More on Suggested Breedings

Darling puppy pile photo courtesy of Shyre Standard Poodles!

Knowing what is good for a breed as a whole is not necessarily easy, and there will always be varying opinions on what’s best.  However there are some very solid basic concepts that are difficult to argue – one is that maximizing existing diversity is better than losing more, and another is that selecting for general good health is better than selecting for some other trait regardless of health.

Both of those keep unseen bad genes from becoming too common in the breed.

In all the different assessments of diversity in various breeds, whether from UC Davis, a comprehensive recent NIH paper, or results from the commercial companies selling versions of diversity testing, we know that every breed is different. Some breeds have more diversity, some have less. However, the same basic principles apply to all breeds.

One aspect a great many people – even some researchers – seem to be confused about is the difference between looking for specific disease genes versus how a diversity test can show risk for disease.  The key is the difference between looking for a tiny mutation or three, and assessing overall genetic similarity.

The concept is this – by isolating breeds (via closed studbook) and selecting for similar and usually simple genetic traits (coat color, the perfect head, ear or tail set, etc.) breeders improved the overall look of a breed, but also concentrated whatever disease genes just happened to be in the founder dogs – or in particular popular sires or other influential ancestors. (Pedersen, et al, 2015) Which disease genes existed in the founders was random, and they often weren’t even noticeable until some tipping point, when finally these sets of gene became common enough throughout the population, and suddenly affected dogs were cropping up everywhere.

Dogs with the most common genetics within the breed were then shown to have higher risks of those breed-specific diseases. Because of this, we don’t have to look for the precise disease genes – which are often illusive in complex diseases – we only have to know whether a dog is more or less similar to the most common dogs in the breed. And in fact, Standard Poodles with the most bottleneck influence were shown to be most at risk for known breed specific diseases – based on genomic data AND pedigree data. We see the same principle in effect in other breeds as well.

So large genetic bottlenecks, the process by which some genetics become very common and drive out other genetics, are bad for reasons we don’t see in our whelping boxes. They can happen when everyone rushes to breed to a single dog or a special line, or a culture of sustained, multi-generational inbreeding, or they can happen due to war or famine – but they have great impact over time. They are bad for whole breeds, and the damage done from them is not perceptible by looking at one dog and then another dog. It’s very perceptible, however, when looking at large numbers of dogs, and that evidence bears out over and over.

That’s probably old news to many of you, and maybe fightin’ words to others, but what is certain is that  neither a “diversity” breeder nor a hardcore linebreeder wants unhealthy puppies. How we produce the healthiest puppies involves a lot of careful considerations.

Among those considerations we can now include taking care of our gene pool so that there will always be an ample source of diversity.  What really matter is not so much whether an individual dog is inbred, or highly homozygous, but rather whether an entire breed is highly related. Two highly inbred dogs of the same breed can be completely unrelated, and two very outbred (highly heterozygous) dogs can be genetically very similar.

What we want to prevent is a breed having too many of the same exact ancestors, because this makes those ancestors’ genes, the good ones and the bad ones, much too common in the population. Having all the same ancestors turns into consistency in type, but also means having the same disease genes. Having more varied ancestors means the disease genes only very rarely end up in the same dog. This is why we want to retain as many different lines – meaning different genetics – in any breed.

To do that is tricky – especially in breeds that already have a bottleneck. BetterBred’s “Suggested Breedings” is a way of maximizing the diversity, by increasing gene flow. This means that the unusual genetics over time become less unusual and the common genes become less common until there is better balance.

Emphasis is put on genetically unusual dogs, not because they are automatically special – but to increase the frequency of their genetics, generally, so that they can dilute the frequency of any common disease genes.

Unusual dogs should be bred to dogs that are equally unusual. These dogs all produce more overall diversity, and they should be tested and the best ones with the lowest Average Genetic Relatedness should be kept intact. The more unusual they are, the more important it is that they are bred, and bred to other unusual dogs.  These dogs are responsible for maintaining diversity, so they should be generally healthy, long lived, and have decent structure and good temperaments, but they don’t have to be perfect in type.

Common dogs usually come from lines that have a long history of selective breeding. These dogs tend to be more like our breed standards – but are also more at risk for breed specific diseases. So we want to keep the generations of selective breeding for good things, but break up the possible disease gene combinations. Common dogs should be selected very carefully – because they are responsible for putting selection pressure on the rest of the breed for proper breed type, temperament and health. A beautiful dog with lousy hips that has otherwise common genetics should not be bred. Excellent quality common dogs should be bred to more unusual dogs and their nicest puppies that have the lowest Average Genetic Relatedness should be kept.

In the graphic above, there’s a visual representation of how it should be managed. The most unusual tiers of diversity have to be producing puppies to contribute to the gene pool. These can then be bred to lower tiers. Dogs that are genetic outliers will have many fewer suggested breedings, but their contributions are very important.  Common dogs can be bred to any dog with an Average Genetic Relatedness that is below average – but breeders must know that some of every litter may be in the more at-risk range if there’s a specific bottleneck in the breed.

Slowly the breed will balance the existing diversity throughout the breed, while retaining quality.

Will this solve all the breed specific diseases? Probably not all, not completely. Will it lower their frequency?  Quite possibly, and it can prevent new diseases from becoming very common.  Each breed has different breed specific diseases and each disease has different modes of inheritance. Some diseases are fixed within the breed, while others can still be bred away from with care.  Some breeds may be so depleted, and have too many common risky alleles for this type of breed management to help much on its own. If that’s really the case, however, determined by both researchers and breed clubs, they’ll  need outcrosses to other breeds – and then this method of breeding management can be used to bring in new diversity from a similar breed and spread it effectively through the breed to bolster the health of the breed without losing the traits and temperament that make the depleted breed distinctively itself.

All gene pools need proper management to keep them genetically healthy and self-sustaining. Of course any breeding program will only get results if people follow it, but serious breeders tend to be very good at following trusted protocol. With more and better tools, we can do more and better as breed communities. It’s an exciting time indeed.

Natalie Green Tessier

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