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 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.
Publication Title
Scientific Reports
Recommended Citation
Qiao, X., Su, R., Wang, Y., Wang, R., Yang, T., Li, X., Chen, W., He, S., Jiang, Y., Xu, Q., Wan, W., Zhang, Y., Zhang, W., Chen, J., Liu, B., Liu, X., Fan, Y., Chen, D., Jiang, H., Fang, D., Liu, Z., Wang, X., Zhang, Y., Mao, D., Wang, Z., Di, R., Zhao, Q., Zhong, T., Yang, H., Wang, J., Wang, W., Dong, Y., & Chen, X. (2017). Genome-wide Target Enrichment-Aided Chip Design: A 66 K SNP Chip for Cashmere Goat. Scientific Reports, 7 (1) https://doi.org/10.1038/s41598-017-09285-z
