Novel coat colour phenotypes often emerge during domestication, and there is strong evidence of genetic selection for the two main genes that control base coat colour in horses—ASIP and MC1R. These genes direct the type of pigment produced, red pheomelanin (MC1R) or black eumelanin (ASIP), as well as the relative concentration and the temporal–spatial distribution of melanin pigment deposits in the skin and hair coat. Here, we describe a genome-wide association study (GWAS) to identify novel genic regions involved in the determination of the shade of bay. In total, 126 horses from five different breeds were ranked according to the extent of the distribution of eumelanin: spanning variation in phenotype from black colour restricted only to the extremities to the presence of some black pigment across nearly all the body surface. We identified a single region associated with the shade of bay ranking spanning approximately 0.5 MB on ECA22, just upstream of the ASIP gene (p = 9.76 × 10−15). This candidate region encompasses the distal 5′ end of the ASIP transcript (as predicted from other species) as well as the RALY gene. Both loci are viable candidates based on the presence of similar alleles in other species. These results contribute to the growing understanding of coat colour genetics in the horse and to the mapping of genetic determinants of pigmentation on a molecular level. Given pleiotropic phenotypes in behaviour and obesity for ASIP alleles, especially those in the 5′ regulatory region, improved understanding of this new Shade allele may have implications for health management in the horse.

中文翻译：

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ASIP 上游的独立基因座控制马湾毛色的深浅变化

新的毛色表型经常在驯化过程中出现，并且有强有力的证据表明，控制马底毛颜色的两个主要基因——ASIP 和 MC1R 存在遗传选择。这些基因指导产生的色素类型，红色褐黑素（MC1R）或黑色真黑素（ASIP），以及皮肤和毛发中黑色素沉积物的相对浓度和时空分布。在这里，我们描述了一项全基因组关联研究（GWAS），以确定参与确定海湾色调的新基因区域。总共，来自 5 个不同品种的 126 匹马根据真黑色素的分布程度进行了排名：表型的变化范围从仅限于四肢的黑色到几乎整个身体表面都存在一些黑色素。我们在 ECA22 上确定了一个与海湾排名阴影相关的单个区域，跨度约为 0.5 MB，位于 ASIP 基因的上游（p = 9.76 × 10−15）。该候选区域包含 ASIP 转录本的远端 5' 端（如从其他物种预测的那样）以及 RALY 基因。基于其他物种中相似等位基因的存在，这两个基因座都是可行的候选基因座。这些结果有助于加深对马毛色遗传学的了解，并有助于在分子水平上绘制色素沉着的遗传决定因素。鉴于 ASIP 等位基因（尤其是 5' 调控区中的 ASIP 等位基因）在行为和肥胖方面的多效性表型，提高对这种新 Shade 等位基因的了解可能对马的健康管理产生影响。