Accuracy of Genomic Prediction from Multi-Breed Sheep Reference Population

Abstract

Genomic estimated breeding values (GEBV) were calculated based on a combination of purebred and crossbred sheep for birth weight, weaning weight and post weaning weight using genomic best linear unbiased prediction (GBLUP). The genomic relationship matrix (G) was calculated based on population wide or breed of haplotype specific allele frequency using the 50k ovine Illumina SNP-chip. The accuracy of genomic prediction was estimated based on the correlation between genomic breeding value and an accurate breeding value based on progeny records. The result showed better genomic prediction accuracy for breeds with higher representation in the combined reference populations. Accuracies slightly decreased when the reference set contained a significant set of additional animals from another breed. This study showed no extra accuracy from across breed information using 50k SNP marker panel. The result showed a small but non-significant increase in accuracy when using breed specific allele frequencies in the calculation of G.