Horse

Agouti Signaling Protein (ASIP) gene on equine chromosome 22. Controls distribution of eumelanin when present (requires E/- at Extension). A (dominant) restricts eumelanin to the points (mane, tail, lower legs) producing BAY. a (recessive, 11-bp deletion in exon 2) allows uniform eumelanin throughout producing BLACK. A has no visible effect on e/e (chestnut) horses.

ID tips: A/-: bay -- brown/red body with black mane, tail, and lower legs. a/a: black -- uniform black body, mane, and tail. On e/e horses, Agouti genotype is hidden but important for breeding predictions.

SLC36A1 gene on equine chromosome 14. Champagne allele (Ch) is a dominant missense mutation (Thr63Arg) diluting both eumelanin and phaeomelanin, producing a distinct metallic appearance from Cream. Ch/Ch and Ch/n are phenotypically similar. Produces Gold Champagne (chestnut base), Amber Champagne (bay base), Classic Champagne (black base). All champagne horses are born with bright blue eyes that change to amber/hazel/green with age. Skin shows pinkish mottling (freckling) around muzzle and eyes.

ID tips: Champagne horses: (1) amber/green/hazel eyes in adults (bright blue at birth), (2) pink/mottled skin around muzzle and eyes, (3) warm metallic coat. Gold champagne: gold body, lighter mane/tail. Amber champagne: warm tan body with chocolate points. Classic champagne: lilac/mousy body with chocolate points.

SLC45A2 gene. Three alleles: Cr (Cream), prl (Pearl), N (wild-type). Cr single copy (Cr/N): dilutes phaeomelanin strongly producing Palomino (chestnut base), Buckskin (bay base), Smoky Black (black base). Cr/Cr: strongly dilutes both pigments producing Cremello (chestnut), Perlino (bay), Smoky Cream (black). prl/N: NO visible effect. prl/prl: mild dilution. Cr/prl compound heterozygote: pseudo-double-dilute appearing cremello/perlino-like despite only one Cream copy.

ID tips: Cr/N: palomino/buckskin/smoky black. Cr/Cr: cremello/perlino/smoky cream. prl/N: no visible dilution -- undetectable without DNA test. prl/prl: mild apricot tint. Cr/prl: pseudo-double-dilute -- appears cremello/perlino-like. DNA test is the ONLY way to distinguish Cr/Cr from Cr/prl.

TBX3 gene on equine chromosome 8. Three alleles: D (Dun, wild-type, dominant), nd1 (non-dun 1), nd2 (non-dun 2). D dilutes the body coat while preserving pigment on primitive markings (dorsal stripe, leg barring, shoulder stripe). nd1 removes most body dilution while preserving some primitive markings. nd2 eliminates both dilution and primitive markings. Most modern horses are nd2/nd2. D produces Dun on bay base, Grullo on black base, Red Dun on chestnut base.

ID tips: D/-: diluted body with dorsal stripe, often leg barring, shoulder stripe. Dun on bay = yellow-tan body with black primitive markings. Grullo = mouse-grey body with black primitive markings. Red dun = peachy-red body with darker red primitive markings. nd1/nd1: may have faint dorsal stripe. nd2/nd2: no dilution, no primitive markings.

Melanocortin 1 Receptor (MC1R) gene on equine chromosome 3. Controls whether eumelanin (black/brown pigment) can be produced. E (wild-type, dominant) allows eumelanin production; e (recessive, missense mutation Ser83Phe) restricts the horse to phaeomelanin (red/yellow) only. E/E and E/e horses can be bay or black depending on Agouti. e/e horses are chestnut/sorrel regardless of other eumelanin-acting loci.

ID tips: E/E and E/e: horse can be bay or black (determined by Agouti). e/e: horse is chestnut/sorrel -- red body with matching or lighter mane and tail. No black pigment on legs or mane/tail. DNA testing recommended to distinguish E/E from E/e.

Endothelin Receptor B (EDNRB) gene on equine chromosome 17. O/n (heterozygous): frame overo pattern -- irregular horizontal white patches framed by base color, rarely crossing the topline, often white face, usually dark legs. O/O (HOMOZYGOUS): ***LETHAL.*** Lethal White Overo Syndrome (LWOS) -- foals born entirely white with intestinal aganglionosis (non-functional GI tract). Cannot pass meconium. Death within 72 hours. NO treatment. MOST CRITICAL BREEDING WARNING IN EQUINE GENETICS.

