Kim Keun-Sik, Noh Choong Hwan, Moon Shin-Joo, Han Seung-Hee, Bang In-Chul
East Sea Environment Research Center, East Sea Research Institute, Korea Institute of Ocean Science & Technology, Uljin, 36315, Republic of Korea.
Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea.
Mol Biol Rep. 2016 Jun;43(6):541-8. doi: 10.1007/s11033-016-3980-4. Epub 2016 Apr 8.
Giant grouper (Epinephelus lanceolatus) is a commercially important species, but its wild population has recently been classified as vulnerable. This species has significant potential for use in aquaculture, though a greater understanding of population genetics is necessary for selective breeding programs to minimize kinship for genetically healthy individuals. High-throughput pyrosequencing of genomic DNA was used to identify and characterize novel tetra- and trinucleotide microsatellite markers in giant grouper from Sabah, Malaysia. In total, of 62,763 sequences containing simple sequence repeats (SSRs) were obtained, and 78 SSR loci were selected to possibly contain tetra- and trinucleotide repeats. Of these loci, 16 had tetra- and 8 had trinucleotide repeats, all of which exhibited polymorphisms within easily genotyped regions. A total of 143 alleles were identified with an average of 5.94 alleles per locus, with mean observed and expected heterozygosities of 0.648 and 0.620, respectively. Among of them, 15 microsatellite markers were identified without null alleles and with Hardy-Weinberg equilibrium. These alleles showed a combined non-exclusion probability of 0.01138. The probability of individual identification (PID) value combined with in descending order 12 microsatellite markers was 0.00008, which strongly suggests that the use of the microsatellite markers developed in this study in various combinations would result in a high resolution method for parentage analysis and individual identification. These markers could be used to establish a broodstock management program for giant grouper and to provide a foundation for genetic studies such as population structure, parentage analysis, and kinship selection.
鞍带石斑鱼（Epinephelus lanceolatus）是一种具有重要商业价值的物种，但其野生种群最近被列为易危物种。该物种在水产养殖方面具有巨大潜力，不过，为了使选择性育种计划能够将亲缘关系降至最低以培育出基因健康的个体，有必要更深入地了解种群遗传学。利用基因组DNA的高通量焦磷酸测序技术，对来自马来西亚沙巴的鞍带石斑鱼新型四核苷酸和三核苷酸微卫星标记进行了鉴定和表征。总共获得了62763个包含简单序列重复（SSR）的序列，并选择了78个SSR位点，这些位点可能包含四核苷酸和三核苷酸重复序列。在这些位点中，16个具有四核苷酸重复序列，8个具有三核苷酸重复序列，所有这些序列在易于进行基因分型的区域内均表现出多态性。总共鉴定出143个等位基因，每个位点平均有5.94个等位基因，观察到的平均杂合度和预期杂合度分别为0.648和0.620。其中，鉴定出15个无微效等位基因且符合哈迪-温伯格平衡的微卫星标记。这些等位基因的联合非排除概率为0.01138。将12个微卫星标记按降序排列组合后的个体识别（PID）值概率为0.00008，这有力地表明，本研究中开发的微卫星标记以各种组合使用，将产生一种用于亲权分析和个体识别的高分辨率方法。这些标记可用于建立鞍带石斑鱼的亲鱼管理计划，并为种群结构、亲权分析和亲属选择等遗传研究提供基础。
