title: Short communication: Imputation of markers on the bovine X chromosome.
abstract: Imputation is a cost-effective approach to augment marker data for genomic selection and genome-wide association studies. However, most imputation studies have focused on autosomes. Here, we assessed the imputation of markers on the X chromosome in Holstein cattle for nongenotyped animals and animals genotyped with low-density (Illumina BovineLD, Illumina Inc., San Diego, CA) chips, using animals genotyped with medium-density (Illumina BovineSNP50) chips. A total of 26,884 genotyped Holstein individuals genotyped with medium-density chips were used in this study. Imputation was carried out using FImpute V2.2. The following parameters were examined: treating the pseudoautosomal region as autosomal or as X specific, different sizes of reference groups, different male/female proportions in the reference group, and cumulated degree of relationship between the reference group and target group. The imputation accuracy of markers on the X chromosome was improved if the pseudoautosomal region was treated as autosomal. Increasing the proportion of females in the reference group improved the imputation accuracy for the X chromosome. Imputation for nongenotyped animals in general had lower accuracy compared with animals genotyped with the low-density single nucleotide polymorphism array. In addition, higher cumulative pedigree relationships between the reference group and the target animal led to higher imputation accuracy. In the future, better marker coverage of the X chromosome should be developed to facilitate genomic studies involving the X chromosome.
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, PO Box 50, DK-8830, Tjele, Denmark; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 75007 Uppsala, Sweden. Electronic address: xiaowei.mao@mbg.au.dk.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Mao
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 75007 Uppsala, Sweden.
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: Johansson
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, PO Box 50, DK-8830, Tjele, Denmark.
authors.forename: Goutam
authors.initials: G
authors.lastname: Sahana
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, PO Box 50, DK-8830, Tjele, Denmark.
authors.forename: Bernt
authors.initials: B
authors.lastname: Guldbrandtsen
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 75007 Uppsala, Sweden.
authors.forename: Dirk-Jan
authors.initials: DJ
authors.lastname: De Koning
mesh_terms: D000818:Animals; D001947:Breeding / Q000379:methods; D002417:Cattle / Q000235:genetics*; D005260:Female; D005819:Genetic Markers / Q000235:genetics*; D016678:Genome; D055106:Genome-Wide Association Study / Q000662:veterinary*; D023281:Genomics; D005838:Genotype; D008297:Male; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D014960:X Chromosome / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: X chromosome; imputation; nongenotyped; pseudoautosomal region