Scientia Agricultura Sinica ›› 2015, Vol. 48 ›› Issue (3): 613-520.doi: 10.3864/j.issn.0578-1752.2015.03.20

• RESEARCH NOTES • Previous Articles    

Detection of Strawberry mild yellow edge virus by RT-LAMP

CHEN Liu1, SHANG Qiao-xia1, CHEN Xiao-yu2, XING Dong-mei3, RAN Ce1, WEI Yan-min1, ZHAO Xiao-yan1, LIU Zheng-ping1   

  1. 1College of Plant Science and Technology, Beijing University of Agriculture/Beijing Key Laboratory of New Technology, Beijing 102206
    2Beijing Plant Protection Station, Beijing 100029; 3Changping Plant Protection and Quarantine Station, Beijing 102200
  • Received:2014-06-26 Online:2015-01-31 Published:2015-01-31

Abstract: 【Objective】Strawberry mild yellow edge virus (SMYEV) is an important virus infecting strawberry plants, reducing fruit yield and quality. The objective of this study is to establish an effective method to detect SMYEV using the reverse transcription loop-mediated isothermal amplification (RT-LAMP). 【Method】 Four specific RT-LAMP primers for SMYEV detection including SMYEV-FIP (5′-CAGATCAGCGACAATTTGGACTCCTGAGGAACTTGCTGCT-3′), SMYEV-BIP (5′-GCTTTGTCGGGGATC CTGGGAAGGCTAAGTCGAAGAGACC-3′), SMYEV-F3 (5′-TCAAGTTGGTGACCCTTTCC-3′) and SMYEV-B3 (5′-CGAGG AACCAATGTCGTAGC-3′) were designed according to the published 3′ end conservative sequences of SMYEV CP gene. Different reaction temperatures (60, 61, 62, 63, 64, 65℃), reaction times (30, 45, 60, 75 min), concentrations of primers SMYEV-FIP/BIP (1.0, 1.2, 1.4, 1.6, 1.8 µmol?L-1) and SMYEV-F3/B3 (0.1, 0.15, 0.2, 0.25, 0.3 µmol?L-1), Mg2+ (2, 4, 6, 8, 10 mmol?L-1), dNTPs (0, 0.4, 0.8, 1.2, 1.6, 2.0 mmol?L-1), betaine (0, 0.4, 0.8, 1.0, 1.2, 1.4 mol?L-1) and DTT (2.0, 2.4, 2.8, 3.2, 3.6, 4.0 µmol?L-1) were used and optimized in the RT-LAMP in order to improve specificity and sensitivity of the detection. The specificity of RT-LAMP was tested by using different RNA templates from other important strawberry viruses and healthy leaves of strawberry plants. The sensitivities of RT-LAMP and RT-PCR for detecting SMYEV were compared by using ten-fold serially diluted RNA templates of SMYEV (including original RNA, 10-1, 10-2, 10-3, 10-4, 10-5, 10-6 and 10-7 dilution). The RT-LAMP products could be detected by electrophoresis and ultraviolet image technology, the typical ladder-like pattern was observed in the positive samples while no amplification of DNA was visible in the negative samples. The RT-LAMP products could be also evaluated by adding SYBR green I, the color of the product for the positive reaction changed from orange to green while the product for a negative reaction remained orange.【Result】The specific RT-LAMP method to detect SMYEV was established and the optimal amplification was achieved by incubation of 1.0 µmol?L-1 SMYEV-FIP/BIP, 0.1 µmol?L-1 SMYEV-F3/B3, 4 mmol?L-1 Mg2+, 1.6 mmol?L-1 dNTPs, 0.4 mol?L-1 betaine, 2.0 µmol?L-1 DTT with template RNA at 60℃ for 45 min. The detection specificity of RT-LAMP was tested by using different RNA templates from SMYEV, Strawberry vein banding virus, Strawberry mottle virus, Strawberry crinkle virus and leaf sample of healthy strawberry plant. The optimized RT-LAMP method had high sensitivity that only reaction within SMYEV RNA template could produce typical ladder-like bands tested by electrophoresis and UV. Test results of RT-PCR detection were positive only with original and 10-1, 10-2, 10-3 diluent RNA templates and no amplified band could be detected when using diluent RNA template with the increase of dilution ratio. While in RT-LAMP detection positive results could be observed with original, 10-1, 10-2, 10-3, 10-4, and 10-5 diluent RNA templates. Sensitivity of the RT-LAMP was 100 times higher than the RT-PCR method for detecting SMYEV. It was time-saving and the results could be directly observed in RT-LAMP which are suitable for SMYEV detection.【Conclusion】 The optimized RT-LAMP proved to be a faster, simpler and specific method for SMYEV detection and could be applied in the process of seedling breeding, field investigation and customs quarantine control in both research institutions and rural areas.

