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1. A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits

Author: Klavdija Poklukar, Camille Mestre, Martin Škrlep, Marjeta Čandek-Potokar, Cristina Ovilo, Luca Fontanesi, Juliette Riquet, Samuele Bovo, Giuseppina Schiavo, Anisa Ribani, Maria Muñoz, Maurizio Gallo, Ricardo Bozzi, Rui Charneca, Raquel Quintanilla, Goran Kušec, Marie-José Mercat, Christoph Zimmer, Violeta Razmaite, Jose P. Araujo, Čedomir Radović, Radomir Savić, Danijel Karolyi, and Bertrand Servin
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments. Results Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene. Conclusions In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.
Published: 2023
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2. Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

Author: Simon Boitard, Laurence Liaubet, Cyriel Paris, Katia Fève, Patrice Dehais, Alban Bouquet, Juliette Riquet, and Marie-José Mercat
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background Numerous genomic scans for positive selection have been performed in livestock species within the last decade, but often a detailed characterization of the detected regions (gene or trait under selection, timing of selection events) is lacking. Cryopreserved resources stored in reproductive or DNA gene banks offer a great opportunity to improve this characterization by providing direct access to recent allele frequency dynamics, thereby differentiating between signatures from recent breeding objectives and those related to more ancient selection constraints. Improved characterization can also be achieved by using next-generation sequencing data, which helps narrowing the size of the detected regions while reducing the number of associated candidate genes. Methods We estimated genetic diversity and detected signatures of recent selection in French Large White pigs by sequencing the genomes of 36 animals from three distinct cryopreserved samples: two recent samples from dam (LWD) and sire (LWS) lines, which had diverged from 1995 and were selected under partly different objectives, and an older sample from 1977 prior to the divergence. Results French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population. Thirty-eight genomic regions under recent selection were detected in these lines and the corresponding selection events were further classified as convergent between lines (18 regions), divergent between lines (10 regions), specific to the dam line (6 regions) or specific to the sire line (4 regions). Several biological functions were found to be significantly enriched among the genes included in these regions: body size, body weight and growth regardless of the category, early life survival and calcium metabolism more specifically in the signatures in the dam line and lipid and glycogen metabolism more specifically in the signatures in the sire line. Recent selection on IGF2 was confirmed and several other regions were linked to a single candidate gene (ARHGAP10, BMPR1B, GNA14, KATNA1, LPIN1, PKP1, PTH, SEMA3E or ZC3HAV1, among others). Conclusions These results illustrate that sequencing the genome of animals at several recent time points generates considerable insight into the traits, genes and variants under recent selection in a population. This approach could be applied to other livestock populations, e.g. by exploiting the rich biological resources stored in cryobanks.
Published: 2023
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3. Mutations on a conserved distal enhancer in the porcine C-reactive protein gene impair its expression in liver

Author: Carles Hernández-Banqué, Teodor Jové-Juncà, Daniel Crespo-Piazuelo, Olga González-Rodríguez, Yuliaxis Ramayo-Caldas, Anna Esteve-Codina, Marie-José Mercat, Marco C. A. M. Bink, Raquel Quintanilla, and Maria Ballester
Subjects: C-reactive protein, fine-mapping, luciferase assays, enhancer, pig, RNA-seq, Immunologic diseases. Allergy, RC581-607
Abstract: C-reactive protein (CRP) is an evolutionary highly conserved protein. Like humans, CRP acts as a major acute phase protein in pigs. While CRP regulatory mechanisms have been extensively studied in humans, little is known about the molecular mechanisms that control pig CRP gene expression. The main goal of the present work was to study the regulatory mechanisms and identify functional genetic variants regulating CRP gene expression and CRP blood levels in pigs. The characterization of the porcine CRP proximal promoter region revealed a high level of conservation with both cow and human promoters, sharing binding sites for transcription factors required for CRP expression. Through genome-wide association studies and fine mapping, the most associated variants with both mRNA and protein CRP levels were localized in a genomic region 39.3 kb upstream of CRP. Further study of the region revealed a highly conserved putative enhancer that contains binding sites for several transcriptional regulators such as STAT3, NF-kB or C/EBP-β. Luciferase reporter assays showed the necessity of this enhancer-promoter interaction for the acute phase induction of CRP expression in liver, where differences in the enhancer sequences significantly modified CRP activity. The associated polymorphisms disrupted the putative binding sites for HNF4α and FOXA2 transcription factors. The high correlation between HNF4α and CRP expression levels suggest the participation of HNF4α in the regulatory mechanism of porcine CRP expression through the modification of its binding site in liver. Our findings determine, for the first time, the relevance of a distal regulatory element essential for the acute phase induction of porcine CRP in liver and identify functional polymorphisms that can be included in pig breeding programs to improve immunocompetence.
Published: 2023
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4. Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data

Author: Christos Dadousis, Maria Muñoz, Cristina Óvilo, Maria Chiara Fabbri, José Pedro Araújo, Samuele Bovo, Marjeta Čandek Potokar, Rui Charneca, Alessandro Crovetti, Maurizio Gallo, Juan María García-Casco, Danijel Karolyi, Goran Kušec, José Manuel Martins, Marie-José Mercat, Carolina Pugliese, Raquel Quintanilla, Čedomir Radović, Violeta Razmaite, Anisa Ribani, Juliet Riquet, Radomir Savić, Giuseppina Schiavo, Martin Škrlep, Silvia Tinarelli, Graziano Usai, Christoph Zimmer, Luca Fontanesi, and Riccardo Bozzi
Subjects: Medicine, Science
Abstract: Abstract Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products.
Published: 2022
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5. Genic and non-genic SNP contributions to additive and dominance genetic effects in purebred and crossbred pig traits

Author: Mahshid Mohammadpanah, Ahmad Ayatollahi Mehrgardi, Hélène Gilbert, Catherine Larzul, Marie-José Mercat, Ali Esmailizadeh, Mehdi Momen, and Llibertat Tusell
Subjects: Medicine, Science
Abstract: Abstract The present research has estimated the additive and dominance genetic variances of genic and intergenic segments for average daily gain (ADG), backfat thickness (BFT) and pH of the semimembranosus dorsi muscle (PHS). Further, the predictive performance using additive and additive dominance models in a purebred Piétrain (PB) and a crossbred (Piétrain × Large White, CB) pig population was assessed. All genomic regions contributed equally to the additive and dominance genetic variations and lead to the same predictive ability that did not improve with the inclusion of dominance genetic effect and inbreeding in the models. Using all SNPs available, additive genotypic correlations between PB and CB performances for the three traits were high and positive (> 0.83) and dominance genotypic correlation was very inaccurate. Estimates of dominance genotypic correlations between all pairs of traits in both populations were imprecise but positive for ADG-BFT in CB and BFT-PHS in PB and CB with a high probability (> 0.98). Additive and dominance genotypic correlations between BFT and PHS were of different sign in both populations, which could indicate that genes contributing to the additive genetic progress in both traits would have an antagonistic effect when used for exploiting dominance effects in planned matings.
Published: 2022
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6. Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Author: Samuele Bovo, Giuseppina Schiavo, Anisa Ribani, Valerio J. Utzeri, Valeria Taurisano, Mohamad Ballan, Maria Muñoz, Estefania Alves, Jose P. Araujo, Riccardo Bozzi, Rui Charneca, Federica Di Palma, Ivona Djurkin Kušec, Graham Etherington, Ana I. Fernandez, Fabián García, Juan García-Casco, Danijel Karolyi, Maurizio Gallo, José Manuel Martins, Marie-José Mercat, Yolanda Núñez, Raquel Quintanilla, Čedomir Radović, Violeta Razmaite, Juliette Riquet, Radomir Savić, Martin Škrlep, Graziano Usai, Christoph Zimmer, Cristina Ovilo, and Luca Fontanesi
Subjects: Medicine, Science
Abstract: Abstract Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a “One Health” perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a “One Health” perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.
Published: 2021
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7. Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets

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

Author: Jean-Pierre BIDANEL, Parsaoran SILALAHI, Thierry TRIBOUT, Laurianne CANARIO, Alain DUCOS, Hervé GARREAU, Hélène GILBERT, Catherine LARZUL, Denis MILAN, Juliette RIQUET, Sandrine SCHWOB, Marie-José MERCAT, Claire HASSENFRATZ, Alain BOUQUET, Christophe BAZIN, and Joel BIDANEL
Subjects: Animal culture, SF1-1100, Aquaculture. Fisheries. Angling, SH1-691
Abstract: 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: 2020
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9. A genome-wide association study points out the causal implication of SOX9 in the sex-reversal phenotype in XX pigs.

Author: Sarah Rousseau, Nathalie Iannuccelli, Marie-José Mercat, Claire Naylies, Jean-Claude Thouly, Bertrand Servin, Denis Milan, Eric Pailhoux, and Juliette Riquet
Subjects: Medicine, Science
Abstract: Among farm animals, pigs are known to show XX sex-reversal. In such cases the individuals are genetically female but exhibit a hermaphroditism, or a male phenotype. While the frequency of this congenital disease is quite low (less than 1%), the economic losses are significant for pig breeders. These losses result from sterility, urogenital infections and the carcasses being downgraded because of the risk of boar taint. It has been clearly demonstrated that the SRY gene is not involved in most cases of sex-reversal in pigs, and that autosomal recessive mutations remain to be discovered. A whole-genome scan analysis was performed in the French Large-White population to identify candidate genes: 38 families comprising the two non-affected parents and 1 to 11 sex-reversed full-sib piglets were genotyped with the PorcineSNP60 BeadChip. A Transmission Disequilibrium Test revealed a highly significant candidate region on SSC12 (most significant p-value
Published: 2013
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10. Immunity traits in pigs: substantial genetic variation and limited covariation.

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

Author: Daniel Crespo-Piazuelo, Hervé Acloque, Olga González-Rodríguez, Mayrone Mongellaz, Marie-José Mercat, Marco C A M Bink, Abe E Huisman, Yuliaxis Ramayo-Caldas, Juan Pablo Sánchez, Maria Ballester
Abstract: In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle.
Published: 2023

12. Genetic determinism of boar taint and relationship with growth traits, meat quality and lesions

Author: Catherine Larzul, B. Blanchet, Marie-José Mercat, Armelle Prunier, C. Dugué, M. Monziols, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut du Porc (IFIP), Unité Expérimentale Porcs Rennes (UE PR), Institut National de la Recherche Agronomique (INRA), French National Research Agency (ANR) - ANR-10-GENOM_BTV-015 UtOpIGe, and ANR-10-GENM-0015,UtOpIGe,Vers une Utilisation Optimale de l'Information Génomique dans les schémas pyramidaux(2010)
Subjects: Male, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Meat, héritabilité, Boar taint, Swine, androstenone, porc mâle entier, oestradiol, Biology, Breeding, heritability, Loin, androsténone, Crossbreed, SF1-1100, comportement animal, Genetic determinism, Genetic Determinism, 03 medical and health sciences, chemistry.chemical_compound, Animal science, Surgical castration, Animals, aggressiveness, carcass, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, sélection génétique, 0402 animal and dairy science, Androstenone, 04 agricultural and veterinary sciences, Heritability, agressivité, 040201 dairy & animal science, Skatole, Animal culture, Phenotype, chemistry, carcasse, Animal Science and Zoology, Purebred, Autre (Sciences du Vivant), Research Article
Abstract: Notice à Reprendre pas de clé UT au 13 Février 2020; International audience; Breeding entire males is an alternative to surgical castration to improve their welfare. However, entire males may have a major quality defect called boar taint. Boar taint is partly due to the presence of androstenone in fat. In this study, we estimated the genetic parameters between androstenone and production traits to evaluate the consequences of selection against boar taint for traits of interest. We focused on growth traits, meat quality, lesions, hormone levels and computerised tomography measurements in purebred Piétrain (P) or Piétrain cross Large White (X) entire males. The number of measured animals varied from 670 P and 734 X for hormones concentrations to 553 P and 645 X for computerised tomography measurements. Skin lesions were measured on live pigs shortly after mixing, at the end of the fattening period, and on carcasses. Heritabilities of traits measured by tomography ranged from low to high: femur density (P: 0.34, X: 0.69), loin eye area (P: 0.53, X: 0.88) and loin eye density (P: 0.12, X: 0.18). The mean number of lesions at each stage was lower in purebred pigs than in crossbreds (entering the fattening stage 4.01 in P and 4.68 in X; before slaughter 3.72 in P and 4.22 in X; on carcass 4.50 in P and 4.96 in X). We also observed a decrease in the average number of lesions between the two stages in live pigs. We found high genetic correlations between stages in purebred pigs (0.74 to 0.76) but low correlations (−0.30 to 0.29) in crossbred pigs. Selection aiming to decrease fat androstenone is feasible ( h2 = 0.57 in P and h2 = 0.71 in X). It would have overall positive effects on meat production and quality traits. Selection aiming to reduce plasma oestradiol would strongly reduce the level of fat androstenone (rg = 0.89 in P and rg = 0.84 in X). Selection against oestradiol is easier and less invasive since it would only require a blood sample rather than a fat biopsy in live animals.
Published: 2020
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13. Discovering genomic regions associated with the phenotypic differentiation of European local pig breeds

