Equine Genetics

Tuesday, September 25, 2012

Equine Genetic Basics

E(Extension)--E is the gene that control the base color of the horse. E is black and e is red(chestnut). E is dominant over e so if you have even one big E you have a black based horse. A black horses gene will either look like this EE or like this Ee. The only way you have a chestnut horse is if its genes are ee. If the horse is EE it will never have a red based foal. This is because you need two copies of e to have a red based foal, one from each parent and this parent does not have an e to give. If the horse is Ee that horse can have either a red based or black based foal depending on the other horses genes. If the horse is ee, the horse will always throw THEIR red based gene, but whether the foal is red based or not depends on what the other parent throws.

A(Agouti)--A is the gene that causes bay. It only acts on a black based horse. A horse that is chestnut, or ee, will show no effects from Agouti. Now if the horse is EE or Ee (black based) and has one copy Aa or two copies AA that horse will be bay. If the horse is EE or Ee (again black based) and no copies of a (so genetically it would look like this-aa) that horse will be black. Again Agouti only effects black pigment so a chestnut horse (ee) can have one two or no copies of Agouti and the horse will still be chestnut. The only time when a chestnut horses agouti gene comes into play is when breeding. If you breed a black horse whose genes look like this EE aa (So homozygous for the black gene and no Agouti-Black horse) to a chestnut whose genes look like this ee AA (So this horse is chestnut and is homozygous for Agouti) you will always get a horse whose genes look like this Ee Aa. That foal is bay. It is black based (Ee) with one copy of Agouti, changing the black horse to bay.

Cr(Cream)--Cream is an incomplete dominate gene that only works on red based pigment. Incompletely dominant means that the effect the gene has is different when there is one copy and when there is two copies.On a black horse one copy of Cr creates a smokey black horse. This color horse is often very hard to distinguish without genetic testing because it looks exactly like a normal black horse because Cr only effects red pigment. On a black horse with two copies of cream the horse is smokey cream. This is the only time that cream effects back pigment. On a bay horse one copy of cream creates a buckskin. The cream gene only effects the red pigment on the bay so the bays mane tail legs and other black points remain black. Two copies of cream on a bay horse creates a perlino. This horses red pigment is diluted even further than one with only one copy of Cr. The black points on a perlino are also diluted. They can be diluted so much to where there is no difference between what were the black points and the body color or the points will be diluted to where the are a chocolate or brown (this is not to be confused with silver that I will cover later.) On a chestnut horse with one copy of Cr creates a palomino. The entire body of this horse including main tail and legs is all diluted. Two copies of Cr on a chestnut horse creates a cremello. This dilutes the pigment even further than a palomino does. Now the breeding aspect of Cr is this. In order for a horse to be smokey black, palomino, or buckskin at least one parent has to have at least one copy of Cr. You CANNOT get a Cr foal out of two NON Cr parents. Also to get a double dilute baby BOTH parents have to have at least one copy of Cr. You CANNOT get a double dilute foal out of one diluted parent (with one copy or two copies) and one NON dilute.

-Gray is a modifying gene. The horse starts out its base color and progressivly gets whiter and whiter every year. Heterozygous grays are more likely to be fleabitten. Homozygous grays are more likely to get melanomas and vitilago. Homozygous grays also gray out quicker.

To(Tobiano)--To is the gene that causes tobiano in horses. It normally causes round smooth markings that NORMALLY do cross the back but they do not have to. Also the head is a solid color. If there is any white on the head that is a sign of another pattern. Normally sabino. A horse can either be heterozygous for Tobiano meaning one copy of the gene or homozygous for Tobiano meaning that the horse has two copies of Tobiano. No matter if it is 100% white or 0% if the horse has To the horse IS tobiano. This is why APHAs color descriptions suck-What pattern is this foal?

