Evaluation of SNP-based parentage panels in commercial beef cattle populations

SNP-based sire assignment was analyzed in a known pedigree population containing 71 calves and 8 sires including two full sibling pairs, in addition to a commercial population with unknown parentage containing 8,480 calves with 460 sires. Parentage panels from the International Society of Animal Genetics (ISAG) were evaluated along with a population specific SNP panel. The ISAG core 100 SNP and 200 SNP panels yielded specificities (single correct sire assigned) of 1.0 and 1.0, respectively, allowing zero exclusions, and 0.92 and 0.99 allowing 1% exclusions in the known pedigree population. Sensitivity (correct sire not excluded) was 1.0 across both panels. The sensitivity and specificity of a 1000 SNP panel selected on high heterozygosity and call rate was 1.0 when allowing up to 2% exclusions. At 2% exclusion allowance paternity from the 1000 SNP panel was in agreement with the ISAG panels. In the larger population allowing 1% exclusions the ISAG 100 panel assigned paternity to 7,426 calves with 416 duplicate sire assignments with 12.4% of calves unassigned. The ISAG 200 panel assigned parentage to 6,944 calves with 1 duplicate sire assignment and 18.1% unassigned. The 1000 SNP panel assigned parentage to 6,121 and 6,964 calves at 0% and 1% respectively, with 0 duplicate sire assignments. These results indicate optimal parentage identification procedures are population specific and depend on the number and relatedness of potential parents.