Technical note: equivalent genomic models with a residual polygenic effect

Liu, Z., Goddard, M. E., Hayes, B. J., Reinhardt, F. and Reents, R. (2016) Technical note: equivalent genomic models with a residual polygenic effect. Journal of Dairy Science, 99 3: 2016-2025. doi:10.3168/jds.2015-10394


Author Liu, Z.
Goddard, M. E.
Hayes, B. J.
Reinhardt, F.
Reents, R.
Title Technical note: equivalent genomic models with a residual polygenic effect
Journal name Journal of Dairy Science   Check publisher's open access policy
ISSN 1525-3198
0022-0302
Publication date 2016-03-01
Sub-type Article (original research)
DOI 10.3168/jds.2015-10394
Open Access Status Not Open Access
Volume 99
Issue 3
Start page 2016
End page 2025
Total pages 10
Place of publication New York, NY, United States
Publisher Elsevier
Language eng
Abstract Routine genomic evaluations in animal breeding are usually based on either a BLUP with genomic relationship matrix (GBLUP) or single nucleotide polymorphism (SNP) BLUP model. For a multi-step genomic evaluation, these 2 alternative genomic models were proven to give equivalent predictions for genomic reference animals. The model equivalence was verified also for young genotyped animals without phenotypes. Due to incomplete linkage disequilibrium of SNP markers to genes or causal mutations responsible for genetic inheritance of quantitative traits, SNP markers cannot explain all the genetic variance. A residual polygenic effect is normally fitted in the genomic model to account for the incomplete linkage disequilibrium. In this study, we start by showing the proof that the multi-step GBLUP and SNP BLUP models are equivalent for the reference animals, when they have a residual polygenic effect included. Second, the equivalence of both multi-step genomic models with a residual polygenic effect was also verified for young genotyped animals without phenotypes. Additionally, we derived formulas to convert genomic estimated breeding values of the GBLUP model to its components, direct genomic values and residual polygenic effect. Third, we made a proof that the equivalence of these 2 genomic models with a residual polygenic effect holds also for single-step genomic evaluation. Both the single-step GBLUP and SNP BLUP models lead to equal prediction for genotyped animals with phenotypes (e.g., reference animals), as well as for (young) genotyped animals without phenotypes. Finally, these 2 single-step genomic models with a residual polygenic effect were proven to be equivalent for estimation of SNP effects, too.
Keyword BLUP with genomic relationship matrix
Equivalent model
Residual polygenic effect
SNP BLUP model
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
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Queensland Alliance for Agriculture and Food Innovation
 
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Created: Thu, 07 Jul 2016, 21:44:09 EST by Anthony Yeates on behalf of Learning and Research Services (UQ Library)