Breeding value estimation combining QTL and polygenic information

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic


Optimal selection is based on breeding values that combine QTL information with polygenic breeding values estimated simultaneously from phenotypic ecords. Generally a large proportion of animals is not genotyped however. The aim of this study was to compare two methods to deal with ungenotyped animals: 1) predicting their marker haplotypes and include them in the marker-assisted breeding value estimation (ma-blup) or 2) perform conventional breeding value estimation and include estimated haplotype effects for genotyped animals in a total EBV by using selection index weights (ma-index). MIXBLUP-software was used for breeding value estimation. To compare both methods, a population was simulated with one additive QTL and an additive polygenic genetic effect (heritability was 0.30; QTL explained 15% of genetic
variance). Using the same estimates of haplotype effects and optimal selection index weights calculated from the true variances and accuracies, both methods resulted in very similar accuracy of total EBV, as expected. However, in practice accuracies need to be approximated and therefore, index weights are not
optimal. For genotyped juveniles without phenotype this resulted in an average accuracy that was 0.01- 0.03 lower with ma-index in comparison to ma-blup. Furthermore, in some replicates (18%) the accuracy for ma-index was even lower than for conventional breeding value estimation without QTL information.
Even with ma-blup and equal weights on haplotype effects and polygenic effects, 12% of the replicates showed lower accuracy than with conventional breeding value estimation. With optimal weights, however, the accuracy was always equal to or higher than that of conventional breeding value estimation. Therefore, it can be concluded that marker-assisted breeding value estimation is better than using a selection index to blend haplotype effects and conventional breeding values. These results were obtained through the ECfunded FP6 Project ‘SABRE’.
Original languageEnglish
Title of host publicationBook of abstracts of the 60th Annual Meeting of the European Association for Animal Production, Barcelona Spain, 24-27 August 2009
Place of PublicationWageningen
PublisherWageningen Academic Publishers
ISBN (Print)9789086861217
Publication statusPublished - 2009
Event60th Annual Meeting of the European Association for Animal Production -
Duration: 24 Aug 200927 Aug 2009


Conference60th Annual Meeting of the European Association for Animal Production


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