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Post by Capriole Admin Account on Aug 5, 2013 1:19:10 GMT -5
The Official Capriole Genetics Guide
Let's be real, genetics can be confusing! And it doesn't help that you may feel like the only person who doesn't know how to use them! Because a majority of our members use realistic genetics, this guide is here to help out those who may feel excluded by not understanding the ins and outs of equine color genetics.
Keep in mind that this is just a basic guide. Equine color genetics are very, very complicated, and are not fully understood, even by the experts. The guide will continue to be updated if any new advancements are made in understanding color genetics.
If any of this appears incorrect, please let an administrator know! Include in your message the part that's incorrect, the correct information, and a reliable source to back up your claim, so we can make sure that this guide is as correct as possible!
This guide only covers the basics of color genetics. It does not include the other aspects of genetics, like diseases, traits, etc.
The Basics of Genetics
The Extension Gene
The Agouti Gene
The Gray Gene
Cream Dilution
Dun Dilution
Champagne
Silver Dapple and Flaxen
Roan, Rabicano and Sooty
Pinto Coloring
The KIT Gene
Appaloosa
Writing the Genotype
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Post by Capriole Admin Account on Jul 21, 2014 16:11:14 GMT -5
The Basics of Genetics
Before you start trying to figure out the genotypes of your horses, it's important to understand the way that genetics work! Without a basic understanding, you'll have a hard time grasping the specifics.
There are two terms we use when describing genetics. The genotype, and the phenotype. The genotype is the genetic code, while the phenotype is how the genotype expresses itself visually. You can think of it as the genotype being the HTML code, and the phenotype being the web page! In terms of horses, the genotype includes the letters, such as Aa. The phenotype includes the color, such as bay.
The traits the foal can inherit from the parent are called genes. Half of a gene, called an allele, are inherited from each parent. (The sire gives one, the dam gives the other). The way the two alleles interact determine which trait from the parent is inherited. (For example, the sire's genotype is XX and the dam's is xx. The foal will inherit one X allele from the sire, and one x allele from the dam, giving it the genotype Xx)
Alleles can either be dominant or recessive. Dominant genes, shown by a capital letter in the genotype, are basically the boss of the recessive genes. If a dominant gene is present, it always shows itself (Unless masked by another gene). When a gene is recessive, in order to be visible, it must have two copies of the recessive gene. Because of this, sometimes horses carry a recessive gene for generations and it'll suddenly show up, especially if it's hidden by other traits!
Genes can either be described on a horse as heterozygous or homozygous. Heterozygous means the horse has different alleles within a gene, and homozygous means the horse has two of the same alleles. (For example, a black horse with Ee is heterozygous and a black horse with EE is homozygous. A horse with ee is also homozygous.)
When breeding two horses, you can either use a genetics calculator, or do it by hand. If you prefer to do it by hand, follow these steps:
Go gene by gene. Usually, it's easiest to start with the extension gene, because this serves as a base. The general format of the genotype goes extension, modifier genes (like gray, cream, dun, etc.), and then pattern genes (like roan, sooty, tobiano, etc.). This is not required, however, and you can write the genotype in whatever order you want.
When doing the inheritance of genes by hand, it's helpful to draw a punnett square. A punnett square is a diagram that predicts the outcome of the crossing between two organisms. Say you're figuring out whether the foal will be bay or black. Here's an example punnett square.
Here, we cross two bay horses. You can have the sire or dam on any side, it doesn't change the outcome. You can see that if both parents pass on the A gene, the genotype will be AA. If one passes A and one passes a, the genotype will be Aa. And if both pass the a gene, the genotype will be aa.
If you want to calculate by hand, you can draw the punnett square for the gene and then use a random number generator to pick 1, 2, 3 or 4. Each section has a 25% chance of being the one the foal has. Do this for each gene and then you're done! |
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Post by Capriole Admin Account on Jul 21, 2014 16:15:52 GMT -5
The Extension Gene (E, e)
The extension gene is the most basic of all the color genes. It answers the simple question: is the horse red, or is the horse black? While there are tons of genes that interact to give the horse its color, they all are built off of the two basic colors, chestnut and black.
