A comparison between multivariate Slash, Student's t and probit threshold models for analysis of clinical mastitis in first lactation cows

Abstract

Robust threshold models with multivariate Student's t or multivariate Slash link functions were employed to infer genetic parameters of clinical mastitis at different stages of lactation, with each cow defining a cluster of records. The robust fits were compared with that from a multivariate probit model via a pseudo-Bayes factor and an analysis of residuals. Clinical mastitis records on 36 178 first-lactation Norwegian Red cows from 5286 herds, daughters of 245 sires, were analysed. The opportunity for infection interval, going from 30 days pre-calving to 300 days postpartum, was divided into four periods: (i) -30 to 0 days pre-calving; (ii) 1-30 days; (iii) 31-120 days; and (iv) 121-300 days of lactation. Within each period, absence or presence of clinical mastitis was scored as 0 or 1 respectively. Markov chain Monte Carlo methods were used to draw samples from posterior distributions of interest. Pseudo-Bayes factors strongly favoured the multivariate Slash and Student's t models over the probit model. The posterior mean of the degrees of freedom parameter for the Slash model was 2.2, indicating heavy tails of the liability distribution. The posterior mean of the degrees of freedom for the Student's t model was 8.5, also pointing away from a normal liability for clinical mastitis. A residual was the observed phenotype (0 or 1) minus the posterior mean of the probability of mastitis. The Slash and Student's t models tended to have smaller residuals than the probit model in cows that contracted mastitis. Heritability of liability to clinical mastitis was 0.13-0.14 before calving, and ranged from 0.05 to 0.08 after calving in the robust models. Genetic correlations were between 0.50 and 0.73, suggesting that clinical mastitis resistance is not the same trait across periods, corroborating earlier findings with probit models.