Cat coat genetics

A chocolate Oriental Shorthair kitten.

The browning gene B/b/b^l codes for TYRP1 (Q4VNX8), an enzyme involved in the metabolic pathway for eumelanin pigment production. Its dominant form, B, will produce black eumelanin. It has two recessive variants, b(chocolate), and b^l(cinnamon), with b^l being recessive to both B and b.[1] Chocolate is a rich brown color, and is referred to as chestnut in some breeds. Cinnamon is a lighter reddish brown.

This cat shows the "red" O- genotype.

The sex-linked Orange locus, O/o, determines whether a cat will produce eumelanin. In cats with orange fur, phaeomelanin (red pigment) completely replaces eumelanin (black or brown pigment).[2] This gene is located on the X chromosome. The orange allele is O, and is codominant with non-orange, o. Males can typically only be orange or non-orange due to only having one X chromosome. Since females have two X chromosomes, they have two alleles of this gene. OO results in orange fur, oo results in black or brown fur, and Oo results in a tortoiseshell cat, in which some parts of the fur are orange and others areas non-orange.[3] Male tortoiseshell cats are known to exist, but, as expected from the genetics involved, they are rare and often exhibit chromosomal abnormalities.[4] In one study, less than a third of male calicos had a simple XXY Klinefelter's karyotype, slightly more than a third were complicated XXY mosaics, and about a third had no XXY component at all.[4]

A female domestic shorthair tortoiseshell cat.

This color is known as red by breeders. Other names include yellow, ginger, and marmalade. Red show cats have a deep orange color, but it can also present as a yellow or light ginger color. Unidentified "rufousing polygenes" are theorized to be the reason for this variance. Orange is epistatic to nonagouti, so all red cats are tabbies. "Solid" red show cats are usually low contrast ticked tabbies.[5]

The precise identity of the gene at the Orange locus is unknown. It has been narrowed down to a 3.5 Mb stretch on the X chromosome in 2009.[5]

The Dense pigment gene, D/d, codes for melanophilin (MLPH; A0SJ36), a protein involved in the transportation and deposition of pigment into a growing hair.[5] When a cat has two of the recessive d alleles (Maltese dilution), black fur becomes "blue" (appearing gray), chocolate fur becomes "lilac" (appearing light brown), cinnamon fur becomes fawn, and red fur becomes cream. The d allele is a single-base deletion that truncates the protein.[5]

• Barrington Brown is a recessive browning gene that dilutes black to mahogany, brown to light brown and chocolate to pale coffee. It is different from the browning gene and has only been observed in laboratory cats.[6]
• The Dilution modifier gene, Dm, "caramelizes" the dilute colors as a dominant trait. The existence of this phenomenon as a discrete gene is a controversial subject among feline enthusiasts.
• A mutation at the extension locus E/e (the melanocortin 1 receptor, MC1R) changes black pigment to amber or light amber. Kittens are born dark but lighten up as they age. Paws and nose still exhibit the original undiluted color, this in contrast to other diluted colors, where paws and nose have the diluted color. This phenomenon was first identified in Norwegian Forest cats.[7]
• Another recessive mutation at extension was discovered which causes the russet color in Burmese cats. It is symbolized as e^r. Like amber cats, russet cats lighten as they age.[8]
• A modifying factor has also been hypothesized in shaded silver and chinchilla Persians whose fur turns pale golden in adulthood, due to low levels of phaeomelanin production. These cats resemble shaded or tipped goldens, but are genetically shaded or tipped silvers. This is probably related to the phenomenon known as "tarnishing" in silvers.

An Abyssinian kitten displaying the ticked tabby pattern.

The Agouti gene, with its dominant A allele and recessive a allele, controls the coding for agouti signaling protein (ASIP; Q865F0). The wild-type A produces the agouti shift phenomenon, which causes hairs to be banded with black and an orangish/reddish brown, this revealing the underlying tabby pattern (which is determined by the T alleles at the separate tabby gene). The non-agouti or "hypermelanistic" allele, a, does not initiate this shift in the pigmentation pathway and so homozygotes aa have pigment production throughout the entire growth cycle of the hair—along its full length.[9] As a result, the non-agouti genotype (aa) is solid and has no obvious tabby pattern (sometimes a suggestion of the underlying pattern, called "ghost striping", can be seen, especially in bright slanted light on kittens and on the legs, tail and sometimes elsewhere on adults). Agouti is found on chromosome A3.

A major exception to the solid masking of the tabby pattern exists: the O allele of the O/o locus is epistatic over the aa genotype. That is, in red or cream colored cats, tabby striping is displayed despite the genotype at the agouti locus. This explains why you can usually see the tabby pattern in the orange patches of non-agouti tortoiseshell cats, but not in the black or brown patches.

However, some red cats and most cream cats show a fainter tabby pattern when they have no agouti allele to allow full expression of their tabby alleles. That is, in genetically red cats (O males and OO and Oo females) the aa does still have an effect, especially in dilute coats (when having dd genotype at the D gene locus), where the tabby pattern is sometimes not expressed except on the extremities.

