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Title: A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation
Contributor(s): Hickey, John (author); Kinghorn, Brian  (author); Tier, Bruce  (author); Van Der Werf, Julius H  (author)orcid ; Cleveland, Matthew A (author)
Publication Date: 2012
Open Access: Yes
DOI: 10.1186/1297-9686-44-9Open Access Link
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Abstract: Background: Efficient, robust, and accurate genotype imputation algorithms make large-scale application of genomic selection cost effective. An algorithm that imputes alleles or allele probabilities for all animals in the pedigree and for all genotyped single nucleotide polymorphisms (SNP) provides a framework to combine all pedigree, genomic, and phenotypic information into a single-stage genomic evaluation. Methods: An algorithm was developed for imputation of genotypes in pedigreed populations that allows imputation for completely ungenotyped animals and for low-density genotyped animals, accommodates a wide variety of pedigree structures for genotyped animals, imputes unmapped SNP, and works for large datasets. The method involves simple phasing rules, long-range phasing and haplotype library imputation and segregation analysis. Results: Imputation accuracy was high and computational cost was feasible for datasets with pedigrees of up to 25 000 animals. The resulting single-stage genomic evaluation increased the accuracy of estimated genomic breeding values compared to a scenario in which phenotypes on relatives that were not genotyped were ignored. Conclusions: The developed imputation algorithm and software and the resulting single-stage genomic evaluation method provide powerful new ways to exploit imputation and to obtain more accurate genetic evaluations.
Publication Type: Journal Article
Grant Details: ARC/LP100100880
Source of Publication: Genetics Selection Evolution, v.44, p. 1-11
Publisher: BioMed Central Ltd
Place of Publication: London, United Kingdom
ISSN: 1297-9686
Field of Research (FOR): 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics)
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
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Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
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