8.6: Breeding value estimation: the Animal Model

Although mass selection is a straight forward way of ranking animals as breeding candidates, it is not always the most accurate way. For example, if all we have is own performance, how would we be able to select animals without own performance? How can we select dairy cattle bulls for improved milk production? Or how can we select animals for meat quality? Meat quality can only be measured after slaughter and then those animals cannot be used for breeding anymore. Fortunately there is a solution for that: we use phenotypic information collected on related animals and use that for estimating breeding values for animals without phenotypes. The success will depend on how much their genetics will resemble that of the animal without own performance: their additive genetic relationship.

Of course for estimating the breeding value of an animal the additive genetic relationship with animals with phenotypes needs to be quite substantial, so that the additional phenotypic information has added value. For example, information on a full brother, who has on average half of its genome the same as your animal (so a=0.5), has more added value than information on a far cousin with additive genetic relationship of only 0.0625. And information on parents or offspring has more added value than information of full brothers and sisters, even though all have additive genetic value of 0.5. That is because parents pass exactly half of their genome on to their offspring. So their additive genetic relationship really is 0.5, whereas full brothers and sisters on average share half of their genome. The Mendelian sampling (the uncertainty of which half of the genetic potential of a parent is passed on to each offspring) determines whether this indeed is the same half or not. In other words: this half is not as certain as the half that parents and offspring share.

The method of combining the additive genetic relationships between animals with the phenotypic information of some of those animals to estimate all of their breeding values is called the Animal Model.  The Animal Model is not only useful in case of missing phenotypic observations, but also to increase the quality of phenotypic information so that the breeding value can be estimated more accurately. So how does the animal model work?