Uncovering genes underlying coat color variation in indigenous cattle breeds through genome-wide positive selection

The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima’s D, CLR, iHS, varLD, ROH, and F_ST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are <i>CRIM1</i> in Gir, <i>MC1R</i> in Sahiwal, <i>MYO5A, PMEL</i> and <i>POMC</i> in Tharparkar, <i>TYRP1, ERBB2,</i> and <i>ASIP</i> in Red Sindhi, <i>MITF, LOC789175, PAX3</i> and <i>TYR</i> in Ongole, and <i>IRF2, SDR165</i> and, <i>KIT</i> in Nelore, <i>ADAMTS19</i> in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development.

鉴定与色素沉着相关且受选择性清除的候选基因，可为解析色素沉着的遗传基础以及塑造该性状变异的进化力量提供重要研究视角。目前针对印度牛群中调控正常被毛颜色的基因所发生的选择性清除事件，仍未有相关研究报道。为筛选本地牛群中携带选择性清除信号的被毛颜色相关基因，我们整理了此前已被报道与被毛颜色及色素沉着相关的候选基因列表。随后，我们使用牛50K SNP基因分型芯片（BovineSNP50K Bead Chip），对7个本地品种的187个个体开展全基因组范围的正选择信号扫描。我们采用多种方法检测选择信号，包括塔伊马D统计量（Tajima’s D）、复合似然比检验（CLR）、整合单倍型得分（iHS）、变异连锁不平衡分析（varLD）、纯合子片段分析（ROH）以及遗传分化系数（F_ST）。本研究共筛选得到16个受选择性清除且参与被毛颜色及色素沉着生理过程的基因，分别为：吉尔牛（Gir）中的CRIM1基因、萨希瓦尔牛（Sahiwal）中的MC1R基因、塔尔帕克萨尔牛（Tharparkar）中的MYO5A、PMEL与POMC基因、红辛迪牛（Red Sindhi）中的TYRP1、ERBB2与ASIP基因、翁格尔牛（Ongole）中的MITF、LOC789175、PAX3与TYR基因、内洛尔牛（Nelore）中的IRF2、SDR165与KIT基因，以及哈里亚纳牛（Hariana）中的ADAMTS19基因。上述基因均与黑色素合成、黑素细胞与黑素体的生物学功能，以及发育过程中黑素细胞的迁移与存活密切相关。