Swiss researchers have taken another step toward unraveling the mystery of the white body hair in horses. In their new whole-genome study, they’ve found yet another variation responsible for yet-unexplained white spotting, one they’ve named W22.
“By now, research from many groups, including our own, has shown that ‘white spotting phenotypes’ in horses are quite heterogeneous,” said Tosso Leeb, PhD, professor at the University of Bern Institute of Genetics, in Switzerland. “This means there is a large number of different genetic variants that leads to horses with nonpigmented body parts. Our research has just uncovered yet one more.”
Leeb’s group sequenced the whole genome of a horse with white spotting patterns that could not be explained by any current genomic testing. They found a variation—a deletion of nearly 2,000 base pairs—in the KIT gene. That gene is the site where other white-pattern variations occur, Leeb said. But his group was the first to discover the existence of the W22 variation, which causes a part of the gene to simply not exist.
“I would call a 2,000 base-pair deletion a ‘medium-sized’ deletion, not huge,” he said. “The functional consequence of a deletion always depends on which specific bases are deleted. It is very likely that this deletion completely inactivates the KIT gene altogether.”
Still, even a couple of missing base pairs can deactivate a gene, he added. And meanwhile, the deletion of a million base pairs might have no known effect whatsoever on a different gene. It all depends on what those base pairs do. “It’s important what information the deletion contains,” Leeb said.
The W22 variant seems, in most cases, to have an aesthetic effect only. When heterozygous (one copy of the allele), it results in white spots on the horse without any other known effects. That might not be true if the W22 variant occurs simultaneously with other KIT alleles that could cause loss of function, he added. And horses receiving two copies of the W22 allele instead of one probably don’t survive past early gestation.
Armed with the W22 deletion information, Leeb and his fellow researchers then found 21 additional horses with the variation and investigated their genomes. They found white spotting varying from 15% to 100% depigmentation (a completely white horse) in these horses, he said. And all the horses with one copy of the W22 allele combined with a copy of another allele, W20, were entirely white.
But, this still doesn’t mean you can simply look at a horse and determine whether he has the W22 variant. White spotting seems to have several genetic causes, and current knowledge doesn’t yet allow us to link the kind of spotting to the genetic variation.
“According to my experience, it is close to impossible to guess the underlying genetics from just looking at the horses’ phenotypes,” Leeb said. “It really requires molecular genetic investigations to determine which variant or which combination of the many possible variants may have caused the white spotting phenotype in any given horse.”
Their finding can contribute to the genetic testing of white spotted horses, he said.
The study, “Whole genome sequencing reveals a novel deletion variant in the KIT gene in horses with white spotted coat colour phenotypes,” was published in Animal Genetics.