Down, awn and guard hairs of a domestic tabby cat

The Tabby gene on chromosome B1 accounts for most tabby patterns seen in domestic cats, including those patterns seen in most breeds. The dominant allele Ta^M produces mackerel tabbies, and the recessive Ta^b produce classic (sometimes or once referred to as blotched) tabbies.[10] The gene responsible for this differential patterning has been identified as transmembrane aminopeptidase Q (Taqpep, M3XFH7), which also produces the king cheetah coat variant.[11]

The wild-type (in African wildcats) is the mackerel tabby (stripes look like thin fishbones and may break up into bars or spots), the most common variant is the classic tabby pattern (broad bands, whorls, and spirals of dark color on pale background usually with bulls-eye or oyster pattern on flank). The classic tabby is most common in Iran, Great Britain and in lands that were once part of the British Empire and Persian Empire.[11]

Spotted tabbies have their stripes broken up into spots, which may be arranged vertically or horizontally. A 2010 study suggests that spotted is caused by the modification of mackerel stripes, and may cause varying phenotypes such as "broken mackerel" tabbies via multiple loci.[10]

The Ticked (Ti) locus on chromosome A1 controls the generation of ticked coats, a non-patterned agouti coat having virtually no stripes or bars but still considered a tabby coat. The Ti^A is the dominant allele that produces ticked coats; Ti⁺ is the recessive one. Stripes often remain to some extent on the face, tail, legs, and sometimes the chest in heterozygotes (Ti^ATi⁺) but are nearly or completely nonexistent in homozygotes (Ti^ATi^A). The Abyssinian breed is fixed for the ticked allele—all Abyssinians are homozygotes for this gene. The ticked tabby allele is ultimately dominant and therefore completely (or mostly) masks all the other tabby alleles, “hiding” the patterns they would otherwise express.[10]

It was once thought that Ti^A is a very dominant allele of the Tabby gene called T^a.[12]

• Other genes (pattern modifier genes) are theorized to be responsible for creating various type of spotting patterns, many of which are variations on a basic mackerel or classic pattern. There are also hypothetical factors which affect the timing and frequency of the agouti shift, affecting agouti band width and the number and quality of alternating bands of eumelanin and phaeomelanin on individual hairs.
• There is a gene not yet identified, but believed to be related to the agouti gene in the Chausie breed that produces silver-tipped black fur similar to Abyssinian ticked fur, known as "grizzled." This phenomenon is purported to have been inherited from the hybridization of the domestic cat to the jungle cat (Felis chaus).
• The inhibited pigment gene, I/i. The dominant allele (I) produces tipped hairs that are fully colored only at the tip and have a white base. This allele appears to interact with other genes to produce various degrees of tipping, ranging from deeply tipped silver tabby to lightly tipped shaded silver and chinchilla silver. The inhibitor gene interacts with the non-agouti genotype (I-aa) to produce the color known as smoke. The homozygous recessive genotype when combined with the agouti gene (iiA-), produces tabby coloration, which can vary along a spectrum ranging from a deeply patterned brown tabby, to a lighter "golden tabby", to the very lightly colored shaded or chinchilla golden colors. Orange cats with the inhibitor gene (I-O-) are commonly called "cameo".

• The basic tortoiseshell pattern has several different colors depending on the color of the eumelanin (the B locus), and dilution (the D locus).
• Tortoiseshell tabbies, also known as torbies, display tabby patterning on both colors. Calico tabbies are also called calibys or tabicos.[16]

The genetic influences on tipped or shaded cats are:

• Agouti gene.
• Tabby pattern genes (such as T^a masking the tabby pattern).
• Silver/melanin inhibitor gene.
• Factors affecting the number and width of bands of color on each hair (such as the hypothetical wide band gene).
• Factors affecting the amount and quality of eumelanin and/or phaeomelanin pigment expression (such as theorized rufousing factors)
• Genes causing sparkling appearance (such as glitter in the Bengal, satin in the Tennessee Rex, grizzle in the Chausie).
• Factors to clear up residual striping (hypothetical Chaos, Confusion, Unconfused, Erase, and Roan factors).

There are various genes producing curly-coated or "rex" cats. New types of rex arise spontaneously in random-bred cats now and then. Here are some of the rex genes that breeders have selected for:

• r = Cornish Rex, recessive.
• gr (provisional) = German Rex, recessive. Same locus as Cornish, but proposed as a different allele. However, most breeders consider the German Rex to have r/r genotype.
• re = Devon Rex, recessive. Identified on KRT71 (E1AB55).[29]
• ro = Oregon Rex (extinct), recessive.
• Se = Selkirk Rex, dominant although sometimes described as an incomplete dominant because the three possible allele pairings relate to three different phenotypes: heterozygous cats (Sese) may have a fuller coat that is preferred in the show ring, while homozygous cats (SeSe) may have a tighter curl and less coat volume. (sese type cats have a normal coat.) This phenomenon may also colloquially be referred to as additive dominance.
• Lp (provisional) = LaPerm, dominant: Lp/lp and Lp/Lp individuals have the same phenotype.

There are also genes for hairlessness:

• h = French hairless cat, recessive.
• hd = British hairless cat, recessive.
• Hp = Russian Donskoy and Peterbald, dominant.
• hr = Canadian Sphynx cat, recessive. Identified on KRT71.[29]

Some rex cats are prone to temporary hairlessness, known as baldness, during moulting.

Here are a few other genes resulting in unusual fur:

• The Wh gene (dominant, possibly incomplete) results in Wirehair cats. They have bent or crooked hair producing springy, crinkled fur.
• A hypothetical Yuc gene, or York Chocolate undercoat gene, results in cats with no undercoat. However, the proportional relationship between guard, awn, and down hair production varies greatly between all breeds.
• A recessive autosomal gene for Onion hair which causes roughness and swelling on the hairs. The swelling is due to enlargement of the inner core of medulla cells.
• A recessive autosomal gene spf for sparse fur. As well as sparse coat, the hairs are thin, straggly and contorted and there is brown exudate around the eyes and nose and on the chest and stomach. A similar condition is linked to Ornithine Transcarbamylase Deficiency in mice.