Journal of Fisheries Research ›› 2023, Vol. 45 ›› Issue (4): 331-340.DOI: 10.14012/j.cnki.fjsc.2023.04.002
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LI Zhaonan(), LI Changzhong, BAO Changhong, HE Caixia, JIN Wenjie, CHEN Yanxia()
Received:
2022-12-05
Online:
2023-08-25
Published:
2023-08-09
李昭楠(), 李长忠, 保长虹, 贺彩霞, 金文杰, 陈艳霞()
通讯作者:
陈艳霞(1987—),女,博士,讲师,主要从事高原动物保护与利用相关研究。E-mail:chenyanxia9568@163.com
作者简介:
李昭楠(1996—),女,硕士,主要从事动物生态学相关研究。E-mail:lizhaonan123456@163.com
基金资助:
CLC Number:
LI Zhaonan, LI Changzhong, BAO Changhong, HE Caixia, JIN Wenjie, CHEN Yanxia. Molecular identification of Oncorhynchus mykiss based on DNA barcode technology[J]. Journal of Fisheries Research, 2023, 45(4): 331-340.
李昭楠, 李长忠, 保长虹, 贺彩霞, 金文杰, 陈艳霞. 基于DNA条形码技术的虹鳟分子鉴定[J]. 渔业研究, 2023, 45(4): 331-340.
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URL: http://www.hyyysci.com/EN/10.14012/j.cnki.fjsc.2023.04.002
物种 Species | 登录号 Accession number | 长度/bp Length |
---|---|---|
帝王鲑 Oncorhynchus tshawytscha | KX958414.1 | 1 204 |
金腹大麻哈鱼 Oncorhynchus chrysogaster | JX960908.1 | 1 247 |
美洲红点鲑 Salvelinus fontinalis | HQ167687.1 | 1 551 |
钝吻鲑 Salmo obtusirostris | JX960948.1 | 1 262 |
多瑙哲罗鱼 Hucho hucho | JX960904.1 | 1 247 |
细鳞鲑 Brachymystax lenok | JX227988.1 | 1 581 |
突唇白鲑 Coregonus lavaretus | JX960890.1 | 1 246 |
北鲑 Stenodus leucichthys | KT630716.1 | 1 201 |
普伦白鲑 Coregonus pollan | JX960898.1 | 1 262 |
茴鱼 Thymallus thymallus | JX960975.1 | 1 262 |
Tab.1 COⅠgene information of Salmonidae
物种 Species | 登录号 Accession number | 长度/bp Length |
---|---|---|
帝王鲑 Oncorhynchus tshawytscha | KX958414.1 | 1 204 |
金腹大麻哈鱼 Oncorhynchus chrysogaster | JX960908.1 | 1 247 |
美洲红点鲑 Salvelinus fontinalis | HQ167687.1 | 1 551 |
钝吻鲑 Salmo obtusirostris | JX960948.1 | 1 262 |
多瑙哲罗鱼 Hucho hucho | JX960904.1 | 1 247 |
细鳞鲑 Brachymystax lenok | JX227988.1 | 1 581 |
突唇白鲑 Coregonus lavaretus | JX960890.1 | 1 246 |
北鲑 Stenodus leucichthys | KT630716.1 | 1 201 |
普伦白鲑 Coregonus pollan | JX960898.1 | 1 262 |
茴鱼 Thymallus thymallus | JX960975.1 | 1 262 |
引物名称 Name of primers | 引物序列 Sequence of primers | 产物长度/bp Length of product | |
---|---|---|---|
COⅠ-1(DNA barcode) | COⅠ-F24 | 5’-GGGATGACCAAATCTATAACGTGA-3’ | 681 |
COⅠ-R24 | 5’-CTCAGACCATTCCTATATACCCGAAG-3’ | ||
COⅠ-F25 | 5’-GATTAATTCCCCTAATAATCGGAGC-3’ | 678 | |
COⅠ-R25 | 5’-ATGTAAAGTAAGCACGAGTGTCCA-3’ | ||
COⅠ-2(Mini barcode) | TEYI-0F | 5’-AACCTCCAGCCATCTCTCAG-3’ | 153 |
TEYI-0R | 5’-CCGGGTCAAAGAAAGTGGTG-3’ | ||
TEYI-1F | 5’-CCGCCCTGAGTCTACTGATT-3’ | 230 | |
TEYI-1R | 5’-TGGAGGAAGGAGTCAGAAGC-3’ |
Tab.2 PCR primer information
引物名称 Name of primers | 引物序列 Sequence of primers | 产物长度/bp Length of product | |
---|---|---|---|
