Analysis of validated and population-specific single nucleotide polymorphism parentage panels in pedigreed and commercial beef cattle populations

Abstract

A pedigreed population containing 71 calves and 8 sires was used to compare sire qualification using three genotyping platforms [14 microsatellite, real-time quantitative PCR, and 100, 200, 500, and 1000 single nucleotide polymorphism (SNP) arrays]. Parentage was also qualified in an unknown-pedigree population containing 8480 calves with 460 sires using SNP arrays. The three platforms qualified the true sire in the known-pedigree population with zero mismatches. The 100 and 200 SNP arrays yielded specificities of 0.92 and 0.99 with a 1% mismatch rate in the known-pedigree population, respectively. In the larger population, SNP panels of the 500 and 1000 highest minor allele frequency SNPs were also evaluated. The 1000 SNP panel qualified paternity to a single sire for 82.1% of calves with 1% or 2% mismatches. Not all commercial sires were genotyped, which accounts for missing paternity for some calves. In this larger population, the 100 SNP array qualified multiple sires to 0.42% of calves and single sires to 80.84% of calves without mismatches. The 200 SNP array assigned unique paternity, and 79.8% of calves were qualified to a sire without mismatches. With a 2% mismatch rate, sire qualifications agreed with the 1000 SNP array. This study highlights the interplay among population size, genotyping error rates, and the specificity and sensitivity of parentage platforms.