Chlamys farreri, which is naturally distributed along the coasts of East Asia, is a commercially important mollusk in China, and its mariculture has been prevalent since the 1970s with the decrease of natural resources in the 1960s. To conserve its genetic resources and avoid genetic disturbance, the population structure of the natural population in Japan and genetic condition of the stock population in China were investigated using morphological, microsatellite, and mtDNA markers. Analysis of morphological variance in C. farreri revealed no distinct difference between the presumed 2 subspecies (C. farreri akazara and C. farreri nipponensis) or between the natural and cultured scallops. Population genetic analysis using 2 DNA markers showed that wild scallops in Japan could be divided into a northern group and a southern group with 2 subgroups. The magnitude of genetic divergence between these groups was below the subspecies level, suggesting that C. farreri comprises 1 species with geographic subpopulations. Analysis of the mtDNA markers indicated the genetic divergence between populations of Japan and China, while that of the microsatellite markers showed that 3 Chinese populations (Qingdao, Weihai, and Yantai) were genetically similar to the northern Japanese group, suggesting the possibility of introduction of foreign genomes from the Tohoku area. On the basis of the present results, the northern and southern groups in Japan and Dalian population in China should ideally be regarded as separate units for management and conserved as the source populations for breeding programs. In addition, the genetic relationship among natural and cultured populations in China and natural populations in Japan should be further investigated for a better genetic management of this species.
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