DNA breed testing and kennel club breeds

Perhaps the first consideration when understanding DNA "breed" identification is just what a "breed" is.

Most breeds have only existed for the last couple of hundred years. They have come about by selecting dogs for a specific look, use, colour or nature etc. By definition this eliminates unwanted genetic features. It does not result in new genes being created. There are no single DNA markers that identify a particular breed. Kennel club breeds, with few exceptions, are closed groups of related dogs and dogs outside of that cannot be added. Embark can use the length of genetic segments a dog shares with their reference dogs to see how many generations it has been since they last shared an ancestor. Long segments of DNA that are identical to known purebred dogs tell Embark's scientists that the dog being tested has a relative from that breed. By testing over 200,000 genetic markers, they build up the dog being tested genes one DNA segment at a time, to learn the ancestry. Other dog DNA tests look at many fewer genetic markers and have to take a guess at breed ancestry based on that. Just what DNA is in a breed can differ in different countries since not every dog in a breed has been used for breeding in geographically separated countries and some DNA may have been lost in one country but not another. It is therefore reasonable for the testing company to know what country a pedigree dog is from. The DNA test in such cases will confirm that the dog does or does not have any other mix in it. Likewise, a dog of unknown origin will reasonably give information of the mix, or otherwise.  It is kennel clubs that decide and control what a breed makeup is and not DNA test companies. Likewise in a breed where an outside dog may be added, when that happens the DNA testing company will of course add that information to their DNA profile for that breed. 

When it comes to our ancient origin dogs much the same applies. It would be impossible to test every such dog in every country and dogs probably do not move between these countries as often as in the past when dog were first introduced to these countries. 

A recent comparison of some DNA test companies showed just how poorly some perform as linked below. The dog from Kuwait shows how many expats still fail to understand that free born dogs in the region are simply not mixes of the "breeds" they are familiar with. Embark remains the only company able to identify our village/desert/wadi/baladi dogs. 

How accurate are dog DNA tests? We unleash the truth | CBC News

Time for pedigree Canaan dog breeders to get serious about genetic health.

As one of the few kennel club breeds still open to new dogs being added it is vital to check such new additions for all known possible genetic health issues before breeding them. If breeders do not do that then they could be adding to the overall problems in the future which could then be difficult to remove. Some of these potential problems increase the chances of a dog developing problems but may not cause a problem in every dog even if it has both copies of the gene. Surely prevention is better than a cure but why take a chance? 

 Intervertebral Disc Disease (Type I)

This has rarely been found in Canaan dogs, but it is present. This is not yet recognized as a problem, and it may be that when it got into the breed testing was not available. Now we do know about it and is still not too late to track it down and eliminate it.  Type I Intervertebral Disc Disease (IVDD) is a back/spine issue that refers to a health condition affecting the discs that act as cushions between vertebrae. With Type I IVDD, affected dogs can have a disc event where it ruptures or herniates towards the spinal cord. This pressure on the spinal cord causes neurologic signs which can range from a wobbly gait to impairment of movement. Embark uses linkage testing for this so positive result should be checked using specific tests. If confirmed, then having a dog checked by a vet who finds no sign of this problem does not mean the DNA test is wrong. The issue mainly shows up in dogs with a long body and short legs, such as Dachshunds so again may not show up in dogs of other morphotypes.

Looking back at pedigree records this could have come from any of a number of dogs including, Ben Yarden Me Dlbaan Jimi, Pereh Me Nachal Yealem, Mocha Givat Har Adar, Keliv El Kashhar, Zahava El Kashar, V'Makole de Solemel, Lilo Me Shaar Hagai, Bayud Bedoui Me Tel Arad, U'nes Ha Bedouim de Solemel, Tihelah de Solemel, or Tofee Me Shaar Hagai. That is eleven dogs that could be the origin of this, some of which are probably no longer alive but could have passed this gene on to any number of offspring. So where to start? 

