Understanding Genetic Diversity in Bearded Collies: Insights for Pedigree Dog Breeders
For pedigree dog breeders, ensuring the health and vitality of our breeds is paramount. A recent study published in Genes (2025), titled “Measures of Homozygosity and Relationship to Genetic Diversity in the Bearded Collie Breed,” offers critical insights into how inbreeding and genetic diversity interact within the Bearded Collie population. Conducted by researchers from institutions such as the University of California, Davis, and Tufts University, the study uses pedigree analysis, single nucleotide polymorphism (SNP) arrays, and whole genome sequencing (WGS) to examine homozygosity—regions of identical DNA inherited from both parents—and its implications for breed health. Here’s what we can learn from this research and how to apply it practically.
The Bearded Collies in this study
The Bearded Collie has a relatively modern lineage, refined largely in the 20th century. Like many purebred dogs, it has undergone inbreeding to lock in traits such as coat furnishings and temperament. However, this practice increases homozygosity, potentially heightening the risk of inherited disorders by unmasking recessive deleterious alleles. The study analysed an extensive pedigree of 11,989 Bearded Collies over 28 generations, SNP data from 244 dogs, and WGS from a subset of 23, comparing these to other pedigree and mixed-breed dogs.
Measuring Inbreeding: Pedigree vs. DNA
The study reveals significant differences in inbreeding estimates based on the method used. Pedigree-based inbreeding coefficients (F_PED) rely on known ancestry, averaging 0.29 across all generations for Bearded Collies—a significant level of inbreeding. When restricted to the most recent five generations, this dropped to 0.07, indicating that shallow pedigrees underrepresent true relatedness. SNP-based genomic inbreeding coefficients (F_ROH), which measure runs of homozygosity (ROH), averaged 0.35. WGS-based F_ROH, averaged 0.32. The F_ROH based on SNP array data was consistently greater than the F_ROH based on WGS variants.
Homozygosity and Diversity: A Balancing Act
Homozygosity is a double-edged sword—crucial for fixing breed-defining traits like the Bearded Collie’s long coat (linked to FGF5) or furnishings (RSPO2), yet potentially reducing genetic diversity. The study found Bearded Collies have longer ROH segments (6854 kb from SNP data) than other pedigree breeds (1.3x longer) and mixed breeds (1.8x), reflecting intense selection. High ROH overlap regions, such as on chromosome 8 (CFA8) where over 94% of dogs shared homozygosity, included olfactory receptor genes vital to canine function. Other selected genes, like MITF (coat color) and FSHR (litter size), also showed elevated homozygosity. However, high-impact variants—potentially harmful mutations—were present in 11-14.6% of dogs in a homozygous state, even in those with lower F_ROH (e.g., 0.18), indicating persistent genetic risks.
Comparing Breeds: Where Bearded Collies Stand
Bearded Collies exhibit higher inbreeding than the average of 41 other pedigree breeds (SNP F_ROH 0.25) and mixed breeds (0.09), though not the highest among purebreds. Their effective population size (N_e)—a gauge of breeding population diversity—has shrunk to 15 in the latest generation, signaling a contracting gene pool. Comparing inbreeding levels 5 generations ago with those 50 generations ago showed a recent surge in inbreeding; a 367% rise over 50 generations.
Health Implications: Beyond the Numbers
The relationship between inbreeding and health is nuanced. While some research ties it to reduced litter sizes and longevity, this study notes that purging deleterious alleles through selection (e.g., as seen in Border Collies for hip and elbow dysplasia) can offset risks. High-impact variants in Bearded Collies were often in shorter ROH, suggesting ancient origins, and neutral variants were twice as likely to be homozygous, implying that high F_ROH doesn’t always signal functional harm.
The Outcrossing Debate
Proposals to outcross purebreds to enhance diversity, inspired by conservation models, are appealing but complex. The study cautions that pedigree breeding intentionally curbs diversity for breed consistency, and outcrossing might disperse deleterious alleles unpredictably, complicating efforts to eliminate them. A cited Finnish study found 57% of dogs, including mixed breeds, carry deleterious alleles, highlighting their deep ancestral roots.
Looking Ahead: Tools for the Future
No single measure—pedigree, SNP, or WGS—fully captures genetic diversity or functionality. SNP arrays overestimate inbreeding compared with pedigree data, while WGS includes individual-specific variants that may not reflect breed-wide diversity. The study calls for algorithms to distinguish beneficial from harmful homozygosity, a gap yet to be filled.
Good Practice Advice for Breeders
- Use Comprehensive Inbreeding Assessments: Avoid relying solely on five-generation pedigrees, which underestimate inbreeding. Opt for deeper pedigree analysis (10+ generations) or SNP testing for a truer picture of genomic homozygosity. While WGS is ideal, its cost makes it less practical for routine use. It is probably best reserved for critical cases.
- Balance Homozygosity and Diversity: Select mates with lower F_ROH (e.g., below the breed average) that still carry key traits. Limit popular sire use to prevent concentrating ROH and shrinking diversity, addressing the recent inbreeding spike seen in Bearded Collies.
- Widen the Gene Pool Strategically: Collaborate with breeders globally or consider controlled outcrossing to related breeds. Use veterinary and genetic guidance to maintain breed type, and monitor N_e, aiming for 50-100 to ensure long-term health.
- Prioritise Health-Driven Selection: Combine genetic testing with health screening to target deleterious variants rather than broadly reducing homozygosity, preserving breed identity. Keep and share detailed health records with breed clubs to manage genetic load.
- Approach Outcrossing Cautiously: If outcrossing, use SNP or WGS data to pair carriers of deleterious variants with non-carriers, ensuring offspring align with standards. Start with small, monitored crosses and assess multi-generational outcomes rather than adopting widespread outcrossing.
- Leverage Emerging Tools: Stay updated on genetic advancements and contribute DNA samples to databases like the BeaCon Bearded Collie Health Database used in this study. Integrate pedigree depth, SNP results, and health data for well-rounded breeding decisions until more precise tools emerge.
Conclusion
For Bearded Collie breeders, this study illuminates the intricate dance between inbreeding and diversity. Inbreeding secures the breed’s unique traits but poses health risks if unchecked. By embracing deeper pedigrees, genomic insights, and targeted selection, breeders can safeguard a breed’s most desirable characteristics. Collaboration, informed choices, and a nuanced view of homozygosity will pave the way for a thriving future for Bearded Collies and other breeds.
