CNV calling in Malagueña goats

The agouti signaling protein (ASIP) gene has a crucial role in pigmentation by encoding a protein that binds the melanocortin 1 receptor and stimulates the synthesis of pheomelanin rather than eumelanin. Several studies have suggested that an increased copy number of the ASIP gene might explain the white pigmentation of certain goat breeds, as previously demonstrated in sheep. In the current work, we have identified the segregation of the ASIP CNV in Murciano-Granadina (black or brown coat), Malagueña (brown, blond or white coat) and Saanen (white coat) goats with available Illumina Goat SNP50 BeadChip (Illumina Inc., San Diego, CA) genotypes by using the PennCNV v1.0.5 and QuantiSNP v2 tools. This result shows that the ASIP CNV segregates in dark-colored breeds. To gain new insights into this issue, we have estimated the copy number of the ASIP gene in 83 goats from 8 breeds with different coloration patterns using a real-time quantitative PCR approach. Our results showed an increased ASIP copy number not only in Saanen (3.50 ± 0.23 copies relative to the calibrator) and white Malagueña (3.51 ± 0.51 copies) goats, but also in the Murciano-Granadina breed (3.33 ± 0.58 copies) as well as in blond/brown individuals from the Malagueña (3.58 ± 0.73 copies) breed. The number of ASIP copies was not significantly different in these four caprine populations (P value > 0.05). Moreover, we did not observe a trend towards increased ASIP copy number in breeds with predominantly white colors, such as Maltese (2.85 ± 0.28 copies), Jonica (2.82 ± 0.39 copies) and Blanca de Rasquera (2.37 ± 0.33 copies). Our results, combined with recent findings demonstrating the high structural complexity of the ASIP locus, indicate that additional functional and expression studies should be performed in order to fully understand the role of ASIP structural variation in goat pigmentation.

刺鼠信号蛋白（agouti signaling protein, ASIP）基因通过编码结合黑皮质素1受体的蛋白质，刺激褐黑素（pheomelanin）而非真黑素（eumelanin）的合成，在色素沉着过程中发挥关键作用。多项前期研究表明，ASIP基因拷贝数增加或许可以解释部分山羊品种的白色被毛表型，这一结论此前已在绵羊中得到验证。本研究借助PennCNV v1.0.5与QuantiSNP v2两款工具，基于已获取的Illumina山羊SNP50基因芯片（Illumina公司，加利福尼亚州圣地亚哥）基因型数据，对穆尔西亚-格拉纳达纳山羊（被毛呈黑色或棕色）、马拉格尼亚山羊（被毛呈棕色、金色或白色）以及萨能山羊（被毛呈白色）群体中ASIP拷贝数变异（copy number variation, CNV）的分离情况进行了鉴定。结果显示，ASIP拷贝数变异在深色被毛品种中存在分离现象。为进一步解析该问题，本研究采用实时定量聚合酶链反应（real-time quantitative PCR）方法，对来自8个具有不同被毛颜色表型的山羊品种的83只个体的ASIP基因拷贝数进行了估算。结果表明，不仅萨能山羊（相对于校准品的拷贝数为3.50±0.23）、白色型马拉格尼亚山羊（3.51±0.51）的ASIP拷贝数有所升高，穆尔西亚-格拉纳达纳山羊群体（3.33±0.58）以及马拉格尼亚山羊中的金色/棕色个体（3.58±0.73）同样呈现出ASIP拷贝数增加的特征。上述四个山羊群体的ASIP拷贝数并无显著差异（P值>0.05）。此外，在以白色被毛为主的马耳他山羊（2.85±0.28）、约尼卡山羊（2.82±0.39）以及拉斯克拉布兰卡山羊（2.37±0.33）群体中，并未观察到ASIP拷贝数升高的趋势。本研究结果结合近期关于ASIP基因座高度结构复杂性的研究发现，提示需开展更多的功能与表达研究，以全面阐明ASIP结构变异在山羊色素沉着过程中的作用。