#macska

Disclaimer: Sometimes I might not use the most common designations of a gene or an allele, and I'd like to apologize to everyone who's bothered by this. I have a very good reason for it: I like it better my way.

Genetics guide

Agouti (agouti signaling protein gene, ASIP): this gene determines whether the individual hairs will be banded or not.

dominant allele: A - banded hairs, tabby cat (wild type)

allele: APb - less banded hairs, charcoal cat (wild type in the leopard cat)

recessive allele: a - no bands, solid cat (variant)

A_ means if there's already an A allele, the other one can be either.

A homozygous solid cat with wild type alleles on every other gene will be solid black. Combined with other allele variants the a allele can produce other solid colors, different types of smokes and several more.

The most typical charcoal carry one APb leopard cat agouti allele and one solid a allele. For more details on charcoals, check out my charcoal tag!

Ticked (dickkopf wnt signaling pathway inhibitor 4, DKK4): this gene determines if there is any full-colored hairs, or only banded.

dominant allele(s - researchers found at least two): Ti - only banded hairs, ticked tabby cat (variant)

recessive allele: ti - some hairs don't have bands, "patterned" tabby cat (wild type)

If this is the only gene with variant allele, we'll have a black ticked tabby [black tabbies are also called brown, and other, mostly breed-specific names]. Ticked tabbies are possible in every color.

Nonagouti covers up the tickedness (this is called recessive epistasis): we won't see what a solid cat's genotype is on this gene. (Except when other genes make it possible. But that's biology for you.)

Spotted (?): this hypothetic gene/genes can break up the tabby pattern's stripes into spots.

spotted tabby cat (variant)

striped tabby cat (wild type)

Alone the spotting modifier(s) makes a black (brown ect) spotted tabby cat; of course, in combinations with other variant alleles, spotted tabbies can come in a wide variety of different colors.

Both a and Ti covers up the spotting: its effect normally only visible on a cat with the A_ titi genotype.

Mackerel (leaverin or transmembrane aminopeptidase Q, LVRN/Taqpep): this gene determines the type of the tabby pattern.

Blotched and classic are synonym terms.

dominant allele: TMc - narrow vertical lines, mackerel tabby cat (wild type)

recessive allele: tbl - wide, swirling lines, blotched or classic tabby cat (variant)

If every other gene is wild type except this, we'll have a black blotched tabby cat, but of course the tbl allele can produce lots of different colored classic tabbies.

All of the previously mentioned genes are able to nullify the effect of this one, so a mackerel or a blotched tabby must have A_ titi genotype. The interaction of spotted and blotched is debated.

Additional annoyed remark: Despite the name, the so-called classic pattern is actually both the newer and the less common worldwide. This is why I prefer the name blotched over classic.

Brown (tyrosinase-related protein-1, TYRP1): this gene determines the quantity of the functional eumelanin.

dominant allele: B - full pigment production, black cat (wild type)

"middle" allele: b - less pigment, chocolate cat (variant)

recessive allele: b'- even less pigment, cinnamon cat (variant)

Order of dominance: B > b > b'

If every other allele is wild type except this, we'll have a chocolate or cinnamon mackerel tabby cat. (On the picture the cinnamon cat is spotted rather than striped, because i couldn't find a decent mackerel. So sad.) Chocolate and cinnamon cats are possible in every pattern.

Color restriction (tyrosinase, TYR): mutations on this gene will result in temperature-sensitivity in the pigment production, the cats will be lighter on the warm and darker on the cooler areas of their bodies.

dominant allele: C - regular pigment production, full colored cat (wild type)

allele: cb - moderately reduced pigment production: burmese color restriction, sepia cat (variant)

allele: cm - reduced pigment production, bangkok color restriction, mocha cat (variant)

allele: cs - highly reduced pigment production: siamese color restriction, pointed cat (variant)

recessive allele: c - no pigment production, albino cat (variant)

Dominance order: C > cb = cm = cs > c

Now this group is a lot. Not only five different alleles (mocha was found relatively recently in Thailand), but the middle three are all intermediate with each other meaning that actually we have eight different phenotypes (illustration from messybeast; full color and albino are absent):

I used solid cats for illustration, because in the thai breed (the cats i used belong to this) they are often preferred over tabbies, so it's easier to find pictures; also, it's much more simple to compare them.

(Photos from The Thai Cat Center and Bangkok Mocha Cat, and Pangur from @pangur-and-grim as an albino cat)

Please note that all of these varieties are very changeable; the pictures (especially those of the heterozygotes) are far from representing all cats carrying the respective genotypes.

Alone these variants makes some type of a black (seal) mackerel tabby point cat, but every type of color restriction can occure together with all possible colors and patterns.

