Genetic Diversity Testing for Akitas
(Phase 2 - Preliminary Results)
The Veterinary Genetics Laboratory (VGL), in collaboration with Dr. Niels C. Pedersen and staff, has developed a panel of short tandem repeat (STR) markers that will determine genetic diversity across the genome and in the Dog Leukocyte Antigen (DLA) class I and II regions. This test panel will be useful to breeders who wish to track and increase genetic diversity of their breed as a long term goal.
Genetic diversity testing of Akitas is nearing completion and we feel that almost all of the existing alleles at the 33 STR loci and DLA class I and II regions have been identified. Any new alleles or haplotypes are likely to occur at very low frequency. We will continue to add new alleles and haplotypes when they are found and to adjust frequencies if necessary. We have confirmed that Akitas exist as two varieties, Japanese (AKJ) and American (AKA). Blends involving crossing between varieties also have been identified and genetically characterized as intermediate. We have now tested 343 dogs from all three of these groups (81 AKA, 197 AKJ and 21 Blends), and the results of our preliminary genetic diversity testing have been updated.
Price: $50 (see below for free testing option)
YOUR DOG MAY QUALIFY FOR A FREE DIVERSITY TEST!
The Akita Club of America donated $2500 that will be used to test Akitas affected with sebaceous adenitis (SA) and Vogt-Koyanagi-Harada disease (VKH)! This is open for all types of Akitas. The goal is to collect samples from 50 SA and VKH Akitas for research under Dr. N.C. Pedersen. The purpose of the research is to see possible genetic connections or risk factors in diseased dogs by comparing their samples to those from healthy Akitas.
If you have any type of Akita dog who has one of these diseases and if you would like to participate in this study, the $50 fee is waived and some additional enrollment information is required.
To see if your dog qualifies for enrollment please email:
Saija Tenhunen firstname.lastname@example.org
If you have already submitted a diversity test for your Akita with one of these diseases, your dog is still valuable to the ongoing Akita research. We will need additional information for enrollment that will take a few moments of your time. If you are willing to have your previously submitted sample used in this project, please contact Saija Tenhunen, email@example.com
ORDER TEST KITS
Allow 5-10 business days for results.
Results reported as:
Short tandem repeat (STR) loci: A total of 33 STR loci from across the genome were used to gauge genetic diversity within an individual and across the breed. The alleles inherited from each parent are displayed graphically to highlight heterozygosity, and breed-wide allele frequency is provided.
DLA haplotypes: STR loci linked to the DLA class I and II genes were used to identify genetic differences in regions regulating immune responses and self/non-self recognition. Problems with self/non-self recognition, along with non-genetic factors in the environment, are responsible for autoimmune disease.
Internal Relatedness: The IR value is a measure of genetic diversity within an individual that takes into consideration both heterozygosity of alleles at each STR loci and their relative frequency in the population. Therefore, IR values heterozygosity over homozygosity and uncommon alleles over common alleles. IR values are unique to each dog and cannot be compared between dogs. Two dogs may have identical IR values but with very different genetic makeups.
The Akita originated from the high regions of Northern Japan (Honshu Island.) Through the last 70 years, they have become separated by breeding, and somewhat by geography, into two breeds or varieties. Both “breeds” originated from the same founder population. During WWII, on the brink of extinction, many Akitas were mixed with other breeds in an effort to save them from government ordered culling in Japan. The American Akita started post war with 166 dogs of all types/colors registered with the Akita Club by 1966. When the stud book was turned over to AKC in 1972, 1,865 Akitas were registered as foundation stock. Akitas continued to be imported and registered with AKC until 1974, at which time the stud book closed to new imports (reopening in 1992). Meanwhile in Japan, after being declared a Japanese Natural Monument in 1931, organized efforts were undertaken, through selective lines, to preserve/restore the Akita to its original breed standard (allowing only three colors of origin). Some of these lines are retained in American Akitas, in the US, Europe and Oceanian countries. Due to American and Japanese Akita breeders pursuing differing standards, the country of origin requested the FCI (Federation Cynologique Internationale) to split the breed, (effective within FCI June 1999.) In the US and Canada, within AKC (American Kennel Club) and CKC (Canadian Kennel Club) the differences are considered two varieties of the same breed. Some favor blending the two types, others vehemently oppose.The genetic information used to formulate the enclosed tables and graphs came from DNA samples of 343 Akitas from around the world and include American Akitas (AKA) (n=81), Japanese Akitas (AKJ) (n=197) and what are known as “blends” (n=19+2=21). Two of the 343 dogs were not identified by variety, but were later determined to be blends. We believe that the dogs currently tested are reasonable representations of the genetic relationships and diversity that still exist in these varieties, although more AKA need to be tested.
