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1. Cinquante années d’amélioration génétique du porc en France : bilan et perspectives

Author

Hélène Gilbert, Claire Hassenfratz, Hervé Garreau, Alain Ducos, Catherine Larzul, Thierry Tribout, Christophe Bazin, J. P. Bidanel, Sandrine Schwob, Denis Milan, Jean Pierre Bidanel, Parsaoran Silalahi, Marie-José Mercat, Juliette Riquet, Alain Bouquet, Laurianne Canario, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Bogor Agricultural University - IPB (INDONESIA), 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], Université Fédérale Toulouse Midi-Pyrénées, Pôle génétique, Institut du Porc, Pôle Génétique, 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 du Porc (IFIP), Institut du Porc (IFIP). FRA., Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Pôle Amélioration de l'animal, Space Science and Engineering Division [San Antonio], Southwest Research Institute [San Antonio] (SwRI), and Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)

Subjects
Porc, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Artificial insemination, medicine.medical_treatment, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Best linear unbiased prediction, Biology, Feed conversion ratio, Agricultural science, Pig breeding, Animal model, medicine, Génétique, Welfare, Genomic selection, media_common
Abstract

International audience; Cette synthèse fait le point sur les principales évolutions de l’amélioration génétique du porc en France depuis la loi sur l’élevage de 1966. Elle évoque rapidement les 20 premières années, qui ont fait l’objet d’une synthèse en 1986, puis décrit plus en détail les évolutions ultérieures. Les objectifs de sélection, initialement limités aux caractères de production, se sont complexifiés avec la prise en compte de la qualité de la viande, puis de la prolificité et enfin des aptitudes maternelles des truies. La mise en place d’une évaluation génétique utilisant la méthodologie du « BLUP - modèle animal » au milieu des années 1990 et le développement de l’insémination artificielle ont profondément changé le travail des sélectionneurs. Une nouvelle évolution majeure, la sélection génomique, a récemment été mise en place. La sélection a conduit à des améliorations importantes des performances pour les principaux caractères de l’objectif de sélection depuis 1970 : plus de 200 g de gain moyen quotidien, plus de 0,5 point d’indice de consommation, plus de 12 points de taux de viande maigre dans la carcasse, jusqu’à près de six porcelets nés vifs par portée supplémentaires. Ces évolutions favorables ont réduit l’empreinte environnementale de la production, mais ont également eu des effets défavorables : une augmentation la mortalité des porcelets avant sevrage et une plus grande hétérogénéité des performances. Les enjeux pour l’avenir en termes d’objectifs d’amélioration génétique (prise en compte de caractères liés au bien-être, à la robustesse et à l’adaptation…), de méthodes et d’outils sont ensuite discutés.

Published
2018

2. Influence of season and feeding resources on the quality of dry-cured hams from Gascon pigs - Noir de Bigorre chain

Author

Lebret, Bénédicte, Lenoir, Herveline, Daré, Sophie, Fonseca, Alexandre, Mercat, Marie-José, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Pôle génétique, Institut du Porc (IFIP), Consortium du Noir de Bigorre, and European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015)

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

Titre publié : Razas porcinas autóctonas para la obtención de productos cárnicos de calidad; International audience

Published
2019

3. Acrosin inhibitor detection along the boar epididymis

Author

Benoit Guyonnet, Miroslav Šulc, Věra Jonáková, Nina Cozlová, Pavla Maňásková-Postlerová, Andriy Dorosh, Laboratory of Reproductive Biology, Institute of Biotechnology, Czech Academy of Sciences [Prague] (ASCR), Department of Biochemistry, Faculty of Science, Charles University, 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), Pôle génétique, Institut du Porc, CIFRE, IFIP, Grant Agency of the Czech Republic P503/12/1834 and P502-14-05547S, ERDF Project BIOCEVCZ.1.05/1.1.00/02.0109, Charles University in Prague (UNCE204025/2012), Czech Academy of Sciences [Prague] (CAS), Charles University [Prague] (CU), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut du Porc (IFIP), 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
Male, 0301 basic medicine, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], endocrine system, medicine.medical_specialty, Glycosylation, BOAR, Swine, acrosin inhibitor, Molecular Sequence Data, Gene Expression, Immunofluorescence, Biochemistry, Mass Spectrometry, Andrology, 03 medical and health sciences, chemistry.chemical_compound, boar epididymis, spermatozoa, Structural Biology, Internal medicine, medicine, Animals, Amino Acid Sequence, Enzyme Inhibitors, Acrosome, Molecular Biology, Epididymis, Acrosin, integumentary system, biology, medicine.diagnostic_test, urogenital system, General Medicine, Sperm, 3. Good health, Protein Transport, 030104 developmental biology, medicine.anatomical_structure, Endocrinology, chemistry, Polyclonal antibodies, Proteolysis, biology.protein, Sequence Alignment, hormones, hormone substitutes, and hormone antagonists
Abstract

Epididymal sperm maturation represents a key step in the reproduction process. Spermatozoa are exposed to epididymal fluid components representing the natural environment essential for their post-testicular maturation. Changes in sperm membrane proteins are influenced by proteolytic, glycosylation and deglycosylation enzymes present in the epididymal fluid. Accordingly, the occurrence of inhibitors of these enzymes in the epididymis is very important for the regulation of sperm membrane protein processing. In the present study, we monitored acrosin inhibitor distribution in boar epididymal fluid and in spermatozoa from different segments of the organ. Using specific polyclonal antibody we registered increasing signal of the acrosin inhibitor (AI) from caput to cauda epididymis. Mass spectroscopy examination of the immunoprecipitated acrosin inhibitor (12 kDa) unequivocally identified sperm-associated acrosin inhibitor (SAAI) in the epididymal tissue. Lectin staining showed N-glycosylation in AI from boar epididymis. Protein detection of AI was supported by the results of semi-quantitative RT-PCR showing the presence of mRNA specifically coding for SAAI and similarly increasing throughout the epididymal duct, from its proximal to distal part. Additionally, the immunofluorescence technique showed the AI localization in the secretory tissue of caput, corpus and cauda epididymis, and in the acrosome region and midpiece of the sperm.