COⅠ-1(DNA barcode) | COⅠ-F24 | 5’-GGGATGACCAAATCTATAACGTGA-3’ | 681 |
COⅠ-R24 | 5’-CTCAGACCATTCCTATATACCCGAAG-3’ | ||
COⅠ-F25 | 5’-GATTAATTCCCCTAATAATCGGAGC-3’ | 678 | |
COⅠ-R25 | 5’-ATGTAAAGTAAGCACGAGTGTCCA-3’ | ||
COⅠ-2(Mini barcode) | TEYI-0F | 5’-AACCTCCAGCCATCTCTCAG-3’ | 153 |
TEYI-0R | 5’-CCGGGTCAAAGAAAGTGGTG-3’ | ||
TEYI-1F | 5’-CCGCCCTGAGTCTACTGATT-3’ | 230 | |
TEYI-1R | 5’-TGGAGGAAGGAGTCAGAAGC-3’ |
种名 Species | 登录号 Accession number | 长度/bp Length | |
---|---|---|---|
帝王鲑 Oncorhynchus tshawytscha | FJ999371.1 | 652 | |
银鲑 Oncorhynchus kisutch | MG951604.1 | 652 | |
虹鳟 Oncorhynchus mykiss | MN850431.1 | 653 | |
大麻哈鱼 Oncorhynchus keta | MN850432.1 | 653 | |
大西洋鲑 Salmo salar | MN850430.1 | 651 | |
花羔红点鲑 Salvelinus malma | EU522414.1 | 652 | |
北极红点鲑 Salvelinus alpinus | KJ128606.1 | 648 | |
远东红点鲑 Salvelinus leucomaenis | MF503661.1 | 697 | |
多瑙哲罗鱼 Hucho hucho | KJ553640.1 | 652 | |
哲罗鱼 Hucho taimen | MG951558.1 | 652 | |
细鳞鲑 Brachymystax lenok | JX261990.1 | 633 | |
远东哲罗鱼 Parahucho perryi | HQ693237.1 | 655 | |
秋白鲑 Coregonus autumnalis | EU202649.1 | 650 | |
高白鲑 Coregonus peled | MF632325.1 | 637 | |
欧白鲑 Coregonus albula | KX457959.1 | 704 | |
茴鱼 Thymallus thymallus | HQ961016.1 | 652 | |
黑龙江茴鱼 Thymallus grubii | MG951577.1 | 652 |
Tab.3 COⅠ gene information of 17 Salmonidae species
种名 Species | 登录号 Accession number | 长度/bp Length | |
---|---|---|---|
帝王鲑 Oncorhynchus tshawytscha | FJ999371.1 | 652 | |
银鲑 Oncorhynchus kisutch | MG951604.1 | 652 | |
虹鳟 Oncorhynchus mykiss | MN850431.1 | 653 | |
大麻哈鱼 Oncorhynchus keta | MN850432.1 | 653 | |
大西洋鲑 Salmo salar | MN850430.1 | 651 | |
花羔红点鲑 Salvelinus malma | EU522414.1 | 652 | |
北极红点鲑 Salvelinus alpinus | KJ128606.1 | 648 | |
远东红点鲑 Salvelinus leucomaenis | MF503661.1 | 697 | |
多瑙哲罗鱼 Hucho hucho | KJ553640.1 | 652 | |
哲罗鱼 Hucho taimen | MG951558.1 | 652 | |
细鳞鲑 Brachymystax lenok | JX261990.1 | 633 | |
远东哲罗鱼 Parahucho perryi | HQ693237.1 | 655 | |
秋白鲑 Coregonus autumnalis | EU202649.1 | 650 | |
高白鲑 Coregonus peled | MF632325.1 | 637 | |
欧白鲑 Coregonus albula | KX457959.1 | 704 | |
茴鱼 Thymallus thymallus | HQ961016.1 | 652 | |
黑龙江茴鱼 Thymallus grubii | MG951577.1 | 652 |
物种 Species | 浓度/(ng/μL) Concentration | OD(260/280) | 260/230 | 260 |
---|---|---|---|---|
三倍体虹鳟Triploid rainbow trout | 164.90 | 2.032 | 1.343 | 3.300 |
金鳟Golden trout | 197.65 | 2.141 | 1.633 | 3.964 |
二倍体虹鳟 Diploid rainbow trout | 119.85 | 2.001 | 1.097 | 2.366 |
大西洋鲑Salmo salar | 170.00 | 1.988 | 1.943 | 3.406 |
大麻哈鱼Oncorhynchus keta | 198.40 | 2.084 | 1.859 | 3.957 |
高白鲑Coregonus peled | 126.05 | 1.982 | 2.030 | 2.507 |
Tab.4 Test results of DNA quality of various samples
物种 Species | 浓度/(ng/μL) Concentration | OD(260/280) | 260/230 | 260 |
