Genetic Diversity Test for Akitas

edited May 2015 in Akita (秋田犬)
The Vet Genetics Lab at UC Davis will shortly be offering a genetic diversity test for Akitas, Japanese and American, so breeders have the best chance of increasing diversity in their breedings and especially increasing the number of different alleles in the MHC region of the genome, which moderates the immune system. I think this is the best chance we've had of trying to decrease the amount of autoimmune problems in Akitas. In the research phase, the test will be $50 with a few free tests available; the regular test will be $100. The test is now available for Poodles and Italian Greyhounds; the write-up for the Poodle test will explain more about what the test and its certificate will show: https://www.vgl.ucdavis.edu/services/dog/GeneticDiversityInStandardPoodles.php

If you have any questions, I can try to find answers for you
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Comments

  • Is there a way to get results based on just the JA population (UKC-registered JA) versus a combined AA+JA population?

    And if UC Davis doesn't offer this segregation service, will they provide raw data so a fancier could compile their own database?
  • edited May 2015
    I don't think they'll separate them but many of the JAs will come from other countries so won't be UKC registered. I'll ask your questions, though. The allele range for each dog would be for an individual dog and wouldn't matter whether it's JA or AA or blend.
  • edited May 2015
    Until I get an answer, I can say the purpose of the test is to choose breeding partners that give the best chance of an efficient immune system. Here's a very good article that explains the importance of that:

    http://www.ashgi.org/home-page/genetics-info/immune-mediated-diseases/the-rising-storm-what-breeders-need-to-know

    If you looked at the certificates issued with the test, there's a bell curve of diversity; the relative positions of two (or more) JAs on the curve wouldn't change. If you look for a breeding partner with more genetic diversity between two JAs, compare their certificates to see their relative positions. Those positions wouldn't change if JAs were separated out. To use the allele chart on the certificates, look for dogs with more alleles or different ones. That again won't change if JAs are separated out.


  • Sorry, forgot to get article in above.
  • If you want to have a JA database, post the certificates online. For a more private one, remove the identifier (reg number, I think) and have one person in charge of it.
  • Actually, the bell curve or relatedness would change if just a subpopulation, the JA, are being calculated. It's why UC Davis also mentions in the original link,

    "This data will be updated as more dogs are tested, so allele and DLA haplotype frequencies may change to a limited extent over time." Conversely, it will change when results are deleted if you were to remove the AA.

  • Why wd that change the relative positions of two dogs? Also, they've looked at Akita alleles in several projects already so not a big chance of many new alleles.

    I can ask if, when they have a good number of samples, well past the research stage, if they could separate JAs or UKC JAs. Would JACA or ?? pay for the extra work if they could do it?
  • aykayk
    edited May 2015
    I'll give a simplified example that demonstrates how things would change if the sample population is different.

    Say for one loci there are 4 alleles.

    In a previous research paper where they blended AA and JA results, they found 100, 200, 300, and 400 for alleles. Say in equal parts.

    But if they had not blended the AA and JA, the distribution would reveal something else.

    ie. in the AA
    100 = 49% of the population
    200 = 49 % of the population
    300 = 1% of the population
    400 = 1% of the population

    in the JA,
    100 = 1% of the population
    200 = 1 % of the population
    300 = 49% of the population
    400 = 49% of the population.


    If a dog is located in a country where the breeds are split, you * should* get two different diversity ratings. An AA with allele of 300 would be very valuable with respect to the rest of the AA population. A JA with an allele of 300 would not be very diverse with respect to the rest of the JA population. But compared against the blended bell curve, you wouldn't know where you stand.



    With respect to who would do the statistics of the JA population, it can be calculated outside of UC Davis. As long as the raw data is provided (ie. dog's registration # which can be cross-checked against breed and DNA results), a volunteer can do the calculations. Calculations are not propriertary.


