Genetic evaluations should become more accurate with the advent of whole genome selection (WGS) based on high density SNP panels. The use of WGS should then accelerate genetic gains for production traits given likely decreases in generation interval due to the greater intent to select more animals based just on their genotypes rather than phenotypes. However, past and current genetic evaluations may not generally connect well to the intended scope of inference. For example, estimating haplotype effects from the data of a single reference population does not bode well for the use of WGS in other diverse environments since the scope of inference is too narrow; conversely, WGS based on estimates, for example, derived from daughter yield deviations of dairy bulls may be too broad to infer upon genetic merit under any one particular environment. The treatment of contemporary group effects as random rather than as fixed, heterogeneous variances, genotype by environment interaction, and multiple trait analyses are all important scope of inference issues that are discussed in this review. Management systems and environments have and will continue to change; hence, it is vital that genetic evaluations are as robust and scope-appropriate as is possible in order to optimize animal adaptation to these changes.
Bayesian inference; genotype by environment interaction; heterogeneous variances; mixed effects models; multiple traits; random effects
