Scientific Reports (2017-08-01)

Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat

  • Xian Qiao,
  • Rui Su,
  • Yang Wang,
  • Ruijun Wang,
  • Ting Yang,
  • Xiaokai Li,
  • Wei Chen,
  • Shiyang He,
  • Yu Jiang,
  • Qiwu Xu,
  • Wenting Wan,
  • Yaolei Zhang,
  • Wenguang Zhang,
  • Jiang Chen,
  • Bin Liu,
  • Xin Liu,
  • Yixing Fan,
  • Duoyuan Chen,
  • Huaizhi Jiang,
  • Dongming Fang,
  • Zhihong Liu,
  • Xiaowen Wang,
  • Yanjun Zhang,
  • Danqing Mao,
  • Zhiying Wang,
  • Ran Di,
  • Qianjun Zhao,
  • Tao Zhong,
  • Huanming Yang,
  • Jian Wang,
  • Wen Wang,
  • Yang Dong,
  • Xiaoli Chen,
  • Xun Xu,
  • Jinquan Li

Journal volume & issue
Vol. 7, no. 1
pp. 1 – 13


Read online

Abstract 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.