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Title: Genomic evaluations using similarity between haplotypes
Contributor(s): Hickey, John (author); Kinghorn, Brian  (author); Tier, Bruce  (author); Clark, Sam A  (author)orcid ; Van Der Werf, Julius H  (author)orcid ; Gorjanc, G (author)
Publication Date: 2013
DOI: 10.1111/jbg.12020
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Abstract: Long-range phasing and haplotype library imputation methodologies are accurate and efficient methods to provide haplotype information that could be used in prediction of breeding value or phenotype. Modelling long haplotypes as independent effects in genomic prediction would be inefficient due to the many effects that need to be estimated and phasing errors, even if relatively low in frequency, exacerbate this problem. One approach to overcome this is to use similarity between haplotypes to model covariance of genomic effects by region or of animal breeding values. We developed a simple method to do this and tested impact on genomic prediction by simulation. Results show that the diagonal and off-diagonal elements of a genomic relationship matrix constructed using the haplotype similarity method had higher correlations with the true relationship between pairs of individuals than genomic relationship matrices built using unphased genotypes or assumed unrelated haplotypes. However, the prediction accuracy of such haplotype-based prediction methods was not higher than those based on unphased genotype information.
Publication Type: Journal Article
Grant Details: ARC/LP100100880
Source of Publication: Journal of Animal Breeding and Genetics, 130(4), p. 259-269
Publisher: Wiley-Blackwell Verlag GmbH
Place of Publication: Germany
ISSN: 1439-0388
Fields of Research (FoR) 2008: 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics)
Fields of Research (FoR) 2020: 310506 Gene mapping
Socio-Economic Objective (SEO) 2008: 830301 Beef Cattle
830302 Dairy Cattle
Socio-Economic Objective (SEO) 2020: 100401 Beef cattle
100402 Dairy cattle
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Journal Article

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