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Agronomically important thrips: development of species-specific primers in multiplex PCR and microarray assay using internal transcribed spacer 1 (ITS1) sequences for identification

Published online by Cambridge University Press:  22 October 2014

W.B. Yeh ,
M.J. Tseng ,
N.T. Chang ,
S.Y. Wu  and
Y.S. Tsai
W.B. Yeh*
Affiliation:
Department of Entomology, National Chung Hsing University, 250 Kuan-Kung Rd., Taichung 40227, Taiwan
M.J. Tseng
Affiliation:
Department of Entomology, National Chung Hsing University, 250 Kuan-Kung Rd., Taichung 40227, Taiwan
N.T. Chang
Affiliation:
Department of Plant Medicine, National Pingtung University of Science and Technology, 1 Shuefu Rd., Neipu, Pingtung 91201, Taiwan
S.Y. Wu
Affiliation:
Department of Entomology, National Chung Hsing University, 250 Kuan-Kung Rd., Taichung 40227, Taiwan
Y.S. Tsai
Affiliation:
Department of Entomology, National Chung Hsing University, 250 Kuan-Kung Rd., Taichung 40227, Taiwan
*
*Author for correspondence Phone: +886-4-22840799 ext. 558 Fax: +886-4-22875024 E-mail: [email protected]
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Abstract

Thrips, the sole vector of plant Tospovirus, are major pests of many agricultural crops throughout the world. Molecular approaches have been applied in recent decades to identify these minute and morphologically difficult to distinguish insects. In this study, sequences of internal transcribed spacer 1 (ITS1) region of 15 agronomically important thrips, including several virus transmission species, have been analyzed in order to design species-specific primers for multiplex PCR and probes for microarray assay. That the ITS1 sequence distances within species were smaller than those among species suggests that the ITS1 fragment can be used for thrips species identification. The specificity and stability of these primers, combined with universal paired primers, were tested and verified in multiplex PCR. Using these specific primers as probes, microarray assay showed that PCR products of all thrips species hybridized consistently to their corresponding probes, though some signals were weak. We have demonstrated that multiplex PCR using specific primers based on ITS1 sequences is a simple, reliable, and cost-effective diagnostic tool for thrips species identification. Moreover, the DNA microarray assay is expected to extend into a reliable high-throughput screening tool for the vast numbers of thrips.

Keywords

thripsITS1multiplex PCRspecies-specific probesmicroarray
Type
Research Papers
Information
Bulletin of Entomological Research , Volume 105 , Issue 1 , February 2015 , pp. 52 - 59
Copyright
Copyright © Cambridge University Press 2014 

