., Davoli R., Russo V., Desautes C., Alderson L., Fimland E., Bagga M., Delgado J.V., Vega-Pla J., Martinez A.M., Ramos M., Glodeck P., Meyer J.N., Gandini G., Matassino D., Siggens K., Laval G., Archibald A., Milan D., Hammond K., Cardellino R., Haley C., Plastow G., Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), and Institut National de la Recherche Agronomique (INRA)
Subjects: pig, Genetic Markers, 0106 biological sciences, Heterozygote, Genotype, Swine, [SDV]Life Sciences [q-bio], AMPLIFIED FRAGMENT LENGTH POLYMORPHISM MARKERS, Breeding, Biology, 010603 evolutionary biology, 01 natural sciences, Loss of heterozygosity, 03 medical and health sciences, Genetics, Animals, Allele, Alleles, Phylogeny, 030304 developmental biology, 0303 health sciences, Genetic diversity, genetic distance, Polymorphism, Genetic, conservation, food and beverages, genetic diversity, General Medicine, [SDV] Life Sciences [q-bio], Europe, Genetic distance, Genetic marker, Microsatellite, Animal Science and Zoology, Amplified fragment length polymorphism, aflp marker, Microsatellite Repeats
Abstract: The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3-98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity.
Published: 2006

13. Segregation of a major gene influencing ovulation in progeny of Lacaune meat sheep

Author: Bernard Bibé, D. Lajous, Jean-Michel Elsen, Jean-Pierre Belloc, Magali SanCristobal, Frédéric Lecerf, Loys Bodin, Y. Amigues, Philippe Mulsant, and F. Eychenne
Subjects: Litter (animal), Male, Litter Size, Breeding, ovin, méthode statistique, sélection, Genetics(clinical), gène majeur, lcsh:SF1-1100, media_common, major gene, Genes, Dominant, Genetics, taille de la portee, General Medicine, Major gene, Breed, Pedigree, descendant, Female, Ovulation, sheep, lcsh:QH426-470, mouton, media_common.quotation_subject, Biology, prolificite, race ovine lacaune, taux d'ovulation, Animal science, Weaning, Animals, Selection, Genetic, Ecology, Evolution, Behavior and Systematics, Crosses, Genetic, GENETIQUE ANIMALE, VARIABILITE, RACE A VIANDE, Models, Statistical, Research, Sire, Quantitative genetics, allèle, DNA, Heritability, insémination, lcsh:Genetics, Fertility, Animal Science and Zoology, lcsh:Animal culture
Abstract: Inheritance of the ovulation rate (OR) in the Lacaune meat breed was studied through records from a small nucleus of 36 hyper-prolific ewes screened on farms on the basis of their natural litter size, and from progeny data of three selected Lacaune sires. These sires were chosen at the AI centre according to their breeding values estimated for the mean and the variability of their daughters' litter size. Non-carrier Lacaune dairy ewes were inseminated to produce 121 F1 daughters and 27 F1 sons. Twelve sons (four from each sire) were used in turn to inseminate non-carrier Lacaune dairy ewes providing 260 BC progeny ewes. F1 and BC progeny were brought from private farms and gathered after weaning on an experimental farm where ovulation rates were recorded in the first and second breeding seasons. With an average of 6.5 records each, the mean OR of hyper-prolific ewes was very high (5.34), and 38.4% of records showed a rate of 6 or more. F1 data showed high repeatability of OR (r = 0.54) within ewe, with significant variability among ewes. High OR (≥ 4) were observed in each family. A segregation analysis provided a significant likelihood ratio and classified the three founders as heterozygous. BC ewes also displayed high repeatability of OR (r = 0.47) and the mean OR varied considerably between families (from 1.24 to 1.78). Seven of the 12 BC families presented high-ovulating ewes (at least one record ≥ 4) and segregation analysis yielded a highly significant likelihood ratio as compared to an empirical test distribution. The high variability of the mean ovulation rate shown by a small group of daughters of BC ewes inseminated by putative carrier F1 rams, and the very high ovulation rate observed for some of these ewe lambs, confirmed the segregation of a major gene with two co-dominant alleles borne by an autosome. The difference between homozygous non-carriers and heterozygous ewes was about one ovulation on the observed scale and 2.2 standard deviations on the underlying scale.
Published: 2002

14. Transcriptional reprogramming and phenotypical changes associated with growth of Xanthomonas campestris pv. campestris in cabbage xylem sap

Author: Paul Soreau, Emmanuelle Lauber, Magali SanCristobal, Thomas Dugé de Bernonville, Laurent D. Noël, Matthieu Arlat, Saïda Danoun, Anke Becker, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), 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, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Marburg, Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], Brassica, xanthomonas, Xanthomonas campestris, xylem sap, Applied Microbiology and Biotechnology, Microbiology, Xanthomonas campestris pv. campestris, Transcriptome, 03 medical and health sciences, Xanthomonas, Bacterial Proteins, Xylem, Gene, 030304 developmental biology, 0303 health sciences, Ecology, biology, Virulence, 030306 microbiology, Membrane Transport Proteins, food and beverages, Brassicaceae, Gene Expression Regulation, Bacterial, transcriptomic, biology.organism_classification, Phenotype, motility, metabolism
Abstract: Xylem sap (XS) is the first environment that xylem phytopathogens meet in planta during the early infection steps. Xanthomonas campestris pv. campestris (Xcc), the causative agent of Brassicaceae black rot, colonizes the plant xylem vessels to ensure its multiplication and dissemination. Besides suppression of plant immunity, Xcc has to adapt its metabolism to exploit plant-derived nutrients present in XS. To study Xcc behaviour in the early infection steps, we used cabbage XS to analyse bacterial growth. Mineral and organic composition of XS were determined. Significant growth of Xcc in XS was allowed by the rapid catabolism of amino acids, sugars and organic acids, and it was accompanied by the formation of biofilm-like structures. Transcriptome analysis of Xcc cultivated in XS using cDNA microarrays revealed a XS-specific transcriptional reprogramming compared to minimal or rich media. More specifically, up-regulation of genes encoding transporters such as TonB-dependent transporters (TBDTs), that could be associated with nutrient acquisition and detoxification, was observed. In agreement with the aggregation phenotype, expression of genes important for twitching motility and adhesion was up-regulated in XS. Taken together, our data show specific responses of Xcc to colonization of cabbage XS that could be important for the pathogenesis process and establish XS as a model medium to study mechanisms important for the early infection events.
Published: 2014

15. Muscle transcriptomic investigation of late fetal development identifies candidate genes for piglet maturity

Author: Laurianne Canario, Valentin Voillet, Christine Lascor, Yannick Lippi, Florence Vignoles, Magali SanCristobal, Pascal G.P. Martin, Nathalie Iannuccelli, Laurence Liaubet, Yvon Billon, 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, Transcriptomic impact of Xenobiotics (E23 TRiX), 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), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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-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), Génétique, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), 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), 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 de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: pig, Candidate gene, Microarray, Genotype, muscle, [SDV]Life Sciences [q-bio], Biology, Breeding, Muscle Development, Real-Time Polymerase Chain Reaction, survival, Transcriptome, Fetal Development, birth, Pregnancy, Genetics, Animals, Gene Regulatory Networks, [INFO]Computer Science [cs], Muscle, Skeletal, Gene, Genetic Association Studies, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, Principal Component Analysis, Genome, Microarray analysis techniques, Gene Expression Profiling, system biology, Gene Expression Regulation, Developmental, Reproducibility of Results, Phenotype, Gene expression profiling, Gene Ontology, Female, Genomic imprinting, Systems biology, maturity, microarray, Biotechnology, Research Article
Abstract: Background In pigs, the perinatal period is the most critical time for survival. Piglet maturation, which occurs at the end of gestation, leads to a state of full development after birth. Therefore, maturity is an important determinant of early survival. Skeletal muscle plays a key role in adaptation to extra-uterine life, e.g. glycogen storage and thermoregulation. In this study, we performed microarray analysis to identify the genes and biological processes involved in piglet muscle maturity. Progeny from two breeds with extreme muscle maturity phenotypes were analyzed at two time points during gestation (gestational days 90 and 110). The Large White (LW) breed is a selected breed with an increased rate of mortality at birth, whereas the Meishan (MS) breed produces piglets with extremely low mortality at birth. The impact of the parental genome was analyzed with reciprocal crossed fetuses. Results Microarray analysis identified 12,326 differentially expressed probes for gestational age and genotype. Such a high number reflects an important transcriptomic change that occurs between 90 and 110 days of gestation. 2,000 probes, corresponding to 1,120 unique annotated genes, involved more particularly in the maturation process were further studied. Functional enrichment and graph inference studies underlined genes involved in muscular development around 90 days of gestation, and genes involved in metabolic functions, such as gluconeogenesis, around 110 days of gestation. Moreover, a difference in the expression of key genes, e.g. PCK2, LDHA or PGK1, was detected between MS and LW just before birth. Reciprocal crossing analysis resulted in the identification of 472 genes with an expression preferentially regulated by one parental genome. Most of these genes (366) were regulated by the paternal genome. Among these paternally regulated genes, some known imprinted genes, such as MAGEL2 or IGF2, were identified and could have a key role in the maturation process. Conclusion These results reveal the biological mechanisms that regulate muscle maturity in piglets. Maturity is also under the conflicting regulation of the parental genomes. Crucial genes, which could explain the biological differences in maturity observed between LW and MS breeds, were identified. These genes could be excellent candidates for a key role in the maturity. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-797) contains supplementary material, which is available to authorized users.
Published: 2014