Published
2016

4. Projet Treasure. Influence de la saison de finition des animaux et des ressources alimentaires sur les qualités des produits

Author

Lebret, Bénédicte, Lenoir, Herveline, Mercat, Marie-José, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Pôle Génétique, Institut du Porc, 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), and Institut du Porc (IFIP)

Subjects
race porcine locale, food supply, facteur génétique, [SDV]Life Sciences [q-bio], système d'élevage, ressource alimentaire, swine, genêtic factor, qualité des produits, porc
Abstract

Projet Treasure. Influence de la saison de finition des animaux et des ressources alimentaires sur les qualités des produits. Réunion de travail

Published
2016

5. Les anomalies congénitales héréditaires chez le porc

Author

Sarah Rousseau, Marie-José Mercat, Juliette Riquet, Eric Pailhoux, Catherine Larzul, 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], Pôle Génétique, Institut du Porc, 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), Université Paris-Saclay, ANOPORC, SwAn, 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 du Porc (IFIP), Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), and Didier Boichard

Subjects
Animal biology, Reproductive Biology, facteur de risque, production porcine, anomalie congénitale porcine, [SDV.BA]Life Sciences [q-bio]/Animal biology, Biologie animale, Biologie de la reproduction, Sexual reproduction, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Reproduction sexuée, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction
Abstract

Les anomalies congénitales sont définies comme des défauts de structure ou de fonction présents à la naissance. Bien que la fréquence des anomalies congénitales soit relativement faible, leur impact en production porcine est significatif. Elles provoquent le plus souvent un mal-être des animaux et une dépréciation des carcasses à l’abattoir induisant des pertes économiques. Les anomalies congénitales peuvent être de nature diverse, mais les défauts les plus courants rencontrés chez le porcelet sont de type urogénital (les hernies inguinales et scrotales, la cryptorchidie et l’intersexualité). Ces défauts peuvent être dus à des problèmes nutritionnels, aux conditions d’environnement ou à la conduite de l’élevage, mais une part de leur déterminisme est très souvent génétique. Les développements récents des outils de génomique permettent désormais d’entreprendre, à grande échelle, des études d’association afin d’identifier les régions chromosomiques des gènes impliqués. L’identification des mutations causales est devenue une priorité afin de proposer de nouveaux schémas de sélection. L’objectif de cet article est de présenter une synthèse des connaissances génétiques sur les anomalies congénitales les plus fréquentes chez le porc et les stratégies mises en œuvre pour gérer ces défauts en sélection., Congenital diseases are defined as physical or functional defects, which are present at birth. Although the incidence of congenital disorders is quite low, it is a significant problem in the pig industry. These defects have a serious impact on animal welfare and induce economic losses due to carcass depreciation. Congenital diseases are various but the most common defects occurring in piglets are urogenital diseases (scrotal or inguinal hernias, cryptorchidism, and intersexuality). Defects can arise from nutritional, environmental, management causes, as well as hereditary. Recently the developed genomics tools enable large scale, genome wide association studies to identify chromosomal regions containing causal genes. Identification of causal mutations became a priority to propose new selection schemes. The aim of this article is to present an overview of genetic knowledge on the most frequent congenital diseases in pigs, and the strategies implemented to manage these defects in selection.

Published
2016

6. Gut microbiota composition in swine: genetic parameters and links with immunity traits

Author

Estelle Fabrellas, Jordi, Mach Casellas, Nuria, RAMAYO CALDAS, Yuliaxis, Levenez, Florence, Lemonnier, Gaetan, Denis, Catherine, Dore, Joel, Billon, Yvon, Mercat, Marie-José, Larzul, Catherine, Lepage, Patricia, Gaillard, Claire, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Génétique, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), Pôle génétique, Institut du Porc (IFIP), UE 1372 Génétique, Expérimentation et Système Innovants, Institut National de la Recherche Agronomique (INRA)-Génétique animale (G.A.)-Physiologie Animale et Systèmes d'Elevage (PHASE), Institut National de la Recherche Agronomique (INRA)-Génétique, Expérimentation et Système Innovants (GenESI), Institut du Porc, and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
pig, microbiote, gut microbiota, [SDV]Life Sciences [q-bio], immunity, genetic parameters, porcin, paramètre génétique, immunité
Abstract

absent

Published
2014

7. A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality

Author

Claire Rogel-Gaillard, Denis Milan, Nathalie Iannuccelli, Thierry Tribout, Patrice Dehais, Bertrand Servin, Hélène Gilbert, Nelly Muller, Jean Pierre Bidanel, Marie-José Mercat, Marie Pierre Sanchez, A.M.M. Tenghe, Marcel Bouffaud, Maria Pilar Del Schneider, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité expérimentale de testage de porcs, Institut National de la Recherche Agronomique (INRA), Pôle génétique, Institut du Porc (IFIP), French National Agency for Research (ANR, Paris) [ANR-07-GANI-001, ANR-06-GANI-008], BIOPORC (ADN, Nucleus and Gene + breeding organizations), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), UE 0450 Unité Expérimentale de Testage de Porcs, Institut National de la Recherche Agronomique (INRA)-Génétique animale (G.A.)-Unité Expérimentale de Testage de Porcs (UETP), and Institut du Porc

Subjects
Male, Meat, Genotype, [SDV]Life Sciences [q-bio], Population, Quantitative Trait Loci, Sus scrofa, Single-nucleotide polymorphism, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Family-based QTL mapping, Genetics, Animals, Genetics(clinical), education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetic association, 2. Zero hunger, 0303 health sciences, education.field_of_study, Autosome, Genome, Research, Haplotype, 0402 animal and dairy science, food and beverages, 04 agricultural and veterinary sciences, General Medicine, 040201 dairy & animal science, Phenotype, Haplotypes, Body Composition, Microsatellite, Animal Science and Zoology, Genome-Wide Association Study
Abstract

Background: Numerous quantitative trait loci (QTL) have been detected in pigs over the past 20 years using microsatellite markers. However, due to the low density of these markers, the accuracy of QTL location has generally been poor. Since 2009, the dense genome coverage provided by the Illumina PorcineSNP60 BeadChip has made it possible to more accurately map QTL using genome-wide association studies (GWAS). Our objective was to perform high-density GWAS in order to identify genomic regions and corresponding haplotypes associated with production traits in a French Large White population of pigs. Methods: Animals (385 Large White pigs from 106 sires) were genotyped using the PorcineSNP60 BeadChip and evaluated for 19 traits related to feed intake, growth, carcass composition and meat quality. Of the 64 432 SNPs on the chip, 44 412 were used for GWAS with an animal mixed model that included a regression coefficient for the tested SNPs and a genomic kinship matrix. SNP haplotype effects in QTL regions were then tested for association with phenotypes following phase reconstruction based on the Sscrofa10.2 pig genome assembly. Results: Twenty-three QTL regions were identified on autosomes and their effects ranged from 0.25 to 0.75 phenotypic standard deviation units for feed intake and feed efficiency (four QTL), carcass (12 QTL) and meat quality traits (seven QTL). The 10 most significant QTL regions had effects on carcass (chromosomes 7, 10, 16, 17 and 18) and meat quality traits (two regions on chromosome 1 and one region on chromosomes 8, 9 and 13). Thirteen of the 23 QTL regions had not been previously described. A haplotype block of 183 kb on chromosome 1 (six SNPs) was identified and displayed three distinct haplotypes with significant (0.0001 < P < 0.03) associations with all evaluated meat quality traits. Conclusions: GWAS analyses with the PorcineSNP60 BeadChip enabled the detection of 23 QTL regions that affect feed consumption, carcass and meat quality traits in a LW population, of which 13 were novel QTL. The proportionally larger number of QTL found for meat quality traits suggests a specific opportunity for improving these traits in the pig by genomic selection.

