A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation

Genetics Selection Evolution

Research

Bruce Tier¹  Matthew A Cleveland²  Brian P Kinghorn³  John M Hickey³  Julius HJ van der Werf⁴ 

[1] Animal Genetics and Breeding Unit, University of New England (AGBU is a joint unit of NSW DPI and the University of New England), Armidale, Australia;Genus plc, 100 Bluegrass Commons Blvd., Suite 2200, 37075, Hendersonville, TN, USA;School of Environmental and Rural Science, University of New England, Armidale, Australia;School of Environmental and Rural Science, University of New England, Armidale, Australia;Cooperative Research Centre for Sheep Industry Innovation, Armidale, Australia;

关键词: Single Nucleotide Polymorphism;    Genomic Selection;    Imputation Accuracy;    Impute Genotype;    Genotyped Animal;   

DOI  :  10.1186/1297-9686-44-9

 received in 2011-11-02, accepted in 2012-03-30,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundEfficient, 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.MethodsAn 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.ResultsImputation 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© Hickey et al.; licensee BioMed Central Ltd. 2012