It would be pretty easy to guess that Garfield was a tomcat even if you didn’t know his name—or didn’t want to peek under his tail. Most orange cats are boys, a quirk of feline genetics that also explains why almost all calicos and tortoiseshells are girls.
Scientists curious about those sex differences—or perhaps just cat lovers—have spent more than 60 years unsuccessfully seeking the gene that causes orange fur and the striking patchwork of colors in calicos and tortoiseshells. Now, two teams have independently found the long-awaited mutation and discovered a protein that influences hair color in a way never seen before in any animal.
“I am fully convinced this is the gene and am happy,” says Carolyn Brown, a University of British Columbia geneticist who was not involved in either study. “It’s a question I’ve always wanted the answer to.”
Scientists have long been fascinated by tortoiseshell and calico cats: the offspring of a black cat and an orange cat. Multicolored cats from such a cross are almost always female, suggesting the gene variant that makes fur orange or black is located on the X chromosome. The male offspring of such a cross are typically unicolor because they inherit just one parent’s X chromosome: We can guess, for instance, that Garfield’s mother is orange because he inherited his only X chromosome from her.
But female cats inherit an X chromosome from each parent. Cells don’t generally need both, so during embryonic development each cell randomly chooses one X to express genes from. The other chromosome rolls up into a mostly inert ball—a phenomenon called X inactivation. As a result, tortoiseshell cats end up with separate patches of black and orange fur depending on which chromosome was inactivated in that part of their skin. Calico cats add white fur into the mix because they have a second, unrelated genetic mechanism that shuts down pigment production in some cells.
In most mammals, including humans, red hair is caused by mutations in one cell surface protein, Mc1r, that determines whether skin cells called melanocytes produce a dark pigment or a lighter red-yellow pigment in skin or hair. Mutations that make Mc1r less active cause melanocytes to get “stuck” producing the light pigment.
But the gene encoding Mc1r didn’t seem explain where cats’ orange fur came from. It isn’t located on the X chromosome in cats or any other species—and most orange cats don’t have Mc1r mutations. “It’s been a genetic mystery, a conundrum,” says Greg Barsh, a geneticist at Stanford University.
To solve it, Barsh’s team collected skin samples from four orange and four nonorange fetuses from cats at spay-neuter clinics. As a proxy to determine how individual skin cells express genes, the researchers measured the amount of RNA that each melanocyte was producing and determined the gene it encoded. Melanocytes from orange cats, they found, made 13 times as much RNA from a gene called Arhgap36. The gene is located on the X chromosome, which led the team to think they had the key to orange color.
But when the researchers looked at Arhgap36’s genetic sequence in orange cats, they didn’t find any mutations in the DNA that encodes the Arhgap36 protein. Instead, they found the orange cats were missing a nearby stretch of DNA that didn’t affect the protein’s amino acid components but might be involved in regulating how much of it the cell produced. Scanning a database of 188 cat genomes, Barsh’s team found every single orange, calico, and tortoiseshell cat had the exact same mutation. The group reports the discovery this month on the preprint server bioRxiv.
A separate study, also posted to bioRxiv this month, confirms these findings. Similar experiments run by developmental biologist Hiroyuki Sasaki at Kyushu University and his colleagues revealed the same genetic deletion in 24 feral and pet cats from Japan, as well as among 258 cat genomes collected from around the world. They also found that skin from calico cats had more Arghap36 RNA in orange regions than in brown or black regions. Moreover Arhgap36 genes in mice, cats, and humans acquire chemical modifications that silence them on one of the two X chromosomes in females, Sasaki’s team documented, suggesting the gene is subject to X inactivation.
When Barsh and Sasaki learned their respective teams had discovered the same mutation, they decided to post their preprints at the same time. (Because they are preprints, neither study has been peer reviewed.) Both groups further found that increasing the amount of Arhgap36 in melanocytes activates a molecular pathway that switches the cells to producing light red pigment regardless of whether MC1r is active.
No one previously knew Arhgap36 could affect skin or hair coloration—it is involved in many aspects of embryonic development, and major mutations that affect its function throughout the body would probably kill the animal, Barsh says. But because the deletion mutation appears to only affect Arhgap36 function in melanocytes, cats with the mutation are not only healthy, but also cute.
Arhgap36’s inactivation pattern in calicos and tortoiseshells is typical of a gene on the X chromosome, Brown says, but it’s unusual that a deletion mutation would make a gene more active, not less. “There is probably something special about cats.”
Experts are thrilled by the two studies. “It’s a long-awaited gene,” says Leslie Lyons, a feline geneticist at the University of Missouri. The discovery of a new molecular pathway for hair color was unexpected, she says, but she’s not surprised how complex the interactions seem to be. “No gene ever stands by itself.”
Lyons would like to know where and when the mutation first appeared: There is some evidence, she says, that certain mummified Egyptian cats were orange. Research into cat color has revealed all kinds of phenomena, she says, including how the environment influences gene expression. “Everything you need to know about genetics you can learn from your cat.”