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A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color
Gertrud Grilz-Seger1, Simone Reiter1, Markus Neuditschko2
1Department of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria.
Researchers identified a specific genetic marker in the KIT gene associated with the roan coat color in horses. This finding helps understand the genetic basis of this common equine coat pattern.
Area of Science:
- Equine genetics
- Coat color genetics
- Animal genomics
Background:
- The roan coat color, characterized by dispersed white hairs and dark points, is observed across many horse breeds, but its genetic basis remains unclear.
- Previous attempts to link the roan locus to the KIT gene on equine chromosome 3 (ECA3) were not consistently validated across breeds.
Purpose of the Study:
- To identify the genetic cause of the roan coat color in horses.
- To investigate the association of specific genetic variants within the KIT gene with the roan phenotype.
- To trace the historical origin of the roan gene pool.
Main Methods:
- Genome-wide association analysis (GWAS) was performed on Noriker horses to identify associated single nucleotide polymorphisms (SNPs).
- Comparative whole-genome sequencing was used to analyze the KIT gene region in roan and non-roan horses.
- Linkage disequilibrium (LD) analysis was conducted to assess the relationship between identified variants and the roan phenotype.
- Pedigree information and historical records were utilized to trace the genetic origin.
Main Results:
- A significant SNP (ECA3:g.79,543.439 A > G) in intron 17 of the KIT gene was strongly associated with the roan coat color in Noriker horses.
- The identified G-allele was present in roan horses of various breeds (Quarter Horse, Murgese, Slovenian, Belgian draught) but absent in non-roan horses.
- Several deletions and a complex insertion-deletion in the KIT gene region were found to be in complete LD with the top SNP in Noriker horses.
- The genetic origin of the roan coat color was traced back to a baroque gene pool.
- Evidence suggests potential allelic heterogeneity and the presence of additional roan alleles in ponies and breeds related to the English Thoroughbred.
Conclusions:
- The study identifies a specific SNP in the KIT gene as a strong candidate marker for the roan coat color in several horse breeds.
- The findings provide a genetic explanation for the roan phenotype and its segregation in diverse equine populations.
- Further research is needed to fully elucidate the allelic heterogeneity and identify additional roan alleles in specific breeds.
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