An C-M, An H S, Lee J W, Hong S W
Biotechnology Research Division, National Fisheries Research and Development Institute, Busan, Korea.
Genet Mol Res. 2013 May 14;12(2):1679-90. doi: 10.4238/2013.May.14.8.
The threadsail filefish, Stephanolepis cirrhifer (Monacanthidae), is found mainly in the western Pacific. It is intensively caught in Korea and is a highly appreciated seafood delicacy. Consequently, the natural population of this species has drastically decreased, despite introductions from hatcheries. To provide information necessary for its conservation and management, we developed 24 polymorphic microsatellite markers using a combination of a total enriched genomic library and a small-scale 454 pyrosequencing. A total of 90,847 raw reads were obtained, and 75,128 unique sequences were generated, with an average length of 477 bp; 5350 (7.12%) sequences contained a minimum of 5 di- to tetranucleotide repeat motifs. Seventy-four sequences were used for microsatellite primer design. They all amplified successfully; 24 were polymorphic, with 8 containing trinucleotide repeats and 3 containing tetranucleotide repeats. The genetic variations based on 15 primer sets were investigated using 45 wild individuals from the coastal waters of Geomun Island. The number of alleles per locus varied from 4 to 15, with an average of 7.47. The observed and expected heterozygosities ranged from 0.333 to 0.956 and from 0.316 to 0.870, with averages of 0.692 and 0.701, respectively. No linkage disequilibrium was found between any pair of loci, indicating their independence. One locus significantly deviated from Hardy-Weinberg equilibrium after Bonferroni's correction; this may be due to the existence of a null allele. Cross-amplification was also tested for all 24 polymorphic loci in another monacanthid species, Thamnaconus modestus; 7 loci were effectively amplified. The high degree of polymorphism that was exhibited by the 15 newly developed microsatellites will be useful for assessing genetic variation and for conservation genetic studies of these 2 monacanthid species.
线纹单棘鲀（Stephanolepis cirrhifer，单棘鲀科）主要分布于西太平洋。在韩国，该物种遭到过度捕捞，是备受青睐的海鲜珍品。因此，尽管有孵化场放流补充，但该物种的自然种群数量仍急剧下降。为提供其保护和管理所需的信息，我们结合全基因组文库富集法和小规模454焦磷酸测序技术，开发了24个多态性微卫星标记。共获得90847条原始 reads，生成75128条独特序列，平均长度为477 bp；其中5350条（7.12%）序列包含至少5个二至四核苷酸重复基序。74条序列用于微卫星引物设计。所有引物均成功扩增；24个具有多态性，其中8个包含三核苷酸重复，3个包含四核苷酸重复。利用来自巨文岛沿海水域的45个野生个体，对基于15对引物的遗传变异进行了研究。每个位点的等位基因数从4到15不等，平均为7.47。观察杂合度和期望杂合度分别在0.333至0.956和0.316至0.870之间，平均值分别为0.692和0.701。未发现任何一对位点之间存在连锁不平衡，表明它们相互独立。经Bonferroni校正后，有一个位点显著偏离哈迪-温伯格平衡；这可能是由于无效等位基因的存在。还对另一种单棘鲀属物种——小鳞单棘鲀的所有24个多态性位点进行了交叉扩增测试；7个位点有效扩增。新开发的15个微卫星所表现出的高度多态性，将有助于评估这两种单棘鲀属物种的遗传变异和开展保护遗传学研究。
