a phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation的血统人口逐步和归责方法在单级基因组评估结果.pdfVIP

Hickey et al. Genetics Selection Evolution 2012, 44:9 Ge n e t i c s /content/44/1/9 Se l e c t i o n Evolution RESEARCH Open Access A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation 1* 1 2 1,3 4 John M Hickey , Brian P Kinghorn , Bruce Tier , Julius HJ van der Werf and Matthew A Cleveland 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