Modeling missing pedigree in single-step genomic BLUP

Simple item page
dc.contributor.authorBradford, Heather L.en
dc.contributor.authorMasuda, Yutakaen
dc.contributor.authorVanRaden, Paul M.en
dc.contributor.authorLegarra, Andresen
dc.contributor.authorMisztal, Ignacyen
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 was to compare methods of modeling missing pedigree in single-step genomic BLUP (ssGBLUP). Options for modeling missing pedigree included ignoring the missing pedigree, unknown parent groups (UPG) based on A (the numerator relationship matrix) or H (the unified pedigree and genomic relationship matrix), and metafounders. The assumptions for the distribution of estimated breeding values changed with the different models. We simulated data with heritabilities of 0.3 and 0.1 for dairy cattle populations that had more missing pedigrees for animals of lesser genetic merit. Predictions for the youngest generation and UPG solutions were compared with the true values for validation. For both traits, ssGBLUP with metafounders provided accurate and unbiased predictions for young animals while also appropriately accounting for genetic trend. Accuracy was least and bias was greatest for ssGBLUP with UPG for H for the trait with heritability of 0.3 and with UPG for A for the trait with heritability of 0.1. For the trait with heritability of 0.1 and UPG for H, the UPG accuracy (SD) was -0.49 (0.12), suggesting poor estimates of genetic trend despite having little bias for validations on young, genotyped animals. Problems with UPG estimates were likely caused by the lesser amount of information available for the lower heritability trait. Hence, UPG need to be defined differently based on the trait and amount of information. More research is needed to investigate accounting for UPG in A(22) to better account for missing pedigrees for genotyped animals.en
dc.description.adminPublic domain – authored by a U.S. government employeeen
dc.description.notesThis 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 US Department of Energy (DOE) and the US 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. A. Legarra is grateful for FEDER (European Regional Development Fund) funds through Poctefa (Programme Interreg V-A Espagne-France-Andorre, Huesca, Spain) project ARDI (Research, Development, Innovation in Sheep). We appreciated the helpful comments by 2 anonymous reviewers.en
dc.description.sponsorshipUS Department of Energy (DOE)United States Department of Energy (DOE); US Department of Agriculture (USDA)United States Department of Agriculture (USDA); DOEUnited States Department of Energy (DOE) [DE-SC0014664]; Poctefa (Programme Interreg V-A Espagne-France-Andorre, Huesca, Spain) project ARDI (Research, Development, Innovation in Sheep)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.3168/jds.2018-15434en
dc.identifier.eissn1525-3198en
dc.identifier.issn0022-0302en
dc.identifier.issue3en
dc.identifier.pmid30638995en
dc.identifier.urihttp://hdl.handle.net/10919/97131en
dc.identifier.volume102en
dc.language.isoenen
dc.rightsCC0 1.0 Universalen
dc.rights.urihttp://creativecommons.org/publicdomain/zero/1.0/en
dc.subjectgenetic groupen
dc.subjectmetafounderen
dc.subjectsingle-step genomic BLUP (ssGBLUP)en
dc.subjectunknown parent groupen
dc.titleModeling missing pedigree in single-step genomic BLUPen
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-S002203021930044X-main.pdf
Size:
529.68 KB
Format:
Adobe Portable Document Format
Description:
Download

Collections

Scholarly Works, School of Animal Sciences