Breeding Decisions: Managing MDR1 in Your Lines

I have worked with hundreds of breeders over my sixteen years in canine genetics, and the question I hear most often is some variant of "Should I stop breeding my carrier or affected dogs?" The answer is almost never a simple yes or no, and the breeders who make the best decisions are those who understand the population genetics underlying their choices.

What frustrates me most about MDR1 discourse is the oversimplification. People treat genetics like a simple good/bad binary when it is actually a complex optimization problem balancing multiple traits, population diversity, and practical constraints. Let me walk you through how I think about MDR1 in breeding programs.

The Fundamental Tradeoff

When you breed dogs, you are making tradeoff decisions whether you acknowledge them or not. Every breeding pair represents a choice to emphasize certain genetics over others. With MDR1, the core question is: how much do you prioritize P-glycoprotein function relative to every other trait?

If MDR1 were the only consideration, breeding would be simple: only use N/N dogs. But MDR1 is not the only consideration. In breeds with high MDR1 frequency, eliminating all carriers and affected dogs would:

• Remove 40-75% of the breeding population
• Dramatically reduce effective population size
• Increase inbreeding coefficients across the breed
• Potentially fix other harmful alleles by eliminating genetic diversity
• Lose valuable traits that happen to be linked with affected dogs

The responsible approach is not elimination but management. Our goal should be to reduce the frequency of M/M puppies over time while maintaining healthy breed diversity.

Understanding the Mathematics

Let me be explicit about the probabilities because I see breeders make poor decisions based on misunderstandings.

Punnett Square Basics

My Breeding Recommendations by Status

For N/N (Clear) Dogs

You have the most flexibility. Your N/N dog can be bred to any partner status and will never produce M/M puppies when bred to N/N or N/M partners. Use this flexibility to prioritize other important traits. An exceptional N/N dog that is also clear for CEA, PRA, and other breed-relevant conditions is a valuable asset to your breeding program.

Consider offering stud services or breedings to carrier dog owners who need clear partners. This helps the broader breed population while using your dog's genetics productively.

For N/M (Carrier) Dogs

Carrier dogs can and should be used in breeding programs when they have other valuable qualities. The rule is simple: ONLY breed to N/N partners. This produces no affected puppies while preserving the carrier dog's other genetic contributions.

Test every puppy from carrier breedings and clearly disclose status to all puppy buyers. Buyers who understand MDR1 will appreciate your transparency and can make informed care decisions.

Do NOT remove excellent carrier dogs from breeding programs unless you have equally excellent N/N alternatives available. The Collie breed, for example, would lose a massive amount of genetic diversity if all carriers were immediately retired from breeding.

For M/M (Affected) Dogs

This is where I diverge from some colleagues. I believe exceptional M/M dogs can be bred, but ONLY to N/N partners. This produces 100% carrier puppies, but zero affected puppies. If the M/M dog has outstanding qualities that are rare in the breed, preserving those genetics through careful breeding may serve the breed better than eliminating the individual entirely.

However, I acknowledge this is controversial. Many breed clubs recommend against breeding M/M individuals entirely. You must weigh your breed's specific circumstances, the individual dog's overall genetic value, and the availability of alternative dogs that preserve similar qualities.

Population-Level Strategies

Individual breeding decisions matter, but the real impact comes from coordinated breed-level strategies. Here is what works:

Mandatory Testing Before Registration

Breed clubs that require MDR1 testing for registration or breeding clearance see faster reduction in affected puppies. The Australian Shepherd Club of America's embrace of mandatory testing for breeding stock has demonstrably reduced M/M frequency in registered populations over the past fifteen years.

Coefficient of Inbreeding Monitoring

Do not let MDR1 selection create inbreeding problems. Track COI across your breedings and across your breed. Some databases (MyDogDNA, Embark, breed-specific registries) now provide COI tools. Use them. A breed with zero MDR1 but high inbreeding will develop other problems.

Multi-Generation Planning

Think beyond the immediate litter. If you breed a carrier today and keep back a puppy, that puppy should be bred to a clear dog. Over two generations, you can preserve excellent genetics while potentially producing N/N grandchildren who carry forward those traits without the mutation.

What I Tell My Clients

When breeders come to me with MDR1 questions, here is my practical advice:

1. Test everything. Test all breeding stock. Test all puppies before placement. No exceptions.
2. Never breed M/M to anything except N/N. This is a hard rule with no exceptions.
3. Avoid N/M to N/M breedings. There is almost always an N/N alternative available.
4. Disclose fully to puppy buyers. Provide written status and explain what it means for care.
5. Price affected and carrier puppies appropriately. Some breeders discount, others do not. Either is fine as long as buyers understand the status.
6. Document everything. Keep records of all test results for your breeding dogs, their offspring, and their ancestors. This data helps you make better decisions over time.

Dealing with Breeder Stigma

Some breeders face criticism for continuing to use carriers in their programs. My response: critics who demand immediate elimination of all carriers do not understand population genetics and are advocating for breed destruction in the name of breed improvement.

The responsible approach is gradual frequency reduction through careful breeding, not sudden elimination of 40-70% of a breeding population. Breeders who test, disclose, and breed responsibly should be celebrated, not attacked.

If your breed club or community pressures you to make decisions that would harm genetic diversity, push back with data. Share this guide. Explain the mathematics. Advocate for evidence-based breeding policies.

Resources for Ongoing Learning

Understanding MDR1 in the context of broader herding breed genetics helps inform breeding decisions. I recommend exploring the genetic landscape of herding breeds to understand how multiple inherited conditions interact in breeding programs.

For specific drug considerations when placing puppies with families who may need to medicate their dogs, review our complete drug avoidance list so you can educate puppy buyers effectively.

If you have not yet established testing protocols for your breeding program, our testing options guide compares laboratories and pricing for both individual and breeder-volume testing.

And please, if you ever encounter an emergency situation with a puppy you have placed, have the owner consult our emergency protocol while seeking immediate veterinary care.

A Final Thought

I have been researching canine genetics for sixteen years. In that time, I have watched MDR1 testing go from research curiosity to widely available standard of care. The breeders who have embraced testing and made informed decisions have improved their breeds without sacrificing genetic diversity.

You can manage MDR1 responsibly. It requires understanding the science, making data-driven decisions, and communicating honestly with puppy buyers. But it does not require eliminating carriers from breeding programs or watching the gene pool collapse in misguided pursuit of genetic purity.

Test. Disclose. Breed thoughtfully. The breeds we love will be healthier for it.