Abstract Splashed white is a coat color pattern in horses characterized by extensive white patterning on the legs, belly, and face often accompanied by blue eyes and deafness. Three mutations in microphthalmia-associated transcription factor (MITF) and two mutations in Paired Box 3 (PAX3) have been identified that explain splashed white patterns (SW1–SW5). An American Paint Horse stallion with a splashed white phenotype and blue eyes, whose parents were not white patterned, was negative for the 5 known splashed white variants and other known white spotting alleles. This novel splashed white phenotype (SW6) was hypothesized to be caused by a de novo mutation in MITF or PAX3. Analysis of whole-genome sequencing using the EquCab3.0 reference genome for comparison identified an 8.7 kb deletion in MITF on ECA16 (NC_009159.3:g.21551060-21559770del). The deletion encompassed part of intron 7 through the 3′ UTR of exon 9 of MITF, including the helix-loop-helix DNA-binding domain (ENSECAT00000006375.3). This variant is predicted to truncate protein and impair binding to DNA. Sanger sequencing confirmed the stallion was heterozygous for the MITF deletion. No single nucleotide polymorphisms (SNPs) or structural variants were identified in PAX3 or any of the other candidate genes that were unique to the stallion or predicted to affect protein function. Genotyping five of the stallion’s splashed white offspring, including one all white foal, found that they were also heterozygous for the deletion. Given the role of MITF in producing white pattern phenotypes, and the predicted deleterious effect of this mutation, this 8.7 kb deletion is the likely causal variant for SW6.

中文翻译：

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De Novo MITF 删除解释了美国油漆马的一种新的泼白色表型

摘要 泼白是马的一种毛色图案，其特征是腿、腹部和面部有大量的白色图案，通常伴有蓝眼睛和耳聋。已鉴定出小眼病相关转录因子 (MITF) 中的三个突变和配对框 3 (PAX3) 中的两个突变，可以解释飞溅的白色图案 (SW1-SW5)。一匹美国油漆马种马具有溅白色表型和蓝眼睛，其父母没有白色图案，对 5 个已知的溅白色变体和其他已知的白色斑点等位基因呈阴性。这种新型飞溅白色表型 (SW6) 被假设是由 MITF 或 PAX3 中的从头突变引起的。使用 EquCab3.0 参考基因组进行全基因组测序分析以进行比较，发现 ECA16 上的 MITF 中存在 8.7 kb 缺失 (NC_009159.3:g.21551060-21559770del)。缺失包括通过 MITF 外显子 9 的 3' UTR 的内含子 7 的一部分，包括螺旋-环-螺旋 DNA 结合域 (ENSECAT00000006375.3)。预计该变体会截断蛋白质并削弱与 DNA 的结合。桑格测序证实这匹种马是 MITF 缺失的杂合子。在 PAX3 或任何其他候选基因中没有发现单核苷酸多态性 (SNP) 或结构变异，这些候选基因是种马独有的或预测会影响蛋白质功能。对这匹种马的五只白色后代进行基因分型，包括一只全白色的小马驹，发现它们也是缺失的杂合子。鉴于 MITF 在产生白色模式表型中的作用，以及该突变的预测有害影响，这个 8.7 kb 缺失可能是 SW6 的因果变异。