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Genetic maps can provide bases for a wide range of genetic and genomic studies.A high-resolution map will greatly facilitate fine mapping of alleles potentially affecting important traits.So far, no high-density map has been constructed for Zhikong scallop (Chlamys farreri, Jones et Preston 1904), which is one of the most important maricultural shellfish in northern China, mostly due to lack of techniques for rapid and cost-effective marker development on a large scale.Recently developed typeⅡB enzyme-based tag sequencing technique enables rapid de novo SNP discovery and genotyping for a mapping population.Using this technique, we sequenced 96 full sib individuals and two parents from an F1 cross of Zhikong scallop based on the Illumina sequencing platform.More than 100 million reads of F1 individuals and 30 million reads of each parent were yielded.After preprocessing, about 80 million high quality tags were remained for F 1 individuals and 25 million for each parent.By clustering these tags using CD-HIT, ~ 1.2 million representing tags were found, which can serve as reference tags for read mapping.Now we are working on SNP calling and genotype assignment for each individual with MAQ.A high-resolution map will be constructed based on identified SNPs and size-related traits will be analyzed to identify the putative quantitative trait loci (QTL) as well.Our approach presents an effective way to discover and genotype genome-wide SNPs for genetic mapping, which should be applicable for any non-model organisms.