Chestnut is not considered an acceptable coat color in some breeds of horses. A fast, cost-effective, and reliable method for the routine genotyping of alleles has been developed by Researchers from the Department of Genetics, Physical Anthropology and Animal Physiology at the University of the Basque Country in Bilbao, Spain.

Chestnut coat color is due to two recessive versions (e and e^a) of the gene called melanocortin-1 receptor. The dominant version of the gene (E) produces black or bay coats.

For the pony breeds of the Cantabrian Coast of the Iberian Peninsula, bay and black are considered to be the original coat colors. Researchers believe that around 1930 local mares were crossed with stallions of other breeds to "improve the capacity for agricultural work and meat production." This also resulted in some chestnut offspring, which are not allowed in the official stud book in the Cantabrian Coast pony breeds.

SNaPshot is a tool capable of detecting single variations in DNA called single nucleotide polymorphisms (SNPs) such as the E, e, and e^a versions of the gene responsible for the chestnut coat color in horses