Modeling missing pedigree in single-step genomic BLUP.

TitleModeling missing pedigree in single-step genomic BLUP.
Publication TypeJournal Article
Year of Publication2019
AuthorsBradford, HL, Masuda, Y, VanRaden, PM, Legarra, A, Misztal, I
JournalJ Dairy Sci
Volume102
Issue3
Pagination2336-2346
Date Published2019 Mar
ISSN1525-3198
Abstract

The 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 to better account for missing pedigrees for genotyped animals.

DOI10.3168/jds.2018-15434
Alternate JournalJ. Dairy Sci.
PubMed ID30638995