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Poster communications

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

Abstract : 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 1100 equidistant SNPs. The relevance of this chip has been studied in French populations of the Landrace, Large White and Pietrainpig 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 estimatedby the correlation between the genomic values obtained for the candidates with imputed genotypes, and those obtained with the high-densitygenotypes. Average error rates of imputation estimated on all the chromosomes were 0.03, 0.11 and 0.14for Landrace, Large White and Pietrain, respectively. The estimated correlations between actual and imputed genotypes were relativelyhigh at 0.93, 0.92 and 0.88forLandrace, Large White and Pietrain populations,respectively. Correlations between genomicbreedingvalues predicted with high-density genomicdata or imputed genomic data from the LD SNP panel rangedfrom0.89-0.97 for Large White and Landrace populations for reproductivetraits. They were higher than those obtained for the Pietrain population (0.80and 0.97for production traits, respectively). In conclusion, despite the limited number of SNPs on the low-density panel used in this study, the imputation accuracyis sufficient to use the imputed genotypes in the genomic evaluations. In practice, genotyping candidates with aLD chip is a solution for selecting future breeding pigsat lower cost.
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Poster communications
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https://hal.inrae.fr/hal-02737254
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Submitted on : Tuesday, June 2, 2020 - 6:58:36 PM
Last modification on : Wednesday, November 3, 2021 - 5:41:50 AM

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  • HAL Id : hal-02737254, version 1
  • PRODINRA : 494012

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Céline Carillier-Jacquin, Alban Bouquet, Yann Labrune, Pauline Brenaut, Juliette Riquet, et al.. Utilisation d’une puce très basse densité (1 100 SNP) pour la sélection génomique chez 3 races porcines françaises. 52. Journées de la Recherche Porcine, Feb 2020, Paris, France. IFIP - Institut du Porc, Journées de la Recherche Porcine en France, 2020, 52èmes journées de la recherche porcine. ⟨hal-02737254⟩

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