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Sci Rep. 2017 Aug 17;7(1):8621. doi: 10.1038/s41598-017-09285-z.

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

Qiao X1, Su R1,2,3,4,5, Wang Y6,7, Wang R1,2,3,4, Yang T6,7, Li X1, Chen W8,9, He S7, Jiang Y10, Xu Q6,11, Wan W12, Zhang Y6,11, Zhang W1,2, Chen J6,7, Liu B13, Liu X6,11, Fan Y1, Chen D7, Jiang H14, Fang D7, Liu Z1,2,3,4, Wang X7, Zhang Y1,2,3,4, Mao D7, Wang Z1,2,3,4, Di R15, Zhao Q15, Zhong T16, Yang H7,17, Wang J7,17, Wang W5, Dong Y7,8,9, Chen X18,19, Xu X20,21, Li J22,23,24,25.

Author information

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
Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, 010018, China.
5
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
6
China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
7
BGI-Shenzhen, Shenzhen, 518083, China.
8
College of Biological big data, Yunnan Agriculture University, Kunming, 650504, China.
9
Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.
10
College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
11
BGI-Qingdao, Qingdao, 266000, China.
12
Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Polytechnical University, Xi'an, 710072, China.
13
Institute of Animal Husbandry, Academy of Agriculture and Stockbreeding Sciences, Hohhot, Inner Mongolia, 010030, China.
14
College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
15
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.
16
Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China.
17
James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China.
18
China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. chenxiaoli@genomics.cn.
19
BGI-Shenzhen, Shenzhen, 518083, China. chenxiaoli@genomics.cn.
20
China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. xuxun@genomics.cn.
21
BGI-Shenzhen, Shenzhen, 518083, China. xuxun@genomics.cn.
22
College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. lijinquan_nd@126.com.
23
Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, 010018, China. lijinquan_nd@126.com.
24
Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, 010018, China. lijinquan_nd@126.com.
25
Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, 010018, China. lijinquan_nd@126.com.

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.

PMID:
28819310
PMCID:
PMC5561203
DOI:
10.1038/s41598-017-09285-z
[Indexed for MEDLINE]
Free PMC Article

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