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Using 1K SNP panel for genomic selection in 3 French pig breeds: Accuracy of Imputation and estimation of genomic breeding values using 1K SNP panel, designed for several breeds in French pig populations

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Céline Carillier-Jacquin (Université de Toulouse, INRA, INPTet ENVT)  et al., World Congress on Genetics Applied to Livestock Production, Auckland, Nouvelle-Zélande, 11–16 février 2018, p. 294-298

The current cost of medium density SNP chips is a limit to the development of genomic selection in pig populations (Badke et al., 2014; Wellmann et al., 2013). To reduce the cost of genotyping, a low density (LD) SNP chip was designed in 2016 and has been used in routine.
This LD panel of around 1100 SNP was optimized for imputation accuracy in the French Landrace (Land) pig population using equally spaced SNP with minor allele frequency (MAF) larger than 0.2. In the present study, we proposed to adapt the panel to two other major French pig breeds i.e. Large White (LW) and Pietrain (PI) lines. Imputation accuracy as well as the impact on genomic estimated breeding value (GEBV) were estimated in the three breeds using this new SNP chip design.

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2018

Relationship between age and body weight at farrowing over 6 parities in Large White × Landrace sow

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Nathalie Quiniou, 69th Annual meeting of the european federation of animal science (EAAP), Dubrovnik, Croatie, 27-31 août 2018 

At the beginning of the gestation, parity and back fat (BT) thickness are frequently used by farmers to choose among different feeding plans the most adapted one to feed each sow if individual feeding is possible. Otherwise, BT is used to allocate the sows to one of the available pens and to adapt the feed allowance at the group level. Usually a single target of BT at farrowing is retained at the herd scale, and each sow is expected to make up its BT for the difference between the target and its own initial BT. According to the factorial approach used to assess nutrient requirements, achieving an expected BT gain implies that enough energy is supplied above maintenance. Based on equation published by Dourmad et al., expected energy retention is obtained by the difference between the initial (calculated from measured BT and BW) and the final amount of energy (calculated from expected BT and BW).
When no information is collected on BW during the gestation, the expected final BW is also used to assess daily BW and corresponding maintenance requirement and to take into account impacts of housing conditions (temperature, activity level). Then, adequacy of the energy supply depends not only on initial and final BT, but also on initial BW and final BW. Individual BW have been collected over successive parities in the IFIP facilities (n=6,288 from Large White × Landrace sows born since 2000). Data of 90 sows born between 2012 and 2015, studied over at least 6 parities and group-housed from the 28th to the 108th day of gestation, were used to characterize the relationship between age and BW after farrowing based on BW at the first farrowing (BW_P1) and BW gain afterwards, with BW at the 6th parity considered as the mature BW: BWi(Age), kg = 145.6 + 0.171 × Age_P1i+ 111.4 × (1 – exp(- 1.453/1000 × (Age-Age_P1i)1.084)), RMSEP=16 kg; with Age_P1i: the individual age at the first farrowing used to adjust the mean BW_P1. Based on this equation, the individual expected BW gain (both growth and recovering parts) can be calculated and, combined with BT gain, used to assess the corresponding energy requirement for precision feeding during gestation. Its calibration for other lines or farms will require specific measurements due to interactions with management.

PDF icon Nathalie Quiniou, 69th EAAP, Dubrovnik, Croatie, 27-31 août 2018
2018

Relationship between age and body weight at farrowing over 6 parities in Large White × Landrace sow

Consulter le resumé

Nathalie Quiniou, 69th Annual meeting of the european federation of animal science (EAAP), Dubrovnik, Croatie, 27-31 août 2018 

