Comparison of genomic predictions using medium-density (∼54,000) and high-density (∼777,000) single nucleotide polymorphism marker panels in Nordic Holstein and Red Dairy Cattle populations

Abstract

This study investigated genomic prediction using medium-density (∼54,000; 54K) and high-density marker panels (∼777,000; 777K), based on data from Nordic Holstein and Red Dairy Cattle (RDC). The Holstein data comprised 4,539 progeny-tested bulls, and the RDC data 4,403 progeny-tested bulls. The data were divided into reference data and test data using October 1, 2001, as a cut-off date (birth date of the bulls). This resulted in about 25% genotyped bulls in the Holstein test data and 20% in the RDC test data. For each breed, 3 data sets of markers were used to predict breeding values: (1) 54K data set with missing genotypes, (2) 54K data set where missing genotypes were imputed, and (3) imputed high-density (HD) marker data set created by imputing the 54K data to the HD data based on 557 bulls genotyped using a 777K single nucleotide polymorphism chip in Holstein, and 706 bulls in RDC. Based on the 3 marker data sets, direct genomic breeding values (DGV) for protein, fertility, and udder health were predicted using a genomic BLUP model (GBLUP) and a Bayesian mixture model with 2 normal distributions. Reliability of DGV was measured as squared correlations between deregressed proofs (DRP) and DGV corrected for reliability of DRP. Unbiasedness was assessed by regression of DRP on DGV, based on the bulls in the test data sets. Averaged over the 3 traits, reliability of DGV based on the HD markers was 0.5% higher than that based on the 54K data in Holstein, and 1.0% higher than that in RDC. In addition, the HD markers led to an improvement of unbiasedness of DGV. The Bayesian mixture model led to 0.5% higher reliability than the GBLUP model in Holstein, but not in RDC. Imputing missing genotypes in the 54K marker data did not improve genomic predictions for most of the traits.