title: Imputation of genotypes in Danish purebred and two-way crossbred pigs using low-density panels.
abstract: BACKGROUND
  Genotype imputation is commonly used as an initial step in genomic selection since the accuracy of genomic selection does not decline if accurately imputed genotypes are used instead of actual genotypes but for a lower cost. Performance of imputation has rarely been investigated in crossbred animals and, in particular, in pigs. The extent and pattern of linkage disequilibrium differ in crossbred versus purebred animals, which may impact the performance of imputation. In this study, first we compared different scenarios of imputation from 5 K to 8 K single nucleotide polymorphisms (SNPs) in genotyped Danish Landrace and Yorkshire and crossbred Landrace-Yorkshire datasets and, second, we compared imputation from 8 K to 60 K SNPs in genotyped purebred and simulated crossbred datasets. All imputations were done using software Beagle version 3.3.2. Then, we investigated the reasons that could explain the differences observed.
  
  
  RESULTS
  Genotype imputation performs as well in crossbred animals as in purebred animals when both parental breeds are included in the reference population. When the size of the reference population is very large, it is not necessary to use a reference population that combines the two breeds to impute the genotypes of purebred animals because a within-breed reference population can provide a very high level of imputation accuracy (correct rate ≥ 0.99, correlation ≥ 0.95). However, to ensure that similar imputation accuracies are obtained for crossbred animals, a reference population that combines both parental purebred animals is required. Imputation accuracies are higher when a larger proportion of haplotypes are shared between the reference population and the validation (imputed) populations.
  
  
  CONCLUSIONS
  The results from both real data and pedigree-based simulated data demonstrate that genotype imputation from low-density panels to medium-density panels is highly accurate in both purebred and crossbred pigs. In crossbred pigs, combining the parental purebred animals in the reference population is necessary to obtain high imputation accuracy.
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, DK-8830, Denmark. Tao.Xiang@mbg.au.dk.|INRA, UR1388 GenPhySE, CS-52627, Castanet-Tolosan, F-31326, France. Tao.Xiang@mbg.au.dk.
authors.forename: Tao
authors.initials: T
authors.lastname: Xiang
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, DK-8830, Denmark. Peipei.Ma@mbg.au.dk.
authors.forename: Peipei
authors.initials: P
authors.lastname: Ma
authors.affiliation: Pig Research Centre, Danish Agricultural and Food Council, Copenhagen, DK-1609, Denmark. TAO@seges.dk.
authors.forename: Tage
authors.initials: T
authors.lastname: Ostersen
authors.affiliation: INRA, UR1388 GenPhySE, CS-52627, Castanet-Tolosan, F-31326, France. Andres.Legarra@toulouse.inra.fr.
authors.forename: Andres
authors.initials: A
authors.lastname: Legarra
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, DK-8830, Denmark. OleF.Christensen@mbg.au.dk.
authors.forename: Ole F
authors.initials: OF
authors.lastname: Christensen
mesh_terms: D000818:Animals; D005838:Genotype; D007178:Inbreeding; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D011156:Population Density; D012641:Selection, Genetic; D012984:Software; D013552:Swine / Q000235:genetics*