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

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	Genome-wide Target Enrichment- aided Chip Design: a 66 K SNP Chip for Cashmere Goat
	Qiao X[1]1; Su R 1,2,3,4,5; Li XK 1; Wang W 5; Dong Y 7,10,17; Chen XL6,7; Xu X6,7; Li JQ*1,2,3,4; Wang Y 6,7; Wang RJ 1,2,3,4
刊名	Scientific Reports
	2017
卷号	7 期号:X 页码:e8621
英文摘要	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.
语种	英语
资助机构	This work was financially supported by National high technology research and development program of China(863plan) (2013AA102506), National Key Basic Research Special Foundation of China(973plan) (2013CB835200), National Natural Science Foundation of China(31660639), and China Agriculture Research System (CARS-40-05). ; This work was financially supported by National high technology research and development program of China(863plan) (2013AA102506), National Key Basic Research Special Foundation of China(973plan) (2013CB835200), National Natural Science Foundation of China(31660639), and China Agriculture Research System (CARS-40-05). ; This work was financially supported by National high technology research and development program of China(863plan) (2013AA102506), National Key Basic Research Special Foundation of China(973plan) (2013CB835200), National Natural Science Foundation of China(31660639), and China Agriculture Research System (CARS-40-05). ; This work was financially supported by National high technology research and development program of China(863plan) (2013AA102506), National Key Basic Research Special Foundation of China(973plan) (2013CB835200), National Natural Science Foundation of China(31660639), and China Agriculture Research System (CARS-40-05).
内容类型	期刊论文
源URL	[http://159.226.149.26:8080/handle/152453/12026]
专题	昆明动物研究所_遗传资源与进化国家重点实验室昆明动物研究所_基因起源组
通讯作者	chenxiaoli@genomics.cn; xuxun@genomics.cn; lijinquan_nd@126.com
作者单位	1.College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China 2.Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, 010018, China 3.Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, 010018, China 4.Institute of Animal Husbandry, Academy of Agriculture and Stockbreeding Sciences, Hohhot, Inner Mongolia, 010030, China 5.College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China. 6.The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China 7.Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China 8.James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China 9.Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China 10.Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, 010018, China
推荐引用方式 GB/T 7714	Qiao X[1],Su R,Li XK,et al. Genome-wide Target Enrichment- aided Chip Design: a 66 K SNP Chip for Cashmere Goat[J]. Scientific Reports,2017,7(X):e8621.
APA	Qiao X[1].,Su R.,Li XK.,Wang W.,Dong Y.,...&lijinquan_nd@126.com.(2017).Genome-wide Target Enrichment- aided Chip Design: a 66 K SNP Chip for Cashmere Goat.Scientific Reports,7(X),e8621.
MLA	Qiao X[1],et al."Genome-wide Target Enrichment- aided Chip Design: a 66 K SNP Chip for Cashmere Goat".Scientific Reports 7.X(2017):e8621.