Author: Klavdija Poklukar, Camille Mestre, Martin Škrlep, Marjeta Čandek-Potokar, Cristina Ovilo, Luca Fontanesi, Juliette Riquet, Samuele Bovo, Giuseppina Schiavo, Anisa Ribani, Maria Muñoz, Maurizio Gallo, Ricardo Bozzi, Rui Charneca, Raquel Quintanilla, Goran Kušec, Marie-José Mercat, Christoph Zimmer, Violeta Razmaite, Jose P. Araujo, Čedomir Radović, Radomir Savić, Danijel Karolyi, and Bertrand Servin
Abstract: BackgroundIntensive selection of modern pig breeds resulted in genetic improvement of productive traits while local pig breeds remained less performant. As they have been bred in extensive systems, they have adapted to specifical environmental conditions resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth and reproductive performance traits. These data were analyzed using a dedicated approach to detect selection signatures linked to phenotypic traits in order to uncover potential candidate genes that may be under adaptation to specific environments.ResultsGenetic data analysis of European pig breeds revealed four main axes of genetic variation represented by Iberian and modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian and Portuguese Alentejano breeds. Principal component analysis of phenotypic data distinguished between larger and leaner breeds with better growth potential and reproductive performance on one hand and breeds that were smaller, fatter, and had low growth and reproductive efficiency on the other hand. Linking selection signatures with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effect on stature, fatness, growth and reproduction performance traits. For example, strong associations were found for stature in two regions containing theANXA4andANTXR1genes, for fatness containing theDNMT3AandPOMCgenes and for reproductive performance containing theHSD17B7gene.ConclusionsThe present study on European local pig breeds used a dedicated approach for searching selection signatures supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems. Results can be useful to define conservation programs of local pig breeds.
Published: 2022
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14. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Author: Christoph Zimmer, Marie-José Mercat, Rui Charneca, Cristina Óvilo, Goran Kušec, Anisa Ribani, Estefania Alves, J.M. Martins, Juliette Riquet, Raquel Quintanilla, G. Usai, Samuele Bovo, Valerio Joe Utzeri, Maurizio Gallo, Ana Isabel Fernández, Yolanda Núñez, Danijel Karolyi, Violeta Razmaite, María Muñoz, Giuseppina Schiavo, Fabián García, Riccardo Bozzi, Luca Fontanesi, Čedomir Radović, Radomir Savić, Marjeta Čandek-Potokar, José Pedro Araújo, University of Bologna, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Polytechnic Institute of Porto, Université de Florence, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Mediterranean Institute for Agriculture, Environment and Development (MED), University of Évora [Portugal], Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Bologna RFO 2016-2019 programs, European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Schiavo G., Bovo S., Munoz M., Ribani A., Alves E., Araujo J.P., Bozzi R., Candek-Potokar M., Charneca R., Fernandez A.I., Gallo M., Garcia F., Karolyi D., Kusec G., Martins J.M., Mercat M.-J., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Usai G., Utzeri V.J., Zimmer C., Ovilo C., Fontanesi L., University of Bologna/Università di Bologna, Università degli Studi di Firenze = University of Florence (UniFI), Agricultural Institute of Slovenia, University of Zagreb, J.J. Strossmayer University of Osijek, Institut du Porc (IFIP), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Inst Anim Husb, Lithuanian Univ Hlth Sci, 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], AGRIS sardegna, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), Università di Bologna, European Commission, Schiavo, G., Bovo, S., Ribani, A., Araújo, J.P., Bozzi, R., Čandek-Potokar, M., Charneca, R., Fernandez, A.I., Kušec, G., Campos Martín, José Miguel, Mercat, M.J., Núñez, Y., Quintanilla, R., Radović, Č., Razmaite, V., Riquet, J., Savić, R., Usai, G., Utzeri, V.J., Fontanesi, L., Géosciences Montpellier, Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Centro de Ciências e Tecnologias Nucleares (C2TN), Instituto Politécnico de Viana do Castelo, UNIVERSITY OF FIRENZE (UNIVERSITY OF FIRENZE), and Spanish National Research Council [Madrid] (CSIC)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Sus scrofa, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Runs of Homozygosity, population genomic, Population genomics, single nucleotide polymorphism, Genotype, Inbreeding, autozygosity, population genomics, selection signature, 2. Zero hunger, education.field_of_study, Genome, [SDV.BA]Life Sciences [q-bio]/Animal biology, Homozygote, Single Nucleotide, 04 agricultural and veterinary sciences, General Medicine, Europe, Genetic structure, Population, Autozygosity, Single-nucleotide polymorphism, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genetics, Animals, Population Density, Polymorphism, education, 0402 animal and dairy science, Selection signature, biology.organism_classification, 040201 dairy & animal science, Single nucleotide polymorphism, 030104 developmental biology, Evolutionary biology, Animal Science and Zoology, Sarda
Abstract: 16 Pág. Departamento de Mejora Genética Animal, ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources., This work has been funded by University of Bologna RFO 2016-2019 programs and by the European Union’s Horizon 2020 research and innovation programme (TREASURE project – grant agreement no. 634476). The content of this work reflects only the authors’ view and the European Union Agency is not responsible for any use that may be made of the information it contains.
Published: 2022
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15. Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Author: Giuseppina Schiavo, Valeria Taurisano, Raquel Quintanilla, Anisa Ribani, Juan García-Casco, Rui Charneca, Valerio Joe Utzeri, Marie-José Mercat, Estefania Alves, Fabián García, Graham J Etherington, Samuele Bovo, Juliette Riquet, Danijel Karolyi, Christoph Zimmer, Ivona Djurkin Kušec, Federica Di Palma, Ana Isabel Fernández, G. Usai, Violeta Razmaite, María Muñoz, Yolanda Núñez, José Pedro Araújo, Martin Škrlep, Radomir Savić, J.M. Martins, Maurizio Gallo, Luca Fontanesi, Čedomir Radović, Mohamad Ballan, Cristina Óvilo, Riccardo Bozzi, University of Bologna, Instituto Nacional de Investigación Agropecuaria (INIA), Centro de Investigação de Montanha [Bragança, Portugal] (CIMO), Instituto Politécnico de Bragança, Department of Agriculture, Food, Environment and Forestry (DAGRI), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Universidade de Évora, University of East Anglia [Norwich] (UEA), Josip Juraj Strossmayer University of Osijek, Earlham Institute [Norwich], University of Zagreb, Associazione Nazionale Allevatori Suini, Institut du Porc (IFIP), Institute of Agrifood Research and Technology (IRTA), Institute for Animal Husbandry, Lithuanian University of Health Sciences [Kaunas, Lithuania], Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], Kmetijski Inštitut Slovenije (KIS), AGRIS sardegna, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), European Cooperation in Science and Technology (COST)Ministry of Foreign Affairs of ItalyUniversity of Bologna RFO 2016-2019 programmesItalian MIUR 2017 PigPhenomics projectEuropean Commission634476European Open Science Cloud (EOSC) Secretariat, project 'Application of animal genomics and data mining to predict and monitor novel coronavirus potential infections (VirAnimalOne)'EGI call for COVID-19 research projects (AnGen1H project)Por Fesr Emilia-Romagna 2014-2020 (actions 1.1.4 and 1.2.2-Bando per sostenere progetti di ricerca ed innovazione per lo sviluppo di soluzioni finalizzate al contrasto dell'epidemia da COVID-19-Project LIVESTOCK-STOP-COVI), European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Producció Animal, Genètica i Millora Animal, University of Bologna/Università di Bologna, Università degli Studi di Firenze = University of Florence (UniFI), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università di Bologna, European Commission, Bovo, Samuele, Schiavo, Giuseppina, Ribani, Anisa, Utzeri, Valerio J, Taurisano, Valeria, Araujo, Jose P, Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Djurkin Kušec, Ivona, Etherington, Graham, Fernandez, Ana I, Suárez García, Fabián, García-Casco, Juan, Karolyi, D 0000-003-0409-9071], Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Škrlep, Martin, Usai, Graziano, Ovilo, Cristina, Bovo S., Schiavo G., Ribani A., Utzeri V.J., Taurisano V., Ballan M., Munoz M., Alves E., Araujo J.P., Bozzi R., Charneca R., Di Palma F., Djurkin Kusec I., Etherington G., Fernandez A.I., Garcia F., Garcia-Casco J., Karolyi D., Gallo M., Martins J.M., Mercat M.-J., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Skrlep M., Usai G., Zimmer C., Ovilo C., and Fontanesi L.
Subjects: 0301 basic medicine, Candidate gene, Population genetics, Swine, MESH: Coronavirus Infections, Sus scrofa, MESH: Angiotensin-Converting Enzyme 2, MESH: One Health, Breeding, MESH: INDEL Mutation, 0302 clinical medicine, Gene Frequency, INDEL Mutation, Receptors, Receptors, Viru, MESH: Animals, MESH: Serine Endopeptidases, MESH: Genetic Variation, MESH: High-Throughput Nucleotide Sequencing, MESH: Swine, 2. Zero hunger, Genetics, education.field_of_study, Multidisciplinary, MESH: Polymorphism, Single Nucleotide, Serine Endopeptidases, High-Throughput Nucleotide Sequencing, Single Nucleotide, Genomics, Virus, Serine Endopeptidase, One Health, 030220 oncology & carcinogenesis, Microsomal aminopeptidase, Medicine, Infectious diseases, Receptors, Virus, Angiotensin-Converting Enzyme 2, Coronavirus Infections, MESH: Whole Genome Sequencing, Human, Agricultural genetics, pig, local breed, whole genome sequencing, coronavirus, Science, Dipeptidyl Peptidase 4, Population, MESH: Genetics, Population, Context (language use), MESH: Breeding, CD13 Antigens, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Animals, Genetics, Population, Humans, Whole Genome Sequencing, Genetic Variation, Genetic variation, MESH: Gene Frequency, Polymorphism, education, Data mining, Gene, CD13 Antigen, Animal breeding, Whole genome sequencing, MESH: Humans, Animal, Coronavirus Infection, Host (biology), Virus receptor, MESH: CD13 Antigens, MESH: Dipeptidyl Peptidase 4, MESH: Receptors, Virus, MESH: Sus scrofa, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Dipeptidyl peptidase IV, Next-generation sequencing, Genetic markers, Serine proteinase
Abstract: 14 Pág. Departamento de Mejora Genética Animal, Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a "One Health" perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a "One Health" perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources., This work has received funding from the University of Bologna RFO 2016-2019 programmes, the Italian MIUR 2017 PigPhenomics project, from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 634476 for the project with acronym TREASURE, from the European Open Science Cloud (EOSC) Secretariat, project “Application of animal genomics and data mining to predict and monitor novel coronavirus potential infections (VirAnimalOne)”, the EGI call for COVID-19 research projects (AnGen1H project) and from the Por Fesr Emilia-Romagna 2014-2020 (actions 1.1.4 and 1.2.2—Bando per sostenere progetti di ricerca ed innovazione per lo sviluppo di soluzioni finalizzate al contrasto dell’epidemia da COVID-19—Project LIVESTOCK-STOP-COVI). The content of this article reflects only the authors' view and the European Union Agency is not responsible for any use that may be made of the information it contains.
Published: 2021
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16. Finishing season and feeding resources influence the quality of products from extensive-system Gascon pigs. Part 2: muscle traits and sensory quality of dry-cured ham

Author: A. Fonseca, Marie-José Mercat, Bénédicte Lebret, Juliette Riquet, H. Lenoir, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut du Porc (IFIP), Consortium du Noir de Bigorre, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO 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 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), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Male, Taste, Pork quality, Sus scrofa, Production system, Sensory system, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, Eating quality, Biology, Processing, 0404 agricultural biotechnology, Animal science, Grazing, [SDV.IDA]Life Sciences [q-bio]/Food engineering, medicine, Animals, Muscle, Skeletal, Flavor, 2. Zero hunger, chemistry.chemical_classification, Local breed, 0402 animal and dairy science, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, 040401 food science, 040201 dairy & animal science, Diet, Tenderness, Odor, chemistry, Pork Meat, Animal Science and Zoology, Intramuscular fat, Seasons, medicine.symptom, Polyunsaturated fatty acid
Abstract: International audience; The quality of pork products from local breeds in extensive systems depends, among other things, on pig production. In particular, the variability in climatic conditions and feeding resources may influence the properties of tissues at slaughter and the quality of pork and processed products. The present study (part 2) was part of a larger project that assessed the influence of the finishing season and feeding resources on carcass and tissue traits and the quality of meat and dry-cured ham from Gascon pigs in an extensive system. Following the specifications of the Protected Designation of Origin “Noir de Bigorre”, castrated Gascon males were reared on rangelands (grassland and forest areas) and received a supplementary diet from 5 to 6 months of age until slaughter at a minimum of 12 months and ca. 170 kg BW. Three finishing seasons were considered: Winter (n = 18), Spring (n = 22) and Autumn (n = 23). To estimate the specific effects of season on quality traits and avoid bias due to effects of genes known to influence these traits, polymorphisms in the RYR1, PRKAG3, MC4R and LEPR genes were included in the analysis models. Compared to Winter pigs, Spring and Autumn pigs had higher ultimate pH in the semimembranosus and gluteus medius (GM) muscles, lower meat lightness (P < 0.05) and tended to have higher GM intramuscular fat (IMF) content (P < 0.10). They also had higher GM contents of saturated, monounsaturated and polyunsaturated fatty acids (FAs) than Winter pigs (P < 0.05). Spring pigs had the lowest n-6:n-3 polyunsaturated FA ratio and the highest GM α-tocopherol content (P < 0.001), indicating pig grazing. The finishing season did not influence the processing yield of dry-cured hams (24-month process). Within each seasonal group, ten hams selected for genetic variability and IMF content were analyzed by a trained sensory panel. The season did not modify the appearance or odor, but influenced texture and taste. Hams from Winter and Spring pigs had higher tenderness and melting fat scores than hams from Autumn pigs (P < 0.01). Hams from Spring pigs had higher taste intensity and salty taste (P < 0.01) but lower positive tastes (e.g. fruits, forest) than hams from the other groups. Overall, finishing season had moderate effects on ham sensory traits. Furthermore, our results reveal high redness, tenderness, taste and odor intensity, and low rancid flavor of hams from Gascon pigs produced in an extensive system.
Published: 2021
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17. Describing variability in pig genes involved in coronavirus infections: towards a One Health perspective in conservation of animal genetic resources

Author: Samuele Bovo, Giuseppina Schiavo, Anisa Ribani, Valerio Joe Utzeri, Valeria Taurisano, Mohamad Ballan, Maria Muñoz, Estefania Alves, Jose P. Araujo, Riccardo Bozzi, Rui Charneca, Federica Di Palma, Ivona Djurkin, Graham Etherington, Ana I. Fernandez, Fabián García, Juan García-Casco, Danijel Karolyi, Maurizio Gallo, José Manuel Martins, Marie-José Mercat, Yolanda Núñez, Raquel Quintanilla, Čedomir Radović, Violeta Razmaite, Juliette Riquet, Radomir Savić, Martin Škrlep, Grazioano Usai, Christoph Zimmer, Cristina Ovilo, and Luca Fontanesi
Abstract: Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a “One Health” perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a “One Health” perspective that should consider conservation programmes of pig genetic resources with twofold objectives: i) genetic resources could be reservoirs of host gene variability useful to design selection programmes to increase resistance to coronaviruses; ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.
Published: 2020
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18. MOESM2 of Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets

Author: Massacci, Francesca, Berri, Mustapha, Lemonnier, Gaetan, Guettier, Elodie, Blanc, Fany, Jardet, Deborah, Rossignol, Marie, Marie-José Mercat, Doré, Joël, Lepage, Patricia, Rogel-Gaillard, Claire, and Estellé, Jordi
Abstract: Additional file 2: Figure S2. NMDS plot of microbiota composition before weaning (A), after weaning (B), and at 60 days of age (C); samples from all the weaning groups were combined.
Published: 2020
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19. Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

Author: Čedomir Radović, Valerio Joe Utzeri, Rui Charneca, Juan García-Casco, Christoph Zimmer, Raquel Quintanilla, Samuele Bovo, Danijel Karolyi, E. Alves, Angeles Fernandez, Luca Fontanesi, João P. Araújo, J.M. Martins, Martin Škrlep, F. Di Palma, Radomir Savić, Marie-José Mercat, Ricardo Bozzi, María Muñoz, Violeta Razmaite, Graham J Etherington, Kristina Gvozdanović, Giuseppina Schiavo, Anisa Ribani, Yolanda Núñez, Maurizio Gallo, G. Usai, Cristina Óvilo, Felisa Laíz García, Juliette Riquet, Bovo S., Ribani A., Munoz M., Alves E., Araujo J.P., Bozzi R., Charneca R., Di Palma F., Etherington G., Fernandez A.I., Garcia F., Garcia-Casco J., Karolyi D., Gallo M., Gvozdanovic K., Martins J.M., Mercat M.J., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Schiavo G., Skrlep M., Usai G., Utzeri V.J., Zimmer C., Ovilo C., Fontanesi L., University of Bologna/Università di Bologna, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Instituto Nacional de Investigación Agropecuaria (INIA), Instituto Politécnico de Viana do Castelo = Polytechnic Institute of Viana do Castelo (IPVC), UNIVERSITY OF FIRENZE (UNIVERSITY OF FIRENZE), Università degli Studi di Firenze = University of Florence (UniFI), Universidade de Évora, Earlham Institute [Norwich], University of Zagreb, Assoc Nazl Allevatori Suini, University of Osijek, Institut du Porc (IFIP), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Lithuanian University of health Sciences, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], Agricultural Institute of Slovenia, Agenzia della Regione Sardegna per la Ricerca Scientifica (AGRIS), Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Institute of animal husbandry, Slovenian Agency of Research / P4-0133, European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), University of Bologna, Instituto Politécnico de Viana do Castelo, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute of Agrifood Research and Technology (IRTA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Producció Animal, and Genètica i Millora Animal
Subjects: 0301 basic medicine, Male, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], DNA Copy Number Variations, Sus scrofa, Breeding, Genome, DNA sequencing, 03 medical and health sciences, Species Specificity, copy number variant, ELOVL6, genetic resource, KIT, MSRB3, next-generation sequencing, ZNF622, Genetics, Animals, Copy-number variation, Gene, 2. Zero hunger, Whole genome sequencing, Genetic diversity, biology, Genetic ressource, Whole Genome Sequencing, Animal, 0402 animal and dairy science, Turopolje pig, 04 agricultural and veterinary sciences, General Medicine, DNA, biology.organism_classification, 040201 dairy & animal science, Breed, 030104 developmental biology, Phenotype, Italy, Evolutionary biology, Animal Science and Zoology, Female
Abstract: In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed‐specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed‐specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems. info:eu-repo/semantics/acceptedVersion
Published: 2020
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20. Towards the quantitative characterization of piglets' robustness to weaning: A modelling approach

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

21. Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

Author: Marie-José Mercat, Christoph Zimmer, Anisa Ribani, I. Djurkin-Kušec, Danijel Karolyi, Luca Fontanesi, Radomir Savić, Giuseppina Schiavo, Jordi Estellé, Martin Škrlep, Čedomir Radović, María Muñoz, Marjeta Čandek-Potokar, Samuele Bovo, Valerio Joe Utzeri, Ana Isabel Fernández, Juliette Riquet, Maurizio Gallo, José Pedro Araújo, Vladimir Margeta, Cristina Óvilo, Riccardo Bozzi, Fabián García, Juan García-Casco, J.M. Martins, Rui Charneca, Raquel Quintanilla, Oreste Franci, Violeta Razmaite, Yolanda Núñez, J. Tibau, Producció Animal, Genètica i Millora Animal, Departamento de Mejora Genética Animal, Instituto Nacional de Investigaciones Agronomicas, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Department of Agricultural and Food Sciences, University of Bologna, Kmetijski Institut Slovenije, Partenaires INRAE, Universidade de Évora, Institute of Agrifood Research and Technology (IRTA), University of Osijek, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), Lithuanian University of health Sciences, Centro de Investigação de Montanha [Bragança, Portugal] (CIMO), Instituto Politécnico de Bragança, Faculty of Agriculture, Université nationale du Rwanda, Department of Animal Science, Faculty of Agriculture, University of Ghana, Associazione Nazionale Allevatori Suini, European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Munoz M., Bozzi R., Garcia-Casco J., Nunez Y., Ribani A., Franci O., Garcia F., Skrlep M., Schiavo G., Bovo S., Utzeri V.J., Charneca R., Martins J.M., Quintanilla R., Tibau J., Margeta V., Djurkin-Kusec I., Mercat M.J., Riquet J., Estelle J., Zimmer C., Razmaite V., Araujo J.P., Radovic C., Savic R., Karolyi D., Gallo M., Candek-Potokar M., Fernandez A.I., Fontanesi L., Ovilo C., Óvilo, C., Università degli Studi di Firenze = University of Florence (UniFI), University of Bologna/Università di Bologna, Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), and Université de Toulouse (UT)-Université de Toulouse (UT)
Subjects: 0301 basic medicine, Linkage disequilibrium, pig, breed, genomic diversity, SNP chip, SNP chips, Molecular biology, Swine, Population genetics, [SDV]Life Sciences [q-bio], Sus scrofa, lcsh:Medicine, Breeding, selection signatures, Linkage Disequilibrium, Effective population size, local pig breeds, lcsh:Science, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, education.field_of_study, Principal Component Analysis, Multidisciplinary, Genome, biology, 04 agricultural and veterinary sciences, Genomics, Breed, SNP genotyping, Alentejana, genomic diversity, selection signatures, local pig breeds, SNPs, Phenotype, Animals, Domestic, Pigs, SNPs, Genotype, Population, SNP, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Genetic variation, Animals, Genetic resource, [INFO]Computer Science [cs], education, Animal breeding, Population Density, genomics, local breeds, diversity, Genetic diversity, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genomic diversity, lcsh:R, 0402 animal and dairy science, Genetic Variation, Phenotypic trait, Selection signature, biology.organism_classification, 040201 dairy & animal science, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Genetics, Population, Evolutionary biology, Local breeds, lcsh:Q
Abstract: Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.
Published: 2019
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22. Projet TREASURE : Diversité des races locales de porcs et des systèmes de production pour des produits traditionnels de qualité élevée et des filières porcines durables

Author: Lebret, Bénédicte, Brossard, Ludovic, Garcia-Launay, Florence, Faure Justine, Servin, Bertrand, Riquet, Juliette, Estellé, Jordi, Marie-José Mercat, Lenoir, Herveline, and Čandek-Potokar, Marjeta
Published: 2019
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23. Integrating blood transcriptome and immunity traits to identify markers of immune capacity in pigs

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

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

Author: Francesca Massacci, El Mostafa Berri, Gaetan Lemonnier, Deborah Jardet, Fany BLANC, Manuel Revilla Sanchez, Marie-José Mercat, Joel Dore, Patricia Lepage, Claire Rogel Gaillard, Jordi Estelle Fabrellas, Pigletbiota Anr Consortium, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Département Santé Animale (DEPT SA), Institut National de la Recherche Agronomique (INRA), Modélisation Systémique Appliquée aux Ruminants (MoSAR), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut du Porc (IFIP), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Projet ANR-14-CE18-0004 PIGLETBIOTA, and European Federation of Animal Science (EAAP). INT.
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2018
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25. 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
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26. Genetic relationships between measures of sexual development, boar taint, health, and aggressiveness in pigs1

Author: Catherine Larzul, Armelle Prunier, Elodie Merlot, Marie-José Mercat, and Séverine Parois
Subjects: endocrine system, medicine.medical_specialty, Boar taint, Androstenone, General Medicine, Biology, Heritability, Crossbreed, chemistry.chemical_compound, Animal science, Endocrinology, chemistry, Internal medicine, Genetics, medicine, Animal Science and Zoology, Skatole, Purebred, Testosterone, Food Science, Hormone
Abstract: Breeding intact boars is a promising alternative to surgical castration of piglets. Genetic selection should enable farmers to solve problems due to boar taint and aggressiveness while taking into account potential consequences on other traits of interest. The aim of the study was to estimate genetic relations between sexual development, boar taint, health, and aggressiveness. About 1,600 Pietrain (purebred) or Pietrain × Large White (crossbred) boars were raised in a testing station. Blood samples were collected at about 105 kg BW for measuring sex hormones (testosterone and estradiol) and indicators of the inflammatory status (C-reactive protein [CRP], pig major acute-phase protein [pigMAP], and blood formula). Animals were slaughtered 9 d later and measured for boar taint compounds present in fat (androstenone and skatole) and skin lesions on carcass, an indicator of aggressiveness. For both genetic types, heritability was moderate for sex hormones (from 0.17 to 0.29) and skatole (0.24 for purebred and 0.37 for crossbred) and high for androstenone (0.63 and 0.70 for purebred and crossbred, respectively). Genetic correlations between sex hormones and boar taint compounds were moderate to high (from 0.31 to 0.95). Heritability was moderate for CRP (0.24 and 0.46 for purebred and crossbred, respectively) and very low for pigMAP (0.06 and 0.05 for purebred and crossbred, respectively. Numbers of leukocytes had moderate to high heritabilities according to the genetic type (from 0.21 to 0.52). Heritability of skin lesions was moderate for both genetic types (0.31). Genetic correlations were negative between sex hormones and inflammatory measures (from -0.46 to -0.05), positive between testosterone and number of lesions (0.43 and 0.53 for purebred and crossbred, respectively), and low between androstenone and lesions (-0.06 and -0.17 for purebred and crossbred, respectively). Overall, both breeds of pigs had very similar estimations of heritabilities, but estimates of genetic correlations were different for some pairs of traits. It would be possible to select boars based on their plasma concentration of sex hormones to decrease boar taint and aggressiveness without important consequences on the immune response. However, because of the strong links between boar taint and reproductive function, the possible consequences on the reproductive performance should be evaluated.
Published: 2015
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27. Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis

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

Author: Marjeta Čandek-Potokar, Rosa Nieto, Carolina Pugliese, Jose P. Araujo, Rui Charneca, Juan M. Garcia Casco, Elena González Sánchez, Francisco I. Hernandez-Garcia, Mercedes Izquierdo, Danijel Karolyi, Goran Kušec, Benedicte Lebret, Marie-José Mercat, Matthias Petig, Čedomir Radović, Radomir Savić, Marjeta Čandek-Potokar, Rosa Nieto, Carolina Pugliese, Jose P. Araujo, Rui Charneca, Juan M. Garcia Casco, Elena González Sánchez, Francisco I. Hernandez-Garcia, Mercedes Izquierdo, Danijel Karolyi, Goran Kušec, Benedicte Lebret, Marie-José Mercat, Matthias Petig, Čedomir Radović, and Radomir Savić
Abstract: TREASURE is a research and innovation project of European Union’s Horizon 2020 programme which is devoted to traditional genetic resources in pig production with aim to improve their potentials for enhanced use. Studying and improving management of local pig breeds in their production systems is one of the challenges in which we address their performances and nutrition with special attention on locally available feeding resources and innovative practices aiming to improved welfare. For that purpose 15 experiments on 12 breeds were designed in the project, which are hereafter shortly presented. Their concepts and main objectives with some highlights on already available results are described.
Published: 2017

29. 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

30. Phenotypic prediction based on metabolomic data for growing pigs from three main European breeds1

Author: Laurence Liaubet, Florian Rohart, Jérôme Molina, Nathalie Iannuccelli, Denis Milan, Marie José. Mercat, Nathalie Villa-Vialaneix, Nelly Muller, M. San Cristobal, Cécile Canlet, Alain Paris, Béatrice Laurent, and Thierry Tribout
Subjects: 2. Zero hunger, 0303 health sciences, Animal breeding, business.industry, 0402 animal and dairy science, Contrast (statistics), Feature selection, 04 agricultural and veterinary sciences, General Medicine, Computational biology, Biology, 040201 dairy & animal science, Phenotype, Cross-validation, 3. Good health, Biotechnology, 03 medical and health sciences, Metabolomics, Wavelet, Genetics, Animal Science and Zoology, business, 030304 developmental biology, Food Science, Lean meat
Abstract: 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 growing pigs. 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 before slaughter, and slaughter is known to have a strong influence on these traits. By contrast, phenotypes of potential economic interest (e.g., lean meat percentage and ADFI) were well predicted (R2 = 0.7; P < 0.0001) using metabolomic data.
Published: 2012
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31. Detection of quantitative trait loci for reproduction and production traits in Large White and French Landrace pig populations(Open Access publication)