Published
2014

8. Mise en évidence de régions QTL sélectionnées dans une lignée synthétique sino-européenne

Author

Labrune, Yann, Gilbert, Hélène, Iannuccelli, Nathalie, Schwob, Sandrine, Delaunay, Isabelle, Bidanel, Jean Pierre, Bellec, Thierry, Riquet, Juliette, 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, Pôle génétique, Institut du Porc (IFIP), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ADN (ADN), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Institut du Porc, and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

The French pig breeding organisation ADN has been developing since 2001 the Chinese European composite line Duochan (25% Meishan, 25% French Landrace, 50% Large White). In order to set up marker assisted selection in the Duochan line, molecular screening was conducted (1) to confirm the effects of QTL identified in the INRA PorQTL (MS x LW) experimental design and (2) to seek for additional chromosomal regions influencing production and reproduction traits included in the breeding goal. Firstly, two groups of 30 individuals, representing the line at its foundation and after two generations of selection, were genotyped using the pig 60K SNP chip to identify regions of the genome that have been affected by selection or drift. In a second step, a set of 384 SNPs tagging these candidate regions was established to test associations between markers and performances of 480 animals born between 2003 and 2006. Each selected animal had a CD (coefficient of determination) greater than 0.25 for a global breeding value combining growth, carcass and reproduction traits). QTLs (Quantitative Trait Loci) were detected in 16 different chromosomal regions. Some of these regions simultaneously affected production and reproduction traits. These results indicated that a marker assisted selection scheme can be proposed for the Duochan selection.

Published
2013

9. Phenotypic prediction based on metabolomic data on the growing pig from three main European breeds

Author

F, Rohart, A, Paris, B, Laurent, C, Canlet, J, Molina, M J, Mercat, T, Tribout, N, Muller, N, Iannuccelli, N, Villa-Vialaneix, L, Liaubet, D, Milan, M, San Cristobal, 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, Méthodologies d'Analyse de Risque Alimentaire (MET@RISK), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Analyse de Xénobiotiques, Identification, Métabolisme (E20 Metatoul-AXIOM), 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-MetaToul-MetaboHUB, 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), 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), BIOPORC, Pôle génétique, Institut du Porc (IFIP), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité expérimentale de testage de porcs, Institut National de la Recherche Agronomique (INRA), Statistique, Analyse et Modélisation Multidisciplinaire (SAmos-Marin Mersenne) (SAMM), Université Paris 1 Panthéon-Sorbonne (UP1), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-MetaToul-MetaboHUB, 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), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), 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), 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), MetaToul AXIOM (E20), 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)-MetaboHUB-MetaToul, MetaboHUB-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)-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)-MetaboHUB-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, pig, Magnetic Resonance Spectroscopy, Meat, Models, Genetic, [SDV.BA]Life Sciences [q-bio]/Animal biology, Sus scrofa, [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH], Breeding, wavelet transformation, Phenotype, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Linear Models, Animals, Metabolomics, Female, metabolome, phenotypic prediction, Blood Chemical Analysis, variable selection
Abstract

"Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access "; International audience; Predicting phenotypes is a statistical and biotechnical challenge, both in medicine (predicting an illness) and animal breeding (predicting the carcass economical value on a young living animal). High-throughput fine phenotyping is possible using metabolomics, which describes the global metabolic status of an individual, and is the closest to the terminal phenotype. The purpose of this work was to quantify the prediction power of metabolomic profiles for commonly used production phenotypes from a single blood sample from the growing pig. Several statistical approaches were investigated and compared on the basis of cross validation: raw data vs. signal preprocessing (wavelet transformation), with a single-feature selection method. The best results in terms of prediction accuracy were obtained when data were preprocessed using wavelet transformations on the Daubechies basis. The phenotypes related to meat quality were not well predicted because the blood sample was taken some time prior to slaughter, and slaughter is known to have a strong influence on these traits. In contrast, phenotypes of potential economic interest (e.g., lean meat percentage and ADFI) were well predicted (R(2) = 0.7; P < 0.0001) using metabolomic data.

Published
2012

10. Fine mapping of production and meat quality QTL in Large White pigs using the PorcineSNP60 Beadchip

Author

Marie Pierre Sanchez, Thierry Tribout, Nathalie Iannuccelli, Marcel Bouffaud, Bertrand Servin, Patrice Dehais, Nelly Muller, Marie-José Mercat, Jordi Estelle Fabrellas, Jean Pierre Bidanel, Claire Rogel Gaillard, Denis Milan, Hélène Gilbert, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité expérimentale de testage de porcs, Institut National de la Recherche Agronomique (INRA), Pôle génétique, and Institut du Porc (IFIP)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2012

11. Cartographie fine de régions QTL à l’aide de la puce Porcine SNP60 pour l’ingestion, la croissance, la composition de la carcasse et la qualité de la viande en race Large White

Author

Sanchez, Marie Pierre, Tribout, Thierry, Iannuccelli, Nathalie, Bouffaud, Marcel, Servin, Bertrand, Dehais, Patrice, Muller, Nelly, Mercat , Marie‐José, Estelle Fabrellas, Jordi, Bidanel, Jean Pierre, Gaillard, Claire, Milan, Denis, Gilbert, Hélène, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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), 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), Pôle génétique, Institut du Porc, ANR Delisus, ANR Immopig, AgroParisTech-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, Unité expérimentale de testage de porcs, Institut National de la Recherche Agronomique (INRA), and Institut du Porc (IFIP)

Subjects
cartographie fine, qtl, composition de la carcasse, [SDV]Life Sciences [q-bio], race porcine large white, croissance animale, qualité de la viande, ingestion alimentaire
Abstract