The dominant allele (E) in the extension gene causes the horse to produce black pigment called eumelanin. Its recessive allele (e) produces pheomelanin. Because black is a dominant color, the horse must have two recessive alleles (ee) to be chestnut, while a black horse could have EE or Ee.  Above is an example of a chestnut horse and a black horse.Source: VenomxBaby |
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Post by Capriole Admin Account on Jul 21, 2014 16:27:16 GMT -5
The Agouti Gene (A, At, A+, a)
The agouti gene is what's known as a modifier gene. Modifier genes work only when certain genes are present. The agouti gene modifies the black pigment on the horse by restricting it to certain areas. Because it only modifies black pigment, it will only express itself if the horse is black based. Chestnut horses can still have all the different agouti genes in their genotype, but the horse will always look chestnut. It is unclear whether the presence of agouti genes changes the shade of chestnut horses, and is still debated among genetics experts.
The agouti gene is different from other genes because it has 4 different alleles instead of 2. This means that there can't be a simple dominant-recessive relationship. Instead, the agouti alleles have a hierarchy, where each allele has a certain level of dominance over the others.
The most recessive agouti allele is the a allele, which does not restrict black pigment, and therefore results in a completely black horse. Because a is recessive, the horse must have two a alleles to show up as black. (Ee aa or EE aa will result in a black horse.)
One step up from this allele is the At gene, which restricts black pigment from the soft areas of the body, resulting in seal brown coloration. This gene is dominant over a, but recessive to A and A+, and therefore will be hidden by these genes. (A/At will not be a seal brown horse, but At/At or At/a will be seal.)
The next step up is the A gene, which causes the normal bay color. A regular bay horse will have black on its legs, which extend up to or above the knees, black points on the ears, and the mane and tail will be black. (A horse with Aa or AA will be bay. Bay horses can also have an A/At genotype and show up as bay)
The most dominant of the agouti alleles is the A+ gene, which causes the color known as wild bay. Wild bay horses have the black mane and tail like a normal bay, but the black pigment on its legs will only extend up to the pastern. The A+ allele is still very new and not widely researched, and is considered very rare. Information regarding it isn't exactly concrete. (No matter what agouti genes the horse has, if the A+ gene is present, the horse will always be wild bay.)    Above are examples of a bay horse (top), a seal brown horse (middle), and a wild bay horse (bottom). Sources: Bay HorseSeal Brown HorseWild Bay Horse |
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Post by Capriole Admin Account on Jul 21, 2014 16:41:11 GMT -5
The Gray Gene (G, g)
The gray gene is sometimes a very confusing gene. But before we go into depth about it, you should know the difference between white and gray. Gray horses are incredibly different than white horses. Gray coloring is caused by a completely separate gene, and begins to show up over time. While gray horses may appear white, they always start out as the color hidden under the white, and "gray out" with age. White horses are born white, and the coloring is caused by a completely different gene than the gray gene. You can tell the difference between a very light gray horse and a white horse by the color of the skin. Gray horses have dark skin, while white horses have pink skin.
The gray gene has two alleles, G and g. The gray gene behaves a bit differently than other genes, because it shows up over time rather than being immediately apparent. The gray gene acts almost like a mask. When a horse has the dominant gray allele, the gray coloring sits on top of the horse's base color. When the gene is present, the horse is born with its normal color, and like human hair, it'll fade as the horse ages until it turns to a snowy white. During the phase of graying out, the horse can show a variety of colors and patterns. Below are a few of the common types of transitional gray colors that horses can show up as. (On Capriole, it's very common for horses to be born with the gray pattern that they keep for their whole lives. While it isn't necessarily realistic, it's definitely easier than creating the base coat and having it gray out over time. Both methods of having a gray horse are accepted on Capriole, and neither one is preferred.)
Dapple gray: An intermediate stage that is not seen on all grays, but is considered very attractive. It consists of dark hair, which can either be concentrated in certain areas or all over the body, with lighter colored circles scattered over the dark areas. (This is not to be confused with the dapples that can show up on horses that don't necessarily have the gray gene.) Rose gray horses are bay or chestnut based with gray hairs starting to show through. It can often be confused for roan, but is genetically different, and the coloring underneath will fade with age, unlike with roan horses. Iron/Steel Gray horses are black based, with similar properties to rose gray. Like with other grays, the base color that shows through underneath fades with age. Mulberry gray horses are horses with a chestnut base coat, where the chestnut shows through the gray on the legs, and the mane and tail are red with light tips. This is mostly seen in Andalusian horses.
