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Utilisation d’une puce très basse densité (1 100 SNP) pour la sélection génomique chez 3 races porcines françaises

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Céline  Carillier-Jacquin (Inrae) et al., 52e Journées de la Recherche Porcine (FRA), 4 et 5 février 2020, p. 45-46, poster


Le coût actuel des puces SNP constitue une limite au développement de la sélection génomique dans les populations porcines (Badke et al., 2014; Wellmann et al., 2013). Afin de réduire les coûts de génotypage, une puce SNP basse densité (LD), conçue en 2016, est utilisée en routine. Ce panel LD d'environ 1100 SNP a été optimisé pour maximiser la précision d'imputation dans la population de porcs Landrace français. Dans la présente étude, nous avons proposé d’étudier l’impact de l’utilisation de ce panel pour deux autres grandes races de porc françaises, le Large White et le Piétrain. 



Design of a very low density chip (1 100 SNP) for genomic selection in 3 French pig breeds 

To reduce genotyping costs for genomic selection, a Low-Density SNP (LD) chip, designed in 2016, is now used routinely. This panel is composed of approximately 1 100 equidistant SNPs. The relevance of this chip has been studied in French populations of the Landrace, Large White and Pietrain pig breeds. The quality of imputation was estimated by the correlation between actual and imputed genotypes and error rates. The impact of imputation on the genomic evaluations was estimated by the correlation between the genomic values obtained for the candidates with imputed genotypes, and those obtained with the high-density genotypes. Average error rates of imputation estimated on all the chromosomes were 0.03, 0.11 and 0.14 for Landrace, Large White and Pietrain, respectively. The estimated correlations between actual and imputed genotypes were relatively high at 0.93, 0.92 and 0.88 for Landrace, Large White and Pietrain populations, respectively. Correlations between genomic breeding values predicted with highdensity genomic data or imputed genomic data from the LD SNP panel ranged from 0.89-0.97 for Large White and Landrace populations for reproductive traits. They were higher than those obtained for the Pietrain population (0.80 and 0.97 for production traits, respectively). In conclusion, despite the limited number of SNPs on the low-density panel used in this study, the imputation accuracy is sufficient to use the imputed genotypes in the genomic evaluations. In practice, genotyping candidates with a LD chip is a solution for selecting future breeding pigs at lower cost.


Utilisation d’une puce basse densité pour la sélection génomique chez 3 races porcines françaises

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Céline Carillier-Jacquin (Inrae) et al., 52e Journées de la Recherche Porcine (FRA), 4 et 5 février 2020, poster


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Use of mate allocation in pig crossbreeding schemes: a simulation study

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González-Diéguez D et al., 70th Annual meeting of the European Federation of Animal science (EAAP), 26-30 août 2019, Ghent, Belgique, visuels d'intervention

One of the main goals in a crossbreeding scheme is to improve the performance of crossbred population by exploiting heterosis and breed complementarity. Dominance is one of the likely genetic bases of heterosis and, nowadays, estimating dominance effects in genetic evaluations has become feasible in a genomic selection context. Mate allocation strategies that account for inbreeding and/or dominance can be of interest for maximizing the crossbred performance. The objective of this study was to simulate scenarios including or not mate allocation strategies in two-breed pig crossbreeding schemes. The different crossbreeding scenarios have been compared in terms of genetic gain (within-breed) and total genetic value in crossbred populations. The benchmark scenario is a crossbreeding scheme where within-line selection is performed on purebred genomic estimated breeding values and crossbreds come from random matings of the best purebreds. The other subsequent scenarios are conceived to evaluate the potential benefits of accounting for inbreeding, dominance and crossbred performances in the genetic evaluation model. Genomic mate allocation is a promising strategy to improve the crossbred performance.

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Relationship between sperm production and boar taint risk of purebred or crossbred entire offspring

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Marie-José Mercat et al., 66th EAAP, Varsovie, Pologne, 31 aout-4 septembre 2015, visuels d'intervention

This study focuses on 100 boars from three Pietrain varieties: 74 V1, 10 V2 and 16 V3. On average, data were recorded on 90 ejaculates collected in artificial insemination centers and boar taint measured on 15.4 entire male offspring, half purebred and half Pietrain × Large-White type. Offspring were reared at INRA UETP (Le Rheu, France) up to 110 kg. Boar taint risk was assessed by androstenone and skatole measurements in fat collected at the slaughterhouse. Sperm production data were corrected for the production site, the age and the collection frequency using a generalized linear mixed model to estimate an average sperm production count per boar and ejaculate. Boar taint odor risk was on the whole low in the tested population. Considering the three Pietrain varieties altogether, boars with the highest sperm production had a lower proportion of offspring without risk of odor compared to boars with low sperm production: the boars ranked in the top quartile of sperm production had 14% less offspring without odor (i.e. androstenone <1.0 &•6;g/g and skatole <0.2 &•6;g/g) compared to the boars in the bottom quartile (P<0.05). The sperm production of the sires of pigs with high androstenone content in fat was on average higher than that of the sires of pigs with low androstenone content: 95.3 and 86.8 billion spermatozoa per ejaculate for the sires of offspring with more than 3.0 &•6;g/g of androstenone and non-detectable androstenone level, respectively (P<0.05). Differences were more pronounced on crossbred offspring than on purebred ones. With V1 sires alone, differences were smaller but still significant. As a conclusion, selection against boar taint might negatively impact semen production if reproduction traits are not included in the breeding goal.

PDF icon Marie-José Mercat et al., 66th EAAP, Varsovie, Pologne, 31 aout-4 septembre 2015

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

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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.


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.


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.

La race cul noir du Limousin

Les races porcines locales françaises (à petits effectifs et en conservation)

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Des fiches pour mieux connaitre les races locales porcines française, à petits effectifs et en conservation.

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