  • I don't know if they'd provide the raw data. How does what you wrote affect comparing one dog to another?
  • aykayk
    edited May 2015
    Under your blended bellcurve, a AA that has the rarer alleles 300/400 is of the same worth as a dog that has the overly represented alleles of 100/200.

    This blended scheme doesn't give a direction on how to proceed in order to preserve the rarer alleles. The population of rarer alleles can easily disappear through genetic drift - which is bad.
  • I don't see how the bellcurve affects the listing of the alleles. If the important thing to you is to preserve particular alleles, wouldn't you look at the listing of alleles and pick two dogs that had those rarer alleles? I'll wait til I get an answer from VGL; it feels like we're talking about "apples and oranges."

    Poodle people, who have a much more organized approach to health than Akita people, have a great slideshow that explains more about the test in regard to their breed, but a lot of it is general useful information: http://poodlesdegrenier.com/geneticspresentation
  • Chapter 3 of the poodle slides states how the IR value is calculated.


    "The IR Value takes into consideration not only how many pairs of genes a dog has that are the same or different, but also how common those genes are, and how many different possible genes have been found at that locus in all dogs."
  • If this really is the best chance at reducing the risk of autoimmune issues then the group running this needs to be willing to separate the Akita by breed. It's easy just take a pedigree and see if it falls under one of these three conditions:

    (a) all ancestors in a three-generation pedigree are registered with the Japanese Kennel Club and/or Akita Inu Hozonkai(AKIHO) as a Japanese Akita or trace all their ancestry back to such dogs OR (b) all ancestors in a three-generation pedigree were registered as a Japanese Akita within a registry created by an FCI Kennel Club since their recognition in October 1998 , the Kennel Club (UK) since 2006, the United Kennel Club since 2012, OR (c) it has a three-generation pedigree which is a combination of the above, provided all eight great-grandparents are either as specified in (a) or (b).

    Sure some data would be off as blends would not follow under these criteria and thus would land as American Akita. Of course the few blends that are registered as Akita Inu would throw it off the other way(example would be the one you helped export to Finland). But over all this would encourage US JA owners to participate.

    Ann, thank you for explaining all of this. I have a hard time wrapping my head around all of this and your replies hell put them into context. I find the idea of genetic tests to be a appealing but I struggle with the analysis part.



  • Why does it matter to separate the two breeds? The same reason breed matters at all in the testing. If breed wasn't relevant, then it wouldn't be limited to Akitas, or Poodles, or Greyhiunds, etc.
  • I won't write more about the test here. It's there if you want to use it; they won't be separating, looking at pedigrees, giving out raw data. Both types/breeds were one historically and still are in the AKC, so looking at both would show which haplotypes were lost in each. If you read the descriptions, two types of Poodles were tested under Poodle and show in different AKC classes; European IGs were different enough from US IGs to be almost another breed. That didn't invalidate the test. JAs have one of the highest rates of autoimmune diseases and this test is the best way now to try to get a better functioning immune system. If you want a UKC JA test, you can set it up and pay for it yourselves. If you're referring to me above, I didn't help anyone export a dog to Finland.
  • I don't think you fully understand how you'll be wrecking the potential good that this research could give by not acknowledging that the AA and JA are currently separate populations.