The Canine Genetic Diversity Test and What It Tells Us
A. Population genetics based on 33 STR loci on 25 chromosomes or 58 STRs on 39 chromosomes
STR markers are highly polymorphic and have great power to determine genetic differences among individuals and breeds. The routine test panel contains 33 STRs that are recommended for universal parentage determination for domestic dogs by the International Society of Animal Genetics (ISAG) with additional markers developed by the VGL for forensic purposes.The diversity of alleles at each of the genomic STR loci and their frequency in the population were used to determine the genetic relatedness and diversity of American Akitas (AKA), Japanese Akitas (AKJ), and Akita blends (AK) from around the world. Allele frequencies differ somewhat between AKA and AKJ and there are some alleles that are specific for AKA or AKJ (Table 1). However, these tend to occur at low frequency and it is possible that they will be found in both breeds if a larger number of AKA or AKJ are tested. Allele frequencies indicate that the Akita blends tested are truly mixtures of AKA and AKJ, but more closely related to AKA than AKJ.
B. Differences in population structure as determined by principal coordinate analysis (PCoA)
The data obtained from genomic STRs were used to determine the relatedness of AKA and AKJ to each other based on principal coordinate analysis (PCoA) (Fig. 1). PCoA uses genetic distance based on allele sharing to demonstrate genetic differentiation between individuals in related or unrelated populations. An optimized two dimensional graph portrays the degree of genetic differentiation between individuals and the more distant two points (dogs) are from each other the greater the genetic differences and vice versa. This analysis showed that AKA and AKJ were genetically distinct varieties and no registered AKJ segregates with AKAs and no AKA with AKJ. One AKA appears to segregate with AKJ and two AKJ with AKA, which indicates errors in registration or classification rather than interrelatedness. Akitas referred to as "blends" by their owners tend to differentiate more with AKA than AKJ, although some are obviously intermediate between AKA and AKJ, indicating that they are true crosses. Only four Akita blends clearly segregate with AKJ and two dogs of unknown classification (AKU) appear to be blends, although one dog is more closely related to AKJ and another to AKA.
Fig. 1. Top- PCoA of 343 Akitas from four different populations – Akita blends (AK), American Akitas (AKA), Japanese Akitas (AKJ) and Akitas of unknown variety (AKU)
C. Assessment of population genetics using standard measurements
1. Genetic assessment of the population as a whole using genomic STR allele frequencies
The allele frequency data obtained from the 33 STR panel can also be used for a standard genetic assessment based on heterozygosity (Table 2). Using the 33 marker panel and 301/343 dogs, the AKA have an average of 6.33 alleles/loci (Na), while the AKJ had 5.94 alleles/loci. The blends had an average of 4.94 alleles/locus. AKA have an average of 3.018 effective alleles/loci, while the AKJ had only 2.410 and blends 2.87. Effective alleles are the proportion of alleles that contribute to most of the heterozygosity. Therefore, AKJ have a smaller genetic base than AKA, possibly from a smaller number of founders. Blends would be expected to have more alleles per locus and higher effective alleles than either AKA or AKJ. However, the number of dogs is small and these values are likely to increase as more blends are tested.
The observed heterozygosity (Ho) and expected heterozygosity (He) can be used to calculate a value (F) that is an estimate of the level of inbreeding in a population. An F value of 0 indicates that the population is in Hardy-Weinberg equilibrium (HWE), i.e. mate selection is totally random. A positive F value means that there is a subpopulation of dogs that are more inbred than the population as a whole, and the higher the value of F, the greater the size of this inbred population. Interestingly, even though AKA are somewhat more genetically diverse based on Na and Ne than the AKJ, the F value for the AKA is positive (0.034), while the F value for the AKJ is lower at 0.008. The Ho for Akita blends is close to that of AKA (0.591 vs. 0.594). The AKJ have the lowest Ho (0.543). The index of inbreeding F is highest for AKA (0.044) and lowest for AKJ (0.008). These F values indicate that there is a larger subpopulation of inbred dogs among AKA than AKJ, while as might be expected, the blends are intermediate (0.029).
