Genomic Prediction of Milk Fat using Fixed Length Haplotypes

  • Melanie K. Hayr (Iowa State University)
  • Xiaochen Sun (Iowa State University)
  • Tom Druet (University of Liège)
  • Dorian J. Garrick (Iowa State University)


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.

How to Cite:

Hayr, M. K., Sun, X., Druet, T. & Garrick, D. J., (2016) “Genomic Prediction of Milk Fat using Fixed Length Haplotypes”, Iowa State University Animal Industry Report 13(1). doi: https://doi.org/10.31274/ans_air-180814-201

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Published on
01 Jan 2016
Peer Reviewed