Unknown‐parent groups in single‐step genomic evaluation |
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Authors: | I Misztal ZG Vitezica A Legarra I Aguilar AA Swan |
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Institution: | 1. Department of Animal and Dairy Science, University of Georgia, , Athens, GA, USA;2. Université de Toulouse, , F‐31326 Castanet‐Tolosan, France;3. INRA, , Castanet‐Tolosan, France;4. Instituto Nacional de Investigación Agropecuaria, , Las Brujas, Uruguay;5. Animal Breeding and Genetics Unit, University of New England, , Armidale, NSW, Australia |
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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. |
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Keywords: | Bias genomic evaluation genomic relationships unknown‐parent groups |
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