For the past several decades, Shetland ponies’ collective past had caught up with them. A portion of the population of these miniature horses is affected by atavism, a phenomenon in which ancient characteristics are accidentally revived by mutations. Traits reincarnated in this way sometimes interact disastrously with the genetic background of the modern organism. For the ponies, a type of skeletal atavism (SA) has tragic consequences: the affected animals are born with some of the bones in their legs fused together, resulting in leg deformity and difficulty moving. Over ten percent of the ponies are carriers, and most affected individuals have to be euthanized at a young age. In an article in the July issue of G3, researchers report not only the cause of this condition, but also a genetic test that can be applied to breeding programs immediately.

Ponies suffering from skeletal atavism have bowed legs. Photo credit: Ove Wattle.

Ponies suffering from skeletal atavism have bowed legs. Photo credit: Ove Wattle.

The researchers first attempted a genome-wide association study, which looks for statistical associations between a disease and variation at a region of the genome, but this approach failed to detect the mutation responsible for SA. To dig a little deeper, they then resequenced the whole genomes of six affected ponies and compared them to the genomes of a pool of control horses—stallions that had at least 50 registered offspring, none of which had SA. They found that the SA-affected ponies suffered from at least one of two partially overlapping deletion mutations, which they labeled Del-1 and Del-2.

These deletions were in sequences unassigned in the Thoroughbred horse reference genome assembly (EquCab2.0), which explains why the genome-wide association study originally failed to find them. These mutations fell in the pseudoautosomal region of the sex chromosomes, a stretch of DNA with a high GC and repeat content that makes it notoriously difficult to sequence and assemble—even in the human genome, about 600 kilobases remain unassembled. The region is very fragmented in the EquCab2.0 genome assembly, and the researchers’ attempts at de novo assembly using short sequence reads from the SA-affected ponies’ genomes also failed.

To circumvent this problem, they used single-molecule real-time (SMRT) sequencing, which enabled them to sequence longer stretches of DNA and pinpoint the deletions to the gene SHOX and the downstream gene CRLF2. Both Del-1 and Del-2 mutants were missing the region downstream of the gene SHOX, which includes the gene CRLF2, but Del-1 mutants were also missing the entire coding region SHOX. Taking into account their functions alone, either gene could plausibly be involved in the deformity. Among the genes’ many roles, CRLF2 is involved in bone metabolism and SHOX is developmentally regulated and activates transcription in cells that develop into bones.

An X-ray image of an atavistic pony's legs. Photo credit: Göran Dalin.

An X-ray image of an atavistic pony’s legs. Photo credit: Göran Dalin.

Although both mutations completely deleted CRLF2, the researchers hypothesize that the effects on SHOX function are the mostly likely cause of SA—whether through deletion of the entire gene or loss of regulatory elements its downstream region. The apparent role of SHOX in humans supports this idea. In humans, haploinsufficiency or deficiency of SHOX is associated with limb deformities, and a 47 kilobase deletion downstream of SHOX is responsible for the skeletal disease Leri-Weill dyschondrosteosis as well as idiopathic short stature. While the results don’t suggest a cure for these human conditions, they did allow the researchers to develop a genetic test for SA in ponies, which—if applied—could allow this crippling condition to be bred out immediately.

CITATION:

Rafati, N.; Andersson, L.; 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, E.; Dalin, G.; Chowdary, B.; Anderssson, L.; Lindgren, G.; Rubin, C. Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies.
G3, 6(7), 2213-2223.
DOI: 10.1534/g3.116.029645
http://www.g3journal.org/content/6/7/2213.full

, , ,

Nicole Haloupek is a freelance science writer and a recent graduate of UC Berkeley's molecular and cell biology PhD program.

View all posts by Nicole Haloupek »

Read more in

  • Ed Grell at his dissecting microscope using ether to anesthetize his flies.

    In Memoriam: Ellsworth Herman Grell (1932–2023), a pioneer of Drosophila genome engineering and annotation

    Ellsworth (Ed) Grell blessed the Drosophila community through three enduring legacies: as a pioneer of chromosome mechanics, as a primary organizer and synthesizer of genetic knowledge in Drosophila, and as a graceful mentor to those fortunate to have known him personally. Ed grew up in rural Nebraska, completed his undergraduate studies at Iowa State, and…

  • Congratulations to the #Fungal24 Poster Award winners!

    We are pleased to announce the recipients of the GSA Poster Awards for posters presented at the 32nd Fungal Genetics Conference! Undergraduate and graduate student members of GSA were eligible for the awards, and a hard-working team of judges made the determinations. Congratulations to all! Felicia Ebot Ojong, The University of Georgia My research is focused…

  • Poster presentation tips for TAGC 2024

    You’ve been selected to present a poster at The Allied Genetics Conference 2024 in March—you’ve celebrated, made plans to attend, now what? This is an exciting opportunity to showcase your research and engage with fellow members of the genetics community, so you want to make sure you’re prepared. We wanted to offer you some tips…

  • Maximize your TAGC 2024 experience 

    A guide to all that National Harbor & DC have to offer Are you joining us for The Allied Genetics Conference 2024 in March? Make the most of your #TAGC24 experience in National Harbor! We know the science will keep you busy, but you deserve to unwind and have some fun, so we’ve curated a…

  • Early Career Leadership Spotlight: Sarah Petrosky

    We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates. Sarah PetroskyMultimedia SubcommitteeUniversity of Pittsburgh Research Interest I am interested in understanding adaptation that has been happening recently in populations by dissecting the ways that genes underlying an adaptation…

  • TAGC 2024 Early Career Award Winners

    GSA is pleased to announce the winners of the early career awards presented at The Allied Genetics Conference 2024. These awards are specific to particular TAGC communities and recognize early career scientists’ outstanding work on their respective research organisms. The awardees will present their talks in keynote sessions at TAGC 2024.  Don’t miss the opportunity…

  • Preeminent geneticists recognized with revamped GSA Awards

    In 2022, GSA’s Board of Directors launched an audit to review the five major awards conferred by the Society. Today, we are thrilled to announce the recipients of the reimagined GSA Awards, including the new Genetics Society of America Early Career Medal. The scientists honored this year are recognized by their peers for their outstanding…

  • Fly Board funds outreach programs to spread the word about Drosophila research

    In 2020, the Fly Board voted to use part of its reserve fund to support efforts to increase trainee participation as well as equity and diversity in the Drosophila community. An awards committee decides how the money will be spent each year, and from 2020–2022, the committee posted a very broad call for applications from…

  • New members of the GSA Board of Directors: 2024–2026

    We are pleased to announce the election of four new leaders to the GSA Board of Directors: 2024 Vice President/2025 President Brenda Andrews Professor, University of Toronto It’s an honor to continue my association with the Society by serving as Vice President of the Board of Directors. I have broad knowledge of the ongoing activities…

  • A rose-ringed parakeet, one of three parrot species used in the study.

    Parrot plumage study aids breeders and endangered natural populations

    Yellow coloration is maladaptive in the wild but prized by breeders. People have long been fascinated with birds, which exhibit one of the widest ranges of coloration among vertebrates. Parrots, in particular, have captivated humans by their ability to mimic human speech and spectacular plumage. Brightly colored feathers are used primarily to attract mates, intimidate…

  • Early Career Leadership Spotlight: Sarah Gilmour

    We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates. Sarah GilmourMultimedia SubcommitteeStowers Institute for Medical Research Research Interest Questions of evolution have always fascinated me. I am extremely fortunate to be starting out my research career in a…