For the dog we know has both copies both parents, Noked Me Shaar Hagai and Angie od Dvou cedru,  must have carried at least one copy, so if breeders want to nip this in the bud they should ideally not be used for any further breeding and all their offspring, if intended to be used for breeding, tested with the aim of not breeding any positive dogs from these. Where did these 2 get it from? Potentially Or Ve-Tel Me Shaar Hagar and Toot Bar (at least one of which must carry it) and Chakede de Solemel and Chanyah de Solomel (at least one of which must carry it. Depending on results of testing these dogs breeders could then go further back to trace the potential presence of this gene in other ancestors and any of their pups intended for breeding. Complicated? Yes. A lot of work? Yes, but do breeders really want to ensure the Canaan breed does not end up with avoidable problems. 

This gene has not shown up yet in any of the "Arabian village dogs" (a small number of which were used to establish the Canaan breed) I have seen, but of course it and others are probably there in small numbers. It is essential that any new dogs brough into the Canaan breed, be fully tested before even being considered as additions. Breeders have the tools available today that Menzel did not have. Why not use them?

Notes on potential genetic health issues and Reference ranges.

 

Most of these are autosomal recessive so dogs need 2 copies of the variant to develop disease, one from each parent.

 

While figures are small, based on a total of 78 village dogs with publicly available health information.

Degenerative Myelopathy (DM) 15 carry 1 copy (19%) It is probably fair to assume there are desert dogs out there that are born with 2 copies even though none showed up in this group. Data of many “village dogs” tested do not show health figures in public profiles, either because only breed was tested or because that is the default set by Embark and has not been changed by owners. It is no surprise that with inbreeding of pedigree Canaan dogs that are derived from a small number of “village dogs” that DM has become a major issue in the breed. When the breed was established, no genetic testing was available.

Von Willebrand type 1 – 2 dogs (2.56%)

Factor VII – 1 dog (1.28%)

Collie Eye Anomaly, so called because it was first found in Collies but more accurately called Choroidal hypoplasia (75% of Collies, 80% of Stabyhoun and 71% of German spitz have this) – 2 related dogs (2.56%)

Bald thigh syndrome – 2 dogs (2.56%)

Lunderhund Syndrome (affects neuroendocrine cells in the intestinal tract causing stomach and intestinal problems) – 1 dog (1.28%)

 

 

ALT potential low normal 39 (50%) have 1 copy, 17 (21.8%) have 2 copies. This is not a health issue as such but may mean that a dog with this gene may have a reference range lower that test books state so could give results that seem to be in range but are somewhat raised for that dog.

Reference ranges for laboratory tests are often incorrectly called “normal ranges”.  These are typically defined as the range of values of the median 95% of the healthy population. It is possible that a given sample even from a healthy individual will show values slightly outside of the range for some tests. Other factors such as race (breed in the case of dogs), altitude, age, and sex etc. can also result in variation. People living at high altitudes will have higher levels of haemaglobin than those at sea level. Few laboratories establish reference ranges for the local healthy population. In one laboratory I worked in where the altitude was around 3500 meters up to a maximum 4000 we went to great lengths to establish local reference ranges. Sadly, some years later with staff changes, no one was aware of this and when doctors raised questions as to why the laboratory reference ranges in the computer were not those to be found in textbooks pathology staff at the time had no answer.

Among a small number of Canaan breed dogs at least 3 have the genes that increase the risk for Chondrodystrophy and Invertebrate disc disease developing, 1 has the gene predisposing it to having Urate crystals forming in the kidney and bladder stones. This does does mean they will have a problem but are at increased risk so need to be watched as time goes on.

Most village dogs that have homes are neutered but Canaan breeders need to be aware of the potential for genetic issues other than DM also being present in the breed, as well as the potential for adding some not yet present when new freeborn dogs are added. Better to test and eliminate all mutations before they become an issue later.