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Abstract:
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In livestock, prediction of an animal's genetic merit using genomic information is becoming increasingly common. The models used to make these predictions typically assume that we are sampling from a homogeneous population. However, in both commercial and experimental populations the sire and dam of an individual may be a mixture of several populations. Haplotype models can capture this population structure. A model based on breed specific haplotype clusters which utilizes the known breed composition from the sire and dam was developed to allow for differences in linkage disequilibrium across multiple breeds. The haplotype clusters were modeled as hidden states in a hidden Markov model where the genomic effects are associated with loci located on the unobserved clusters. Similar to the Bayes C model, we can model the genomic effects at the loci using a prior, which consists of a mixture of a multivariate normal and a point mass at zero distribution. The model was evaluated in an F1 population, which was a cross between two independent lines, using age of puberty records on 1,654 swine genotyped for 48,408 mapped SNPs.
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