Genomic Prediction with 12.5 Million SNPs for 5503 Holstein Friesian Bulls

This study reports the first preliminary results of genomic prediction with whole-genome sequence data (12,590,056 SNPs) for 5503 bulls with accurate phenotypes. Two methods were compared: genome-enabled best linear unbiased prediction (GBLUP) and a Bayesian approach (BSSVS). Results were compared with results using BovineHD genotypes (631,428 SNPs). Results were reported for somatic cell score, interval between first and last insemination, and protein yield. For all traits, and both methods genomic prediction with sequence data showed similar results compared to BovineHD and GBLUP showed similar results compared to BSSVS. However, it remains to be seen if reliability of BSSVS with sequence data will improve after more sampling cycles have been finished.