DataSheet_1_Identification of polymorphisms in TYRP1, DCT and RAB38 genes and their association with coat color in alpacas.pdf

ObjectiveThe goal of this study was to characterize and investigate the effect of single nucleotide polymorphisms (SNPs) or InDels in tyrosinase related protein 1 (TYRP1), dopachrome tautomerase (DCT), and Ras-related protein 38 (RAB38) genes on coat color in South American camelids. TYRP1 is among one of the major regulators of pigmentation in mammals. DCT is a pigment cell-specific gene that plays an important role in the melanin synthesis pathway and the expression of skin color. RAB38 is involved in the transport of tyrosinase (TYR) and TYRP1, which are key enzymes in melanin production.
MethodsFive fleece color tones from 327 alpacas (white, black, brown, gray and light fawn) were investigated to characterize and identify polymorphisms that play a role in coat color. Among the SNPs and Indels identified in the coding region, statistical analysis was performed to determine the association between the polymorphisms and fleece color in camelids, as well as the determination of allelic frequencies.
ResultsTwenty two polymorphisms in the coding region, seven of them were nonsynonymous, eleven were synonymous, three located in the 5’UTR region and one deletion in the 3’UTR region were identified in the TYRP1 gene; in the DCT gene were identified twenty two polymorphisms, where five of them were non-synonymous, twelve were synonymous, one polymorphism in the 5’UTR region and four in the 3’UTR region; in adition, in the RAB38 gene six polymorphisms were identified, one was nonsynonymous, two were synonymous, in addition to three polymorphisms in the 3’UTR region were found in the RAB38 gene. There were low to moderate polymorphisms in the populations. Significant differences (P<0.001) were found with color fiber in the alpaca populations studied for TYRP1 and DCT genes.

研究目的
本研究旨在解析并探究南美骆驼科动物酪氨酸酶相关蛋白1（tyrosinase related protein 1, TYRP1）、多巴色素互变异构酶（dopachrome tautomerase, DCT）以及Ras相关蛋白38（Ras-related protein 38, RAB38）基因中的单核苷酸多态性（single nucleotide polymorphisms, SNPs）与插入缺失变异（InDels）对被毛颜色的影响。其中，TYRP1是哺乳动物色素沉着的核心调控因子之一；DCT为色素细胞特异性基因，在黑色素合成通路及皮肤色泽表达中发挥关键作用；RAB38则参与黑色素生成关键酶——酪氨酸酶（tyrosinase, TYR）与TYRP1的转运过程。

研究方法
本研究对327头羊驼的5种被毛色调（白色、黑色、棕色、灰色及浅黄褐色）开展分析，以鉴定并表征与被毛颜色相关的多态性变异。针对编码区鉴定得到的SNPs与InDels，本研究通过统计学分析明确了骆驼科动物中多态性与被毛颜色的关联，并测定了等位基因频率。

研究结果
本研究在TYRP1基因编码区共鉴定得到22处多态性变异，其中7处为错义突变、11处为同义突变，另有3处位于5'UTR、1处为3'UTR区域的缺失变异；在DCT基因编码区共鉴定得到22处多态性变异，其中5处为错义突变、12处为同义突变，另有1处位于5'UTR、4处位于3'UTR区域；此外，在RAB38基因中鉴定得到6处多态性变异，其中1处为错义突变、2处为同义突变，另有3处位于3'UTR区域。受试羊驼群体的多态性水平处于低至中等区间。针对TYRP1与DCT基因的分析显示，受试羊驼群体的被毛颜色与上述基因存在极显著关联（P<0.001）。