Animal Industry Report

Extension Number

ASL R3071



Summary and Implications

Performance of genomic prediction from haplotype models utilizing fixed length haplotype blocks ranging from 125 kb – 2 Mb and haplotype allele frequency cutoffs ranging from 1-10% were compared to a model using SNP genotypes. Milk fat yield deviations and genotypes at 37,740 SNPs were from 38,385 Holstein Friesian, Jersey and KiwiCross cows (Training=23,907; Validation=14,478) from New Zealand. This study showed slight improvement in accuracy and bias of genomic prediction when using 125 kb haplotype blocks with a 1% filter; however this was associated with a large increase in run-time. Haplotype blocks larger than 1 Mb are not appropriate for genomic prediction in this population.

Copyright Holder

Iowa State University