The French dairy cattle genomic evaluation uses an extension of Marker-Assisted BLUP (MA-BLUP) based on a haplotype model with a residual polygenic effect. A two-step approach to select SNP and construct haplotypes linked to QTL was tested by cross-validation for two breeds with moderate (Montbéliarde) and large (Holstein) reference populations. The comparison with other genomic evaluation approaches showed MA-BLUP validation performances which are very similar for Montbéliarde and slightly lower for Holstein. Some simplifying or ad-hoc assumptions explaining these results have been identified and reveal directions for improvement. In particular, a genome-wide strategy to pinpoint the most informative haplotypes linked to QTL is highly desirable. The robustness and computing simplicity of MA-BLUP remain two appealing features for routine genomic evaluations. The use of haplotypes is expected to give more robust and reliable predictions over more distantly related animals.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Genetic Improvement Programs: Selection using molecular information, , 054, 2014
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