Cookies Policy
X

This site uses cookies. By continuing to browse the site you are agreeing to our use of cookies.

I accept this policy

Find out more here

Development and validation of real-time PCR assays based on novel molecular markers for the simultaneous detection and identification of Globodera pallida, G. rostochiensis and Heterodera schachtii

No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
The full text of this article is not currently available.

Brill’s MyBook program is exclusively available on BrillOnline Books and Journals. Students and scholars affiliated with an institution that has purchased a Brill E-Book on the BrillOnline platform automatically have access to the MyBook option for the title(s) acquired by the Library. Brill MyBook is a print-on-demand paperback copy which is sold at a favorably uniform low price.

Access this article

+ Tax (if applicable)
Add to Favorites
You must be logged in to use this functionality

image of Nematology
For more content, see Nematologica.

Considering the growing trade of seed potato, reliable diagnostic protocols are required for the detection of regulated nematode species. In this study, a specific and sensitive multiplex Taqman-based real-time PCR method was developed in order to detect and identify Globodera pallida, G. rostochiensis and Heterodera schachtii. The newly designed primers and probes enabled the detection of all the target populations tested and with no cross-reaction for closely related non-target species (55 populations tested). The limit of detection (LOD) was one juvenile for G. rostochiensis and G. pallida and five juveniles for H. schachtii. For monitoring potato cyst nematodes, this analytical tool would extend the number of cyst investigated as five juveniles can be detected among 50 cysts in a sample. Furthermore, this multiplex assay detects DNA of the three targeted species in template DNA obtained directly from float material after nematode extraction from soil.

Affiliations: 1: 1Anses, Plant Health Laboratory, Nematology unit, Domaine de la Motte au Vicomte, BP35327, 35653 Le Rheu, France ; 2: 2INRA, UMR1349 IGEPP (Institute of Genetics, Environment and Plant Protection), Domaine de la Motte au Vicomte, BP35327, 35653 Le Rheu, France

*Corresponding author, e-mail: sylvie.gamel@anses.fr
Loading

Full text loading...

/content/journals/10.1163/15685411-00003086
Loading

Data & Media loading...

