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J. Dairy Sci. 2009. 92:369-374. doi:10.3168/jds.2008-1086
© 2009 American Dairy Science Association ®
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The number of single nucleotide polymorphisms and on-farm data required for whole-herd parentage testing in dairy cattle herds

P. J. Fisher*,{dagger},1, B. Malthus*, M. C. Walker*, G. Corbett{ddagger} and R. J. Spelman*

* Livestock Improvement Corporation Ltd., Hamilton 3240, New Zealand
{dagger} AgResearch, Invermay, Mosgiel 9053, New Zealand
{ddagger} ZyGEM Corporation Ltd, Hamilton 2001, New Zealand

1 Corresponding author: paul.fisher{at}agresearch.co.nz

New platforms utilizing single nucleotide polymorphisms (SNP) offer operational advantages over the conventional microsatellite-based ones, making them a promising alternative for parentage exclusion. Through simulation and empirical data, a 40-SNP panel (where the minor allele frequency was 0.35 on average) was shown to be a comparable or better diagnostic tool than the current 14-microsatellite panel that is used to parentage test New Zealand dairy animals. The 40 SNP alone did not have sufficient power of exclusion to match more than 75% of the progeny to the correct sire and dam. Utilizing mating records and grouping progeny and dams by birth and calving dates, respectively, decreased the number of sire-dam combinations that each progeny was tested against and dramatically increased the utility of the SNP. These results highlight the importance of combining genotypes with on-farm data to maximize the ability to assign parentage in the New Zealand dairy herd.

Key Words: bovine • parentage testing • pedigree record • single nucleotide polymorphism






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