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


Autoria(s): Frischknecht, Mirjam; Neuditschko, Markus; Jagannathan, Vidhya; Drögemüller, Cord; Tetens, Jens; Thaller, Georg; Leeb, Tosso; Rieder, Stefan
Data(s)

2014

Resumo

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.

Formato

application/pdf

Identificador

http://boris.unibe.ch/71093/1/s12711-014-0063-7.pdf

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 <http://dx.doi.org/10.1186/s12711-014-0063-7>

doi:10.7892/boris.71093

info:doi:10.1186/s12711-014-0063-7

info:pmid:25927638

urn:issn:1297-9686

Idioma(s)

eng

Publicador

BioMed Central

Relação

http://boris.unibe.ch/71093/

Direitos

info:eu-repo/semantics/openAccess

Fonte

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 <http://dx.doi.org/10.1186/s12711-014-0063-7>

Palavras-Chave #570 Life sciences; biology #590 Animals (Zoology) #630 Agriculture
Tipo

info:eu-repo/semantics/article

info:eu-repo/semantics/publishedVersion

PeerReviewed