Genomic prediction of health traits using a mixed reference bull and cow reference population for German Holsteins

Abstract

German breeding organizations started a long-term project of whole-herd genotyping, called KuhVision, in 2016. The main goal of the project KuhVision was to establish a cow reference population for more accurate genomic prediction. In addition to recording of currently evaluated traits, more than half of the participating herds recorded also direct health traits. A conventional genetic evaluation for the health traits has been set up and running for German Holsteins for several years. The health traits included clinical mastitis, six claw traits, three reproduction and three metabolic health traits. To increase the size of genomic reference population for the novel health traits, genotyped cows were added to the current reference population composing only genotyped bulls. For April 2019 genomic evaluation, 100,319 or 67,994 cows were included in the German Holstein reference population for clinical mastitis or digital dermatitis, respectively. In contrast to the newly recorded health traits, calf fitness, defined as survival of female calves from day 3 to 458, had a much larger reference population containing 298,499 female calves and 10,424 bulls. Genomic prediction of the health traits was optimized and validated via Interbull GEBV test. Reasonable increase in R2 values was observed for the health traits from the conventional EBV to the genomic model, despite a short history of whole-herd cow genotyping. Phenotypes of youngest genotyped cows that were not included in the mixed reference population were compared in four groups that were defined based on their candidate GEBV. A strong association was observed between their early candidate GEBV and later own phenotypes. Since April 2019, the mixed bull and cow reference population has been used in routine genomic evaluation of the health traits for German Holsteins.