Frame/Lethal White Overo
--If a horse has LWO the horse IS FRAME. Frame is lethal white overo, lethal white overo is frame. You cannot have one without the other. Frame horses generally have irregular patches of white that are very jagged around the edges. The normally does not cross the back, but it can. The legs are also normally solid. Any white on the leg is a sign of another pattern, again normally sabino. Frame horses normally have white markings on there head. A horse can only have one copy of this gene. If it gets two copies his intestinal track does not develope correctly and within three days of birth the horse will either die or have to be put down because of it. Frame horses are the only horses that have Lethal White. If your tobiano horse tests positive for Lethal white than your horse is frame and tobiano. It can hide very very easily and be very very minimal. If you are breeding paints you MUST test your horses to see if they have LWO. If not you risk a lethal white foal. Also if breeding to a paint stallion, ask to see the papers stating that the horse is LWO negative. A fellow posted on another board bred to a stallion she was told was negative and he wasnt. She had a LW baby. This horse (he is a miniature but it doesnt matter) is frame. He is frame because he has LWO. This is to show you just how minimal frame overo can be.

-Sabino is the gene (s) that we know the least about surprisingly. Geneticists can only test for one form of sabino. It is thought that there are many maybe even hundreds of different sabinos. It is also thought that any white on a horse not from another pattern, so white legs or face markings on horses that have no paint genes, is caused by some form of sabino. Sabino can also cause some roaning but NOT TRUE ROAN. There is also a Dominant White that is like sabino. That gene is kind of complicated so I wont get into it on here, but will in a future post.

-Rabicano can cause what is called a "skunk tail."It is when white hairs appear on either side of the tail head like this. It also cause roaning on the sides of the horse, but again NOT to be confused with true roan. This is an extensively marked rabicano horse. The gene for rabicano is thought to be dominant but the exact gene or genes has not been located yet.

And now my favorite Splash White-The gene has not been located yet sadly. They have been trying and trying but so far nothing. Splash can be extremely minimal just like frame. The most obvious markings of a splash white is a horse that looks like it is dipped in paint. The face is normally a big wide blaze, that gets wider at the bottom (called a bottom heavy blaze) and it normally appears to be falling off the edge of the face. Splash is also known for extremely high white stockings. Another tell tale sign of splash white, is that the bottom half of a splashed whites tail will be white. It really looks like the horse was dipped in paint. It has been proven that deafness is caused by lack of pigmentation inside the ear. Not all splash whites are deaf however it is theorized that the close the white markings on the face come to the ears the more likely it is that the horse is deaf. It is also theorized but not proven that horses that are homozygous for whatever gene causes splash will be more heavily marked. That however is all theory. (I will go into heavier detail about splash in a later post.) The foal I posted under the tobiano section is Mile High Party from Cedar Rock Farms. She is Splash White and Sabino. NO tobiano, or frame at all. Her sire is a QH and her dam is splash white and sabino, NO tobiano from either parent so no tobiano for the foal.

Rn(True Roan)-Rn is thought to be a dominant gene. If the horse has Rn he will be true roan there is no getting around that. The horses head and legs will be solid colored but everywhere else will have white roaning. This is most commonly found in Quarter Horses and Paint Horses. Thoroughbreds with true roan is a hard one. The only TBs that have True Roan are descendants from Catch a Bird. There is no known cause for why he has passed on true roan as it is not found in TBs. It was also thought that homozygous Roan is lethal however there are geneticists who believe that it is not. Also there is a line in QH (Hancock line I believe) that appear to be homozygous for roan. The common thought is that it can be homozygous lethal but it doesnt have to be, unlike Lethal White where homozygous horses are lethal.

Dun-So far there is no test for the exact dun gene. HOWEVER there is a test that is quite close. This test tests for markers that are around the gene that they believe is dun. The problem is some horses that are NOT dun HAVE these markers and some horse that ARE dun DO NOT have these markers. Dun in horses is characterized by a distinct dorsal stripe, leg and wither barring, and shading. Dun is NOT homozygous lethal. A bay horse with the dun gene becomes Dun, and red horse with the dun gene becomes Red Dun and a black horse with a dun genes becomes Grulla/o.

Z(Silver)-Silver effects black pigment. It turns black pigment a brown color. It also turns black mains and tails some shade of flaxen of white. It dilutes the black points on a bay to a mousey brown color.

