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Genetics, Vol. 178, 553-561, January 2008, Copyright © 2008
doi:10.1534/genetics.107.080838

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Accuracy of Genomic Selection Using Different Methods to Define Haplotypes

M. P. L. Calus*,1, T. H. E. Meuwissen{dagger}, A. P. W. de Roos{ddagger} and R. F. Veerkamp*

* Animal Breeding and Genomics Centre, Animal Sciences Group, Wageningen University and Research Centre, 8200 AB Lelystad, The Netherlands, {dagger} University of Life Sciences, Department of Animal and Aquacultural Sciences, N-1432 Ås, Norway and {ddagger} HG, 6802 EB Arnhem, The Netherlands

1 Corresponding author: Animal Breeding and Genomics Centre, Animal Sciences Group, Wageningen University and Research Centre, P.O. Box 65, 8200 AB Lelystad, The Netherlands.
E-mail: mario.calus{at}wur.nl

Genomic selection uses total breeding values for juvenile animals, predicted from a large number of estimated marker haplotype effects across the whole genome. In this study the accuracy of predicting breeding values is compared for four different models including a large number of markers, at different marker densities for traits with heritabilities of 50 and 10%. The models estimated the effect of (1) each single-marker allele [single-nucleotide polymorphism (SNP)1], (2) haplotypes constructed from two adjacent marker alleles (SNP2), and (3) haplotypes constructed from 2 or 10 markers, including the covariance between haplotypes by combining linkage disequilibrium and linkage analysis (HAP_IBD2 and HAP_IBD10). Between 119 and 2343 polymorphic SNPs were simulated on a 3-M genome. For the trait with a heritability of 10%, the differences between models were small and none of them yielded the highest accuracies across all marker densities. For the trait with a heritability of 50%, the HAP_IBD10 model yielded the highest accuracies of estimated total breeding values for juvenile and phenotyped animals at all marker densities. It was concluded that genomic selection is considerably more accurate than traditional selection, especially for a low-heritability trait.




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