Harlequin Genetics

There seems to be a lot of information (and misinformation) on breeding the harlequin pattern available, so we thought we'd try to put here some things we have learned along the way specific to Harlequin breeding.

When breeding Harlequins, we touch on nearly all the major color genes. There are many sites that go over these genes like Three Little Ladies and The Nature Trail that offer great introductions to genetics. I suggest starting there, getting a decent understanding of the major color (and pattern) genes, and then we can look a little deeper at the japanese/magpie genetics.

AA, AAt, AtAt, Ata, aa ... All Harlequin

When we first started with this breed, we were told like so many that you "have to breed Agouti rabbits to get good Harlequins". Surprise surprise when a torted Harlequin (aaeje - NOT agouti) had decent markings other than her little tort nose. Let's dig deeper then.

First, some clarification on what "Agouti" means. Agouti is the name of a gene location and a specific mutation and a coat pattern in domestic rabbits. Gets kind of confusing, but stay with me here. The Agouti gene is carried by all mammals (as far as I know). It is a physical location on the chromosome. The Agouti "gene" (actually allele) that most rabbit breeders refer to is the "A" when looking at a genotype (so Aaejej = one Agouti gene, one "self" gene and two japanese genes). Agouti, tan and self are the three known mutations of the Agouti gene in rabbits. Now, a third option - the Agouti coat pattern/color refers to the "wild type" - think a cottontail rabbit or a Flemish Giant. This coat pattern is only expressed this way with other genes (all dominant). If you bred all the rabbits together you would end up with a bunch of Agoutis hiding all the other color genes.

You can find heavily torted harlequin marked rabbits that do not look good, and you can see those that are torted but still have otherwise very nice markings. It is not a simple tort/non-tort. Ask any tort breeder if all their torts are nicely marked. No, they are not. There are many modifiers at play and all have to be bred for, most of which are unnamed and unknown to breeders. If you have a good one, you breed to that and hope for more good ones.

The tort pattern cannot show up in an Aa or AA (the agouti masks the tort). Similar with At (tan). I have not seen many harlequin marked tans in person, but knowing other breeders that have worked with tan genetics in their other breeds (and also harlequin/tri) they do happen and some, I am told, look pretty nice. In conclusion, You do not have to have Agouti to get a good Harlequin, but Agouti will mask the self gene (e), thus prevent torted Harlequins from SHOWING.

If you are going to keep Agouti based Harlequins (AA or Aa) know that you could still be carrying torted harlequin markings (eje) in your herd. However if you are breeding self based Harlequins (aa) torts will show up 9/10 times in some varying level. Some may only have slightly darker ears or legs and that's your only indicator. Others will be very obvious - this all depends on the modifiers that are carried along with that rabbit, and can also even depend on nestbox temperature! If you keep self based Harlequins be careful when bringing in new blood that is Agouti based - they could carry tort hiding under the mask of the Agouti genes and you might not know for several generations.

What is far more important than the base agouti/tan/self is the double japanese genes (ejej) and breeding to the Harlequin standard.

The Truth About Tris puts all of this more eloquently than I can with some great photo examples of a true torted harlie vs. a self based non torted.

Torted Harlequins

Torted Harlequins are aaeje rabbits. They are jokingly referred to as "tortequins" and are a major fault in a Harlequin breeding program. They will come out of normally marked Harlequin parents, if at least one of the parents is genotype Aaeje. As agouti (A) will mask non-extension (e), this parent may look like a perfectly well marked Harlequin. I would love to say that they will be brindled or lightly marked but that's just not the case - they can be grand champion three and four part frontals with excellent body banding/barring and still have only one japanese gene. Some of my best marked animals have shown themselves to only have one japanese gene - a confounding issue when trying to select for double japanese carriers!

Hardway Inodorum

Inodorum was kept as a test animal to verify the above theory. Inodorum came out of two Harlequin marked parents, though her mother was known to be A_eje due to an outcross with a New Zealand (A_ee). We knew when doing the cross that there were chances of bringing in the e gene into the next generation, but had been told by experienced breeders that Harlequins have to be Agouti to be Harlequin marked, so we thought we were safe with breeding back to a cleanly marked Harlequin buck. No.

Hardway Inodorum, Torted Harlequin Hardway Inodorum, Torted Harlequin
Torted Harlequin - aaeje

Hardway Inodorum as a young kit, her tort-y nose was apparent right away.
As you can see the tort on her nose expanded as she grew - harlequin genetics fix the dark and light bars
on the hair shafts before birth, wheras non-extension (e) is development and temperature dependent.

