Genetics and DNA testing for Diversity

Improving Genetic Diversity for the Stabyhoun

Increasingly, it is clear that the Stabyhoun breed, like most others, is in danger.    Why?   Because the nature of creating a particular breed with a mostly solid-colored head (or a cute blaze in the solid one!) of a certain height, length and weight, with all-rounder qualities and a quirky temperament means that type was heavily selected over genetic diversity.   Simply put, but you get the drift.  Over time, selective breeding has narrowed the breed founders down to less than 14 dogs.

The ASA has partnered with EMBARK to study what we, as a group and as individual breeders, can do to improve our odds by using our average relatedness of the worldwide Staby population to lower our coefficients of inbreeding in the future.   Our Dutch friends in the NVSW are undertaking a study on these genetic diversity issues for both Stabys and Wetterhoun.   Many possible solutions will be addressed in producing outcross models as well as searching for "look-alikes" or unused dogs that might add diversity.   We have already discovered some purebred material that is at least partially unique and something we can use to build a stronger genetic base.   Dogs with genes that are rare in the breed have the highest "genetic value". Similarly, dogs with genes that are common in the breed have low genetic value. Dogs with high genetic value should be prioritized for breeding so rare genes are not lost from the gene pool.

The genomes of dogs that are closely related are more similar to each other than those of dogs that are from unrelated ancestry. The chart to the right is similar to a family tree. It shows clustered dogs on the x and y axis with the center matrix colors showing the relative relatedness of one dog with another.  Obviously, the red squares on the diagonal are the most related, as they are the same dog on both the x and y axis!  You can see that the clustered dogs  (meaning genetically similar)  in this case has created two major groups with several minor groups in each. Each branch that touches the matrix is an individual dog. So for example, in the orange cluster in the upper left, there are 4 dogs, and the length of the branches reflect the degree of similarity between them (shorter lines are more similar). Looking to the matrix, the most genetically similar group of dogs is the pale green group (upper left of the matrix). The color of the squares (with the key in the upper left) reflects the degree of genetic similarity between each pair of dogs.

The ASA has negotiated an excellent breeder price with EMBARK of just $129 to analyze each DNA sample (collected by a simple cheek swab).  Starting in May 2020, the price for testing all the pups in your litter (4 to 11 pups) is just $99/puppy with this link.  Our Breeding Advisors suggest that every Stabyhoun owner consider having their dog's DNA test done by EMBARK.    A newborn litter tested will help you make even better choices of which dogs would be best for future breeding so we are adding this requirement for all litters in the ASA.

If you wish to do this test, you should use the current EMBARK password - STABYDNA.   The website to visit with that password is embarkvet.com/STABYHOUN.

Please note that the results are sent to you and you alone.   The ASA would love to receive the raw data results for your Staby to be included in the genetic study for the breed.   The raw data will be the basis for looking at genetic diversity, or the lack thereof in our case, and putting together charts and analyses like the ones on this website.  This information will be thoroughly studied against pedigree data to give us guidelines for our breeding program, hopefully worldwide.  It also is helpful in research to discover gene mutations that affect the health of our breed.  New advances are constantly being made in the field of genetics.

Of course, it is even more beneficial to the breed if you make your health, breed, and trait information public on the EMBARK site so it can be utilized in the new exciting Matchmaker Tool!  For a dog to be viewed in Matchmaker:

  • The dog must have been DNA tested using an Embark for Breeders DNA Test (and have a breeder account created)
  • The dog must be marked as intact on his/her profile
  • The owner must have not opted out of the tool--Be sure to go to “Breeder Tools” and then “Dog Settings” to include your dogs in Matchmaker as well as set their health and traits results to public.
  • Owner must have set up a "kennel" profile under your main settings tab.  This tool is for Breeders, so even without a specific kennel name (use your own name if you don't have a kennel name) you must register as a "breeder".

Of particular interest to the individual dog owner may be the coat color and trait tests that are listed below:

*Coat Color:

A Locus (Agouti): Ay, Aw, At, a

B Locus (Brown): B, b

K Locus (Dominant Black): KB, Ky

Embark provides you with a coefficient of inbreeding at the chromosome level, which is a measure of how closely related the ancestors of your dog were.  We also learn the Y haplotype and the Mitochondrial Haplotypes which are especially helpful in finding some rarer genes in our population.  Use this Matchmaker Tool to discover the potential DNA inbreeding level of your next litter!  Maybe there is a dog of lower Mean Kinship that would be a terrific match for your Staby.

For a tutorial on how to use the Matchmaker tool, please click on this link: https://www.stabyhouns.org/wp-content/uploads/2020/09/INTRO-TO-EMBARK-MATCHMAKER.pptx

Knowing the coat color -- having brown or tri-color genes like a few of our Stabys will make mating choices easier.  We will also learn whether or not your Staby is a possible carrier of von Willebrand disease, or a few other genetic mutations.  The tests do look at degenerative myelopathy, which is seen in the dna, but rarely appears clinically in our breed;  the genetics of DM appear to be more complex than originally believed. You should read this article for background on the current state of our understanding about DM. (See The lesson(s) from SOD1 and degenerative myelopathy).

These are currently the only DNA markers that have been discovered for our breed, other than the Cerebral Dysfunction DNA test, which is still a non-peer reviewed test, so must be done separately.  The BAC will require that test for all possible carriers of CD who are breeding.  We know that when the research done by the University of Utrecht on Cerebral Dysfunction in 2016 is peer reviewed, this DNA test can be included in the DNA testing done by EMBARK.   We would also like to include the ISAG 2006 parentage markers, so it would be "one stop" for all required tests and much more data on the breed can be gained.

Please note, it will be continual and cross-the-board testing that will be most valuable to our breed -- these tests are mostly for learning trends and to hopefully discover the markers for Stabyhoun specific diseases not yet known.    One very interesting piece of information will be the actual COI of your dog, based on the chromosome level analysis -- many dogs are actually 6-10% less inbred than statistics would think!   Good news, but we still have a long way to go.

What will my DNA test show?   Below is an example of one part of the DNA results from Tulip, Sante Yfke fan Bûten Út (click on the image to see the full results).   All individuals in a finite population are related if traced back far enough and will, therefore, share segments of their genomes that are "Identical by Descent" (shown below in blue). During meiosis segments of IBD chromosomes are broken up by recombination. Therefore, the expected length of an IBD segment depends on the number of generations since the most recent common ancestor at that segment.

Tulip's DNA

Please contact the BAC for more information on this DNA offer!   

We already have over 250 Stabys who have done the DNA swab with EMBARK!!   Now we will work on bringing more into the program.  😉

What else can I do to help the breed?

While you are waiting for the results of your dog's DNA test, we highly recommend that you visit the Institute of Canine Biology site for their amazing articles and courses on genetics for breeders.  This is very easy information to understand, and once you know the basics, Breeders and stud owners will be much better at picking good choices for mating and for choosing the offspring to stay intact.

And we'll all be on the same page when we start looking at results!  The courses below are FREE and enrollment is not required:

Useful Genetics  - a primer on genetics that is easy to follow

COI Bootcamp -- understanding the coefficient of inbreeding.  They actually are fun as well as highly informative.

With the basic knowledge of genetics understood, you can also enroll in other courses at
http://www.instituteofcaninebiology.org/courses.html for additional education on this topic.

Once enrolled, you can go back and retake the courses as many times as you like!  A great reference tool.

 Let's get started on changing the future now, shall we?  Thank you!

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