On estimation and identifiability issues of sex‐linked inheritance with a case study of pigmentation in Swiss barn owl ( Tyto alba )

Genetic evaluation using animal models or pedigree‐based models generally assume only autosomal inheritance. Bayesian animal models provide a flexible framework for genetic evaluation, and we show how the model readily can accommodate situations where the trait of interest is influenced by both autosomal and sex‐linked inheritance. This allows for simultaneous calculation of autosomal and sex‐chromosomal additive genetic effects. Inferences were performed using integrated nested Laplace approximations (INLA), a nonsampling‐based Bayesian inference methodology. We provide a detailed description of how to calculate the inverse of the X‐ or Z‐chromosomal additive genetic relationship matrix, needed for inference. The case study of eumelanic spot diameter in a Swiss barn owl ( Tyto alba ) population shows that this trait is substantially influenced by variation in genes on the Z‐chromosome ( σ z 2= 0.2719 andσ a 2= 0.4405 ). Further, a simulation study for this study system shows that the animal model accounting for both autosomal and sex‐chromosome‐linked inheritance is identifiable, that is, the two effects can be distinguished, and provides accurate inference on the variance components.