P.M. VanRaden*,1, M.E. Tooker*, T.C.S. Chud†, H.D. Norman‡, J.H. Megonigal, Jr.‡, I.W. Haagen‡, and G.R. Wiggans‡
*USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
†Departamento de Ciências Exatas, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, SP, 14884-900, Brazil
‡Council on Dairy Cattle Breeding, Bowie, MD 20716
2019 J. Dairy Sci. (?)
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Genomic evaluations are useful for crossbred as well as purebred populations when selection is applied to commercial herds. Genomic breed composition was estimated from 60,671 markers using the known breeds of daughter-proven Holstein, Jersey, Brown Swiss, Ayrshire, and Guernsey bulls as the five traits (breed fractions) to be predicted. In initial research, 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 percentages were negative or exceeded 100 and the breed percentages summed to 100. A final adjustment was applied to set percentages above 93.5% equal to 100% and the resulting value was termed breed base representation and implemented in 2016. 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 combinations. Larger percentages of alleles were imputed by using a crossbred reference population rather than the closest purebred reference. Crossbred predictions were averages of genomic predictions computed using marker effects for each pure breed, weighted by the animal’s genomic breed composition. The marker and polygenic effects were estimated separately for each breed on the all-breed scale instead of the within-breed scales previously used. For crossbreds, genomic predictions weighted by breed base representation were more accurate than parent average and slightly more accurate than predictions using only the predominate breed. For purebreds, single-trait predictions using only within-breed data were as accurate as multiple-trait predictions treating allele effects in different breeds as correlated effects. The crossbred genomic predicted transmitting abilities will aid producers in managing their breeding programs and selecting replacement heifers.
Key Words: genomic evaluation, multiple breed, crossbreeding, imputation