| 应用单核苷酸多态性(SNP)标记鉴定短颌鲚、湖鲚和刀鲚 |
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| 引用本文： | 程方圆,陶紫玉,李晨虹.应用单核苷酸多态性(SNP)标记鉴定短颌鲚、湖鲚和刀鲚[J].上海海洋大学学报,2019,28(1):10-19. |
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| 作者姓名： | 程方圆 陶紫玉 李晨虹 |
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| 作者单位： | 上海海洋大学海洋动物系统分类与进化上海高校重点实验室;上海海洋大学水产动物遗传育种上海市协同创新中心;上海海洋大学水产科学国家级实验教学示范中心 |
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| 基金项目： | 上海市协同创新水产动物遗传育种中心（A1-2041-18-0000） |
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| 摘 要： | 为了快速区分长江流域各水体中的鲚属鱼类,利用单核苷酸多态性(Single nucleotide polymorphism,SNP)标记对短颌鲚(Coilia brachygnathus)、湖鲚(C. nasus taihuensis)和刀鲚(C. nasus)进行物种鉴定。从120个在短颌鲚和刀鲚之间分化指数(Fst)为1的SNP位点中随机挑选出20个用于引物设计,从21个在湖鲚和刀鲚之间分化指数较高的SNP位点中随机挑选出10个设计引物。随机挑20尾短颌鲚、20尾湖鲚和12尾刀鲚用设计的引物扩增、测序。结果表明:洞庭湖和鄱阳湖的短颌鲚与刀鲚可以使用以上19个SNP分子标记中的任何一个完全分开,剩下1个SNP标记在所扩增的样本中没有发现多样性变异而被弃用。用于区分湖鲚与刀鲚的10个SNP分子标记中有8个在所测样本中可以扩增并用于物种鉴定。其中单独使用Ct-Cn_wtap位点时,湖鲚和刀鲚的基因频率相差最大,当使用Ct-Cn_wtap和Ct-Cn_eif2b4位点时,对湖鲚和刀鲚的鉴别准确率可以达到100%。本研究提供了稳定、高效和低成本识别短颌鲚和刀鲚、湖鲚和刀鲚的方法,为今后鲚属鱼类的物种鉴定和资源保护提供了有效的工具。
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| 关 键 词： | SNP分子标记 刀鲚 短颌鲚 湖鲚 物种鉴定 |
| 收稿时间： | 2018/5/14 0:00:00 |
| 修稿时间： | 2018/10/27 0:00:00 |
Species identification of Coilia brachygnathus, C. nasus and C. nasus taihuensis with SNP markers |
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| CHENG Fangyuan,TAO Ziyu and LI Chenhong.Species identification of Coilia brachygnathus, C. nasus and C. nasus taihuensis with SNP markers[J].Journal of Shanghai Ocean University,2019,28(1):10-19. |
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| Authors: | CHENG Fangyuan TAO Ziyu and LI Chenhong |
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| Institution: | Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China;Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China;National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China,Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China;Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China;National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China and Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China;Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China;National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China |
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| Abstract: | To identify the species of the tapertail anchovies rapidly, Coilia brachygnathus, C. nasus and C. nasus taihuensis distributed in freshwater lakes of the Yangtze River Basin, single nucleotide polymorphism (SNP) molecular markers were developed to distinguish them. Twenty SNP markers were randomly selected with fixation index (Fst) of 1 from the 120 loci found between C. brachygnathus and C. nasus; and 10 SNP markers were ramdomly selected with high Fst value from the 21 loci found between C. nasus and C. nasus taihuensis for primers designing. Twenty C. brachygnathus, 20 C. nasus taihuensis and 12 C. nasus were randomly amplified and sequenced using the primers designed. The results showed that each of the 19 SNP markers can be used to completely distinguish C. brachygnathus and C. nasus, and no polymorphic sites were found in the other locus in the samples tested. Eight SNP makers were successfully amplified and used to distinguish C. nasus and C. nasus taihuensis. Marker Ct-Cn_wta showed the highest difference in genotype frequency between C. nasus and C. nasus taihuensis. When marker Ct-Cn_wtap and Ct-Cn_eif2b4 SNP were used, the successful identification rate on C. nasus and C. nasus taihuensis reached 100%. In conclusion, a robust and efficient method is provided to identify the tapertail anchovies, C. brachygnathus, C. nasus and C. nasus taihuensis using SNP molecular marker, which would provide an important tool for identification and conservation of the tapertail anchovies. |
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| Keywords: | SNP marker Coilia brachygnathus Coilia nasus Coilia nasus taihuensis species identification |
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