At the beginning of the gestation, parity and back fat (BT) thickness are frequently used by farmers to choose among different feeding plans the most adapted one to feed each sow if individual feeding is possible. Otherwise, BT is used to allocate the sows to one of the available pens and to adapt the feed allowance at the group level. Usually a single target of BT at farrowing is retained at the herd scale, and each sow is expected to make up its BT for the difference between the target and its own initial BT. According to the factorial approach used to assess nutrient requirements, achieving an expected BT gain implies that enough energy is supplied above maintenance. Based on equation published by Dourmad et al., expected energy retention is obtained by the difference between the initial (calculated from measured BT and BW) and the final amount of energy (calculated from expected BT and BW).
When no information is collected on BW during the gestation, the expected final BW is also used to assess daily BW and corresponding maintenance requirement and to take into account impacts of housing conditions (temperature, activity level). Then, adequacy of the energy supply depends not only on initial and final BT, but also on initial BW and final BW. Individual BW have been collected over successive parities in the IFIP facilities (n=6,288 from Large White × Landrace sows born since 2000). Data of 90 sows born between 2012 and 2015, studied over at least 6 parities and group-housed from the 28th to the 108th day of gestation, were used to characterize the relationship between age and BW after farrowing based on BW at the first farrowing (BW_P1) and BW gain afterwards, with BW at the 6th parity considered as the mature BW: BWi(Age), kg = 145.6 + 0.171 × Age_P1i+ 111.4 × (1 – exp(- 1.453/1000 × (Age-Age_P1i)1.084)), RMSEP=16 kg; with Age_P1i: the individual age at the first farrowing used to adjust the mean BW_P1. Based on this equation, the individual expected BW gain (both growth and recovering parts) can be calculated and, combined with BT gain, used to assess the corresponding energy requirement for precision feeding during gestation. Its calibration for other lines or farms will require specific measurements due to interactions with management.

PDF icon Nathalie Quiniou, 69th EAAP, Dubrovnik, Croatie, 27-31 août 2018, visuels
2018

Modélisation de l'évolution moyenne du poids vif après la mise bas selon l'âge chez des truies croisées Large White x Landrace

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51es Journées de la Recherche Porcine, 5 et 6 février 2019, Paris, p. 123-128, par Nathalie Quiniou

Le rang de portée et l'épaisseur de lard dorsal au début de la gestation sont deux critères utilisés par de nombreux éleveurs pour grouper les truies et choisir le niveau de rationnement appliqué à l'échelle de la case ou de l'individu. Ignorer la variabilité du poids vif et de l'âge à un rang de portée donné peut induire un accroissement de l’hétérogénéité dans l'état des réserves entre truies d’une même bande. Mieux ajuster la ration à la dynamique des changements de poids au cours de la carrière de la truie implique de peser les truies et de définir l’objectif de poids vif en fin de gestation en fonction de l'âge. A partir des données obtenues en station expérimentale sur 90 truies Large White x Landrace, nées entre 2012 et 2015 et suivies sur au moins six cycles, plusieurs modèles de croissance sont étudiés pour modéliser l’évolution du poids après la mise bas (PV) en fonction de l’âge (t). La précision de prédiction (hors primipares) est environ de 15 kg quand le poids (P1i) et l’âge (t1i) individuel à la première mise bas sont pris en compte (e.g. modèle de Weibull : P1i + (326,3 – P1i)(1 - exp(-(2,288/1000 x (t – t1i))1,041))) contre environ 16 kg quand ce n'est pas le cas (e.g. modèle de Brody : 331,4 x (1 - 0,821 x exp(-2,121/1000t))). L’évaluation de ces équations à partir de trois autres jeux de données obtenues dans le même élevage indique une évolution du PV avec l'âge similaire à celle du jeu initial. Le calibrage d’un modèle adapté à chaque élevage de production sera possible dans un futur proche dès lors que les truies seront pesées avec des bascules automatiques, développées dans une optique d’élevage de précision.

Modelling the relationship between body weight and age at farrowing in Large White x Landrace sow

Parity and backfat thickness are frequently used by farmers to group gestating sows and thereafter choose a feeding plan at the pen- or individual-scale. At a given parity, ignoring differences in body weight with age contributes to the increase in variability of body reserves at farrowing. Therefore, improving the adequacy of the feed allowance relies on better knowledge of the dynamic change in body weight over the productive lifetime. Data collected routinely on an experiment station from 90 crossbred Large White x Landrace sows were used to characterise the relationship between individual age (t) and body weight after farrowing (BW). Sows were born from 2012-2015 and studied over at least six parities. Accuracy of the prediction (without primiparous sows) was around 15 kg when the individual BW (P1i) and age (t1i) at first parity were considered (e.g., Weibull model: P1i + (326.3 – P1i)(1 - exp(-(2.288/1000 x (t – t1i))1.041))), otherwise 16 kg (e.g., Brody model : 331.4 x (1 – 0.821 exp(-2.121/1000t))). Models were evaluated using three other datasets obtained within the same herd from sows born over a period of 12 years. Relationships between BW and age obtained from these datasets were relatively similar to those of the initial dataset. It appeared that the more homogeneous the herd was, the more accurate was the prediction. Calibration of such models for a commercial herd should be possible in the near future from automatic BW measurement, using tools developed in the context of precision farming.

