Druml T Grilz-Seger G Neuditschko M Brem G 2017 The aim of this study was to determine the allele frequency of the glycogen synthase 1 (GYS1) mutation associated with polysaccharide storage myopathy type 1 in the Austrian Noriker horse. Furthermore, we examined the influence of population substructures on the allele distribution. The study was based upon a comprehensive population sample (208 breeding stallions and 309 mares) and a complete cohort of unselected offspring from the year 2014 (1553 foals). The mean proportion of GYS1 carrier animals in the foal cohort was 33%, ranging from 15% to 50% according to population substructures based on coat colours. In 517 mature breeding horses the mutation carrier frequency reached 34%, ranging on a wider scale from 4% to 62% within genetic substructures. We could show that the occurrence of the mutated GYS1 allele is influenced by coat colour; genetic bottlenecks; and assortative, rotating and random mating strategies. Highest GYS1 carrier frequencies were observed in the chestnut sample comprising 50% in foals, 54% in mares and 62% in breeding stallions. The mean inbreeding of homozygous carrier animals reached 4.10%, whereas non-carrier horses were characterized by an inbreeding coefficient of 3.48%. Lowest GYS1 carrier frequencies were observed in the leopard spotted Noriker subpopulation. Here the mean carrier frequency reached 15% in foals, 17% in mares and 4% in stallions and inbreeding decreased from 3.28% in homozygous non-carrier horses to 2.70% in heterozygous horses and 0.94% in homozygous carriers. This study illustrates that lineage breeding and specified mating strategies result in genetic substructures, which affect the frequencies of the GYS1 gene mutation. https://sonar.ch/global/documents/93189 eng info:eu-repo/semantics/altIdentifier/doi/10.1111/age.12481 info:eu-repo/semantics/altIdentifier/pmid/27476720 Animal genetics. - 2017 GYS1 gene Noriker horse coat colour genetic substructures inbreeding polysaccharide storage myopathy Alleles Animals Austria Breeding Female Gene Frequency Genetic Predisposition to Disease Genetics, Population Genotype Glycogen Synthase Hair Color Heterozygote Homozygote Horse Diseases Horses Inbreeding Male Muscular Diseases Mutation Pedigree Association between population structure and allele frequencies of the glycogen synthase 1 mutation in the Austrian Noriker draft horse. http://purl.org/coar/resource_type/c_6501