title: The number of single nucleotide polymorphisms and on-farm data required for whole-herd parentage testing in dairy cattle herds.
abstract: 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.
authors.affiliation: Livestock Improvement Corporation Ltd., Hamilton 3240, New Zealand. paul.fisher@agresearch.co.nz
authors.forename: P J
authors.initials: PJ
authors.lastname: Fisher
authors.forename: B
authors.initials: B
authors.lastname: Malthus
authors.forename: M C
authors.initials: MC
authors.lastname: Walker
authors.forename: G
authors.initials: G
authors.lastname: Corbett
authors.forename: R J
authors.initials: RJ
authors.lastname: Spelman
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D003198:Computer Simulation; D003612:Dairying / Q000379:methods*; D005260:Female; D005787:Gene Frequency; D005838:Genotype; D008297:Male; D018895:Microsatellite Repeats; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*