Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat
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...
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oai:doaj.org-article:305b6b80156c4ed4bb452744fb5087772021-12-02T12:30:13ZGenome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat10.1038/s41598-017-09285-z2045-2322https://doaj.org/article/305b6b80156c4ed4bb452744fb5087772017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-09285-zhttps://doaj.org/toc/2045-2322Abstract 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.Xian QiaoRui SuYang WangRuijun WangTing YangXiaokai LiWei ChenShiyang HeYu JiangQiwu XuWenting WanYaolei ZhangWenguang ZhangJiang ChenBin LiuXin LiuYixing FanDuoyuan ChenHuaizhi JiangDongming FangZhihong LiuXiaowen WangYanjun ZhangDanqing MaoZhiying WangRan DiQianjun ZhaoTao ZhongHuanming YangJian WangWen WangYang DongXiaoli ChenXun XuJinquan LiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-13 (2017) |
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Medicine R Science Q |
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Medicine R Science Q 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 Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat |
| description |
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. |
| format |
article |
| author |
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 |
| author_facet |
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 |
| author_sort |
Xian Qiao |
| title |
Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat |
| title_short |
Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat |
| title_full |
Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat |
| title_fullStr |
Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat |
| title_full_unstemmed |
Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat |
| title_sort |
genome-wide target enrichment-aided chip design: a 66 k snp chip for cashmere goat |
| publisher |
Nature Portfolio |
| publishDate |
2017 |
| url |
https://doaj.org/article/305b6b80156c4ed4bb452744fb508777 |
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