Author: Hélène Gilbert, Thierry Tribout, Pascale Le Roy, Juliette Riquet, Denis Milan, R. Gueblez, Tom Druet, Nathalie Iannuccelli, Jean Pierre Bidanel, and Marie-José Mercat
Subjects: 2. Zero hunger, Genetics, Litter (animal), 0303 health sciences, media_common.quotation_subject, 0402 animal and dairy science, Population genetics, 04 agricultural and veterinary sciences, General Medicine, Quantitative genetics, Quantitative trait locus, Biology, Selective breeding, 040201 dairy & animal science, Sexual reproduction, 03 medical and health sciences, Animal science, Microsatellite, Animal Science and Zoology, Reproduction, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, media_common
Abstract: A genome-wide scan was performed in Large White and French Landrace pig populations in order to identify QTL affecting reproduction and production traits. The experiment was based on a granddaughter design, including five Large White and three French Landrace half-sib families identified in the French porcine national database. A total of 239 animals (166 sons and 73 daughters of the eight male founders) distributed in eight families were genotyped for 144 microsatellite markers. The design included 51 262 animals recorded for production traits, and 53 205 litter size records were considered. Three production and three reproduction traits were analysed: average backfat thickness (US_M) and live weight (LWGT) at the end of the on-farm test, age of candidates adjusted at 100 kg live weight, total number of piglets born per litter, and numbers of stillborn (STILLp) and born alive (LIVp) piglets per litter. Ten QTL with medium to large effects were detected at a chromosome-wide significance level of 5% affecting traits US_M (on SSC2, SSC3 and SSC17), LWGT (on SSC4), STILLp (on SSC6, SSC11 and SSC14) and LIVp (on SSC7, SSC16 and SSC18). The number of heterozygous male founders varied from 1 to 3 depending on the QTL.
Published: 2007
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32. 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
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33. Le metabolome, un moyen pour trouver de nouveaux biomarqueurs ?

Author: Magali San Cristobal, Marie Pierre Sanchez, Marie‐josé Mercat, Florian Rohart, Laurence Liaubet, Thierry Tribout, Cecile Canlet, Nelly Muller, Jerome Molina, Nathalie Iannuccelli, Béatrice Laurent, Nathalie Villa-Vialaneix, Alain Paris, Denis Milan, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut du Porc (IFIP), Australian Institute for Bioengineering & Nanotechnology, University of Southern Queensland (USQ), Toxicologie Alimentaire (UTA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Unité expérimentale de testage de porcs, 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), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Statistique, Analyse et Modélisation Multidisciplinaire (SAmos-Marin Mersenne) (SAMM), Université Paris 1 Panthéon-Sorbonne (UP1), Physiologie de la Nutrition et du Comportement Alimentaire (PNCA), Muséum national d'Histoire naturelle (MNHN), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National des Sciences Appliquées (INSA), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut du Porc, University of Queensland (UQ), 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 Panthéon-Sorbonne (UP1), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, University of Queensland ( UQ ), Toxicologie Alimentaire ( UTA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique ( INRA ) -Génétique animale ( G.A. ) -Unité Expérimentale de Testage de Porcs ( UETP ), Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ), Unité de Biométrie et Intelligence Artificielle ( UBIA ), Institut National de la Recherche Agronomique ( INRA ), Statistique, Analyse et Modélisation Multidisciplinaire (SAmos-Marin Mersenne) ( SAMM ), Université Panthéon-Sorbonne ( UP1 ), Physiologie de la Nutrition et du Comportement Alimentaire ( PNCA ), and Muséum National d'Histoire Naturelle ( MNHN )
Subjects: [ SDV ] Life Sciences [q-bio], prédiction de phénotype, [SDV]Life Sciences [q-bio], analyse métabolomique, porc
Abstract: Cette étude visait à quantifier le pouvoir prédictif du métabolome sur des phénotypes de production dans la filière porcine. Des données métabolomiques ont été obtenues par Résonance Magnétique Nucléaire à partir d’une prise de sang réalisée pendant la période de croissance de l’animal. Selon le type de phénotype considéré, un spectre métabolomique peut être envisagé comme une source de biomarqueurs intéressants. Ainsi, le taux de muscle des pièces de la carcasse a pu être correctement prédit à partir des mesures prises sur des prélèvements réalisés à environ 60 kg., This study was aimed at quantifying the predictive power of metabolomic data on production phenotypes in the pig. Metabolomic data were obtained by Nuclear Magnetic Resonance from one blood sample during the growing period of the animals. Depending on the phenotype, a metabolomic spectrum can be envisioned as a source of suitable biomarkers. In particular, the lean meat percentage was correctly predicted from samples taken at around 60 kg
Published: 2014

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

Author: Claire Rogel-Gaillard, Denis Milan, Nathalie Iannuccelli, Thierry Tribout, Patrice Dehais, Bertrand Servin, Hélène Gilbert, Nelly Muller, Jean Pierre Bidanel, Marie-José Mercat, Marie Pierre Sanchez, A.M.M. Tenghe, Marcel Bouffaud, Maria Pilar Del Schneider, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité expérimentale de testage de porcs, Institut National de la Recherche Agronomique (INRA), Pôle génétique, Institut du Porc (IFIP), French National Agency for Research (ANR, Paris) [ANR-07-GANI-001, ANR-06-GANI-008], BIOPORC (ADN, Nucleus and Gene + breeding organizations), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), UE 0450 Unité Expérimentale de Testage de Porcs, Institut National de la Recherche Agronomique (INRA)-Génétique animale (G.A.)-Unité Expérimentale de Testage de Porcs (UETP), and Institut du Porc
Subjects: Male, Meat, Genotype, [SDV]Life Sciences [q-bio], Population, Quantitative Trait Loci, Sus scrofa, Single-nucleotide polymorphism, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Family-based QTL mapping, Genetics, Animals, Genetics(clinical), education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetic association, 2. Zero hunger, 0303 health sciences, education.field_of_study, Autosome, Genome, Research, Haplotype, 0402 animal and dairy science, food and beverages, 04 agricultural and veterinary sciences, General Medicine, 040201 dairy & animal science, Phenotype, Haplotypes, Body Composition, Microsatellite, Animal Science and Zoology, Genome-Wide Association Study
Abstract: Background: Numerous quantitative trait loci (QTL) have been detected in pigs over the past 20 years using microsatellite markers. However, due to the low density of these markers, the accuracy of QTL location has generally been poor. Since 2009, the dense genome coverage provided by the Illumina PorcineSNP60 BeadChip has made it possible to more accurately map QTL using genome-wide association studies (GWAS). Our objective was to perform high-density GWAS in order to identify genomic regions and corresponding haplotypes associated with production traits in a French Large White population of pigs. Methods: Animals (385 Large White pigs from 106 sires) were genotyped using the PorcineSNP60 BeadChip and evaluated for 19 traits related to feed intake, growth, carcass composition and meat quality. Of the 64 432 SNPs on the chip, 44 412 were used for GWAS with an animal mixed model that included a regression coefficient for the tested SNPs and a genomic kinship matrix. SNP haplotype effects in QTL regions were then tested for association with phenotypes following phase reconstruction based on the Sscrofa10.2 pig genome assembly. Results: Twenty-three QTL regions were identified on autosomes and their effects ranged from 0.25 to 0.75 phenotypic standard deviation units for feed intake and feed efficiency (four QTL), carcass (12 QTL) and meat quality traits (seven QTL). The 10 most significant QTL regions had effects on carcass (chromosomes 7, 10, 16, 17 and 18) and meat quality traits (two regions on chromosome 1 and one region on chromosomes 8, 9 and 13). Thirteen of the 23 QTL regions had not been previously described. A haplotype block of 183 kb on chromosome 1 (six SNPs) was identified and displayed three distinct haplotypes with significant (0.0001 < P < 0.03) associations with all evaluated meat quality traits. Conclusions: GWAS analyses with the PorcineSNP60 BeadChip enabled the detection of 23 QTL regions that affect feed consumption, carcass and meat quality traits in a LW population, of which 13 were novel QTL. The proportionally larger number of QTL found for meat quality traits suggests a specific opportunity for improving these traits in the pig by genomic selection.
Published: 2014
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35. A genome-wide association study points out the causal implication of SOX9 in the sex-reversal phenotype in XX pigs

