Evaluation and Development of SNP-Based Parentage Identification 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 specificity of a 1000 SNP panel selected on high heterozygosity and call rate was 1.0, 1.0 and 1.0 when allowing 0, 1% and 2% exclusions, respectively, and sensitivity was 0.51, 0.67 and 1.0. 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 7,010 calves with 416 duplicate sire assignments with 17.3% 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 4410 and 6,948 calves at 1% and 2% respectively, with 0 duplicate sire assignments. This meant 48.0% and 18.1% calves were unassigned at 1% and 2% exclusions, respectively.  These results indicate optimal parentage identification procedures are population specific and depend on the number and relatedness of potential parents.