Analysis of Single Nucleotide Polymorphism Panels for Bovine DNA Identification

Single nucleotide polymorphisms (SNPs) have great power in resolving questions of unknown parentage on ranches or dairies where errors could have been made in pedigree record keeping or when such records were simply not kept. Currently a panel of 88 SNPs based on a panel originally created by USDA-MARC is commercially available from the company Fluidigm®. Our objective was to determine whether or not the number of SNPs could be reduced to form a smaller, more cost-efficient parentage-testing panel. A smaller panel would be beneficial to farmers and researchers alike in the reduction of time spent running and preparing chips for the Fluidigm® machine, as well as a reduction in cost for the procedure. Genotype data for over 3000 cattle samples from offspring and potential parents were run through parentage calling software against nine SNP panels of varying size. It was determined that the minimum number of SNPs chosen from the existing pool of 88, that will make bovine parentage calls without a loss of accuracy or reliability compared to the original panel, is 71 SNPs