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Multi-varietal genomic selection in French pig populations

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visuel de Céline Carillier-Jacquin et al., 67e  EAAP, 31 août 2016, Belfast, Irlande du nord, session 35 : advances in genomic selection, theatre 13, 19 pages.

Document réservé Espace Pro, veuillez vous identifier
2016

L’évaluation génomique dans un schéma de croisement terminal

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Poster

FR

L’intérêt d’utiliser le croisement est de bénéficier de la complémentarité entre les lignées parentales et des effets d’hétérosis au niveau des terminaux. Dans les schémas d’amélioration génétique, les individus des lignées parentales de race pure sont généralement sélectionnés sur des performances enregistrées sur des animaux de race pure, alors que la sélection vise à améliorer la performance des descendants croisés. Ainsi, l’amélioration génétique observée au niveau du noyau de sélection peut ne se retrouver que partiellement chez les descendants croisés élevés en conditions commerciales en raison de corrélations génétiques inférieures à 1 entre des phénotypes enregistrés sur les deux types d’animaux. Dans le contexte de la sélection génomique, il est opportun d'explorer les nouvelles possibilités offertes par le génotypage des animaux pour mieux prendre en compte les phénotypes d’animaux croisés pour sélectionner les animaux des lignées parentales. Dans cette étude, nous avons développé et testé un modèle en une seule étape (modèle SSt pour « single step ») (Aguilar et al., 2010) pour l'estimation des paramètres génétiques et des valeurs génétiques dans une population constituée d’animaux purs et d’animaux croisés apparentés.

ENG

Genomic evaluation of pigs using a terminal-cross model

In crossbreeding schemes, within-line selection of purebred lines mainly aims at improving performance of crossbred progeny in field conditions. The genetic correlation between purebred and crossbred performance is an important parameter to be assessed to ascertain that purebred performance is a good predictor of crossbred performance. With the availability of high density markers, feasibility of using crossbred information for evaluating purebred candidates can be reevaluated. This study implements and applies to real data a single-step terminal-cross model to estimate genetic parameters of several production traits in Pietrain and Pietrain x Large White pigs.
Piglets were recorded for growth rate between 35 and 110 kg. Animals were genotyped using the 60K SNP chip. For each trait, purebred and crossbred performances were jointly analyzed. The purebred animals were evaluated through an animal model, whereas the additive genetic effect of a crossbred individual was decomposed into its purebred sire and dam allelic contribution effects. Piétrain genotypes were introduced in genetic evaluation in a single-step procedure. The same model but only accounting for pedigree information was compared to the genomic model in terms of breeding value accuracies obtained from the mixed model equations.
Genetic correlation between purebreds and sire allelic contribution to crossbred performance was high (0.84 and 0.79 for the genomic and the pedigree model, respectively). Breeding value accuracies of the genotyped animals obtained with the genomic model outperformed the pedigree model.

2016

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

Pedigree and genomic evaluation of pigs using a terminal-cross model

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In crossbreeding schemes, within-line selection of purebreds is performed mainly to improve the performance of crossbred descendants under field conditions. The genetic correlation between purebred and crossbred performance is an important parameter to be assessed because purebred performance can be a poor predictor of the performance of crossbred offspring. With the availability of high-density markers, the feasibility of using crossbred information to evaluate purebred candidates can be reassessed. This study implements and applies a single-step terminal-cross model (GEN) to real data to estimate the genetic parameters of several production and quality traits in pigs.

2016

Développement de la sélection génomique

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Fiche n° 059 : réduction des coûts d'élevage

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. Plusieurs actions ont été engagées en 2015 en vue de définir le coût d’opportunité de la sélection génomique pour une utilisation en routine dans les lignées collectives.

