Please use this identifier to cite or link to this item:
|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) ; Cleveland, Matthew A (author)||Publication Date:||2012||Open Access:||Yes||DOI:||10.1186/1297-9686-44-9||Handle Link:||https://hdl.handle.net/1959.11/12527||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||Statistics to Oct 2018:||Visitors: 441
|Appears in Collections:||Animal Genetics and Breeding Unit (AGBU)|
Files in This Item:
checked on Nov 30, 2018
checked on Feb 18, 2019
Items in Research UNE are protected by copyright, with all rights reserved, unless otherwise indicated.