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Title: Unknown-parent groups in single-step genomic evaluation
Contributor(s): Misztal, I (author); Vitezica, Z G (author); Legarra, A (author); Aguilar, I (author); Swan, Andrew (author)
Publication Date: 2013
DOI: 10.1111/jbg.12025
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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.
Publication Type: Journal Article
Source of Publication: Journal of Animal Breeding and Genetics, 130(4), p. 252-258
Publisher: Wiley-Blackwell Verlag GmbH
Place of Publication: Germany
ISSN: 1439-0388
Field of Research (FOR): 070201 Animal Breeding
060408 Genomics
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
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