Technical note: Adjustment of all cow evaluations for yield traits to be comparable with bull evaluations

Authors: Wiggans, George; Vanraden, Paul; Cooper, Tabatha

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2012
Publication Date: 6/1/2012
Citation: Wiggans, G.R., Van Raden, P.M., Cooper, T.A. 2012. Technical note: Adjustment of all cow evaluations for yield traits to be comparable with bull evaluations. Journal of Dairy Science. 95(6):3444-3447.

Interpretive Summary: An adjustment for traditional evaluations of yield traits of all US cows was developed to make evaluations of genotyped and nongenotyped cows more comparable. Traditional cow evaluations were adjusted within birth year to have characteristics similar to those of bull evaluations. A second adjustment was applied to evaluations of some genotyped cows based on comparison with direct genomic values. The second adjustment also was applied to cows with converted evaluations from other countries; those cows were excluded from the predictor population. The adjustment method was implemented in April 2011.

Technical Abstract: Traditional evaluations of cows with genotypes have been adjusted since April 2010 to be comparable with evaluations of bulls so that their value for estimation of SNP effects would be improved. However, that adjustment made them not comparable with traditional evaluations of nongenotyped cows. To create an adjustment for all cows with an evaluation based on US data, Mendelian sampling, which is the difference between predicted transmitting ability (PTA) and parent average (PA), was calculated for milk, fat, and protein yields and then deregressed by dividing by a function of reliability with PA contribution removed. Standard deviations for the deregressed Mendelian sampling (DMS) were grouped by reliability. A multiplicative adjustment to reduce the DMS standard deviation for cows so that it would be the same as for bulls with similar reliability was represented as a linear function of reliability. Mean PA by birth year was subtracted from PA to create within-year PA deviation groups, and mean DMS was calculated for bulls and cows by PA deviation group. Means decreased for bulls and increased for cows with increasing deviation. The differences were fit by linear regression on PA deviation and used to adjust cow DMS. The adjustment reduced PTA of cows with a high PA and increased PTA of cows with a low PA but did not change estimated genetic trend because adjustment was within birth year. The adjustment also reduced variance of cow evaluations within birth year. Traditional evaluations of genotyped cows with a reliability (excluding PA contribution) of '55% were further adjusted so that the difference between those evaluations and direct genomic values calculated using only bulls as predictors was similar to that for bulls. The second adjustment was small compared with a 2010 adjustment and, therefore, had little effect on the comparability of evaluations for genotyped and nongenotyped cows. Cows with converted evaluations from other countries were excluded from the predictor population, and their converted evaluations were adjusted so that the difference between their mean PTA and direct genomic value was the same as the corresponding difference for bulls. For cows with converted evaluations the adjustment amount differed depending on if the reliability (excluding PA contribution) of '55% or not. The new adjustment was implemented by USDA in April 2011 and lets breeders more fairly compare nongenotyped with genotyped cows.