Hardway Inodorum, Torted Harlequin Hardway Inodorum, Torted Harlequin
Her first litter, test mated to confirm to a tort buck (non harlequin). Torted and Tortequin kits day one.
At several days old torting is very clear on these kits. Nice rufus though.
You can see that some of the kits are both torted and have faint japanese barring - they are "tortequins".

Why no Magpie x Japanese

There is nothing wrong with breeding Mags and Japs together, but know that if you are trying to breed to get more Japanese from the litter, that your magpies can hide du genes (white feet/toes/nose snips/even full dutch belts) because they ARE white. White spots don't exactly stand out on them. Nickie Raines noticed that those Magpies that have a dark leg with a white foot that looks like it was dipped in paint are indeed white footed - and their Japanese kits are more likely to have white.

In addition, Magpies will hide really poor rufus (the factors that play into our good rich orange color). For all you know their black Japanese kits will look lighter fawn than some blues and have big white eye circles with flank streaks that border solid white.

We think another issue is that Magpies usually look better than they really are. When we see a Mag we think we like, imagine the white replaced with orange. Is it still that nice? Do they really have clarity and evenness of color, or is a bit of an optical illusion (nothing has better contrast than black and white, so it will appear cleaner at first glance). The same goes with the blues and other colors - would that blue look good over fawn, or is it so washed out it only really looks dark because it's against a white background? While color itself is not a lot of points in the breed, and neither is clarity, they both lend to overall impression and a rabbit with neither is not pleasing to the eye.


Something we're still trying to find out. Currently doing test matings that might lead to more information, but if you have knowledge of the wideband gene's effects on the japanese genes and visa versa, please let us know!

So far my best guess to the effects of wideband is that ww Harlequins are more likely to show an overwhelming majority of one color or another. Because the wideband pattern is poorly understood in general, it is hard to find ww animals to test to. I have also heard conflicting information on wideband being dominant or recessive - this pattern seems to behave on its own terms (much like our ej!).

Crossing Out... Satins

I am not sure why so many are dead set on using Satins for crossing their Harlequins out to, but many have tried then decided to ditch the project because they kept having satin fur pop up. Satin fur is hollow hair shaft and not okay in the Harlequin breed. If you MUST breed in a Satin to jump-start type or increase genetic diversity, be prepared to raise several kits to breeding age + dedicate several years to the project. Below is the formula for test mating for satin (or any simple recessive gene, really)...

F1 - Satin x Harlequin litter. Keep best typed animal from this litter, preferrably a buck if you have several Harlequin does you can breed him to.
F2 - 1/2 Harlequin x Harlequin (several if you can). Try to keep at least 3-4 good quality excellent type animals with nice markings, fur density and texture.
F3 - Take these 3/4 Harlequin kits and test mate them to Satins. You want at least 20 kits from each animal to test mate them. If a SINGLE satin kit is born in these litters, your Harlequin Cross is still carrying a satin gene. You may choose to go one more generation out (breed again to a Harlequin, grow up kits, test mate) or simply cull this animal and try the next best typed animal that you kept out of the 3/4 Harlequin litter.

As you can see it is a difficult road to test mate and eliminate carriers of a recessive gene like satin. You may go several generations before your test matings come back clean. If you CAN get the type to breed through into the next several generations you've done what many could not. However. By the time you've done all this you have spent more money growing up all those test kits than to offer the best Harlequin breeder in the country enough to buy their star herd buck. Not to mention time and cage space. And that's if you don't bring in funky color genes!

Crossing to a New Zealand (red only, with only red on the pedigree) or a Palomino has its risks but less so than crossing to Satins. Ideally only crossbred bucks will be retained (as you can more quickly test mate them to get enough kits to know if they carry a particular recessive gene) but if an exceptional female shows herself and you are willing to wait longer to know her genotype then by all means keep her around.

Crossing to another breed is NOT the quick easy fix many are looking for. Even the best New Zealands and Californians and Satins in the country have litters with lots of culls. They are the best because their breeders only use the best from each litter - and you must continue that tradition if you wish to bring in those quality traits from these crosses.

Dutch Spotting Genes, White Markings

I wish I knew more about dutch spotting genes, but haven't been able to find a lot of great information on them. On our rabbit's pedigrees we note if the rabbit is Dudu that means we know they have thrown white feet/snips/etc. I know that's not exactly accurate, but until more research is done on our part it allows us to track this major fault and make better breeding decisions to eventually eliminate it from our bloodline. Because of the limited availability of Japanese harlequins when we first started, our only options for purebred does were those that throw white feet. Our purebred bucks have been the same situation. In the future I hope that more knowledge on our part and more strict culling standards for this fault will eliminate it entirely from our breeding pool. At this time, we do not use any Japanese known to throw white markings in our Magpie program either.