Genome-Wide Target Enrichment-Aided Chip Design: A 66K SNP Chip for Cashmere Goat

    August 2017 in “ Scientific reports ”
    Xuguang Qiao, Rui Su, Yan Wang, Ruijun Wang, Ting Yang, Xiaokai Li, Wei Chen, Shiyang He, Yu Jiang, Qiwu Xu, Wenting Wan, Yaolei Zhang, Wenguang Zhang, Chen Jiang, Bin Liu, Xin Liu, Yixing Fan, Duoyuan Chen, Jiang Huai-zhi, 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
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    TLDR Researchers developed a cost-effective 66 K SNP chip for cashmere goats that is accurate and useful for genetic studies.
    In 2017, researchers developed a 66 K SNP chip for cashmere goats using a solution hybrid selection (SHS)-based target enrichment strategy, which is more flexible and cost-effective than the existing Bead Chip technology. The chip was created using whole-genome sequencing data from 73 individuals and was validated with data from 436 cashmere goats, achieving SNP call rates of 95.3% to 99.8% and an average sequencing depth of 40X for target SNPs. The chip, which targets regions 200 bp around the SNPs, was also used in a genome-wide association study for cashmere fineness and identified several loci marginally associated with hair growth signaling pathways. This demonstrates the chip's utility in genomic analyses and suggests that the SHS-based strategy could be applied to other species.
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