Researchers have moved beyond the so-called gait-keeper gene, identifying genetic variants that clearly distinguish trotters from pacers.
They even developed an algorithm that, based on the analysis of seven genetic variations, can tell with 99.4% accuracy whether a horse is a trotter or pacer.
Certain horse breeds have been developed over generations specifically for the ability to perform alternative patterns of movement, or gaits.
Our current understanding of the genetic basis for these gaits is limited to one known mutation in the DMTR3 gene – the so-called gait-keeper gene.
This mutation is apparently necessary for gaitedness in breeds, but is not sufficient to explain variability in “gaitedness”.
Standardbreds provide a good example. They comprise two distinct groups. Trotters have a two-beat gait in which the opposite forelimb and hind limb move together, while pacers exhibit an alternative two-beat gait where the legs on the same side of the body move together.
Researcher Annette McCoy and an international team of scientists set out to identify genetic variants underlying the ability of certain Standardbreds to pace.
In their study, reported in PLOS Genetics, they were able to identify several regions of the genome highly associated with pacing.
Within these regions were several specific highly associated variants, known as single nucleotide polymorphisms (SNPs).
Although the biological function of these variants has yet to be determined, the study team was able to develop a model based on seven SNPs that proved to be more than 99% accurate in predicting whether an individual was a pacer or a trotter in two independent populations.
“This predictive model,” they said, “can be used by horse owners to make breeding and training decisions related to this economically important trait, and by scientists interested in understanding the biology of coordinated gait development.”
Their research began with a genome-wide association analysis performed in 542 Standardbred horses from North America, Sweden and Norway, comprising 176 pacers and 366 trotters.
Nineteen SNPs on nine chromosomes reached genome-wide significance. These defined regions of interest were on nine chromosomes and comprised more than two dozen named genes.
The pool was extended to 659 Standardbreds (231 pacers and 428 trotters) for more work to be carried out on these genetic regions of interest. This revealed a set of 303 variants from 22 chromosomes with likely modifying effects on gait.
The algorithm they went on to develop proved to be highly accurate when tested in an independently sampled population of 166 North American Standardbreds, evenly split between trotters and pacers.
They say more work is needed to see determine the algorithm’s usefulness in other gaited breeds.
The authors say there is still much that is not known about the development of normal limb coordination in horses, which makes it challenging to identify biologically compelling candidate genes for gait.
“It is likely that many genes that play a role in the development of alternative gaits have not previously been associated with any aspect of neurobiology,” they said.
“This is aptly illustrated by DMRT3 which had initially been described as primarily playing a role in gonadal development and sexual differentiation.”
The DMRT3 nonsense mutation originally reported in 2012 has now been reported to occur in 68 out of 141 breeds tested from around the world, and at high frequency (more than 50%) in all “gaited” breeds.
“This example demonstrates that a strongly associated mutation cannot be ruled out as having a functional role in the development of alternative gaits simply because it falls within a gene that does not have a described role in neural development or locomotion.”
They said that, of the tens of thousands of SNPs discovered within regions of interest via whole-genome sequencing, only a small fraction could be selected for follow-up.
“It is likely that we have not identified any truly functional alleles despite our prioritization process.”
The full study team comprised McCoy, Samantha Beeson, Carl-Johan Rubin, Leif Andersson, Paul Caputo, Sigrid Lykkjen, Alison Moore, Richard Piercy, James Mickelson, and Molly McCue.
McCoy and McCue are named as inventors on a pending patent application for the predictive model, which has been submitted by the University of Minnesota.
McCoy AM, Beeson SK, Rubin C-J, Andersson L, Caputo P, Lykkjen S, et al. (2019) Identification and validation of genetic variants predictive of gait in standardbred horses. PLoS Genet 15(5): e1008146. https://doi.org/10.1371/journal.pgen.1008146