Haplotype Tests for Diagnosis of QTL and Genes

Tests based on haplotypes are usually considered to be temporary measures until causal mutations are found. An alternative view is that for livestock improvement they may be sufficient. Haplotype tests can be delivered quickly and cheaply, requiring no knowledge of the causal mutation. Appropriately applied, they are robust to uncertainty in the number of alleles at the mutation. With a haplotype based test for polled in beef cattle we found that most animals carried common haplotypes, and for these there was very high concordance in their association with the underlying genotypes. Phenotyped animals tested commercially can contribute to the accuracy of haplotype effect estimates, especially for rare or previously unseen haplotypes. For livestock, haplotype based tests may be competitive with causal mutation tests in delivering genetic improvement.