Simulation was used to compare the accuracy of using genetic markers to assign an animal or animal product to its breed of origin when loci were considered independently segregating versus when haplotypes were constructed for linked loci. The simulated population of animals included three breeds of 10 000 animals each. Assignment was based on 60 biallelic, neutral loci, which could be arranged into twenty 3-locus haplotypes. The frequency method was used to compute likelihoods of breed origins. The Expectation-Maximization approach was used to reconstruct haplotypes and estimate their breed-wise frequencies. Considering haplotypes in breed assignment was only of value when sufficient population-wide linkage disequilibrium was present. Decreasing the size of founder populations increased accuracy of assignment, but did not alter the relative utility of considering haplotypes or individual loci.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 22.20, 2006
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