Table 2. F-Statistics of Akitas (n=301) using 33 STR loci on 25 chromosomes
2. Genetic assessment of allele and allele frequencies at each genomic STR locus
D. Genetic assessment of individuals within a population using internal relatedness (IR)
The Na, Ne, Ho, He and F values apply mainly to the population as a whole and not to individual dogs within the population. The genetic diversity of an individual depends not only on the alleles present at each locus, but also on how common or rare each of the two possible alleles is in the population. The commonness or rarity of the two possible alleles at each STR loci can be used to calculate what is called "internal relatedness" or IR. The IR values of a population can then be used to construct a graph with values ranging from -1 to +1. An IR of -1 indicates that the parents of that dog are totally unrelated, while an IR score of +1 indicates that the parents are genetically identical. The average IR scores of puppies born to full-sibling parents from a random breeding population would be +0.25. The comparison graphs of IR scores for AKA and AKJ provide a great deal of additional information about how individuals in the population are related to their parents.
The median IR value for AKA population is +0.074 (Table 3; Fig. 2), but with individuals scoring as low as -0.270 (most outbred) and as high as +0.383 (most inbred). One half of the population had IR scores of +0.074 to +0.383 and one fourth between+ 0.159 and +0.383. An IR of +0.25 would be the average score for a litter of puppies born to full siblings from a random breeding population.
Fig. 2: Distribution of IR estimates in 81 AKA based on intra-breed diversity (Red line), compared with IR adjusted for diversity lost during breed development (Blue line). Diversity lost as a result of breed development was determined by comparing allele frequencies at the same loci between AKA and randomly breeding village dogs from the Middle East, SE Asia, and the Pacific Islands.
IR scores for AKJ are given in Fig. 3 and Table 3. The least inbred dog scored -0.394 and the most inbred dog 0.470. One half of the dogs have IR scores from +0.017 to +0.472 and one fourth have scores from +0.100 to +0.472. However, the IR peak is actually bimodal, suggesting that there are actually two populations within one. It can be concluded that the AKJ population contains more inbred dogs than the AKA. It is also visually apparent by the degree of overlap between IR and IRVD curves (Figs. 2, 3) that AKJ have less genetic diversity than AKA, i.e., the parents of AKJ are more related to each other than the parents of AKA.
Fig. 3: Distribution of IR estimates in 197 AKJ based on intra-breed diversity (Red line), compared with IR adjusted for diversity lost during breed development (Blue line). Diversity lost as a result of breed development was determined by comparing allele frequencies at the same loci between AKA and randomly breeding village dogs from the Middle East, SE Asia, and the Pacific Islands.
Table 3: Statistical parameters used to interpret IR and IRVD curves for Akita varieties
E. Estimation of genetic diversity lost during breed creation using village dogs as a gold standard
The IR values can also be used to give an approximation of how much genetic diversity has been lost during breed development and subsequent evolution. This is done by comparing the frequency of a given allele in an Akita variety with the frequency of that allele in a population of village dogs from the Middle East, SE Asia, Taiwan and other Pacific island nations such as Brunei and the Philippines. Contemporary village dogs are largely unchanged from the ancestors of almost all modern dog breeds. This adjusted value is known as the IR-Village Dogs or IRVD.
Adjustment of the IR values for diversity lost, using village dogs as the gold standard (blue curve), caused a marked shift of the curve to the right in the AKA (Fig. 2). The median IRVD value was +0.268, with a range of -0.077 to +0.468. This means that the average AKA is about as closely related as offspring of full sibling village dog parents, providing that the parents of the sibling pair were random members of the village dog population. IRVD values progressively greater than +0.25 would mean that the parents of the sibling pair were also increasingly more related than dogs from a large, genetically diverse, random breeding population.
The graph of IRVD values for the AKJ shows an even greater shift to the right than for the AKA, with the median value for the population being 0.301 with individuals ranging from -0.023 to +0.625 (Fig. 3). This is another indication that AKJ have lost more genetic diversity than AKAs.
F. Population genetics based on STR-associated DLA class I and II haplotypes
In addition to the markers used to estimate relatedness, which reflect genome-wide diversity, a set of STRs associated with specific genes in the DLA region (the canine Major Histocompatibility Complex) was identified and used to measure genetic diversity associated with immune function (see sidebar).