Près de 500 porcs Large White (106 familles de pères) ont été génotypés pour la puce PorcineSNP60 et contrôlés pour 21 caractères d’ingestion, de croissance, de composition de carcasse et de qualité de la viande. Sur les 64432 marqueurs SNP (Single Nucleotide Polymorphism) de la puce, 44412 ont passé le contrôle qualité et ont donc été utilisés pour des analyses d’association avec la méthode FASTA (estimation conjointe des effets individuels des SNP et de l’effet polygénique). Au total, 45 régions avec des effets significatifs (P, About 500 Large White pigs (106 sire families) were genotyped using the PorcineSNP60 Beadchip and controlled for feed intake, growth, carcass composition and meat quality. Of the 64,432 SNP (Single Nucleotide Polymorphism) of the chip, 44,412 passed the quality control and were thus used for genome‐wide association analyses (GWAS) with the FASTA method (individual effects of SNP and polygenic effect are estimated jointly). A total of 45 regions with significant effects (P < 10‐4) have been identified for SNP distributed on all chromosomes (SSC) except on SSC5 and SSC12. In 18 of these regions (from 7 to 1,251kb), several SNP had significant effects on growth and feed intake (3 regions), on carcass composition traits (10 regions) and meat quality traits (5 regions). Eight of these regions had never been described before. The region which had the greatest number of significant effects (a region of 183kb on SSC1 for meat quality) was submitted to haplotype analyses. Three haplotypes of 6 SNP were found in the studied Large White population, they had significant effects on all meat quality traits included in the analyses. These results show that GWAS analyses with the PorcineSNP60 Beadchip allow QTL to be mapped with a good accuracy. Therefore considering the selection of the favorable alleles (or haplotypes) and also analysing the genetic architecture of complex traits can now be envisaged in commercial pig populations.

Published
2012

12. Cartographie fine de régions QTL à l’aide de la puce PorcineSNP60 pour la qualité de la viande en race Large White

Author

Marie Pierre Sanchez, Thierry Tribout, Nathalie Iannuccelli, Marcel Bouffaud, Bertrand Servin, Patrice Dehais, Nelly Muller, Marie-José Mercat, Jordi Estelle Fabrellas, Jean Pierre Bidanel, Claire Gaillard, Denis Milan, Hélène Gilbert, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), 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), Pôle génétique, Institut du Porc, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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), and Institut du Porc (IFIP)

Subjects
cartographie fine, [SDV]Life Sciences [q-bio], qtl, composition de la carcasse, race porcine large white, croissance animale, qualité de la viande, ingestion alimentaire
Abstract

A total of 389 French Large White pigs (106 sire families) were controlled for ultimate pH of [i]semimembranosus[/i] muscle, L* a* b* Minolta values and water holding capacity of [i]gluteus superficialis[/i] muscle, and a meat quality index was computed. Pigs were genotyped using the [i]PorcineSNP60[/i] Beadchip containing 64,432 SNP (Single Nucleotide Polymorphism) markers. A genome-wide association study (GWAS) was then performed with the FASTA method. Thirty-three significant SNP effects (P

Published
2012

13. Recherche de causes génétiques des anomalies congénitales majeures chez le porc

Author

Juliette Riquet, Marie‐josé Mercat, Nathalie Iannuccelli, Bertrand Servin, Eric Pailhoux, Catherine Larzul, 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, Pôle génétique, Institut du Porc (IFIP), 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), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ANR-08-GENM-040, Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Institut du Porc, Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
approche génétique, anomalie congénitale, [SDV]Life Sciences [q-bio], porcin
Abstract

Bien que la fréquence des anomalies congénitales soit relativement faible (environ 1%), leur impact en production porcine estsignificatif. Elles provoquent le plus souvent un mal‐être des animaux et une dépréciation des carcasses à l’abattoir induisant despertes économiques. Les anomalies les plus courantes chez le porc sont les hernies inguinales/scrotales, la cryptorchidie etl’intersexualité. En 2006, BIOPORC (l’IFIP et les Organisations de Sélection Porcine ADN, GENE+, Nucleus et Pen Ar Lan) a inscritcette problématique dans ses priorités et deux programmes de recherche, ANOPORC (Ministère de l’Agriculture 2007‐2008) etSwAn (ANR 2009‐2012), ont été mis en place en partenariat entre l’INRA et BIOPORC. L’objectif de cette présentation est de faireun état des lieux de la banque de données phénotypiques et moléculaires mise en place dans le cadre d’ANOPORC et de présenterles premiers résultats d’utilisation de cette collection pour la recherche des gènes responsables de l’apparition de ces anomalies(SwAn). Les outils moléculaires disponibles chez le porc permettent en effet de réaliser aujourd’hui une analyse systématique del’ensemble du génome et de mettre en évidence les régions chromosomiques portant des gènes responsables de ces défauts ou deleur apparition en interaction avec l’environnement. Un signal fort d’association entre le caractère intersexué et des marqueursd’une petite région du chromosome 12 a été identifié. Ces résultats prometteurs seront présentés afin d’illustrer la stratégieégalement mise en oeuvre sur les hernies scrotales/inguinales et la cryptorchidie.

Published
2011

14. Décryptage du contrôle génétique des réponses immunitaires innées et adaptatives chez le porc Large White : une étude combinant des approches génétiques et fonctionnelles

Author

Gaillard, Claire, Flori, Laurence, Gao, Yu, Oswald, Isabelle, Lefèvre, Francois, Bouffaud, Marcel, Mercat, Marie-José, Bidanel, Jean Pierre, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Biosynthèse & Toxicité des Mycotoxines (ToxAlim-BioToMyc), ToxAlim (ToxAlim), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Unité expérimentale de testage de porcs, BIOPORC, Pôle génétique, Institut du Porc (IFIP), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Unité de recherche Virologie et Immunologie Moléculaires (VIM), Unité Expérimentale de Testage de Porcs, and Institut du Porc

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, réponse immunitaire, race porcine Large White, caractères de production, héritabilité, race porcine Large White, porc, génétique, réponse immunitaire, caractères de production, héritabilité
Abstract

