Chestnut coat color in horses is determined by a missense mutation within the MC1R gene. However, the intensity of the chestnut color can vary widely within individuals possessing this genotype. Here, we investigated this variation using standardized photographs of 96 horses. Each horse was ranked lightest to darkest within the cohort for phenotype by 3 blinded observers. A genome-wide association study utilizing the relative shade ranking as the phenotype and using 268 487 single-nucleotide polymorphisms (SNPs) genotyped using the Affymetrix Equine 670k array identified a single significantly associated region on chromosome 3 (P = 2.934 × 10–8). Analysis of whole-genome sequences for horses spanning the diverse range of chestnut color identified candidate SNPs within the coding sequence of the only gene in the region: SALL1. The function of SALL1 is largely unknown, though it is predicted to interact with the Hermansky-Pudlak Syndrome type 1 (HPS1) protein, which causes partial albinism in humans. However, with only one study suggesting a circumstantial influence of the SALL1 protein on pigmentation, additional work is needed to confirm this new coat color locus in larger populations and investigate the function of this protein for impacts on equine health.

中文翻译：

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GWAS 识别出马栗色毛色内色素沉着强度变化中包含 SALL1 基因的区域

马的栗色毛色是由 MC1R 基因中的错义突变决定的。然而，栗色的强度在拥有这种基因型的个体中可能有很大差异。在这里，我们使用 96 匹马的标准化照片研究了这种变化。由 3 名盲观察者将每匹马的表型从最轻到最黑排列。一项利用相对阴影等级作为表型并使用 Affymetrix Equine 670k 阵列进行基因分型的 268 487 个单核苷酸多态性 (SNP) 的全基因组关联研究确定了 3 号染色体上的单个显着相关区域 (P = 2.934 × 10-8) . 对跨越不同栗色范围的马的全基因组序列的分析确定了该区域唯一基因的编码序列中的候选 SNP：SALL1。SALL1 的功能在很大程度上是未知的，尽管预计它会与导致人类部分白化病的 Hermansky-Pudlak 综合征 1 型 (HPS1) 蛋白相互作用。然而，只有一项研究表明 SALL1 蛋白对色素沉着有间接影响，因此需要额外的工作来在更大的人群中确认这种新的毛色基因座，并研究这种蛋白对马健康影响的功能。