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.

The ASA would like to cooperate with the Institute of Canine Biology in studying 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 about to undertake a study on possible outcross models as well as searching for "look-alikes" or unused dogs that might add diversity.   They may even discover 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 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). Similarly, the most genetically similar group of dogs is  the 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 type of information that we can gain for our breed may be similar to another study done for the Berners:  Please follow this link.

The ASA has negotiated an excellent price with EMBARK of just $129 to analyze each DNA sample (collected by a simple cheek swab) and get the individual results back.  Our Breed Advisors suggest that each Stabyhoun owner, even those owning neutered/spayed Stabys, consider having their dogs DNA test done by EMBARK.  This is completely elective -- not a requirement by any means. If you wish to do this test, you should select the option for $179 (Embark for Breeders: Dog DNA Test w/o breed identification) and enter the coupon code, STABYHUN.  And yes, it is intentionally misspelled!.  If you have a dog of unknown pedigree, you may also use the coupon for the $199 test which includes the breed identification.  In both cases, you will receive a discount of $50.   The results of this testing 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 described above.  This information will be thoroughly studied against pedigree data to give us guidelines for our breeding program.

The most interesting to the individual dog owner may be the coat color and trait tests that are listed below:
 
*Coat Color:
A Locus (Agouti): Ay, Aw
B Locus (Brown): B, b
D Locus (Dilute): D, d
E Locus (Mask/Grizzle): Em, Eg
H Locus (Harlequin): H, h
K Locus (Dominant Black): Kb, Ky
 
*Other traits included are:
Curly Coat (KRT71)
Long Hair (FGF5)
Shedding (MC5R)
Hind Dewclaws (LMBR1)
Altitude Adaptation (EPAS1)
Brachycephaly (BMP3)
Body Size (IGF1, IGF1R, GHR, STC2)
 
For both pure and mixed breed dogs, Embark provides you with a coefficient of inbreeding, which is a measure of how related the parents of your dog were, and immune diversity at the Dog Leukocyte Antigen DQA1-DQB1 and DRB1 loci.
 

It will be particularly helpful to know 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 cleft palates, degenerative myelopathy, dilated cardiomyopathy, cataracts, skin issues and glaucoma; all of which we do see in our breed, although quite rarely to date.

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 patent protected test so must be done separately.  The BAC will still require that test for all possible carriers of CD and who are breeding.

You will also learn your dogs mitochondrial makeup, and if a male, their Y haplotype as well.  "Dogs of the same breed share similarities in their mtCR sequence, even if the sequences are not identical. This shows that it is necessary to collect multiple individuals from the same breed to build a thorough database of mtCR polymorphisms. Also purebred and mixed breed individuals can be combined into one database. The same is true for dogs from separate geographic locations. " ¹

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.   Other than for a specific gene like coat color or a known mutation like vWD, you will not really have an "AHA moment" from your individual dog's data.  Mostly, at this time, it is a fishing expedition.  But we do hope to catch a BIG FISH!   One very interesting piece of information will be the actual COI of your dog, based on the chromosome level analysis -- many dogs are actually 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 long 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!

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!  Do you really need to take a genetics course?   Read this article to find out!

Maybe you or someone else you know recently lost a "heart dog" to cancer or another deadly genetic disease?  Well, this article will give you hope for the future.

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 as they become available.

Taking the "pay" courses helps our breed directly, as the funds contribute to the amount of time that the Institute of Canine Biology can afford for analyzing the Stabyhoun pedigree data and the DNA data from all the Embark testing.

Pertinent courses that we encourage you to consider in addition to the free basic courses are:

Managing Genetics for the Future,  Understanding Hip and Elbow Dysplasia   and  Genetics for Preservation Breeders

NOTE:  The Hip and Elbow course just started on November 2, 2017!!  Be sure to enroll as it is fabulous.

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

Footnotes:

¹  from Building a Genetic Reference Database for Dog mtDNA Sequences and SNPs, by Marc W. Allard, Ph.D. , May 2009

NEFA-NMO7V-64GS