Genetic Properties of Animal Models

Abstract

For traits controlled by a large number of loci acting additively, use of an animal model with the additive genetic relationship matrix can account for changes in genetic mean and variance due to chance or selection. Changes in genetic variance can result from inbreeding and linkage disequilibrium as a result of selection. Through the relationship matrix, breeding values are expressed as linear functions of breeding values of base population animals and subsequent Mendelian sampling contributions that are unaffected by selection and account for inbreeding. Correct definition of the base population is important. With finite numbers of loci, an animal model does not account for changes in genetic variance due to changes in gene frequency. Genotypic values can be expressed in terms of separate gametic contributions of each parent by gametic models, and a gametic relationship matrix can be constructed. With dominance, use of an animal model with the dominance relationship matrix leads to BLUP of dominance genetic merit if number of loci is sufficiently large and no inbreeding occurs. With inbreeding, inclusion of the dominance relationship matrix (even if modified to account for inbreeding contributions) does not account for inbreeding depression. However, effects of inbreeding depression might be accommodated by including the inbreeding coefficient as a covariate in the model.