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A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation
- Source :
- Genetics, Selection, Evolution : GSE, Hickey, J M, Kinghorn, B P, Tier, B, van der Werf, J H J & Cleveland, M A 2012, ' A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation ', Genetics Selection Evolution, vol. 44, no. n/a, 9 . https://doi.org/10.1186/1297-9686-44-9, Genetics Selection Evolution, Vol 44, Iss 1, p 9 (2012)
- Publication Year :
- 2011
-
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.
- Subjects :
- Male
INFORMATION
ACCURACY
Sus scrofa
Pedigree chart
Bayes' theorem
Gene Frequency
Quantitative Biology::Populations and Evolution
Genetics(clinical)
lcsh:SF1-1100
Genetics
education.field_of_study
Genome
Statistics::Applications
FULL PEDIGREE
ASSOCIATION
General Medicine
Quantitative Biology::Genomics
Pedigree
MISSING GENOTYPES
Female
Algorithms
lcsh:QH426-470
Population
UNIFIED APPROACH
HAPLOTYPE IMPUTATION
PREDICTIONS
Single-nucleotide polymorphism
Computational biology
Biology
GENOTYPE IMPUTATION
Polymorphism, Single Nucleotide
GENETIC EVALUATION
SNP
Animals
education
Allele frequency
Ecology, Evolution, Behavior and Systematics
Alleles
Models, Genetic
Research
Haplotype
Bayes Theorem
lcsh:Genetics
Haplotypes
Animal Science and Zoology
Cattle
lcsh:Animal culture
Imputation (genetics)
Subjects
Details
- ISSN :
- 12979686
- Volume :
- 44
- Database :
- OpenAIRE
- Journal :
- Genetics, selection, evolution : GSE
- Accession number :
- edsair.doi.dedup.....8dbaaaa16f54c8b8c40ddae0412f1fc9