The Agouti Locus

Location: Chromosome 22 - Agouti-Signaling Protein (ASIP) Gene
Inheritance: Autosomal
Alleles: Two
The A Locus Alleles

• A+ - Agouti, dominant. Permits the expression of eumelanin in the hair coat on the points of the horse. e.g. mane, tail, legs.
• a - Self, recessive. Expands the area where eumelanin is permitted to be expressed to cover the entire body.

The Champagne Locus

Location: Unmapped
Inheritance Mode: Autosomal
Alleles: Two Theorized
The Ch Locus Alleles

• Ch - Champagne, dominant. Lightens eumelanin to a lilac/chocolate color, and phaeomelanin to a buff/gold color in the adult coat. Foal coats typically do not show the champagne affect. Eyes are lightened, being bright blue at birth, and turning to hazel as adults. Skin is bright pink at birth, gaining a freckled appearance with age.
• ch+ - Non champagne, recessive.

The Cream Locus

Location: Chromosome 21 - Membrane-Associated Transporter Protein (MATP) Gene
Inheritance Mode: Autosomal
Alleles: Two
The Cr Locus Alleles

• Cr+ - Normal color, incomplete dominant. This means it takes two copies of the Cr+ gene to have normal color.
• cr - Cream. This allele has a stronger dilution effect on phaeomelanin than it does on eumelanin. In heterozygous form it has little if any visible effect on eumelanin. This results in 'cryptic' blacks who are often only identified after producing a cream dilute foal, or being DNA tested.

The Dun Locus

Location: Chromosome 8 - exact gene unknown
Inheritance Mode: Autosomal
Alleles: Two Theorized
The D Locus Alleles

• D+ - Dun, dominant. Dilutes the barrel area, neck and upper legs. Leaves a dark dorsal stripe, zebra stripes on the upper legs. Often has a dark face mask, ear barring, neck cape, and wither bars.
• d - Non dun, recessive.

The Extension Locus

Location: Chromosome 3 - Melanocortin-1 Receptor (MC1R) Gene
Inheritance Mode: Autosomal
Alleles: Two
The E Locus Alleles

• E+ - Full extension, dominant. The presence of this gene allows for the expression of eumelanin in the hair shaft.
• e - Recessive red, recessive. Red factor. In its homozygous form (e/e) it prevents the expression of eumelanin in the hair, but does not affect phaeomelanin. This locus is epistatic to the A and K loci.

The Flaxen Locus

Location: Unmapped
Inheritance Mode: Autosomal
Alleles: Two Theorized
The F Locus Alleles

• F+ - Non flaxen, dominant.
• f - Flaxen, recessive. In its homozygous form (f/f) it will result in a bleaching effect on the mane and/or tail of e/e recessive red horses. It has no effect on eumelanin.

The Grey Locus

Location: Chromosome 25
Inheritance Mode: Autosomal
Alleles: Two
The G Locus Alleles

• G - Grey, dominant to non grey. Causes progressive loss of pigment in the hair shafts as the horse ages. This mutation causes an increased formation of melanomas. This is further increased in horses homozygous for the grey mutation. It is also increased if the horse is also a/a at the Agouti locus. Horses that are a/a G/G will have the highest incidence of melanoma formation. Homozygous horses also have a higher incidence of vitiligo. Horses that are homozygous for this mutation will grey faster than horses that are heterozygous. Heterozygous horses have a higher incidence of being flea bitten grey.
• g+ - Non Grey, recessive.

The Dominant Dark Locus

Location: Theoretical
Inheritance: Autosomal
Alleles: Two Theorized
The K Locus Alleles

• K - Dominant self, dominant. Epistatic to the A locus, this gene will allow for expression of eumelanin over the entire coat regardless of what alleles are present at the A locus. i.e. A+/a E+/E+ K/- without dilutions will be a black horse. The presence of e/e will suppress the expression of K. -- This is a theorized allele.
• k+ - normal, recessive.

The Pangare Locus

Location: Unmapped
Inheritance: Autosomal
Alleles: Two Theorized
The Pa Locus Alleles

• Pa+ - Pangare, dominant. Also known as mealy. It has no effect on eumelanin, but lightens phaeomelanin on the soft parts of the horse such as flanks and muzzles. The late Dr. Bowling attributed this gene for turning chestnut into sorrel as seen in Haflingers.
• pa - Non mealy, recessive.

