H.L. Bradford*,1, Y. Masuda†, J.B. Cole,* I. Misztal†, and P.M. VanRaden*
*Animal Genomics and Improvement Laboratory, Agriculture Research Service, USDA, Beltsville, MD 20705-2350
†Department of Animal and Dairy Science, University of Georgia, Athens 30605
2018 J. Dairy Sci. (?)
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The objective was to model differences in pedigree accuracy caused by selective genotyping. Because genotypes were used to correct pedigree errors, some pedigree relationships were more accurate than others were. These accuracy differences could be modeled with uncertain parentage models that distribute the paternal (maternal) contribution across multiple sires (dams). In our case, the parents were the parent on record and an unknown parent group to account for pedigree relationships that were not confirmed through genotypes. Pedigree accuracy was addressed through simulation and Holstein data. Data were simulated to be representative of the dairy industry with heterogeneous pedigree depth, pedigree accuracy, and genotyping. Holstein data were obtained from the official evaluation for milk, fat, and protein. Two models were compared: the traditional approach assuming accurate pedigrees and uncertain parentage assuming variable pedigree accuracy. The uncertain parentage model was used to add pedigree relationships for alternative parents when pedigree relationships were not certain. The uncertain parentage model included 2 possible sires (dams) when the sire (dam) could not be confirmed with genotypes. The 2 sires (dams) were the sire (dam) on record with probability 0.90 (0.95) and the unknown parent group for the birth year of the sire (dam) with probability 0.10 (0.05). In simulation, small bias differences occurred between models based on pedigree accuracy and genotype status. Rank correlations were strong between traditional and uncertain parentage models in simulation (≥ 0.99) and in Holstein (≥ 0.96). For Holsteins, estimated breeding value differences between models were small for most animals. Thus, traditional models can continue to be used for dairy genomic prediction despite using genotypes to improve pedigree accuracy. Those genotypes can also be used to discover maternal parentage, specifically maternal grandsires and great grandsires when the dam is not known. More research is needed to understand how to use discovered maternal pedigrees in genetic prediction.