13.6.2 Consequences of GxE for the breeding program

Genotype by environment interaction occurs in any situation where one population is more sensitive to changes than others, indicated by a steeper slope in the reaction norm. What are consequences for the breeding program? When do you need to take into account that the offspring is supposed to perform in a different type of environment than what the parents are selected in?

An answer to these questions lays in the genetic correlation between performance in both environments. If the correlation is low, or even negative, selection based on performance in one environment may result in poor performance of the offspring in the other environment. For example, if you would select the best performing animals in an environment that is optimised in all possible ways (perfect housing, feeding, health care, etc), you may get the animals with the best genetic potential for your trait if interest IN THAT ENVIRONMENT. However, if you would use those animals as parents for offspring in a more average environment, they may perform poorly because they miss the prerequisites that it takes to perform in that average environment. The genetic correlation between performance in two environments is a measure of how applicable the genotype in one environment is to perform in the other environment. In other words, that genetic correlation provides an indication of whether the same breeding program can be used for both environments or not. Obviously, performance testing of sibs or offspring in the environment that the offspring is supposed to perform in is very valuable information to optimise the selection decisions.

If the same breeding program is supposed to serve a too large range of environments, it may become wiser to split the breeding program in two. That decision will depend on the outcome of a number of questions. What is the genetic progress now and how will that improve when the breeding program is split? Very important in relation to that is your competitive position with respect to others that operate in the same market. As a breeding company, you can save money by maintaining a single breeding program, but you can lose much more by losing genetic gain, and thus market share, to your competitor. Obviously this is the case in farm animal breeding, but it also is the case in riding horse breeding! The KWPN, for example, has decided to split its breeding program in two: one for dressage and one for show-jumping. The selection criteria for both specializations are different. Stallions for the dressage specialization are no longer tested on their show jumping skills but they should have excellent gaites and show real potential in the performance test. Stallions for the show jumping specialization are not punished for having less superior gaites, but they should show real potential for show jumping. The idea was that this would allow more genetic progress through specialisation. There were costs involved, but the idea was that the benefits would outweigh the costs and market share could be further increased. Because the split of the breeding program into two has been relatively recent, the results have not been evaluated yet. But preliminary results suggest that from genetic progress point of view the split has been a success.

A rule of thumb for running a breeding program is that if the genetic correlation between performance in two environments drops below 0.6, so if different genetics is required to perform well in either environment, it becomes worthwhile to split the breeding program into two: one for each environment. A correlation higher than 0.6 indicates that even though the selection of the parents may be sub-optimal, it still outweighs the costs of running two separate breeding programs. Costs involve not only the financial consequences, but the costs with respect to loss in genetic response to selection if the population is reduced in size, and with respect to maintaining genetic diversity (of the two smaller populations).