Identification of sources of heterogeneous residual and genetic variances in milk yield data from the Spanish Holstein-Friesian population and impacton genetic evaluation

Data from the Spanish Holstein-Friesian milk recording system were used to investigate sources of heterogeneity of genetic and residual variation and to evaluate the impact in the genetic evaluation. Factors such as period of time, herd level of production, geographical region, herd size and year of calving were found to be associated with heterogeneity of genetic and resi dual variation. This stratified the 7664 herd-year of calving into 395 stra ta defined by combinations of levels of these factors. In order to improve the accuracy of estimates of strata dispersion a mixed model structure in t he log-linear model was considered which included the single factors acting additively as fixed effect plus the random third order interaction for res idual variance and the single factor acting additively as fixed effect for sire variance. The average value for heritabilities estimated was 0.26, wit h maximum and minimum values being 0.52 and 0.11, respectively. The 25 and 75 percentiles were 0.20 and 0.32, respectively. Genetic evaluations were c ompared using three alternative models differed in the dispersion structure : Homogeneous genetic and residual variance, homogeneous genetic and residu al variance after data standardization and the heterogeneous variance model with the current genetic and residual variance estimated. Assuming a homog eneous variance model produced an overdispersion with respect to the expect ed dispersion of both yield deviations and predicted genetic values in larg e variance environments and the contrary was observed in low variance envir onments. Precorrection by phenotypic standardization seems to correct for t he phenotypic adequately but dispersion of predicted genetic values of anim al in environments with large heritability was underestimated with respect to the heterogeneous variance model. (C) 1999 Elsevier Science B.V. All rig hts reserved.