    I do understand that you are coming from the AKC Akita outlook and there is a remote possibility that someone may import a JA and register it as AA, but that is a tiny trickle compare to the majority who would stay within their own types/breeds. I understand that you're convinced that people will change and in hindsight appreciate your pro-blend work, but for me, I'd rather educate people on diversity within the separated breeds. I see that as more international and more apt to encourage participation.
  • edited May 2015
    Until I get an answer, I can say the purpose of the test is to choose breeding partners that give the best chance of an efficient immune system.
    As an AKIHO member I will only be breeding to AKIHO member owned JA. AA and tweenies are outside the the breeding partners allowed for us anyways. So if it's no breed split, there is no incentive for me to participate.
  • Sorry to butt in but I think this needs to be said. The way you split the breed shouldn't be an issue here. This isn't a matter of American vs Japanese but one of breeding populations. 99 times out of 100 you won't find an AKC registered Akita being bred to an Akiho Akita. For the most parts they are separate and the gene pools don't mix. This will ruin the study if you include dogs from two different breeding populations and then draw conclusions for one population on a mixed set of data as it won't apply to either and is therefor, worthless.
    Don't misunderstand I'm not saying "they are two different breeds and need to be separated" I'm trying to be objective. If you consider them different, that's wonderful and many think so to. If you consider them the same, that's fantastic and many agree with you. But you can't draw conclusions for inaccurate data and that will happen here if you aren't careful. If AAs that aren't regularly being bred to JAs are included and you draw conclusions for JAs then the conclusions are inherently incorrect as they aren't an accurate representation. If JAs that aren't regularly being bred to AAs are included and you draw conclusions for AAs then the conclusions are inherently incorrect as they aren't an accurate representation. If a dog from Japan Akiho registered and by all accounts is a JA is being bred to an AKC fullblodded american regularly and it's pups are entering the gene pool, and you want to drew conclusions for the American gene pool, include it! That dog is an important part of the study and contributes to the population your drawing conclusions from. Otherwise the populations need to be separated for the good of BOTH!
    At the end of the day the health of the dogs is all that matters and politics or preferences shouldn't end this study as it will be priceless to the health of this breed, no matter how you divide it.
  • edited May 2015
    I wasn't going to reply more but Dr Pedersen had a response to what ayk wrote. He says,

    "I have no idea what the concern is about. Without actually testing a number of American
    and Japanese Akitas, this is all just theoretical. The two breeds may be
    very different, or at the extreme, exactly the same. Perhaps this person
    should study the Standard Poodle, Italian Greyhound and Alaskan Klee Kai
    links on the VGL website. The Standard Poodle is genetically diverse but
    diversity is out of balance. Also, there is no difference in Standard
    Poodles across the world. The IGs are also diverse, but out of balance.
    Interestingly, the European and USA dogs are genetically distinct, almost
    to the point of being two different breeds. Are the Akitas like IGs? The
    AKK are another story, because they started with a few founders and they
    seriously lack genetic diversity. Are Akitas like AKK? This should give
    her a better idea of what is being tested and how genetic diversity is
    determined. What do these breeders have to lose by having their dogs
    tested? They will be given all of the information on each dog and if they
    want to study the information on their own, that is ok. At the least, they
    will have some good background information to make sense of their data."

    As I said, JACA/UKC JA people will have the results on each individual dog entered, identified by registration number. These data can be collected and studied for just these JAs. rikumom doesn't understand the principle of the test; it has nothing to do with what she thinks it's about. ayk, I don't understand what you mean: you can educate people about diversity within a breed even if I don't mind blends.

    I dislike the paranoia I've encountered in this forum. I have no "agenda" other than wanting healthier Akitas of any breed/type. I've been interested and involved in Akita health since 1990, shortly after I got my first Akita. I've been interested in genetic diversity since my veterinarian introduced me to Dr Pedersen in 1995. I've contributed to and taken part in many Akita health-related studies but gradually came to see research for gene tests for diseases and research for disease cures as band-aid approaches. I'd rather see emphasis on genetic diversity for the future of this breed (or any breed). I see a growing turning away from the purebred concept: "A closed stud book puts an expiration date on a breed." Just because my outlook may seem extreme, it doesn't mean there's no value in the test. I wish I could explain it better.

    I'd just like to see an end to the suffering of dogs with autoimmune diseases and the suffering of their owners. I've had 25 or so Akitas and none have had autoimmune diseases, probably because they were almost all rescues from "backyard breeders" with more genetic diversity than inbred show dogs.
  • edited May 2015
    The study is for a breed of dog, to learn something about that breed. Including dogs of another breed muddies the data and makes the study useless. You wouldn't include a Husky in the AKK study (same root stock - and only ~25 years apart instead of 60). Including non-AAs in a study about AAs is exactly the same.
  • The goal for the is to help combat Autoimmune disorders right? So if splitting the samples leads to more participation how on earth could someone be against that?







