Submitted to: Interbull Annual Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 8/8/2015
Publication Date: 8/19/2015
Citation: Van Raden, P.M., Cooper, T.A. 2015. Genomic evaluations and breed composition for crossbred U.S. dairy cattle. Interbull Annual Meeting Proceedings. Interbull Bulletin 49:19–23.
Interpretive Summary: Genomic evaluations are desired for crossbred as well as purebred dairy cattle populations in commercial and breeding herds. The goals of this study were to compute genomic breed composition (GBC) for all animals in the national database, examine categories of animals genotyped, compare imputation strategies for crossbreds, and evaluate crossbreds using GBC to weight marker effects computed for each pure breed. Genotypes of 6,296 crossbred animals were examined for inclusion in routine genomic evaluations. Two imputation strategies with findhap were compared yielding similar results to obtain the 60,671 markers used officially. The first included crossbred animals and 3,119 genotyped ancestors, the second included all 834,367 purebred and crossbred animals available in March 2015. Genomic predicted transmitting abilities (GPTAs) were computed by applying marker effects from each of the four breeds then weighting those GPTAs by GBC. Crossbred GPTAs were correlated by about 0.91 to GPTAs obtained from a common set of marker effects for all breeds. The methods developed should allow accurate evaluations for nearly all dairy cattle. In application, thousands of crossbred animals are genotyped because many commercial producers apply genomic selection to whole herds.
Technical 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.