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

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.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.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.Genome-wide association studies and genetic evaluation systems using genomic information require large numbers of individuals that are both intensively phenotyped and densely genotyped for SNP across the genome to give reliable results. Dense SNP genotyping of the required number of individuals is still expensive. Therefore, research effort has focused on developing methods and strategies to impute genotypes from low-density platforms that are cheaper and easier to obtain. These imputation methods can be divided into two main categories, those that use linkage disequilibrium information (e.g. fastPHASE [1]; MaCH [2]; Beagle [3]; IMPUTE2 [4]) and those that use pedigree and linkage information e.g. [5-8]. Methods that use linkage disequilibrium information are suboptimal because they require at least some genotypes on each individual for which imputation is to be carried out. Some of the methods that use pedigree and linkage information are also less than optimal because they require all immediate ancestors to be densely genotyped. An optimal im