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Genome-wide association studies in purebred and crossbred entire male pigs

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A total of 654 purebred Piétrain entire male pigs and 716 crossbred Piétrain × Large White entire male pigs issued from about 70 Piétrain sires were tested in a French test station for production traits (feed intake, feed efficiency, growth rate, carcass composition and meat quality). All were genotyped with the 60K Porcine SNPchip. Genome wide association studies were run using linear mixed models with a genomic kinship matrix to account for relatedness between individuals, and the fixed effect of each SNP was tested separately. In a first step, separate analyses of the two populations showed suggestive results (P<0.0001) for almost all traits in the two populations. For production traits, eight 1-Mb regions affected multiple correlated traits in the purebred pigs, and only one in the crossbred pigs. Only two regions with P<0.0001 were detected in common in purebred and crossbred individuals after correction for the halothane mutation, on SSC1 and SSC2. Breed differences in linkage disequilibrium between markers and causal variants, or different gene effects due to the purebred vs crossbred polygenic background could explain these discrepancies. Genotypes were phased and chromosome breed origins were identified in all progeny. Analyses were thus run to estimate within breed allelic effects in the crossbred population, and combining the two populations. After accounting for differences in allele frequencies in the two populations, only few SNP estimates showed significantly different allelic effects depending on the genetic background. If confirmed in a larger design, this suggests that genes affecting production traits act similarly in purebred and crossbred commercial pigs, as suggested by high genetic correlations between purebred and crossbred pigs for these traits.

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2015

La sélection collective inaugure sa station de phénotypage

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France Génétique Porc, consortium regroupant les organismes de sélection porcine (OSP) ADN, GENE+, NUCLEUS et l’IFIP, et l’INRA ont inauguré la station porcine de phénotypage située au Rheu. La volonté collective des opérateurs économiques et des instituts de recherche dote la filière porcine française d’un outil performant pour répondre aux enjeux de la sélection génomique.

PDF icon le plan de la station porcine de phénotypage du rheu -Inra/ifip, PDF icon dossier de vite de la station porcine de phénotypage du Rheu (ifip/inra)
2015

Programmes de recherche en biologie moléculaire et en génomique

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Fiche n° 057 : progrès génétiques

La sélection des animaux s’appuie de plus en plus sur des données moléculaires et de génomique.
C’est pourquoi l’IFIP anime l’association BIOPORC dont l’objectif est de conduire des programmes de recherche en génomique répondant aux attentes des organisations de sélection porcine (OSP).
Les OSP ADN, CHOICE GENETICS FRANCE, GENE+ et NUCLEUS et l’IFIP sont membres de BIOPORC.
L’action est prioritairement conduite auprès des OSP, mais les thématiques abordées dans ces programmes répondent à des préoccupations sociétales et des éleveurs (odeur de mâle entier, sensibilité au sevrage …), et des attentes de l’aval de la filière (qualité des viandes).

PDF icon fiche_bilan2014_057.pdf
2015

Mise en place de la sélection génomique

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Fiche n° 056 : progrès génétiques

La sélection génomique fait l’objet d’un intérêt croissant dans les schémas de sélection porcins.
Malgré un surcoût important par rapport au schéma conventionnel, elle permet de réaliser un choix plus précis des reproducteurs à un âge relativement précoce. Les gains de précision sont particulièrement importants pour les critères dont les quantités d’information sont limitées au moment de la sélection : critères de reproduction, de qualité des carcasses et de la viande, de longévité, etc.
En outre, la sélection génomique ouvre de nouvelles perspectives pour intégrer de façon appropriée les performances issues d’individus croisés
pour la sélection des reproducteurs des lignées de race pure.

PDF icon fiche_bilan2014_056.pdf
2015

Nouvelle station collective de phénotypage FG Porc-Inra : un site dédié à la génomique

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Outil central pour l'obtention de populations de référence dans le cadre de programmes d'amélioration génétique, la station collective FG Porc sera inaugurée fin juin. Présentation et enjeux.

