Abstract
Phloem-limiting phytoplasmas are known to be causal agents of phyllody, which is recognized by the abnormal development of floral structures resulting in serious yield losses in sesame plants. Currently, identification of the various groups of phytoplasmas that cause sesame phyllody (SP) is conducted by nested PCR, RFLP, and multiplex real-time qPCR assays. However, these methods require intensive labor and are costly and time-consuming so can only be undertaken in well-equipped labs. Here, diagnostic loop-mediated isothermal amplification (LAMP)–based assays allowing rapid detection of specific groups of phytoplasmas within 30 min were developed based on detection of the 16S rRNA sequence of phytoplasmas. Universal 16S rRNA phytoplasma primers and seven primer sets of different 16Sr group phytoplasmas (16SrI, 16SrII, 16SrIII, 16SrIV, 16SrV, 16SrX, 16SrXI) and universal plant cytochrome oxidase (cox) gene primers were used to detect 16S rRNA group phytoplasma sequences and the cox gene in sesame plants. The LAMP assays were carried out using a real-time fluorometer with amplification plots and annealing curves visualized directly. Results demonstrated that the 16SrI and 16SrII group phytoplasmas were causal agents of sesame phyllody in Vietnam. LAMP-based assays for in-field detection of sesame phyllody-causing phytoplasmas revealed advantages and potential applicability in comparison with conventional approaches. To the best of our knowledge, this is the first assessment of multiple phytoplasma infection associated with sesame phyllody disease in Vietnam using LAMP-based assays.
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References
Abraham E, Natarajan V, Murugaesanm K (1977) Damage by pests and phyllody to S. indicum in relation to time sowing. Madras Agric J 64:298–301
Akhtar KP, Dickinson M, Sarwar G, Jamil FF, Haq MA (2008) First report on the association of a 16SrII phytoplasma with sesame phyllody in Pakistan. Plant Pathol 57:771. https://doi.org/10.1111/j.1365-3059.2008.01872.x
Akhtar KP, Sarwar G, Dickinson M, Ahmad M, Haq MA, Hameed S, Iqbal MJ (2009) Sesame phyllody disease: its symptomatology, etiology, and transmission in Pakistan. Turk J Agric For 33:477–486. https://doi.org/10.3906/tar-0901-23
Al-Sakeiti MA, Al-Subhi AM, Al-Saady NA, Deadman ML (2005) First report of witches’-broom disease of sesame (Sesamum indicum) in Oman. Plant Dis 89:530–530. https://doi.org/10.1094/PD-89-0530C
Alvarez E, Pardo JM, Mejia JF, Bertaccini A, Thanh ND, Hoat TX (2013) Detection and identification of ‘Candidatus Phytoplasma asteris’-related phytoplasmas associated with a witches’ broom disease of cassava in Vietnam. Phytopatho Moll 3:77–81. https://doi.org/10.5958/j.2249-4677.3.2.018
Angamuthu R, Baskaran S, Gopal DR, Devarajan J, Kathaperumal K (2012) Rapid detection of the Marek’s disease viral genome in chicken feathers by loop-mediated isothermal amplification. J Clin Microbiol 50:961–965. https://doi.org/10.1128/JCM.05408-11
Bedendo IP, Davis RE, Dally EL (2000) Detection and identification of the maize bushy stunt phytoplasma in corn plants in Brazil using PCR and RFLP. Int J Pest Manage 46:73–76. https://doi.org/10.1080/096708700227606
Bertaccini A, Duduk B (2009) Phytoplasma and phytoplasma diseases: a review of recent research. Phytopathol Mediterr 48:355–378. https://doi.org/10.14601/Phytopathol_Mediterr-3300
Bhat AI, Siljo A, Deeshma KP (2013) Rapid detection of Piper yellow mottle virus and cucumber mosaic virus infecting black pepper (Piper nigrum) by loop-mediated isothermal amplification (LAMP). J Virol Methods 193:190–196. https://doi.org/10.1016/j.jviromet.2013.06.012
Catal M, Ikten C, Vol E, Ustun R, Uzun B (2013) First report of a 16SrIX group (pigeon pea witches’-broom) phytoplasma associated with sesame phyllody in Turkey. Plant Dis 97:835. https://doi.org/10.1094/PDIS-11-12-1100-PDN
Dickinson M (2015) Loop-mediated isothermal amplification (LAMP) for detection of Phytoplasmas in the field. Methods Mol Biol 1302:99–111. https://doi.org/10.1007/978-1-4939-2620-6_8
Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
Duduk B, Paltrinieri S, Lee IM, Bertaccini A (2013) Nested PCR and RFLP analysis based on the 16S rRNA gene. In: Dickinson M, Hodgetts J (eds) In Phytoplasma: Methods and Protocol, methods in molecular biology. Springer Science+Business Media, New York, pp 159–171