Un programme d'analyse fine du contrôle génétique de la réponse immunitaire (RI) combinant des approches génétiques et fonctionnelles a été développé. Plus de 400 animaux de race Large White mesurés pour des caractères de production ont été caractérisés pour un large éventail de paramètres de l'immunité trois semaines après vaccination contre Mycoplasma hyopneumoniae. Ces paramètres incluent : i) une numération‐formule sanguine et un comptage par cytométrie de flux de cinq sous‐populations leucocytaires caractérisées par la présence à leur surface des marqueurs IgM, TCRγδ, CD4/CD8, CD16/CD2 et CD16/CD172a/MHCII, ii) des paramètres de la RI innée (phagocytose et production in vitro des cytokines IL1B, IL6, IL8, TNF, IL12 et IFNα après stimulation du sang total), iii) des paramètres de RI adaptative (prolifération lymphocytaire, production in vitro des cytokines IL2, IL4, IL10 et IFNγ, dosages sériques des immunoglobulines (Ig) totales A, G, M et des IgG spécifiques anti‐Mycoplasma hyopneumoniae) et iv) deux protéines de la phase inflammatoire aiguë (protéine C‐réactive et haptoglobine). Les estimations d'héritabilité atteignent 0,4 en moyenne (SE = 0,1) et 42 des 54 paramètres mesurés ont montré des valeurs d'héritabilité estimées modérées à élevées (≥ 0,2). Ces valeurs confirment que de nombreux paramètres sont sous contrôle génétique et pourraient être inclus dans les programmes de sélection. Les analyses fonctionnelles ont révélé que le transcriptome sanguin est informatif pour une partie des caractères d'immunité mesurés et pourrait être utile pour affiner nos connaissances sur l'immunocompétence chez le porc., Improving animal robustness and resistance to pathogens by adding health criteria to selection schemes is one of the challenging objectives of the next decade. In order to better understand the genetic control of immunity in French Large White pigs, we have launched a program combining genetic and genomic studies that do not focus on any particular pathogen. More than 400 animals recorded for production traits were scored for a wide range of immunity parameters three weeks after vaccination against Mycoplasma hyopneumoniae: i) total white blood cells and lymphocyte counts and proportions of various leucocyte subsets including cells harbouring IgM, γδTCR, CD4/CD8, CD16/CD2 and CD16/CD172a/MHCII, ii) innate immune response parameters (phagocytosis and in vitro production of IL1B, IL6, IL8, TNF, IL12 and IFNα after blood stimulation), iii) adaptive immune response parameters (lymphocyte proliferation, in vitro production of IL2, IL4, IL10 and IFNγ after blood stimulation, total IgG, IgA, IgM and specific IgG levels) and iv) two acute phase proteins (C‐reactive protein and haptoglobin). Heritability estimates were 0.4 on average (SE=0.1) and 42 of the 54 measured parameters showed moderate to high heritabilities (≥ 0.2), confirming that many parameters are under genetic control and could be included in selection protocols. Functional analyses revealed that blood transcriptome is informative for some of the immunity traits and could be relevant to refine our knowledge on pig immunocompetence.

Published
2011

15. Alternative rearing systems in pigs: consequences on stress indicators at slaughter and meat quality

Author

Aline Foury, P. Chevillon, Bénédicte Lebret, Pierre Mormède, Claudia Terlouw, A. Vautier, Nutrition et Neurobiologie intégrée (NutriNeuro), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Centre National de la Recherche Scientifique (CNRS), 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), Pôle génétique, Institut du Porc (IFIP), Unité de Recherches sur les Herbivores (URH), Institut National de la Recherche Agronomique (INRA), and French 'Action de Coordination Technique Agricole'

Subjects
2. Zero hunger, pig, 0303 health sciences, Veterinary medicine, 0402 animal and dairy science, pigs, food and beverages, rearing system, 04 agricultural and veterinary sciences, Biology, Straw, SF1-1100, 040201 dairy & animal science, Animal culture, Urine levels, meat quality, Blood creatine, 03 medical and health sciences, stress, Semimembranosus muscle, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, Animal Science and Zoology, Muscle activity, Skin lesion, 030304 developmental biology
Abstract

Chantier qualité GA; International audience; The objective of this study was to evaluate the effects of three alternative (ALT) rearing systems for growing pigs (outdoor: 150 m2/pig; straw bedding: 1.30 m2/pig; and hut with access to a courtyard: 1.30 m2/pig) compared with a conventional system (fully slatted floor: 0.65 m2/pig, considered as control), on pre-slaughter stress indicators in relation with meat quality. To that end, the number of skin lesions on whole carcasses, as well as blood creatine kinase (CK) activity and urine levels in cortisol and catecholamines (adrenaline and noradrenaline) were determined at slaughter. Glycolytic potential (GP) and ultimate pH of the semimembranosus muscle were also measured. The global correlation network calculated between all these parameters shows that the indicators of pre-slaughter muscle activity (plasma CK) and/or stress indicators (e.g. adrenaline) are negatively (r = −0.26, P < 0.01; r = −0.29, P < 0.05, respectively) correlated with muscle GP and positively (r = 0.17, P < 0.05; r = 0.44, P < 0.001, respectively) with meat ultimate pH. Although some traits measured were sensitive to the degree of pre-slaughter mixing, they differed across rearing systems. The differences were most pronounced for the comparison of outdoors v. slatted floor. The lower levels of plasma CK and urinary catecholamines, and the lower number of carcass skin lesions of pigs reared outdoors, were related to a lower meat ultimate pH. Thus, ALT rearing systems influence animal welfare and meat quality, by providing enriched environmental conditions to the animals.

Published
2011

16. SwAn, anomalies congénitales chez le porc : cartographie génétique fine des gènes sous-jacents

Author

Riquet, Juliette, Mercat, Marie-José, Iannuccelli, Nathalie, Servin, Bertrand, Pailhoux, Eric, Larzul, Catherine, Pôle génétique, Institut du Porc, 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), Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ANR, Institut du Porc (IFIP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Biologie du développement et reproduction (BDR), and Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

absent

Published
2010

17. Genetic parameters for tissue and fatty acid composition of backfat, perirenal fat and longissimus muscle in Large White and Landrace pigs

Author

Pierre Sellier, Laurence Maignel, Jean Pierre Bidanel, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Pôle génétique, Institut du Porc, Centre Canadien pour l'Amélioration des Porcs (CCAP), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut du Porc (IFIP), and Sellier, Pierre

Subjects
pig, muscle, compositional trait, Adipose tissue, tissu adipeux, Biology, Genetic correlation, SF1-1100, Adipose capsule of kidney, compositional traits, genetic parameter, 03 medical and health sciences, Animal science, sus scrofa, genetic parameters, porcin, lipide, 030304 developmental biology, 2. Zero hunger, Longissimus muscle, 0303 health sciences, Degree of unsaturation, adipose tissue, acide gras, 0402 animal and dairy science, Large white, 04 agricultural and veterinary sciences, Science des productions animales, 040201 dairy & animal science, Animal culture, Biochemistry, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, carcasse, Animal Science and Zoology, Composition (visual arts), Fatty acid composition, Animal production studies, porc
Abstract

