| Occurring along the coast of northern China, South Korea, North Korea and Japan, the Chinese scallop (Chlamys farreri) has been one of the major species of the shellfish industry in the northern coast China for several decades. In recent years, however, scallop culture has been haunted by a high mortality problem. It is believed that the problem was caused by a combination of overcrowding N high summer temperature and deteriorating water quality. Additionally, one more possible reason for the problem to some extent, is that the scallop stock may be deteriorating genetically. Based upon this reason, refreshing scallop stock by introducing new stocks from other populations outside the coast of north China was considered. Consequently, investigation and evaluation on its stock structure throughout its geographic range are required.For benthic marine species with pelagic larvae, it has been proposed that they have population genetic structures reflecting the dispersal capacity of larvae. Most of them are supposed to have less or little genetic structure reflecting the dispersal capacity of larvae. Mitochondrial DNA sequences (including 16S rDNA) were used for many of these studies. In C. farreri, this hypothesis has almost never been tested. So, this also lead to our interest to examine population genetic structure using mitochondrial gene sequence data, with two more population samples (Korea and Japan) as well as four samples from China, within its geographic range of the species.Ribosomal Internal Transcribed Spacer Regions ITS-1 and ITS-2 in Scallop C. farreri were amplified via PCR, Fragments of the 16S rRNA gene and COI gene were amplified using two pairs of universal primers:The PCR products of ITS-1 and ITS-2 fragments from Scallop C.farrei were ligated into T-vector, cloned and sequenced. 340 bp (ITS-1, AF245687 ) and 510 bp (ITS-2, AF245688) nucleotide sequences were got respectively, and the contents of A, T, G and C were 32.06%, 20.59%, 22.35% and 25.00% in ITS-1, 30.00%, 21.37%, 24.12% and 24.51% in ITS-2. The primers of ITS-1 and ITS-2 proved to be very universal in a variety of mollusk species.Mitochondria! 16S rRNA gene fragments from Scallop C. farrei and Argopecten irradians were amplified via PCR. 634bp and 542bp nucleotide sequences were retrieved respectively. The content of A, T, G and C were 25.08%, 29.65%, 27.60% and 17.67% in C. farreri, 25.65%, 29.52%, 27.31% and 17.53% in A. irradians. Alignment indicated that the homology of two fragments was 68.1%, the nucleotide difference number was 80, and several small deletion/insertion sections, which contributed to length difference of the two fragments in two species, occurred in the middle of fragments (around 130bp) .A 592 base pairs fragment of the mitochondrial 16S ribosomal RNA gene in 47 Zhikong scallop (C. farreri) specimens was sequenced in order to examine its intra-specific genetic variation and geographic structure. These samples were collected from six populations (four from China, and one each from South Korea and Japan respectively) across its range. Thirty-one nucleotide positions were found variable and twenty-three haplotypes were detected in all samples, which showed that more 16S rDNA variation existed in C. farreri when compared with several oyster species. Analysis at the intra-population level showed that the South Korea samples had the richest sequence diversity. However, analysis of haplotype frequency distribution and analysis of molecular variance (AMOVA) indicated that little geographic structure was present among all samples, and an absolute majority (99.65%) of the genetic variation was distributed within populations, suggesting that the populations in this study may belong to a single panmictic unit. Relative smaller distribution range and various currents may account for sufficient gene flow among these populations for this benthic species.With 14 polymorphic sites and 8 hyplotypes, SK population showed the richest variation in all 6 populations, this may support the idea of stock introduction from South Ko...
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