Accounting for variance heterogeneity in French dairy cattle genetic evaluation

A linear mixed model assuming heterogeneous residual variances and known co nstant variance ratios was applied to the analysis of milk, fat, and protei n yields, and fat and protein contents in the French Holstein, Montbeliarde , and Normande dairy cattle populations. The method was based on a log-line ar model for residual variances. This log-linear model included a region-ye ar fixed effect and a herd-year random effect with a within-herd autocorrel ation. The estimates of this correlation coefficient varied from 0.64 to 0. 92, according to trait and breed. Residual standard deviation for yields do ubled over the last 20 years, whereas differences across regions were more limited and decreased over time. This model was compared with the homogeneo us model and with the multiplicative model of Meuwissen el al. (1996) [Meuw issen, T.H.E., De Jong, G., Engel, B., 1996. Joint estimation of breeding v alues and heterogeneous variances of large data files. J. Dairy Sci. 79, 31 0-316]. Both heteroskedastic models provided very similar results. Accounti ng for heterogeneous variances had important consequences on cow ranking. C onsequences on AI bull ranking were very limited, although the method affec ted estimated genetic trend and within birth year estimated breeding values (EBV) variability.