1. Adams I., Woodhall J., Glover R., Shah F., Hockland S., Boonham N., Marshall J. (2009). Validation of quantitative DNA detection systems for PCN. Final Report, Potato Council, Kenilworth, UK.
2. Alenda C., Montarry J., Grenier E. (2014). "Human influence on the dispersal and genetic structure of French Globodera tabacum populations". Infection, Genetics and Evolution Vol 27, 309-317. DOI: 10.1016/j.meegid.2014.07.027 [Crossref]
3. Amiri S., Subbotin S.A., Moens M. (2002). "Identification of the beet cyst nematode Heterodera schachtii by PCR". European Journal of Plant Pathology Vol 108, 497-506. DOI: 10.1023/A:1019974101225 [Crossref]
4. (2000). "Council Directive 2000/29/EC of 8 May 2000 on protective measures against the introduction into the Community of organisms harmful to plants or plant products and against their spread within the Community". Official Journal of the European Communities Vol 43(L169), 1-112.
5. (2007). "Council Directive 2007/33/EC of 11 June 2007 on the control of potato cyst nematodes and repealing Directive 69/465/EEC". Official Journal of the European Union Vol 50(L156), 12-22.
6. (2010a). Preliminary tests for the identification of different species of Heterodera. Anses-LSV-Nematology unit internal document 10/02.
7. (2010b). Comparative evaluation of different molecular tools for the identification of Globodera pallida and Globodera rostochiensis. Anses-LSV-Nematology unit internal document 10/03.
8. Blok V.C. (2005). "Achievements in and future prospects for molecular diagnostics of plant-parasitic nematodes". Canadian Journal of Plant Pathology Vol 27, 176-185. DOI: 10.1080/0706660509507214 [Crossref]
9. Boucher A.C., Mimee B., Montarry J., Bardou-Valette S., Bélair G., Moffett P., Grenier E. (2013). "Genetic diversity of the golden potato cyst nematode Globodera rostochiensis and determination of the origin of populations in Quebec, Canada". Molecular Phylogenetics and Evolution Vol 69, 75-82. DOI: 10.1016/j.ympev.2013.05.020 [Crossref]
10. Buckler E.S., Ippolito A., Holtsford T.P. (1997). "The evolution of ribosomal DNA divergent paralogues and phylogenetic implications". Genetics Vol 145, 821-832.
11. Bulman S., Marshall J. (1997). "Differentiation of Australasian potato cyst nematode (PCN) populations using the polymerase chain reaction (PCR)". New Zealand Journal of Crop and Horticultural Science Vol 25, 123-129. [Crossref]
12. Castagnone-Sereno P., Danchin E.G.J., Deleury E., Guillemaud T., Malausa T., Abad P. (2010). "Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita". BMC Genomics Vol 11, 598. DOI: 10.1186/1471-2164-11-598 [Crossref]
13. Delmotte F., Sabater-Muñoz B., Prunier-Leterme N., Latorre A., Sunnucks P., Rispe C., Simon J.-C., Crespi B. (2003). "Phylogenetic evidence for hybrid origins of asexual lineages in an aphid species". Evolution Vol 57, 1291-1303. DOI: 10.1554/02-557 [Crossref]
14. Dong K., Dean R.A., Fortnum B.A., Lewis S.A. (2001). "Development of PCR primers to identify species of root-knot nematodes: Meloidogyne arenaria, M. hapla, M. incognita and M. javanica". Nematropica Vol 31, 271-280.
15. Eoche-Bosy D., Gauthier J., Juhel A.S., Esquibet M., Fournet S., Grenier E., Montarry J. (2016). "Experimentally evolved populations of the potato cyst nematode Globodera pallida allow the targeting of genomic footprints of selection due to host adaptation". Plant Pathology Vol 66, 1022-1030. DOI: 10.1111/ppa.12646 [Crossref]
16. EPPO (2013a). "EPPO Standard PM 7/40 (3). Globodera rostochiensis and Globodera pallida". EPPO Bulletin Vol 43, 119-138. DOI: 10.1111/epp.12025 [Crossref]
17. EPPO (2013b). "EPPO Standard PM 7/119 (1). Nematode extraction". EPPO Bulletin Vol 43, 471-495. DOI: 10.1111/epp.12077 [Crossref]
18. EPPO (2014). "EPPO Standard PM 7/98 (2). Specific requirements for laboratories preparing accreditation for a plant pest diagnostic activity". EPPO Bulletin Vol 44, 117-147. DOI: 10.1111/epp.12118 [Crossref]
19. Eves-van den Akker S., Laetsch D.R., Thorpe P., Lilley C.J., Danchin E.G.J., Da Rocha M., Rancurel C., Holroyd N.E., Cotton J.A., Szitenberg A. , et al (2016). "The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence". Genome Biology Vol 17, 124. DOI: 10.1186/s13059-016-0985-1
20. Fenton B., Malloch G., Germa F. (1998). "A study of variation in rDNA ITS regions shows that two haplotypes coexist within a single aphid genome". Genome Vol 41, 337-345. [Crossref]
21. Fredholm M., Winterø A.K. (1995). "Variation of short tandem repeats within and between species belonging to the Canidae family". Mammalian Genome Vol 6, 11-18. [Crossref]
22. Fullaondo A., Barrena E., Viribay M., Barrena I., Salazar A., Ritter E. (1999). "Identification of potato cyst nematode species Globodera rostochiensis and G. pallida by PCR using specific primer combinations". Nematology Vol 1, 157-163. DOI: 10.1163/156854199508126 [Crossref]
