«Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats»

Anderson et al 2022

Heidi Anderson at WisdomPanel/MyCatDNA and her colleagues have just published the largest cat study to date on cats genetics. 11036 cats, 90 breeds/types, a total of 10419 pedigree cats, 617 cats housecats/non-pedigree were analyzed.

Here are some short impressions with excerpts from the paper, which can be found in full-text here.

Samples came from MyCatDNA and Optimal Selection Feline tests done between 2016 and 2021 (Wisdom Panel of Helsinki, Finland and Vancouver, WA, USA. The tested cats were from:

• USA (54.9%)
• Finland (17.4%)
• Canada (5.3%)
• United Kingdom (3.5%)
• Norway (3.5%)
• Sweden (3.3%)
• Russia (2.5%)
• France (1%)

«The maximum number of different disease-associated variants present in a single breed was 9; this was observed in the Maine Coon, which was the breed that was represented by the most individuals (N = 1971) tested in this dataset.» (p 9)

The cat fancy can learn a lot from the results. For instance it is clear that broad panel tests help breeders make good choices for combinations, without losing genetic variation in the breed. «For more than a decade, it has been common practice to eradicate disease-associated variants from pedigreed cat breeding populations using DNA testing. However, the focus on eradicating single DNA variants from a breed could contribute to severe loss of genetic diversity, especially if implemented strictly instead of thoughtfully.» (p 3)

«Our data indicate that known disease-associated variant frequencies are now lower for many conditions (GM2 and Hypokalemia in Burmese, Glycogen Storage Disease in Norwegian Forest Cats, HCM and Spinal Muscular Atrophy in Maine Coon, HCM in Ragdoll and PKD in Persian) compared to the frequencies at the time of their discovery, perhaps reflecting change over time within the breed, presumably due to genetic testing combined with informed breeding selection.» (p 22) The known HCM risk mutation for Maine Coon, HCM1-A31p was tested for all cats, and showed that only 169 cats had 1 copy, 9 cats had 2 copies. The SMA frequency showed that 13 cats had 1 copy, none with 2. This means that these two risk mutations are well under control and that very few cats today have them.

Diversity – Heterozygosity

Genetic diversity is essential for the overall health status of a breed. This is tested: «Genome-wide genetic diversity was measured as a percentage of heterozygous SNPs across a set of 7,815 informative SNPs.» (p 4)
«In the pedigreed cat population, the median heterozygosity was 34.0% and the typical range (defined as the 10th and 90th percentile) was 27.2%-38.3%, in the non-pedigreed population, the median heterozygosity was 38.8%; and the typical range was 29.8%-41.3% (Fig 2).» (p 19)

«The most diverse breeds include three of the newer cat breeds: the short-legged Munchkin, produced from a sibling mating followed by regular non-pedigreed cat outcrosses; the Highlander, a crossbreed of two recent experimental hybrid cat breeds, the Desert Lynx and Jungle Curl; and the Lykoi breed founded by unrelated cats expressing hypotrichosis, whose unique sparse and roaned coat phenotype may be caused by any of six different variants of the HR gene from six independent lineages found in four different states of the United States, Canada and France. The heterozygosity levels of the European Shorthair, Norwegian Forest Cat, Siberian, and Manx, which were developed from the local domestic populations that likely had a larger diversity in the founder population, were above average compared with the entire pedigreed cat population. The lowest median heterozygosity measures in any pedigreed cat population were observed in the Burmese, Birman, Havana Brown, Korat, Singapura and breeds of the Siamese group (such as Balinese, Siamese and Oriental Shorthair), in line with previous observations.» (p 20)

A list of median diversity for the most popular cat breeds in Norway:

• Neva Masquerade 38%
• Siberian 37%
• Norwegian Forest Cat 37%
• Selkirk Rex 37%
• British Shorthair 35%
• Maine Coon 34%
• Ragdoll 35%
• Average all cats 33,9%
• Exotic 33%
• Persian 33%
• Bengal 33%
• Somali 30%
• Abyssinian 28%
• Birman 25%
• Siamese 24%
• Oriental shorthair 24%
• Burmese 21%

AB Blood Type

Knowing a queen’s blood type is essential to avoid problems with her kittens. The test panel analyzes 4 different allels: «After determining the suitability of 2019 typing panel, we based genetic blood typing on the variants: c.268T>A, (b1); c.179G>T, (b2); c.364C>T, (c—resulting in blood type AB); and c.1322delT (b3). The variants b1, b2 and c were observed widely distributed across breeds with frequencies of 12.6%, 1.6% and 1.5% in all cats, respectively.» (p 9)

«Though generally uncommon in all cats, variant b2 was a major variant associated with blood type in the breeds Chartreux, Donskoy, Egyptian Mau, Minuet Longhair, Pixiebob, Siberian, Tennessee Rex, Tonkinese, Toybob, Turkish Angora and Turkish Van. Variant b3 was exclusively found in Ragdolls (16.9% allele frequency) and in a Ragdoll mix across the subset of 2,186 genotyped cats representing 69 breeds and varieties (S4 Table).» (p 9)

Blood type B was most common in: American Curl (40.4%), British Shorthair breed types (20.3%), Cornish Rex (33%), Devon Rex (30.3%) and Havana Brown (20%).

