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The Yesso scallop, Patinopecten yessoensis (Jay, 1857) has become one of the most important commercial maricultural shellfish in the north of China since it was introduced in 1982.Molecular breeding programs for genetic improvement of cultured Yesso scallops are currently ongoing.A high-resolution genetic linkage map would allow for high-resolution QTL mapping of important economic traits, achievement of which however requires cost-effective SNP discovery and genotyping technique suitable for non-model organisms whose genome information is usually very limited.Here we applied the typeⅡB enzyme-based tag sequencing technique based on high-throughput Illumina sequencing platform to identify and type SNPs in 96 of F1 individuals from a self-fertile inbred line generated from a hermaphrodite Yesso scallop.In total, we got more than 133 million reads from the parent and its progenies.After preprocessing raw reads, over 27 million (81%) and 80 million (80%) tags retained for the parent and its progenies, respectively.About 600,000 representing tags were obtained by self-alignment of all tags using CD-Hit-est.Ongoing works include discovery and genotyping of SNPs for each individual, linkage mapping, and QTL analysis.The accomplishment of this study will provide the first high-density of linkage map for Yesso scallop, and lay the important foundation for future genetic studies on this species.