Differences among methods to validate genomic evaluations for dairy cattle

Two methods of testing predictions from genomic evaluations were investigated. Data used were from the August 2006 and April 2010 official USDA genetic evaluations of dairy cattle. The training data set consisted of both cows and bulls that were proven (had own or daughter information) as of August 2006 and included 8,022, 1,959, and 1,056 Holsteins, Jerseys, and Brown Swiss, respectively. The validation data set consisted of bulls that were unproven as of August 2006 and were proven by April 2010 with 2,653, 411, and 132 Holsteins, Jerseys, and Brown Swiss for the production traits. Method 1 used the training animal's predicted transmitting ability (PTA) from August of 2006. Method 2 used the training animal's April 2010 PTA to estimate single nucleotide polymorphism effects. Both methods were tested using several regressions with the same validation animals. In both cases, the validation animals were tested using the deregressed April 2010 PTA. All traits that had genomic evaluations from the official USDA April 2010 genetic evaluations were tested. Results included bias, differences from expected regressions (calculated using selection intensities), and the coefficients of determination. The genomic information increased the predictive ability for most of the traits in all of the breeds. The 2 methods of testing resulted in some differences that would affect interpretation of results. The coefficient of determination was higher for all traits using method 2. This was the expected result as the data were not independent because evaluations of the validation bulls contributed to their sires' evaluations. The regression coefficients from method 2 were often higher than the regression coefficients from method 1. Many traits had regression coefficients that were higher than 2 standard deviations from the expected regressions when using method 2. This was partially due to the lack of independence of the training and validation data sets. Most traits did have some level of bias in the prediction equations, regardless of breed. The use of method 1 made it possible to evaluate the increased accuracy in proven first-crop bull evaluations by using genomic information. Proven first-crop bulls had an increase in accuracy from the addition of genomic information. It is advised to use method 1 for validation of genomic evaluations.