Poodle Pulse: UC Davis and Betterbred DNA Mapping – a deeper look

🧬 How UC Davis and BetterBred Map DNA – And What It Actually Means

This is a follow-up to my post on Understanding Canine Genetic Diversity Research.

When we talk about “mapping DNA” in canine genetic diversity testing, what we’re referring to is the process of analyzing specific markers across the genome to measure diversity and breed relationships. UC Davis, through its Canine Genetic Diversity Project, and BetterBred, a partner platform, use a specific kind of DNA testing known as Short Tandem Repeat (STR) genotyping.

What Are STR Markers?

STRs are regions in DNA where short sequences of base pairs repeat. These regions are highly variable from one dog to another, making them perfect for measuring genetic diversity.

UC Davis tests:

• 33 autosomal STR loci (the main body chromosomes)

• 7 DLA (Dog Leukocyte Antigen) loci (important for immune system function)

This test is used across all breeds, allowing both within-breed and cross-breed comparisons.

🧪 How Much of the Dog’s DNA Is This?

Let’s put it into perspective:

• The entire dog genome has around 2.5 billion base pairs.

• The STR-based test covers just a tiny fraction of that—a few hundred to a few thousand base pairs total.

• So, the sample represents much less than 0.0001% of the dog’s entire genome.

But even this small slice can tell us a huge amount about diversity, population structure, and relatedness—think of it as using fingerprints rather than full body scans.

BetterBred and Risky Haplotypes:

BetterBred uses data from UC Davis’s canine genetic diversity study to analyze haplotypes—clusters of genes inherited together. These clusters can give breeders insight into how genetically diverse or similar a dog is, especially across the DLA (Dog Leukocyte Antigen) region, which is part of the immune system.

Here’s how it works:

• Each haplotype is labeled as common, uncommon, or rare within the breed’s established database.

• BetterBred identifies “risky” matings when a sire and dam share identical or highly similar haplotypes, especially in both DLA Class I and II. Too much similarity here can increase the risk of autoimmune issues and reduce overall immune diversity in offspring.

• Risky haplotypes may also reflect limited ancestral diversity, meaning the pair may have a greater chance of producing genetically bottlenecked litters with less long-term resilience.

Breeding with diverse but compatible dogs helps maintain health, fertility, and longevity in the breed.

🎯 Why It Matters to Breeders

This kind of testing does not predict health outcomes, but it does help breeders:

• Avoid excessive inbreeding.

• Preserve rare alleles that might otherwise be lost.

• Make informed pairings that improve the genetic health and longevity of the breed.

For SPFL, it means we can maintain the classic structure, temperament, and function of the Standard Poodle while also keeping an eye on preserving the genetic richness that makes the breed sustainable for generations to come.

Why Adding Intervariety-Bred Poodles is Problematic for the Standard Poodle Database:

The Standard Poodle has a distinct genetic fingerprint developed over decades. The addition of Miniature (or Toy) poodles—who have different historical breeding selections and sometimes unrelated health concerns—can introduce genetic noise that skews the data.

Key issues:

• Distorted Diversity Metrics: Including dogs from other varieties inflates perceived diversity in the Standard Poodle gene pool. It may look like we have more unique haplotypes or better outcross potential than truly exists.

• False Security in Matchmaking: A breeder could unintentionally match two dogs thinking they are genetically diverse, when in fact that diversity comes from incompatible intervariety outcrosses that don’t reflect the historical standard poodle population.

• Health Risk Confusion: Intervariety dogs may carry different mutation frequencies or traits not typical in standard lines, complicating interpretation of results and breeding decisions.

You can think of it like trying to measure the nutritional diversity of apples… but someone added pears to the study. It may still look “diverse,” but it’s no longer accurate to what apple growers need to know.

Cause for Concern?

💢 1. Inflated Genetic Diversity Metrics

Intervariety poodles (those with Miniature or Toy ancestry) introduce haplotypes not native to the Standard Poodle population. These “new” haplotypes may be labeled rare or unique, giving the false impression that the breed has more diversity than it actually does.

➡️ Why it matters: Standard breeders might feel encouraged to breed two dogs based on seemingly diverse genetics, when in reality that diversity was artificially introduced from another variety—not historically present in Standard lines.

🧬 2. Misleading Outcross Potential

When evaluating potential pairings, BetterBred’s tools try to identify the best matches to increase genetic diversity. But if the database includes dogs with intervariety ancestry, it can recommend outcrosses that are not actually appropriate for Standards.

➡️ Result: Breeders aiming for thoughtful preservation may end up compromising structure, temperament, or health consistency by unknowingly introducing Miniature traits.

🧪 3. Diluted Breed-Specific Data

Standard Poodles have unique breed-related trends in autoimmune risks, DLA haplotype frequencies, and genetic bottlenecks. Mixing in intervariety data confuses these patterns, making it harder to:

• • Identify which DLA combinations are truly rare or risky in Standards

  • Understand real diversity within the Standard population

  • Make informed breeding decisions based on Standard-specific history

🐩 4. Undermines Preservation Goals

Preservation breeding isn’t just about health—it’s about maintaining the distinct identity of the Standard Poodle: their size, structure, coat, temperament, and working aptitude.

➡️ Including intervariety dogs in the database erodes the historical record of Standard Poodle genetics and confuses efforts to maintain the breed’s integrity.

Summary

“As a preservation breeder, I believe that intervariety breeding introduces traits, haplotypes, and potential health risks not representative of the true Standard Poodle gene pool. Including these dogs in diversity databases may distort the data, mislead breeding choices, and ultimately undermine efforts to preserve the breed as it was intended.”