23. Handoo Z.A., Carta L.K., Skantar A.M., Chitwood D.J. (2012). "Description of Globodera ellingtonae n. sp. (Nematoda: Heteroderidae) from Oregon". Journal of Nematology Vol 44, 40-57.
24. Hockland S., Inserra R., Millar L., Lehman P. (2006). "International plant health-putting legislation into practice". In: Perry R.N., Moens M. (Eds). Plant nematology. Wallingford, UK, CAB International, pp.  327-345. [Crossref]
25. Ibrahim S.K., Perry R.N., Burrows P.R., Hooper D.J. (1994). "Differentiation of species and populations of Aphelenchoides and of Ditylenchus angustus using a fragment of ribosomal DNA". Journal of Nematology Vol 26, 412-421. [Crossref]
26. Kim J., Kim T., Lee Y.C., Chun J.Y., Kern E.M.A., Jung J., Park J.K. (2016). "Characterization of 15 microsatellite loci and genetic analysis of Heterodera schachtii (Nematoda: Heteroderidae) in South Korea". Biochemical Systematics and Ecology Vol 64, 97-104. DOI: 10.1016/j.bse.2015.11.013 [Crossref]
27. Madani M., Subbotin S.A., Moens M. (2005). "Quantitative detection of the potato cyst nematode, Globodera pallida, and the beet cyst nematode, Heterodera schachtii, using Real-Time PCR with SYBR green I dye". Molecular and Cellular Probes Vol 19, 81-86. DOI: 10.1016/j.mcp.2004.09.006 [Crossref]
28. Madani M., Ward L.J., De Boer S.H. (2011). "Hsp90 gene, an additional target for discrimination between the potato cyst nematodes, Globodera rostochiensis and G. pallida, and the related species, G. tabacum tabacum". European Journal of Plant Pathology Vol 130, 271-285. DOI: 10.1007/s10658-011-9752-z [Crossref]
29. Malausa T., Gilles A., Meglécz E., Blanquart H., Duthoy S., Costedoat C., Dubut V., Pech N., Castagnone-Sereno P., Délye C. , et al (2011). "High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries". Molecular Ecology Resources Vol 11, 638-644. DOI: 10.1111/j.1755-0998.2011.02992.x [Crossref]
30. Mallez S., Castagnone C., Espada M., Vieira P., Eisenback J.D., Mota M., Guillemaud T., Castagnone-Sereno P. (2013). "First insights into the genetic diversity of the pinewood nematode in its native area using new polymorphic microsatellite loci". PLoS ONE Vol 8, e59165. DOI: 10.1371/journal.pone.0059165 [Crossref]
31. Manachini B. (2000). "First report of Heterodera glycines Ichinohe on soybean in Italy". Bolletino di Zoologia Agraria e di Bachicoltura Serie II Vol 32, 261-267.
32. Meglécz E., Costedoat C., Dubut V., Gilles A., Malausa T., Pech N., Martin J.-F. (2010). "QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects". Bioinformatics Vol 26, 403-404. DOI: 10.1093/bioinformatics/btp670 [Crossref]
33. Montarry J., Jan P.L., Gracianne C., Overall A.D.J., Bardou-Valette S., Olivier E., Fournet S., Grenier E., Petit E.J. (2015). "Heterozygote deficits in cyst plant-parasitic nematodes: possible causes and consequences". Molecular Ecology Vol 24, 1654-1677. DOI: 10.1111/mec.13142 [Crossref]
34. Mulet K., Fargette M., Richaud M., Genson G., Castagnone-Sereno P. (2011). "Isolation of microsatellites from an enriched genomic library of the plant-parasitic nematode Meloidogyne incognita and their detection in other root-knot nematode species". European Journal of Plant Pathology Vol 129, 501-505. DOI: 10.1007/s10658-010-9721-y [Crossref]
35. Mulholland V., Carde L., O’Donnell K. (1996). Use of the polymerase chain reaction to discriminate potato cyst nematode at the species level. In: BCPC symposium proceedings No. 65: Diagnostics in crop production. Farnham, UK, BCPC, pp. 247-252.
36. Müller J. (1999). "The economic importance of Heterodera schachtii in Europe". Helminthologia Vol 36, 205-213.
37. Nakhla M.K., Owens K.J., Li W.B., Wei G., Skantar A.M., Levy L. (2010). "Multiplex real-time PCR assays for the identification of the potato cyst and tobacco cyst nematodes". Plant Disease Vol 94, 959-965. DOI: 10.1094/PDIS-94-8-0959 [Crossref]
38. Papayiannis L.C., Christoforou M., Markou Y.M., Tsaltas D. (2013). "Molecular typing of cyst-forming nematodes Globodera pallida and G. rostochiensis, using real-time PCR and evaluation of five methods for template preparation". Journal of Phytopathology Vol 161, 459-469. DOI: 10.1111/jph.12091 [Crossref]
39. Plantard O., Porte C. (2003). "Isolation and characterization of microsatellite loci in the sugar beet cyst nematode Heterodera schachtii". Molecular Ecology Notes Vol 3, 139-141. DOI: 10.1046/j.1471-8286.2003.00383.x [Crossref]
40. Plantard O., Picard D., Valette S., Scurrah M., Grenier E., Mugniéry D. (2008). "Origin and genetic diversity of western European populations of the potato cyst nematode (Globodera pallida) inferred from mitochondrial sequences and microsatellite loci". Molecular Ecology Vol 17, 2208-2218. DOI: 10.1111/j.1365-294X.2008.03718.x [Crossref]
