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A genetic and functional analysis of innate and adaptive immunity in pigs

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PDF icon A genetic and functional analysis of innate and adaptive immunity in pigs
2010

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

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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.

2014

A genome-wide association study points out the causal implication of SOX9 in the sex-reversal phenotype in XX pigs

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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<4.65.10-10) containing the SOX9 gene. SOX9, one of the master genes involved in testis differentiation, was sequenced together with one of its main regulatory region Tesco.
However, no causal mutations could be identified in either of the two sequenced regions. Further haplotype analyses did not identify a shared homozygous segment between the affected pigs, suggesting either a lack of power due to the SNP properties of the chip, or a second causative locus. Together with information from humans and mice, this study in pigs adds to the field of knowledge, which will lead to characterization of novel molecular mechanisms regulating sexual differentiation and dysregulation in cases of sex reversal. 

2013

Accuracy of genomic selection to improve litter traits in the French Landrace pig population

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Poster.

• To assess gains in accuracy due to integration of genomic information in genomic evaluations of pigs,
• Focus on litter traits and on the French Landrace dam line.

PDF icon poster ifip de Alain Bouquet et al., 67th EAAP Meeting, 29/08-02/09/2016, Belfast, Irlande, Royaume-Uni, session 67, poster 23
2016

Additive and dominance genomic parameters for backfat thickness in purebred and crossbred pigs

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Mohammadpanah M (Shahid Bahonar University of Kerman, Iran) et al., 70th Annual meeting of the European Federation of Animal science (EAAP), 26-30 août 2019, Ghent, Belgique, p. 291, poster

In pig crossbreeding programs, genetic evaluation has been based predominantly on purebred data accounting only for additive genetic effects, whereas improving crossbred performance is the ultimate goal. Theoretically, a combined crossbred and purebred selection method is advised if genetic correlation between purebred and crossbred populations differ from unity. If dominance effects are large enough, assortative mating strategies can enhance the total genetic values of the offspring. Hence, estimates of genetic parameters for purebreds and crossbreds are needed to assess the best selection crossbreeding scheme strategies. In this study, additive and dominance genetic variance components and additive and dominance genotypic correlations between a Piétrain and a Piétrain × Large White populations were estimated for backfat thickness (BFT). A total of 607 purebreds and 620 crossbred BFT records were analysed with a genotypic bivariate model that included hot carcass weight and inbreeding coefficient as covariates, an additive and a dominance genotypic effects, and a pen nested within batch random effect. Genetic parameters were estimated with EM-REML plus an additional iteration of AIREML to obtain the asymptotic standard deviations of the estimates. The additive genotypic correlation between purebreds and crossbreds was high, 0.82, indicating that the genetic progress attained in the purebreds can mostly be transferred to the crossbreds. Dominance genetic variance represented about 10% of the BFT phenotypic variance in both populations, suggesting that assortative matings could slightly enhance both purebred and crossbred performances. However, the underlying genetic mechanisms responsible for the dominance effects could differ between populations since dominance genotypic correlation was 0.49.

Document réservé Espace Pro, veuillez vous identifier
2019

An online phenotype database: first step towards breeding programs in local pig breeds

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Marie-José Mercat et al., 69th Annual Meeting of the European Federation of Animal Science (EAAP), Dubrovnik, Croatie, le 27-31 août 2018, visuels d'intervention

In order to further allow implementation of breeding programs in local pig breeds, with selection objectives defined for each local breed, we aimed at developing a standardised recording of carcass and meat quality traits. These data have to be connected with herdbooks to estimate genetic parameters of the traits (heritabilities and genetic correlations) which are necessary to define breeding objectives. Today the situation is very different from one local breed to another. No or very few phenotypes are recorded in some of them, while breeding programs already exist for a few breeds. To promote phenotyping, a dedicated database and a website were developed in the frame of the TREASURE project. First, the required variables have been collected for six local breeds: Basque (FR), Bísaro (PT), Crna slavonska (HR), Gascon (FR), Krškopoljski (SI) and Schwäbisch-Hällisches (DE). In total 74 variables have been identified dealing with animal herdbook information (10), rearing and growth (22), carcass (22) and meat quality (20) attributes. The database is compatible with the various identifiers used in the different countries: animal IDs, breed, farm… codifications. Major attention has been paid to the description of measurement methods of traits. Thus, each carcass and meat quality phenotype is associated to a method description representing 35 additional variables. The website can be easily translated into several languages. The website and database are currently on test until the end of the TREASURE project. All the breeds studied in TREASURE are free to use these tools. The database can be duplicated so that each partner can host its own data. Funded by European Union H2020 RIA program (grant agreement no. 634476).