The Pearl Locus

Location:
Inheritance: Autosomal
Alleles: Two
The Prl Locus Alleles

• Prl+ - Normal color, dominant.
• prl - Pearl, recessive. In its homozygous form, this mutation will alter Chestnut horses to a gold color with freckled pink skin. This phenotype is virtually indistinguishable from Buff. In either its heterozygous or homozygous form combined with heterozygous cream, this mutation creates a phenotype that is indistinguisable from homozygous cream. It dilutes the skin to pink, coat to off white, and eyes to blue.

The Roan Locus

Location: Chromosome 3 - Believed to be KIT Gene.
Inheritance: Autosomal
Alleles: Two Theorized
The Rn Locus Alleles

• Rn - True or Classic Roan, dominant. Produces a very distinct pattern of roaning, leaving the head, mane, tail, and legs unroaned. The forelegs will sport inverted V's over the knees.
• rn+ - Non roan, recessive.

The Rabicano Locus

Location: Unmapped
Inheritance: Autosomal
Alleles: Two Theorized
The Rb Locus Alleles

• Rb - Rabicano, dominant. Creates minor to moderate roaning of the flanks and in some cases the barrel. Causes the distinct 'skunk tail', turning the tail head white.
• rb+ - Non rabicano, recessive.

The Silver Locus

Location: Chromosome 6 - PMEL17/SILV Gene
Inheritance: Autosomal
Alleles: Two
The Z Locus Alleles

• Z - Silver, dominant. Silver acts on eumelanin only, diluting black to liver/chocolate brown. Manes and tails are often show a stronger dilution affect, turning flaxen to white.
• z+ - Non silver, recessive.

A few helpful hints:

G - All horses that are G/- will grey out with age.
A G/G horse will always have foals that grey out with age.
Greying may not be visible on double cream (cr/cr) horses, or horses with many dilution factors, or extensive white markings due to their extreme lack of pigment.

e/e - Recessive red will prevent the expression of bay, brown, black, and silver. Two e/e horses bred to each other will never have a Bay, Black, or Brown based foal.
An E+/E+ horse is not Red Factored, and will never have a Chestnut based foal.
Horses that are E+/e are Red Factored, and can have e/e offspring if paired with a mate that is also Red Factored.

Ch - Silver, Cream, or Dun will show on a Champagne that does not also have another dilution gene present. Combining Champagne with multiple dilutions makes it virtually impossible to detect which are present without DNA testing. Neither Roan nor Rabicano are distinguisable on a Champagne. Champagne is not visible on double cream (cr/cr) horses.

prl - Neither Silver, Roan, nor Rabicano are distinguisable on a Fawn.

Cr+/cr will make bay into buckskin, black into smoky black, and chestnut into palomino.
cr/cr will make bay into perlino, black into smoky cream, and chestnut into cremello.

Ch will make bay into amber, brown into dove, black into lilac, and chestnut into buff.

prl combined with Cr+/cr will make bay into sesame, black into ash, and chestnut into platinum. prl/prl with Cr+/Cr+ will turn chestnut into fawn.

Pattern information:

The Frame Locus

Location: Chromosome 17 - Endothelin Receptor Type B (EDNRB) Gene
Inheritance: Autosomal
Alleles: Two
The Ov Locus Alleles

• Ov - Frame Overo, incomplete dominant. Lethal in its homozygous (Ov/Ov) form
• o - Not Frame.

The Lp Locus - Autosomal

Location: Chromosome 1
Inheritance: Autosomal
Alleles: Two Theorized
The Lp Locus Alleles

• Lp - Appaloosa Spotted aka Leopard Complex, incomplete dominant.
• lp+ - Not appaloosa spotted, recessive.

The Sabino 1 Locus

Location: Chromosome 3 - c-Kit (KIT) Gene
Inheritance: Autosomal
Alleles: Two
The Sa1 Locus Alleles

• Sa1 - Sabino 1, co-dominant. In its homozygous form (Sa1/Sa1) it results in Maximum Sabino which can result in a nearly all white to all white horse. This theory has been confirmed by DNA test with the discovery of the Sabino1 gene. It would appear there is at least one other Sabino gene, possibly on another locus that results in the 'clean' Sabino markings seen in Clydesdales.
• sa1+ = Not Sabino 1, co-dominant.