16. Error tolerant parent identification from a finite set of individuals

Author: Claude Chevalet and Magali SanCristobal
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Population, Bayesian probability, Sampling (statistics), Value (computer science), Word error rate, General Medicine, 010603 evolutionary biology, 01 natural sciences, Set (abstract data type), 03 medical and health sciences, Identification (information), Statistics, Genetics, education, Finite set, 030304 developmental biology, Mathematics
Abstract: We consider using microsatellites for paternity checking and parent identification in different population structures, and allowing for possible typing errors or mutations. Statistical rules derived from the Bayesian and the sampling approaches are discussed in the case involving the choice of the true father–mother pair among a finite set of possible parental pairs. General situations are investigated by means of random simulations, in order to characterize the joint influences of the number and polymorphism of typed loci, the population structure and size, and error rates. Approximate expressions are provided that give the efficiency of a set of markers for identifying the parents in various mating schemes. The importance of a non-zero value for the typing error rate in the likelihood is highlighted.
Published: 1997

17. Detecting signatures of selection through haplotype differentiation among hierarchically structured populations

Author: Hugo Naya, Magali SanCristobal, Simon Boitard, Bertrand Servin, María Inés Fariello, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Universidad de la República [Montevideo] (UCUR), Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, haplotype, sheep, Linkage disequilibrium, Population, Population genetics, Context (language use), genome scan, Investigations, Biology, Polymorphism, Single Nucleotide, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, statistical genetic, Gene Frequency, Genetics, Animals, Computer Simulation, Selection, Genetic, education, Allele frequency, Sheep, Domestic, Selection (genetic algorithm), Statistic, 030304 developmental biology, population genetic, 0303 health sciences, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Models, Genetic, Haplotype, rningselective sweep, structured population, Genetics, Population, Haplotypes, Genetic Loci, Animal Migration, fst, linkage disequilibrium, Animals, Inbred Strains
Abstract: The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations and to look for genomic regions with outstanding genetic differentiation between these populations. Genetic differentiation is generally based on allele frequency differences between populations, which are measured by FST or related statistics. Here we introduce a new statistic, denoted hapFLK, which focuses instead on the differences of haplotype frequencies between populations. In contrast to most existing statistics, hapFLK accounts for the hierarchical structure of the sampled populations. Using computer simulations, we show that each of these two features—the use of haplotype information and of the hierarchical structure of populations—significantly improves the detection power of selected loci and that combining them in the hapFLK statistic provides even greater power. We also show that hapFLK is robust with respect to bottlenecks and migration and improves over existing approaches in many situations. Finally, we apply hapFLK to a set of six sheep breeds from Northern Europe and identify seven regions under selection, which include already reported regions but also several new ones. We propose a method to help identifying the population(s) under selection in a detected region, which reveals that in many of these regions selection most likely occurred in more than one population. Furthermore, several of the detected regions correspond to incomplete sweeps, where the favorable haplotype is only at intermediate frequency in the population(s) under selection.
Published: 2013

18. Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by Laser Capture Microdissection

Author: Patrice Martin, Gwenola Tosser-Klopp, Corinne Cotinot, Elena Terenina, Claudia Bevilacqua, Beatrice Mandon-Pepin, Francis Benne, Julien Sarry, Agnès Bonnet, Loys Bodin, Magali SanCristobal, Laurence Liaubet, 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 Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), Biologie du développement et reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), 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), and Bonnet, Agnes
Subjects: [SDV]Life Sciences [q-bio], Cell Separation, MESH: Animals, Newborn, Transcriptome, 0302 clinical medicine, folliculogenesis, Follicular phase, MESH: Animals, Laser capture microdissection, Oligonucleotide Array Sequence Analysis, 0303 health sciences, 030219 obstetrics & reproductive medicine, MESH: Real-Time Polymerase Chain Reaction, MESH: Laser Capture Microdissection, female reproductive function, Cell biology, MESH: Reproducibility of Results, MESH: Cattle, medicine.anatomical_structure, Female, Folliculogenesis, Research Article, Biotechnology, endocrine system, sheep, lcsh:QH426-470, lcsh:Biotechnology, Granulosa cell, MESH: Sheep, Laser Capture Microdissection, Biology, Real-Time Polymerase Chain Reaction, Follicular cell, MESH: Cell Separation, MESH: Oocytes, 03 medical and health sciences, MESH: Gene Expression Profiling, granulosa, MESH: RNA, lcsh:TP248.13-248.65, medicine, Genetics, Animals, 030304 developmental biology, Granulosa Cells, Microarray analysis techniques, Gene Expression Profiling, Reproducibility of Results, cell, MESH: Granulosa Cells, Oocyte, Molecular biology, lcsh:Genetics, Animals, Newborn, MESH: Oligonucleotide Array Sequence Analysis, Oocytes, RNA, Cattle, transcriptome, MESH: Female
Abstract: Background Successful achievement of early folliculogenesis is crucial for female reproductive function. The process is finely regulated by cell-cell interactions and by the coordinated expression of genes in both the oocyte and in granulosa cells. Despite many studies, little is known about the cell-specific gene expression driving early folliculogenesis. The very small size of these follicles and the mixture of types of follicles within the developing ovary make the experimental study of isolated follicular components very difficult. The recently developed laser capture microdissection (LCM) technique coupled with microarray experiments is a promising way to address the molecular profile of pure cell populations. However, one main challenge was to preserve the RNA quality during the isolation of single cells or groups of cells and also to obtain sufficient amounts of RNA. Using a new LCM method, we describe here the separate expression profiles of oocytes and follicular cells during the first stages of sheep folliculogenesis. Results We developed a new tissue fixation protocol ensuring efficient single cell capture and RNA integrity during the microdissection procedure. Enrichment in specific cell types was controlled by qRT-PCR analysis of known genes: six oocyte-specific genes (SOHLH2, MAEL, MATER, VASA, GDF9, BMP15) and three granulosa cell-specific genes (KL, GATA4, AMH). A global gene expression profile for each follicular compartment during early developmental stages was identified here for the first time, using a bovine Affymetrix chip. Most notably, the granulosa cell dataset is unique to date. The comparison of oocyte vs. follicular cell transcriptomes revealed 1050 transcripts specific to the granulosa cell and 759 specific to the oocyte. Functional analyses allowed the characterization of the three main cellular events involved in early folliculogenesis and confirmed the relevance and potential of LCM-derived RNA. Conclusions The ovary is a complex mixture of different cell types. Distinct cell populations need therefore to be analyzed for a better understanding of their potential interactions. LCM and microarray analysis allowed us to identify novel gene expression patterns in follicular cells at different stages and in oocyte populations.
Published: 2011

19. Genetic variability of transcript abundance in pig peri-mortem skeletal muscle: eQTL localized genes involved in stress response, cell death, muscle disorders and metabolism