ID tips: O/n: horizontal white patches not crossing topline. Dark legs. White face. Blue eyes common. Irregular patch edges. Minimal-expression carriers can appear nearly solid -- DNA testing essential. O/O (LETHAL): foal born entirely white, blue eyes, cannot pass meconium, progressive colic, death within 72 hours.

STX17 gene on equine chromosome 25. Gray allele (G) causes progressive depigmentation. Dominant -- one copy (G/n) produces full graying phenotype. Horses are born their base color and progressively lighten with each shed cycle, typically appearing white by age 8-15 (skin remains dark). G/G grayes faster. Gray is epistatic to all other color genes. Associated with increased melanoma risk -- up to 80% of gray horses over age 15 develop melanoma, higher in G/G.

ID tips: Gray horses change color throughout life. Foal born bay/black/chestnut. White hairs appear around eyes first. "Dapple gray" stage. "Flea-bitten gray": small colored spots on otherwise white coat. Fully grayed: appears white but has dark skin (distinguishes from cremello/perlino which have pink skin).

TRPM1 gene on equine chromosome 1. LP is incomplete dominant: LP/n produces varnish roan, mottled skin, striped hooves, and visible white sclera. LP/LP produces more extensive white patterning. LP/LP is associated with Congenital Stationary Night Blindness (CSNB). PATN genes are separate modifiers controlling pattern extent -- only active with LP present. LP+PATN produces blanket, leopard, few-spot, snowcap, and varnish roan patterns.

ID tips: LP/n with PATN: appaloosa patterns -- white blanket over hips, or leopard pattern with colored spots. Mottled skin around muzzle/eyes/genitalia. Striped hooves. Visible white sclera. LP/LP with PATN: few-spot leopard -- nearly all white with scattered spots. n/n: no appaloosa characteristics.

KIT gene on equine chromosome 3. Roan (Rn) is dominant -- even intermixing of white hairs with colored hairs throughout body while head and lower legs (points) remain fully colored. Present from birth and stable (unlike progressive gray). Produces Blue Roan (black base), Bay/Red Roan (bay base), Strawberry Roan (chestnut base). "Corn marks" (areas where injured skin grows back in base color) are diagnostic. Rn/Rn is viable -- historical reports of homozygous roan being lethal are discredited.

ID tips: Rn/-: even mix of white and colored hairs on body. Head fully colored. Lower legs fully colored. "Corn marks" diagnostic. Blue roan: dark head and legs with blue-grey frosted body. Bay/red roan: pinkish-roan body. Strawberry roan: pinkish body. Pattern stable year to year (distinguish from progressive graying).

PMEL17 gene on equine chromosome 6. Silver allele (Z) specifically dilutes eumelanin but has NO visible effect on phaeomelanin. On black base: produces chocolate/silver dapple body with flaxen/silver mane and tail. On bay base: lightens black points to flaxen/chocolate. On chestnut: NO visible effect. Associated with Multiple Congenital Ocular Anomalies (MCOA) / Anterior Segment Dysgenesis (ASD), more severe in Z/Z homozygotes.

ID tips: Z/- on black: chocolate/dark brown body with bright flaxen/silver-white mane and tail ("silver dapple"). Z/- on bay: black points lighten to flaxen/chocolate ("silver bay"). Z/- on chestnut: NO visible effect -- DNA test required. Eye abnormalities (ASD/MCOA) may be present.

KIT gene (chromosome 3) -- chromosomal inversion. Tobiano (TO) is dominant white spotting. TO/n produces tobiano: large, regular white patches crossing the topline, colored flanks and head, usually white legs, smooth patch borders. TO/TO tends to have more white. Most common and genetically simplest pinto/paint pattern.

ID tips: TO/-: large white patches crossing back/topline with smooth edges. Legs typically white. Head usually colored. Colored areas often on flanks. Homozygous TO/TO often have more extensive white and may show "ink spots" within white areas.