The Sabino 2 Locus

Location: Theorized
Inheritance: Autosomal
Alleles: Two Theorized
The Sa2 Locus Alleles

• Sa2+ - Not Sabino 2, dominant.
  
• sa2 = Sabino, recessive. This sabino is only expressed in its homozygous form. With the discovery of the Sabino 1 gene, it is now known there are multiple loci that can result in sabino type markings. To this end I have implemented a second sabino gene, Sabino 2 in the game. While we now know for fact there are multiple genes that cause sabino type markings, this is a strictly theorized locus and mutation.

The Splash Locus

Location: Unmapped
Inheritance: Autosomal
Alleles: Two Theorized
The Spl Locus Alleles

• Spl - Splashed White, dominant.
• spl+ - Not Splashed White, recessive.

The Tobiano Locus

Location: Chromosome 3 - Believed to be KIT
Inheritance: Autosomal
Alleles: Two
The To Locus Alleles

• To - Tobiano, dominant. One of the Tobiano markers is kn1, found at the KIT gene.
• t - Not Tobiano, recessive.

The White Locus

Location: Chromosome 3 - c-Kit (KIT) Gene
Inheritance: Autosomal
Alleles: Two
The W Locus Alleles

• W - White, dominant with occassional possible incomplete penetrance. Homozygous lethal during gestation. W/W embryos are not viable, and the pregnancy aborts. In its heterozygous form, dominant white prevents pigment in all, or the majority of the skin and coat. Its phenotype can vary widely. It appears to have incomplete penetrance in some cases, and the horse will have some skin pigment. In some cases the horse will even some pigmented hair, creating a sabino pattern.
• w+ - Not White, recessive.

More about the game genetics:

Extension, Roan, Sabino1, Tobiano, and White are inherited on the same "chromosome" just as in real life. Thus they will rarely separate during "meiosis." During genetic recombination it is very, very rare for roan, sabino1, tobiano, and white to separate. The recombination frequency at which extension will separate from the other four loci is much higher, but it is still a fairly rare occurance. Mares recombine at a slightly higher frequency than stallions.

Shade of phaeomelanin is controlled by rufusing genes, also referred to as intensifiers. Phaeomelanin can vary in shade from a very pale sandy color to near black.

Base color affects the amount of white spotting seen in appaloosa and pinto markings. White markings are suppressed by black, enhanced slightly by bay, and are maximally expressed on chestnut. There are other white enhancers/suppressors that have an additive effect on the amount of white in the coat. While I did not apply this to all pinto markings due to the sheer complexity of it, I did apply it to toveros.
Appaloosa spotting is further affected by the PATN1 locus which has been added to the game. If you want leopards/fewspots, you will have to find the family lines that carry PATN1!

Genetic Disorder:

I have included a generic unnamed genetic disorder in the game. This disorder is an autosomal recessive trait which means that it occurs equally in males and females and it takes two copies of the gene to be affected. Carriers will not have any "symptoms" so the only way to find them is to DNA test the horses. Affecteds will be affected in the show ring. Their scores will be cut in half making it impossible to show them to any legitimate wins. The point of adding this disorder to the game was twofold. One to help educate about genetic disease and how to "breed through them" to a clear line and two to add challenge to the game. When you DNA test your horses you will get one of three results (provided all is working as it should LOL): Clear, Carrier or Affected. It is each individual breeders choice how they go about clearing their lines of the disorder and there are several methods. One is to discard any carrier or affected but this can cost the breed some valuable genetics for the other inherited traits. One can also formulate a plan to breed through to clears using the carriers or even the affecteds. By utilizing clears to breed to them they are assured of never producing any affecteds and at worst more carriers. Eventually they will be able to produce a clear line that still retains the other desired inherited traits. I hope this gives you some insight into breeding and the choices that must be made as well as making the game more challenging and fun.

I could lay all the color combos out nice tables that would lead you straight to every combination, but where would the fun be in that? LOL What I've given you above is plenty to get you started. Studying real horse genetics will be necessary for finding out how to produce the color/pattern combinations you desire. There are now over 288 quadrillion unique genetic combinations in the game for color and pattern so the possibilities are virtually endless!