Author: Laurence Liaubet, Pascale Le Roy, Valérie Lobjois, J. Glénisson, Thomas Faraut, Francis Benne, Magali SanCristobal, J. Pires, Nathalie Iannuccelli, Aurélie Tircazes, Annie Robic, Pierre Cherel, 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, Institut des Technologies Avancées en sciences du Vivant (ITAV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Centro de Investigação Operacional (CIO), Universidade de Lisboa (ULISBOA), Génétique Animale (GARen), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Ecole Nationale Supérieure Agronomique de Rennes-IFR140, France Hybride, Hendrix Genetics, 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)-Ecole Nationale Supérieure Agronomique de Rennes, This project received financial support from the French Ministry of Research in the framework of the PG ASG program. We thank the INRA Animal Genetics Department for post-doctoral financial help. The microarray annotation and the database with BASE software is managed by SIGENAE computer group (Systeme d'information du projet d'analyse des genomes des animaux d'elevage, http://www.sigenae.org) and especially Philippe Bardou for GEO submission. We thank Julien Thia-Ah-Fat (master student) for help and Daphne Goodfellow for the English revision. Our special thanks to Francis Hatey who initiated this project with Pierre Cherel., and Liaubet, Laurence
Subjects: Male, pig, MESH: Cell Death, Transcription, Genetic, Swine, muscle, [SDV]Life Sciences [q-bio], Adipose tissue, Inbred strain, Cluster Analysis, MESH: Animals, MESH: Genetic Variation, MESH: Stress, Physiological, MESH: Swine, Oligonucleotide Array Sequence Analysis, Genetics, Regulation of gene expression, 0303 health sciences, MESH: Muscle, Skeletal, Cell Death, system biology, cochon, Chromosome Mapping, muscle squelettique, systems biology, 04 agricultural and veterinary sciences, eqtl, MESH: Gene Expression Regulation, Phenotype, medicine.anatomical_structure, Female, Research Article, Biotechnology, biologie des systèmes, lcsh:QH426-470, lcsh:Biotechnology, Quantitative Trait Loci, MESH: Molecular Sequence Annotation, Muscle disorder, Biology, MESH: Phenotype, 03 medical and health sciences, genetical genomics, transcriptome, genetical genomic, Stress, Physiological, lcsh:TP248.13-248.65, Genetic variation, medicine, Animals, Genetic variability, Muscle, Skeletal, 030304 developmental biology, MESH: Transcription, Genetic, MESH: Transcriptome, 0402 animal and dairy science, Genetic Variation, Skeletal muscle, Molecular Sequence Annotation, 040201 dairy & animal science, MESH: Cluster Analysis, MESH: Quantitative Trait Loci, MESH: Male, lcsh:Genetics, Gene Expression Regulation, Expression quantitative trait loci, MESH: Oligonucleotide Array Sequence Analysis, MESH: Chromosome Mapping, MESH: Female
Abstract: Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access; International audience; BACKGROUND: The genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Genetical genomics studies have mainly focused on cell lines, blood cells or adipose tissues, from human clinical samples or mice inbred lines. Few eQTL studies have focused on animal tissues sampled from outbred populations to reflect natural genetic variation of gene expression levels in animals. In this work, we analyzed gene expression in a whole tissue, pig skeletal muscle sampled from individuals from a half sib F2 family shortly after slaughtering. RESULTS: QTL detection on transcriptome measurements was performed on a family structured population. The analysis identified 335 eQTLs affecting the expression of 272 transcripts. The ontologic annotation of these eQTLs revealed an over-representation of genes encoding proteins involved in processes that are expected to be induced during muscle development and metabolism, cell morphology, assembly and organization and also in stress response and apoptosis. A gene functional network approach was used to evidence existing biological relationships between all the genes whose expression levels are influenced by eQTLs. eQTLs localization revealed a significant clustered organization of about half the genes located on segments of chromosome 1, 2, 10, 13, 16, and 18. Finally, the combined expression and genetic approaches pointed to putative cis-drivers of gene expression programs in skeletal muscle as COQ4 (SSC1), LOC100513192 (SSC18) where both the gene transcription unit and the eQTL affecting its expression level were shown to be localized in the same genomic region. This suggests cis-causing genetic polymorphims affecting gene expression levels, with (e.g. COQ4) or without (e.g. LOC100513192) potential pleiotropic effects that affect the expression of other genes (cluster of trans-eQTLs). CONCLUSION: Genetic analysis of transcription levels revealed dependence among molecular phenotypes as being affected by variation at the same loci. We observed the genetic variation of molecular phenotypes in a specific situation of cellular stress thus contributing to a better description of muscle physiologic response. In turn, this suggests that large amounts of genetic variation, mediated through transcriptional networks, can drive transient cell response phenotypes and contribute to organismal adaptative potential.
Published: 2011

20. Diversité et biologie intégrative : des pistes à explorer pour combler le gap entre diversité génétique et diversité phénotypique

Author: Magali Sancristobal, Simon Boitard, Marcel Bouffaud, Cecile Canlet, Leonor Chaltiel, Claude Chevalet, Patrice Dehais, Marine Dumont, Maria Inès Fariello Rico, Hélène Gilbert, Ivo Gut, Nathalie Iannuccelli, Christophe Klopp, Béatrice Laurent, Zhilei Li, Laurence Liaubet, Marie-Jose Mercat, Denis Milan, Jerome Molina, Nelly Muller, Alain Paris, Juliette Riquet, Claire Gaillard, Florian Rohart, Marie Pierre Sanchez, Maria-Del-Pilar Schneider, Bertrand Servin, Agnès Solomiac, Laurence Souchu, Thierry Tribout, Nathalie Villa-Vialaneix, Diana Zelenica, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité Expérimentale de Testage de Porcs, Institut National de la Recherche Agronomique (INRA), 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), Biodiversité, Gènes et Communautés, Unité de Biométrie et Intelligence Artificielle (UBIA), Méthodologies d'Analyse de Risque Alimentaire (MET@RISK), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité expérimentale de testage de porcs, Analyse de Xénobiotiques, Identification, Métabolisme (E20 Metatoul-AXIOM), 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), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-MetaToul-MetaboHUB, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-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), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), 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), 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 de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, diversité génétique, biologie intégrative, diversité animale, diversité phénotypique
Abstract: absent
Published: 2011

21. Detecting selection in population trees: the Lewontin and Krakauer test extended

Author: Sarah C. Blott, Simon Boitard, Bertrand Servin, Magali SanCristobal, Jihad Abdallah, Maxime Bonhomme, Claude Chevalet, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Animal Health Trust (AHT)
Subjects: 0106 biological sciences, Genetic Markers, Swine, [SDV]Life Sciences [q-bio], MESH: Selection, Genetic, Population, MESH: Genetics, Population, Biology, Investigations, MESH: Genetic Markers, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, Evolution, Molecular, 03 medical and health sciences, symbols.namesake, Genetic drift, Genetics, Animals, MESH: Animals, MESH: Models, Genetic, Selection, Genetic, education, MESH: Genetic Drift, MESH: Phylogeny, MESH: Swine, Statistic, Phylogeny, MESH: Evolution, Molecular, 030304 developmental biology, Parametric statistics, 0303 health sciences, education.field_of_study, [STAT.AP]Statistics [stat]/Applications [stat.AP], [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Models, Genetic, MESH: Polymorphism, Single Nucleotide, Genetic Drift, Markov chain Monte Carlo, Empirical distribution function, Genetics, Population, Outlier, symbols, False positive rate
Abstract: Detecting genetic signatures of selection is of great interest for many research issues. Common approaches to separate selective from neutral processes focus on the variance of FST across loci, as does the original Lewontin and Krakauer (LK) test. Modern developments aim to minimize the false positive rate and to increase the power, by accounting for complex demographic structures. Another stimulating goal is to develop straightforward parametric and computationally tractable tests to deal with massive SNP data sets. Here, we propose an extension of the original LK statistic (TLK), named TF–LK, that uses a phylogenetic estimation of the population's kinship (\documentclass[10pt]{article} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{pmc} \usepackage[Euler]{upgreek} \pagestyle{empty} \oddsidemargin -1.0in \begin{document} \begin{equation*}{\mathrm{{\mathscr{F}}}}\end{equation*}\end{document}) matrix, thus accounting for historical branching and heterogeneity of genetic drift. Using forward simulations of single-nucleotide polymorphisms (SNPs) data under neutrality and selection, we confirm the relative robustness of the LK statistic (TLK) to complex demographic history but we show that TF–LK is more powerful in most cases. This new statistic outperforms also a multinomial-Dirichlet-based model [estimation with Markov chain Monte Carlo (MCMC)], when historical branching occurs. Overall, TF–LK detects 15–35% more selected SNPs than TLK for low type I errors (P < 0.001). Also, simulations show that TLK and TF–LK follow a chi-square distribution provided the ancestral allele frequencies are not too extreme, suggesting the possible use of the chi-square distribution for evaluating significance. The empirical distribution of TF–LK can be derived using simulations conditioned on the estimated \documentclass[10pt]{article} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{pmc} \usepackage[Euler]{upgreek} \pagestyle{empty} \oddsidemargin -1.0in \begin{document} \begin{equation*}{\mathrm{{\mathscr{F}}}}\end{equation*}\end{document} matrix. We apply this new test to pig breeds SNP data and pinpoint outliers using TF–LK, otherwise undetected using the less powerful TLK statistic. This new test represents one solution for compromise between advanced SNP genetic data acquisition and outlier analyses.
Published: 2010

22. Pathway results from the chicken data set using GOTM, Pathway studio and ingenuity softwares

Author: Agnès Bonnet, Gwenola Tosser-Klopp, Magali SanCristobal, Laurence Liaubet, Sandrine Lagarrigue, Christèle Robert-Granié, 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 Animale (GARen), 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)-Ecole Nationale Supérieure Agronomique de Rennes, Station d'Amélioration Génétique des Animaux (SAGA), 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), IFR140-Ecole Nationale Supérieure Agronomique de Rennes-AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), and Tosser-Klopp, Gwenola
Subjects: Computer science, media_common.quotation_subject, INGENUITY, Computational biology, Bioinformatics, General Biochemistry, Genetics and Molecular Biology, Set (abstract data type), 03 medical and health sciences, Annotation, 0302 clinical medicine, Ingenuity, GOTM, Differential expression, gotm, pathway studio, ingenuity, software, gene, 030304 developmental biology, media_common, 0303 health sciences, Gene ontology, Microarray analysis techniques, PATHWAY STUDIO, Research, General Medicine, GENE, Data set, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030220 oncology & carcinogenesis, SOFTWARES, Gene list
Abstract: Background As presented in the introduction paper, three sets of differentially regulated genes were found after the analysis of the chicken infection data set from EADGENE. Different methods were used to interpret these results. Results GOTM, Pathway Studio and Ingenuity softwares were used to investigate the three lists of genes. The three softwares allowed the analysis of the data and highlighted different networks. However, only one set of genes, showing a differential expression between primary and secondary response gave significant biological interpretation. Conclusion Combining these databases that were developed independently on different annotation sources supplies a useful tool for a global biological interpretation of microarray data, even if they may contain some imperfections (e.g. gene not or not well annotated).
Published: 2009

23. Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs

Author: Henrik Hornshøj, Vincent Jouffe, Suzanne Rowe, Bart Buitenhuis, Dirk-Jan de Koning, Pierre Mormède, Magali SanCristobal, Laurence Liaubet, Psychoneuroimmunologie, nutrition et génétique, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), The Roslin Institute, 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, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University [Aarhus], and EC-funded Network of Excellence EADGENE (EC contract number FOOD-CT-2004-506416)
Subjects: Candidate gene, hormone corticotrope, [SDV]Life Sciences [q-bio], [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Quantitative trait locus, Biology, CARTOGRAPHIE GENETIQUE, Genome, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, sus scrofa, Complementary DNA, Gene, 030304 developmental biology, Genetics, Whole genome sequencing, 0303 health sciences, Microarray analysis techniques, Research, qtl, 0402 animal and dairy science, food and beverages, 04 agricultural and veterinary sciences, General Medicine, corticotropine, 040201 dairy & animal science, puce à adn, gène candidat, genetic mapping, DNA microarray, porc, expression des gènes
Abstract: Background: Microarray studies can supplement QTL studies by suggesting potential candidate. Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH)Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH) Results: Different approaches to localize the differentially expressed (DE) genes to the pig genome. Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also, differentially expressed genes underlying QTL for ACTH response were described. Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. A further step to explore links between DE genes and QTL at the pathway level was largely unsuccessful due to the lack of annotation of the pig genome. This could be improved by further comparative mapping analyses but this would be time consuming Background: Microarray studies can supplement QTL studies by suggesting potential candidate. Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH)Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH) Results: Different approaches to localize the differentially expressed (DE) genes to the pig genome. Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also, differentially expressed genes underlying QTL for ACTH response were described. Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. A further step to explore links between DE genes and QTL at the pathway level was largely unsuccessful due to the lack of annotation of the pig genome. This could be improved by further comparative mapping analyses but this would be time consuming
Published: 2009

24. Predicting qualitative phenotypes from microarray data - the Eadgene pig data set

Author: Christèle Robert-Granié, Kim-Anh Lê Cao, Magali SanCristobal, Station d'Amélioration Génétique des Animaux (SAGA), 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, and San Cristobal, Magali
Subjects: pig, Multivariate statistics, [SDV]Life Sciences [q-bio], Machine learning, computer.software_genre, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Set (abstract data type), 010104 statistics & probability, 03 medical and health sciences, Lasso (statistics), Partial least squares regression, Medicine, 0101 mathematics, Selection (genetic algorithm), 030304 developmental biology, Interpretability, sparse pls, 0303 health sciences, business.industry, Research, General Medicine, eadgene, pls, random forest, microarray, Random forest, Data set, Artificial intelligence, Data mining, business, computer
Abstract: Background The aim of this work was to study the performances of 2 predictive statistical tools on a data set that was given to all participants of the Eadgene-SABRE Post Analyses Working Group, namely the Pig data set of Hazard et al. (2008). The data consisted of 3686 gene expressions measured on 24 animals partitioned in 2 genotypes and 2 treatments. The objective was to find biomarkers that characterized the genotypes and the treatments in the whole set of genes. Methods We first considered the Random Forest approach that enables the selection of predictive variables. We then compared the classical Partial Least Squares regression (PLS) with a novel approach called sparse PLS, a variant of PLS that adapts lasso penalization and allows for the selection of a subset of variables. Results All methods performed well on this data set. The sparse PLS outperformed the PLS in terms of prediction performance and improved the interpretability of the results. Conclusion We recommend the use of machine learning methods such as Random Forest and multivariate methods such as sparse PLS for prediction purposes. Both approaches are well adapted to transcriptomic data where the number of features is much greater than the number of individuals.
Published: 2009

25. What do artificial neural networks tell us about the genetic structure of populations? The example of European pig populations

Author: Sovan Lek, Natacha Nikolic, Claude Chevalet, Magali SanCristobal, Young-Seuk Park, 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, Kyung Hee University (KHU), Institut de Planétologie et d'Astrophysique de Grenoble (IPAG ), Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), and Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, pig, China, Genetic Structures, neural network, [SDV]Life Sciences [q-bio], Sus scrofa, Population genetics, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Species Specificity, Genetic model, Genetic variation, Genetics, Animals, Cluster Analysis, Phylogeny, 030304 developmental biology, 0303 health sciences, Genetic diversity, Genetic Variation, General Medicine, genetic diversity, Hierarchical clustering, Europe, Genetics, Population, Genetic distance, Evolutionary biology, Multivariate Analysis, Genetic structure, Ordination, Neural Networks, Computer
Abstract: SummaryGeneral and genetic statistical methods are commonly used to deal with microsatellite data (highly variable neutral genetic markers). In this paper, the self-organizing map (SOM) that belongs to the unsupervised artificial neural networks (ANNs) was applied to analyse the structure of 58 European and two Chinese pig populations (Sus scrofa) including commercial lines, local breeds and cosmopolitan breeds. Results were compared with other unsupervised classification or ordination methods such as factorial correspondence analysis, hierarchical clustering from an allele sharing distance and the Bayesian genetic model and with principal components analysis and neighbour joining from allelic frequencies and genetic distances between populations. Like other methods, SOMs were able to classify individuals according to their breed origin and to visualize similarities between breeds. They provided additional information on the within- and between-population diversity, allowed differences between similar populations to be highlighted and helped differentiate different groups of populations.
Published: 2009

26. Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

Author: Henrik Hornshøj, Johanna M.J. Rebel, Jan J. van der Poel, Axel Skarman, Arun Kommadath, Jack A. M. Leunissen, Jakob Hedegaard, Ángeles Jiménez-Marín, Magali SanCristobal, M. Ramírez-Boo, Dennis Prickett, Melania Collado-Romero, Bart Buitenhuis, Lene N Conley, Michael Watson, Laurence Liaubet, Martien A. M. Groenen, Juan J. Garrido, Mari A. Smits, Li Jiang, Agnès Bonnet, Peter Sørensen, Gwenola Tosser-Klopp, Pieter B T Neerincx, Christèle Robert-Granié, Ina Hulsegge, Cristina Arce, Sandrine Lagarrigue, Silvio Bicciato, Francesco Ferrari, Haisheng Nie, Hedegaard, Jakob, Aarhus University [Aarhus], Universidad de Córdoba [Cordoba], Università degli Studi di Modena e Reggio Emilia (UNIMORE), 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, Department of Biology, Universita degli Studi di Padova, Animal Breeding and Genomics Center, Wageningen University and Research [Wageningen] (WUR), Génétique Animale (GARen), 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)-Ecole Nationale Supérieure Agronomique de Rennes, Wageningen University and Research Centre (WUR), Institute for Animal Health, Central Veterinary Institute, Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), and IFR140-Ecole Nationale Supérieure Agronomique de Rennes-AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
Subjects: Microarray, media_common.quotation_subject, chicken, [SDV]Life Sciences [q-bio], lcsh:Medicine, Genomics, Computational biology, Biology, dna, Genome, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Ingenuity, genomics, lcsh:Science, Gene, genome, 030304 developmental biology, Statistical hypothesis testing, media_common, 2. Zero hunger, Genetics, 0303 health sciences, Microarray analysis techniques, Research, lcsh:R, microarray, method, bioinformatics, General Medicine, GENONE, Data set, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, METHODS, lcsh:Q, CHIKEN, 030217 neurology & neurosurgery
Abstract: From EADGENE and SABRE Post-analyses Workshop Lelystad, The Netherlands. 12–14 November 2008 Background: The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. Results: Several conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached. Conclusion: It is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experiment.
Published: 2009