Genetic parameters pertaining to the same chemical characteristics of three porcine tissues, that is backfat (BF), perirenal fat (PF) and longissimus muscle (LM), were estimated in centrally tested Large White and Landrace pigs. Animals were fed ad libitum. They were slaughtered at an average BW of 99.6 kg, and samples of BF (both inner and outer layers) and LM were removed at the 13th to 14th rib level of the carcass on the day after slaughter. The data set included 2483 animals recorded for average daily gain (ADG; 35 to 100 kg), estimated carcass lean percentage (LEAN) and lean tissue growth rate (LTGR). Among these animals, around 950 pigs were recorded for lipid content (L%) and water content (W%) of BF and LM and for fatty acid composition (FAC) of BF, whereas FAC of LM was measured on 297 pigs and L%, W%, and FAC of PF on around 210 pigs. Heritabilities (h2) and genetic correlations (ra) were estimated using REML-animal model methodology. Estimates of h2 for L%, W% and FAC of BF, PF and LM were of moderate-to-high magnitude: for example 0.47 ± 0.09 for L% of LM, 0.59 ± 0.11 for W% of BF, 0.45 ± 0.08 for the ratio of polyunsaturated to saturated fatty acids (P/S) of BF, 0.61 ± 0.15 and 0.29 ± 0.10 for the coefficient of unsaturation of lipids (UNSAT, average number of double bonds of unsaturated fatty acids) of PF and LM, respectively. Genetic correlations of L% with P/S or UNSAT were strongly negative (from −0.4 to −0.9) in BF and LM, but not in PF. The ‘between-tissue’ genetic correlations for homologous compositional traits were far from being unity (e.g. ra = 0.57 ± 0.05 ‘between’ BF and PF for UNSAT). Genetic relationships between ADG and tissue compositional traits were globally weak. By contrast, genetic correlations were moderate-to-high between carcass leanness and tissue compositional traits, especially those of fat depots: for example −0.66 ± 0.14 between LEAN and L% of BF, 0.50 ± 0.07 between LEAN and UNSAT of PF, −0.44 ± 0.08 between LEAN and L% of LM, and 0.27 ± 0.03 between LEAN and UNSAT of LM. On the basis of the parameter estimates found here, breeding for higher LTGR is expected to increase the ratio of water to lipids and the unsaturation degree of lipids in subcutaneous BF and, to a lesser extent, in PF. Tissue composition and FAC of LM would be less affected.

Published
2010

18. The adult boar testicular and epididymal transcriptomes

Author

Guillemette Marot, Sandrine Schwob, Benoît Guyonnet, Jean-Louis Dacheux, Marie-José Mercat, Jean-Luc Gatti, Florence Jaffrézic, 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), Haras Nationaux, Pôle génétique, Institut du Porc (IFIP), Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), This work was in part financed by a grant from the AGENAE French program (Analyse du GENome des Animaux d'Elevage)., 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
Male, Swine, sperme, [SDV]Life Sciences [q-bio], reproduction animale, Mice, 0302 clinical medicine, Gene expression, Testis, Cluster Analysis, Oligonucleotide Array Sequence Analysis, Genetics, Epididymis, 0303 health sciences, 030219 obstetrics & reproductive medicine, Vas deferens, adn, spermatozoide, medicine.anatomical_structure, Convoluted tubule, Gamete, testicule, Biotechnology, Research Article, expression génique, lcsh:QH426-470, lcsh:Biotechnology, Biology, Andrology, 03 medical and health sciences, Complementary DNA, lcsh:TP248.13-248.65, medicine, Animals, Humans, porcin, [INFO]Computer Science [cs], RNA, Messenger, verrat, 030304 developmental biology, Gene Library, épididyme, Gene Expression Profiling, fertilité animale, Efferent ducts, Rats, Gene expression profiling, lcsh:Genetics, transcriptome
Abstract

Background Mammalians gamete production takes place in the testis but when they exit this organ, although spermatozoa have acquired a specialized and distinct morphology, they are immotile and infertile. It is only after their travel in the epididymis that sperm gain their motility and fertility. Epididymis is a crescent shaped organ adjacent to the testis that can be divided in three gross morphological regions, head (caput), body (corpus) and tail (cauda). It contains a long and unique convoluted tubule connected to the testis via the efferent ducts and finished by joining the vas deferens in its caudal part. Results In this study, the testis, the efferent ducts (vas efferens, VE), nine distinct successive epididymal segments and the deferent duct (vas deferens, VD) of four adult boars of known fertility were isolated and their mRNA extracted. The gene expression of each of these samples was analyzed using a pig generic 9 K nylon microarray (AGENAE program; GEO accession number: GPL3729) spotted with 8931 clones derived from normalized cDNA banks from different pig tissues including testis and epididymis. Differentially expressed transcripts were obtained with moderated t-tests and F-tests and two data clustering algorithms based either on partitioning around medoid (top down PAM) or hierarchical clustering (bottom up HCL) were combined for class discovery and gene expression analysis. Tissue clustering defined seven transcriptomic units: testis, vas efferens and five epididymal transcriptomic units. Meanwhile transcripts formed only four clusters related to the tissues. We have then used a specific statistical method to sort out genes specifically over-expressed (markers) in testis, VE or in each of the five transcriptomic units of the epididymis (including VD). The specific regional expression of some of these genes was further validated by PCR and Q-PCR. We also searched for specific pathways and functions using available gene ontology information. Conclusion This study described for the first time the complete transcriptomes of the testis, the epididymis, the vas efferens and the vas deferens on the same species. It described new genes or genes not yet reported over-expressed in these boar tissues, as well as new control mechanisms. It emphasizes and fulfilled the gap between studies done in rodents and human, and provides tools that will be useful for further studies on the biochemical processes responsible for the formation and maintain of the epididymal regionalization and the development of a fertile spermatozoa.

Published
2009

19. Estimation of genetic trends from 1977 to 2000 for stress-responsive systems in French Large White and Landrace pig populations using frozen semen

Author

Thierry Tribout, J. Gogué, Yvon Billon, Marcel Bouffaud, Jean Pierre Bidanel, Christophe Bazin, Aline Foury, Pierre Mormède, Psychoneuroimmunologie, nutrition et génétique, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Génétique Expérimentale en Productions Animales (GEPA), Institut National de la Recherche Agronomique (INRA), Unité expérimentale de testage de porcs, Domaine expérimental Bourges-La Sapinière (BOURGES), Unité de Psychoneuroimmunologie, Nutrition et Génétique (PsyNuGen), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Pôle génétique, Institut du Porc, 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), Université Victor Segalen, Psychoneuroimmunologie, Nutrition et Génétique (PsyNuGen), Université Bordeaux Segalen - Bordeaux 2, Institut du Porc (IFIP), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2

Subjects
Veterinary medicine, viande, STRESS, muscle, Offspring, acceptabilité, [SDV]Life Sciences [q-bio], Semen, Urine, Biology, cortisol, Insemination, SF1-1100, meat quality, GENETIC TREND, 03 medical and health sciences, sus scrofa, medicine, porcin, PIGS, Landrace pig, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 0402 animal and dairy science, food and beverages, Large white, Science des productions animales, 04 agricultural and veterinary sciences, insémination artificielle, medicine.disease, 040201 dairy & animal science, Obesity, Breed, fatness, Animal culture, catecholamine, genetic trend, stress, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, carcasse, Animal Science and Zoology, catecholamines, Animal production studies, porc
Abstract