Maine Coon

A total of 1971 Maine Coons were tested, and 9 disease variants were found present in the breed. Here is an overview of what was found:

HCM1-A31p 0,8% 163 of the 1971 MCO. Poly MCO had 10 out of 150 cats with the mutation. It was also found in 1 Pixiebob, 1 Siberian, and 2 housecats. For comparison 3% of RAG had the HCM3-R820W variant, a total of 33 of 1115 tested RAG. «Two independent variants of the MYBPC3 gene c.91G>C p.(A31P) and c.2453C>T p. (R818W) (published as 2060C>T p.(R820W); coordinates updated to reference genome Fel-Cat9) have been associated with HCM in the Maine Coon and Ragdoll breeds, respectively.» (p 14)

PK-deficiency was found in 14,3% of MCO, 280 of 1955 tested MCO. For poly MCO the number was 20,2%, 30 of 150 tested cats. «PK-def shows a marked clinical variability, including variation in the age of disease onset and severity.» (p 13). Furthermore, «Our veterinarians interviewed owners of ten Maine Coons (including two Maine Coon Polydactyls) […]. All the Maine Coons were 3 years old or younger at the time of interview. In three out of ten cases owners reported occurrence of at least one mild potential episode with clinical signs such as lethargy, anorexia, weight loss, and/or jaundice (S7 Table). One male Maine Coon, at the age of 1 year and 5 months, become severely ill with anorexia, lethargy, and significant weight loss (down to approximately 8 lbs from 17 lbs), another male had had episodes of mild lethargy and hyporexia, and the one female cat may have potentially manifested mild symptoms directly after giving birth. […] Compared to the Abyssinian, all owner-reported episodes in the Maine Coon and Maine Coon Polydactyl are milder and should be considered preliminary results as they lack a complete blood count taken during the episode and PK-def diagnoses by a veterinarian.» (p 14)

The SMA mutation was found in 11 MCO, 1 poly MCO and 1 Highlander. All carriers, none affected. So this mutation is really rare, and we already know it occurs only in a few known lines.

Blood type analysis showed: 0,8 % had blood type B, b/b. No Maine Coons were found with blood type AB (c allele).

Some disorder mutations are discovered more recently:
Cystinuria Type B was found in 0,2%, 3 of the 1971 MCO.

Factor XII Deficiency was found in 9,9%, 195 of the 1971 MCO – it gives coagulation problems, but is not considered a very serious disorder.

MDR1 medication sensivity was discovered in 5,4%, 107 of the 1971 MCO. This gives sensibility to some medications. «Feline MDR1 Medication Sensitivity is a disorder associated with severe adverse reactions after exposure to medications that use the p-glycoprotein drug transporter. This genetic condition is caused by a two base pair deletion within exon 15 of the ABCB1 gene resulting in abnormal p-glycoprotein. While functional p-glycoprotein plays a significant part in the bloodbrain barrier that prevents various drugs and chemicals in the bloodstream from entering the brain, a defective p-glycoprotein allows more drugs to cross this barrier, thus increasing the neurological effects of some medications. […] Severe macrocyclic lactone-induced neurologic toxicosis has previously been reported in cats homozygous for the MDR1 variant receiving either a subcutaneously administered dose of ivermectin or a topically administered eprinomectincontaining antiparasitic product labeled for cats [59,60].» (p 16).

PKD1 was alarmingly found in 5 of 1966 tested MCO, making 0,5% positive! Breeders should try to identify the lines these are from. The mutation should be eradicated from Maine Coon.

PRA rcAc (CEP290) was found in 0,1%, 2 of 1971 MCO – these two cats were earlier shown as public results on the MyCatDNA website, and are F3-F4 cats after a known F1 PRA carrier. Hopefully all breeders with this particular F1 in their lines have all offspring tested to remove the PRA mutation from the breed.

The Birman Gloves mutation is recessive and found on the KIT gene. «Maine Coon, Ragdoll and Siberian breeds, in which they were not associated with Gloving based on photographic evidence and owner reports. Of the phenotyped individuals some white areas of hair were seen on the belly or toes in (3/17) Maine Coons and (1/2) Siberian cats. Our findings are supportive of a potential additional candidate locus that may play a role in the regulation of the Gloves phenotype» (p 18) This also supports the theory we have discsussed between Maine Coon breeders, that «gloves» or similar recessive KIT mutations are causative for lockets and small white spots in our breed.

Source

Anderson et al. 2022. “Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats”. Heidi Anderson , Stephen Davison, Katherine M. Lytle, Leena Honkanen, Jamie Freyer, Julia Mathlin, Kaisa Kyöstilä, Laura Inman, Annette Louviere, Rebecca Chodroff Foran, Oliver P. Forman, Hannes Lohi, Jonas Donner PLOS Published: June 16, 2022