PDF icon fiche_bilan2015_059.pdf
2016

Utilisation des informations génomiques des animaux croisés pour la sélection

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Fiche n° 058 : réduction des coûts d'élevage

Dans les schémas de sélection porcin et avicole, des animaux de race pure sont sélectionnés dans un environnement de haut niveau sanitaire dans
l’objectif de produire des terminaux croisés élevés dans un milieu de production moins favorable. Le projet UtOpIGe (2011-2015) avait pour objectif
de fournir les informations nécessaires à la mise en oeuvre d’une sélection génomique optimale dans ces deux espèces. Ce document se focalise sur les résultats obtenus sur le porc.

PDF icon fiche_bilan2015_058.pdf
2016

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

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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 < 0.001). The functional analysis highlighted that gene expression diversity is mainly linked to cellular signaling pathways such as the PI3K (phosphoinositide 3-kinase) pathway. The PI3K pathway is known to be involved in the control of development of the skeletal muscle mass by affecting extracellular matrix - receptor interactions, regulation of actin cytoskeleton pathways and some metabolic functions. This study also highlighted 228 spots (171 unique genes) that differentiate the breeds from each other. A common subgroup of 15 genes selected by three statistical methods was able to differentiate Duroc, Large White and Piétrain breeds.

Conclusions

This study on transcriptomic differentiation across Western pig breeds highlighted a global picture: mainly signaling pathways were affected. This result is consistent with the selection objective of increasing muscle mass. These transcriptional changes may indicate selection pressure or simply breed differences which may be driven by human selection. Further work aiming at comparing genetic and transcriptomic diversities would further increase our understanding of the consequences of human impact on livestock species.

2015

Sélection génomique : un nouvel outil pour la sélection collective

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Méthode de sélection prometteuse
- Sélection plus précise des candidats dans les meilleures portées
- Principalement sur les critères de reproduction pour les lignées maternelles
- Ouvre des perspectives pour l’amélioration d’autres critères
-> Plus grande efficacité de la sélection
Utilisation de l’outil à optimiser en raison de son coût
- Stratégies de génotypages des candidats
- Des opportunités liées à la baisse du prix de génotypage
Mise en place de l’évaluation génomique Landrace fin 2015

PDF icon Intervention de Alban Bouquet Space 2015
2015

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.

Document réservé Espace Pro, veuillez vous identifier
2015

Pedigree and genomic evaluation of pigs using a terminal cross model

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This study presents a single-step terminal-cross model (GEN) to estimate genetic parameters of growth rate and pH of longissimus dorsi in pigs. The model is compared in terms of parameter estimates and breeding value accuracies with a pedigree-based terminal-cross model (PED) and 2 univariate single-step models (GEN_UNI) for purebred (PB) and crossbred (CB) performance. Ninety Piétrain sires were mated with 306 Piétrain and 306 Large White dams leading a total of 654 PB and 716 CB male piglets. Sires and PB offspring were genotyped using the 60K SNP chip. PB and CB performances were jointly analyzed as 2 traits. The PB animals were accounted for through an animal model, whereas the additive genetic effect of a CB individual was decomposed into its sire and dam allelic contribution effects plus a Mendelian sampling confounded with the residual. Genetic correlation between the PB and the sire contribution for CB performance was estimated. The inverse of a matrix combining both genomic and pedigree relationship matrices was used in the mixed model equations for the Piétrain line as in a single-step procedure. The PED model was of the same form as GEN but accounted only for pedigree information. The GEN_UNI models contained same effects as the GEN model for either the PB or CB performance. (Co)variance components were estimated by Gibbs sampling. Genetic correlations [HPD95%] between PB and CB traits obtained with the GEN model were close to unity: 0.84 [0.45, 1.00] and 0.97 [0.83, 1.00] for growth rate and pH, respectively, suggesting that PB line selection is already successful to improve CB performance. Genotyped animals obtained higher breeding value accuracies with the GEN model than with the PED and GEN_UNI models. Accounting for PB and CB information together with genomic information improves the precision of the genetic evaluation in breeding programs based on crossbreeding.

PDF icon tusell et al., 66th EAAP, Varsovie, Pologne, 31 aout-4 septembre 2015, abstract
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.

Document réservé Espace Pro, veuillez vous identifier
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

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