8.15.1 Composition of the reference population

Apart from sufficient size of the reference population it is also important that the reference population is related to the main population to assure that the estimated associations between SNP and the phenotypes also exist in the main population. The smaller the genetic relationship between reference and main population, the more associations will be different in the main population due to recombination between SNP and genes that determine the effect on the phenotype. Also with little genetic relationships still many of the association will exist because the animals in both populations are of the same breed, but the closer the relationship the better the estimates of the associations.

The need for genetic relationships between reference and main population is the reason for a restricted working life of the reference population. The accuracy of the estimated associations between phenotype and SNP reduces across generations. Main reason is recombination between the genes that are affecting the phenotype and the SNP. The larger the number of SNP that are used in genotyping the reference population, the longer its shelf life. But the linkage between SNP and genes will reduce across generations. The only solution is to update the reference population. It is still unclear what would be the best strategy for increasing the working life of a reference population. Should the population have a very large number of animals from the start? Or is it better to start smaller but add new animals every generation? And how many animals? It has become clear that even though the reference population is very large, it remains essential to add new animals at regular basis to update the estimated SNP associations.