Author: Denis Milan, Juliette Riquet, Nathalie Iannuccelli, Marie-José Mercat, Bertrand Servin, Sarah Rousseau, Claire Naylies, Jean-Claude Thouly, Eric Pailhoux, 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, Domaine expérimental de la Motte au Vicomte (RENN RHEU UE), Institut National de la Recherche Agronomique (INRA), Domaine expérimental Bourges-La Sapinière (BOURGES), 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), French National Research Agency (Agence Nationale de la Recherche) ANR-08-GENM-040 SwAn, BIOPORC, LABOGENA, Research Ministry (CIFFRE grant), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), and Biologie du Développement et Reproduction (BDR)
Subjects: Male, Candidate gene, Sterility, Science, Population, Disorders of Sex Development, Locus (genetics), Biology, 03 medical and health sciences, 0302 clinical medicine, Biologie de la reproduction, Animals, education, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, Genetics, Reproductive Biology, 0303 health sciences, education.field_of_study, Multidisciplinary, Sexual differentiation, génome, inversion sexuelle, Haplotype, Biologie du développement, SOX9 Transcription Factor, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, hermaphrodisme, Sex reversal, Development Biology, phénotype, Testis determining factor, Haplotypes, 030220 oncology & carcinogenesis, Medicine, Female, adn génomique, différenciation sexuelle, porc, gène sry, Genome-Wide Association Study, Research Article
Abstract: Among farm animals, pigs are known to show XX sex-reversal. In such cases the individuals are genetically female but exhibit a hermaphroditism, or a male phenotype. While the frequency of this congenital disease is quite low (less than 1%), the economic losses are significant for pig breeders. These losses result from sterility, urogenital infections and the carcasses being downgraded because of the risk of boar taint. It has been clearly demonstrated that the SRY gene is not involved in most cases of sex-reversal in pigs, and that autosomal recessive mutations remain to be discovered. A whole-genome scan analysis was performed in the French Large-White population to identify candidate genes: 38 families comprising the two non-affected parents and 1 to 11 sex-reversed full-sib piglets were genotyped with the PorcineSNP60 BeadChip. A Transmission Disequilibrium Test revealed a highly significant candidate region on SSC12 (most significant p-value
Published: 2013
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36. 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

37. 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

38. 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

39. Deciphering the genetic control of innate and adaptive immune responses in pig: a combined genetic and genomic study

Author: François Lefèvre, Yu Gao, Marcel Bouffaud, Jean Pierre Bidanel, Marie-José Mercat, Claire Rogel-Gaillard, Isabelle P. Oswald, Laurence Flori, 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, Pôle Amélioration de l'animal, Institut du Porc (IFIP), ANR IMMOPIG, 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 moléculaire et cellulaire, Unité Expérimentale de Testage de Porcs, Institut du Porc, Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Unité de recherche Virologie et Immunologie Moléculaires (VIM)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Lymphocyte, chemical and pharmacologic phenomena, Lymphocyte proliferation, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Immune system, Immunity, medicine, resistance to pathogens, animal robustness, blood stimulation, immunity traits, 030304 developmental biology, Genetics, 0303 health sciences, Innate immune system, 0402 animal and dairy science, immunity trait, 04 agricultural and veterinary sciences, General Medicine, Heritability, Acquired immune system, 040201 dairy & animal science, 3. Good health, Vaccination, medicine.anatomical_structure, Proceedings, Immunology
Abstract: Improving animal robustness and resistance to pathogens by adding health criteria in 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 not focussing on any particular pathogen. 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 IFNαafter 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 haploglobin). Across traits, heritability estimates reached 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 the blood transcriptome is informative for part of the immunity traits and should provide relevant phenotypic information to better characterize some immunity traits.
Published: 2011
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40. Immunity traits in pigs: substantial genetic variation and limited covariation

Author: Marcel Bouffaud, Yu Gao, Jean-Jacques Leplat, Angélique Teillaud, Isabelle P. Oswald, Claire Rogel-Gaillard, Joëlle Laffitte, Gaetan Lemonnier, Denis Laloë, Christiane de Vaureix, Laurence Flori, Anne-Marie Cossalter, Jean Pierre Bidanel, Marie-José Mercat, Philippe Pinton, François Lefèvre, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche Pharmacologie-Toxicologie (UPT), Institut National de la Recherche Agronomique (INRA), Unité de recherche Virologie et Immunologie Moléculaires (VIM), Unité Expérimentale de Testage de Porcs, Pôle Amélioration de l'animal, Institut du Porc, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Unité expérimentale de testage de porcs, Institut du Porc (IFIP), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: Male, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, deoxynivalenol, lcsh:Medicine, Lymphocyte proliferation, Adaptive Immunity, medicine.disease_cause, paramètre, Genetics of the Immune System, sélection, lcsh:Science, Immune Response, innate immunity, large white, Animal Management, immune trait, Swine Diseases, 2. Zero hunger, Genetics, Principal Component Analysis, 0303 health sciences, Multidisciplinary, response, Vaccination, Mycoplasma hyopneumoniae, 04 agricultural and veterinary sciences, Pneumonia of Swine, Mycoplasmal, Flow Cytometry, Phenotype, parameter, Cytokines, Female, performance, Research Article, Veterinary Medicine, Genetic Markers, Immunology, lymphocyte sanguin, selection, Biology, Veterinary Immunology, 03 medical and health sciences, breeding, resistance to pathogen, livestock, blood lymphocyte, cell, swine, pathogène, Genetic variation, Heredity, medicine, Animals, Selection, Genetic, 030304 developmental biology, Animal Performance, Innate immune system, lcsh:R, 0402 animal and dairy science, Genetic Variation, Robustness (evolution), Heritability, élevage, 040201 dairy & animal science, Immunity, Innate, Genetic marker, Veterinary Science, lcsh:Q, cellule, Animal Genetics
Abstract: Chantier qualité GA; Background: Increasing robustness via improvement of resistance to pathogens is a major selection objective in livestock breeding. As resistance traits are difficult or impossible to measure directly, potential indirect criteria are measures of immune traits (ITs). Our underlying hypothesis is that levels of ITs with no focus on specific pathogens define an individual's immunocompetence and thus predict response to pathogens in general. Since variation in ITs depends on genetic, environmental and probably epigenetic factors, our aim was to estimate the relative importance of genetics. In this report, we present a large genetic survey of innate and adaptive ITs in pig families bred in the same environment.[br/] Methodology/Principal Findings: Fifty four ITs were studied on 443 Large White pigs vaccinated against Mycoplasma hyopneumoniae and analyzed by combining a principal component analysis (PCA) and genetic parameter estimation. ITs include specific and non specific antibodies, seric inflammatory proteins, cell subsets by hemogram and flow cytometry, ex vivo production of cytokines (IFNa, TNFa, IL6, IL8, IL12, IFNc, IL2, IL4, IL10), phagocytosis and lymphocyte proliferation. While six ITs had heritabilities that were weak or not significantly different from zero, 18 and 30 ITs had moderate (0.1,h2#0.4) or high (h2.0.4) heritability values, respectively. Phenotypic and genetic correlations between ITs were weak except for a few traits that mostly include cell subsets. PCA revealed no cluster of innate or adaptive ITs. [br/] Conclusions/Significance: Our results demonstrate that variation in many innate and adaptive ITs is genetically controlled in swine, as already reported for a smaller number of traits by other laboratories. A limited redundancy of the traits was also observed confirming the high degree of complementarity between innate and adaptive ITs. Our data provide a genetic framework for choosing ITs to be included as selection criteria in multitrait selection programmes that aim to improve both production and health traits.
Published: 2011
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41. Effects of 6 QTL on growth, carcass composition and ultimate PH of Longissimus Dorsi in 65 commercial or experimental sire pig families

