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With recently rapid decline in sequencing costs, there is an urgent need for developing new tools based on next-generation sequencing platforms for non-model organisms that would enable rapid and cost-effective SNP genotyping on a genome-wide scale without requiring any prior genome information.Here we describe such a technique called TETSeq, the core feature of which is that the typeⅡB restriction enzyme such as BsaⅪ that produces uniform 33-bp tags is utilized for genome complexity reduction-based tag sequencing.The feasibility and potential power of this technique have been demonstrated in the model plant species Arabidopsis thaliana.It can achieve high level of genotyping accuracy, and genotyping results are highly reproducible across sequencing platforms.We are initiating several pilot projects by applying this technique to scallop genetic and phylogenomic studies.