• About This Guide
  
• How This Guide is Being Developed
  
• Philosophy of this guide
  
• Using this Guide
  
• Thinking Scientifically
  
• About the Author
  
• Documented Genes
  
• What is a documented gene?
  
• Black/Red (MC1R)
  
• Bay (ASIP)
  
• Cream/Pearl (SLC45A2)
  
• Dun (TBX3)
  
• Gray (STX17)
  
• Silver (PMEL17)
  
• Champagne (SLC36A1)
  
• Roan/Tobiano/Sabino/White Spotting (KIT)
  
• Splash White (MITF/PAX3)
  
• Leopard Complex (TRPM1/ECA3P)
  
• Frame (EDNRB)
  
• Tiger Eye (SLC24A5)
  
• Height Regulation (HMGA2/LCORL)
  
• Mushroom (MFSD12)
  
• Hypothetical Genes
  
• What is a hypothetical gene?
  
• Borrowed Genes
  
• Glossaries
  
• Glossary of Colors
  
• Glossary of Terms
  

Hypothetical Genes

What is a hypothetical gene?

• Hypothetical genes have not been documented in horses. These genes range from genetic factors that we are highly certain exist like sooty and flaxen to things that could exist but we can be pretty sure do not. I have broken them into the following categories: well supported, moderately supported, unsupported, and borrowed.

Borrowed Genes

• What is a borrowed gene?

  Borrowed genes are documented genes in other mammals that are being used as models for genes in HorseGeneticsGame.com Not all documented genes have been fully mapped and made testable as some species do not have as much economic incentives for testing as horses do.
• Satin (Rabbits and Cats)

  • Last updated: 2026-02-4

    Common Names: Satin

    General Overview:

    The satin gene is theorized to be found in Akhal Teke horses but as of yet no research has been published about it. HorseGeneticsGame.com uses the satin gene found in rabbits as our model for the game.  Satin, denoted as sa/sa, is recessive and modifies the hair shaft to make the outer layer smoother, and make the hair finer. This creates a shinier than normal coat.[1]

    
    

    A similar gene in cats is called glitter. [2]

    
    

    In the game satin horses will have a higher than normal amount of shine to their coat. Rerolling the image seed can increase or decrease the total amount of shine.

  • Citations:

    1. Steven Lukefahr 2022. Rabbit Production, 10th Edition (S.D. Lukefahr et al.) DOI: 10.1079/9781789249811.0016
    2. Kaelin CB, McGowan KA, Hutcherson AD, Delay JM, Li JH, Kiener S, Jagannathan V, Leeb T, Murphy WJ, Barsh GS. Ancestry dynamics and trait selection in a designer cat breed. Curr Biol. 2024 Apr 8;34(7):1506-1518.e7. doi: 10.1016/j.cub.2024.02.075. Epub 2024 Mar 25. PMID: 38531359; PMCID: PMC11162505.

  • Examples:

    A brown horse without and with satin.

    

    
    
• Chocolate (TYRP1 - Dog)

  • Last updated: 2026-02-4

    Common Names: Chocolate, Brown

    Scientific Name: tyrosinase-related protein 1

    General Overview:

    The chocolate or brown gene is a mutation of the gene TYRP1. It converts black pigment into a chocolate brown color. This is found in a large number of breeds but is most famously the gene that turns black labrador retrievers into chocolate labs. Chocolate is recessive and requires two copies to show. [1] Listed in HorseGeneticsGame.com as b/b.

    
    

    Similar TYRP1 mutations can also be found in cats, pigs, chickens, mice and more.

  • Citations:

    1. Schmutz SM, Berryere TG, Goldfinch AD. TYRP1 and MC1R genotypes and their effects on coat color in dogs. Mamm Genome. 2002 Jul;13(7):380-7. doi: 10.1007/s00335-001-2147-2. PMID: 12140685. https://pubmed.ncbi.nlm.nih.gov/12140685/

  • Examples:

    Bay, Brown and Black horses homozygous for chocolate

    

    
    
• Merle (PMEL17 - Dog)

  • Last updated: 2026-02-6

    Common Names: Merle

    Scientific Name: Premelanosome protein 17 (PMEL17)

    General Overview:

    Merle is found in a wide variety of dog breeds and is a SINE found in the regulatory region of the PMEL17 gene. This is the same gene responsible for the silver coat color in horses. Merle is a dramatic coat pattern characterized by dark colored patches on a diluted background. Only black pigment (eumelanin) is diluted by merle. So called red merles are actually dogs with other genes that lighten eumelanin, for example the chocolate/brown gene. Merle is known to cause blue eyes and can cause significant health issues at high expression levels. [1]]

    
    

    SINE in genetics stands for Short Interspersed Nuclear Elements. It’s a bit of DNA that replicates like a parasite. SINEs hijack the enzymes that copy DNA to copy itself as much as possible instead. [2]

    
    

    We think of most genes as being in an on or off state. If a horse has one copy of the E allele it’s “on” and that horse can make eumelanin. Merle is not an on or off state. It’s a volume knob. By their nature SINEs are highly unstable.[2] Every time a cell divides, the number of copies of that SINE fluctuates. With merle, more copies of this SINE in the regulatory region means more shut down PMEL17 and more extreme merle markings.
    
