The dun gene is a dilution gene that affects both red and black pigments in the coat color of a horse. The dun gene lightens most of the body while leaving the mane, tail, legs, and primitive markings the shade of the undiluted base coat color. A dun horse always has a dark dorsal stripe down the middle of its back, usually has a darker face and legs, and may have transverse striping across the shoulders or horizontal striping on the back of the forelegs. Body color depends on the underlying coat color genetics. A classic "bay dun" is a gray-gold or tan, characterized by a body color ranging from sandy yellow to reddish brown. Duns with a chestnut base may appear a light tan shade, and those with black base coloration are a steel gray. Manes, tails, primitive markings, and other dark areas are usually the shade of the undiluted base coat color. The dun gene may interact with all other coat color alleles.
Dun is believed to be the ancestral or wild type color of horses. Many equines appearing in prehistoric cave paintings such as in Chauvet cave are dun, and several closely related species in the genus Equus show dun characteristics. These include the Przewalski's horse, onager, kiang, African wild ass, an extinct subspecies of plains zebra, the quagga, and an extinct subspecies of horse, the tarpan. Zebras can also be considered a variant of dun where the dilution is so extreme it turns the hair nearly white, and the primitive markings (like the striped leg barring) extend across the entire body.
Neither the non-dun1 nor the non-dun2 mutations were found in any other equids.
The dun gene has a stronger dilution effect on the body than on the primitive markings and on the point coloration of the mane, tail, ears, and legs. Thus it lightens the body coat more. This explains why points on a dun are darker than the coat, or in the case of a "classic" dun, the mane, tail, and legs often are black.
Dun traits include the following primitive markings and other features:
- Dorsal stripe down the center of the back, along the spine, seen almost universally on duns
- Horizontal striping on the back of forelegs, common on most duns, although at times, rather faint
- Facial mask, a darker area around the nasal bone and forehead, sometimes making the head close to the undiluted color, some patterns colloquially called "Cobwebbing."
- Transverse stripe, a crosswise stripe along the shoulders perpendicular to the dorsal stripe, less common in horses, very common in donkeys.
- Frosting: light hairs found on either side of the mane and on both sides of the dock of the tail.
- Dun, also called bay dun, classic dun, or zebra dun is the most common type of dun, and has a tan or gold body with black mane, tail, and primitive markings. Genetically, the horse has an underlying bay coat color, acted upon by the dun gene.
- Red dun, also called claybank, horses have reddish instead of black points, as there is no black on the horse to be affected. Instead, the points and primitive markings are a darker shade Reflecting that genetically, the horse has an underlying chestnut coat color, acted upon by the dun gene.
- Grullo or grulla, also called blue dun or mouse dun,is a smoky, blue-gray to mouse-brown color and can vary from light to dark. They consistently have black points and they often have a dark or black head. The primitive markings are usually all black. Genetically, the horse has an underlying black coat color, acted upon by the dun gene.
Other variations result from the interplay of additional genes:
- Chestnut + dun + cream gene (single copy) = "dunalino" or "palomino dun"
- Bay + dun + cream gene (single copy) = "dunskin" or "buckskin dun"
A single copy of the cream gene on a black base coat does not significantly lighten black hair, though it may have a subtle effect, and thus a single copy generally has no visible effect on a grullo, either. Conversely, double copies of the cream gene create very light-colored horses (cremello, perlino, and smoky cream). Thus, if a horse with two cream dilution alleles also carries the dun gene, it also will be cream-colored, with primitive markings not visible to any significant degree.
Dorsal striping alone does not guarantee the horse carries the dun gene. There two types of non-dun, called non-dun1 and non-dun2. Non-dun 1 removes the diluting effect of dun, but keeps the primitive markings, while non-dun 2 removes both the diluting effect and the primitive markings. The non-dun1 allele is over 40,000 years old, while non-dun2 is relatively recent, and is thought to have first appeared within the past several thousand years.
A countershading gene can also produce faint dorsal striping, even in breeds where dun coloration is not known to be carried in the gene pool. There are three known alleles of the dun gene, dun (D), non-dun1 (d1), and non-dun2 (d2). These appear to affect primitive markings. Dun is dominant over the other two, so a horse with D is dun regardless of whether the second allele is dun or non-dun. Horses that are d1/d1 or d1/d2 may have some asymmetry in pigment distribution, but much less than dun horses. Homozygous non-dun1/non-dun1 horses typically have clearer primitive markings than heterozygous d1/d2 horses. The primitive markings from non-dun 1 are more visible on a bay or chestnut horse than on black. A horse with two copies of non-dun2 lacks primitive markings as the hair color is completely saturated.
The Fjord horse breed, which is predominantly dun, uses unique Norwegian-based terminology to distinguish between the different shades of dun horses. "Brown dun," or brunnblakk is a zebra dun, rødblakk is a red dun, grå - literally "gray" - is a grullo, buckskin duns are called ulsblakk or white dun, and a dunalino (dun + palomino) is called a "yellow dun" or gulblakk. A cremello, perlino or smoky cream is called "white" or kvit.
Historically, before modern genetic studies distinguished between alleles, diluted colors were sometimes lumped together and simply called "dun".
The dun gene, when on a "bay dun" horse, can closely resemble buckskin, in that both colors feature a light-colored coat with a dark mane and tail, classic duns frequently are confused with buckskins. Buckskins with non-dun 1 primitive markings can easily be confused with dun.:32 The difference between these two colors is the dun is a tan color, somewhat duller than the more cream or gold buckskin, and duns also possess primitive markings. Genetically, a bay dun is a bay horse with the dun gene. A buckskin is bay horse with the addition of the cream gene, causing the coat color to be diluted from red to gold, often without primitive markings. Today, pedigree analysis, DNA testing, studying possible offspring, and the presence of other primitive markings are used to determine whether a horse is a dun.
