Effect of ignoring random sire and dam effects on estimates and standard errors of breed comparisons

Data were weights of F1 calves and weaning weights of top-cross progeny from sires and maternal grandsires of 13 breeds. Three analyses were performed on each trait to obtain estimates and standard errors of breed effects needed to calculate across-breed EPD and accuracies. Model (R) for records of F1 progeny contained fixed effects for birth year and date of birth, sex, age and breed of dam, and breed of sire, and a random residual effect. The second analysis included random effects for sires (RS), and the third analysis included random effects for sires and dams (RSD). In maternal analysis of top-cross progeny, model (Rm) contained fixed effects for cycle of experiment, age of dam, year of birth, sex, breeds of maternal grandam and grandsire, and breed of sire, and a random residual effect. In addition, the second and third analyses fit random effects for maternal grandsires (RSm) and for maternal grandsires and daughters of maternal grandsires (RSDm). Estimates of breed of sire effects changed only slightly for different models. Total variance increased in RSD and RS relative to R. Standard errors of breed of sire comparisons were underestimated with Model R, compared to Models RS and RSD. Standard errors of other contrasts were generally not affected. Variance components, breed effects, and standard errors followed patterns for Rm, RSm, and RSDm similar to those for R, RS, and RSD. Ignoring random variation due to sires and dams underestimated standard errors of breed of sire comparisons.