title: Genome-wide association studies based on sequence-derived genotypes reveal new QTL associated with conformation and performance traits in the Franches-Montagnes horse breed.
abstract: To identify novel quantitative trait loci (QTL) within horses, we performed genome-wide association studies (GWAS) based on sequence-level genotypes for conformation and performance traits in the Franches-Montagnes (FM) horse breed. Sequence-level genotypes of FM horses were derived by re-sequencing 30 key founders and imputing 50K data of genotyped horses. In total, we included 1077 FM horses genotyped for ~4 million SNPs and their respective de-regressed breeding values of the traits in the analysis. Based on this dataset, we identified a total of 14 QTL associated with 18 conformation traits and one performance trait. Therefore, our results suggest that the application of sequence-derived genotypes increases the power to identify novel QTL which were not identified previously based on 50K SNP chip data.
authors.affiliation: Agroscope, Swiss National Stud Farm, Les Longs-Prés, 1580, Avenches, Switzerland.|Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland.|Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
authors.forename: M
authors.initials: M
authors.lastname: Frischknecht
authors.affiliation: Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, Bremgartenstrasse 109a, 3001, Bern, Switzerland.|Bern University of Applied Sciences, School of Agricultural, Forest and Food Sciences, Länggasse, 85 3052, Zollikofen, Switzerland.
authors.forename: H
authors.initials: H
authors.lastname: Signer-Hasler
authors.affiliation: Agroscope, Swiss National Stud Farm, Les Longs-Prés, 1580, Avenches, Switzerland.|Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
authors.forename: T
authors.identifier: http://orcid.org/0000-0003-0553-4880
authors.initials: T
authors.lastname: Leeb
authors.affiliation: Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland.|Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
authors.forename: S
authors.initials: S
authors.lastname: Rieder
authors.affiliation: Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012, Bern, Switzerland.|Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, Bremgartenstrasse 109a, 3001, Bern, Switzerland.
authors.forename: M
authors.initials: M
authors.lastname: Neuditschko
mesh_terms: D000818:Animals; D001827:Body Height / Q000235:genetics; D001947:Breeding; D005684:Gait / Q000235:genetics; D056726:Genetic Association Studies; D005838:Genotype; D006736:Horses / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
keywords: GWAS; NGS; imputation