Champagne-This site http://www.equinecolor.com/champagne.html Explains it much much better than I can.

Lp/Patn(Appy coloring)-This one is sightly confusing. Lp and PATN can make base colors do very weird things, such as make chestnuts look like bays, or change shades A LOT. By itself LP is only the charecteristics of Appys like mottling ect and Patn is the gene that actually causes white. But the only way Patn is expressed is if the horse has Lp. Patn without Lp is just a normal horse no appy charecteristics at all. I can go into more detail but that is the basics anything more than that and it gets confusing. PM however if you would like a more in depth explaination.

Pearl-Pearl is one of the more complicated dilution genes. By itself pearl is recessive, meaning the horse needs two copies of the gene for it to have any effect. In its homozygous form it creates the appearance of a single cream dilutes. The only time pearl acts in its heterozygous form is in association with cream. If the horse has one copy of pearl and one copy of cream it creates a fake double dilute, except it is slightly too dark and has darker skin instead of pink. This is a homozygous Pearl horse with NO cream. And this is a horse who is heterozygous for cream and heterozygous for pearl.

And finally Brindle-There are two causes to brindle. One is a chimera. This is when two embryos are fertilized. One ends up getting absorbed by the other, but not fully. The resulting foal ends up being two horses fused as one. The horse can have two different colors, but each color will genetically test as I different horse. The TB Catch a Bird was a chimeric brindle. He never passed his brindle on to any of his foals. His roan offspring were the product of a mutation that most likely had little to do with his chimerism. The other cause is a genetic cause. The Warmblood Natal Classi is one example of a non chimeric brindle. His owner had him tested, and it was found out that he was infact not chimeric, and is believed to have passed his coloring on to at least one offspring. The other horses that have shown to be able to pass their brindle coloring to foals are these horses http://www.geocities.com/sbatteate/brindlehos/index.htm

Monday, September 24, 2012

Extension AKA Black or Red

Extension is the gene that controls whether a horse is black based (E) or red based (e), the only two colors that are true base colors. Every other horse color is a caused by a modifier or dilution. As I said in my last post black (E) is dominant over red (e). A black based horses genetic composition will be either Ee or EE, and a red based horses genetic composition will always be ee.

Here are some examples of black horses
This is Aloha. He is a black Mecklenburg stallion, standing at Gray Fox Farms. His genetic composition is Ee.

This is Redwine he is a Hannoverian stallion, who also stands at Gray Fox Farms, and also has a genetic composition of Ee.

This is Zorro. A homozygous black (EE) Friesian Stallion standing at Mon Cheval.

This is Sjoerd, another homozygous black (EE) Friesian stallion, standing at Three Day Ranch.

And here are the red based horses.
This is AC's Painted Lace. She, like all red bases is ee. (Photo copyright ACCPhotography)

This is the grand prix show jumping stallion Baloubet du Rouet. He of course is ee.

This is Couleur Rubin, a chestnut (ee) Oldenburg stallion

This is Don Schufro, a dark or liver chestnut stallion

Within the next week or so, I will be doing at least one other post on the Agouti modifier, and hopefully the Cream dilution as well!! See you then!

Sunday, September 23, 2012

Agouti aka The gene that makes black horses bay

This post covers agouti, the gene that makes a black horse into a bay. Agouti is dominant, meaning you only need one copy for it to express HOWEVER the horse also needs an "E" or black gene. If the horse is red based (ee) then the agouti gene will not express. So, in order for a horse to be bay based his genetic composition has to be either EeAa, EEAa, EeAA, or EEAA. A horse who is ee Aa, ee aa, or ee AA, will always be chestnut based. Here are a few examples of horses with at least one copy of agouti, and at least one copy of black. They are E?A?

This is Abra Khadabra, an Arabian mare from Epic Arabians. She is EEAa.

This is Galea MHF. She is a Pura Raza Espanola from WATCHMAN P.R.E. She is also EEAa.

This is Magic, a thoroughbred mare from Swan Creek Andalusians . She is ee Aa, and notice how her "A" has no effect on her chestnut color.

