Multibreed genomic evaluations using purebred Holsteins, Jerseys, and Brown Swiss

Abstract

Multibreed models are currently used in traditional US Department of Agriculture (USDA) dairy cattle genetic evaluations of yield and health traits, but within-breed models are used in genomic evaluations. Multibreed genomic models were developed and tested using the 19,686 genotyped bulls and cows included in the official August 2009 USDA genomic evaluation. The data were divided into training and validation sets. The training data set comprised bulls that were daughter proven and cows that had records as of November 2004, totaling 5,331Holstein, 1,361 Jersey, and 506 Brown Swiss. The validation data set had 2,508Holstein, 413 Jersey, and 185 Brown Swiss bulls that were unproven (no daughter information) in November 2004 and proven by August 2009. A common set of 43,385 single nucleotide polymorphisms (SNP) was used for all breeds. Three methods of multibreed evaluation were investigated. Method 1 estimated SNP effects separately within breed and then applied those breed-specific SNP estimates to the other breeds. Method 2 estimated a common set of SNP effects from combined genotypes and phenotypes of all breeds. Method 3 solved for correlated SNP effects within each breed estimated jointly using a multitrait model where breeds were treated as different traits. Across-breed genomic predicted transmitting ability (GPTA) and within-breed GPTA were compared using regressions to predict the deregressed validation data. Method 1 worked poorly, and coefficients of determination (R2) were much lower using training data from a different breed to estimate SNP effects. Correlations between direct genomic values computed using training data from different breeds were less than 30% and sometimes negative. Across-breed GPTA from method 2had higher R2 values than parent average alone but typically produced lower R2 values than the within-breed GPTA. The across-breed R2 exceeded the within-breed R2 for a few traits in the Brown Swiss breed, probably because information from the other breeds compensated for the small numbers of Brown Swiss training animals. Correlations between within-breed GPTA and across-breed GPTA ranged from 0.91 to 0.93. The multibreed GPTA from method 3 were significantly better than the current within-breed GPTA, and adjusted R2 for protein yield (the only trait tested for method 3) were highest of all methods for all breeds. However, method 3 increased the adjusted R2 by only 0.01 for Holsteins, ≤0.01 for Jerseys, and 0.01 for Brown Swiss compared with within-breed predictions. © 2012 American Dairy Science Association.