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The development and molecular characterization of a rapid detection method for Rice root-knot nematode (Meloidogyne graminicola)

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Abstract

The root-knot nematode Meloidogyne graminicola is a major constraint in rice production in the world. Using rDNA-ITS sequences data alignments, the genetic variation among twenty-one populations of M. graminicola (sixteen from Myanmar and five from China) was investigated. The results showed that all the populations were clearly separated from other species and that there was a low level of genetic variation among the isolates. A set of species-specific primers was designed to develop a species-specific molecular tool for the precise identification of M. graminicola. The primer reliability, specificity and sensitivity tests showed that the primer set (Mg-F3 and Mg-R2) amplified the expected fragment size of 369 bp from the template DNA of target nematode populations but not from non-target organisms. A duplex PCR test allows for saving diagnostic time and costs by amplifying the species of interest from a nematode mixture. Therefore, this species-specific primer set may be a powerful tool to improve taxonomic identification by non-specialists and the design of successful management practices as well.

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References

  • Besnard, G., Juhling, F., Chapuis, E., Zedane, L., Lhuillier, E., Mateille, T., et al. (2014). Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing. Comptes Rendus Biologies, 337(5), 295–301.

    Article  PubMed  Google Scholar 

  • Birchfield, W. (1965). Host-parasite relations and host range studies of a new Meloidogyne species in Southern U.S.A. Phytopathology, 55(12), 1359–1361.

    Google Scholar 

  • Blok, V. C., & Powers, T. O. (2009). Biochemical and molecular identification. In R. N. Perry, M. Moens, & J. Starr (Eds.), Root-knot nematodes (pp. 98–112). Lincoln: CABI.

    Chapter  Google Scholar 

  • Correa, V. R., dos Santos, M. F. A., Almeida, M. R. A., Peixoto, J. R., Castagnone-Sereno, P., & Carneiro, R. M. D. G. (2013). Species-specific DNA markers for identification of two root-knot nematodes of coffee: Meloidogyne arabicida and M. Izalcoensis. European Journal of Plant Pathology, 137(2), 305–313.

    Article  CAS  Google Scholar 

  • De Luca, F., Reyes, A., Troccoli, A., & Castillo, P. (2011). Molecular variability and phylogenetic relationships among different species and populations of Pratylenchus (nematoda: pratylenchidae) as inferred from the analysis of the ITS rDNA. European Journal of Plant Pathology, 130(3), 415–426.

    Article  Google Scholar 

  • De Waele, D., & Elsen, A. (2007). Challenges in Tropical Plant nematology. Annual Review of Phytopathology, 45(1), 457–485.

    Article  PubMed  Google Scholar 

  • Eisenback, J. D., Hirschmann, H., Sasser, J. N., & Triantaphyllou, A. C. (1981). A More Complete Characterization of the Four Most Common Species of Root-Knot Nematodes (Meliodogyne Spp.) with Pictorial Key. IMP Publication, Raleigh, N.C.U.S.A.

  • Elnifro, E., Ashshi, A., Cooper, R., & Klapper, P. (2000). Multiplex PCR: optimization and application in diagnostic virology. Clinical Microbiology Reviews, 13(4), 559–570.

    Article  CAS  PubMed  Google Scholar 

  • Gilabert, A., & Wasmuth, J. D. (2013). Unravelling parasitic nematode natural history using population genetics. Trends in Parasitology, 29(9), 438–448.

    Article  PubMed  Google Scholar 

  • Hooper, D. J. (1990). Extraction and processing of plant and soil nematodes. In M. Luc, R. A. Sikora, & J. Bridge (Eds.), Plant parasitic nematodes in subtropical and tropical agriculture (pp. 45–68). Wallingford: CABI.

    Google Scholar 

  • Hu, M. X., Zhuo, K., & Liao, J. L. (2011). Multiplex PCR for the simultaneous identification and detection of Meloidogyne incognita, M. enterolobii, and M. javanica using DNA extracted directly from individual galls. Phytopathology, 101(11), 1270–1277.

