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Pedigree and genomic evaluation of pigs using a terminal cross model

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

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.

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2017

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

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?

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2014