| Feng Yanyan,Zhang Dening,Lv Jianjian,Gao Baoquan,Li Jian,Liu Ping. 2019. Identification of SNP markers correlated with the tolerance of low-salinity challenge in swimming crab (Portunus trituberculatus). Acta Oceanologica Sinica, 38(8):41－47 |
| Identification of SNP markers correlated with the tolerance of low-salinity challenge in swimming crab (Portunus trituberculatus) |
| 三疣梭子蟹低盐适应相关的SNP开发 |
| Received:July 19, 2018 |
| DOI：10.1007/s13131-019-1428-0 |
| Key words:Portunus trituberculatus low salinity time-of-flight mass spectrometry single nucleotide polymorphism SNP |
| 中文关键词: 三疣梭子蟹 低盐 飞行质谱 单核苷酸多态性 SNP |
| 基金项目:The Modern Agro-industry Technology Research System under contract No. CARS-48; the program of Shandong Leading Talent under contract No. LJNY2015002; the National Natural Science Foundation of China under contract No. 31472275; the Qingdao Industrial Development Program (Science and Technology Benefit Special Project) under contract No. 17-3-3-62-nsh. |
| Author Name | Affiliation | E-mail | | Feng Yanyan | Key Laboratory of Sustainable Development of Marine Fisheries of Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China | | | Zhang Dening | Key Laboratory of Sustainable Development of Marine Fisheries of Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China | | | Lv Jianjian | Key Laboratory of Sustainable Development of Marine Fisheries of Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China | | | Gao Baoquan | Key Laboratory of Sustainable Development of Marine Fisheries of Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China | | | Li Jian | Key Laboratory of Sustainable Development of Marine Fisheries of Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China | lijian@ysfri.ac.cn | | Liu Ping | Key Laboratory of Sustainable Development of Marine Fisheries of Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China | |
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| Abstract: |
| Water salinity condition is an important factor for artificial propagation of the swimming crab (Portunus trituberculatus). Low salinity (LS)-resistant strains are preferred by crab industries. Single nucleotide polymorphism (SNP), the third generation of molecular markers, can be utilized in the breeding of LS-resistant species of P. trituberculatus. Our earlier study identified 615 genes differentially expressed in low-salinity stress compared to the controls. Although thousands of SNP loci have been found, it is hard to identify a SNP marker in correlation with a desired trait. In this study, time-of-flight mass spectrometry (TOF-MS), as an efficient method to select SNPs for the tolerance of LS challenge, was utilized for SNP typing. Fifty gene segments were amplified based on comparative transcriptomics in our earlier study, a total of 18 511 bp DNA fragments were amplified, and eighty-five SNP markers were found. The frequency of the SNPs was estimated to be 0.46 per 100 base pairs of DNA sequences. The rate of the conversion mutation was 81%, while the transversion mutation was 19%. The mutation rate of the G/T (C/A), A/T and G/C was 26%, 12% and 7%, respectively. Eight SNP markers were found to significantly correlate with the adaption of low salinity. Of the eight SNP markers, three linked-SNPs were found in the cuticle proportion gene, and another three SNPs were found in three new genes, and the rest two were found in aquaporin gene and chloride channel gene. The development of these SNP markers found in our study could be primarily used for breeding LS-resistant strains of P. trituberculatus. |
| 中文摘要: |
| 盐度是影响三疣梭子蟹人工繁育非常重要的一个环境因素，抗低盐品系的三疣梭子蟹受到水产养殖界的广泛喜爱。分子标记辅助育种可以大大加快良种选育和性状改良的的过程，目前作为第三代的分子标记技术的SNP，广泛应用到三疣梭子蟹耐低盐品系选育过程中。本实验室已有的研究中，通过不同群体分别在盐度11和33下的基因表达差异，构建的比较转录组学数据中总共包含了615条与低渗调节相关的基因片段。为了发掘三疣梭子蟹与低盐适应相关SNP，本研究基于三疣梭子蟹比较转录组学数据研究结果，筛选出低盐调节相关候选基因片段50条，设计引物进行PCR扩增，共得到总长为18511 bp的DNA片段。通过直接测序法在低盐相关片段上发现了85个SNP位点，分布频率为0.46/100 bp，其中转换突变的比例为81%，颠换突变的比例为19%，转换的比例远远大于颠换，符合“transition bias”原理。C/T或G/A突变所占比例为55%；G/T或C/A比例为26%，A/T突变所占比例为12%，G/C突变比例为7%。通过飞行质谱法，在三疣梭子蟹低盐适应性状分离群体中各成功分型了23个SNP位点。通过卡方检验分析发现，8个SNPs与低盐适应显著相关（P<0.05）。其中有三个关联性SNP位点位于表皮蛋白基因上，有三个SNP位点位于三个新基因上，其他两个SNP位点分别位于水通道蛋白和氯离子通道蛋白基因上。这些标记的开发为三疣梭子蟹耐低盐新品种选育方法的建立奠定了良好的基础。 |
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