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Genomic evaluation using QTL information
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.
Keywords:
dairy cattle
genomic evaluation
genomic selection
quantitative trait locus
