Genetic Testing in the Horse

Breed Distribution and Allele Frequencies of Base Coat Color, Dilution, and White Patterning Variants across 28 Horse Breeds

“…The number of individuals per breed ranged from 36 (Hanoverian) to 5519 (Quarter Horse) (mean = 403 horses/breed; median = 96 horses/breed; Supplementary Table S1 ). Genotyping data included five alleles contributing to base coat color: agouti ( A or a ) and extension ( E , e a , e ); eight alleles that cause dilution of pigment or primitive marks: champagne ( Ch ), cream ( Cr ), dun ( D ), non-dun1 ( nd1 ), non-dun2 ( nd2 ), mushroom ( Mu ), pearl ( Prl ), and silver ( Z ); and 16 white patterning alleles: appaloosa pattern-1 ( PATN1 ), dominant white 5, 10, 20, 22 ( W5 , W10 , W20 , W22 ), gray ( G ), leopard Complex ( LP ), lethal white overo ( O ), splashed white 1–6 ( SW1 – SW6 ), sabino 1 ( SB1 ), and tobiano ( TO ) [ 3 , 28 , 29 ]. The details of the genetic variants tested and their respective nomenclatures can be found in Supplementary Table S2 .…”

“…One of the first variants discovered in the horse was a recessive mutation in the melanocortin 1 receptor ( MC1R ), which causes the chestnut phenotype, characterized by red-pigmented hair in the body and points (mane, tail, lower legs, and ear rims) [ 2 ]. Since then, over 60 variants contributing to equine pigmentation have been identified [ 3 ].…”

“…White patterning variants are the most numerous among those identified to impact pigmentation in horses, with 49 mutations in seven genes—endothelin receptor type B ( EDNRB ), KIT proto-oncogene, receptor tyrosine kinase ( KIT ), melanocyte inducing transcription factor ( MITF ), paired box 3 ( PAX3 ), ring finger and WD repeat domain 3 ( RFWD3 ), syntaxin 17 ( STX17 ), and transient receptor potential cation channel subfamily M member 1 ( TRPM1 )—identified to date [ 3 , 16 , 17 , 18 , 19 , 20 , 21 , 22 ]. Of those, 35 were identified in or thought to regulate the KIT gene (dominant white 1–16, 17a–b, 18–28, 30–33, sabino 1, and tobiano) [ 3 ]. White patterns occur on any base color and/or dilution background.…”

“…White patterns occur on any base color and/or dilution background. The phenotypic expression of white patterning variants is extremely variable, ranging from minimal white patches on the body to an all-white horse [ 3 , 20 ]. Genetic tests are available and routinely performed for 16 of these variants (lethal white overo, sabino 1, tobiano, W4 , W5 , W10 , W20 , W22 , SW1 – SW6 , gray, leopard complex spotting, and Appaloosa Pattern-1) to assist breeders in producing horses with desired white patterns while avoiding potential health concerns [ 3 ].…”

“…The phenotypic expression of white patterning variants is extremely variable, ranging from minimal white patches on the body to an all-white horse [ 3 , 20 ]. Genetic tests are available and routinely performed for 16 of these variants (lethal white overo, sabino 1, tobiano, W4 , W5 , W10 , W20 , W22 , SW1 – SW6 , gray, leopard complex spotting, and Appaloosa Pattern-1) to assist breeders in producing horses with desired white patterns while avoiding potential health concerns [ 3 ]. Studies suggest that homozygosity for some white patterning variants is embryonic lethal, and some white patterning mutations are thought to be restricted to a specific breed, lineage, or a single individual, although more work is needed in both areas.…”