As a last little note, if researching for this post has taught me one thing, its that if you are planning to breed to a homozygous bay stallion because you only want a bay foal, make sure you ASK SPECIFICALLY what he is homozygous for. Some stallion owners call their bays that are homozygous black(EE), but only heterozygous for agouti(Aa) homozygous bay, but you still have a chance for a black foal there. Also they sometimes say homozygous for bay, but the horse is only EeAA, so you can end up with a chestnut foal.

Which is part of the reason I want to do this blog. IMO Homozygous bay should mean the horse is EEAA. If he is EE?? he is homozygous black. If he is ??AA he is homozygous agouti. The only thing that should be homozygous bay IS a horse who will only throw bays, and that is EEAA.

If you have any questions in regards to this post, feel free to leave them in the comments!

Saturday, September 22, 2012

Palominos, Buckskins, and Perlinos OH MY!

The cream gene (CR) is the gene that creates palominos, buckskins, smoky blacks, cremellos, perlinos, and smoky its. It is an incomplete dominant gene; this means that you get a different result when a horse is heterozygous for cream, than when it is homozygous for cream. For example it changes a chestnut to a palomino with one cream gene and then to a cremello with two cream genes. It changes a a bay into a buckskin with one cream gene and then into a perlino with two cream genes. It changes a black horse into a smoky black with one cream gene and then a smokey cream with two cream genes.

A chestnut will have a genetic composition of ee??crcr
A palomino will have a genetic composition of ee??CRcr
A cremello will have a genetic composition of ee??CRCR

A bay will have a genetic composition of E?A?crcr
A buckskin will have a genetic composition of E?A?CRcr
A perlino will have a genetic composition of E?A?CRCR

A black will have a genetic composition of E?aacrcr
A smoky black will have a genetic composition of E?aaCRcr
A smoky cream will have a genetic composition of E?aaCRCR

Here are two examples of palomino.
This is Lourinho AFA from Abacus Farms. He is eeAACRcr

This is BNWD Footloose Nfancyfree from Benwood Morgan Stables . Her genetic composition is eeAaCRcr.

Here are two cremellos.
This is Guaranteed Gold from True Colours Farm. He is ee Aa CRCR.

This is Son of a Gun's Moonwalker from Walk N Express. He is eeaaCRCR

Here are two buckskins.
This is Abacus Xanton from Abacus Farms. He is EeAaCRcr.

This is a buckskin stallion by Moret II out of Canela-R. He is EEAACRcr.

Here are two perlinos.
This is RS Hollywood Command from RR Bar Ranch. He is EEAACRCR.

This is Hmstd Rum Runner from Homestead Morgans. He is EeAaCRCR.

Here are two smoky black horses.
This is TCF Nightlight from True Colours Farm. She is EeaaCRcr.

This is Hopes Black Maria from Coosa Valley Farm. She is EEaaCRcr.

Here are two smoky creams.
This is The Key from The Brand Farm. He is EeaaCRCR.

This is Scott Creek Scrimshaw from Gold Vision Farm. He is EeaaCRCR.

If you have any questions in regards to this post, feel free to leave them in the comments.
Thanks to Audrey Crosby for help locating some of these horses!

Friday, September 21, 2012

Gray-The color eraser.

Gray (G) is a color modifying gene. It is also a dominant gene, which means one parent must be gray in order for the foal to be gray. Two non-grays cannot produce a gray. It gradually turns any color of horse, including any dilutes or pintos, white. The horse starts out its base color and then gradually turns white. One way to tell if a horse is going to gray when they are born is that they tend to be born their "adult" color rather than the tan or mousey color non gray foals are born. However not all foals born their adult color will gray and not all that are born tan/mousey wont gray, but I have found it to be pretty reliable. The study covering the gray gene in horses has just recently been released, in it they found a few things I personally found interesting.

1. Heterozygous grays are more likely to have fleabites.
2. Homozygous grays go gray faster.
3. Horses that are aa have a higher chance of getting melanomas.
4. Homozygous grays have a higher chance of getting melanomas.
5. Homozygous grays also have a higher chance of having vitiligo, or depigmentation of the skin.