  • Very informative and interesting discussion. The linked slide show was great and helped me get my head around all the conflicts that cross one's mind like when reading A. Akita books by authors such as Andrews, Killilea (especially), Bouyet, etc... lots of pro line-breeding and setting "type" advocation, which flies in the face of the dog's smell test shown in the slides fascinatingly directly linked to pheromones (human subjects have performed the same way w/ women smelling sweaty t-shirts of unseen males, they prefer scents out of their own gene code as more "pleasant" smells) - all sex related stuff as most of life evolved into opposite partner sex for reproduction for... well, for better "armed" offspring to fight disease, parasites, etc. Suffice to say, very mixed messages when reading about beloved Akita breeding (uhh "inbreeding").

    So, am I wrong to guess that JA's likely have less genetic diversity the AA's? After all, as I reread parts of "Dog Man", Morie Sawataish was breeding AA looking dogs the vast majority of his life (one could loosely argue the breed look of AA has been around at least 200 years, granted along w/ other versions of "Akita" - floppy eared etc,). The less stout and leggy, very oriental eye and thick coat but limited acceptable colors and markings of the modern JA, according him, didn't really get started until the 80's and 90's. Ironically (to me anyway), he accused the look of being the latest Akita taste in Japan(and predicted that too would change as well, as fashion does? Morie had seen a lot of changes after all), not a sentimental recapturing of the "pure" Japanese dogs of his distant historic youth.
  • Dogs are now being chosen for free participation in UC Davis's Vet Genetics Lab Genetic Diversity Test. Pedigree research from the database in Akita Inu Pedigree is being used to try to find as unrelated Japanese Akitas as possible. Preliminary work with samples from American Akitas shows the breed to be much more inbred that was thought. For directions on how to participate, see http://www.akita-unleashed.info/2015/07/08/diversity-test-for-akitas/
  • I am wondering if a DNA test could even tell the difference between a JA and an AA? I am not sure if DNA test are accurate enough to recognize the difference under the scope. But I do see how mixing the two populations might mess the accuracy of the test. But I don't claim to know anything about this. I think when I was reading about the AKC DNA test that they require before you breed. They can't tell the precise breed. Just that it it's 75% or above in matching DNA that it's likely a purebred, and UKC says they go off of the pedigree of reciprocal registries. Because DNA is not accurate enough. I might be all mixed up Cuz I am kinda new to this.
  • Yes, it can, and has in the past.
  • edited November 2015
    Saw this in a FB group I'm in and was wondering if someone could explain the results in layman terms? https://www.vgl.ucdavis.edu/services/dog/GeneticDiversityInAkitas.php
  • edited November 2015
    @akitarise
    AA, JA and blend were tested. The point of the test was to tell how closely related the Akitas tested were to each other (not exactly that but that's the basic idea/ genetic diversity). Dogs were labeled as either JA, AA, or blend. The number of dogs tested is small so only general results could be made. Two panels testing 33 and 58 different genetic factors were done, the results were basically the same even though the number of factors tested to see a difference was changed.

    They found that the JA has alleles (genetic information that lead to real life physical traits) that the AA does not have and that the AA has alleles the JA does not have. This means that they each have unique genetic information the other does not have. Blends in this study shared more genetic similarities with AAs than JAs.

    If any one else has anything else to add or clarify feel free, I'm not an expert by any means:)!
  • @Vulpesvulpes89 Seems pretty good.

    I will add that since most blends are not actually 1/2 but many are 1/4 or 1/8 JA (and 3/4 or 7/8 AA) it makes sense that they favored the AA genetics.
  • Thank you Vulpesvulpes89.
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