Author: Marie-Pierre Sanchez, Nathalie Iannuccelli, Guillaume Le Mignon, Sophie Ruzafa, Marie-José Mercat, Nicolas Dechamp, Yvon Billon, Marcel Bouffaud, Sandrine Schwob, Hélène Gilbert, Juliette Riquet, Jean Pierre Bidanel, Denis Milan, 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), Institut du Porc, Génétique Expérimentale en Productions Animales (GEPA), 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), 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, Institut du Porc (IFIP), and Unité expérimentale de testage de porcs
Subjects: musculoskeletal diseases, viande, muscle, QTL, LONGISSIMUS DORSI, [SDV]Life Sciences [q-bio], education, GENETIQUE, musculoskeletal system, sus scrofa, carcasse, croissance animale, porcin, porc
Abstract: CD-ROM; absent
Published: 2010

42. 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
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43. The adult boar testicular and epididymal transcriptome

Author: Benoît Guyonnet, Jean-Luc Gatti, Anne Lacoste, Jean-Louis Dacheux, Guillemette Marot, Sandrine Schwob, Marie-José Mercat, 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 (UT)-Centre National de la Recherche Scientifique (CNRS), Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), Institut Technique du Porc (ITP), ProdInra, Migration, 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: 0303 health sciences, 030219 obstetrics & reproductive medicine, BOAR, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Cell Biology, General Medicine, Biology, Transcriptome, Andrology, 03 medical and health sciences, 0302 clinical medicine, Reproductive Medicine, [SDV.BDLR] Life Sciences [q-bio]/Reproductive Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience
Published: 2008

44. Detection of quantitative trait loci for reproduction and production traits in Large White and French Landrace pig populations (Open Access publication)

Author: Thierry Tribout, Tom Druet, Pascale Le Roy, Riquet Juliette, Denis Milan, Gueblez Ronan, Marie-José Mercat, Hélène Gilbert, Jean Pierre Bidanel, and Nathalie Iannuccelli
Subjects: Genetic Markers, Male, pig, Litter (animal), production trait, Genotype, Litter Size, lcsh:QH426-470, Swine, media_common.quotation_subject, Quantitative Trait Loci, French landrace pig, commercial population, Live weight, Efficiency, Biology, Quantitative trait locus, 03 medical and health sciences, quantitative trait locus, Animal science, Genetics, Animals, Genetics(clinical), ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, lcsh:SF1-1100, 030304 developmental biology, media_common, 2. Zero hunger, 0303 health sciences, Research, Reproduction, Body Weight, 0402 animal and dairy science, Chromosome Mapping, Large white, 04 agricultural and veterinary sciences, General Medicine, 040201 dairy & animal science, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, reproduction trait, lcsh:Genetics, Microsatellite, Female, Animal Science and Zoology, National database, lcsh:Animal culture
Abstract: A genome-wide scan was performed in Large White and French Landrace pig populations in order to identify QTL affecting reproduction and production traits. The experiment was based on a granddaughter design, including five Large White and three French Landrace half-sib families identified in the French porcine national database. A total of 239 animals (166 sons and 73 daughters of the eight male founders) distributed in eight families were genotyped for 144 microsatellite markers. The design included 51 262 animals recorded for production traits, and 53 205 litter size records were considered. Three production and three reproduction traits were analysed: average backfat thickness (US_M) and live weight (LWGT) at the end of the on-farm test, age of candidates adjusted at 100 kg live weight, total number of piglets born per litter, and numbers of stillborn (STILLp) and born alive (LIVp) piglets per litter. Ten QTL with medium to large effects were detected at a chromosome-wide significance level of 5% affecting traits US_M (on SSC2, SSC3 and SSC17), LWGT (on SSC4), STILLp (on SSC6, SSC11 and SSC14) and LIVp (on SSC7, SSC16 and SSC18). The number of heterozygous male founders varied from 1 to 3 depending on the QTL.
Published: 2008
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45. Effects of six QTL regions on growth, carcass composition and meat quality traits in French comercial pig populations: first results of BIOMARK project

Author: Sanchez, Marie-Pierre, Marie-José Mercat, Dechamp, Nicolas, Iannuccelli, Nathalie, Gilbert, Hélène, Billon, Yvon, Bouffaud, Marcel, Schwob, Sandrine, Riquet, Juliette, Bidanel, Jean-Pierre, and Milan, Denis
Published: 2008
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46. Growth, carcass and meat quality of gascon pigs produced according to the noir de bigorre pdo specifications: variability and influence of local feeding resources on phenotypic pigs

Author: Benedicte Lebret, Herveline Lenoir, Alexandre Fonseca, Justine Faur, and Marie-José Mercat
Subjects: 2. Zero hunger, pork quality, local resources, Noir de Bigorre chain, Gascon breed
Abstract: The Noir de Bigorre (NB) pork chain (pure Gascon breed) recently obtained the national "AOC" label required for further Protected Designation Origin (PDO) registration, for both fresh meat and dry cured hams.

47. 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

48. Influence de l’agressivité sur le comportement alimentaire, le développement sexuel et les odeurs sexuelles chez le porc mâle entier

Author: Séverine Parois, Geoffrey Bissianna, Sabine Herlemont, Marie-José Mercat, Benoit Blanchet, Catherine Larzul, Armelle Prunier, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Institut du Porc, Unité Expérimentale de Testage de Porcs, 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), 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], ANR UtOpIGe, Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut du Porc (IFIP), Unité expérimentale de testage de porcs, École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV]Life Sciences [q-bio], stéroïde sexuel, swine, porc mâle entier, androsténone, comportement animal, porc
Abstract: Chez le porc mâle entier, le comportement social pourrait influencer le développement sexuel et le comportement alimentaire. Les objectifs de cette étude sont d’étudier 1) les relations entre agressivité et comportement alimentaire ou développement sexuel ; 2) les répercussions sur les odeurs sexuelles ; 3) le lien entre comportement alimentaire et développement sexuel. L’étude porte sur 216 porcs issus de deux types génétiques croisés distincts, élevés en loge collective de 12. Les animaux sont observés 10 heures par jour sur deux périodes de deux jours : à l’entrée et en fin d’engraissement. Les comportements agonistiques (combat, coup de tête, morsure, menace, poursuite) sont dénombrés par individu. Les lésions (indicateur de l’agressivité) sont dénombrées 48 heures après l’entrée en engraissement, en élevage avant les premiers départs à l’abattoir ainsi que sur la carcasse. Les données de distributeurs automatiques de concentré ont été utilisées pour renseigner le comportement alimentaire (le nombre de repas, leur durée et la quantité consommée) sur des périodes de 96 heures. En fin d’engraissement, du sang est prélevé pour mesurer deux hormones sexuelles (oestradiol, testostérone). A l’abattage, du gras est récupéré pour doser les odeurs (androsténone). Dans l’un des deux génotypes, des corrélations significatives positives ont été estimées entre le nombre de lésions à l’abattoir et les hormones sexuelles et l’androsténone. Ces corrélations sont faibles voire nulles dans l’autre génotype probablement parce que les concentrations en hormones sexuelles mesurées sont beaucoup plus faibles. Dans les deux génotypes, il existe des corrélations significatives positives entre les nombres de comportements sexuels et de comportements agonistiques en début d’engraissement. Enfin, les porcs avec le plus de lésions en début d’engraissement sont également les plus gros mangeurs en milieu d’engraissement., In entire male pigs, social behavior could impact sexual development and feeding behavior. The objectives of the study were to study 1) relationships between aggressiveness and feeding behavior or sexual development; 2) impacts on boar taint; 3) relationships between feeding behavior and sexual development. A total of 216 boars of two different crossbred genotypes were used in the study. They were raised in groups of 12 pigs per pen. Animals were observed for 10 hours per day over two periods of two days: at the beginning and at the end of fattening. Agonistic behaviors (fighting, hitting with the head, biting, threatening, chasing) were counted per boar. Skin lesions (an indicator of aggression) were counted: 48 hours after the start of fattening, in farm before the first departure for slaughtering, and on the carcass. Data obtained from the electronic feeders were used to determine the feeding behavior (the number of meals, their duration and the feed intake) over 96-hour periods. At the end of the fattening period, blood was sampled to measure two sexual hormones (estradiol, testosterone). At slaughter, fat was collected to measure boar taint (androstenone). For one of the genotypes, significant positive correlations were demonstrated between the number of skin lesions at slaughter and sexual hormones and androstenone. These correlations were low if not zero in the other genotype probably because the measured concentrations of sexual hormones were too weak. In both genotypes, significant positive correlations were found between the numbers of sexual behavior and agonistic behavior at the beginning of fattening. Finally, boars with the most numerous skin lesions at the beginning of the fattening period were also the biggest eaters in the middle of the fattening period.

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