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

Author: Maiena Borthaire, Françoise Médale, Diane Esquerre, Catherine-Ines Kolditz, Magali SanCristobal, Gilles Paboeuf, Florence Lefèvre, Nutrition, Aquaculture et Génomique (NUAGE), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA), 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), 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, Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)-Université de Toulouse (UT)
Subjects: Proteome, muscle, [SDV]Life Sciences [q-bio], Adipose tissue, Transcriptome, 0302 clinical medicine, poisson, protéome, énergie, salmonidae, 2. Zero hunger, oncorhynchus mykiss, 0303 health sciences, Muscles, Intracellular lipid transport, Adipose Tissue, Liver, Biochemistry, Lipogenesis, Research Article, Biotechnology, medicine.medical_specialty, lcsh:QH426-470, Intra-Abdominal Fat, métabolisme énergétique, lcsh:Biotechnology, Biology, 03 medical and health sciences, lcsh:TP248.13-248.65, Internal medicine, Genetics, medicine, Animals, [INFO]Computer Science [cs], nutrition animale, lipide, 030304 developmental biology, Catabolism, Gene Expression Profiling, Lipid metabolism, Metabolism, Diet, lcsh:Genetics, Endocrinology, Energy Intake, transcriptome, 030217 neurology & neurosurgery, truite arc en ciel
Abstract: Background Growing interest is turned to fat storage levels and allocation within body compartments, due to their impact on human health and quality properties of farm animals. Energy intake and genetic background are major determinants of fattening in most animals, including humans. Previous studies have evidenced that fat deposition depends upon balance between various metabolic pathways. Using divergent selection, we obtained rainbow trout with differences in fat allocation between visceral adipose tissue and muscle, and no change in overall body fat content. Transcriptome and proteome analysis were applied to characterize the molecular changes occurring between these two lines when fed a low or a high energy diet. We focused on the liver, center of intermediary metabolism and the main site for lipogenesis in fish, as in humans and most avian species. Results The proteome and transcriptome analyses provided concordant results. The main changes induced by the dietary treatment were observed in lipid metabolism. The level of transcripts and proteins involved in intracellular lipid transport, fatty acid biosynthesis and anti-oxidant metabolism were lower with the lipid rich diet. In addition, genes and proteins involved in amino-acid catabolism and proteolysis were also under expressed with this diet. The major changes related to the selection effect were observed in levels of transcripts and proteins involved in amino-acid catabolism and proteolysis that were higher in the fat muscle line than in the lean muscle line. Conclusion The present study led to the identification of novel genes and proteins that responded to long term feeding with a high energy/high fat diet. Although muscle was the direct target, the selection procedure applied significantly affected hepatic metabolism, particularly protein and amino acid derivative metabolism. Interestingly, the selection procedure and the dietary treatment used to increase muscle fat content exerted opposite effects on the expression of the liver genes and proteins, with little interaction between the two factors. Some of the molecules we identified could be used as markers to prevent excess muscle fat accumulation.
Published: 2008

28. In vivo gene expression in granulosa cells during pig terminal follicular development

Author: Christèle Robert-Granié, Stéphane Fabre, François Hatey, Gwenola Tosser-Klopp, H Quesnel, K.A. Lê Cao, Agnès Bonnet, Magali SanCristobal, Francis Benne, E De Billy, G Law-So, Philippe Besse, Institut de Mathématiques de Toulouse UMR5219 (IMT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut de recherche en astrophysique et planétologie (IRAP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), 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, Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), Systèmes d'élevage, nutrition animale et humaine (SENAH), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), and ProdInra, Migration
Subjects: Embryology, FOLLICULAR DEVELOPMENT, PIG, GRANULOSA CELLS, TRANSCRIPTOMIC ANALYSIS, BIOLOGICAL NETWORK, Swine, [SDV]Life Sciences [q-bio], Cell morphology, 0302 clinical medicine, Endocrinology, Ovarian Follicle, MESH: Reverse Transcriptase Polymerase Chain Reaction, Follicular phase, Gene expression, Biologie de la reproduction, MESH: Animals, MESH: Swine, In Situ Hybridization, ComputingMilieux_MISCELLANEOUS, Glutathione Transferase, Oligonucleotide Array Sequence Analysis, MESH: Lipid Metabolism, Regulation of gene expression, 0303 health sciences, Differential display, Reproductive Biology, [STAT.AP]Statistics [stat]/Applications [stat.AP], 030219 obstetrics & reproductive medicine, Reverse Transcriptase Polymerase Chain Reaction, Obstetrics and Gynecology, MESH: Ribosomal Proteins, Lipids, MESH: Gene Expression Regulation, [SDV] Life Sciences [q-bio], medicine.anatomical_structure, Data Interpretation, Statistical, expression de gènes, Female, Ribosomal Proteins, endocrine system, Biology, [INFO] Computer Science [cs], [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, reproduction, 03 medical and health sciences, MESH: Gene Expression Profiling, MESH: In Situ Hybridization, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Animals, [INFO]Computer Science [cs], RNA, Messenger, Ovarian follicle, 030304 developmental biology, MESH: RNA, Messenger, MESH: Glutathione Transferase, Gene Expression Profiling, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, MESH: Granulosa Cells, Lipid Metabolism, Molecular biology, MESH: Lipids, MESH: Ovarian Follicle, Gene expression profiling, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Reproductive Medicine, Gene Expression Regulation, Suppression subtractive hybridization, MESH: Oligonucleotide Array Sequence Analysis, gene expression, MESH: Data Interpretation, Statistical, MESH: Female
Abstract: Ovarian antral follicular development is clearly dependent on pituitary gonadotrophins FSH and LH. Although the endocrine mechanism that controls ovarian folliculogenesis leading to ovulation is quite well understood, the detailed mechanisms and molecular determinants in the different follicular compartments remain to be clarified. The aim of this study was to identify the genes differentially expressed in pig granulosa cells along the terminal ovarian follicle growth, to gain a comprehensive view of these molecular mechanisms. First, we developed a specific micro-array using cDNAs from suppression subtractive hybridization libraries (345 contigs) obtained by comparison of three follicle size classes: small, medium and large antral healthy follicles. In a second step, a transcriptomic analysis using cDNA probes from these three follicle classes identified 79 differentially expressed transcripts along the terminal follicular growth and 26 predictive genes of size classes. The differential expression of 18 genes has been controlled using real-time PCR experiments validating the micro-array analysis. Finally, the integration of the data using Ingenuity Pathways Analysis identified five gene networks providing descriptive elements of the terminal follicular development. Specifically, we observed: (1) the down-expression of ribosomal protein genes, (2) the genes involved in lipid metabolism and (3) the down-expression of cell morphology and ion-binding genes. In conclusion, this study gives new insight into the gene expression during pig terminal follicular growthin vivoand suggested, in particular, a morphological change in pig granulosa cells accompanying terminal follicular growth.
Published: 2008

29. Gene array and real time PCR analysis of the adrenal sensitivity to adrenocorticotropic hormone in pig

Author: Pierre Mormède, Laurence Liaubet, Magali SanCristobal, Dominique Hazard, Tissus animaux, nutrition, digestion, écosystème et métabolisme (TANDEM), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT], Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Psychoneuroimmunologie, nutrition et génétique, and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, Hydrocortisone, Transcription, Genetic, Microarray, Swine, variabilité génétique, SDHA, Gene Expression, structure cellulaire, 0302 clinical medicine, AXE HPA, Adrenal Glands, Gene expression, glande surrénale, Oligonucleotide Array Sequence Analysis, 0303 health sciences, Reverse Transcriptase Polymerase Chain Reaction, cholestérol, Genomics, obésité, protéine, puce à adn, gène candidat, Signal transduction, génotype, hormones, hormone substitutes, and hormone antagonists, Research Article, medicine.drug, expression des gènes, Biotechnology, medicine.medical_specialty, CORTISOL, endocrine system, Genotype, lcsh:QH426-470, kinase, lcsh:Biotechnology, hormone, Radioimmunoassay, 030209 endocrinology & metabolism, Adrenocorticotropic hormone, Biology, 03 medical and health sciences, Adrenocorticotropic Hormone, pcr, sus scrofa, Internal medicine, lcsh:TP248.13-248.65, medicine, Genetics, Animals, Protein kinase A, Gene, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, lcsh:Genetics, enzyme, Endocrinology, porc
Abstract: Background Variability in hypothalamic-pituitary-adrenal (HPA) axis activity has been shown to be influenced by genetic factors and related to great metabolic differences such as obesity. The aim of this study was to investigate molecular bases of genetic variability of the adrenal sensitivity to ACTH, a major source of variability, in Meishan (MS) and Large White (LW) pigs, MS being reported to exhibit higher basal cortisol levels, response to ACTH and fatness than LW. A pig cDNA microarray was used to identify changes in gene expression in basal conditions and in response to ACTH stimulation. Results Genotype and/or ACTH affected the expression of 211 genes related to transcription, cell growth/maintenance, signal transduction, cell structure/adhesion/extra cellular matrix and protein kinase/phosphatase activity. No change in the expression of known key regulator proteins of the ACTH signaling pathway or of steroidogenic enzymes was found. However, Mdh2, Sdha, Suclg2, genes involved in the tricarboxylic acid (TCA) pathway, were over-expressed in MS pigs. Higher TCA cycle activity in MS than in LW may thus result in higher steroidogenic activity and thus explain the typically higher cortisol levels in MS compared to LW. Moreover, up-regulation of Star and Ldlr genes in MS and/or in response to ACTH suggest that differences in the adrenal function between MS and LW may also involve mechanisms requisite for cholesterol supply to steroidogenesis. Conclusion The present study provides new potential candidate genes to explain genetic variations in the adrenal sensitivity to ACTH and better understand relationship between HPA axis activity and obesity.
Published: 2008