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References

Asokan, R., Kumar, N.K.K., Kumar, V. & Ranganath, H.R. (2007) Molecular differences in the cytochrome oxidase I (mtCOI) gene and development of a species-specific marker for onion thrips, Thrips tabaci Lindeman, and melon thrips, T. palmi Karny (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae). Bulletin of Entomological Research 97, 461–470.CrossRefGoogle ScholarPubMed
Brunner, P.C. & Frey, J.E. (2010) Habitat-specific population structure in native western flower thrips Frankliniella occidentalis (Insecta, Thysanoptera). Journal of Evolutionary Biology 23, 797–804.CrossRefGoogle ScholarPubMed
Brunner, P.C., Chatzivassiliou, E.K., Katis, N.I. & Frey, J.E. (2004) Host-associated genetic differentiation in Thrips tabaci (Insecta: Thysanoptera), as determined from mtDNA sequence data. Heredity 93, 364–370.CrossRefGoogle ScholarPubMed
Buckman, R., Mound, L.A. & Whiting, M.F. (2013) Phylogeny of thrips (Insecta: Thysanoptera) based on five molecular loci. Systematic Entomology 38, 123–133. doi: 10.1111/j.1365-3113.2012.00650.x.CrossRefGoogle Scholar
Chung, I.H., Kang, S., Kim, Y.R., Kim, J.H., Jung, J.W., Lee, S., Lee, S.H. & Hwang, S.Y. (2011) Development of a low-density DNA microarray for diagnosis of target-site mutations of pyrethroid and organophosphate resistance mutations in the whitefly Bemisia tabaci . Pest Management Science 67, 1541–1548. doi: 10.1002/ps.2209.CrossRefGoogle ScholarPubMed
de Luca, F.M., Ribeiro, R.M., Sakai, K., Muraosa, Y., Lyra, L., Gonoi, T., Mikami, Y., Tominaga, K., Kamei, K., Zaninelli, S.A., Trabasso, P. & Moretti, M.L. (2013) Visual analysis of DNA microarray data for accurate molecular identification of non-albicans Candida isolates from patients with candidemia episodes. Journal Clinical Microbiology 51, 3826–3829. doi: 10.1128/JCM.01050-13.CrossRefGoogle Scholar
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792–1797.CrossRefGoogle ScholarPubMed
Farris, R.E., Ruiz-Arce, R., Ciomperlik, M., Vasquez, J.D. & DeLeón, R. (2010) Development of a ribosomal DNA ITS2 marker for the identification of the thrips, Scirtothrips dorsalis . Journal of Insect Science 10, 26.CrossRefGoogle ScholarPubMed
Gent, D.H., du Toit, L.J., Fichtner, S.F., Mohan, S.K., Pappu, H.R. & Schwartz, H.F. (2006) Iris yellow spot virus: an emerging threat to onion bulb and seed production. Plant Disease 90, 1468–1480.CrossRefGoogle ScholarPubMed
Glover, H., Collins, D.W., Walsh, K. & Boonham, N. (2010) Assessment of loci for DNA barcoding in the genus Thrips (Thysanoptera:Thripidae). Molecular Ecology Resources 10, 51–59.CrossRefGoogle ScholarPubMed
Han, Y.F. (1997) Economic Insect Fauna of China Fascicule 55 Thysanoptera. Beijing, China, Fauna Sinica Chinese Academy of Science, 514 pp.Google Scholar
Hoddle, M.S., Heraty, J.M., Rugman-Jones, P.F., Mound, L.A. & Stouthamer, R. (2008) Relationships among species of Scirtothrips (Thysanoptera: Thripidae, Thripinae) using molecular and morphological data. Annals of the Entomological Society of America 101, 491–500.CrossRefGoogle Scholar
Huang, K.S., Lee, E., Yeh, Y., Shen, G.S., Mei, E. & Chang, C.M. (2010) Taqman real-time quantitative PCR for identification of western flower thrip (Frankliniella occidentalis) for plant quarantine. Biology Letters 6, 555–557. doi: 10.1098/rsbl.2009.1060.CrossRefGoogle ScholarPubMed
Inoue, T. & Sakurai, T. (2007) The phylogeny of Thrips (Thysanoptera: Thripidae) based on partial sequences of cytochrome oxidase I, 28S ribosomal DNA and elongation factor-1α and the association with vector competence of tospoviruses. Applied Entomology and Zoology 42, 71–81.CrossRefGoogle Scholar
Jacobson, A.L., Booth, W., Vargo, E.L. & Kennedy, G.G. (2013) Thrips tabaci population genetic structure and polyploidy in relation to competency as a vector of Tomato Spotted Wilt Virus . Public Library of Science One 8, e54484. doi: 10.1371/journal.pone.0054484.Google ScholarPubMed