Esmailzadeh Hosseini SA, Khodakaramian G, Salehi M, Fani SR, Mirchenari SR, Elham S (2015a) Incidence, distribution and economic importance of alfalfa witches’ broom disease in Sistan-Baluchestan (Iran) and characterization of associated phytoplasma. Phytopath Moll 5:1–7. https://doi.org/10.5958/2249-4677.2015.00065.1
Esmailzadeh Hosseini SA, Salehi M, Khodakaramian G, Bolok Yazdi HR, Salehi M, Jafari Nodooshan A, Jadidi O, Bertaccini A (2015b) Status of sesame phyllody and its control methods in Yazd, Iran. Phytopath Moll 5(1-Suppl):S119–S120. https://doi.org/10.5958/2249-4677.2015.00051.1
Esmailzadeh-Hosseini SA, Mirzaie A, Jafari-Nodooshan A, Rahimian H (2007) The first report of transmission of a phytoplasma associated with sesame phyllody by Orosius albicinctus in Iran. Australas Plant Dis Notes 2:33–34. https://doi.org/10.1071/DN07016
Goto M, Honda E, Ogura A, Nomoto A, Hanaki K (2009) Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue. Biotechniques 46:167–172. https://doi.org/10.2144/000113072
Hoat TX, Thanh DVT, Dickinson M, Bon NG, Quan MV, Hien VD, Thanh ND, Thuy LT, Vien NV (2012) Disease problems of sugarcane in Vietnam, with special reference to phytoplasma. Funct Plant Sci Biotechnol 6:117–123
Hodgetts J (2019) Rapid sample preparation and LAMP for phytoplasma detection. Methods Mol Biol 1875:187–201. https://doi.org/10.1007/978-1-4939-8837-2_15
Ikten C, Catal M, Yol E, Ustam R, Furat S, Toker C, Uzun B (2014) Molecular identification, characterization and transmission of phytoplasmas associated with sesame phyllody in Turkey. Eur J Plant Pathol 139:217–229. https://doi.org/10.1007/s10658-014-0384-y
Ikten C, Ustun R, Catal M, Yol E, Uzun B (2016) Multiplex real-time qPCR assay for simultaneous and sensitive detection of phytoplasmas in sesame plants and insect vectors. PLoS One 11:e0155891. https://doi.org/10.1371/journal.pone.0155891
Junior EJG, Segana LG, Kitajima EW, Bedendo IP (2019) Sesame phyllody associated with a 16SrI-B phytoplasma, a ‘Candidatus phytoplasma asteris’ – related strain, in Paraguay. Sci Agric 76:47–50. https://doi.org/10.1590/1678-992x-2017-0140
Khan AJ, Botti S, Al-Subhi AM, Gundersen-Rindal DE, Bertaccini AF (2002) Molecular identification of new phytoplasma associated with alfalfa witches’-broom in Oman. Phytopathology 92:1038–1047. https://doi.org/10.1094/PHYTO.2002.92.10.1038
Khan MS, Raj SK, Snehi SK (2007) First report of ‘Candidatus Phytoplasma astris’ affecting sesame cultivation in India. J Plant Pathol 89:301–301
Kogovsek P, Mehle N, Pugelj A, Jakomin T, Schroers HJ, Ravnikar M, Dermastia M (2017) Rapid loop-mediated isothermal amplification assays for grapevine yellows phytoplasmas on crude leaf-vein homogenate has the same performance as qPCR. Eur J Plant Pathol 148:75–84. https://doi.org/10.1007/s10658-016-1070-z
Lau YL, Meganathan P, Sonaimuthu P, Thiruvengadam G, Nissapatorn V, Chen Y (2010) Specific, sensitive and rapid diagnosis of active toxoplasmosis by a loop-mediated isothermal amplification method using blood samples from patients. J Clin Microbiol 48:3698–3702. https://doi.org/10.1128/JCM.00462-10
Le DT, Netsu O, Uehara-Ichiki T, Shimizu T, Choi IR, Omura T, Sasaya T (2010) Molecular detection of nine rice viruses by a reverse-transcription loop-mediated isothermal amplification assay. J Virol Methods 170:90–93. https://doi.org/10.1016/j.jviromet.2010.09.004
Li W, Hartung JS, Levy L (2007) Evaluation of DNA amplification methods for improved detection of “Candidatus liberibacter species” associated with Citrus Huanglongbing. Plant Dis 91:51–58. https://doi.org/10.1094/PD-91-0051
McCoy RE, Caudwell A, Chang CJ, Chen TA, Chi-Ykowski LN, Cousin MT, Dale JL, De Leeuw GTN, Golino DA, Hackett KJ, Kirkpatrick BC, Mar Witz R, Petzold H, Sinha RC, Sugiura M, Whitcomb RF, Yang IL, Zhu BM, Seemüller E (1989) Plant diseases associated with mycoplasma-like organisms, pp. 545-640. In: Whitcomb RF, Tully JG (eds) The mycoplasmas, vol 5. Academic Press, San Diego
Monti M, Martini M, Tedeschi R (2013) EvaGreen real-time PCR protocol for specific “Candidatus Phytoplasma Mali” detection and quantification in insects. Mol Cell Probes 27:129–136. https://doi.org/10.1016/j.mcp.2013.02.001
Nabi SU, Priya M, Dubey DK, Rao GP, Baranwal VK, Sharma P (2015) Molecular characterization of ‘Candidatus Phytoplasma asteris’ subgroup I-B associated with sesame phyllody disease and identification of its natural vector and weed reservoir in India. Australas Plant Pathol 44:289–297. https://doi.org/10.1007/s13313-015-0345-8