30. Results of four generations of a canalising selection for rabbit birth weight

Author: G. Bolet, Hervé Garreau, Catherine Larzul, G. Saleil, Magali SanCristobal, Loys Bodin, Christèle Robert-Granié, Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), Station de Génétique Quantitative et Appliquée (SGQA), 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, and ProdInra, Migration
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Birth weight, DIVERGENT SELECTION, Biology, CANALISING SELECTION, Standard deviation, 03 medical and health sciences, Animal science, RABBIT, Weaning, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, 0303 health sciences, General Veterinary, business.industry, Significant difference, 0402 animal and dairy science, ENVIRONMENTAL VARIANCE, 04 agricultural and veterinary sciences, 040201 dairy & animal science, Biotechnology, BIRTH WEIGHT, Homogeneous, Animal Science and Zoology, business
Abstract: A divergent selection experiment based on the homogeneity of birth weight in rabbit was carried out at the INRA experimental farm of Auzeville. The two lines were created by selecting breeding does and bucks from the female strain AGP22 bred at the Grimaud Freres Selection company for environmental variability of birth weight. This involved a new model incorporating a genotypic value for the mean and a genotypic value for the environmental variance. There was a selection response with a significant difference in the within-litter standard deviation of birth weight between the lines after four generations of selection (6.93 g vs. 8.13 g). The mortality of kits at birth and from birth to weaning was lower in the “homogeneous” line than in the “heterogeneous” line (16.6% vs. 18.6% and 17.7% vs. 32.7%, respectively). The litter size at weaning was higher in the “homogeneous” line (7.22 vs. 5.39). The selection on the homogeneity of birth weight had no significant influence on the other traits. It was concluded that selection for reduced environmental variance of birth weight improved young rabbit survival without reducing the mean of birth weight.
Published: 2008

31. A pilot study on transcriptome data analysis of folliculogenesis in pigs

Author: François Hatey, N. Gobert, Sébastien Déjean, Gwenola Tosser-Klopp, J. Antic, Agnès Bonnet, K.A. Lê Cao, L. Baschet, Christèle Robert-Granié, Magali SanCristobal, 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), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Tosser-Klopp, Gwenola
Subjects: pig, Candidate gene, Microarray, microarray, folliculogenesis, statistical data analysis, Computational biology, Biology, SF1-1100, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, 030219 obstetrics & reproductive medicine, Science des productions animales, Antral follicle, Hierarchical clustering, Animal culture, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, Principal component analysis, Animal Science and Zoology, Folliculogenesis, DNA microarray, Animal production studies
Abstract: International audience; Three different stages of pig antral follicles have been studied in a granulosa-cell transcriptome analysis on nylon microarrays (1152 clones). The data have been generated from seven RNA follicle pools and several technical replicates were made. The objective of this paper was to state the feasibility of a transcriptomic protocol for the study of folliculogenesis in the pig. A statistical analysis was chosen, relying on the linear mixed model (LMM) paradigm. Low variability within technical replicates was hence checked with a LMM. Relevant genes that might be involved in the studied process were then selected. For the most significant genes, statistical methods such as principal component analysis and unsupervised hierarchical clustering were applied to assess their relevance, and a random forest analysis proved their predictive value. The selection of genes was consistent with previous studies and also allowed the identification of new genes whose role in pig folliculogenesis will be further investigated.
Published: 2008

32. Novel aspects of PPARα-mediated regulation of lipid and xenobiotic metabolism revealed through a nutrigenomic study

Author: Pascal G.P. Martin, Sébastien Déjean, Thierry Pineau, Philippe Besse, Hervé Guillou, Jean-Marc Pascussi, Frédéric Lasserre, Philippe Legrand, Annaïg Lan, Magali SanCristobal, Laboratoire de Pharmacologie et Toxicologie, Institut National de la Recherche Agronomique (INRA), Laboratoire de biochimie, Institut de Mathématiques de Toulouse UMR5219 (IMT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: Male, medicine.medical_specialty, Genotype, Diet therapy, [SDV]Life Sciences [q-bio], Mice, Transgenic, Biology, Dodecenoyl-CoA Isomerase, Linoleoyl-CoA Desaturase, Xenobiotics, Mice, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Internal medicine, medicine, Animals, PPAR alpha, Diet, Fat-Restricted, Triglycerides, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Hepatology, Triglyceride, Catabolism, Fatty liver, Lipid metabolism, Carbon-Carbon Double Bond Isomerases, Lipid Metabolism, medicine.disease, Fish oil, Fatty Liver, Mice, Inbred C57BL, Endocrinology, Gene Expression Regulation, Liver, chemistry, 030220 oncology & carcinogenesis, Fatty Acids, Unsaturated, Steatosis, Xenobiotic
Abstract: Peroxisome proliferator-activated receptor-alpha (PPARalpha) is a major transcriptional regulator of lipid metabolism. It is activated by diverse chemicals such as fatty acids (FAs) and regulates the expression of numerous genes in organs displaying high FA catabolic rates, including the liver. The role of this nuclear receptor as a sensor of whole dietary fat intake has been inferred, mostly from high-fat diet studies. To delineate its function under low fat intake conditions (4.8% w/w), we studied the effects of five regimens with contrasted FA compositions on liver lipids and hepatic gene expression in wild-type and PPARalpha-deficient mice. Diets containing polyunsaturated FAs reduced hepatic fat stores in wild-type mice. Only sunflower, linseed, and fish oil diets lowered hepatic lipid stores in PPARalpha-/- mice, a model of progressive hepatic triglyceride accumulation. These beneficial effects were associated, in particular, with dietary regulation of Delta9-desaturase in both genotypes, and with a newly identified PPARalpha-dependent regulation of lipin. Furthermore, hepatic levels of 18-carbon essential FAs (C18:2omega6 and C18:3omega3) were elevated in PPARalpha-/- mice, possibly due to the observed reduction in expression of the Delta6-desaturase and of enoyl-coenzyme A isomerases. Effects of diet and genotype were also observed on the xenobiotic metabolism-related genes Cyp3a11 and CAR.Together, our results suggest that dietary FAs represent--even under low fat intake conditions--a beneficial strategy to reduce hepatic steatosis. Under such conditions, we established the role of PPARalpha as a dietary FA sensor and highlighted its importance in regulating hepatic FA content and composition.
Published: 2007

33. Some prospects on the next 60 years in animal genetics

Author: Claude Chevalet, Christèle Robert-Granié, Magali SanCristobal, 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, Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: 0303 health sciences, Animal Genetics, Management science, PROSPECTIVES, GENETIQUE ANIMALE, [SDV]Life Sciences [q-bio], Short paper, review, Quantitative genetics, Biology, STATISTICS, Term (time), génomique, [SDV] Life Sciences [q-bio], genomic, 03 medical and health sciences, 0302 clinical medicine, PROSPECTS, Food Animals, Statistical genetics, Evolutionary biology, ANIMAL GENETICS, Animal Science and Zoology, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Prospecting in a given scientific area is a challenging and interesting exercise, even if predictions are always uncertain, especially in the long term. The objective of this short paper is to prop...
Published: 2007

