Using whole genome sequencing data to identify novel pigmentation phenotypes in horses.
Splashed white in horses is characterized by extensive white patterning on the legs, face, and abdomen and may be accompanied by deafness. To date, seven variants in microphthalmia-associated transcription factor (MITF) and two variants in Paired Box 3 (PAX3) have been identified to explain this phenotype. A splashed white Thoroughbred stallion, whose sire and dam were not patterned, was hypothesized to have a de novo mutation leading to his white coat pattern. A whole-genome sequencing candidate gene approach identified two SNPs in SOX10, four SNPs in MITF, and a 2.3 kb deletion in MITF with the alternate allele present in this stallion but absent in the other 18 horses analyzed. All six SNPs were annotated as modifiers and were not further considered.  The deletion in MITF (NC_009159.3:g.21555811_21558139delinsAAAT) encompasses a region of the helix-loop-helix domain and is predicted to truncate the protein impacting DNA binding. Sanger sequencing and parentage testing confirmed that this deletion was a de novo mutation of maternal origin. Consistent with the published nomenclature, we denote this likely causal variant as SW8.  Genotyping three of this stallion's offspring identified SW8 only in the nearly all-white foal that was confirmed deaf by Brainstem Auditory Evoked Response (BAER) testing.  This foal was also a compound heterozygote for dominant white variants (W20/W22), but to date, W variants have not been connected to deafness.  SW8 marks the fourth de novo MITF variant in the horse reported to cause white patterning.  The link between all MITF variants and deafness needs to be further explored.