Horses can gray out into two ending stages. White gray horses have had their coats, manes, and tails completely lightened, with the dark skin still showing through where the hair is thin. Fleabitten gray horses are completely grayed out, except flecks of the base color are retained in the coat. This is more common in Arabian horses.      Examples of (in order): a dapple gray horse, a rose gray horse, a steel gray horse, a mulberry gray horse, a white gray horse and a fleabitten gray horse.Sources:
Dapple Gray
Rose Gray
Steel Gray
Mulberry Gray
White Gray
Fleabitten Gray |
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Post by Capriole Admin Account on Jul 21, 2014 16:45:28 GMT -5
Cream Dilution (CR, cr, prl)
The cream gene is what's known as an incomplete dominant. This means that a single dominant allele, expressed as CR, will have a different effect on the base color than if two dominant alleles are present. When talking about the cream gene, we can differentiate the two by calling them single dilute and double dilute.
Single dilute colors will lighten the base color and the mane and tail, while double dilutes will lighten the horse to near white and give them pink skin and blue eyes.
When layered over a chestnut horse, a single cream allele will give you a palomino, which are gold in color with a white mane and tail. Black horses will give you smoky black, which shows up as a dark brown horse, sometimes with light brown mixed in. Over a bay horse, the cream gene will show up as buckskin, which is like a bay except with a golden coat instead of a red coat. The points remain starkly black.
The double dilute colors include cremello and perlino. Cremello is when two cream genes are layered over a chestnut horse. The horse will appear near-white, with the coat being varying light shades of red and the mane and tail being white. Perlino horses are caused by two cream genes being layered over bay, and appear like a cremello, except black points from the bay coloring will show up as a dark reddish color on the legs and mane and tail.
Recently, a third allele has been discovered, called pearl. Pearl, on its own, will do nothing, but when a dominant cream allele is in the mix, it will enhance that allele and result in a pseudo-double dilute. Two pearl genes will result in a warm dilution color, which is sometimes called apricot.      Examples of (in order) a Palomino horse, a Smoky Black horse, a Buckskin horse, a Cremello horse, a Perlino horse, and an Apricot horse.Sources:
Palomino, Cremello, Perlino
Smoky Black and Apricot
Buckskin |
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Post by Capriole Admin Account on Jul 22, 2014 13:42:53 GMT -5
Dun Dilution (D, d)
The dun dilution gene works by diluting pigment to reveal "primitive" markings, which are patterns in the original base color. These are classified as a dorsal stripe, leg barring, shoulder stripes, ear barring, forehead spider-webbing and face masks.
The dun gene affects all colors, and all duns will have the dorsal stripe and most have leg barring.
On a black horse, the dun gene will cause the grullo color. Grullo is a dark, silvery color with black primitive markings. Over chestnut, the gene will cause the red dun color, which is best described as a light apricot color with dark red primitive markings. Over bay coloring, the dun gene will cause the classic dun color, which is a tan color with black points and black primitive markings.    Examples of (in order): a Grullo horse, a Red Dun horse, and a Classic Dun horse. Note the dorsal stripes and primitive markings. Source for all 3 images |
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Post by Capriole Admin Account on Jul 23, 2014 8:50:41 GMT -5
Champagne (CH, ch)
The champagne gene is an incredibly rare gene. It affects both red and black pigment, and dilutes the skin of the horse to a freckled pink. Champagne horses also have hazel eyes.
Over a black horse, the champagne gene will cause the classic champagne color, which is a silvery color with darker silver mane and tail. Bay horses with the champagne gene are amber champagne, and are a golden color with a darker mane and tail and darker points. Over chestnut, it'll create the gold champagne color, which is very similar to amber champagne, except the mane and tail match the coat color, and there are no points.    Above are examples of (in order): Classic Champagne, Amber Champagne, Gold Champagne. Please note that the classic champagne horse has tobiano coloring, so the white in the mane and tail is caused by the tobiano gene. If you look at the top part of the mane, the forelock and the dark color in the tail, you'll see the general mane/tail color classic champagnes have. Source for all 3 images |
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Post by Capriole Admin Account on Jul 23, 2014 8:54:58 GMT -5
Silver Dapple (Z, z) and Flaxen (F, f)
Silver Dapple and Flaxen are categorized together, because they both affect the mane and tail more than the body, and each only affect one type of base color. Silver dapple only shows up on black horses. Because it's dominant, it will show up with only one copy of Z. It mostly affects the mane and tail, but does dilute the black pigment. On an all-black horse, the body will be a dark, silvery color that may have dapples. On a bay horse, the gene will only affect the black pigment. The horse will maintain its red body color, with the mane, tail and points diluting to silver. Silver does not affect chestnut horses at all, so chestnuts may silently carry the gene.