PDF icon Nathalie Quiniou, 51es JRP, 5 et 6 février 2019, Paris, p. 123-128
2019

Intérêt des performances de truies croisées pour la sélection en race pure de caractères de reproduction de la lignée maternelle Large White

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51es Journées de la Recherche Porcine, 5 et 6 février 2019, Paris, p. 309-314, par Raphaël Boré et al.

L’objectif de cette étude est d’évaluer l’intérêt des performances de reproduction de truies croisées Large White x Landrace pour l’évaluation génomique de la lignée maternelle Large White Français (LW). Les performances de 24 771 truies croisées (103 305 portées) ayant eu une carrière dans un élevage de production entre 2007 et 2017 ont été analysées conjointement avec les performances de 24 377 femelles LW de race pure utilisées sur la même période (69 415 portées). Deux caractères ont été considérés : le nombre de porcelets nés vivants (NbNv) et le nombre de mort-nés (NbMn). Les performances exprimées en race pure et en croisement ont été analysées comme deux caractères différents génétiquement corrélés. Les composantes de la variance de chaque caractère ont été estimées par Gibbs Sampling en remontant cinq générations de pedigree pour construire les matrices de parenté et en intégrant l’information génomique de 1 439 reproducteurs LW. Pour les deux caractères les héritabilités estimées sont faibles en race pure (h²NbNv=0,12 ± 0,01 et h²NbMn=0,11 ±0,01%-) et en croisement (h²NbNv=0,07 ± 0,01 et h²NbMn=0,06 ± 0,01). Des corrélations génétiques élevées (rg > 0,90) ont été estimées entre la performance exprimée en race pure et en croisement. Ce résultat confirme que le progrès génétique cumulé dans le schéma de sélection de race pure est pour l’essentiel transféré à la truie croisée sur les critères de reproduction. Une étude de validation croisée suggère que l’intégration de cet échantillon de performances en croisement dans l’évaluation génomique de race pure permettrait d’obtenir un gain de fiabilité (CD) modéré des index génomiques des candidats à la sélection. Ce gain de CD d’environ 2 points de pourcentage correspondrait à une augmentation de 10% de la fiabilité actuelle des index.

Interest of crossbred sow performance for the selection of reproduction traits in the purebred Large White maternal line

The objective of this study was to evaluate benefits of use of Large White x Landrace sow reproduction performance for genomic evaluation of the French Large White (LW) dam line. The performances of 24 771 crossbred sows (103 305 litters) used on production farms from 2007-2017 were analysed along with those of 24 377 purebred LW sows used during the same period (69 415 litters). Two traits were considered: the number of live born piglets (NbNv) and the number of stillbirths (NbMn). The purebred and crossbred performances were analysed as two different traits that are genetically correlated. Variance components were estimated for each breed by Gibbs Sampling using five generations of pedigree to construct relationship matrices and integrate the genomic information of 1 439 LW breeding animals. Estimated heritabilities were low for purebred (h²NbNv= 0.12 ± 0.01 and h²NbMn=0.11 ± 0.01) and crossbred performances (h²NbNv= 0.07 ± 0.01 and h²NbMn=0.06 ± 0.01). For both traits, high genetic correlations (rg > 0.90) were estimated between purebred and crossbred performances. This result confirms that most of the genetic progress cumulated in purebred parental lines should be transferred to the crossbred sows. A cross-validation study suggested that integration of crossbred performances into the purebred genomic evaluation could provide a slight increase in reliability of the genomic indices for selection candidates. This increase in index reliability of approximately 2 points of percentage would correspond to a 10% increase compared to the current reliability of the indices.

PDF icon Raphaël Boré et al., 51es JRP, 5 et 6 février 2019, Paris, p. 309-314
2019

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

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. 

ENG

Poster.

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.

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

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

Poster.

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2020

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