Comparison of methods for estimation of genetic covariance matrix from SNP or pedigree data utilised to predict breeding value

BACKGROUND: The aim was to predict breeding values of non-phenotyped individuals based on a dataset prepared for the 13(th) QTL-MAS Workshop in Wageningen. METHODS: Genetic co-variance matrices between animals were estimated with three methods: one using pedigree information only and two based on SNP markers from the first chromosome. Quadratic regression of breeding values, estimated separately in each of the five time points, was used to predict the breeding values in the 6(th) time point. RESULTS: Based on the comparison (true - estimated BV) it can be concluded that SNP based methods provided better estimates (accuracy between 0.75 and 0.80) than pedigree (0.65). CONCLUSIONS: Even though only SNPs from chromosome 1 were used it was still possible to achieve fairly high accuracies. Most likely this was due to the fact that chromosome 1 contained the QTLs with the largest effects.