Heterogeneity of herd-period phenotypic variances in the Spanish Holstein-Friesian cattle: Sources of heterogeneity and genetic evaluation

Data from the Spanish Holstein-Friesian milk recording system were used to investigate sources of heterogeneity of phenotypic herd-period variances for milk yield and to evaluate the impact of data standardization in the genetic evaluation. Factors such as region, year of calving and management level of the herd were found to be associated to heterogeneity of herd-period variances in a correspondence analysis. Applying clustering techniques, initial 36781 herd-periods were stratified into 38 subclasses defined by combinations of levels of those factors. A statistical analysis that used a structural model on log-variances showed that a significant amount of the observed variability among herd-period variances could be explained by the defined subclasses. Variability between subclasses was 62.8% of the total between and within true variability. The herd-period stratification was used to obtain estimates of herd-period milk yield variances in a Bayesian analysis. These estimates were then applied to produce standardized milk yield records. Genetic evaluations were run on standardized and unstandardized data. Genetic evaluation of cows was noticeably affected by standardization. Twenty percent of cows in the 1000 best cows list were excluded from the list when standardization was performed. Estimated correlation coefficient between the two evaluations for these cows was 0.82, Bulls evaluation was affected to a less extent. Only 9% of the top 100 bulls were out of the 100 top list after standardization. A slight tendency to use North American bulls from the most variable herds was observed, However, this fact did not imply significant changes in ranking of North American bulls compared to domestic bulls when standardization was performed.