Modeling pedigree accuracy and uncertain parentage in single-step genomic evaluations of simulated and US Holstein datasets

Simple item page
dc.contributor.authorBradford, Heather L.en
dc.contributor.authorMasuda, Yutakaen
dc.contributor.authorCole, John B.en
dc.contributor.authorMisztal, Ignacyen
dc.contributor.authorVanRaden, Paul M.en
dc.contributor.departmentAnimal and Poultry Sciencesen
dc.date.accessioned2020-03-04T13:59:08Zen
dc.date.available2020-03-04T13:59:08Zen
dc.date.issued2019-03en
dc.description.abstractThe objective of this study was to model differences in pedigree accuracy caused by selective genotyping. As genotypes are used to correct pedigree errors, some pedigree relationships are more accurate than others. These accuracy differences can 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 through North American 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). An additional set of assumptions was tested in simulation to mimic an extensive dairy production system by using a sire probability of 0.75, a darn probability of 0.85, and the remainder attributed to the unknown parent groups. In the 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 ( >= 0.99). For Holsteins, the 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.en
dc.description.adminPublic domain – authored by a U.S. government employeeen
dc.description.notesThe authors thank the Council on Dairy Cattle Breeding (Bowie, MD) for providing data under USDA Nonfunded Cooperative Agreement 58-1245-3-228N. We also thank L. R. Bacheller and M. E. Tooker (Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD) for providing technical assistance. This research was supported in part by an appointment to the Agricultural Research Service (ARS) Research Participation Program administered by the Oak Ridge Institute for Science and Education (ORISE; Oak Ridge, TN) through an interagency agreement between the U.S. Department of Energy (DOE) and the U.S. Department of Agriculture (USDA); ORISE is managed by Oak Ridge Associated Universities (ORAU) under DOE contract number DE-SC0014664. All opinions expressed in this paper are the authors and do not necessarily reflect the policies and views of USDA, ARS, DOE, or ORAU/ORISE. Mention of trade names or commercial products is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. The authors appreciate the helpful comments of 2 anonymous reviewers.en
dc.description.sponsorshipUSDAUnited States Department of Agriculture (USDA) [58-1245-3-228N]; U.S. Department of Energy (DOE)United States Department of Energy (DOE); U.S. Department of Agriculture (USDA)United States Department of Agriculture (USDA); DOEUnited States Department of Energy (DOE) [DE-SC0014664]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.3168/jds.2018-15419en
dc.identifier.eissn1525-3198en
dc.identifier.issn0022-0302en
dc.identifier.issue3en
dc.identifier.pmid30639024en
dc.identifier.urihttp://hdl.handle.net/10919/97130en
dc.identifier.volume102en
dc.language.isoenen
dc.rightsCC0 1.0 Universalen
dc.rights.urihttp://creativecommons.org/publicdomain/zero/1.0/en
dc.subjectaverage relationship matrixen
dc.subjectgenotypeen
dc.subjectpedigree erroren
dc.subjectselective genotypingen
dc.titleModeling pedigree accuracy and uncertain parentage in single-step genomic evaluations of simulated and US Holstein datasetsen
dc.title.serialJournal of Dairy Scienceen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
1-s2.0-S0022030219300426-main.pdf
Size:
502.07 KB
Format:
Adobe Portable Document Format
Description:
Download

Collections

Scholarly Works, School of Animal Sciences