Kadirvel, P., Srinivasan, R., Hsu, Y.C., Su, F.C. & de la Peña, R. (2013) Application of cytochrome oxidase I sequences for phylogenetic analysis and identification of thrips species occurring on vegetable crops. Journal of Economic Entomology 106, 408–418.CrossRefGoogle ScholarPubMed
Katoh, K., Kuma, K.I., Toh, H. & Miyata, T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33, 511–518.CrossRefGoogle ScholarPubMed
Kjer, K.M., Baldridge, G.D. & Fallon, A.M. (1994) Mosquito large subunit ribosomal RNA: simultaneous alignment of primary and secondary structure. Biochimica et Biophysica Acta 1217, 147–155.CrossRefGoogle ScholarPubMed
Kobayashi, K. & Hasegawa, E. (2012) Discrimination of reproductive forms of Thrips tabaci (Thysanoptera: Thripidae) by PCR with sequence specific primers. Journal of Economic Entomology 105, 555–559.CrossRefGoogle ScholarPubMed
Lee, W.S., Choi, H., Kang, J., Kim, J.H., Lee, S.H., Lee, S. & Hwang, S.Y. (2013) Development of a DNA microarray for species identification of quarantine aphids. Pest Management Science 69, 1399–14061. doi: 10.1002/ps.3520.CrossRefGoogle ScholarPubMed
Lin, J.S., Wang, C.L. & Yeh, W.B. (2003) Molecular identification of multiplex-PCR and PCR-RFLP for the quarantine pest, Frankliniella occidentalis (Pergande). Formosan Entomologist 23, 353–366.Google Scholar
Liu, Y.C. (2004) Molecular identification of a plant quarantine pest (Frankliniella occidentalis) by one-tube nested PCR targeting ribosomal DNA internal transcribed spacer regions. Plant Protection Bulletin 46, 27–46.Google Scholar
Mound, L.A. & Kibby, B. (1998) Thysanoptera: an IdentificationGuide. 2nd edn. Wallingford, UK, CAB International. 70 pp.Google Scholar
Mound, L.A. & Morris, D.C. (2007) The insect order Thysanoptera: classification versus systematics. Zootaxa 1668, 395–411.CrossRefGoogle Scholar
Prins, M. & Goldbach, R. (1998) The emerging problem of tospovirus infection and nonconventional methods of control. Trends in Microbiology 6, 31–35.CrossRefGoogle ScholarPubMed
Rugman-Jones, P.F., Hoddle, M.S., Mound, L.A. & Stouthamer, R. (2006) Molecular identification key for pest species of Scirtothrips (Thysanoptera: Thripidae). Journal of Economic Entomology 99, 1813–1819.CrossRefGoogle ScholarPubMed
Rugman-Jones, P.F., Hoddle, M.S. & Stouthamer, R. (2010) Nuclear-mitochondrial barcoding exposes the global pest western flower thrips (Thysanoptera: Thripidae) as two sympatric cryptic species in its native California. Journal of Economic Entomology 103, 877–886.CrossRefGoogle ScholarPubMed
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28, 2731–2739.CrossRefGoogle ScholarPubMed
Tautz, D., Hancock, J.M., Webb, D.A., Tautz, C. & Dover, G.A. (1988) Complete sequences of the rRNA genes of Drosophila melanogaster . Molecular Biology and Evolution 54, 366–376.Google Scholar
Toda, S. & Murai, T. (2007) Phylogenetic analysis based on mitochondrial COI gene sequences in Thrips tabaci Lindeman (Thysanoptera: Thripidae) in relation to reproductive forms and geographic distribution. Applied Entomology and Zoology 42, 309–316.CrossRefGoogle Scholar
Tseng, L.Y., Chang, N.T., Tseng, M.J. & Yeh, W.B. (2010) Genetic variation of Thrips tabaci Lindeman (Thysanoptera: Thripidae) in the Pacific Rim. Formosan Entomologist 30, 219–234.Google Scholar
Walsh, K., Boonham, N., Barker, I. & Collins, D.W. (2005) Development of a sequence-specific real-time PCR to the melon thrips Thrips palmi (Thysan., Thripidae). Journal of Applied Entomology 129, 272–279.CrossRefGoogle Scholar
Wang, C.L. (2002) Thrips of Taiwan: Biology and Taxonomy. Taichung, Taiwan, Special Publication No. 99, Taiwan Agricultural Research Institute, 328 pp.Google Scholar
Wang, C.L. (2007) Hydatothrips and Neohydatothrips (Thysanoptera, Thripidae) of east and south Asia with three new species from Taiwan. Zootaxa 1575, 47–68.CrossRefGoogle Scholar
Yeh, W.B., Lee, H.C., Tseng, M.J., Chang, N.T. & Wu, S.Y. (2012) Molecular identification and genetic variations of importantly agricultural thrips. pp. 33–50 in Symposium on the management of thrips pests of agriculture and quarantine, 25–26 Oct 2012 Pingtung, Formosan Entomologist Special Publishing 5, Taiwan Entomological Society.Google Scholar