Genomic predictions for crossbred dairy cattle

摘要

Genomic evaluations are useful for crossbred as wellas purebred populations when selection is applied tocommercial herds. Dairy farmers had already spentmore than $1 million to genotype over 32,000 crossbredanimals before US genomic evaluations became availablefor those animals. Thus, new tools were neededto provide accurate genomic predictions for crossbreds.Genotypes for crossbreds are imputed more accuratelywhen the imputation reference population includespurebreds. Therefore, genotypes of 6,296 crossbredanimals were imputed from lower-density chips byincluding either 3,119 ancestors or 834,367 genotypedanimals in the reference population. Crossbreds inthe imputation study included 733 Jersey × HolsteinF_1 animals, 55 Brown Swiss × Holstein F_1 animals,2,300 Holstein backcrosses, 2,026 Jersey backcrosses,27 Brown Swiss backcrosses, and 502 other crossbredsof various breed combinations. Another 653 animalsappeared to be purebreds that owners had miscodedas a different breed. Genomic breed composition wasestimated from 60,671 markers using the known breedidentities for purebred, progeny-tested Holstein, Jersey,Brown Swiss, Ayrshire, and Guernsey bulls as the 5traits (breed fractions) to be predicted. Estimates ofbreed composition were adjusted so that no percentageswere negative or exceeded 100%, and breed percentagessummed to 100%. Another adjustment set percentagesabove 93.5% equal to 100%, and the resulting valuewas termed breed base representation (BBR). Largerpercentages of missing alleles were imputed by usinga crossbred reference population rather than only theclosest purebred reference population. Crossbred predictionswere averages of genomic predictions computedusing marker effects for each pure breed, which wereweighted by the animal’s BBR. Marker and polygeniceffects were estimated separately for each breed on theall-breed scale instead of within-breed scales. For crossbreds,genomic predictions weighted by BBR were moreaccurate than the average of parents’ breeding valuesand slightly more accurate than predictions using onlythe predominant breed. For purebreds, single-trait predictionsusing only within-breed data were as accurateas multi-trait predictions with allele effects in differentbreeds treated as correlated effects. Crossbred genomicpredicted transmitting abilities were implemented bythe Council on Dairy Cattle Breeding in April 2019 andwill aid producers in managing their breeding programsand selecting replacement heifers.