Model comparison for genetic evaluation of milk yield in Uruguayan Holsteins

Abstract

Three models for genetic evaluation of milk yield of Uruguayan Holstein cattle were compared using 159 169 lactation records from 81 928 cows calving between 1989 and 1998. Model I included the effects of herd-year-season, parity by age group, additive genetic merit, permanent environment, and residual. Model II included all effects in Model I, as well as number of days open and length of the dry period. Model III included all factors in Model II, and it accommodated heterogeneity of variance within contemporary groups (CG) through a pre-adjustment of the data based on empirical Bayes estimates of the CG variance. Estimates of heritability for milk yield were 0.23, 0.24 and 0.25, and estimates of repeatability were 0.55, 0.56 and 0.57 for Models I, II and III, respectively. Models were contrasted by examining changes in sire ranking and by a cross-validation procedure, based on the ability of the models to predict first, second and later lactations. Data were divided into two subsets, and records from one subset were predicted using location parameters estimated from the other subset. A resampling procedure was used to minimise the dependency on the sample structure. Correspondence between observed and predicted values was assessed in terms of square root of empirical mean square errors of prediction, percentage squared bias and the coefficient of determination ‘ R 2’. Adjustment for heterogeneous CG variance had a marked effect on rankings of animals, especially elite cows, where correlations between solutions from Models I and II versus Model III ranged from 0.53 to 0.80. The percentage of animals selected in common by each pair of models decreased when selection intensity increased. Cross-validation analyses suggested that an assumption of heterogeneity of CG variance is tenable, especially in later lactations, whereas some doubts arise in first lactations, most probably due to the data structure used in the analyses.