Abstract
In order to promote the widespread application of single-nucleotide polymorphism (SNP)-based genotyping, a new method was developed and called target SNP-seq which combined the advantages of multiplex polymerase chain reaction (PCR) amplification and high throughput sequencing on Illumina X Ten platform. Compared with kompetitive allele-specific PCR (KASP), microchips, and genotyping by sequencing (GBS), target SNP-seq uses perfect SNPs based on the analysis of variome (whole-genome sequence data of different accessions) and is flexible, cost-effective, and highly accurate for genotyping middle-scale SNPs. It could genotype hundreds of SNPs in massive DNA samples within 3 days at the cost of $7 for each DNA sample. The high efficiency and low cost of target SNP-seq make it more competitive than current SNP genotyping methods, and it has excellent potential for application in genetic research, as well as in promoting plant-breeding processes in the near future.
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Acknowledgments
Authors would like to thank Jianan Zhang (MolBreeding Biotechnology Co., Ltd., Shijiazhuang, China) for their valuable comments and corrections to this protocol.
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Zhang, J., Yang, J., Wen, C. (2023). A New SNP Genotyping Technology by Target SNP-Seq. In: Shavrukov, Y. (eds) Plant Genotyping. Methods in Molecular Biology, vol 2638. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3024-2_26
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DOI: https://doi.org/10.1007/978-1-0716-3024-2_26
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