---|---|---|---|---|
三倍体虹鳟Triploid rainbow trout | 164.90 | 2.032 | 1.343 | 3.300 |
金鳟Golden trout | 197.65 | 2.141 | 1.633 | 3.964 |
二倍体虹鳟 Diploid rainbow trout | 119.85 | 2.001 | 1.097 | 2.366 |
大西洋鲑Salmo salar | 170.00 | 1.988 | 1.943 | 3.406 |
大麻哈鱼Oncorhynchus keta | 198.40 | 2.084 | 1.859 | 3.957 |
高白鲑Coregonus peled | 126.05 | 1.982 | 2.030 | 2.507 |
Fig.1 DNA barcode PCR results Notes: M indicated DL 2000 molecular quality standard; 1-6 used COⅠ-F24 and COⅠ-R24 primers; 7-12 used COⅠ-F25 and COⅠ-R25 primers; 1 and 7 were triploid rainbow trout; 2 and 8 were golden trout; 3 and 9 were diploid rainbow trout; 4 and 10 were S.salar; 5 and 11 were O.keta; 6 and 12 were C.peled.
Fig.2 Mini barcode PCR results Notes: M indicated DL 2000 molecular quality standard; 13-18 used TEYI-0F and TEYI-0R primers; 19-24 used TEYI-1F and TEYI-1R primers; 13 and 19 were triploid rainbow trout; 14 and 20 were golden trout; 15 and 21 were diploid rainbow trout; 16 and 22 were S.salar; 17 and 23 were O.keta; 18 and 24 were C.peled.
标签名称 Label name | DNA barcode鉴定结果 (序列相似度/%) DNA barcode identification results (sequence similarity) | Mini barcode鉴定结果 (序列相似度/%) Mini barcode identification results (sequence similarity) | 结合两个片段鉴定结果 Combining the identification results of the two fragment |
---|---|---|---|
三倍体虹鳟 Triploid rainbow trout | 虹鳟(100) | 虹鳟(98.69) | 虹鳟 |
金鳟Golden trout | 虹鳟(100) | 虹鳟(98.69) | 虹鳟 |
二倍体虹鳟 Diploid rainbow trout | 虹鳟(100) | 虹鳟(98.69) | 虹鳟 |
大西洋鲑Salmo salar | 大西洋鲑(100) | 大西洋鲑(100) | 大西洋鲑 |
大麻哈鱼 Oncorhynchus keta | 大麻哈鱼(100) | 大麻哈鱼(97.06) | 大麻哈鱼 |
高白鲑 Coregonus peled | 欧白鲑(100) | 欧白鲑(98.52) | 欧白鲑 |
Tab.5 Identification results of NCBI database of 6 species of Salmonidae by DNA barcode technology
标签名称 Label name | DNA barcode鉴定结果 (序列相似度/%) DNA barcode identification results (sequence similarity) | Mini barcode鉴定结果 (序列相似度/%) Mini barcode identification results (sequence similarity) | 结合两个片段鉴定结果 Combining the identification results of the two fragment |
---|---|---|---|
三倍体虹鳟 Triploid rainbow trout | 虹鳟(100) | 虹鳟(98.69) | 虹鳟 |
金鳟Golden trout | 虹鳟(100) | 虹鳟(98.69) | 虹鳟 |
二倍体虹鳟 Diploid rainbow trout | 虹鳟(100) | 虹鳟(98.69) | 虹鳟 |
大西洋鲑Salmo salar | 大西洋鲑(100) | 大西洋鲑(100) | 大西洋鲑 |
大麻哈鱼 Oncorhynchus keta | 大麻哈鱼(100) | 大麻哈鱼(97.06) | 大麻哈鱼 |
高白鲑 Coregonus peled | 欧白鲑(100) | 欧白鲑(98.52) | 欧白鲑 |
[1] |
刘小鹏, 马存霞, 魏丽, 等. 黄河上游地区减贫转向与高质量发展[J]. 资源科学, 2020, 42(1):197-205.
DOI |
[2] | 简生龙. 基于生态优先前提下推动青海鲑鳟鱼养殖绿色发展的探讨[J]. 青海农林科技, 2019(3):78-81. |
[3] | 简生龙, 关弘弢, 李柯懋, 等. 青海沿黄鲑鳟鱼网箱养殖水体环境监测研究[J]. 中国水产, 2020(5):53-58. |
[4] |
Berthelot C, Brunet F, Chalopin D, et al. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates[J]. Nature Communication, 2014, 5: 3657.
