𧏠How UC Davis and BetterBred Map DNA â 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.
𧪠How Much of the Dog’s DNA Is This?
Letâs 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 thatâa 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 relatednessâthink of it as using fingerprints rather than full body scans.
BetterBred and Risky Haplotypes:
BetterBred uses data from UC Davisâs canine genetic diversity study to analyze haplotypesâclusters 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.
Hereâs how it works:
Each haplotype is labeled as common, uncommon, or rare within the breedâs established database.
BetterBred identifies âriskyâ 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.
đŻ 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) poodlesâwho have different historical breeding selections and sometimes unrelated health concernsâcan 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 âdiverse,â but itâs no longer accurate to what apple growers need to know.
Cause for Concern?
đ˘ 1. Inflated Genetic Diversity Metrics
Intervariety poodles (those with Miniature or Toy ancestry) introduce haplotypes not native to the Standard Poodle population. These ânewâ haplotypes may be labeled rare or unique, giving the false impression that the breed has more diversity than it actually does.
âĄď¸ 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 varietyânot historically present in Standard lines.
𧏠2. Misleading Outcross Potential
When evaluating potential pairings, BetterBredâs 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.
âĄď¸ Result: Breeders aiming for thoughtful preservation may end up compromising structure, temperament, or health consistency by unknowingly introducing Miniature traits.
𧪠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
đŠ 4. Undermines Preservation Goals
Preservation breeding isnât just about healthâitâs about maintaining the distinct identity of the Standard Poodle: their size, structure, coat, temperament, and working aptitude.
âĄď¸ Including intervariety dogs in the database erodes the historical record of Standard Poodle genetics and confuses efforts to maintain the breedâs integrity.
Summary
âAs 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.â
Hi there,
I appreciate your taking the time to explain how some of this works. As the founder of BetterBred, I have thought deeply about the quality of our data and whether poodles with Miniature and Toy ancestry skew the data.
First, let me say that the AKC recognizes all poodles as a single breed and that choice is governed by the Poodle Club of America. Mixing of varieties is generally frowned upon, but is not against the rules. Thus, the varieties, dependent solely on height, as all poodles are meant to fit the same breed standard, are split only artificially.
Second, prior to the mid century bottleneck, when the Standard Poodle gene pool was severely narrowed due to the inbreeding and proliferation of a single successful line based on ten dogs, the varieties were genetically more similar. That line became overly dominant because they were tall and elegant, and everyone with Standard Poodles bred to them, over and over, until much of the ancestral genetics were bred out. That line had both positive and negative effects on the variety, and about 20 years ago breeders became especially alarmed at the rise in autoimmune diseases, specifically Addisonâs and sebaceous adenitis. They could not find any traditional ways to avoid these diseases, especially in otherwise well bred show lines. They also saw a rise in epilepsy and juvenile renal dysplasia. Breed away from one disease and youâd run into another. Through pedigree research the bottleneck was recognized, but breeding for low COI based on pedigrees did not offer any relief. At that time there were a handful of breeders crossing varieties with a range of success. It was no magic solution, though it did mitigate risks of the common diseases, it also became clear that a return to the Standard size and type now expected after the bottleneck would take generations of careful selection.
Starting in 2014, a large number of Standard breeders helped an effort to turn to DNA, and we worked with Dr Niels Petersen at UC Davis to develop a test that could help us breed for true diversity more accurately than we could with pedigrees. We discovered that while the breed still had much diversity, that diversity was found in a relatively tiny number of dogs.
We also found that dogs with unusual DLA haplotypes had lower risks of Addisonâs or SA, and that two of the DLA haplotypes conferred more risk of those diseases. We were only able to do that because we had robust numbers of both affected and healthy dogs. We also could not say for sure whether those DLA haplotypes themselves were problematic or if they just coincidentally were carried in risky lines.
The handful of Standard Poodles that were genetically different from the bottleneck lines were different also in type and disease risk, not unlike the other varieties. Just as with intervariety crosses, they also needed selection to improve type, but they also retained traits that had become rare in the main population, such as good fronts.
Fast forward ten years, and those old Standard lines have increased in population, most breeders of all kinds are careful about not inbreeding too closely, and autoimmune disease incidence, anecdotally, has gone down. There are lines with mini behind them, but most lines used by conscientious breeders are now a number of generations away from those original intervariety crosses.
Selection is the most powerful driver of preservation for desirable traits, aside from inbreeding, and far less risky than inbreeding.
As for hidden Miniature traits or diseases cropping up unexpectedly, remember that all Standards have Minis far back in their pedigrees and vice versa. Any simple Mini diseases like PRA or CDDY can be tested for and safely bred away from. Any complex traits are far less likely to appear in very outbred dogs because outbreeding is the way to avoid them. You pick your best options from each litter and breed to a dog that has more of what your pick needs, and then select again. Return to type takes a few generations but it is perfectly doable while still retaining diversity. Of course you must test your dogs to be sure you arenât losing the added diversity when breeding each generation, because pedigrees are no guarantee that youâll retain any diversity.
As for whether the database is somehow skewed by adding intervariety crosses, when these dogs are now part of the Standard variety, and fit the height requirements, itâs not actually skewing the data. It is changing the population, but only very slightly, since there are relatively few of them and many thousands of full Standards.
Lastly, BetterBred doesnât ever recommend that breeders select the most extreme numbers. Just because a dog has good diversity numbers doesnât mean itâs a good dog, or one you should breed your bitch to. There are many great options to choose from, and your selection should be based on far more than diversity numbers.
I hope that clarifies some things. Feel free to ask any questions.