Gene Test, Research Unravel Severe Skeletal Atavism Limb Deformity in Shetland Ponies

Limbs of a 16-week old Shetland pony with Skeletal Atavism, often described as "bow legs". (Left) caudal view when standing; (center) caudal view when walking and (right) view from the front when standing square.  Complete, or "fused", fibulas and ulnas cause instability in the tarsocrural and antebrachiocarpal joints respectively; the angular limb deformity becomes more severe at the walk. Photo: Ove Wattle

Skeletal Atavism is a genetic defect that can cause skeletal deformities in Shetland ponies. The deformity has now been genetically identified by researchers at Uppsala University and the Swedish University of Agricultural Sciences (SLU), in cooperation with colleagues in the USA at Texas A&M University, the University of Kentucky's Gluck Center, and the University of Washington, as well as at the University of Qatar in the Middle East. The discovery means that healthy carriers now can be identified for better breeding decisions with the use of a gene test.

Fossil records show that in the ancestors of modern equids, the ulna and fibula were reduced in size. Moreover, they were fused to the radius and tibia, respectively. The reappearance of properties previously seen at an earlier evolutionary stage of a species is referred to as an atavism (Hall 1995) and the disease in Shetland ponies has therefore been referred to as Skeletal Atavism (SA).

Other examples of atavisms include rare conditions such as hind limbs in whales and equine polydactyly, or extra digits, in the horse. "Double paws" on cats are a type of atavism, as well.

The disease in Shetlands, called Skeletal Atavism, has been known since the 1950s, and has since been reported across Europe. In the mid-1990s, the disease was prevalent in Sweden, where several breeding stallions were found to be carriers.

Skeletal atavism in Shetland Ponies causes abnormal growth in the ulna (front limb) and fibula (hind limb), as pointed out by red arrows in this anatomy chart. The metacarpal and metatarsal bones, below the knee and hock, develop more normally. The result is a conformation you might describe as "bow legged". In simplest terms, think of it as a "shortened thigh" above a normal calf. Illustration courtesy of WikipedianProlific at the English language Wikipedia.

In Shetland Ponies, such a serious malformation of the legs represents a significant problem. Affected foals suffer from abnormal growth of the ulna and fibula, which extend the carpal and tarsal joints, respectively. A shorter than normal humerus, femur and tibia, in relation to the third metatarsal bone, are also observed. The result is abnormal skeletal structure, impaired movements, and progressively more curved legs, which in turn leads to incorrect conformation and lameness. Affected foals must often be euthanized at a young age.

Shetland Pony with bowed legs typical of Skeletal Atavism. Photo: Sofia Mikko

To reduce the risk of having affected foals, carrier stallions were prohibited from further breeding. Skeletal Atavism follows a so-called recessive inheritance in which both parents must contribute with a disease variant (disease allele) of the gene to produce affected offspring.

The genetic study was published May 20 in the journal G3: Genes, Genomes, Genetics. By sequencing the entire genomes of both affected and healthy individuals, the researchers found that genetic deletions within and around the SHOX gene causes Skeletal Atavism.

Radiograph of the hind limb of a foal with Skeletal Atavism. Photo: Göran Dalin

Mutations in the SHOX gene cause also cause skeletal deformities, as well as dwarfism, in humans.

"Since most disease gene carriers are healthy, it's almost impossible to eliminate the disease from the population by traditional breeding", says Carl-Johan Rubin,  the researcher at Uppsala University responsible for the study.

"Our discovery will now help breeders...to screen for carriers in their breeding stock", adds Sofia Mikko, Director of the Animal Genetics Laboratory at SLU.

The SHOX gene is located in a region shared between the two sex chromosomes X and Y; it is known to be difficult to study by traditional methods because of its complex structure. To reveal the sequence of this chromosomal region, the researchers used a newly developed method, known as Single Molecule Real Time (SMRT) sequencing. The technique is available at SciLifeLab in Uppsala and is used to sequence very long stretches of DNA.

"We are now very pleased to describe some characteristics of one of the most problematic regions in the genome of mammals. That we also contribute to improved animal welfare, as fewer affected foals will be born, feels great," says Nima Rafati, PhD student at UU.

Initially, the study was funded by a grant from the Swedish-Norwegian Foundation for Equine Research. Information from Swedish University of Agricultural Sciences and the G3 journal facilitated the preparation of this article.

To learn more:

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies.
Rafati N, Andersson LS, Mikko S, Feng C, Raudsepp T, Pettersson J, Janecka J, Wattle O, Ameur A, Thyreen G, Eberth J, Huddleston J, Malig M, Bailey E, Eichler EE, Dalin G, Chowdary B, Anderssson L, Lindgren G, Rubin CJ.
G3 Genes, Genomes, Genetics (Bethesda), published online May 20, 2016.
doi: 10.1534/g3.116.029645.

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Note: The paper is published under an Open Access copyright. The complete paper may be read online or downloaded by any interested readers thanks to this publishing permission. Just click on the link.

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