Nagamine K, Hase T, Notomi T (2002) Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol Cell Probes 16:223–229. https://doi.org/10.1006/mcpr.2002.0415
Nakashima K, Hayashi T, Wongkaew P, Sirithorn P (1995) Detection of DNA of phytoplasmas associated with phyllody disease of sesame in Thailand. Ann Phytopathol Soc Jpn 61:519–528. https://doi.org/10.3186/jjphytopath.61.519
Nakashima K, Chaleeprom W, Wongkaew P, Sirithorn P, Kato S (1999) Analysis of phyllody disease caused by phytoplasma in sesame and Richardia plants. Journal of Japan International Research Center for Agricultural Science 7:19–27
Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28:E63. https://doi.org/10.1093/nar/28.12.e63
Obura E, Massiga D, Wachira F, Gurja B, Khan ZR (2011) Detection of phytoplasma by loop-mediated isothermal amplification of DNA (LAMP). J Microbiol Methods 84:312–316. https://doi.org/10.1016/j.mimet.2010.12.011
Parida M, Sannarangaiah S, Dash PK, Rao PV, Morita K (2008) Loop mediated isothermal amplification (LAMP): a new generation of innovative gene amplification technique; perspectives in clinical diagnosis of infectious diseases. Rev Med Virol 18:407–421. https://doi.org/10.1002/rmv.593
Perez-Lopez E, Oliver CY, Luna-Rodriguez M, Rodriguez V, Iglesias LG, Castro-Luna A, Adame-Garcia J, Dumonceaux TJ (2016) Maize bushy stunt phytoplasma affects native corn at high evaluations in Southeast Mexico. Eur J Plant Pathol 145:963–971. https://doi.org/10.1007/s10658-016-0883-0
Perez-Lopez E, Rodriguez-Martinez D, Oliver CY, Luna-Rodriguez M, Dumonceaux TJ (2017) Molecular diagnostic assays based on cnp60UT sequences reveal the geographic distribution of subgroup 16SrXIII-(A/I)I phytoplasma in Mexico. Sci Rep 7:950. https://doi.org/10.1038/s41598-017-00895-1
Salehi M, Izadpanah K (1992) Etiology and transmission of sesame phyllody in Iran. J Phytopathol 135:37–47. https://doi.org/10.1111/j.1439-0434.1992.tb01248.x
Schneider B, Cousin MT, Klinkong S, Seemüller E (1995) Taxonomic relatedness and phylogenetic positions of phytoplasmas associated with diseases of faba bean, sunnhemp, sesame, soybean, and eggplant. J Plant Dis Prot 102:225–232
Sertkaya G, Martini M, Musetti R, Osler R (2007) Detection and molecular characterization of phytoplasmas infecting sesame and solanaceous crops in Turkey. Bull of Insectology 60:141–142
Siemonsmeier A, Hadersdorfer J, Neumuller M, Schwab W, Treutter D (2019) A LAMP protocol for the detection of “Candidatus phytoplasma pyri”, the causal agent of pear decline. Plant Dis 103:1397–1404. https://doi.org/10.1094/PDIS-12-18-2150-RE
Tamura K, Stecher G, Peterson D, Filipski A, Sudhir Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. https://doi.org/10.1093/molbev/mst197
Tazehkand SA, Hosseinipour A, Heydarnejad J, Rahimian H, Massumi H (2017) Identification of phytoplasmas associated with sesame phyllody disease in southeastern Iran. Arch Phytopathol Pflanzenschutz 50:761–775. https://doi.org/10.1080/03235408.2017.1379757
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal_X windows interface: flexible strategies for multiple sequences alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882. https://doi.org/10.1093/nar/25.24.4876
Tseng YW, Deng WL, Chang CJ, Huang JW, Jan FJ (2014) First report on the association of a 16SrII-A phytoplasma with sesame (Sesamum indicum) exhibiting abnormal stem curling and phyllody in Taiwan. Plant Dis 98:990–990. https://doi.org/10.1094/PDIS-12-13-1212-PDN
Win NKK, Back CG, Jung HY (2010) Phyllody Phytoplasma infecting sesame (Sesamum indicum) in Myanmar. Trop Plant Pathol 35:310–313. https://doi.org/10.1590/S1982-56762010000500006
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This study was financially supported by the FIRST Project, Ministry of Science and Technology, Hanoi, Vietnam (No. 21/FIRST/1a/HUAF).
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Quoc, N.B., Xuan, N.T.T., Nghiep, N.M. et al. Loop-mediated isothermal amplification (LAMP) assay for detection of sesame phyllody phytoplasmas in Vietnam. Folia Microbiol 66, 273–283 (2021). https://doi.org/10.1007/s12223-020-00842-0
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DOI: https://doi.org/10.1007/s12223-020-00842-0