Flaxen only affects chestnut horses. Unlike silver dapple, it is recessive, and will only show up on a chestnut horse if the horse has the ff genotye. Ff or FF do not show flaxen. Flaxen only affects the mane and tail, making them a blonde color, while the body retains its red coloring. Flaxen does not affect black horses, so black horses may silently carry the gene. Even with an ff genotype, flaxen will not show itself on black based horses.   Examples of (in order) a silver dapple horse and a flaxen chestnut horse. Sources: Silver DappleFlaxen Chestnut |
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Post by Capriole Admin Account on Jul 23, 2014 9:22:18 GMT -5
Roan, Rabicano and Sooty (RN, rn+, RB, rb, STY, sty)
While roan, rabicano and sooty are not genetically related, they're categorized together because they change the color of stray hairs that are mixed into the normal coloring of the horse.
The dominant roan allele (RN) creates a roan horse. Roan horses have white hairs mixed in with the base color in a relatively even distribution, with the concentration being on the body, with less roaning occuring on the head, legs, mane, and tail. On a black coat, it'll cause blue roan coloring. Chestnut horses with roaning are called strawberry roans, and on bays roaning causes bay roans.
Rabicano is similar to roan, though they are genetically separate, and rabicano horses do not have separate colors from their base color. Rabicano causes roaning only on the belly.
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Post by Capriole Admin Account on Jul 23, 2014 9:38:00 GMT -5
Pinto Coloring (TO, to+, O, o+, SB1, sb1+, SPL, spl)
There are four distinct pinto colorings, caused by four different genes.
Tobiano coloring refers to when the white patches of the horse cross the topline. The legs normally have a lot of white. Tobiano spots are generally rounded and in a vertical pattern, and the face is usually colored. Tobiano is a dominant gene, and will show up whenever the dominant allele is present.
Frame Overo is classified by irregular, jagged white patches arranged in a horizontal fashion. Frame overo horses never have white crossing the topline, and the legs are usually colored. The face is at least partially white, and blue eyes are not uncommon. Frame overo is associated with Lethal White Syndrome, and if two dominant overo alleles are present, the foal will die.
Sabino is an incomplete dominant allele within the KIT gene. When sabino is heterozygous, white markings will generally show up as rough-edged white markings on the legs and the face. They also can have white patches or roaning on the belly or flanks. The white patches will have pink skin, but never have blue eyes. Homozygous sabino horses are typically 90% white at birth, and sometimes it's difficult to tell them apart from a dominant white horse.
Splashed white is a pattern where it appears like the horse's legs and face were dipped in white paint. They often have blue eyes, even if the white doesn't cross the eyes. They often have a white tail tip. Splashed white is similar to sabino, but splashed white markings are crisp and clean, while sabino markings are rough on the edges. It can be difficult to tell when a horse is minimally splashed, and not all splash whites are identified as such.
Tovero horses occur when both tobiano and overo genes are present. It's very difficult to determine whether a horse is tovero without a genetic test. Tovero horses generally exhibit both tobiano and overo patterns, but might be minimally expressed.Splash and sabino can be difficult to identify in some horses, especially when it's minimally expressed, so below I've included photos of both maximum expression (or "loud") and minimal expression.        Above are examples of (in order): a tobiano horse, an overo horse, a "loud" sabino, a minimal sabino, a "loud" splash, a minimal splash, and a tovero. Note how in the minimal splash, blue eyes are present, even though there are very few white markings, and how on the tovero horse, it can be difficult to identify it as such. Sources: Tobiano and ToveroOvero
Maximum SabinoMinimal SabinoMaximum Splash
Minimal Splash |
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Post by Capriole Admin Account on Jul 23, 2014 9:44:47 GMT -5
The KIT Gene
The KIT gene is responsible for many different white patterns. The four known white pattern alleles linked to KIT are roan, tobiano, sabino, and dominant white. Because these are all linked, each horse can only have two of them present at one time. (A horse can only have two KIT alleles at one time. For example, a horse cannot be homozygous tobiano and be roan)
The KIT gene is complicated and is not fully understood.