This is Fuerst Gotthard from Rainbow Equus Meadows. He is homozygous for gray.

This is Lavita from Wild Turkey Farms. He is heterozygous for gray.

Thursday, September 20, 2012


Tobiano (TO) is a dominant gene. If tobiano is there it will express. Tobiano tends to create smooth round white patches on a horse. It also tends to travel up the back of the hind legs and over the rump to the other side. Sometimes the entire rump of the horse will be covered in white.Other times the white will stop just above the hocks, but will leave a stripe of white over the rump, or even in the tail. Tobiano in its minimal form can be as little as four white stockings. It rarely presents minimal enough to be mistaken for just white socks. Tobiano is also one of the few white patterns that never truly "hides." If a horse does not present as tobiano, even if its minimal, it is very likely NOT a tobiano. Tobiano wont be a completely solid horse, and it definitely will not hide for generations. Tobiano also does not cause blue eyes, nor any type of face white.

Here are a few examples of some tobianos.

This is Tru One Ina Million. He is by A Tru Rolex and was bred by Pine Springs Farm. He is homozygous for tobiano. He is Ee Aa TOTO. The movement of the white on his back left leg is very typical for a tobiano marked horse.

This is Sempatico. He is a Dutch Warmblood owned by Silver Wood Farm. He is EEaaTOTO. Notice the white going up the back of the leg and over the rump. Also notice the way the white travels from the front leg white up and over the neck.

This is Hall of Fame, another Dutch Warmblood owned by Silver Wood Farm. He is EeAaTOto. He has the classic tobiano pattern.

This is Extra Heir. He is heterozygous for tobiano. He is ee TOto. He is also marked like a classic tobiano, just a bit louder in expression. He stands at Riley Paint Horses.

If you have any questions regarding this post, or tobiano in general, post a comment and I will do my best to answer it.

Wednesday, September 19, 2012

Frame Overo AKA Lethal White and why the word Overo should no longer exist.

Since Frame Overo is the pattern most people think of when they hear the word "Overo" I think this is the perfect point in time to have the "Never use the word Overo" discussion.

What does the word "Overo" mean?

Well it truly means "Not tobiano." A horse in APHA who was not tobiano, but had qualifying white was registered as "Overo". The horses who had the splash pattern, the sabino pattern, dominant white, and frame overo were all registered as "overo".

Whats the problem with this you ask? Well, only one of those patterns has a horrible genetic disease associated with it, and lumping them all together can cause confusion over this genetic disease. Two options that would create less confusion, and better systems for registering would be to either have a separate category for tobiano, frame overo, splash white, sabino and dominant white or to have a category for LWO positive horses, and lethal white negative horses within the tobiano grouping and the overo grouping. This would help owners avoid creating more lethal white foals.

And now that we have had that discussion lets talk about Frame Overo/Lethal White.

Frame Overo is known by a few names. Its known as "Frame", Lethal White, LWOS, LWO, OLW, OLWS, and sometimes (though by now you know why this is bad, or you should LOL) just "Overo".

All of those names refer to the exact same gene and that is the "O" gene. It is technically an incomplete dominant gene like the cream gene is. In its heterozygous form it can cause anything from a completely solid animal, to a mostly white animal, with the majority being somewhere in the middle. Its homozygous form is an animal that is 95% or more white, and dies from complications caused by being homozygous for the frame gene.

Frame itself, does not usually cause leg white. How much face white frame will cause is up for debate. I personally believe frame will not cause more than a wide blaze. Others believe it will cause any amount of white on the face including a completely white head. Others even believe that frame will not cause any face white at all. Frame is also one of the only two patterns that can cause blue eyes.

Frames body white tends to move in a horizontal fashion across the horses body. It tends to start on the neck and the sides of the horse too, and then expand from there. Frame also tends to avoid the mid line of the horse, and avoids crossing the back especially between the whithers and the tail.

This is Nite Spot. He is a deceased thoroughbred stallion who was owned by Gestuet Falkenhorst. Notice the way his white has concentrated to his sides and his neck. This is a fairly typical presentation for a more minimal frame.

