Inbreeding Depression

In my last post, I mentioned inbreeding depression — a concept that may be unfamiliar to newer breeders. I thought it would be helpful to take a moment to explain what it means and why it matters.

Inbreeding depression is a term used to describe the reduced biological fitness (health, fertility, lifespan, vitality) that can occur when closely related animals are bred together over multiple generations. This happens because inbreeding increases the likelihood of homozygosity—where an animal inherits two identical copies of a gene, including potentially harmful recessive ones.

Homozygosity isn’t always bad — but too much of it can be a problem, especially across large portions of the genome. When an animal inherits two identical alleles (one from each parent) at many locations, it limits genetic variety. This becomes a risk because:

1. 1. Loss of Genetic Flexibility: With less diversity, the dog has fewer tools to respond to environmental stressors, disease, or injury. Think of it like having a toolbox full of the same wrench — not helpful for all jobs.
   2. Expression of Recessive Disorders: Homozygosity increases the chance that recessive mutations (which might be harmless when only one copy is present) will pair up and be expressed. This is where many inherited diseases come from.
   3. Genomic Instability (the “hiccup”): The “hiccup” BetterBred refers to is a simplified way to describe what can happen when DNA replication or gene expression is affected by repetitive, identical sequences.

What Does “Homozygosity Hiccup” Really Mean?

When a dog inherits identical copies of a gene from both parents (homozygosity), it’s like reading the same instruction twice. In small amounts, that’s fine — it helps set breed type. But too much can cause problems.

Imagine you’re copying a big paragraph, and the same sentence shows up over and over:
“Turn left at the tree. Turn left at the tree. Turn left at the tree…”
Eventually, you might lose your place, misread, or skip something important.

That’s what can happen in DNA. When parts of the genome are too repetitive or too similar, the body’s cellular machinery can:

• • • • Misread instructions

      • Fail to make proteins correctly

      • Miss key genetic defenses (like immune responses)

These “errors” don’t always happen, but they become more likely when homozygosity is high — especially in important areas like the immune system (DLA genes) or metabolic pathways.

4. Inbreeding Depression: The cumulative result of too much homozygosity over generations: reduced fertility, smaller litters, shorter lifespan, weakened immune systems, and lower overall vitality.

So the goal isn’t zero homozygosity — it’s to balance it, maintaining breed type while preserving enough diversity for long-term health.

Inbreeding depression in simple terms:

• Every dog carries some recessive genes that may not cause problems on their own.

• When two dogs with the same recessive gene are bred, their offspring have a higher chance of expressing that gene as a disorder or weakness.

• When this happens repeatedly over generations, the population may start showing issues like:

  • Smaller litter sizes

  • Increased puppy mortality

  • Lower fertility

  • Weakened immune systems

  • Poorer temperament or resilience

  • Reduced lifespan

Why It Matters:

In breeds with small gene pools or limited diversity (which includes many preservation breeds), inbreeding depression can quietly erode the health and soundness of a line—even if all visible traits look good.

Maintaining Health and Diversity in Breeding Programs

This is why tools like COI (Coefficient of Inbreeding), AVK (Ancestor Loss Coefficient) and canine genetic diversity testing are so important. They help breeders track and manage genetic relationships to maintain both breed type and long-term health.

• COI measures how closely related the dog’s ancestors are. A higher COI means more inbreeding and less genetic variation, which may increase the risk of inherited health issues.

• AVK shows how many unique ancestors are in a pedigree — measures the percentage of unique ancestors in a pedigree. A lower AVK means the same ancestors appear multiple times, signaling a loss of genetic diversity — even if the COI appears low. This reduction in variety can contribute to issues like inbreeding depression, including reduced fertility, smaller litters, and weaker immune systems.

• Genetic diversity tools (like UC Davis diversity testing) evaluate diversity at the DNA level by analyzing genetic variation across the genome, analyzing STR markers, including markers in the DLA region associated with immune function. This provides a representative sample of the dog’s actual DNA diversity — not just what’s recorded on paper — and helps breeders make informed decisions to preserve or increase genetic health within their lines. I talk more about the benefit and limitations of canine genetic diversity testing in a previous blog post.

So yes — these are all important, especially when you’re trying to:

• Maintain long-term genetic health

• Avoid bottlenecks in a breeding program

• Track how unique a pedigree truly is

It’s best to consider all three: COI, AVK, and DNA diversity when available. Each one gives you a piece of the bigger picture.

📚 References

1. “Canine Inbreeding Depression and Lifespan.” Functional Breeding. Accessed April 17, 2025. https://functionalbreeding.org/inbreeding-depression-and-lifespan/.
2. “Inbreeding Depression Reduces Litter Sizes in Golden Retrievers.” Morris Animal Foundation. Accessed April 17, 2025. https://www.morrisanimalfoundation.org/article/inbreeding-depression-reduces-litter-sizes-golden-retrievers.
3. “Inbreeding Depression and Reduced Fecundity in Golden Retrievers.” Embark Veterinary. Accessed April 17, 2025. https://embarkvet.com/resources/inbreeding-depression-golden-retrievers/.
4. “Inbreeding Impact on Litter Size and Survival in Selected Canine Breeds.” Wikipedia. Accessed April 17, 2025. https://en.wikipedia.org/wiki/Canine_reproduction.
5. “Purebred Dogs Show Higher Levels of Genomic Damage Compared to Mixed-Breed Dogs.” PubMed Central. Accessed April 17, 2025. https://pmc.ncbi.nlm.nih.gov/articles/PMC10884103/.
6. “Inbreeding Depression Causes Reduced Fecundity in Golden Retrievers.” PubMed Central. Accessed April 17, 2025. https://pmc.ncbi.nlm.nih.gov/articles/PMC6606663/.
7. “Understanding Inbreeding Depression in Dogs.” Breeding Business. Accessed April 17, 2025. https://breedingbusiness.com/inbreeding-depression/.
8. “Genetic Health Testing and Inbreeding: A Key to Breeding Better Dogs.” BetterBred. Accessed April 17, 2025. https://www.betterbred.com/blog/genetic-health-testing-and-inbreeding.