Unknown-parent groups in single-step genomic evaluation

Title
Unknown-parent groups in single-step genomic evaluation
Publication Date
2013
Author(s)
Misztal, I
Vitezica, Z G
Legarra, A
Aguilar, I
Swan, Andrew
( author )
OrcID: https://orcid.org/0000-0001-8048-3169
Email: aswan@une.edu.au
UNE Id une-id:aswan
Type of document
Journal Article
Language
en
Entity Type
Publication
Publisher
Wiley-Blackwell Verlag GmbH
Place of publication
Germany
DOI
10.1111/jbg.12025
UNE publication id
une:14762
Abstract
In single-step genomic evaluation using best linear unbiased prediction (ssGBLUP), genomic predictions are calculated with a relationship matrix that combines pedigree and genomic information. For missing pedigrees, unknown selection processes, or inclusion of several populations, a BLUP model can include unknown-parent groups (UPG) in the animal effect. For ssGBLUP, UPG equations also involve contributions from genomic relationships. When those contributions are ignored, UPG solutions and genetic predictions can be biased. Options to eliminate or reduce such bias are presented. First, mixed model equations can be modified to include contributions to UPG elements from genomic relationships (greater software complexity). Second, UPG can be implemented as separate effects (higher cost of computing and data processing). Third, contributions can be ignored when they are relatively small, but they may be small only after refinements to UPG definitions. Fourth, contributions may approximately cancel out when genomic and pedigree relationships are constructed for compatibility; however, different construction steps are required for unknown parents from the same or different populations. Finally, an additional polygenic effect that also includes UPG can be added to the model.
Link
Citation
Journal of Animal Breeding and Genetics, 130(4), p. 252-258
ISSN
1439-0388
0931-2668
Start page
252
End page
258

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