DOI |
[5] | Habte-Tsion H, Ren M, Liu B, et al. Threonine modulates immune response, antioxidant status and gene expressions of antioxidant enzymes and antioxidant-immune-cytokine-related signaling molecules in juvenile blunt snout bream (Megalobrama amblycephala)[J]. Fish & Shellfish Immunology, 2016, 51: 189-199. |
[6] |
Meiler K A, Kumar V. Organic and inorganic zinc in the diet of a commercial strain of diploid and triploid rainbow trout (Oncorhynchus mykiss): effects on performance and mineral retention[J]. Aquaculture, 2021, 545: 737126.
DOI URL |
[7] |
Gonçalves J F M, Hinzmann M, Machado J, et al. Oxidative effect of L-carnitine on energy metabolism in diploid and triploid rainbow trout (Oncorhynchus mykiss): impact on metabolites[J]. International Aquatic Research, 2018, 10(2): 133-143.
DOI |
[8] |
Huang T, Gu W, Liu E, et al. Comprehensive analysis of miRNA-mRNA/lncRNA during gonadal development of triploid female rainbow trout (Oncorhynchus mykiss)[J]. Genomics, 2021, 113(6): 3533-3543.
DOI PMID |
[9] |
Xu G, Huang T, Gu W, et al. Effects of letrozole and 17α-methyltestosterone on gonadal development in all-female triploid rainbow trout (Oncorhynchus mykiss)[J]. Aquaculture Research, 2021, 52(6): 2460-2469.
DOI URL |
[10] |
Meiler K A, Cleveland B, Radler L, et al. Oxidative stress-related gene expression in diploid and triploid rainbow trout (Oncorhynchus mykiss) fed diets with organic and inorganic zinc[J]. Aquaculture, 2021, 533: 736149.
DOI URL |
[11] |
Weber G M, Ma H, Birkett J, et al. Effects of feeding level and sexual maturation on expression of genes regulating growth mechanisms in rainbow trout (Oncorhynchus mykiss)[J]. Aquaculture, 2022, 551: 737917.
DOI URL |
[12] |
Carvalho D C, Palhares R M, Drummond M G, et al. DNA barcoding identification of commercialized seafood in South Brazil: a governmental regulatory forensic program[J]. Food Control, 2015, 50: 784-788.
DOI URL |
[13] |
Hwang I K, Lee H Y, Kim M, et al. Development of real-time PCR assay for genetic identification of the mottled skate, Beringraja pulchra[J]. Forensic Science International, 2015, 255: 80-84.
DOI PMID |
[14] | 时圣明, 潘明佳, 王洁, 等. 分子鉴定技术在中药中的应用[J]. 中草药, 2016, 47(17):3121-3126. |
[15] |
Handy S M, Deeds J R, Ivanova N V, et al. A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance[J]. Journal of AOAC International, 2011, 94(1): 201-210.
PMID |
[16] |
Rhee J S, Seo J S, Raisuddin S, et al. Gonadotropin-releasing hormone receptor (GnRHR) gene expression is differently modulated in gender types of the hermaphroditic fish Kryptolebias marmoratus by endocrine disrupting chemicals[J]. Comparative Biochemistry and Physiology C Toxicology Pharmacology, 2008, 147(3): 357-365.
DOI URL |
[17] |
Ash K T, Drake K M, Gibbs W S, et al. Genomic diversity of type B3 bacteriophages of Caulobacter crescentus[J]. Current Microbiology, 2017, 74(7): 779-786.
DOI |
[18] |
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Molecular Biology and Evolution, 2016, 33(7): 1870-1874.
DOI PMID |
[19] |
Jaffe A, Amsel N, Aizenbud Y, et al. Spectral neighbor joining for reconstruction of latent tree models[J]. SIAM Journal on Mathematics of Data Science, 2021, 3(1):113-141.
DOI PMID |
[20] |
Dudgeon C L, Blower D C, Broderick D, et al. A review of the application of molecular genetics for fisheries management and conservation of sharks and rays[J]. Journal of Fish Biology, 2012, 80(5): 1789-1843.
DOI PMID |
[21] |
Teletchea F. Molecular identification methods of fish species: reassessment and possible applications[J]. Reviews in Fish Biology and Fisheries, 2009, 19(3): 265-293.