The DLA consists of four gene rich regions making up a small part of canine chromosome 12. Two of these regions contain genes that help regulate normal cell- (Class I) and antibody-mediated (Class II) immunity. Polymorphisms in these regions have also been associated with abnormal immune responses responsible for autoimmune diseases. The Class I region contains several genes, but only one, DLA-88, is highly polymorphic (with many allelic forms) and is therefore most important for immune regulation. Specific alleles at the four STR loci associated with the DLA88 are linked together in various combinations, forming specific haplotypes (Table 5). Groups of genes and their alleles that are inherited as a block, rather than singly, are called haplotypes. The class II region also contains several genes, three of which are highly polymorphic, DLA-DRB1, DLA-DQB1 and DLA-DQA1. Specific alleles at STR loci associated with each of the three Class II genes are strongly linked and also inherited as a single block or haplotype (Table 6). One haplotype comes from each of the parents. The linkages between alleles within Class I or II regions are very strong; while linkages between regions of the DLA that are more distant from each other, such as Class I and II, are weaker. There are almost two million base pairs separating the class I and II regions, thus allowing for some genetic recombination to occur. This recombination is most apparent between the common DLA class I and II haplotypes, forming unique "extended DLA class I-II haplotypes. Extended class I-II haplotypes are inherited as a single block of genes.
The STR-based haplotype nomenclature used in this breed diversity analysis is based on numerical ranking with the first haplotypes being identified (in Standard Poodles) being named 1001, 1002, … for DLA class I haplotypes and 2001, 2002, … for DLA class II haplotypes. It is not unusual for various dog breeds to share common and even rare haplotypes, depending on common ancestry. Haplotypes with lower numbers have been recognized in other breeds, while higher numbers are more apt to be more breed specific. The numerical nomenclature used by VGL for DLA class I and II haplotypes does not correlate with numerical rankings used by others.
Each dog has two DLA class I and two DLA class II haplotypes, one inherited from each parent. There are more than 150 known class I and nearly 100 known class II haplotypes among all dogs, but as a result of genetic bottlenecks involved in breed development, most breeds will only end up with a small portion of these haplotypes. AKA possess 11 different class I and 10 different class II haplotypes, while AKJ have 10 class I and 9 class II haplotypes (Table 3), indicating that both varieties came from a similar number of founders. Six of 11 class I haplotypes in AKA and 5 of 10 class II haplotypes are shared between the two varieties. AKA have 6 unique DLA class I haplotypes and AKJ have five, while AKA have five unique DLA class II haplotypes and AKJ also have five. This suggests that about one-half of founders for AKA and AKJ came from related lines, while the other half were from different lines.
AKA and AKJ tend to share the same major haplotypes, such as 1029, 1081, 2037 and 2056. However, relative frequencies of these haplotypes vary between AKA and AKJ, with 1029 occurring 16.4% vs 27.8%, 1081 40.3% vs 15.3%, 2037 16.4% vs 27.6%, and 2056 59% vs 16.6% in respective varieties (Table 3). Three DLA class I haplotypes in AKA (1029, 1081 and 1082) and four in AKJ (1029, 1061, 1081 and 1092) were found in 75.4% and 89.2% of each respective variety. Two DLA class II haplotypes in AKA (2037, 2056) and four in AKJ (2035, 2037, 2056, and 2057) were found in 75.4% and 89.8% of the respective variety. The major class I and II markers in AKJ were present at similar frequency, while 1081 (40.3%) and 2056 (59.0%) were much higher than other major haplotypes. The haplotype and haplotype frequencies of Akita blends were more closely related to AKA than to AKJ (Table 3).
DLA haplotypes and haplotype frequencies were unbalanced in both varieties, suggesting either that dogs with certain haplotypes were being positively selected or that these haplotypes go back to the creation of the breed and subsequently reverted to a state of random selection. The answer was provided by doing a standard type genetic assessment of allele frequencies of the seven STR loci that were associated with the various DLA class I and II haplotypes (Table 3).