    We can tell how strong the merle markings will be by looking at the combined “volume” of all the SINE copies that animal has. That means an individual who is homozygous for merle but has a hypothetical 6 copies of the merle SINE insertion, will have less extreme merle expression than a heterozygous individual who has 8 copies of the merle SINE. [3]

  • Mosaicism:

    The dramatic range of expression from merle is caused by the highly unstable nature of SINEs. Dark patches form when there are less SINE copies messing up PMEL17 expression. The diluted areas are where more SINE copies are messing up PMEL17. When the number of SINEs active in a region are very high all pigment is disabled, and if that region happens to be the eyes or ears of the individual they can be deaf and with malformed eyes.

    
    

    That means an individual can have many different SINE lengths over their body, which is referred to as mosaicism. [3] This also means that inheritance of merle is unpredictable; offspring can have a merle expression that is very different from the parents.

  • Types of Merle:

    You may see the following terms used to describe merle dogs, but they are not used in HorseGeneticsGame.com.

    
    

    Cryptic - An animal that has the merle SINE mutation but at a number small enough not to show

    
    

    Dilute - A merle, normally with lower SINE length, that shows silver like dilution but not classic merle patches

    
    

    Standard/Classic - The typical merle expression

    
    

    Double - An animal with excessive SINE length, often but not always caused by being homozygous. These individuals have large amounts of white markings, and a very high incidence of hearing and vision problems.

    
    

    Harlequin gene- A homozygous lethal gene found in Great Danes that removes the diluted area of merle individuals but leaves the dark patches intact.

    
    

    Harlequin pattern - A variant of merle caused by long sine lengths having strong dilution and a lot of white. Not related to the harlequin gene.

    
    

    Tweed - A variant of merle with lighter patches mixed into the normal dilute and darker patch areas. Caused by the SINE length increasing in the lighter areas.

  • Double Merle:

    Long before the true nature of merle was uncovered by geneticists, dog breeders realized that breeding two merle dogs together was very risky. Many of those merle to merle breedings resulted in a condition they dubbed “double merle.” Most double merle individuals are homozygous for merle, have extensive white markings over most of their body, and normally have heavily impaired vision and hearing.

    
    

    Remember though that merle works like a volume knob. Not all “double merles” are homozygous, and not all homozygous merles have negative health impacts. The shorter the merle SINE tail the less likely there is to be health impairment. [4] Because of the unpredictable way SINEs replicate though it is good practice to avoid merle to merle breeding. 

  • True Red (e/e) Merles

    The PMEL gene is specifically responsible for the fixing of black pigment. That is why the silver mutation only shows on black and bay horses, not on red/chestnut horses. The same is true for merle. ee individuals do not show the classic merle patterning. However they can end up with spontaneous blue eyes from the merle gene and can have health impacts at high SINE levels just like their black based counterparts. Not enough research exists yet on merle’s impacts on ee individuals for us to have the complete picture. We do know, however; that there is some impact at high levels.

  • Merle in HorseGenetics Game:

    To calculate how big the total amount of SINE length your HorseGeneticsGame.com horses have:

    1) Find the silver gene in the gene test results

    2) The merle gene is written like Mrl(65). The number inside the parentheses () is the SINE length. If your horse is homozygous for merle, add both numbers together.

    3) If your horse has a copy of the silver gene, add 15 to the total SINE length.

    4) The - symbol means no mutation is found and does not add to the total SINE length.

    
    

    In HorseGeneticsGame.com foals will start developing health problems at a combined SINE length of 80. Unhealthy horses in the game have a reduced training ability, though breeding ability is not impacted. The health impact is listed as a percentage. The health impact increases proportionally. A foal with a 120 combined SINE length will have much worse health than a foal with an 80 SINE length.

    
    

    SINE lengths over 142 are embryonic lethal.

    
    

    Health impacted foals can be corrected by the HGG University using the ability max out feature to give them normal showing ability. For simplicity, e/e horses in game will have negative health impacts at the same SINE levels as E/? horses. 

