Apart from sufficient size of the reference population it is also important that the reference population is 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.
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