Table 3: DLA class I and II haplotype and their frequencies in different Akita populations
|DLA Class I Haplotype Frequencies (Updated Mar 17, 2017)|
|American Akita (n=71)||Japanese Akita (n=242)||Blend Akita (n=16)||Unknown Akita (n=3)|
|1006||387 375 293 180||0.049||--||--||--|
|1014||375 373 287 178||--||--||--||0.2|
|1029||380 365 281 182||0.176||0.281||0.16||0.3|
|1040||380 371 277 186||0.014||--||--||--|
|1045||376 371 277 186||0.007||--||--||--|
|1061||380 365 281 183||0.042||0.180||0.06||--|
|1067||376 373 277 178||0.014||0.006||--||--|
|1081||395 379 289 178||0.394||0.149||0.38||0.2|
|1082||390 373 277 184||0.197||0.019||0.06||0.2|
|1083||395 375 277 186||0.092||0.081||0.28||0.2|
|1087||380 371 277 178||0.007||--||--||--|
|1092||376 379 277 181||--||0.275||0.03||--|
|1094||386 369 289 176||0.007||--||--||--|
|1108||382 371 277 180||--||0.002||--||--|
|1114||380 373 287 183||--||0.002||--||--|
|1135||388 385 281 180||--||0.004||0.03||--|
|1149||395 377 277 186||--||0.002||--||--|
|DLA Class II Haplotype Frequencies (Updated Mar 17, 2017)|
|American Akita (n=71)||Japanese Akita (n=242)||Blend Akita (n=16)||Unknown Akita (n=3)|
|2007||351 327 280||0.049||--||--||--|
|2012||345 322 280||--||0.002||--||--|
|2017||343 322 280||0.014||0.006||--||--|
|2033||339 323 282||0.007||--||--||--|
|2035||341 323 280||--||0.275||0.03||--|
|2036||341 327 276||--||0.004||--||--|
|2037||341 327 280||0.176||0.277||0.16||0.3|
|2039||345 327 276||0.092||0.087||0.31||0.2|
|2056||339 323 286||0.592||0.167||0.44||0.3|
|2057||341 327 286||0.042||0.176||0.06||--|
|2058||345 323 288||0.014||--||--||--|
|2060||343 323 284||0.007||--||--||--|
|2061||341 327 296||--||0.004||--||--|
|2062||345 327 282||--||--||--||0.2|
|2063||345 327 286||0.007||--||--||--|
|2069||349 322 280||--||0.002||--||--|
AKA have a higher average number of alleles per DLA class I or II STR loci (5.29) than AKJ (5.00). The number of effective alleles was also slightly higher for AKA than AKJ (2.79 vs 2.64). Observed heterozygosity (Ho) was the same for AKA and AKJ, but expected heterozygosity (He) was higher than Ho for AKA than for AKJ. This resulted in an inbreeding index (F) of 0.092 for AKA and 0.039 for AKJ. Therefore, the data indicate that the major DLA class I and II haplotypes were under a degree of positive selection, more so for AKA than AKJ. The F value for blends (0.171) was even higher and indicates that blends were often products of parents that shared these same major haplotypes (Tables 3, 4)
Table 4: Genetic assessment of Akita (n=286) using the 7 STRs in the DLA region
Certificates Providing Genetic Information on Individual Dogs
After a sample is submitted for genetic testing, the identity of the dog and owner will be replaced by a laboratory barcode identifier. This identifier will be used for all subsequent activities. After testing, each owner will be provided with a certificate that reports the internal relatedness, genomic STR genotypes and DLA class I and II haplotypes for the dog(s) tested. The internal relatedness value for the dog being tested is related to the population as a whole.
Genetic Goals for Breeders
The goal for Akita breeders should be to produce a greater and greater proportion of puppies with IR scores less than 0, and with time even lower scores. This can be achieved by selecting parents that are as different as possible in their genomic STR alleles and allele frequencies. It is also important to rebalance diversity within the DLA region, especially for AKA. Even though genetic diversity is limited, it is nonetheless important to properly manage the diversity that exists. Maintaining existing diversity will require using different combinations of breeding stock, including even those from inbred lines with high IR values. IR values, because they reflect the unique genetics of each individual, cannot be used as the criteria for selecting ideal mates. A breeding pair with identical IR values can have genetically distinct parents and produce puppies significantly more or less diverse than their parents. Conversely, a mating between dogs with high IR values, providing they are genetically different, may produce puppies having much lower IR scores than either parent. A mating between a dog with a high IR value and a low IR value, providing the latter is much different in genomic allele and allele frequencies and DLA haplotypes, will produce puppies much more diverse than the highly inbred parent. Breeders should also realize that a litter of puppies may have a wide range of IR values, depending on the comparative contributions of each of the parents as a result of genetic recombination. The more genetically diverse and different the parents, the greater the range of IR values in their offspring.
In brief, potential sires and dams should be first screened for genetic differences in the genome and in the DLA regions by first comparing allele differences at each STR locus, and then at the DLA class I and II haplotypes. Some thought should be given to rare vs common alleles. This information is included on all certificates and on the website. This preliminary comparison will identify promising pairings and if desired, genetic information on the potential sires and dams can then be used to calculate actual IR expectations for their puppies. Puppies, once born, should be tested for their actual IR values, which will reflect the actual genetic impact of each parent on internal diversity. Considerations of mate choices for genetic diversity should be balanced with other breeding goals, but improving genetic diversity in puppies should be paramount.
