Kim E M, An H S, Kang J H, An C M, Dong C M, Hong Y K, Park J Y
Biotechnology Research Division, National Fisheries Research and Development Institute, Busan, Republic of Korea.
Department of Biotechnology, College of Fisheries Science, Pukyong National University, Busan, Republic of Korea.
Genet Mol Res. 2014 Oct 7;13(4):8163-73. doi: 10.4238/2014.October.7.11.
Manila clam (Ruditapes philippinarum) is a valuable and intensively exploited shellfish species in Korea. Despite its importance, information on its genetic background is scarce. For the genetic characterization of R. philippinarum, expressed sequence tag-derived microsatellite markers were developed using next-generation sequencing. A total of 5879 tandem repeats containing di- to hexanucleotide repeat motifs were obtained from 236,746 reads (mean = 413 bp). Of the 62 loci screened, 24 (38.7%) were successfully amplified, and 10 were polymorphic in 144 individuals from 2 manila clam populations (Incheon and Geoje, Korea). The number of alleles ranged from 2 to 17 in the Incheon population and from 3 to 13 in the Geoje population (overall AR = 7.21). The mean observed and expected heterozygosities were estimated to be 0.402 and 0.555, respectively. Hence, there is less genetic variability in the Geoje population than in the Incheon population, although no significant reductions of genetic diversity were found between the populations (P > 0.05). However, significant genetic differentiation was detected between the populations (FST = 0.064, P < 0.001). Significant deviations from Hardy-Weinberg equilibrium and high inbreeding coefficients (mean FIS = 0.22-0.26) were detected in both populations. The 10 novel polymorphic microsatellite loci used in this study will be useful for future genetic mapping studies and for characterizing population structures, monitoring genetic diversity for successful aquaculture management, and developing conservation strategies for manila clam populations in Korea.
菲律宾蛤仔（Ruditapes philippinarum）是韩国一种具有重要价值且被大量开发利用的贝类物种。尽管其具有重要性，但其遗传背景信息却很匮乏。为了对菲律宾蛤仔进行遗传特征分析，利用下一代测序技术开发了基于表达序列标签的微卫星标记。从236,746条 reads（平均长度 = 413 bp）中总共获得了5879个包含二至六核苷酸重复基序的串联重复序列。在筛选的62个位点中，24个（38.7%）成功扩增，其中10个在来自韩国两个菲律宾蛤仔种群（仁川和巨济）的144个个体中表现出多态性。仁川种群的等位基因数范围为2至17，巨济种群为3至13（总体等位基因丰富度AR = 7.21）。观察到的平均杂合度和期望杂合度分别估计为0.402和0.555。因此，巨济种群的遗传变异性低于仁川种群，尽管在两个种群之间未发现遗传多样性的显著降低（P > 0.05）。然而，在两个种群之间检测到显著的遗传分化（FST = 0.064，P < 0.001）。在两个种群中均检测到显著偏离哈迪 - 温伯格平衡以及高近亲繁殖系数（平均FIS = 0.22 - 0.26）。本研究中使用的10个新的多态性微卫星位点将有助于未来的遗传图谱研究、种群结构特征分析、监测遗传多样性以实现成功的水产养殖管理以及制定韩国菲律宾蛤仔种群的保护策略。