Chantier qualité GA; An experimental design aiming at analysing the consequences of genetic selection from 1977 to 1998–2000 on the evolution of stress-responsive systems in the French Large White (LW) and Landrace (LR) pig populations was conducted by INRA and IFIP-Institut du Porc. Large White sows were inseminated with semen from LW boars born in 1977 (frozen semen) or in 1998 and their second-generation offspring were station-tested. Landrace sows were inseminated with semen from LR boars born in 1977 (frozen semen) or in 1999 to 2000, and their progeny was station-tested. Urinary concentration of stress hormones (cortisol and catecholamines) and traits related to carcass composition (estimated carcass lean content (ECLC) and global adiposity) and meat quality (pH 24 h) were measured. For the two populations, selection carried out since 1977 led to an increase in ECLC and a decrease in carcass adiposity. Between 1977 and 1998 to 2000, urinary concentrations of stress hormones were unchanged in the LR breed, but were decreased in the LW breed. Moreover, for the animals generated from LW boars born in 1977 and in 1998, urinary cortisol levels were negatively correlated with ECLC. Therefore, in the LW breed, selection carried out for higher ECLC resulted in a decrease in cortisol production, as well as a reduction of catecholamine production that may be responsible for the lower ultimate pH of meat. Therefore, selection carried out for increased carcass lean content led, in this breed, to large modifications in the functioning of the stress-responsive systems, thereby influencing a large range of physiological regulations and technical properties such as carcass composition and meat pH, which remained however in the normal range for acceptable meat quality.

Published
2009

20. Recherche de QTL pour des caractères de production et de reproduction dans les populations porcines collectives Large White type femelle et Landrace Français à l'aide d'un dispositif grand-parental

Author

Thierry Tribout, Nathalie Iannuccelli, Tom Druet, Hélène Gilbert, Juliette Riquet, Ronan Guéblez, Marie-José Mercat, Jean Pierre Bidanel, Denis Milan, Pascale Le Roy, Station de Génétique Quantitative et Appliquée (SGQA), 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, Institut du Porc (IFIP), Pôle génétique, Génétique Animale (GARen), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Ecole Nationale Supérieure Agronomique de Rennes

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS, QTL, porcs
Abstract

National audience

21. Clinical validation of a novel automated cell-free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma.

Author

Ericsson O, Ahola T, Dahl F, Karlsson F, Persson F, Karlberg O, Roos F, Alftrén I, Andersson B, Barkenäs E, Boghos A, Brandner B, Dahlberg J, Forsgren PO, Francois N, Gousseva A, Hakamali F, Janfalk-Carlsson Å, Johansson H, Lundgren J, Mohsenchian A, Olausson L, Olofsson S, Qureshi A, Skarpås B, Svahn P, Sävneby A, Åström E, Sahlberg A, Fianu-Jonasson A, Gautier J, Costa JM, Jacobsson B, and Nicolaides K

Subjects
Chromosomes, Human, Pair 13, Chromosomes, Human, Pair 18, Chromosomes, Human, Pair 21, Female, Humans, Pregnancy, Noninvasive Prenatal Testing methods, Trisomy diagnosis
Abstract

Objective: To evaluate clinical performance of a new automated cell-free (cf)DNA assay in maternal plasma screening for trisomies 21, 18, and 13, and to determine fetal sex., Method: Maternal plasma samples from 1200 singleton pregnancies were analyzed with a new non-sequencing cfDNA method, which is based on imaging and counting specific chromosome targets. Reference outcomes were determined by either cytogenetic testing, of amniotic fluid or chorionic villi, or clinical examination of neonates., Results: The samples examined included 158 fetal aneuploidies. Sensitivity was 100% (112/112) for trisomy 21, 89% (32/36) for trisomy 18, and 100% (10/10) for trisomy 13. The respective specificities were 100%, 99.5%, and 99.9%. There were five first pass failures (0.4%), all in unaffected pregnancies. Sex classification was performed on 979 of the samples and 99.6% (975/979) provided a concordant result., Conclusion: The new automated cfDNA assay has high sensitivity and specificity for trisomies 21, 18, and 13 and accurate classification of fetal sex, while maintaining a low failure rate. The study demonstrated that cfDNA testing can be simplified and automated to reduce cost and thereby enabling wider population-based screening., (© 2019 The Authors. Prenatal Diagnosis Published by John Wiley & Sons Ltd.)

Published
2019
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22. PUB1 Interacts with the Receptor Kinase DMI2 and Negatively Regulates Rhizobial and Arbuscular Mycorrhizal Symbioses through Its Ubiquitination Activity in Medicago truncatula.

Author

Vernié T, Camut S, Camps C, Rembliere C, de Carvalho-Niebel F, Mbengue M, Timmers T, Gasciolli V, Thompson R, le Signor C, Lefebvre B, Cullimore J, and Hervé C

Subjects
Colony Count, Microbial, Glomeromycota physiology, Mycorrhizae growth & development, Phosphorylation, Plant Proteins chemistry, Protein Domains, Saccharomyces cerevisiae metabolism, Ubiquitin-Protein Ligases metabolism, Medicago truncatula metabolism, Medicago truncatula microbiology, Mycorrhizae physiology, Plant Proteins metabolism, Rhizobium physiology, Symbiosis, Ubiquitination
Abstract

PUB1, an E3 ubiquitin ligase, which interacts with and is phosphorylated by the LYK3 symbiotic receptor kinase, negatively regulates rhizobial infection and nodulation during the nitrogen-fixing root nodule symbiosis in Medicago truncatula In this study, we show that PUB1 also interacts with and is phosphorylated by DOES NOT MAKE INFECTIONS 2, the key symbiotic receptor kinase of the common symbiosis signaling pathway, required for both the rhizobial and the arbuscular mycorrhizal (AM) endosymbioses. We also show here that PUB1 expression is activated during successive stages of root colonization by Rhizophagus irregularis that is compatible with its interaction with DOES NOT MAKE INFECTIONS 2. Through characterization of a mutant, pub1-1, affected by the E3 ubiquitin ligase activity of PUB1, we have shown that the ubiquitination activity of PUB1 is required to negatively modulate successive stages of infection and development of rhizobial and AM symbioses. In conclusion, PUB1 represents, to our knowledge, a novel common component of symbiotic signaling integrating signal perception through interaction with and phosphorylation by two key symbiotic receptor kinases, and downstream signaling via its ubiquitination activity to fine-tune both rhizobial and AM root endosymbioses., (© 2016 American Society of Plant Biologists. All Rights Reserved.)

Published
2016
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23. Acrosin inhibitor detection along the boar epididymis.