2015

Pedigree and genomic evaluation of pigs using a terminal cross model

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Poster.

In a terminal cross, individuals from purebred parental lines are selected to produce crossbred individuals. Up to now, the inclusion of crossbred information for selecting parental lines has not led to a clear advantage compared to within line selection. Can this scenario change with the use of genomic information?

PDF icon tusell2014.pdf
2014

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

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Poster.

The intestinal microbiome plays a major role in host's physiology and homeostasis. It participates in the immunological barrier against infections, helps to develop and mature the immune system, and contributes to extract nutrients and energy from food. Despite large scale studies in human, little is known on gut microbiota composition and potential associations with individual traits in livestock species. The objective of this study was to estimate the genetic parameters of the gut microbiota composition and analyze its links with immunity traits in French Large White pigs. A cohort of 60 days old piglets was assessed for fecal microbiota composition by pyrosequencing the 16S rRNA gene. First results on 299 piglets showed a predominance of Prevotella followed by Oscillibacter, Dialister, Roseburia and Treponema. Among a set of 63 genera, 7 had low (0.1<h2<0.2), 15 medium (0.2<h2<0.4) and 8 high (h2>0.4) heritabilities for abundance variations. At the genetic level, the relative abundance of Prevotella, Oribacterium, Selenomonas, Dialister and Megasphaera were found positively correlated with each other and tended to be negatively correlated to other genera. Finally, regularized canonical correlations (rCCA) and sparse Partial Least Squares (sPLS) analyzes highlighted both positive and negative correlations between various immunity traits (e.g. monocytes, eosinophils, platelets) and genera such as Prevotella, Roseburia and Dialister. In this report we demonstrate for the first time that the gut microbiota composition in swine is influenced by the genetics of the host. In addition, we have found covariations between microbiota composition and immunity traits. These results pave the way for studying the microbiota as a new component of phenotype construction in pigs. Microbiota parameters together with zootechnical and immunity traits will help to better decipher the driving forces that shape animal performances and robustness.

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2014

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

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

RN gene polymorphism effects in a family-based scheme in French purebred pig populations

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The study was based on performance recording (with 23 meat quality traits) in progeny testing station of half-sib families composed of 50 offspring (castrates and females) from purbred sires. The aim of this scheme was to estimate, in French purebred pig populations, the effect  of polymorphisms. Data will be presented for 1,740 genotyped anmals belonging to 4 groups of breeds : LW (3 Large-White type populations), LF (French Landrace), D (3 Duroc populations) and CH (4 Chinese-European lines). Eight polymorphisms in RN (PRKG3) gene were analyzed : R200Q, V1991, G52S, K131R, P134L, T30N, V41I, L53P. No polymorphism was found for R200Q and L53P. Six haplotypes were defined with the remaining mutations. Effect of haplotypes was estimated with MIXED procedure (SAS software) with sex and slaughter date as fixed effects, mother and father as random effects and carcass weight as covariate. Most significant results were observed for pHSM (semi-membraneous pH 24 h post mortem) and MQI (Meat Quality Index combining pHSM, Minolta L* and water holding capacity both on gluteus superficialis) in LW, LF, and D, for drip loss in LW and LF and for color traits (Minolta L*, a*, b*) in LW, LF and CH. Results will be illustrated focusing on 2 meat quality traits (MQI, and drip loss) and 2 haplotypes. Haplotypic frequencies estimated on parents are 26% and 10% in LW, 64% and 20% in LF, 40% and 47% in D and 12% and 21% in CH for haplotype 1 and 2 respectively. haplotype 1 is favorable for the 2 considered traits. Regarding combinations of haplotypes, 11 is significantly better than 16 in LW, LF and D and even more than 66 in D. Estimated effects between 11 and 16 are between 0.2 and 0.8 phenotpic standard deviation; the highest being observed in LW. In D, differences between 11 and 66 animals are estimated to be 0.9 phenotypic standard deviation for MQI.