Dilute (melanophilin, MLPH): this gene determines the distribution of the pigments.

dominant allele: D - even pigment distribution, dark cat (wild type)

recessive allele: d - clumped, uneven pigment distribution, diluted cat (variant)

The diluted version of the previous mentioned colors: black -> blue, chocolate -> lilac, cinnamon -> fawn.

Further comparison of undiluted and diluted color pairs on one picture (to eliminate differences in lightening):

black vs blue and red vs cream

Every possible color and pattern can be diluted (with the only exception of white).

Orange (rho GTPase activating protein 36, ARHGAP36): this gene determines the type of the most prominent pigment: eumelanin on pheomelanin.

allele: O - mainly pheomelanin, red-based cat (variant)

allele: o - mainly eumelanin, black-based cat (wild type)

This gene is special in two related ways: first, it's located on the X chromosome, which means tomcats only have one allele; second, the alleles are codominant - if a cat carries both of them, it'll show both phenotypes: this is how we get tortoiseshell cats. This explains why almost all tortoiseshell cats are females - every tortie needs two different X chromosomes.

Combined with other variant alleles every possible color and pattern can occure as tortoiseshell, but the O allele is epistatic over a lot of genes: for example agouti (the phenotype of every orange cat is tabby, even the genetically solid ones) and brown (since eumelanin is mostly absent thus can't change - the genotypes OO B_, OO b_and OO blbl all mean a red cat).

The dilute version of red is called cream.

The dilution level is always the same in the colors of a tortoiseshell: the undiluted black, chocolate and cinnamon is paired with red, the diluted blue, lilac and fawn are paired with cream.

White (receptor tyrosine kinase, KIT): this gene determines the size of the area the pigment producing cells (the melanocytes) reach.

dominant allele: W - basically no melanocytes, white cat (variant)

allele(s): ws - limited area is covered, white-spotted cat (variant)

allele: w - all of the body is covered by the melanocytes, full-colored cat (wild type)

recessive allele: wg - only the paws remain white, gloved cat (variant)

recessive allele: wsal - salmiak - the paws and the chest is white, the body is finely roaned.

Order of dominance: W > ws = w > wg ? wsal

Salmiak is a very rare allele found in finnish randombred cats; gloving is the characteristic allele of the birman breed.

Lots of alleles here! At least since these variant are all mapped to KIT or near to it, I consider them alleles.

If every other gene shows the wild type except for this, we'll have a white, or a white-spotted black mackerel tabby cat, but thanks to the ws allele(s) every color and pattern can be combined with white patches. However, the W allele is epistatic over every other gene: if a cat has one or two copies of W, it will be white regardless everything else.

ws is interesting: it has an additive effect, a cat with the wsws genotype will have more white than a cat with only one copy of it.

wg and salmiak both seems to be recessive: the gloved phenotype only present if the cat's genotype is wgwg, and salmiak cats were all genotyped wsalwsal.

Dominant blue eyes (paired box 3, PAX3): this is a white spotting gene that affects most strongly the melanocytes of the eye.

alleles: DBEcel, DBEalt, DBEre, DBEago - usually one or two blue eyes and small amount of white spotting in heterozygotes, mostly or entirely white color, possible lethality in homozygotes (variants)

allele: N - normal melanocyte coverage in the eyes and on the body (wild type)

Latency (a cat with DBE/N genotype but without blue eyes) and odd or segmented eyes are not rare. Heterozygotes (including latents) usually have a little white on their muzzle, chin, neck and/or paws (often on only one or two paw, unlike ws white spotting, which almost always affects all four paws). The white spotting level of homozygotes varies, see this post.

Low-grade white (?): Even with the extreme variability of the white spotting allele(s), the existence of some independently inherited low-white genes is suspected. (At least by me. Not everyone agrees.) Their effects most commonly manifest as a white locket: a small white patch on the chest or the belly, and/or a white tail tip. I'm not sure if there is any consensus whether these are more likely to be recessive or dominant alleles, or both.

Karpati (?): This unidentified gene causes a roaning effect: scatters white hairs everywhere on the body, concentrating most on the extremeties (muzzle/nose, ears, legs, tail).

dominant allele: K - whited extremities and roaning, karpati cat (variant)

recessive alleles: k - normal pigmant production, full colored cat (wild type)

Karpati is either dominant or intermediate with significantly more white on homozygotes; it's hard to tell because the gene is still unidentified yet and has been studied for only a few years.

The cats' appearence changes during their life and also with the seasons: when they are born, they look very similar to a fever coated kitten but with white ears - or, sometimes, very pale, almost white - then by the end of their first year they darken considerably.

The karpati mutation is present in the stray cat population in middle-east Europe (including Hungary where I live, wahoo! and indeed, I can regularly see one or two karpaties in facebook adoptions groups and such). It's also introduced to some established breeds (LaPerm, Sphynx, ect) and the creation of its own breed also began under the Transylvanian name.

