Weller, J.I., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Glick, G., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
Ezra, E., Israel Cattle Breeders Association, Caesaria Industrial Park 38900, Israel
Zeron, Y., Sion, AI Institute, Shikmim 79800, Israel
Seroussi, E., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
Ron, M., Institute of Animal Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel

Incorrect paternity assignment in cattle can have a major effect on rates of genetic gain. Of the 576 Israeli Holstein bulls genotyped by the BovineSNP50 BeadChip, there were 204 bulls for which the father was also genotyped. The results of 38 828 valid single nucleotide polymorphisms (SNPs) were used to validate paternity, determine the genotyping error rates and determine criteria enabling deletion of defective SNPs from further analysis. Based on the criterion of >2% conflicts between the genotype of the putative sire and son, paternity was rejected for seven bulls (3.5%). The remaining bulls had fewer conflicts by one or two orders of magnitude. Excluding these seven bulls, all other discrepancies between sire and son genotypes are assumed to be caused by genotyping mistakes. The frequency of discrepancies was >0.07 for nine SNPs, and >0.025 for 81 SNPs. The overall frequency of discrepancies was reduced from 0.00017 to 0.00010 after deletion of these 81 SNPs, and the total expected fraction of genotyping errors was estimated to be 0.05%. Paternity of bulls that are genotyped for genomic selection may be verified or traced against candidate sires at virtually no additional cost. © 2010 Stichting International Foundation for Animal Genetics.