Two Variants of KIT Causing White Patterning in Stock-Type Horses

Abstract

Over 30 polymorphisms in the KIT Proto-Oncogene Receptor Tyrosine Kinase (KIT) gene have been implicated in white spotting patterns ranging from small areas to full dermal depigmentation in the horse. We performed a candidate-gene exon sequencing approach on KIT and MITF, 2 known causatives of white spotting patterns, within 2 families of horses of unknown white spotting. Family 1 (Fam1, N = 5) consisted of a Quarter Horse stallion and 4 offspring with white spotting pattern ranging from legs, lower ventral, and head regions with jagged borders, to almost complete white. The second family (Fam2, N = 7) consisted of 6 half-sibling American Paint Horse/Quarter Horse and their dam, demonstrating unpigmented limbs with belly spots and an extensive white patterning on the face. This approach resulted in 2 variants significantly associated with familial phenotypes, where Fam1 variant is an indel leading to a frameshift mutation, and Fam2 a non-synonymous SNP. We validated the variants within an unrelated population of horses (Fam2 variant, P = 0.00271944) as well as for protein functional impact with ExPASy, Protter, Phyre2, SMART, PROVEAN, SIFT, and I-TASSER, confirming the reported associations. Fam1 associated variant, deemed W31, alters the protein sequence, leading to an early stop codon truncating the normal amino acid sequence from 972 to just 115 amino acids. Fam2 associated variant, deemed W32, may have a subtle impact on receptor function or could be in linkage with a non-coding or regulatory change creating the mild spotting pattern observed in this family.

Identification of W13 in the American Miniature Horse and Shetland Pony Populations

“…Six variants in five genes have been shown to dilute pigment, and these are known as cream (Cr), pearl (Prl), champagne (Ch), dun (D), mushroom (Mu), and silver (Z) [ 8 , 9 , 10 , 11 , 12 , 13 ]. Variants in seven genes ( KIT , EDNRB , TRPM1 , MITF , PAX3 , RFWD3 , STX17 ) have been documented to cause white patterning in domestic horses [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 ]. The majority of the white patterning variants described are within or are thought to regulate the KIT proto-oncogene, receptor tyrosine kinase ( KIT ) [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ].…”

“…Variants in seven genes ( KIT , EDNRB , TRPM1 , MITF , PAX3 , RFWD3 , STX17 ) have been documented to cause white patterning in domestic horses [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 ]. The majority of the white patterning variants described are within or are thought to regulate the KIT proto-oncogene, receptor tyrosine kinase ( KIT ) [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. These variants explain several different but overlapping phenotypes including sabino-1 (SB1), tobiano (TO), and dominant white (W1–W17a, W17b–W28, W30–32) [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 …”

“…The majority of the white patterning variants described are within or are thought to regulate the KIT proto-oncogene, receptor tyrosine kinase ( KIT ) [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. These variants explain several different but overlapping phenotypes including sabino-1 (SB1), tobiano (TO), and dominant white (W1–W17a, W17b–W28, W30–32) [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. The sabino phenotype is characterized by white patterning on the face and legs and white patches and/or white hairs dispersed on the belly that can extend upward on the barrel [ 14 ].…”

“…Dominant white variants are thought to produce a range of phenotypes from a minimal sabino-like phenotype to a horse that is completely white. In the heterozygous state, W5, W10, W12, W19, W21, W22, W26, W31, and W32 have been reported to cause a sabino-like phenotype [ 17 , 18 , 20 , 21 , 22 , 25 , 28 ]. W20 is thought to have a subtler impact on white patterning but, in the presence of other known white-causing alleles, modifies the extent of white patterning [ 20 ].…”

“…W20 is thought to have a subtler impact on white patterning but, in the presence of other known white-causing alleles, modifies the extent of white patterning [ 20 ]. In the strictest sense, those variants termed dominant white were originally reserved for KIT alleles thought to be homozygous lethal [ 16 ], but there are known exceptions including W15, W20, and W32 [ 19 , 20 , 28 ].…”