PDF icon Marie-José Mercat et al., 69th EAAP, Dubrovnik, Croatie, le 27-31 août 2018
2018

Applications moléculaires et génomiques en sélection porcine

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Fiche n° 49 : Progrès génétiques

Les données moléculaires tiennent une place croissante dans les programmes de sélection animaux. C'est pourquoi l'IFIP assure l'animation de l'association Bioporc dont l'objectif est de conduire des programmes de recherche en génomique qui répondent aux attentes des organisations de sélection porcine (OSP). Les OSP ADN, Choice Genetics France, Gène+ et Nucléus et l'IFIP sont membres de Bioporc.

En particulier, à travers le programme UtOpIGe, l'IFIP, l'INRA et les OSP membres de Bioporc mettent en place les pré-requis indispensables à la mise en œuvre d'une sélection génomique chez le porc.

Bien que l'action soit prioritairement conduite auprès des OSP, le programme UtOpIGe et les projets qui lui sont liés cherchent à répondre à des préoccupations sociétales (odeur de mâles entier) et de l'aval (qualités de viande).

PDF icon fiche_bilan2013_49.pdf
2014

Biologie moléculaire et génomique : de nouveaux outils pour la sélection

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Les programmes de sélection animale reposent de plus en plus sur des données d’analyses moléculaires.

L’IFIP gère ces informations pour les organisations de sélection partenaires.

Il coordonne et assure le suivi de projets de recherche en génomique, à l’interface entre les professionnels de la sélection regroupés au sein de BIOPORC et les organismes de recherche.

PDF icon Biologie moléculaire et génomique : de nouveaux outils pour la sélection
2011

BIOMARK : Une évaluation minutieuse de plusieurs QTL en ségrégation dans les lignées commerciales françaises en vue de leur cartographie fine et de la mise en place d'une sélection assistée par marqueur

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Des très nombreux QTL ont été détectés influençant pratiquement tous les caractères pour lesquels des QTL ont été recherchés (Bidanel et Rothschild, 2002). La plupart du temps, ces études ont été réalisées sur des animaux F2 issus du croisement entre animaux de races différentes voire très différentes afin de maximiser la probabilité d’identifier de tels QTL. Pour les QTL les plus importants, il convient ensuite de les cartographier précisément afin de chercher à identifier le gène responsable des effets observés, et de pouvoir sélectionner les animaux porteurs des allèles favorables.
PDF icon BIOMARK : Une évaluation minutieuse de plusieurs QTL en ségrégation dans les lignées commerciales françaises en vue de leur cartographie fine et de la mise en place d'une sélection assistée par marqueur
2009

Building and evaluation of SNPs panels for parentage tests issue in swine

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G Even et al., World Congress on Genetics Applied to Livestock Production, Auckland, Nouvelle Zélande, 11-16 février 2018, posters

Three SNPs panels have been defined for parentage testing in swine containing 100, 200 and 329 SNPs, respectively. Markers have been chosen from the Illumina 60K version 2 chip based on Minor Allele Frequencies (MAF) estimated on twelve breeds used in France. A validation test has been performed confronting products genotypes with those of their right parents or those of animals related or unrelated to their right parents.