This is Dillon Ryan owned by Exclusive Equines. He is a 2006 APHA colt. Notice how the white has expanded further over his sides and his neck.

This is one of the loudest versions of the frame overo pattern. This is On Ice a 1982 APHA stallion. Notice how the white has moved horizontally across his body, and has avoided his mid line from whithers to tail.

Now, how do people unknowingly have LWO effected foals you ask since this pattern seems very easy to spot? Well frame overo has the incredible ability to be nearly invisible on horses. For example these three miniature horses (all three are separate horses) from Strebor Mini Horse Ranch, are all LWO positive.

Tuesday, September 18, 2012

Sabino-The "Everything" Gene

Sabino(SB) is an incomplete dominant gene, like Frame Overo and Cream. In Sabino's heterozygous form it creates minimal to normal white markings. In its homozygous form it creates a horse that is solid white. It is believed that any white marking not caused by any of the other "white marking genes," including splash, frame overo, tobiano, dominant white, and the appaloosa patterns, is caused by some form of sabino. It is also believed that there is more than one form of sabino.

Now, despite what many people think, horses do not need four high white stockings,a big blaze with lip spots, and belly spots to be sabino. A horse doesnt even need ONE of those things to be a sabino. Sabino can be as minimal as a sock or a star, and possibly even have no white at all. Sabino also has the ability to cause roaning on a horse, but this is not to be confused with True Roan, Rabicano, or Appaloosa Roaning.

The only sabino mutation that has been located is called Sabino 1. The researchers put the "1" after it because, like stated above, they believe there is more than one form of sabino out there. Sabino 1 is found in many breeds, but is most often found in Tennesse Walking Horses, Missouri Fox Trotters, and Miniature Horses.

These next horses are Missouri Fox Trotters from Mikarma Farms.
This is their stallion Color Master. He was used in the study for Sabino 1, and is homozygous for Sabino 1. This means he carries two copies of Sabino 1 and that every one of his offspring will have at least one copy of Sabino 1.

Here are pictures of four of his offspring. You can see just how minimal a sabino can truly be. All are heterozygous for Sabino 1

Monday, September 17, 2012

Dominant White--NOT sabino

Dominant White (DW) is a dominant gene. It is also believed to be EMBRYONIC lethal in its homozygous form. Meaning the homozygous foal is never born and is aborted/absorbed by the mare early during the pregnancy, unlike Lethal White Overo, where the foal is born and will die shortly after birth.

There have now been at least 11 different Dominant White mutations found, and like they started with Sabino, all have a number i.e. DW 1, DW 2....DW 10, DW 11. Now despite the name "Dominant White" not all horses who are Dominant White are solid white. According to research most are at least 50% white.

The reason I am breaking from my pattern of going in order down the genes in my first post on this blog is because Dominant White is a new thing, and many horses previously thought to be Sabino are, in fact, Dominant white. Most notably is the Puchilingui line in Thoroughbreds.

Puchilingui himself was tested in the most recent Dominant White study, and was found to be positive for Dominant White

His son Sato, from Blazing Colours Farm, was also used in the study, and he was found to be positive for Dominant White as well.

This mare is Puchi Trap, from True Colours Farm. She is a daughter of Puchilingui, and while she was not used in the Dominant White study, based on her appearance, and her bloodlines, it is a very good bet that she is also Dominant White.

Another separate line of Dominant Whites, is the "Patchen" line. This first horse is Patchen Beauty, with her foal Patchen Prince running at her side.

This is an older photo of Patchen Prince running in a race

And here is another of Patchen Beautys foals, The White Fox. All three of these horses are confirmed Dominant White

This is Airdrie Apache. He has NOT been confirmed to be Dominant White, however his pattern, and his production record really lend credence to the theory that the Airdrie Apache line is Dominant White

This is a son of Airdri Apache named Allamystique from Reed Hill Farm

This mare is also from Reed Hill Farm, and is a daughter of Allamystique, and a grand daughter of Airdrie Apache