title: A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation.
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.
authors.affiliation: School of Environmental and Rural Science, University of New England, Armidale, Australia. john.hickey@une.edu.au
authors.forename: John M
authors.initials: JM
authors.lastname: Hickey
authors.forename: Brian P
authors.initials: BP
authors.lastname: Kinghorn
authors.forename: Bruce
authors.initials: B
authors.lastname: Tier
authors.forename: Julius H J
authors.initials: JH
authors.lastname: van der Werf
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Cleveland
mesh_terms: D000465:Algorithms; D000483:Alleles; D000818:Animals; D001499:Bayes Theorem; D002417:Cattle / Q000235:genetics; D005260:Female; D005787:Gene Frequency; D016678:Genome; D006239:Haplotypes; D008297:Male; D008957:Models, Genetic; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D011153:Population; D034421:Sus scrofa / Q000235:genetics