In other species: golden hamster

Categories: Pigmentation phene

Single-gene trait/disorder: yes

Mode of inheritance: X-linked

Disease-related: no

Key variant known: yes

Year key variant first reported: 2024

Species-specific name: ginger, tortoishell; tortoiseshell; calico (tortoiseshell with white patches)

History: The tortoiseshell coat colour in cats has long been notable for its anomalous occurrence.
In the first (1859) edition of Origin of Species, for example, Darwin asks "What can be more singular than the relation between blue eyes and deafness in cats, and the tortoise-shell colour with the female sex"? (page 144). 
The first person to attempt to explain this mystery was Doncaster (1904) who, after examining the results of many matings reported to him by cat breeders, concluded (correctly) that tortoiseshell cats are heterozygous. Not knowing of X and Y chromosomes, let alone X-linked inheritance, his explanation for most tortoiseshells being female was valiant and the best available at the time: "in the male orange is completely dominant over black, while in the female the dominance is incomplete, and tortoiseshell results." Doncaster was also aware of the other intriguing aspect of the occurrence of orange/tortoiseshell cats, namely "that orange females are very rare, although males are common". He noted that his hypothesis also explained the latter phenomenon. As XX/XY sex determination in cats became ever more likely (as explained below), Doncaster;'s explanation for both phenomena was discarded.
Eight years later, sex chromsomes were still not known in cats, but Little (1912) reported that by then, it was accepted that there was a sex-producing factor "commonly designated by X, its absence by —. Thus one sex would be homozygous, XX, and the other would be heterozygous, X—." The question of which sex was homozygous and which heterozygous in cats was still undecided! So, Little suggested: "If we adopt, tentatively, the hypothesis that the female is a homozygote, XX, and the male is a heterozygote, X—, and if we suppose that black, B, is always coupled with the sex-producing factor, X, we should conclude that the black female is of the gametic constitution, BB, and that the black male is of the composition B—". He continued " The yellow male lacks the factor for the  production of black pigment in the coat and is of the gametic composition Y—, while the yellow female is YY." This is the essence of current understanding, noting that Little uses the symbol B for what is now called the non-Orange allele, and the symbol Y for the Orange allele.
Six years later, Sewall Wright (1918) provided a similar explanation, using the symbols E for black and e for yellow, provided a similar explanation, which included the term sex-linked. Wright's words: "A color which depends on a sex-linked factor is inherited by males wholly from their mothers. Thus black females (EE) should have only black sons (E-), yellow females (ee) only yellow sons (e-), and tortoiseshell females (Ee) both blacks (E-) and yellows (e-) in equal numbers, regardless of the colors of the sires." Noting that Cutler and Doncaster (1915) had "presented evidence that tortoiseshell males are generally sterile", Wright also (correctly) hypothesised that "rare tortoiseshell males may be cats with the two X chromosomes of females, but in which some other cause has overbalanced the sex-determining tendency of the X chromosomes, and produced males or near males."
By 1925, even though the karyotype of cats had not yet been determined, the understanding of the inheritance at what we now call the Orange locus had reached the stage where the first textbook of animal genetics (Crew, 1925) could include the following words: "The allelomorphic factors B (black) and b (yellow) are resident in the X-chromosomes, and the Y-chromosome of the male does not carry these factors. The female, possessing two X-chromosomes can have one bearing the factor for black, another bearing the factor for yellow; she can be tortoiseshell. The male can have either the factor for black or for yellow in his single X-chromosome. He cannot be tortoiseshell." In essence, and the occasional tortoiseshell male notwithstanding, this is still the understanding 100 years later.

Mapping: Despite it having been agreed for decades that the Orange locus is located on the X chromosome (see History section above), it was not until 2005 that the first attempt was made to determine where on the X chromosome the Orange locus is located. Using microsatellite markers, Grahn et al. (2005) were able to exclude most of the X chromosome, leaving just one 14 cM region near the centromere, flanked by the genes TIMP1 and ARAF1, in which the Orange locus could be located. 
Armed with more porwerful tools, Schmidt-Küntzel et al. (2009) refined the location to a 3.5Mb region of the q arm "between markers at positions 106 and 116.8 Mb in the [then] current 1.9x-coverage sequence assembly of the cat genome".
Gandolfi et al. (2018) narrowed this region down to a 1.5Mb region that contains 12 genes.
Hernandez et al. (2022) reported that in "a GWAS on the presence of orange fur in random bred cats", conducted with "Hill’s custom Illumina feline high density [340k] mapping array", the "most significantly associated SNP" was located "within the 1.5Mb haplotype block identified by Gandolfi et al. (2018)". Frustratingly, "only 4 markers within the 1.5Mb haplotype block remain after minor allele frequency (MAF) and missingness filters, preventing the refinement of this region".

Molecular basis: On 21st November 2024, a preprint by Toh et al. (2024) was uploaded to bioRxiv, announcing the long-awaited discovery that the gene for the long-known X-linked Orange locus is ARHGAP36, encoding a Rho GTPase activating protein; and that the Orange variant is "a 5.1-kilobase (kb) deletion within an intron" of ARHGAP36.
One day later, a preprint by Kaelin et al. (2024) was uploaded to bioRxiv, announcing, in essence, the same result: "Sex-linked orange is caused by a 5 kb deletion that leads to ectopic and melanocyte-specific expression of the Rho GTPase Activating Protein 36 (ARHGAP36) gene".
At the time of writing (28 November), neither of these preprints has been peer-reviewed. However, a Science commentary was posted on 27 November, and two articles have been published in The Conversation on 4 December and 5 December. 

Associated gene: