Looking for a needle in a hay-stack: diagnostic kits for the detection of plant parasitic nematodes in complex DNA backgrounds.

R. Landeweert, W. Mulder, S.J.J. van den Elsen, P.J.W. Mooijman, J. Helder

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

Abstract

Recently, many agricultural laboratories have invested in the set up of a molecular laboratory in the expectation that DNA-based identification and detection of plant pathogens, including nematodes, will be the golden standard in the near future. However, as molecular methods for the detection of some specific (quarantine) nematodes have the potential to fully replace the current microscopic routine screening of (soil) samples, there is a strong need to check for their accuracy and performance. Whereas a molecular method in itself may be far more precise and accurate than a microscopic method ever can be, its accuracy will largely depend on the biological information that was used to develop it. Its performance will depend on the robustness of the method and the test performed. On the basis of a phylum-wide, small subunit ribosomal DNA (SSU rDNA)-based framework consisting of ~ 2,500 full-length nematode sequences, we have developed over 20 diagnostic Q-PCR tests for plant pathogenic nematodes. Some nematode species have a dubious reputation as parasites of major crops such as potato, sugar beet and soybean. Among the most notorious ones are cyst (e.g. Globodera rostochiensis and G. pallida), root knot (e.g. Meloidogyne chitwoodi, M. fallax and M. minor), stem and bulb (e.g Ditylenchus dipsaci and D. destructor), and foliar nematodes (various Aphelenchoides species). By using this SSU rDNA framework, we could define unique DNA sequence signatures that enable ‘blind’ identification of these individual nematode species in highly complex DNA backgrounds. A number of examples will be presented during this meeting.
Original languageEnglish
Title of host publicationThe 31th International Sy.mposium of the European Society of Nematologists, Adana, Turkey, 23-27 September 2012
Place of PublicationAdana, Turkey
Pages61-61
Publication statusPublished - 2012
EventThe 31th International Symposium of the European Society of Nematologists - Adana
Duration: 23 Sep 201227 Sep 2012

Conference

ConferenceThe 31th International Symposium of the European Society of Nematologists
CityAdana
Period23/09/1227/09/12

Fingerprint

analytical kits
plant parasitic nematodes
hay
Nematoda
DNA
ribosomal DNA
Ditylenchus destructor
Meloidogyne chitwoodi
Ditylenchus dipsaci
Aphelenchoides
Globodera pallida
Globodera rostochiensis
knots
quarantine
methodology
plant pathogens
sugar beet
bulbs
soil sampling
testing

Cite this

Landeweert, R., Mulder, W., van den Elsen, S. J. J., Mooijman, P. J. W., & Helder, J. (2012). Looking for a needle in a hay-stack: diagnostic kits for the detection of plant parasitic nematodes in complex DNA backgrounds. In The 31th International Sy.mposium of the European Society of Nematologists, Adana, Turkey, 23-27 September 2012 (pp. 61-61). Adana, Turkey.
Landeweert, R. ; Mulder, W. ; van den Elsen, S.J.J. ; Mooijman, P.J.W. ; Helder, J. / Looking for a needle in a hay-stack: diagnostic kits for the detection of plant parasitic nematodes in complex DNA backgrounds. The 31th International Sy.mposium of the European Society of Nematologists, Adana, Turkey, 23-27 September 2012. Adana, Turkey, 2012. pp. 61-61
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Landeweert, R, Mulder, W, van den Elsen, SJJ, Mooijman, PJW & Helder, J 2012, Looking for a needle in a hay-stack: diagnostic kits for the detection of plant parasitic nematodes in complex DNA backgrounds. in The 31th International Sy.mposium of the European Society of Nematologists, Adana, Turkey, 23-27 September 2012. Adana, Turkey, pp. 61-61, The 31th International Symposium of the European Society of Nematologists, Adana, 23/09/12.

Looking for a needle in a hay-stack: diagnostic kits for the detection of plant parasitic nematodes in complex DNA backgrounds. / Landeweert, R.; Mulder, W.; van den Elsen, S.J.J.; Mooijman, P.J.W.; Helder, J.