An additional goal of this study is to contribute this genetic information to a web repository, hopefully under the control of the registry. This information could be incorporated into a mate selection service that will allow a breeder to identify, among all of the dogs tested, potential mates that would be most ideal for increasing genetic diversity in their litters.
Heritable diseases problems of the Akita
Akitas suffer from a long list of disease conditions, most of which are heritable either as complex (polygenic) or Mendelian (usually simple recessive) traits. A list of diseases identified in Akitas can be found at: http://akitarescue.rescuegroups.org/info/file?file=s197m7036.pdf and at https://en.wikipedia.org/wiki/Akita_%28dog%29#Health. The largest number of heritable diseases on this list involves the immune system, either in the form of autoimmune disease or allergies. Autoimmune disorders include several skin disorders (sebaceous adenitis, pemphigus foliaceous, pemphigus vulgaris, uveodermatitis syndrome or VKH), autoimmune thrombocytopenia, autoimmune hemolytic anemia, Addison’s disease, thyroiditis/hypothyroidism, immune mediated polyarthritis and SLE or SLE-like syndromes, myasthenia gravis, and renal amyloidosis. Allergic conditions include atopic dermatitis. Simple Mendelian diseases include VonWillebrand’s disease, microphthalmia, glaucoma, progressive retinal atrophy, degenerative myelopathy, oligodontia and enamel hypoplasia. Complex genetic traits involving the skeleton include hip and elbow dysplasia, chondrodysplasia, osteochondritis dissecans, spondylosis, patellar luxation and dwarfism. Like many larger breeds of dogs, Akitas suffer a high incidence of specific cancers, usually tumors of connective tissue (sarcomas) such as hemangiosarcoma, undifferentiated sarcomas, malignant melanoma, osteosarcoma, or of the lymphoid system (lymphoma/lymphosarcoma). Cryptorchidism and umbilical hernias are commonly seen in puppies of breeds that are more highly inbred. Epilepsy is another complex genetic condition that appears to increase in frequency as a breed suffers more inbreeding. Bloat is a problem seen in many larger deep chested breeds.
A number of these health problems can prove rapidly fatal, but many are either tolerable or manageable with treatment. Therefore, the reported lifespan is 10-12 years. Although many of the health conditions of the breed are manageable, the cost of veterinary care and difficulties coping with managing treatment has led to many Akitas being euthanized or abandoned to shelters, where breed specific rescue groups may find them and try to place them in new homes. The fact that Akitas are long-lived leads some to conclude that the breed is genetically sound, when in fact it suffers more from heritable disorders than almost any other breed.
Except for a small number of unique genetic conditions, usually of a simple recessive nature, most of the heritable disorders of Akitas are ancestral in origin, i.e., the genetic risk factors have been in domestic dogs for a long time and many precede the Victorian era when pure breeding became a norm. The more inbred a breed becomes, the more simple and complex risk factors are concentrated and the more heritable disease problems occur. Pure breeding involves closing registries to new genetic diversity and inbreeding to fix certain phenotypic traits. Because of closed registries, pure breeds are susceptible to many different types of artificial genetic bottlenecks, including small founder populations, geographic isolation, catastrophes such as famines and war, popular sire and bloodline effects, changes in popularity and population size, etc. There is no doubt that both AKA and AKJ are quite inbred, although the conditions behind this inbreeding are somewhat different. AKJ most likely suffer from a small founder population, while AKA started with a larger genetic base. However, the AKA has suffered more from inadvertent or deliberate non-random mating with dogs having 1081 and 2056 class I/II haplotypes. This is most likely a result of a popular sire effect, but further research is required to make this determination. Further research is also required to see if there is an association between specific DLA haplotypes and autoimmune disease.
There is some wisdom in outcrossing between the two varieties, as each contains some unique DLA class I and II haplotypes and there are some differences in allele frequencies at the genomic level. Attempts should also be made to identify additional diversity by testing DNA from dogs across a wider geographic area as well as in long isolated pockets from the home or other countries. Additional genetic diversity may also be present in related breeds.
American and Japanese Akitas are two varieties of a single breed. The founding dogs for these two varieties were originally selected from a larger pool of dogs more than six decades ago. This parent population may still exist independent of modern registered Akita, but more likely as a collective of both American and Japanese dogs. Both breeds contain individuals that are much more inbred than the population as a whole. There is strong positive selection among AKA and blends for a specific DLA class I and II haplotype. This is suggestive of a popular sire effect, which can be confirmed by deep pedigree analysis.