    Article  CAS  PubMed  Google Scholar 

  • Hübschen, J., Kling, L., Ipach, U., Zinkernagel, V., Bosselut, N., Esmenjaud, D., et al. (2004a). Validation of the specificity and sensitivity of species-specific primers that provide a reliable molecular diagnostic for Xiphinema diversicaudatum. X. index and X. vuittenezi. European Journal of Plant Pathology, 110(8), 779–788.

    Article  Google Scholar 

  • Hübschen, J., Kling, L., Ipach, U., Zinkernagel, V., Brown, D., & Neilson, R. (2004b). Development and validation of species-specific primers that provide a molecular diagnostic for virus-vector longidorid nematodes and related species in German viticulture. European Journal of Plant Pathology, 110(9), 883–891.

    Article  Google Scholar 

  • Jaiswal, R. K., & Singh, K. P. (2010). A technique for studying the life cycle of Meloidogyne graminicola in rice roots (pp. 1–3). International Rice Research Notes: Pest science and management.

    Google Scholar 

  • Joyce, S. A., Reid, A., Driver, F., & Curran, J. (1994). Application of polymerase chain reaction (PCR) methods to the identification of entomopathogenic nematodes. Paper presented at the COST 812 Biotechnology: Genetics of entomopathogenic nnematode-bacterium complexes, St Patrick’s College, Maynooth, Co. Kildare, Ireland. DG XII, Luxembourg: European Commission.

  • Le, H. T. T., Padgham, J. L., & Sikora, R. A. (2009). Biological control of the rice root-knot nematode Meloidogyne graminicola on rice, using endophytic and rhizosphere fungi. International Journal of Pest Management, 55(1), 31–36.

    Article  CAS  Google Scholar 

  • Long, H., Liu, H., & Xu, J. (2006). Development of a PCR Diagnostic for the root-knot nematode Meloidogyne enterolobii. Acta Physica Sinica, 36(2), 109–115.

    Google Scholar 

  • MacGowan, J. B., & Langdon, K. R. (1989). Hosts of the rice root-knot nematode, Meloidogyne graminicola. Nematology Circular, 172.

  • Meng, Q. P., Long, H., & Xu, J. H. (2004). PCR Assays for rapid and sensitive identification of three Major Root-Knot Nematodes, Meloidogyne incognita, M. javanica and M. arenaria. Acta Physica Sinica, 34, 204–210.

    Google Scholar 

  • Nunn, G. B. (1992). Nematode molecular evolution. U.K.: Ph.D. dissertation University of Nottingham.

    Google Scholar 

  • Oliveira, C. M. G., Fenton, B., Malloch, G., Brown, D. J. F., & Neilson, R. O. Y. (2005). Development of species-specific primers for the ectoparasitic nematode species Xiphinema brevicolle, X. diffusum, X. elongatum, X. ifacolum and X. longicaudatum (nematoda: longidoridae) based on ribosomal DNA sequences. Annals of Applied Biology, 146(3), 281–288.

    Article  CAS  Google Scholar 

  • Ou, S., Peng, D., Liu, X., Li, Y., & Moens, M. (2008). Identification of Heterodera glycines using PCR with sequence characterised amplified region (SCAR) primers. Nematology, 10(3), 397–403.

    Article  CAS  Google Scholar 

  • Padgham, J. L., Duxbury, J. M., Mazid, A. M., Abawi, G. S., & Hossain, M. (2004). Yield loss caused by Meloidogyne graminicola on lowland rainfed Rice in Bangladesh. Journal of Nematology, 36(1), 42–48.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pankaj, S. H. K., & Prasad, J. S. (2010). The rice root-knot nematode Meloidogyne graminicola: An emerging nematode pest of rice-wheat cropping system. Indian Journal of Nematology, 40(1), 1–11.

