Exon skipping in the KIT gene causes a Sabino spotting pattern in horses.

Sabino (SB) is a white spotting pattern in the horse characterized by white patches on the face, lower legs, or belly, and interspersed white hairs on the midsection. Based on comparable phenotypes in humans and pigs, the KIT gene was investigated as the origin of the Sabino phenotype. In this article we report the genetic basis of one type of Sabino spotting pattern in horses that we call Sabino 1, with the alleles represented by the symbols SB1 and sb1. Transcripts of KIT were characterized by reverse transcriptase polymerase chain reaction (RT-PCR) and sequencing cDNA from horses with the genotypes SB1/SB1, SB1/sb1, and sb1/sb1. Horses with the Sabino 1 trait produced a splice variant of KIT that did not possess exon 17. Genomic DNA sequencing of KIT revealed a single nucleotide polymorphism (SNP) caused by a base substitution for T with A in intron 16, 1037 bases following exon 16. The SNP associated with SB1 was designated KI16+1037A. This substitution eliminated a MnlI restriction site and allowed the use of PCR-RFLP to characterize individuals for this base change. Complete linkage was observed between this SNP and Sabino 1 in the Tennessee Walking Horse families (LOD = 9.02 for Theta = 0). Individual horses from other breeds were also tested. All five horses homozygous for this SNP were white, and all 68 horses with one copy of this SNP either exhibited the Sabino 1 phenotype or were multipatterned. Some multipatterned individuals appeared white due to the additive effect of white spotting patterns. However, 13 horses with other Sabino-type patterns did not have this SNP. Based on these results we propose the following: (1) this SNP, found within intron 16, is responsible for skipping of exon 17 and the SB1 phenotype, (2) the White and Sabino phenotypes are heterogeneous and this mechanism is not the only way to produce the pattern described as "Sabino" or "White," and (3) homozygosity for SB1 results in a complete or nearly completely white phenotype.