DNA-based paternity analysis and genetic evaluation in a large, commercial cattle ranch setting1

Deoxyribonucleic acid-based tests were used to assign paternity to 625 calves from a multiple-sire breeding pasture. There was a large variability in calf output and a large proportion of young bulls that did not sire any offspring. Five of 27 herd sires produced over 50% of the calves, whereas 10 sires produced no progeny and 9 of these were yearling bulls. A comparison was made between the paternity results obtained when using a DNA marker panel with a high (0.999), cumulative parentage exclusion probability (P(E)) and those obtained when using a marker panel with a lower P(E) (0.956). A large percentage (67%) of the calves had multiple qualifying sires when using the lower resolution panel. Assignment of the most probable sire using a likelihood-based method based on genotypic information resolved this problem in approximately 80% of the cases, resulting in 75% agreement between the 2 marker panels. The correlation between weaning weight, on-farm EPD based on pedigrees inferred from the 2 marker panels was 0.94 for the 24 bulls that sired progeny. Partial progeny assignments inferred from the lower resolution panel resulted in the generation of EPD for bulls that actually sired no progeny according to the high-P(E) panel, although the Beef Improvement Federation accuracies of EPD for these bulls were never greater than 0.14. Simulations were performed to model the effect of loci number, minor allele frequency, and the number of offspring per bull on the accuracy of genetic evaluations based on parentage determinations derived from SNP marker panels. The SNP marker panels of 36 and 40 loci produced EPD with accuracies nearly identical to those EPD resulting from use of the true pedigree. However, in field situations where factors including variable calf output per sire, large sire cohorts, relatedness among sires, low minor allele frequencies, and missing data can occur concurrently, the use of marker panels with a larger number of SNP loci will be required to obtain accurate on-farm EPD.