In the previous chapter we have seen how we can model the phenotype into genetic and environmental components. That chapter was quite theoretical, but we need that theory to continue with our breeding program. We have collected a lot of information on the performance of the animals, of their pedigree, and of their relatives, and now we want to know which animals are the best to be used in breeding. In other words: how can we rank the animals to be able to select the best? How do we know which have the best genetic potential and thus have the highest value for breeding (best breeding value)? We have observations on the phenotypes of the animals, but the phenotype is not only determined by the genetic potential, but also by environmental influences. In order to rank the animals according to their breeding value we need to find a way to quantify that breeding value, given the information we have: phenotypes and pedigree (i.e. the genetic relationships between animals). In this chapter we will present different techniques to do just that: rank the animals in order of estimated breeding value. We will also discuss which technique is most suitable in which situation as each technique has its own advantages, but also disadvantages. There are two main reasons why ‘breeding is gambling’: first of all the breeding value needs to be estimated and this may involve inaccuracy of the estimated breeding value. Second, even if you know the breeding value of an animal with 100% accuracy, so you know its true breeding value, you can’t predict which half of the genetic potential is passed on to each of the progeny. This factor will always remain a factor of insecurity in breeding decisions because until now it is not possible to know the exact genotypes of a spermatozoid and an oocyte prior to conception.
If we look at the diagram again with the stages involved in the breeding program circle, then we are still at the stage number 4: determining selection criteria. After having developed the genetic model in the previous chapter we will now consider estimating the breeding values of the animals.