Author

Maňásková-Postlerová P, Cozlová N, Dorosh A, Šulc M, Guyonnet B, and Jonáková V

Subjects
Amino Acid Sequence, Animals, Enzyme Inhibitors blood, Enzyme Inhibitors chemistry, Gene Expression, Glycosylation, Male, Mass Spectrometry, Molecular Sequence Data, Protein Transport, Proteolysis, Sequence Alignment, Spermatozoa metabolism, Swine, Acrosin antagonists & inhibitors, Enzyme Inhibitors metabolism, Epididymis metabolism
Abstract

Epididymal sperm maturation represents a key step in the reproduction process. Spermatozoa are exposed to epididymal fluid components representing the natural environment essential for their post-testicular maturation. Changes in sperm membrane proteins are influenced by proteolytic, glycosylation and deglycosylation enzymes present in the epididymal fluid. Accordingly, the occurrence of inhibitors of these enzymes in the epididymis is very important for the regulation of sperm membrane protein processing. In the present study, we monitored acrosin inhibitor distribution in boar epididymal fluid and in spermatozoa from different segments of the organ. Using specific polyclonal antibody we registered increasing signal of the acrosin inhibitor (AI) from caput to cauda epididymis. Mass spectroscopy examination of the immunoprecipitated acrosin inhibitor (12 kDa) unequivocally identified sperm-associated acrosin inhibitor (SAAI) in the epididymal tissue. Lectin staining showed N-glycosylation in AI from boar epididymis. Protein detection of AI was supported by the results of semi-quantitative RT-PCR showing the presence of mRNA specifically coding for SAAI and similarly increasing throughout the epididymal duct, from its proximal to distal part. Additionally, the immunofluorescence technique showed the AI localization in the secretory tissue of caput, corpus and cauda epididymis, and in the acrosome region and midpiece of the sperm., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Published
2016
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24. Eliminating anti-nutritional plant food proteins: the case of seed protease inhibitors in pea.

Author

Clemente A, Arques MC, Dalmais M, Le Signor C, Chinoy C, Olias R, Rayner T, Isaac PG, Lawson DM, Bendahmane A, and Domoney C

Subjects
Amino Acid Sequence, Animals, Chymotrypsin antagonists & inhibitors, Chymotrypsin genetics, Diet, Humans, Mutation, Pisum sativum genetics, Pisum sativum metabolism, Plant Proteins chemistry, Plant Proteins metabolism, Seeds chemistry, Seeds genetics, Trypsin chemistry, Trypsin genetics, Trypsin Inhibitors chemistry, Chymotrypsin chemistry, Pisum sativum chemistry, Plant Proteins genetics, Protease Inhibitors chemistry
Abstract

Several classes of seed proteins limit the utilisation of plant proteins in human and farm animal diets, while plant foods have much to offer to the sustainable intensification of food/feed production and to human health. Reduction or removal of these proteins could greatly enhance seed protein quality and various strategies have been used to try to achieve this with limited success. We investigated whether seed protease inhibitor mutations could be exploited to enhance seed quality, availing of induced mutant and natural Pisum germplasm collections to identify mutants, whilst acquiring an understanding of the impact of mutations on activity. A mutant (TILLING) resource developed in Pisum sativum L. (pea) and a large germplasm collection representing Pisum diversity were investigated as sources of mutations that reduce or abolish the activity of the major protease inhibitor (Bowman-Birk) class of seed protein. Of three missense mutations, predicted to affect activity of the mature trypsin / chymotrypsin inhibitor TI1 protein, a C77Y substitution in the mature mutant inhibitor abolished inhibitor activity, consistent with an absolute requirement for the disulphide bond C77-C92 for function in the native inhibitor. Two further classes of mutation (S85F, E109K) resulted in less dramatic changes to isoform or overall inhibitory activity. The alternative strategy to reduce anti-nutrients, by targeted screening of Pisum germplasm, successfully identified a single accession (Pisum elatius) as a double null mutant for the two closely linked genes encoding the TI1 and TI2 seed protease inhibitors. The P. elatius mutant has extremely low seed protease inhibitory activity and introgression of the mutation into cultivated germplasm has been achieved. The study provides new insights into structure-function relationships for protease inhibitors which impact on pea seed quality. The induced and natural germplasm variants identified provide immediate potential for either halving or abolishing the corresponding inhibitory activity, along with associated molecular markers for breeding programmes. The potential for making large changes to plant protein profiles for improved and sustainable food production through diversity is illustrated. The strategy employed here to reduce anti-nutritional proteins in seeds may be extended to allergens and other seed proteins with negative nutritional effects. Additionally, the novel variants described for pea will assist future studies of the biological role and health-related properties of so-called anti-nutrients.

Published
2015
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25. New susceptibility locus for rheumatoid arthritis suggested by a genome-wide linkage study.

Author

Cornélis F, Fauré S, Martinez M, Prud'homme JF, Fritz P, Dib C, Alves H, Barrera P, de Vries N, Balsa A, Pascual-Salcedo D, Maenaut K, Westhovens R, Migliorini P, Tran TH, Delaye A, Prince N, Lefevre C, Thomas G, Poirier M, Soubigou S, Alibert O, Lasbleiz S, Fouix S, Bouchier C, Lioté F, Loste MN, Lepage V, Charron D, Gyapay G, Lopes-Vaz A, Kuntz D, Bardin T, and Weissenbach J

Subjects
Genetic Predisposition to Disease, Genome, Genotype, HLA Antigens genetics, Humans, Arthritis, Rheumatoid genetics, Genetic Linkage
Abstract

Rheumatoid arthritis (RA), the most common autoimmune disease, is associated in families with other autoimmune diseases, including insulin-dependent diabetes mellitus (IDDM). Its genetic component has been suggested by familial aggregation (lambdas = 5), twin studies, and segregation analysis. HLA, which is the only susceptibility locus known, has been estimated to account for one-third of this component. The aim of this paper was to identify new RA loci. A genome scan was performed with 114 European Caucasian RA sib pairs from 97 nuclear families. Linkage was significant only for HLA (P < 2.5.10(-5)) and nominal for 19 markers in 14 other regions (P < 0.05). Four of the loci implicated in IDDM potentially overlap with these regions: the putative IDDM6, IDDM9, IDDM13, and DXS998 loci. The first two of these candidate regions, defined in the RA genome scan by the markers D18S68-D18S61-D18S469 (18q22-23) and D3S1267 (3q13), respectively, were studied in 194 additional RA sib pairs from 164 nuclear families. Support for linkage to chromosome 3 only was extended significantly (P = 0.002). The analysis of all 261 families provided a linkage evidence of P = 0. 001 and suggested an interaction between this putative RA locus and HLA. This locus could account for 16% of the genetic component of RA. Candidate genes include those coding for CD80 and CD86, molecules involved in antigen-specific T cell recognition. In conclusion, this first genome scan in RA Caucasian families revealed 14 candidate regions, one of which was supported further by the study of a second set of families.

Published
1998
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