Document réservé Espace Pro, veuillez vous identifier
2018

Cartographie fine de QTL porcins : projet Biomark. BIOMARK : Une évaluation minutieuse de plusieurs QTL en ségrégation dans les lignées commerciales françaises en vue de leur cartographie fine et de la mise en place d'une sélection assistée par marqueur

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Des très nombreux QTL ont été détectés influençant pratiquement tous les caractères pour lesquels des QTL ont été recherchés (Bidanel et Rothschild, 2002). La plupart du temps, ces études ont été réalisées sur des animaux F2 issus du croisement entre animaux de races différentes voire très différentes afin de maximiser la probabilité d’identifier de tels QTL. Pour les QTL les plus importants, il convient ensuite de les cartographier précisément afin de chercher à identifier le gène responsable des effets observés, et de pouvoir sélectionner les animaux porteurs des allèles favorables.
PDF icon Cartographie fine de QTL porcins : projet Biomark. BIOMARK : Une évaluation minutieuse de plusieurs QTL en ségrégation dans les lignées commerciales françaises en vue de leur cartographie fine et de la mise en place d'une sélection assistée par marqueur
2008

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

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Près de 500 porcs Large White (106 familles de pères) ont été génotypés pour la puce PorcineSNP60 et contrôlés pour 21 caractères d’ingestion, de croissance, de composition de carcasse et de qualité de la viande. Sur les 64432 marqueurs SNP (Single Nucleotide Polymorphism) de la puce, 44412 ont passé le contrôle qualité et ont donc été utilisés pour des analyses d’association avec la méthode FASTA (estimation conjointe des effets individuels des SNP et de l’effet polygénique).

PDF icon g2jrp44.pdf
2012

Complete genome sequence of Salmonella enterica subsp. enterica Serotype Derby, associated with the pork sector in France

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Yann Sévellec et al., Microbiology Resource Announcements, volume 7, n° 12, septembre, 4 pages

In the European Union, Salmonella enterica subsp. enterica serovar Derby is the most abundant serotype isolated from pork. Recent studies have shown that this serotype is polyphyletic. However, one main genomic lineage, characterized by sequence type 40 (ST40), the presence of the Salmonella pathogenicity island 23, and showing resistance to streptomycin, sulphonamides, and tetracycline (STR-SSS-TET), is pork associated. Here, we describe the complete genome sequence of a strain from this lineage isolated in France.

https://mra.asm.org/content/ga/7/12/e01027-18.full-text.pdf

2018

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

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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.
2010

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

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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.
PDF icon Deciphering the genetic control of innate and adaptive immune responses in pig: a combined genetic and genomic study
2011

Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis

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T. Maroilley et al., BMC Genomics, 2017, 13 décembre, volume 18, n° 1, 13 décembre,19 pages

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.

2017

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

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Un programme d'analyse fine du contrôle génétique de la réponse immunitaire (RI) combinant des approches génétiques et fonctionnelles a été développé. Plus de 400 animaux de race Large White mesurés pour des caractères de production ont été caractérisés pour un large éventail de paramètres de l'immunité trois semaines après vaccination contre Mycoplasma hyopneumoniae.
PDF icon Décryptage du contrôle génétique des réponses immunitaires innées et adaptatives chez le porc Large White : une étude combinant des approches génétiques et fonctionnelles
2011

DéLiSus : variabilité haplotypique et phénotypage haut-débit chez le porc

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Le projet DéLiSus est un projet intégré ayant pour but l'étude de la variabilité haplotypique du génome porcin à haute densité (puce SNP 60k). Les principales races francaises, et les races synthétiques dérivées détenues par les sélectionneurs de BIOPORC sont étudiées. Les animaux des races principales sont phénotypés au sein de la station de contrôle du Rheu. Outre les paramètres zootechniques détaillés et une analyse metabolomique du sérum, une mesure de paramètres de la réponse immune est réalisée sur certains animaux.
PDF icon DéLiSus : variabilité haplotypique et phénotypage haut-débit chez le porc
2010

Détection de QTL avec la puce PorcineSNP60 pour les indicateurs de la qualité technologique de la viande dans une population Large White

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De nombreux locus à effets quantitatifs (QTL) ont été détectés à l’aide de marqueurs microsatellites chez le porc

PDF icon Détection de QTL avec la puce PorcineSNP60 pour les indicateurs de la qualité technologique de la viande dans une population Large White
2012

Detection of quantitative trait loci for reproduction and production traits in Large White and French Landrace pig populations

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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.
2008

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