Inhibitor (?): this unidentified gene reduces the pheomelanin production, thus removes the warm tones of the fur (the hairs have white-black banding instead of yellow-black).

dominant allele: I - reduced pheomelanin, cooler toned cat (variant)

recessive allele: i - normal pheomelanin, warmer toned cat (wild type)

If every other allele is wild type except for this, we'll have a black silver mackerel tabby cat. Combined with other alleles it can produce lots of different silver (tabby) and smoke (solid) varieties.

Wide band, general (?): These (mostly) undescribed gene(s) make the yellow bands on the agouti hairs wider, resulting in a lighter, yellowish pelt. Based on the width of the pale bands we can differentiate between golden tabby (middle band width) and shaded/tipped/chinchilla/shell (maximal band width, color is pushed up into the tip).

dominant allele: Wb - reduced area of eumelanin, warmer toned cat (variant)

recessive allele: wb - normal area of eumelanin, cooler toned cat (wild type)

If every other gene stays wild type except for this, we'll have a black golden mackerel tabby or a black golden shaded cat. Combined with other alleles we'll get a terrifyingly wide range of golden and silver varieties.

Golden genetics is quite a mess; right now there is one identified gene (found first in siberians, see below), but persians and the many other breeds that allow golden must have different gene(s) instead or besides that, based on the interaction with the inhibitor gene (siberian golden (sunshine) + silver = bimetallic, persian golden + silver = silver shaded or chinchilla) and on the inheritance patterns (the siberian alleles are recessive, while persian golden appears to be dominant).

Wide band, sunshine/copper (corin, serine peptidase, CORIN): This gene makes the yellow bands on the agouti hairs wider, resulting in a lighter, yellowish pelt.

dominant allele: Wb - eumelanin on normal sized area, darker cat (wild type)

recessive alleles: wbSIB, wbeSIB, wbBRI - eumelanin on reduced area, lighter cat (variant)

In the moment, we have three mutations found on this gene: the sunshine (wbSIB) and extreme sunshine (wbeSIB) in the siberian breed, and the copper (wbBRI) in british cats. (I only show the sunshine and the copper here.) The novelty of these mutations means that the breeders still often call them simply golden instead of the new names, so it's difficult to find reliable data. Further complicating the situation, most likely both breeds have more wide band gene(s) beyond CORIN, and especially the copper cat above is the result of the combination of several wb genes.

Extension (melanocortin 1 receptor, MC1R): This gene replaces eumelanin with pheomelanin, resulting in a yellowish or reddish furred cat. The change sometimes happens gradually during the first years of the cat's life.

dominant allele: E - eumelanin remains, black adjacent cat (wild type)

intermediate allele: ec - pheomelanin takes over, yellow/red adjacent cat: carnelian (variant)

recessive alleles: ea, er - pheomelanin takes over, yellow/red adjacent cat: amber and russet (variant)

Amber and russet are recessives, they only affect homozygotes - but carnelian is intermediate: agouti heterozygotes are warm brownish tabbies called copals (or, more commonly, simply goldens).

All three recessive variants are new mutations found recently in different breeds: amber in the 1990s in norwegian forest cats, russet in 2007 in burmese, and carnelian in 2018 in kurilian bobtails (at least that's the first mention). We don't know anything about their interactions, or their effects on cats outside of their respective breeds.

The gene only affects eumelanin, so the O allele is epistatic over the it. However, because of the properties of the overpowering pheomelanin, every e allele is epistatic over agouti, so the tabby patterns will show up on aa cats as well. (The only exception here is the carnelian-carrier copals: while an A_ eaea differs considerably from an A_ E_ black tabby, an aa eaea looks identical to an aa E_.)

Dilute modifier (?): This unidentified gene changes the color of a diluted cat, the coloration becomes more brownish.

dominant allele: Dm - (variant)

recessive allele: dm - (wild type)

Blue, lilac, fawn -> caramel, cream -> apricot.

I put here a cat in all three diluted colors (blue, lilac and fawn) to compare them with the caramel tabby. It's hard to spot the differences, isn't it?

Since this is a dilute modifier, the D allele covers it, and we see its effect only on cats with dd genotype.

It can be found only in a few breeds: orientals (including related breeds), british, burmese, different rexes. To our current knowledge, of course.

Phoenix (?): This unidentified, but very likely X-linked gene produces a dark brown color.

The mutation appeared in maine coons recently. Warning: the following section is my own speculation, not confirmed, or maybe even shared by others. So. Based on both the phenotypes and the family tree data I was able to find, so far it seems to me that phoenix is either allelic or very closely linked with the orange gene. A tom is either phoenix or not. A phoenix molly is either solid phoenix, black-phoenix tortie or red-phoenix tortie; this means phoenix is not simply a modification of red as it can replace both the red or the black in a tortie.