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

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...

Full description

Saved in:
Bibliographic Details
Published in:Scientific reports 2017-08, Vol.7 (1), p.8621-13, Article 8621
Main Authors: Qiao, Xian, Su, Rui, Wang, Yang, Wang, Ruijun, Yang, Ting, Li, Xiaokai, Chen, Wei, He, Shiyang, Jiang, Yu, Xu, Qiwu, Wan, Wenting, Zhang, Yaolei, Zhang, Wenguang, Chen, Jiang, Liu, Bin, Liu, Xin, Fan, Yixing, Chen, Duoyuan, Jiang, Huaizhi, Fang, Dongming, Liu, Zhihong, Wang, Xiaowen, Zhang, Yanjun, Mao, Danqing, Wang, Zhiying, Di, Ran, Zhao, Qianjun, Zhong, Tao, Yang, Huanming, Wang, Jian, Wang, Wen, Dong, Yang, Chen, Xiaoli, Xu, Xun, Li, Jinquan
Format: Article
Language:English
Subjects:
45/22
45/23
45/43
45/61
631/114/2407
631/1647/48
631/208/1348
Association analysis
Cashmere
Design
Genomes
Genomic analysis
Goats
Humanities and Social Sciences
International cooperation
multidisciplinary
Science
Science (multidisciplinary)
Single-nucleotide polymorphism
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-017-09285-z