Key words: Strawberry mild yellow edge virus; RT-LAMP, detection

[1]    Tzanetakis I E, Martin R R. Expanding field of strawberry viruses which are important in North America. International Journal of Fruit Science, 2013, 13: 184-195.
[2]    Andrew M Q K, Michael J A, Eric B C, Elliot J L. Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, 2012.
[3]    Cho J D, Choi G S, Chung B N, Kim J S, Choi H S. Strawberry mild yellow edge potexvirus from strawberry in Korea. Plant Pathology,2011, 27(2): 187-190.
[4]    Zhang Z H, Chang L L, Yang H Y, Xiao M, Li H, Dai H Y. Diagnosis and molecular analysis of strawberry viruses in China. Acta Horticulturae, 2009, 842: 187-190.
[5]    Ragab M, El-Dougdoug K, Mousa S, Attia A, Sobolev I, Spiegel S, Freeman S, Zeidan M, Tzanetakis I E, Martin R R. Detection of strawberry viruses in Egypt. Acta Horticulturae,2009, 842: 319-322.
[6]    Thompson J R, Wetzel S, Klerks M M, Vaskova D, Schoen C D, Spak J, Jelkmann W. Multiplex RT-PCR detection of four aphid-borne strawberry viruses in Fragaria spp. in combination with a plant mRNA specific internal control. Journal of Virological Methods, 2003, 111(2): 85-93.
[7]    周厚成, 何水涛. 草莓病毒病研究进展. 果树学报, 2003, 20(5): 421-426.
Zhou H C, He S T. Advances in strawberry virus research. Journal of Fruit Science, 2003, 20(5): 421-426. (in Chinese)
[8]    Maas J L. Compendium of Strawberry Diseases. Minnesota: The American Phytopathological Society Press, 1998: 62-71.
[9]    Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T. Loop-mediated isothermal amplification of DNA. Nucleic Acids Research, 2000, 28(12): e63.
[10]   刘佳, 黄丛林, 吴忠义, 张秀海, 王永勤. 环介导等温扩增技术检测菊花中番茄不孕病毒. 中国农业科学, 2010, 43(6): 1288-1294.
Liu J, Huang C L, Wu Z Y, Zhang X H, Wang Y Q. Detection of Tomato aspermy virus infecting chrysanthemums by LAMP. Scientia Agricultura Sinica, 2010, 43(6): 1288-1294. (in Chinese)
[11]   陈先锋, 张吉红, 崔俊霞, 张慧丽, 郭立新, 余澍琼. 南芥菜花叶病毒的RT-LAMP检测试剂盒的研制. 植物保护学报, 2013, 40(2): 189-190.
Chen X F, Zhang J H, Cui J X, Zhang H L, Guo L X, Yu S Q. Detection of Arabis mosaic virus by RT-PCR. Acta Phytophylacica Sinica, 2013, 40(2): 189-190. (in Chinese)
[12]   闻伟刚, 杨翠云, 崔俊霞, 张颖. RT-LAMP技术检测菜豆荚斑驳病毒的研究. 植物保护, 2010, 36(6): 139-141.
Wen W G, Yang C Y, Cui J X, Zhang Y. Detection of Bean pod mottle virus by RT-PCR. Plant Protection, 2010, 36(6): 139-141. (in Chinese)
[13]   范旭东, 董雅凤, 张尊平, 任芳, 胡国君, 朱红娟. 沙地葡萄茎痘相关病毒的RT-LAMP检测方法. 植物病理学报, 2013, 43(3): 286-293.
Fan X D, Dong Y F, Zhang Z P, Ren F, Hu G J, Zhu H J. RT-LAMP assay for detection of Grapevine rupestris stem pitting-associated virus. Acta Phytopathologica Sinica, 2013, 43(3): 286-293. (in Chinese)
[14]   Thompson J R, Jelkmann W. Strain diversity and conserved genome elements in Strawberry mild yellow edge virus. Archives of Virology, 2004, 149: 1897-1909.
[15]   Tang Y, Diao Y, Yu C, Gao X, Chen L, Zhang D. Rapid detection of Tembusu virus by reverse-transcription, loop-mediated isothermal amplification (RT-LAMP). Transboundary and Emerging Diseases, 2012, 59: 208-213.
[16]   Fukuta S, Iida T, Mizukami Y, Ishida A, Ueda J, Kanbe M, Ishimoto Y. Detection of Japanese yam mosaic virus by RT-LAMP. Archives of Virology, 2003, 148: 1713-1720.
[17]   Hadersdorfer J, Neumuller M, Treutter D, Fischer T C. Fast and reliable detection of Plum pox virus in woody host plants using the Blue LAMP protocol. Annals of Applied Biology, 2011, 159: 456-466.
[18]   Zhu H X, Zhang Q, Wu G H, Yan X M, Li J, Zhao Z X. Advance of the research on testing of animal viruses by LAMP technology in abroad. Agricultural Science & Technology, 2011, 12(7):1029-1030.
[19]   Chang L, Zhang Z, Yang H, Li H, Dai H. Detection of strawberry RNA and DNA viruses by RT-PCR using total nucleic acid as a template. Journal of Phytopathology, 2007, 155: 431-436.
[20]   Babini A R, Cieslinska M, Karesova R, Thompson J R, Cardoni M, Malinowski T, Paprstein F, Jelkmann W. Occurrence and identification of strawberry viruses in five European countries. Acta Horticulturae, 2004, 656: 39-43.
[21]   王永江, 周彦, 李中安, 苏华南, 黄爱军, 唐科志, 周常勇. 柑橘衰退病毒RT-LAMP快速检测方法的建立. 中国农业科学, 2013, 46(3): 517-524.
Wang Y J, Zhou Y, Li Z A, Su H N, Huang A J, Tang K Z, Zhou C Y. A RT-LAMP assay for detection of Citrus tristeza virus. Scientia Agricultura Sinica, 2013, 46(3): 517-524. (in Chinese)
[22]   周彤, 杜琳琳, 范永坚, 周益军. 水稻黑条矮缩病毒RT-LAMP快速检测方法的建立. 中国农业科学, 2012, 45(7): 1285-1292.
Zhou T, Du L L, Fan Y J, Zhou Y J. Development of a RT-LAMP assay for rapid detection of Rice black-streaked dwarf virus. Scientia Agricultura Sinica, 2012, 45(7): 1285-1292. (in Chinese)
[23] Soliman H, El-Matbouli. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS). Veterinary Microbiology, 2006, 114: 205-213.
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