Adjustment for Heterogeneous Variance in Genetic Evaluations for Conformation of United States Holsteins

Abstract

A method was developed to account for heterogeneous phenotypic variance for final type (conformation) score within herd-year-month-classifier subclasses for national genetic evaluations of US Holsteins. Phenotypic variances decreased 3.5-fold as within-subclass means increased from 70 to 89 points, and variances increased slightly over time and with increases in subclass size and proportion of registered animals. A model containing known management characteristics was fitted to phenotypic standard deviations within subclass, and resulting solutions were used to estimate the prior variance for each subclass. Prior estimates and phenotypic variance estimates within subclass were combined using Bayesian methods, resulting in posterior estimates that contained more information than either the prior estimates or the within-subclass statistics. Observations were standardized to a common variance using the mean of the posterior density of the phenotypic standard deviation within subclass. Moderate changes in PTA occurred for low reliability bulls, bulls with many progeny in a single herd, and foreign bulls subjected to positive assortative mating. Significant increases occurred in ETA of superior cows in subclasses with high means. Incorporation of a heterogeneous variance adjustment into national genetic evaluations should increase fairness of selection among cows and young bulls and may increase the rate of genetic gain from female selection.