Dominant white (W, w+), which is within the KIT gene, is responsible for pure white horses with pink skin and blue eyes. These are not albino horses (albinism has not been proven in horses). Dominant white behaves like gray in the sense that it completely masks the color under it, but white horses do not gray out, and instead are born white. Like overo, the dominant white gene is linked to Lethal White Syndrome, and can only have one copy of W at a time or else it will die.    The first photo is NOT a white horse. It's a white gray horse, caused by the gray gene instead of the white gene. You can spot the difference in the skin around the muzzle and eyes. Gray horses have black skin, white horses have pink skin. The second and last photos are examples of dominant white horses. The first dominant white horse has a more minimal expression, and the last one has the most maximum expression of white. Sources: Gray HorseMinimal Dominant White
Maximum Dominant White |
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Post by Capriole Admin Account on Jul 23, 2014 9:54:03 GMT -5
Appaloosa (LP, lp, PATN1, patn1, PATN2, patn2)
Appaloosa patterning is a bit complicated, and is not caused by a single gene. Instead, it's part of a gene "complex" called the "leopard complex". The key gene in the complex is referred to as LP for leopard complex, and by itself will result in varnish roan coloring. Despite the name, it is not related to the roan gene. The other genes in the complex, PATN1 and PATN2, are responsible for the other spotting patterns within the leopard complex. Without LP, these genes will not show up, as they're reliant on the LP gene being present. A horse carrying one of these pattern genes without LP will show up as a solid horse.
The different patterns of appaloosa are caused by two factors. One is the LP gene, and whether or not it's present, heterozygous, or homozygous. The other factor is which pattern gene is present.
When PATN1 and PATN2 are not present, the horse will be a varnish roan. The horse must either be heterozygous or homozygous in LP for PATN1 and PATN2 to show. PATN1, with LP being heterozygous, will cause the leopard appaloosa color. When LP is homozygous, it will cause few-spot appaloosa. PATN2, with LP being heterozygous, will cause the blanket appaloosa color. When LP is homozygous, it will cause snowcap appaloosa.
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Post by Capriole Admin Account on Jul 23, 2014 9:54:47 GMT -5
Writing The Genotype
Writing the genotypes for the horse can be very complicated, but once you get the hang of it, you'll find it super easy! To start, look at the color of your horse. If you don't know the actual color of the horse (for example, you know your horse is a bay tobiano), take a look at the traits of the color to figure it out. The guide below is an easy, step-by-step way to write your genotype, and might not be completely accurate or the way you want to write your genotype. If anything is wrong, let us know!
Step one is to see if the horse is red or black based. If the horse is red based, its genotype will always be ee. If it's black based, the horse can either have Ee or EE. If the horse is a foundation, and you're able to make up the genotype yourself, feel free to choose either Ee or EE. If the horse is second generation or higher, consult either the breeder of the horse, or look at the genotypes of the sire and dam. The only difference between EE and Ee, for example, is whether or not the foals can possibly be chestnut. A horse with EE cannot produce chestnut foals, even with a chestnut mate.
With almost all genes, when writing the genotype, you write uppercase for dominant and lowercase for recessive. This does not apply to the KIT genes, however. When writing the KIT genes, instead of doing something like TO/to (though you can), you denote the absence of the dominant gene as "n" or "to+". This basically says that the horse only has one tobiano gene, instead of having one dominant tobiano gene and one recessive tobiano gene. So if you're writing tobiano, you write TO/to+ or TO/n. This applies also to roan, sabino, white, and overo.
Why do we write slashes? It's just to make it easier to read! Which one is easier for you? TO/to+ or TOto+? It's honestly just aesthetics.
An example of a complete genotype would be Ee Aa TO/to+. When the horse does not have a certain gene, like recessive flaxen, dun, champagne, etc., you just simply don't have to write it in. You can, but it makes the genotype look cluttered, and provides unnecessary specification. By looking at the above genotype, we can see, for example, the horse has no chance of passing on gray, flaxen, champagne, roan, silver, etc., so we don't need to add it in. The exception here is for genes like agouti and extension, where it DOES matter to see that, for example, the horse is homozygous dominant for extension. |
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Post by Capriole Admin Account on Jul 23, 2014 9:55:42 GMT -5
Helpful Links
Guide to Horse Colors and Patterns - A handy-dandy image guide showing the interactions between different genes, and gives a small visual aid to show all the different colors.
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