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

Abstract

Since domestication, horses have been selectively bred for various coat colors and white spotting patterns. To investigate breed distribution, allele frequencies, and potential lethal variants for recommendations on genetic testing, 29 variants within 14 genes were investigated in 11,281 horses from 28 breeds. The recessive chestnut ea allele in melanocortin 1 receptor (MC1R) (p.D84N) was identified in four breeds: Knabstrupper, Paint Horse, Percheron, and Quarter Horse. After filtering for relatedness, ea allele frequency in Knabstruppers was estimated at 0.035, thus illustrating the importance of testing for mate selection for base coat color. The Rocky Mountain Horse breed had the highest allele frequency for two of the dilution variants under investigation (Za.f. = 0.32 and Cha.f. = 0.026); marker-assisted selection in this breed could aid in the production of horses with desirable dilute coats with less severe ocular anomalies caused by the silver (Z) allele. With regard to white patterning, nine horses homozygous for the paired box 3 (PAX3) splashed white 2 (SW2) allele (p.C70Y) and six horses homozygous for the KIT proto-oncogene, receptor tyrosine kinase (KIT) sabino 1 (SB1) allele (ECA3g.79544206A>T) were identified, thus determining they are rare and confirming that homozygosity for SW2 is not embryonic lethal. The KIT dominant white 20 (W20) allele (p.R682H) was identified in all but three breeds: Arabian (n = 151), Icelandic Horse (n = 66), and Norwegian Fjord Horse (n = 90). The role of W20 in pigmentation across breeds is not well understood; given the different selection regimes of the breeds investigated, these data provide justification for further evaluating the functional role of this allele in pigmentation. Here, we present the largest dataset reported for coat color variants in horses to date, and these data highlight the importance of breed-specific studies to inform on the proper use of marker-assisted selection and to develop hypotheses related to pigmentation for further testing in horses.

Predicted genetic burden and frequency of phenotype-associated variants in the horse

“…The A (non-reference) allele was the major allele in all 12 breed groups and the other breed group, with a breed frequency > 0.86 in Arabians, Belgians, Morgans, Thoroughbreds, and Quarter Horses suggesting more work is needed to determine if this is causal for reduction in pigmentation. The g.79,548,220C > T (EquCab3.0, coordinates from OMIA and manual remapping using the NCBI remapper tool) variant in KIT, named W20 has been reported in multiple breeds and is thought to impact the amount of white patterning was originally reported to increase the size of facial white markings 61 , 62 . This variant was the major allele in Clydesdale horses (frequency: 0.95) and was common (frequency 0.10) in Warmbloods, Belgians, Shetlands, Standardbreds, Quarter Horses, Welsh ponies, Thoroughbreds, Franches Montagnes horses and the ‘other’ breed group.…”

A de novo 2.3 kb structural variant in MITF explains a novel splashed white phenotype in a Thoroughbred family

“…The only known variant detected out of the 46 alleles screened was W20. W20 is a missense variant in the KIT gene (NC_009146.3: g.79548220C>T, ENSECAP00000011188.2:p.His794Arg) with a wide breed distribution that is thought to have a subtle impact on pigmentation, mostly related to white face and leg markings, unless combined with other variants (Avila et al, 2022; Dürig, Jude, Holl, et al, 2017; Haase et al, 2013; Negro et al, 2017). This is further supported by photographic records and the genetic testing of the two foals who inherited the W20 allele and only have white face markings (O‐3) or white face and leg markings (O‐2).…”

“…While a comprehensive study on white patterning alleles and deafness has not yet been performed, recent studies have identified one SW2 homozygote, six SW5 heterozygotes and one SW1/SW7 compound heterozygote as deaf. Still clinical BAER phenotyping for deafness was not reported for these cases (Avila et al, 2022; Henkel et al, 2019; Rosa, Martin, Vierra, Foster, et al, 2022). Until the present study, the MITF de novo variant in a dilute splashed white Franches‐Montagnes horse was the only horse with a MITF variant confirmed deaf by BAER testing (Blatter et al, 2013; Hauswirth et al, 2012).…”

“…Additionally, an inversion thought to impact KIT gene expression causes the tobiano pattern, but there are no reported adverse health effects (Brooks et al, 2007). An intronic variant that alters splicing in this same gene causes a sabino pattern (SB1), white on the abdomen and high white on the legs, with homozygotes being almost all white (Avila et al, 2022; Brooks & Bailey, 2005). Variants in TRPM1 and RFWD3 are involved in leopard complex spotting, a group of white spotting patterns that tend to be symmetrical and centered over the hips (Bellone et al, 2013; Holl et al, 2016).…”

“…The first splashed white variant identified was an 11 bp indel in the promoter of MITF , which is predicted to impair the binding of its transcription factor PAX3 (Hauswirth et al, 2012). This variant has the widest breed distribution of all splashed‐white variants to date (Avila et al, 2022). Since this promoter variant was among the first to be identified for the splashed white phenotype, it was described as SW1.…”