A common reference population from four European Holstein populations increases reliability of genomic predictions

This paper assesses the increase in reliability achieved when combining four Holstein reference populations of 4000 bulls each, from European breeding organizations, i.e. UNCEIA (France), VikingGenetics (Denmark, Sweden, Finland), DHV-VIT (Germany) and CRV (The Netherlands, Flanders). Each partner validated its own bulls using their national reference data and the combined data, respectively.Combining the data significantly increased the reliability of genomic predictions for bulls in all four populations. Reliabilities increased by 10%, compared to reliabilities obtained with national reference populations alone, when they were averaged over countries and the traits evaluated. For different traits and countries, the increase in reliability ranged from 2% to 19%.Genomic selection programs benefit greatly from combining data from several closely related populations into a single large reference population.Genomic predictions rely on linkage disequilibrium between Single Nucleotide Polymorphisms (SNP) and polymorphisms in genes with effects on traits of interest. Linkage disequilibrium induces associations between SNP genotypes and phenotypes. SNP effects can then be estimated and combined to form genomic predictions. The accuracies of estimated SNP effects are expected to increase with the number and accuracy of available phenotypes. Therefore, the reliability of genomic predictions increases with the size of the reference population (RP) from which the relationship between phenotypes and SNP markers is determined [1,2]. Currently, a RP generally consists of genotyped and progeny tested bulls [1,2]. Because of the importance of the size of the RP, US and Canadian RP have been combined and it has been reported that exchanging data from reference populations is beneficial [3,4]. In European countries, the size of national Holstein RP is moderate, compared to that of the combined North American RP. In September 2009, four regional breeding organizations: UNCEIA (France)