Improving the Accuracy of Multi-Breed Prediction in Admixed Populations by Accounting for the Breed Origin of Haplotype Segments

Numerically small breeds have often been upgraded with mainstream breeds. This historic introgression predisposes the breeds for joint genomic evaluations with mainstream breeds. The linkage disequilibrium structure differs between breeds. The marker effects of a haplotype segment may, therefore, depend on the breed from which the haplotype segment originates. An appropriate method for genomic evaluation would account for this dependency. This study proposes a method for the computation of genomic breeding values for small admixed breeds that incorporate phenotypic and genomic information from large introgressed breeds by considering the breed origin of alleles (BOA) in the evaluation. The proposed BOA model classifies haplotype segments according to their origins and assumes different but correlated SNP effects for the different origins. The BOA model was compared in a simulation study to conventional within-breed genomic best linear unbiased prediction (GBLUP) and conventional multi-breed GBLUP models. The BOA model outperformed within-breed GBLUP as well as multi-breed GBLUP in most cases.