Genomic evaluations and breed composition for crossbred U.S. dairy cattle

Abstract

Genomic evaluations are desired for crossbred as well as purebred populations when selection is applied to commercial and not only breeding herds. Genomic breed composition was estimated from 60 671 markers using the known breeds of daughter-proven Holstein, Jersey, Brown Swiss and Ayrshire bulls as the four traits (breed fractions) to be predicted. Genotypes of 6 296 crossbred animals were imputed from lower density chips together with either their 3 119 ancestors or all 834 367 genotyped animals. Estimates of breed composition were adjusted so that no values were negative or exceeded 100 and the four breed percentages summed to 100. The crossbreds included 733 Jersey x Holstein crossbreds with >40% of both breeds (F1 crosses), 55 Brown Swiss x Holstein F1, 2 300 Holstein backcrosses with >67% and <90% Holstein, 2 026 Jersey backcrosses, 27 Brown Swiss backcrosses and 502 other crossbreds of various mixtures. Crossbred evaluations were averages of direct genomic values computed using marker effects for each pure breed, weighted by the animal’s genomic breed composition. The marker effects were estimated separately for each breed on the all-breed scale instead of the within-breed scales currently used.