Imputation of sequence level genotypes in the Franches-Montagnes horse breed

Frischknecht, Mirjam; Neuditschko, Markus; Jagannathan, Vidhya; Drögemüller, Cord; Tetens, Jens; Thaller, Georg; Leeb, Tosso; Rieder, Stefan (2014). Imputation of sequence level genotypes in the Franches-Montagnes horse breed. Genetics, selection, evolution, 46, p. 63. BioMed Central 10.1186/s12711-014-0063-7

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BACKGROUND A cost-effective strategy to increase the density of available markers within a population is to sequence a small proportion of the population and impute whole-genome sequence data for the remaining population. Increased densities of typed markers are advantageous for genome-wide association studies (GWAS) and genomic predictions. METHODS We obtained genotypes for 54 602 SNPs (single nucleotide polymorphisms) in 1077 Franches-Montagnes (FM) horses and Illumina paired-end whole-genome sequencing data for 30 FM horses and 14 Warmblood horses. After variant calling, the sequence-derived SNP genotypes (~13 million SNPs) were used for genotype imputation with the software programs Beagle, Impute2 and FImpute. RESULTS The mean imputation accuracy of FM horses using Impute2 was 92.0%. Imputation accuracy using Beagle and FImpute was 74.3% and 77.2%, respectively. In addition, for Impute2 we determined the imputation accuracy of all individual horses in the validation population, which ranged from 85.7% to 99.8%. The subsequent inclusion of Warmblood sequence data further increased the correlation between true and imputed genotypes for most horses, especially for horses with a high level of admixture. The final imputation accuracy of the horses ranged from 91.2% to 99.5%. CONCLUSIONS Using Impute2, the imputation accuracy was higher than 91% for all horses in the validation population, which indicates that direct imputation of 50k SNP-chip data to sequence level genotypes is feasible in the FM population. The individual imputation accuracy depended mainly on the applied software and the level of admixture.

Item Type:

Journal Article (Original Article)


05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Frischknecht, Mirjam; Jagannathan, Vidya; Drögemüller, Cord and Leeb, Tosso


500 Science > 570 Life sciences; biology
500 Science > 590 Animals (Zoology)
600 Technology > 630 Agriculture




BioMed Central




Cord Drögemüller

Date Deposited:

19 Aug 2015 10:24

Last Modified:

06 Oct 2015 08:39

Publisher DOI:


PubMed ID:





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