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.
Iowa State University
Hayr, Melanie K.; Sun, Xiaochen; Druet, Tom; and Garrick, Dorian J.
"Genomic Prediction of Milk Fat using Fixed Length Haplotypes,"
Animal Industry Report:
AS 662, ASL R3071.
Available at: https://lib.dr.iastate.edu/ans_air/vol662/iss1/32