The 31th International Sy.mposium of the European Society of Nematologists, Adana, Turkey, 23-27 September 2012. Adana, Turkey, 2012. p. 61-61.

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

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T1 - Looking for a needle in a hay-stack: diagnostic kits for the detection of plant parasitic nematodes in complex DNA backgrounds.

AU - Landeweert, R.

AU - Mulder, W.

AU - van den Elsen, S.J.J.

AU - Mooijman, P.J.W.

AU - Helder, J.

PY - 2012

Y1 - 2012

N2 - Recently, many agricultural laboratories have invested in the set up of a molecular laboratory in the expectation that DNA-based identification and detection of plant pathogens, including nematodes, will be the golden standard in the near future. However, as molecular methods for the detection of some specific (quarantine) nematodes have the potential to fully replace the current microscopic routine screening of (soil) samples, there is a strong need to check for their accuracy and performance. Whereas a molecular method in itself may be far more precise and accurate than a microscopic method ever can be, its accuracy will largely depend on the biological information that was used to develop it. Its performance will depend on the robustness of the method and the test performed. On the basis of a phylum-wide, small subunit ribosomal DNA (SSU rDNA)-based framework consisting of ~ 2,500 full-length nematode sequences, we have developed over 20 diagnostic Q-PCR tests for plant pathogenic nematodes. Some nematode species have a dubious reputation as parasites of major crops such as potato, sugar beet and soybean. Among the most notorious ones are cyst (e.g. Globodera rostochiensis and G. pallida), root knot (e.g. Meloidogyne chitwoodi, M. fallax and M. minor), stem and bulb (e.g Ditylenchus dipsaci and D. destructor), and foliar nematodes (various Aphelenchoides species). By using this SSU rDNA framework, we could define unique DNA sequence signatures that enable ‘blind’ identification of these individual nematode species in highly complex DNA backgrounds. A number of examples will be presented during this meeting.

AB - Recently, many agricultural laboratories have invested in the set up of a molecular laboratory in the expectation that DNA-based identification and detection of plant pathogens, including nematodes, will be the golden standard in the near future. However, as molecular methods for the detection of some specific (quarantine) nematodes have the potential to fully replace the current microscopic routine screening of (soil) samples, there is a strong need to check for their accuracy and performance. Whereas a molecular method in itself may be far more precise and accurate than a microscopic method ever can be, its accuracy will largely depend on the biological information that was used to develop it. Its performance will depend on the robustness of the method and the test performed. On the basis of a phylum-wide, small subunit ribosomal DNA (SSU rDNA)-based framework consisting of ~ 2,500 full-length nematode sequences, we have developed over 20 diagnostic Q-PCR tests for plant pathogenic nematodes. Some nematode species have a dubious reputation as parasites of major crops such as potato, sugar beet and soybean. Among the most notorious ones are cyst (e.g. Globodera rostochiensis and G. pallida), root knot (e.g. Meloidogyne chitwoodi, M. fallax and M. minor), stem and bulb (e.g Ditylenchus dipsaci and D. destructor), and foliar nematodes (various Aphelenchoides species). By using this SSU rDNA framework, we could define unique DNA sequence signatures that enable ‘blind’ identification of these individual nematode species in highly complex DNA backgrounds. A number of examples will be presented during this meeting.

M3 - Abstract

SP - 61

EP - 61

BT - The 31th International Sy.mposium of the European Society of Nematologists, Adana, Turkey, 23-27 September 2012

CY - Adana, Turkey

ER -

Landeweert R, Mulder W, van den Elsen SJJ, Mooijman PJW, Helder J. Looking for a needle in a hay-stack: diagnostic kits for the detection of plant parasitic nematodes in complex DNA backgrounds. In The 31th International Sy.mposium of the European Society of Nematologists, Adana, Turkey, 23-27 September 2012. Adana, Turkey. 2012. p. 61-61