  • Citations:

    1. Clark, L. A., et al. “From the Cover: Retrotransposon Insertion in SILV Is Responsible for Merle Patterning of the Domestic Dog.” Proceedings of the National Academy of Sciences, vol. 103, no. 5, 9 Jan. 2006, pp. 1376–1381, .https://www.researchgate.net/publication/7365182_Clark_LA_Wahl_JM... 
    2. Schmitz, Juergen. (2012). SINEs as Driving Forces in Genome Evolution. Genome dynamics. 7. 92-107. 10.1159/000337117. https://www.researchgate.net/publication/228114354_SINEs_as_Driving_Forces_in_Genome_Evolution 
    3. Ballif BC, Ramirez CJ, Carl CR, Sundin K, Krug M, Zahand A, Shaffer LG, Flores-Smith H. The PMEL Gene and Merle in the Domestic Dog: A Continuum of Insertion Lengths Leads to a Spectrum of Coat Color Variations in Australian Shepherds and Related Breeds. Cytogenet Genome Res. 2018; https://www.researchgate.net/publication/326814469_... 
    4. Langevin, Mary & Synkova, Helena & Jancuskova, Tereza & Pekova, Sona. (2018). Merle phenotypes in dogs – SILV SINE insertions from Mc to Mh. PLOS ONE. 13. e0198536. 10.1371/journal.pone.0198536. https://www.researchgate.net/publication/327785306_Merle_phenotypes_in_dogs_-_SILV_SINE_insertions_from_Mc_to_Mh

  • Examples:

    Brown Merle SINE 20, Brown Merle SINE 40, Brown Merle SINE 60

    

    
    

    Brown Merle SINE 80, Brown Merle SINE 100

    

    
    

    Silver Brown Merle SINE 20, Silver Brown Merle SINE 40, Silver Brown Merle SINE 60

    

    
    

    Silver Brown Merle SINE 80, Silver Brown Merle SINE 100

    

    
    
• Harlequin (PSMB7 - Dog)

  • Last updated: 2026-02-4

    Common Names: Harlequin

    Scientific Name: Proteasome 20S Subunit Beta 7

    General Overview:

    Harlequin in HorseGeneticsGame.com is based on the harlequin gene found in great danes. Harlequin is a mutation of PSMB7. It normally has no effect when heterozygous, but is lethal when homozygous. If the individual has a copy of harlequin, and merle and has black pigment it will create the great dane harlequin merle pattern. Harlequin turns the diluted area of merle dogs white and leaves the undiluted patches behind.

    
    

    In HorseGeneticsGame.com harlequin is denoted as Hq/-. It also interacts with the silver gene, as both merle and silver are mutations of PMEL17. The combination of silver and harlequin turns all previously black pigment white.

    
    

    Citations:

    1. Clark LA, Tsai KL, Starr AN, Nowend KL, Murphy KE. A missense mutation in the 20S proteasome β2 subunit of Great Danes having harlequin coat patterning. Genomics. 2011 Apr;97(4):244-8. doi: 10.1016/j.ygeno.2011.01.003. Epub 2011 Jan 20. PMID: 21256207. https://pubmed.ncbi.nlm.nih.gov/21256207/ 

  • Examples:

    Bay Hq/- -/-, Bay -/- Mrl/-, Bay Hq/- Mrl/-

    

    
    

    Silver Bay, Silver Bay Harlequin

    

    
    
• Chinchilla (Rabbits)

  • Last updated: 2026-02-4

    Common Names: Chinchilla

    General Overview:

    Chinchilla in HorseGeneticsGame.com is based on a simplified version of the chinchilla gene in rabbits.[1] Chinchilla in game ignores eumelanin (black) pigment and disables pheomelanin (red) pigment. In rabbits this results in red eyed albino animals but horses are too large to show true red eyes. Instead chinchilla horses in game will have a pale blueish lavender eye color similar to albino humans.[2]

    
    

    Listed in HorseGeneticsGame.com as chn/chn.

    
    

    Citations:

    1. Covrig I., Oroian I., Patrutoiu T. C., 2013 The C locus: rabbit genetics for full color development, chinchilla, seal, sable, pointed black and red-eyed full white. Rabbit Gen 3(1):23-32. https://rg.bioflux.com.ro/docs/2013.23-32.pdf 
    2. Vogel P, Read RW, Vance RB, Platt KA, Troughton K, Rice DS. Ocular albinism and hypopigmentation defects in Slc24a5-/- mice. Vet Pathol. 2008 Mar;45(2):264-79. doi: 10.1354/vp.45-2-264. PMID: 18424845. https://journals.sagepub.com/doi/10.1354/vp.45-2-264

  • Examples:

    Chestnut, Bay and Black horses homozygous for chinchilla