Imputation of sequence level genotypes in the Franches-Montagnes horse breed.
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.
Agroscope - Swiss National Stud Farm, 1580, Avenches, Switzerland. mirjam.frischknecht@vetsuisse.unibe.ch.|Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland. mirjam.frischknecht@vetsuisse.unibe.ch.|Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland. mirjam.frischknecht@vetsuisse.unibe.ch.|Graduate School for Cellular and Molecular Biology, University of Bern, 3012, Bern, Switzerland. mirjam.frischknecht@vetsuisse.unibe.ch.
Mirjam
M
Frischknecht
Agroscope - Swiss National Stud Farm, 1580, Avenches, Switzerland. markus.neuditschko@agroscope.admin.ch.|Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland. markus.neuditschko@agroscope.admin.ch.
Markus
M
Neuditschko
Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland. vidhya.jagannathan@vetsuisse.unibe.ch.|Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland. vidhya.jagannathan@vetsuisse.unibe.ch.
Vidhya
V
Jagannathan
Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland. cord.droegemueller@vetsuisse.unibe.ch.|Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland. cord.droegemueller@vetsuisse.unibe.ch.
Cord
C
Drögemüller
Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118, Kiel, Germany. jtetens@tierzucht.uni-kiel.de.
Jens
J
Tetens
Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118, Kiel, Germany. gthaller@tierzucht.uni-kiel.de.
Georg
G
Thaller
Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland. tosso.leeb@vetsuisse.unibe.ch.|Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland. tosso.leeb@vetsuisse.unibe.ch.
Tosso
T
Leeb
Agroscope - Swiss National Stud Farm, 1580, Avenches, Switzerland. stefan.rieder@agroscope.admin.ch.|Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland. stefan.rieder@agroscope.admin.ch.
Stefan
S
Rieder
D000818:Animals; D005260:Female; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006736:Horses / Q000235:genetics*; D008297:Male; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D012984:Software