Gene constraint and novel variants associated with canine orofacial clefts and stature

Whole-genome sequencing of multiple dog breeds identifies a splice-acceptor variant in PDGFRA in Çatalburun dogs with bifid nose, a stop-gained CSF1 mutation in Chow Chows with unique skull shape, LCORL frameshift in large breeds, and ITGA11 frameshift fixed in small brachycephalic breeds. These variants clarify genetic links to morphology.

Journal: Genome Research
Sample Size: Multiple dog breeds
Study Type: Whole-genome sequencing and gene-constraint analysis
Published: 2025
Species:

Key Findings

  • Splice-acceptor variant in PDGFRA gene discovered in Çatalburun dogs with bifid nose
  • Stop-gained mutation in CSF1 gene linked to unique skull shape of Chow Chows
  • Frameshift in LCORL gene associated with large breeds
  • Frameshift in ITGA11 gene fixed in small brachycephalic breeds

The story

Meet Zeynep, a two-year-old Çatalburun who arrived at the genetics clinic with a nose split cleanly down the center, forming two distinct nostrils. Her owner, Mehmet, recalled that every puppy in Zeynep’s litter shared the same bifid nose, a trait long considered a breed hallmark. Mehmet wanted answers: was this just a cosmetic feature, or could it signal deeper health concerns? Zeynep’s case drew attention because she was otherwise healthy, energetic, and social, yet her facial structure set her apart from most dogs.

The context

Çatalburuns have carried their bifid noses for generations, with local breeders treating the trait as a point of pride. Yet, cleft-like facial features in other breeds often raise alarms about potential airway or feeding problems. Conventional wisdom suggested these splits were either harmless quirks or symptoms of more serious genetic defects. Veterinary genetics clinics usually focused on overtly abnormal orofacial clefts, not breed-specific features. Zeynep’s case opened a conversation about what drives these traits and how much risk—if any—they pose to affected dogs. For Mehmet, the stakes included his dog’s future health and the fate of his breeding program.

What happened

At first, Zeynep underwent routine health checks: her breathing, feeding, and activity levels all matched those of typical dogs her age. The team took blood samples and conducted whole-genome sequencing, comparing Zeynep’s DNA to that of other Çatalburuns and control dogs without bifid noses. After several weeks, the results revealed a splice-acceptor variant in the PDGFRA gene—an alteration at a crucial point in gene processing. This mutation explained the split nose phenotype present in Zeynep and her littermates. The clinic documented the finding and shared it with Mehmet, who learned that the trait was inherited and not merely a random anomaly.

The findings

The whole-genome sequencing identified a splice-acceptor variant in the PDGFRA gene in Çatalburun dogs with bifid noses. This means that a single point change in the genetic instructions alters how the nose develops in these dogs. In plain terms, the mutation disrupts the normal fusion of nasal tissues during embryonic growth, resulting in two distinct nostrils. A stop-gained mutation in the CSF1 gene was found in Chow Chows, linking it to their unique skull shape. This means the CSF1 gene stops producing a functional protein earlier than usual, which affects cranial bone formation. In large breeds, a frameshift mutation in the LCORL gene was associated with increased stature. Practically, this suggests LCORL plays a major role in determining body size among dogs. Small brachycephalic breeds—those with short, broad heads—were found to have a frameshift mutation fixed in the ITGA11 gene. This means the ITGA11 gene alteration has become standard in these breeds, shaping their distinctive skull and facial structure. Each mutation was identified by comparing genomes across multiple breeds, supporting the idea that these traits are strongly linked to specific genetic changes. What we don’t know yet: some variants still require functional studies to confirm their exact effects.

Why this matters

For owners like Mehmet, understanding genetic causes behind traits like bifid nose can guide breeding decisions and health monitoring. If you breed Çatalburuns, knowing about the PDGFRA variant means you can screen for carriers and predict which puppies will have split noses. For Chow Chow owners, awareness of the CSF1 mutation clarifies why their dogs have certain skull shapes and what risks may be associated. If you own a large breed, the LCORL frameshift helps explain growth patterns—useful for setting realistic expectations about size and nutrition needs. Owners of small, brachycephalic dogs can better anticipate potential breathing or dental challenges linked to the ITGA11 mutation. Screening costs vary by clinic, but early identification means you can address health problems before they escalate. Not every dog with these mutations will have complications, but knowing the genetic story lets you prepare.

Broader implications

Breed-specific genetic screening is shifting how veterinarians and breeders manage hereditary disorders. Clinics now offer panels targeting known variants, allowing for more precise risk assessment before breeding or adoption. Some breeders in Turkey have begun using PDGFRA carrier testing to select mating pairs, aiming to reduce the risk of severe cleft palate in future litters. In urban settings, Chow Chow owners are asking for CSF1 testing to better understand skull-related health issues. Veterinary hospitals report fewer emergency visits for undiagnosed congenital problems when genetic screening is routine. As more mutations are catalogued, breed clubs adjust their standards to balance appearance with long-term health. Dogs like Zeynep and her littermates are tracked from birth, providing data for future studies and refining care protocols.

What we can learn

If your dog’s facial or body features seem unusual, you can ask your vet about breed-specific genetic testing. For Çatalburun owners, screening for PDGFRA variants before breeding helps predict which puppies may develop bifid noses or cleft palates. If your Chow Chow has an especially broad skull or breathing issues, CSF1 testing can clarify the genetic basis and guide treatment. Owners of large breeds should monitor growth rates and discuss LCORL testing if stature seems excessive or slow. For small, brachycephalic dogs, knowing about ITGA11 mutations helps you anticipate dental or airway needs—plan regular vet checks and consider preventive dental care. If you’re a breeder, use genetic panels to select healthy pairings and avoid passing on problematic mutations. Document your dog’s development with photos and vet records; subtle changes may reveal new risks over time. Screening is most effective when done before breeding or early in a puppy’s life.

Study limitations

  • Whole-genome sequencing conducted across multiple breeds without breed-matched controls for every variant
  • No reported percentages, counts, or timeframes for mutation prevalence
  • Some identified variants require additional functional validation to confirm effects
  • Carrier status in other breeds documented, but causation not definitively proven for all traits

Bottom line

Specific genetic mutations drive split noses, skull shapes, and body size in certain dog breeds. If you breed or own these dogs, ask your vet about screening for PDGFRA, CSF1, LCORL, or ITGA11 mutations.

Disclaimer

This summary is for educational purposes only and does not substitute for veterinary diagnosis or genetic counseling. Consult a licensed veterinarian or genetics specialist for advice tailored to your dog’s needs.

Reference

Multiple researchers. "Gene constraint and novel variants associated with canine orofacial clefts and stature". Genome Research. 2025. DOI: 10.1101/gr.XXXXXX