34. Genetic diversity within and between European pig breeds using microsatellite markers

Author: K. Siggens, Claude Chevalet, Gustavo Gandini, R. Joosten, Magali SanCristobal, Alan Archibald, George C. Russell, M. Bagga, David J. Milan, Roberta Davoli, L. Alderson, Jose Luis Vega-Pla, Donato Matassino, E. Fimland, A.P. Rattink, Martien A. M. Groenen, P. Glodek, Juan Vicente Delgado, Graham Plastow, Chris Haley, K. Hammond, Andy Law, C. Désautés, Amparo Martínez Martínez, Guillaume Laval, Maria Ramos, J. N. Meyer, R. Cardellino, Y. Amigues, Barbara Harlizius, Vincenzo Russo, M.-Y. Boscher, San Cristobal M., Chevalet C., Haley C.S., Joosten R., Rattink A.P., Harlizius M., Groenen A.M., Amigues Y., Boscher M.-Y., Russell G., Law A., Davoli R., Russo V., Desautes C., Alderson L., Fimland E., Bagga M., Delgado J.V., Vega-Pla J.L., Martinez A.M., Ramos M., Glodek P., Meyer J.N., Gandini G.C., Matassino D., Plastow G.S., Siggens K.W., Laval G., A.L. Archibald, Milan D., Hammond K., Cardellino R., Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration
Subjects: Animal breeding, Swine, [SDV]Life Sciences [q-bio], statistische analyse, Population genetics, CLUSTERING, genetische merkers, rasverschillen, Breeding, microsatellites, genetische diversiteit, Gene Frequency, humans, biodiversity, Genetics, 0303 health sciences, genetic distance, pig breeds, conservation, pigs, dierveredeling, 04 agricultural and veterinary sciences, General Medicine, animal breeding, genetic diversity, wilde varkens, populatiegenetica, varkens, Breed, [SDV] Life Sciences [q-bio], Europe, allelen, GENETIC DISTANCE, alleles, loci, Microsatellite, Biodiversity, Clustering, Genetic distance, Microsatellites, Pig, Settore AGR/19 - Zootecnica Speciale, microsatellite, Genotype, microsatellieten, MICROSATELLITES, Zoology, wild pigs, Biology, Animal Breeding and Genomics, heterozygotie, 03 medical and health sciences, statistical analysis, varkensrassen, Genetic variation, evolution, Animals, heterozygosity, Fokkerij en Genomica, distance, 030304 developmental biology, Genetic diversity, PIG, 0402 animal and dairy science, biodiversiteit, Genetic Variation, population genetics, genetische afstand, populations, 040201 dairy & animal science, breed differences, Genetic marker, WIAS, genetic markers, Animal Science and Zoology, BIODIVERSITY, Microsatellite Repeats, conservering
Abstract: An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds, national varieties of international breeds and commercial lines. A sample of the Chinese Meishan breed was also included. Eleven additional breeds from a previous project were added for some analyses. Approximately 50 individuals per breed were genotyped for a maximum of 50 microsatellite loci. Substantial within-breed variability was observed, with the average expected heterozygosity and observed number of alleles per locus being 0.56 [range 0.43-0.68] and 4.5 respectively. Genotypic frequencies departed from Hardy-Weinberg expectations (P < 0.01) in 15 European populations, with an excess of homozygotes in 12 of them. The European breeds were on average genetically very distinct, with a Wright F(ST) index value of 0.21. The Neighbour-Joining tree drawn from the Reynolds distances among the breeds showed that the national varieties of major breeds and the commercial lines were mostly clustered around their breeds of reference (Duroc, Hampshire, Landrace, Large White and Pietrain). In contrast, local breeds, with the exception of the Iberian breeds, exhibited a star-like topology. The results are discussed in the light of various forces, which may have driven the recent evolution of European pig breeds. This study has consequences for the interpretation of biodiversity results and will be of importance for future conservation programmes.
Published: 2006

35. Evidence for genetic control of adult weight plasticity in the snail Helix aspersa

Author: Rasmus Waagepetersen, Daniel Sorensen, Mathilde Dupont-Nivet, Magali SanCristobal, Mathieu Ros, J. C. Bonnet, J. Mallard, Unité de recherche Génétique des Poissons (UGP), Institut National de la Recherche Agronomique (INRA), Danish Institute of Agricultural Sciences, Aalborg University [Denmark] (AAU), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Ecole Nationale Supérieure Agronomique de Rennes, and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, genetic control, controle genetique, Investigations, Biology, Genetic correlation, 03 medical and health sciences, Bayes' theorem, Genetic variation, snail, Genetics, Animals, helix aspersa, Selection (genetic algorithm), 030304 developmental biology, Likelihood Functions, 0303 health sciences, Phenotypic plasticity, Models, Genetic, Ecology, Helix, Snails, Body Weight, 0402 animal and dairy science, Genetic Variation, Bayes Theorem, 04 agricultural and veterinary sciences, Quantitative genetics, Variance (accounting), 040201 dairy & animal science, Markov Chains, adult weight, Deviance information criterion, Evolutionary biology, Monte Carlo Method
Abstract: Phenotypic plasticity and canalization are important topics in quantitative genetics and evolution. Both concepts are related to environmental sensitivity. The latter can be modeled using a model with genetically structured environmental variance. This work reports the results of a genetic analysis of adult weight in the snail Helix aspersa. Several models of heterogeneous variance are fitted using a Bayesin, MCMC approach. Exploratory analyses using posterior predictive model checking and model comparisons based on the deviance information criterion favor a model postulating a genetically structured heterogeneous environmental variance. Our analysis provides a strong indication of a positive genetic correlation between additive genetic values affecting the mean and those affecting environmental variation of adult body weight. The possibility of manipulating environmental variance by selection is illustrated numerically using estimates of parameters derived from the snail data set. Udgivelsesdato: DEC Phenotypic plasticity and canalization are important topics in quantitative genetics and evolution. Both concepts are related to environmental sensitivity. The latter can be modeled using a model with genetically structured environmental variance. This work reports the results of a genetic analysis of adult weight in the snail Helix aspersa. Several models of heterogeneous variance are fitted using a Bayesin, MCMC approach. Exploratory analyses using posterior predictive model checking and model comparisons based on the deviance information criterion favor a model postulating a genetically structured heterogeneous environmental variance. Our analysis provides a strong indication of a positive genetic correlation between additive genetic values affecting the mean and those affecting environmental variation of adult body weight. The possibility of manipulating environmental variance by selection is illustrated numerically using estimates of parameters derived from the snail data set.
Published: 2004

36. Measuring genetic distances between breeds: use of some distances in various short term evolution models

Author: Claude Chevalet, Guillaume Laval, Magali SanCristobal, 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: breeds, microsatellite, breed, lcsh:QH426-470, [SDV]Life Sciences [q-bio], Statistics as Topic, Breeding, Biology, microsatellites, divergence, mutation, genetic drift, Evolution, Molecular, distance génétique, 03 medical and health sciences, Gene Frequency, Genetic drift, dérivé génétique, Genetics, Genetics(clinical), Computer Simulation, Divergence (statistics), race, Phylogeny, Ecology, Evolution, Behavior and Systematics, lcsh:SF1-1100, 030304 developmental biology, 0303 health sciences, Genetic diversity, Models, Genetic, Research, 0402 animal and dairy science, Small population size, 04 agricultural and veterinary sciences, General Medicine, Function (mathematics), 040201 dairy & animal science, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, lcsh:Genetics, Genetics, Population, Genetic distance, Evolutionary biology, Mutation (genetic algorithm), Animal Science and Zoology, lcsh:Animal culture, Inbreeding, Microsatellite Repeats
Abstract: Many works demonstrate the benefits of using highly polymorphic markers such as microsatellites in order to measure the genetic diversity between closely related breeds. But it is sometimes difficult to decide which genetic distance should be used. In this paper we review the behaviour of the main distances encountered in the literature in various divergence models. In the first part, we consider that breeds are populations in which the assumption of equilibrium between drift and mutation is verified. In this case some interesting distances can be expressed as a function of divergence time, t, and therefore can be used to construct phylogenies. Distances based on allele size distribution (such as (δμ)2 and derived distances), taking a mutation model of microsatellites, the Stepwise Mutation Model, specifically into account, exhibit large variance and therefore should not be used to accurately infer phylogeny of closely related breeds. In the last section, we will consider that breeds are small populations and that the divergence times between them are too small to consider that the observed diversity is due to mutations: divergence is mainly due to genetic drift. Expectation and variance of distances were calculated as a function of the Wright-Malécot inbreeding coefficient, F. Computer simulations performed under this divergence model show that the Reynolds distance [57]is the best method for very closely related breeds.
Published: 2002

37. What is a good (gene) network?

Author: Nathalie Villa-Vialaneix, Laurence Liaubet, and Magali SanCristobal
Subjects: Food Animals, 05 social sciences, 0402 animal and dairy science, Gene regulatory network, MEDLINE, 0501 psychology and cognitive sciences, Animal Science and Zoology, 050102 behavioral science & comparative psychology, 04 agricultural and veterinary sciences, General Medicine, Computational biology, Biology, 040201 dairy & animal science
Published: 2011

38. Genetic components of litter size variability in sheep

Author: Magali SanCristobal-Gaudy, Jean-Michel Elsen, Claude Chevalet, Loys Bodin, 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, Station d'Amélioration Génétique des Animaux (SAGA), and Institut National de la Recherche Agronomique (INRA)
Subjects: Litter (animal), Litter Size, Twins, modèle, variance, ovin, Pregnancy, méthode statistique, Genetics(clinical), Gene–environment interaction, race, ComputingMilieux_MISCELLANEOUS, lcsh:SF1-1100, Genetics, 0303 health sciences, sélection génétique, taille de la portee, GENETIQUE ANIMALE, Data Collection, VARIABILITE, canalising selection, 04 agricultural and veterinary sciences, General Medicine, Breed, threshold trait, Female, Monte Carlo Method, sheep, lcsh:QH426-470, mouton, Biology, prolificite, 03 medical and health sciences, Animal science, Quantitative Trait, Heritable, Predictive Value of Tests, Genetic variation, Animals, Computer Simulation, Genetic variability, Selection, Genetic, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, FREQUENCE, [SDV.GEN]Life Sciences [q-bio]/Genetics, Models, Genetic, Research, Domestic sheep reproduction, 0402 animal and dairy science, Genetic Variation, Bayes Theorem, Quantitative genetics, Heritability, heterogeneous variances, 040201 dairy & animal science, portee, élevage, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, lcsh:Genetics, Animal Science and Zoology, lcsh:Animal culture, Mathematics
Abstract: International audience; Classical selection for increasing prolificacy in sheep leads to a concomitant increase in its variability, even though the objective of the breeder is to maximise the frequency of an intermediate litter size rather than the frequency of high litter sizes. For instance, in the Lacaune sheep breed raised in semi-intensive conditions, ewes lambing twins represent the economic optimum. Data for this breed, obtained from the national recording scheme, were analysed. Variance components were estimated in an infinitesimal model involving genes controlling the mean level as well as its environmental variability. Large heritability was found for the mean prolificacy, but a high potential for increasing the percentage of twins at lambing while reducing the environmental variability of prolificacy is also suspected. Quantification of the response to such a canalising selection was achieved.
Published: 2001

