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Journal of Dairy Science
Article . 2012 . Peer-reviewed
License: Elsevier Non-Commercial
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Journal of Dairy Science
Article
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Different methods to calculate genomic predictions—Comparisons of BLUP at the single nucleotide polymorphism level (SNP-BLUP), BLUP at the individual level (G-BLUP), and the one-step approach (H-BLUP)

Authors: Koivula, Minna; Strandén, Ismo; Su, G.; Mäntysaari, Esa A.;

Different methods to calculate genomic predictions—Comparisons of BLUP at the single nucleotide polymorphism level (SNP-BLUP), BLUP at the individual level (G-BLUP), and the one-step approach (H-BLUP)

Abstract

Several strategies to use genomic data in predictions have been proposed. The aim of this study was to compare different genomic prediction methods. The response variables used in the genomic predictions were deregressed proofs, which were derived from 2 estimated breeding value (EBV) data sets. The full EBV data set from March 2010 included the EBV for production and mastitis traits for all Nordic red bulls. The reduced data set included the same animals as the full data set, but the EBV were predicted from a data set that excluded the last 5 yr of observations. Genomic predictions were obtained using different BLUP models: BLUP at the single nucleotide polymorphism level (SNP-BLUP), BLUP at the individual level (G-BLUP), and the one-step approach (H-BLUP). For the selection candidate bulls, the SNP-BLUP and G-BLUP models gave the same direct genomic breeding values (e.g., correlation of direct genomic breeding values between SNP-BLUP and G-BLUP for protein was 0.99), but slightly different from genomic EBV obtained from H-BLUP (correlations of SNP-BLUP or G-BLUP with H-BLUP were about 0.96). For all traits, SNP-BLUP and G-BLUP gave the same validation reliability, whereas H-BLUP led to slightly higher reliability. Therefore, the results support a slight advantage of using H-BLUP for genomic evaluation.

Country
Finland
Keywords

Genetic Markers, Male, 570, Models, Genetic, dairy cattle, breeding value, Ko, forecasting, Genomics, Breeding, genominen arvostelu, Polymorphism, Single Nucleotide, Dairying, ayrshire, genomics, Linear Models, Animals, Cattle, Female, genomic evaluation, jalostusarvo, lypsykarja

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
47
Top 10%
Top 10%
Top 10%
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