Reliability Increases from Combining 50,000- and 777,000-Marker Genotypes from Four Countries

Abstract

Genomic predictions were compared on U.S. scale after combining 50,000 (50K) and 777,000 (HD) marker genotypes across countries. The genotyped Holsteins included 161,341 animals with five marker densities including 1,510 with HD. Imputation was more accurate with FImpute than with findhap across the five densities. Reliability of HD predictions minus reliability of 50K predictions averaged only 0.4%. For 50K predictions, reliability for the combined reference population was higher than for domestic only, with the gain averaging 2.6% for Holsteins and 3.2% for Brown Swiss when 50K genotypes were added for 3,593 foreign Holstein and 732 Brown Swiss bulls that had no U.S. daughters prior to August 2008. Gains should be larger with 7,974 foreign Holstein and 870 Brown Swiss bulls in the May 2012 reference population. Multi-trait methods were not more accurate than single-trait for Holsteins, but multi-trait reliability averaged 1.4% higher than single-trait for Brown Swiss, perhaps because of lower genetic correlations between Brown Swiss populations. International exchange improves accuracy and decreases cost of obtaining additional phenotypes and genotypes.