Some horses’ ability to pace is associated with the “Gaitkeeper” gene (DMRT3). But being homozygous (having copies of the gene from both the dam and the sire) for the Gaitkeeper gene doesn’t seem to be enough, because some horses with the gene still don’t pace. So could these genetically capable foals learn how to pace by watching their dams?

“Although there is a traditional belief that foals learn the gait from their mothers in Hokkaido Native Horses, the mother’s gait did not affect the choice of gait of the foals in our study,” said Tomoko Amano, PhD, of the Laboratory of Animal Genetics at Rakuno Gakuen University College of Agriculture, Food, and Environment Sciences Department of Sustainable Agriculture, in Hokkaido, Japan. “We now speculate that several other genes which have less effect than the DMRT3 work with the DMRT3 on the pacing trait.”

The Hokkaido horse is a four-gaited breed native to Japan’s Hokkaido region. People traditionally used them to transport goods over mountainous regions inaccessible by wheeled vehicles. They preferred the pace to the trot because the gait is smoother, resulting in less damage to transported goods, Amano said. Today, Hokkaido horses are mostly used for local sporting competitions such as mounted archery.

In their recent study, Amano and colleagues analyzed 130 Hokkaido horses’ gaits and ran genomic tests to investigate chromosomal regions that might be related to pacing.

As expected, they found that all the pacers were homozygous for DMRT3. However, 14% of the homozygous horses didn’t pace. They ran additional tests, from which they identified 23 SNPs (genetic coding regions) on six chromosomes that might be related to the pacing trait. While they didn’t find a specific gene that seemed to reinforce the pace compared as a complement to the DMRT3, they were able to conclude one major finding: Pacing in homozygous DMRT3 horses doesn’t seem to be related to whether the mother paces.

“We hypothesized that the foals would learn the pace—if they’re genetically capable of doing it—from their mothers,” Amano said. “But that was not the case.”

Foals have greater environmental influences from their dams than from their sires since most foals spent little, if any time, with their sires, she said. However, the horses in her study spent about 10 months with their dams, giving them plenty of time to learn the gait.

As such, she said, “we suspect a genetic explanation rather than an environmental one.”

Although the Hokkaido breed is no longer used for transport, it’s still in demand among enthusiasts who seek its pacing gait, Amano said. As such, the breed is at risk of genetic bottlenecking as breeders try to select for the pace. Her ongoing research could help maintain the pacing trait while preventing inbreeding.

The study, “Genome-wide association mapping and examination of possible maternal effect for the pace trait of horses,” was published in Animal Genetics.