The genetics of Appaloosa horses



Please note that these pages on appaloosa need updating to reflect more recent research. I will be doing some updating when and as I get chance and time, with the kind help of the people of the The Appaloosa Project . Many thanks to Sheila Archer for volunteering information and help with this.

Spotting only shows in horses with at least one copy of the dominant Appaloosa spotting allele LpLp, although it is then influenced by several other genes. Horses with this gene but no other spotting genes show at least one of the three minimal appaloosa characteristics. These are mottled skin pigment on the face and/or genitals, hooves striped with narrow vertical bands and white sclera of the eye. The skin pigmentation may not be present at birth, but the other two characteristics are. Pink and black mottled skin is one of the most indicative characteristics. It is always evident in the genital region and may also occur around the lips, muzzle, nostrils and/or eyes. An appaloosas eye is sometimes called the "human eye" due to the white sclera encircling the eye. Most other horses have a dark sclera.

Horses showing all three traits are said to be mottled. The expression of appaloosa characteristics is thought to be influenced by sex, possibly through an hormonal effect. There is some evidence that stallions show more patterning than mares. Jeanette Gower (1999) suggests the following phenotypes for horses with no other spotting genes:





Genotype at the appaloosa locus stallions mares
Lp+Lp+ solid solid
LpLpLp+ mottled 1 or 2 minimal characteristics
LpLpLpLp false snowflake mottled




Spotted horses come in an enormous variety of patterns. There are many names for the different patterns observed and some patterns are known by more than one name depending on the breed and the local customs. From a genetic perspective Jeanette Gower (1999) proposed a model based on four genetically distinct patterns, some of the genes involved are now being studied. The presence of one or more of these patterns in various combinations provides for the array of patterns actually observed. I will follow this model, and apply what has been found out since, as it seems to me the best available based on current understanding. The four patterns identified by Gower are snowcap or blanket (discussed below), appaloosa dark spots, appaloosa white spots and varnish. In the discussions of these it is assumed that there is at least one copy of the dominant spotting allele LpLp.



Congenital stationary night blindness

Homozygosity for LP is associated with congenital stationary night blindness (CSNB). CSNB is the name given to any inherited disorder that causes either impaired or absent night vision, which is present at birth but not progressive. Several forms of CSNB are known, not only in horses, but also in humans and other animals.

In a study of 30 horses by Sandmeyer et al (2007) all 10 horses homozygous for LP were affected by CSNB, while none of the heterozygous or homozygous lp horses were affected (so that the LP allele is recessive for this character). In the expression study (Bellone et al, 2008) the average expression levels of TRPM1 in the retina of homozygous horses (LPLP) was only 0.05% of the level found in the other horses.

Although the exact roles of TRPM1 in patterning and night blindness aren’t yet established TRP proteins in general are thought to have a role in controlling intracellular calcium ion concentration. Decreased expression of TRPM1 in the eye and the skin may alter both cell signaling and melanocyte function (another example of a gene showing pleiotropy). The mechanisms of action are yet to be determined.




Snowcap (white blanket)



Image of Style Image of Style snowcap filly

White patterning (often termed snowcap or white blanket) in Appaloosas appears to also be a polygenic, and the generic name “PATN” (for “pattern”) has been given to these genes. Horses inheriting both LP and one or more of these PATN genes it will have white appaloosa-type patterns, the extent of white varying according to which and how many PATN genes it has. Minimal white patterning can be just a sprinkling of white over the hips. Extensive white can cover most of the body, although usually some colour is retained just above the hooves, on the knees and hocks, stifles and elbows, hips, points of shoulder, mane and tail, and the bony parts of the face.

A solid horse may have PATN, with no effect in the absence of LP. If bred to a horse with LP allele the foal might inherit both LP and PATN, and display coat patterns not seen in either parent. A solid horse can thus potentially contribute patterns to its foal. This explains why a solid horse and a minimally marked Appaloosa can together produce a loudly marked foal.


Black roan few spot Blue Dove Mighty Ghost Few Spot  Stallion

A gene causing high white patterns (PATN-1) is thought to be on chromosome 3. Researchers intend to try and identify the gene and produce a test for it. PATN-1 may cause common-size "blankets" in heterozygotes and extensive "blankets" in homozygotes.

In the most extreme form of snowcap the white may cover the whole body with perhaps just dark “flash” markings on legs. This form is called few spot. According to Gower (2000) this type is true-breeding, and therefore homozygous (possibly for PATN-1, but time will tell). When crossed to non snowcap appaloosas the offspring show a white blanket (snowcap), providing they also least one copy of LP.




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