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

John M. Hickey*, Brian P. Kinghorn, Bruce Tier, Julius H. J. van der Werf, Matthew A. Cleveland

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number9
Number of pages11
JournalGenetics Selection Evolution
Volume44
Issue numbern/a
DOIs
Publication statusPublished - 19 Jun 2012

Keywords

  • INFORMATION
  • GENOTYPE IMPUTATION
  • MISSING GENOTYPES
  • GENETIC EVALUATION
  • UNIFIED APPROACH
  • ACCURACY
  • ASSOCIATION
  • HAPLOTYPE IMPUTATION
  • PREDICTIONS
  • FULL PEDIGREE

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