PDF icon eaap_mercat.pdf
2013

RN gene polymorphism effects in a family-based scheme in French purebred pig populations

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The study was based on performance recording (with 23 meat quality traits) in progeny testing station of half-sib families composed of 50 offspring (castrates and females) from purbred sires. The aim of this scheme was to estimate, in French purebred pig populations, the effect  of polymorphisms. Data will be presented for 1,740 genotyped anmals belonging to 4 groups of breeds : LW (3 Large-White type populations), LF (French Landrace), D (3 Duroc populations) and CH (4 Chinese-European lines). Eight polymorphisms in RN (PRKG3) gene were analyzed : R200Q, V1991, G52S, K131R, P134L, T30N, V41I, L53P. No polymorphism was found for R200Q and L53P. Six haplotypes were defined with the remaining mutations. Effect of haplotypes was estimated with MIXED procedure (SAS software) with sex and slaughter date as fixed effects, mother and father as random effects and carcass weight as covariate. Most significant results were observed for pHSM (semi-membraneous pH 24 h post mortem) and MQI (Meat Quality Index combining pHSM, Minolta L* and water holding capacity both on gluteus superficialis) in LW, LF, and D, for drip loss in LW and LF and for color traits (Minolta L*, a*, b*) in LW, LF and CH. Results will be illustrated focusing on 2 meat quality traits (MQI, and drip loss) and 2 haplotypes. Haplotypic frequencies estimated on parents are 26% and 10% in LW, 64% and 20% in LF, 40% and 47% in D and 12% and 21% in CH for haplotype 1 and 2 respectively. haplotype 1 is favorable for the 2 considered traits. Regarding combinations of haplotypes, 11 is significantly better than 16 in LW, LF and D and even more than 66 in D. Estimated effects between 11 and 16 are between 0.2 and 0.8 phenotpic standard deviation; the highest being observed in LW. In D, differences between 11 and 66 animals are estimated to be 0.9 phenotypic standard deviation for MQI.

PDF icon eaap_mercat.pdf
2013

Génétique : les enjeux du contrôle de performances

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La sélection génomique ouvre la possibilité de sélectionner de nouveaux caractères. Son développement passera par la capacité que la recherche et les OSP auront à réaliser de nouvelles mesures. Pour se préparer à ces nouveaux enjeux, FG Porc* et l'Inra se mobilisent pour la création d'une nouvelle station de contrôle de performance, tout en consolidant l'expertise du contrôle en ferme.
*FG Porc (France Génétique Porc) regroupe les OSP ADN, GENE+, NUCLEUS et l'IFIP

PDF icon techporc_bidanel_n8_2012.pdf
2012

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

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

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About 500 Large White pigs (106 sire families) were genotyped using the PorcineSNP60 Beadchip and controlled for feed intake, growth, carcass composition and meat quality. Of the 64,432 SNP (Single Nucleotide Polymorphism) of the chip, 44,412 passed the quality control and were thus used for genome-wide association analyses (GWAS) with the FASTA method (individual effects of SNP and polygenic effect are estimated jointly). A total of 45 regions with significant effects (P<10-4) have been identified for SNP distributed on all chromosomes (SSC) except on SSC5 and SSC12.

PDF icon Fine mapping of production and meat quality QTL in Large White pigs using the PorcineSNP60 Beadchip
2012

Estimation, dans un dispositif familial issu des populations porcines françaises en sélection, de l’effet quantitatif de mutations dans des gènes majeurs et des gènes candidats

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L’étude repose sur le contrôle de performances en station (croissance, composition corporelle et qualité de viande) de familles composées d’une cinquantaine de descendants (mâles castrés et femelles) d’un même père de race pure. Ce dispositif a vocation à estimer, dans les populations porcines françaises en sélection, l’effet de mutations publiées dans la bibliographie, certaines parfois exploitées commercialement.
PDF icon Estimation, dans un dispositif familial issu des populations porcines françaises en sélection, de l’effet quantitatif de mutations dans des gènes majeurs et des gènes candidats
2012

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

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

Immunity Traits in Pigs: Substantial Genetic Variation and Limited Covariation

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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.
2011

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

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