A red dun may also be confused with a perlino, which is genetically a bay horse with two copies of the cream gene, which creates a horse with a cream-colored body but a reddish mane and tail. However, perlinos usually are significantly lighter than a red dun and have blue eyes.
Grullos are sometimes confused with roans or grays. However, unlike blue roan, dun has no intermingled black and white hairs, and unlike a true gray, which also intermingles light and dark hairs, the color does not change to a lighter shade as the horse ages. With a dun, the hair color itself is one solid shade and remains so for life.
To further confuse matters, it is possible for a horse to carry both dun and cream dilution genes; such horses with golden buckskin coloring and a complete set of primitive markings are referred to as a "buckskin dun" or a "dunskin". On such horses, the light-shaded primitive markings are most noticeable during the summer months, when the winter hair sheds.
Countershading may be harder to differentiate between countershading and a dorsal stripe on light-colored horses such as red duns.
The dun allele is dominant, so the phenotype of a horse with either one or two copies of the gene is dun. In effect, two non-dun parents cannot produce a dun foal. It has a stronger effect than other dilution genes, such as the silver dapple gene, which acts only on black-based coats, or the cream gene, an incomplete dominant which must be homozygous to be fully expressed, and when heterozygous is visibly expressed only on red (bay and chestnut) pigment.
The dun dilution effect is caused by pigment only being placed in a part of each hair. Specifically, body hairs only have pigment along one side of them, while hairs from darker parts such as the dorsal stripe have pigment all the way around. Dun was the original color of horses, but most horses today are non-dun.
A primary characteristic of the dun gene is the dorsal stripe, and most duns also have visual leg striping. The shoulder stripes are less common and often fainter, but usually visible on horses with a short summer coat.
Genetic analysis and DNA sequencing results published in 2015 link dun color to the T-box 3 (TBX3) transcription factor. When functional, it creates dun coloring, including the primitive markings, and when recessive, a horse is not dun. In humans and lab mice, TBX3 affects affect bones, breast tissue, and cardiac conduction; inactivation of the TBX3 gene affects a protein function and is linked to ulnar–mammary syndrome. The study demonstrated that TBX3 also affects skin and hair. In non-dun horses, the TBX3 protein is still functional, just not expressed in the hair. Where diluted color exists, the color is not uniform, but rather is more intense on the outward-facing side of the hair shaft and lighter underneath. In the darker areas, where the primitive markings occur, the hair shaft is of uniform color. One of the researchers involved in the study said it could be called a "microscopic spotting pattern".: This phenomenon is new to science and has not been observed in rodents, primates, or carnivores.
The 2015 study also identified the two forms of non-dun color, non-dun1 and non-dun2, caused by different mutations. Non-dun1 horses have some primitive markings, while non-dun2 horses do not. It is thought that the non-dun2 genetic mutation occurred after domestication, whereas dun and non-dun1 predate domestication. Ancient DNA from a horse that lived about 43,000 years ago, long before horses were domesticated, carried both dun and non-dun1 genes. The location of TBX3 expression may also determine the striping pattern of zebras.
Both non-dun1 and non-dun2 are found in a region of equine chromosome 8 whose only gene is TBX3. Non-dun1 has a guanine where dun has an adenine at chromosome 8 base pair 18,226,905, which appears to be sufficient to cause non-dun1 coloration. In addition, non-dun1 has another single nucleotide polymorphism compared to the version of dun that is most common in domestic horses, where a guanine in dun is replaced with thymine in non-dun1 at chr. 8: 18,227,267. However, that SNP was also found in some dun Estonian native horses, so is not necessary for dun. Non-dun2 has a 1,609 bp deletion and another very near 8 bp deletion. Comparison with TBX3 in other species showed that the non-dun2 deletion is a more derived allele. Nucleotide diversity across the flanking regions of chromosome 8 for the various alleles indicates that the non-dun2 mutation most likely occurred on a chromosome that already had non-dun1.
In some hair bulb keratinocytes, non-dun1 and non-dun2 are thought to disrupt the function of a transcriptional enhancer that regulates the expression of TBX3 during hair growth. The region deleted in non-dun2 is predicted to include binding sites for the transcription factors ALX4 and MSX2, which are both known to be involved in hair follicle development. TBX3 was significantly downregulated in non-dun horses compared to dun horses, while the neighboring gene, TBX5, was expressed in about the same amount. In dun horses, the pattern of TBX3 expression mirrored the pattern of pigment deposition in the hair, that is, TBX3 was found wherever the pigment wasn't. TBX3 was not found in the hair cortex keratinocytes from non-dun horses, nor in those from the dorsal stripe of dun horses. However, all of the horses had a thin outer layer of the hair where TBX3 was expressed. Two markers of mature melanocytes, KIT and MITF, were found only in the pigmented areas of the hair. This indicates that the hair follicles of dun and non-dun horses have different distributions of pigment producing cells. KITLG encodes KIT ligand, a molecule required for melanocyte migration and survival in the skin and hair follicle. Keratinocytes expressing KITLG were found all the way around the hair in non-dun horses, but only on the pigmented side in dun horses. The region where KITLG was not expressed was similar to, but not exactly the same as, the region where TBX3 was expressed. TBX3 is not thought to directly affect KITLG expression.
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