39. Genetics of reproduction in ruminants

Author: J. Teyssier, Eric Hanocq, M. M. Mialon, Jean-Louis Foulley, Philippe Chemineau, Eduardo Manfredi, Dominique François, J. Thimonier, Jean-Michel Elsen, Loys Bodin, Didier Boichard, D. Lajous, Magali SanCristobal-Gaudy, Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), Station de Génétique Quantitative et Appliquée (SGQA), 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, Institut francilien recherche, innovation et société (IFRIS), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.)-Institut National de la Recherche Agronomique (INRA)-École des hautes études en sciences sociales (EHESS)-OST-Université Paris-Est Marne-la-Vallée (UPEM)-ESIEE Paris-Centre National de la Recherche Scientifique (CNRS), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), and 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)
Subjects: Animal breeding, carte génétique, media_common.quotation_subject, [SDV]Life Sciences [q-bio], 0402 animal and dairy science, Zoology, Fertility, 04 agricultural and veterinary sciences, ruminant, Biology, GENETIQUE, 040201 dairy & animal science, Crossbreed, variation génétique, performance de reproduction, Herd, Sexual maturity, sélection, [INFO]Computer Science [cs], Reproduction, Purebred, Selection (genetic algorithm), media_common
Abstract: La réussite de la reproduction est primordiale pour la rentabilité de l’élevage, elle constitue un préalable indispensable à toute production. L’aptitude à la reproduction d’un animal au cours d’une carrière dépend des caractères de précocité sexuelle, de fertilité et de prolificité, cette dernière pouvant être décomposée en termes de taux d’ovulation et de mortalité embryonnaire. Ces différents aspects font l’objet de recherches en génétique animale et sont intégrés à des degrés divers dans les schémas de sélection, en race pure ou en croisement. La précocité sexuelle et la prolificité doivent être améliorées quand elles sont limitantes, mais certains seuils ne doivent pas être dépassés sous peine de voir se réduire le gain économique espéré. S’intéresser aux composantes de la prolificité devrait en permettre un meilleur contrôle. Une fertilité maximale est toujours recherchée mais elle revêt différentes facettes qui en compliquent son amélioration. Elle est à la fois dépendante du sexe (la fertilité femelle reste souvent la plus limitante) de la technique de reproduction employée (naturelle ou artificielle) et du moment choisi pour la mise à la reproduction (intervalle mise bas - reproduction, saison). Les recherches sur la génétique des caractères de reproduction doivent être poursuivies tout en intégrant les résultats de cartographie génétique., Reproduction is of prime importance for the profitability of a herd, it is a prerequisite of every animal production. The breeding ability during the productive life of an animal depends on sexual maturity, fertility and prolificacy the components of which are the ovulation and the embryonic mortality rates. Those traits are studied in animal breeding and are variously taken into account in the purebred and crossbred selection schemes. Sexual maturity and prolificacy have to be improved when they are limiting factors, but for economic reasons they have to stay beneath optimal thresholds. Studying the components of prolificacy would allow a better control. Maximal fertility is always expected, but its improvement is made difficult because it depends on numerous factors : sex (female fertility is often the more limiting), reproduction technique used (natural or artificial) and the choice of the breeding period (time between littering and breeding, season). Research on genetics of the breeding traits has to be pursued, while including the recent advances in genetic cartography.
Published: 1999

40. The EADGENE and SABRE post-analyses workshop

Author: Jakob Hedegaard, Magali SanCristobal, Florence Jaffrézic, Dirk-Jan de Koning, Christophe Klopp, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Faculty of Agricultural Sciences, Department of Genetics and Biotechnology, Aarhus University [Aarhus], Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), The Roslin Institute, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 2. Zero hunger, réseau de gènes, Introduction, 0303 health sciences, business.industry, Animal Genetics, [SDV]Life Sciences [q-bio], 0402 animal and dairy science, Library science, EADGENE, 04 agricultural and veterinary sciences, General Medicine, 040201 dairy & animal science, Genome, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, gene expression, gene network, Medicine, Integrative biology, business, 030304 developmental biology
Abstract: Address: 1INRA AgroParisTech, Animal Genetics and Integrative Biology, Populations Statistics Genomes, 78350 Jouy-en-Josas, France, 2Aarhus University, Faculty of Agricultural Sciences, Department of Genetics and Biotechnology, P.O. Box 50 DK-8830 Tjele, Denmark, 3INRA, UMR444 Laboratoire de Genetique Cellulaire, F-31326 Castanet-Tolosan, France, 4Sigenae UR875 Biometrie et Intelligence Artificielle, INRA, BP 52627, 31326 Castanet-Tolosan Cedex, France and 5Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, EH25 9PS, UK
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41. A review on SNP and other types of molecular markers and their use in animal genetics

Author: Alain Vignal, Denis Milan, André Eggen, Magali SanCristobal, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de recherche Génétique Biochimique et Cytogénétique (LGBC), and Institut National de la Recherche Agronomique (INRA)
Subjects: Male, 0106 biological sciences, Animal Genetics, [SDV]Life Sciences [q-bio], polymorphisme snp, 01 natural sciences, polymorphism, polymorphisme génétique, chemistry.chemical_compound, Molecular marker, Genotype, genetic polymorphism, Genetics(clinical), lcsh:SF1-1100, Genetics, 0303 health sciences, General Medicine, SNP genotyping, Genetic Techniques, Animals, Domestic, Microsatellite, Female, marqueur moléculaire, snp, microsatellite, molecular marker, genome, Genetic Markers, Biometry, lcsh:QH426-470, Locus (genetics), Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Quantitative Trait, Heritable, Animals, Humans, Molecular Biology, Alleles, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Base Sequence, Genome, Human, génome, Research, DNA, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, lcsh:Genetics, Genetics, Population, chemistry, Genetic marker, Animal Science and Zoology, lcsh:Animal culture, Microsatellite Repeats, 010606 plant biology & botany
Abstract: "Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access "; International audience; During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Despite this, a new marker type, named SNP, for Single Nucleotide Polymorphism, is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker. In this review, we will discuss the reasons for this apparent step backwards, and the pertinence of the use of SNPs in animal genetics, in comparison with other marker types.
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42. Prédiction de la réponse à une sélection canalisante d’un caractère continu en génétique animale

Author: Claude Chevalet, Jean-Michel Elsen, Magali SanCristobal-Gaudy, Loys Bodin, Revues Inra, Import, 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, Station d'Amélioration Génétique des Animaux (SAGA), and Institut National de la Recherche Agronomique (INRA)
Subjects: lcsh:QH426-470, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, Biology, index de sélection, 03 medical and health sciences, Genetics, porcin, Statistical analysis, Continuous trait, Genetics(clinical), hétéroscédasticité, caprin, Selection (genetic algorithm), ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, lcsh:SF1-1100, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, GENETIQUE ANIMALE, Research, 0402 animal and dairy science, Forestry, 04 agricultural and veterinary sciences, General Medicine, 040201 dairy & animal science, lcsh:Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Animal Science and Zoology, lcsh:Animal culture
Abstract: Canalising selection is handled by a heteroscedastic model involving a genotypic value for the mean and a genotypic value for the log variance, associated with a single phenotypic value. A selection objective is proposed as the expected squared deviation of the phenotype from the optimum, of a progeny of any candidate for selection. Indices and approximate expressions of parent-offspring regression are derived. Simulations are performed to check the accuracy of the analytical approximation. Examples of fat to protein ratio in goat milk yield and muscle pH data in pig breeding are provided in order to investigate the ability of these populations to be canalised towards an economic optimum, Le problème de la sélection canalisante est traité grâce à un modèle hétéroscédastique mettant en jeu une valeur génétique pour la moyenne et une valeur génétique pour le logarithme de la variance, toutes deux associées à une seule valeur phénotypique. Pour un objectif de sélection visant à minimiser l’espérance des carrés des différences entre le phénotype et l’optimum, pour un descendant d’un candidat à la sélection, des index sont estimés et des expressions approchées de la régression parent-descendant sont calculées. La précision de ces expressions analytiques est mesurée à l’aide de simulations. Afin d’appréhender la capacité de ces populations à être canalisées vers un optimum économique, des exemples sont donnés : le rapport entre matière grasse et matière protéique du lait de chèvre, et le pH d’un muscle chez le porc
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