DOI URL |
[22] | 衣洁菡, 王桐, 郭德慧, 等. 利用SNP分子标记对阿根廷滑柔鱼和科氏滑柔鱼的分子鉴定[J]. 食品科技, 2018, 43(10):311-316. |
[23] |
Kress W J, García-Robledo C, Uriarte M, et al. DNA barcodes for ecology,evolution,and conservation[J]. Trends in Ecology & Evolution, 2015, 30(1):25-35.
DOI URL |
[24] |
Hulley E N, Taylor N D J, Zarnke A M, et al. DNA barcoding vs. morphological identification of larval fish and embryos in Lake Huron: advantages to a molecular approach[J]. Journal of Great Lakes Research, 2018, 44(5): 1110-1116.
DOI URL |
[25] |
Nedunoori A, Turanov S V, Kartavtsev Y P. Fish product mislabeling identified in the Russian far east using DNA barcoding[J]. Gene Reports, 2017, 8: 144-149.
DOI URL |
[26] |
Cline E. Marketplace substitution of Atlantic salmon for Pacific salmon in Washington State detected by DNA barcoding[J]. Food Research International, 2012, 45(1): 388-393.
DOI URL |
[27] |
Clark L F. The current status of DNA barcoding technology for species identification in fish value chains[J]. Food Policy, 2015, 54: 85-94.
DOI URL |
[28] |
Chang C, Lin H, Ren Q, et al. DNA barcode identification of fish products in Taiwan: government-commissioned authentication cases[J]. Food Control, 2016, 66: 38-43.
DOI URL |
[29] |
Zahn R J, Silva A J, Hellberg R S. Development of a DNA mini-barcoding protocol targeting COⅠfor the identification of elasmobranch species in shark cartilage pills[J]. Food Control, 2020, 109: 106918.
DOI URL |
[30] |
Sultana S, Ali M E, Hossain M A M, et al. Universal mini COⅠbarcode for the identification of fish species in processed products[J]. Food Research International, 2018, 105: 19-28.
DOI URL |
[31] |
Xiong X, Yuan F, Huang M, et al. DNA barcoding revealed mislabeling and potential health concerns with roasted fish products sold across China[J]. Journal of Food Protection, 2019, 82(7): 1200-1209.
DOI PMID |
[32] |
Shedko S V, Miroshnichenko I L, Nemkova G A. Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: analysis of nuclear RAG1 gene[J]. Russian Journal of Genetics, 2012, 48: 575-579.
DOI URL |
[33] |
Esin E V, Markevich G N. Evolution of the charrs, genus Salvelinus (Salmonidae). 1. origins and expansion of the species[J]. Journal of Ichthyology, 2018, 58(2): 187-203.
DOI |
[34] | 李瑶瑶, 刘云国, 刘凌霄, 等. 鲑科鱼类线粒体全基因组序列结构特征及其系统发育信息分析[J]. 烟台大学学报(自然科学与工程版), 2016, 29(4):271-279. |
[35] | 孙毅. 基于线粒体基因COX1、Cyt b和ND4的鲑科鱼类的系统发育[J]. 畜牧与饲料科学, 2015, 36(9):9-17. |
[36] |
Mariani S, Griffiths A M, Velasco A, et al. Low mislabeling rates indicate marked improvements in Eusropean seafood market operations[J]. Frontiers in Ecology and the Environment, 2015, 13(10):536-540.
DOI URL |
[37] |
Tang Q, Luo Q I, Duan Q, et al. DNA barcode identification of fish products from Guiyang markets in southwestern People’s Republic of China[J]. Journal of Food Protection, 2022, 85(4): 583-590.
DOI URL |
[38] |
Cordes J F, Stephens M R, Blumberg M A, et al. Identifying introgressive hybridization in native populations of California golden trout based on molecular markers[J]. Transactions of the American Fisheries Society, 2006, 135(1): 110-128.
DOI URL |
[39] |
Stephens M R, Clipperton N W, May B. Subspecies-informative SNP assays for evaluating introgression between native golden trout and introduced rainbow trout[J]. Molecular Ecology Resources, 2009, 9(1): 339-343.
DOI PMID |
[40] |
Maxime V. The physiology of triploid fish: current knowledge and comparisons with diploid fish[J]. Fish and Fisheries, 2008, 9(1): 67-78.
DOI URL |
[41] |
Manor M L, Weber G M, Cleveland B M, et al. Expression of genes associated with fatty acid metabolism during maturation in diploid and triploid female rainbow trout[J]. Aquaculture, 2015, 435: 178-186.
DOI URL |
[42] | 王庆龙. 金鳟和虹鳟繁殖与育种关键技术研究[D]. 青岛: 中国海洋大学, 2013. |
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