College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, 010018, China.
Sci Rep. 2017 Aug 17;7(1):8621. doi: 10.1038/s41598-017-09285-z.
Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to design an animal SNP chip using the SHS-based target enrichment strategy for the first time. As an update to the international collaboration on goat research, a 66 K SNP chip for cashmere goat was created from the whole-genome sequencing data of 73 individuals. Verification of this 66 K SNP chip with the whole-genome sequencing data of 436 cashmere goats showed that the SNP call rates was between 95.3% and 99.8%. The average sequencing depth for target SNPs were 40X. The capture regions were shown to be 200 bp that flank target SNPs. This chip was further tested in a genome-wide association analysis of cashmere fineness (fiber diameter). Several top hit loci were found marginally associated with signaling pathways involved in hair growth. These results demonstrate that the 66 K SNP chip is a useful tool in the genomic analyses of cashmere goats. The successful chip design shows that the SHS-based target enrichment strategy could be applied to SNP chip design in other species.
与基于 Bead Chip 技术的商业单核苷酸多态性 (SNP) 芯片相比，基于溶液杂交选择 (SHS) 的靶向富集 SNP 芯片不仅设计灵活，而且对于基因型测序具有成本效益。在这项研究中，我们首次提出使用基于 SHS 的靶向富集策略来设计动物 SNP 芯片。作为国际合作研究山羊的更新，从 73 个个体的全基因组测序数据中创建了一个用于羊绒羊的 66K SNP 芯片。对 436 只羊绒羊的全基因组测序数据进行的这种 66K SNP 芯片的验证表明，SNP 调用率在 95.3%到 99.8%之间。目标 SNP 的平均测序深度为 40X。捕获区域显示为侧翼目标 SNP 的 200bp。该芯片进一步在羊绒细度（纤维直径）的全基因组关联分析中进行了测试。发现几个顶级命中基因座与涉及毛发生长的信号通路呈边缘相关。这些结果表明，66K SNP 芯片是分析羊绒羊基因组的有用工具。成功的芯片设计表明，基于 SHS 的靶向富集策略可应用于其他物种的 SNP 芯片设计。
