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

文献类型： 外文期刊

第一作者： Qiao, Xian

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

作者机构：

期刊名称：SCIENTIFIC REPORTS （ 影响因子：4.379； 五年影响因子：5.133 ）

ISSN： 2045-2322

年卷期： 2017 年 7 卷

页码：

收录情况： SCI

摘要： 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.

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