Thai Binh Thanh, Tan Mun Hua, Lee Yin Peng, Gan Han Ming, Tran Trang Thi, Austin Christopher M
Fisheries College, Dinh Bang, Tu Son, Bac Ninh, Vietnam.
Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.
Mol Biol Rep. 2016 May;43(5):391-6. doi: 10.1007/s11033-016-3966-2. Epub 2016 Feb 27.
The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation sequencing technology to streamline the identification and genotyping of microsatellite loci from this clam species. Based on an initial partial genome scan, 48 microsatellite markers with similar melting temperatures were identified and characterised. The 12 most suitable polymorphic loci were then genotyped using 51 individuals from a population in Quang Ninh Province, North Vietnam. Genetic variation was low (mean number of alleles per locus = 2.6; mean expected heterozygosity = 0.41). Two loci showed significant deviation from Hardy-Weinberg equilibrium (HWE) and the presence of null alleles, but there was no evidence of linkage disequilibrium among loci. Three additional populations were screened (n = 7-36) to test the geographic utility of the 12 loci, which revealed 100 % successful genotyping in two populations from central Vietnam (Nha Trang). However, a second population from north Vietnam (Co To) could not be successfully genotyped and morphological evidence and mitochondrial variation suggests that this population represents a cryptic species of Lutraria. Comparisons of the Qang Ninh and Nha Trang populations, excluding the 2 loci out of HWE, revealed statistically significant allelic variation at 4 loci. We reported the first microsatellite loci set for the marine clam Lutraria rhynchaena and demonstrated its potential in differentiating clam populations. Additionally, a cryptic species population of Lutraria rhynchaena was identified during initial loci development, underscoring the overlooked diversity of marine clam species in Vietnam and the need to genetically characterise population representatives prior to microsatellite development. The rapid identification and validation of microsatellite loci using next-generation sequencing technology warrant its integration into future microsatellite loci development for key aquaculture species in Vietnam and more generally, aquaculture countries in the South East Asia region.
海蛤Lutraria rhynchaena作为一种水产养殖物种在亚洲越来越受欢迎。越南各地的野生环境中都有Lutraria种群，并且已经建立了几个种群并进行了迁移，用于繁殖和水产养殖养成。在本研究中，我们证明了利用Illumina下一代测序技术简化该蛤类微卫星位点鉴定和基因分型的可行性。基于初步的部分基因组扫描，鉴定并表征了48个具有相似解链温度的微卫星标记。然后使用来自越南北部广宁省一个种群的51个个体对12个最合适的多态性位点进行基因分型。遗传变异较低（每个位点的平均等位基因数 = 2.6；平均期望杂合度 = 0.41）。两个位点显示出与哈迪-温伯格平衡（HWE）的显著偏差以及无效等位基因的存在，但没有证据表明位点之间存在连锁不平衡。另外筛选了三个种群（n = 7 - 36）以测试这12个位点的地理实用性，结果显示越南中部（芽庄）的两个种群基因分型成功率为100%。然而，越南北部的另一个种群（Co To）未能成功进行基因分型，形态学证据和线粒体变异表明该种群代表了Lutraria的一个隐性物种。比较广宁和芽庄种群（不包括偏离HWE的2个位点），发现在4个位点存在统计学上显著的等位基因变异。我们报告了首个针对海蛤Lutraria rhynchaena的微卫星位点集，并展示了其在区分蛤类种群方面的潜力。此外，在初始位点开发过程中鉴定出了Lutraria rhynchaena的一个隐性物种种群，强调了越南海蛤物种多样性被忽视的情况以及在微卫星开发之前对种群代表进行遗传特征分析的必要性。利用下一代测序技术快速鉴定和验证微卫星位点保证了其可整合到越南关键水产养殖物种以及更广泛地说东南亚地区水产养殖国家未来的微卫星位点开发中。
