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This article is part of the supplement: Proceedings of the 12th European workshop on QTL mapping and marker assisted selection

Open Access Proceedings

Estimating genomic breeding values from the QTL-MAS Workshop Data using a single SNP and haplotype/IBD approach

Mario PL Calus1*, Sander PW de Roos2 and Roel F Veerkamp1

Author Affiliations

1 Animal Breeding and Genomics Centre, Animal Sciences Group, Wageningen University and Research Centre, P. O. Box 65, 8200 AB Lelystad, The Netherlands

2 CRV, PO Box 454, 6800 AL Arnhem, The Netherlands

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BMC Proceedings 2009, 3(Suppl 1):S10  doi:10.1186/1753-6561-3-S1-S10

Published: 23 February 2009


Genomic breeding values were estimated using a Gibbs sampler that avoided the use of the Metropolis-Hastings step as implemented in the BayesB model of Meuwissen et al., Genetics 2001, 157:1819–1829.

Two models that estimated genomic estimated breeding values (EBVs) were applied: one used constructed haplotypes (based on alleles of 20 markers) and IBD matrices, another used single SNP regression. Both models were applied with or without polygenic effect. A fifth model included only polygenic effects and no genomic information.

The models needed to estimate 366,959 effects for the haplotype/IBD approach, but only 11,850 effects for the single SNP approach. The four genomic models identified 11 to 14 regions that had a posterior QTL probability >0.1. Accuracies of genomic selection breeding values for animals in generations 4–6 ranged from 0.84 to 0.87 (haplotype/IBD vs. SNP).

It can be concluded that including a polygenic effect in the genomic model had no effect on the accuracy of the total EBVs or prediction of the QTL positions. The SNP model yielded slightly higher accuracies for the total EBVs, while both models were able to detect nearly all QTL that explained at least 0.5% of the total phenotypic variance.