41. Powers T. (2004). "Nematode molecular diagnostics: from bands to barcodes". Annual Review of Phytopathology Vol 42, 367-383. DOI: 10.1146/annurev.phyto.42.040803.140348 [Crossref]
42. Pylypenko L., Uehara T., Phillips M., Sigareva D., Blok V. (2005). "Identification of Globodera rostochiensis and G. pallida in the Ukraine by PCR". European Journal of Plant Pathology Vol 111, 39-46. DOI: 10.1007/s10658-004-2732-9 [Crossref]
43. Reid A., Kenyon D.M., Evans F.F., Mulholland V., Pickup J., Blok V.C., Paterson A., Phillips M.S. (2010). "Development of a high-throughput method for the detection and species determination of PCN". Aspects of Applied Biology Vol 103, 13-16.
44. Reid A., Evans F., Mulholland V., Cole Y., Pickup J. (2015). "High-throughput diagnosis of potato cyst nematodes in soil samples". In: Lacomme C. (Ed.). Plant pathology: techniques and protocols. New York, NY, USA, Springer, pp.  137-148. DOI: 10.1007/978-1-4939-2620-6_11 [Crossref]
45. Rotmistrovsky K., Jang W., Schuler G.D. (2004). "A web server for performing electronic PCR". Nucleic Acids Research Vol 32, W108-W112. DOI: 10.1093/nar/gkh450 [Crossref]
46. Selkoe K.A., Toonen R.J. (2006). "Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers". Ecology Letters Vol 9, 615-629. DOI: 10.1111/j.1461-0248.2006.00889.x [Crossref]
47. Shields R., Fleming C.C., Stratford R. (1996). "Identification of potato cyst nematodes using the polymerase chain reaction". Fundamental and Applied Nematology Vol 19, 167-173.
48. Skantar A.M., Handoo Z.A., Carta L.K., Chitwood D.J. (2007). "Morphological and molecular identification of Globodera pallida associated with potato in Idaho". Journal of Nematology Vol 39, 133-144.
49. Subbotin S.A., Waeyenberge L., Moens M. (2000). "Identification of cyst forming nematodes of the genus Heterodera (Nematoda: Heteroderidae) based on the ribosomal DNA-RFLP". Nematology Vol 2, 153-164. DOI: 10.1163/156854100509042 [Crossref]
50. Subbotin S.A., Cid del Prado Vera I., Mundo-Ocampo M., Baldwin J.G. (2011). "Identification, phylogeny and phylogeography of circumfenestrate cyst nematodes (Nematoda: Heteroderidae) as inferred from analysis of ITS-rDNA". Nematology Vol 13, 805-824. DOI: 10.1163/138855410X552661 [Crossref]
51. Sunnucks P. (2000). "Efficient genetic markers for population biology". Trends in Ecology and Evolution Vol 15, 199-203. DOI: 10.1016/S0169-5347(00)01825-5 [Crossref]
52. Szalanski A.L., Sui D.D., Harris T.S., Powers T.O. (1997). "Identification of cyst nematodes of agronomic and regulatory concern with PCR-RFLP of ITS1". Journal of Nematology Vol 29, 255-267.
53. Thiéry M., Mugniéry D. (1996). "Interspecific rDNA restriction fragment length polymorphism in Globodera species, parasites of solanaceous plants". Fundamental and Applied Nematology Vol 19, 471-479.
54. Thiéry M., Mugniéry D. (2000). "Microsatellite loci in the phytoparasitic nematode Globodera". Genome Vol 43, 160-165. [Crossref]
55. Van Riel H., Mulder A. (1998). "Potato cyst nematodes (Globodera species) in western Europe". In: Marks J., Brodie W. (Eds). Potato cyst nematodes: biology, distribution and control. Wallingford, UK, CAB International, pp. 271-298.
56. Vejl P., Skupinova S., Sedlak P., Domkarova J. (2002). "Identification of PCN species (Globodera rostochiensis, G. pallida) by using of ITS-1 region’s polymorphism". Rostlinna Vyroba Vol 48, 486-489.
57. Villate L., Esmenjaud D., Van Helden M., Stoeckel S., Plantard O. (2010). "Genetic signature of amphimixis allows for the detection and fine scale localization of sexual reproduction events in a mainly parthenogenetic nematode". Molecular Ecology Vol 19, 856-873. DOI: 10.1111/j.1365-294X.2009.04511.x [Crossref]
58. Volossiouk T., Robb E.J., Nazar R.N. (1995). "Direct DNA extraction for PCR-mediated assays of soil organisms". Applied and Environmental Microbiology Vol 61, 3972-3976.
59. Wang H.-M., Zhao H.-H., Chu D. (2015). "Genetic structure analysis of populations of the soybean cyst nematode, Heterodera glycines, from north China". Nematology Vol 17, 591-600. DOI: 10.1163/15685411-00002893 [Crossref]
http://brill.metastore.ingenta.com/content/journals/10.1163/15685411-00003086
Loading

Article metrics loading...

/content/journals/10.1163/15685411-00003086
2017-08-22
2018-07-19

Sign-in

Can't access your account?
  • Tools

  • Add to Favorites
  • Printable version
  • Email this page
  • Subscribe to ToC alert
  • Get permissions
  • Recommend to your library

    You must fill out fields marked with: *

    Librarian details
    Your details
    Why are you recommending this title?
    Select reason:
     
    Nematology — Recommend this title to your library
  • Export citations
  • Key

  • Full access
  • Open Access
  • Partial/No accessInformation