The number of single nucleotide polymorphisms and on-farm data required for whole-herd parentage testing in dairy cattle herds

J Dairy Sci. 2009 Jan;92(1):369-74. doi: 10.3168/jds.2008-1086.


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.

MeSH terms

  • Animals
  • Cattle / genetics*
  • Computer Simulation
  • Dairying / methods*
  • Female
  • Gene Frequency
  • Genotype
  • Male
  • Microsatellite Repeats
  • Pedigree
  • Polymorphism, Single Nucleotide / genetics*