    Google Scholar 

  • Pokharel, R. R., Abawi, G. S., Zhang, N., Duxbury, J. M., & Smart, C. D. (2007). Characterization of isolates of Meloidogyne from Rice-wheat production fields in Nepal. Journal of Nematology, 39(3), 221–230.

    CAS  PubMed  Google Scholar 

  • Randig, O., Bongiovanni, M., Carneiro, R. M. D. G., & Castagnone-Sereno, P. (2002). Genetic diversity of root-knot nematodes from Brazil and development of SCAR markers specific for the coffee-damaging species. Genome, 45(5), 862–870.

    Article  CAS  PubMed  Google Scholar 

  • Sambrook, J., Fritsch, E. F., & Maniatis, T. (1989). Composition of the electrophoresis buffer. In In Molecular Cloning: A Laboratory Manual ((second edition) ed.). Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.

  • Soriano, I. R. S., Prot, J. C., & Matias, D. M. (2000). Expression of tolerance for Meloidogyne graminicola in Rice cultivars as affected by soil type and flooding. Journal of Nematology, 32(3), 309–317.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Subbotin, S., Peng, D., & Moens, M. (2001). A rapid method for the identification of the soybean cyst nematode Heterodera glycines using duplex PCR. Nematology, 3(4), 365–371.

    Article  CAS  Google Scholar 

  • 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(10), 2731–2739.

    Article  CAS  PubMed Central  Google Scholar 

  • Tigano, M., De Siqueira, K., Castagnone-Sereno, P., Mulet, K., Queiroz, P., Dos Santos, M., et al. (2010). Genetic diversity of the root-knot nematode Meloidogyne enterolobii and development of a SCAR marker for this guava-damaging species. Plant Pathology, 59(6), 1054–1061.

    Article  CAS  Google Scholar 

  • Whitehead, A. G. (1998). Plant nematode control. New York: CAB International.

    Google Scholar 

  • Whitehead, A. G., & Hemming, J. R. (1965). A comparison of some quantitative methods of extracting small vermiform nematodes from soil. Annals of Applied Biology, 55(1), 25–38.

    Article  Google Scholar 

  • Williamson, V. M., Caswell-Chen, E. P., Westerdahl, B. B., Wu, F. F., & Caryl, G. (1997). A PCR assay to identify and distinguish single juveniles of Meloidogyne hapla and M. chitwoodi. Journal of Nematology, 29(1), 9–15.

    CAS  PubMed  PubMed Central  Google Scholar 

  • ZijIstra, C., Lever, A. E. M., Uenk, B. J., & Van Silfhout, C. H. (1995). Differences between ITS regions of isolates of root-knot nematodes Meloidogyne hapla and M. chitwoodi. Phytopathology, 85(10), 1231–1237.

    Article  Google Scholar 

Download references

Acknowledgments

This study was supported by the Organization for Women in Science for the Developing World (OWSD) and the Swedish International Development Cooperation Agency (SIDA). Research facilities were provided by the Special Fund for Agro-scientific Research in the Public Interest (No. 201103018) the National Key Basic Research Program of China (973 Program, 2013CB127502).

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Authors and Affiliations

  1. State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China

    ChoCho Htay, Huan Peng, Wenkun Huang, Lingan Kong, Wenting He & Deliang Peng

  2. Norwegian Institute of Bioeconomy Research, Høgskoleveien 7, 1430, Ås, Norway

    Ricardo Holgado

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  1. ChoCho Htay
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  2. Huan Peng
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  3. Wenkun Huang
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  4. Lingan Kong
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  5. Wenting He
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  6. Ricardo Holgado
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  7. Deliang Peng
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Correspondence to Deliang Peng.

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ChoCho Htay & Huan Peng contributed equally to this work.

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Htay, C., Peng, H., Huang, W. et al. The development and molecular characterization of a rapid detection method for Rice root-knot nematode (Meloidogyne graminicola). Eur J Plant Pathol 146, 281–291 (2016). https://doi.org/10.1007/s10658-016-0913-y

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