Depending on the breed and breeder, white markings on horses might be something to strive for or against. Swiss and Australian researchers have recently tuned into the genetics of white leg and face markings, and they've learned that these features are the result of complex genetic processes—but not too complex for modern science.

“Our analysis indicated that there are three major genes involved and that the complex interaction of these three genes determines the extent of white markings,” said Bianca Haase, PhD, genetics researcher at the University of Sydney and lead author of the study.

The researchers examined more than 1,000 Franche-Montagne horses, native to Switzerland, for the presence and degree of white markings. A genome-wide study on the horses revealed seven specific locations on the genome that appeared to be responsible for the markings. Through a novel computer approach to analyzing genetic codes (technically speaking, applying phylogenetic relationships among haplotypes to study their effects on quantitative traits), the researchers narrowed the genes down to three of interest: two principle genes and one minor.

While the study focused solely on Franche-Montagne horses, the researchers have begun running the same genetic tests on other breeds and are finding a similar pattern, Haase said.

Understanding the genetics behind white markings could help breeders make more informed decisions for reaching personal, cultural, and business objectives.

“The general breeding goal in the Franches-Montagnes breed is a horse with as minimal white marking as possible,” Haase said. “While the breeding goal is an aesthetic one, there is an economic imperative as well as a desire to maintain the historic appearance of the breed, which is of broad and conservational interest to most horse breeders.”

But the benefits of the study are not limited to breeding goals. Working with complex genetic traits that result in something easily visible (coat colors and markings) is helping scientists better understand how to decipher all the complicated codes of genes. By testing different computer calculation models against a clear physical trait, they’re honing in on calculation systems that will allow them to work through genetics that don’t lead to clear physical traits—like temperament or susceptibility to certain diseases.

“We developed a novel approach that allowed us to better understand some complex regulatory mechanisms, and this is likely to facilitate future work possibly outside the area of coat color,” Haase said.

The success of their project was heavily reliant on the positive cooperation of the breeding association and the horse owners, who readily contributed to the research, she added.

The study, "Accumulating Mutations in Series of Haplotypes at the KIT and MITF Loci Are Major Determinants of White Markings in Franches-Montagnes Horses," was published in the open-access journal PLoS One