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Use of whole sequence GWAS to improve genomic evaluation in dairy cattle

Abstract : The 1000 bull genomes reference population makes it possible to impute whole genome sequences for a large number of animals. Even if imputation accuracy is still limited for rare variants, it becomes possible to directly pinpoint the causal mutations, or at least variants in very high linkage disequilibrium with them. However, sequence data (i.e. tens of millions of variants for several thousand animals) cannot be used in routine genomic evaluation and only the most predictive part of them should be identified and used. In this study, we propose to construct virtual chips containing 50k variants (V50K) selected from the whole genome sequence, compatible with a routine use. About 3,000 bulls from the French Montbéliarde breed were studied for a panel of ten traits related to milk production and composition, fertility, and conformation. This population was divided in training and validation sets. GWAS analyses were carried out at the sequence level on the training population using Wombat software. V50K were then designed considering different criteria: GWAS results, minor allele frequency, variant distribution over the genome, and functional annotations. BayesCπ approach was applied on these V50K and on the Illumina Bovine SNP50 Beadchip® (IB50K) to predict breeding values in the validation set based on the phenotypes (DYD) and genotypes of the training set. GEBV accuracy for each chip was then estimated through correlations between DYD and GEBV in the validation set. Most of the tested scenarios failed to improve accuracy of GEBV obtained with the IB50K. Nevertheless, a good choice of the variants can outperform results of the standard IB50K.
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Contributor : Pascal Croiseau <>
Submitted on : Thursday, September 24, 2020 - 4:30:32 PM
Last modification on : Tuesday, June 15, 2021 - 2:56:30 PM
Long-term archiving on: : Thursday, December 3, 2020 - 5:15:34 PM


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  • HAL Id : hal-02948451, version 1



T Tribout, D Boichard, M Sanchez, Sebastien Fritz, Pascal Croiseau. Use of whole sequence GWAS to improve genomic evaluation in dairy cattle. World Congress on Genetics Applied to Livestock Production, Feb 2018, Auckland, Australia. ⟨hal-02948451⟩



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