A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color.

This research article investigates the genetic factors associated with the roan coat color in Noriker horses. It pinpointed a specific genetic mutation linked with this coat color and found that it originated from a baroque gene pool, suggesting allelic heterogeneity and the existence of more roan alleles in certain equine breeds.

Genetic Analysis of Roan Coat Color in Horses

• The study identified a genotype linked to the roan coloring in Noriker horses. This phenotype, a mixture of white and colored hairs, is seen in a range of horse breeds, but its genetic basis has remained largely unknown.
• Previous research had connected the roan chromosomal locus to the KIT gene on equine chromosome 3 (ECA3), but this link had not been consistently proven across multiple horse breeds.
• In this research, a Genome-Wide Association Analysis (GWAS) was performed on Noriker horses to further investigate this.

Identification of a Single Nucleotide Polymorphism (SNP)

• The study discovered a specific SNP in the intron 17 of the KIT gene. This SNP (ECA3:g.79,543.439 A > G) could potentially help in identifying the roan coloration in horses.
• The G -allele of the SNP was also noted in other roan horse breeds, such as the Quarter Horse, Murgese, Slovenian, and Belgian draught horse. At the same time, it did not appear in a group of 657 non-roan horses from 15 different breeds.
• Interestingly, out of an additional 379 gray Lipizzan horses, eight were found to have a heterozygous genotype (A/G), adding to the evidence that this SNP might be linked to roan coloration.

Further Genetic Findings and Implications

• Continuing their analysis, the researchers found two deletions in the downstream region of the KIT region across the equine genome. Another mutation, a 3 bp deletion coupled with a 17 bp insertion, was spotted in intron 20 of KIT.
• In the Noriker samples, these genetic locations were in total linkage disequilibrium (LD) with the earlier identified SNP, suggesting a strong correlation with the roan phenotype.
• Using this information, coupled with historical records and pedigree data, the researchers inferred the roan coat color genetic origin dates back to a baroque gene pool.
• This raises the possibility of allelic heterogeneity and the existence of additional roan alleles in ponies and breeds that share lineage with the English Thoroughbred. For a more conclusive understanding, more studies geared towards verifying these findings will be necessary.