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Development of qPCR assays for quantitative detection of Heterodera avenae and H. latipons

Fateh Toumi, Lieven Waeyenberge, Nicole Viaene UGent, Abdelfattah Amer Dababat, Julie M Nicol, Francis C Ogbonnaya and Maurice Moens UGent (2015) EUROPEAN JOURNAL OF PLANT PATHOLOGY. 143(2). p.305-316
abstract
Twelve Heterodera species are considered of major economic significance in cereals, of which Heterodera avenae, H. latipons and H. filipjevi are the most important. Precise identification and quantification of these nematodes are necessary to develop effective integrated pest control. This study reports on the use of the mitochondrial cytochrome oxidase subunit 1 (COI) gene to develop qPCR assays that could be used for the identification and quantification of H. avenae and H. latipons. Two qPCR primer sets, each comprising two primers and a probe, were designed for each of both species. After optimization, the qPCR assays using a single second-stage juvenile (J2) were able to identify and quantify H. avenae and H. latipons. Their specificity was confirmed by the lack of amplification of J2 of 14 other Heterodera species. A qPCR using DNA extracted from 120 J2 + eggs of H. avenae and H. latipons resulted in steady Ct-values (Ct = 22.33 +/- 0.1 and Ct = 21.83 +/- 0.12, respectively). Dilution series of DNA extracted from 120 J2 + eggs of the two species were made. The assays for both species resulted in a standard curve showing a highly significant linearity between the Ct-values and the dilution rates (R-2 = 0.99; slope = -3.03 and R-2 = 0.99; slope = -3.28 for H. avenae and H. latipons, respectively). The two qPCR assays provide a sensitive and valid tool for rapid detection and quantification of the two species whether they occur alone or in mixtures with other species.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
H. avenae, H. latipons, quantification., qPCR, cytochrome oxidase subunit 1 (COI) gene, REAL-TIME PCR, EVOLUTION, IDENTIFICATION, SOIL, FILIPJEVI, POTATO CYST, QUANTIFICATION, CYST-NEMATODE, RIBOSOMAL DNA, ROOT-LESION NEMATODE
journal title
EUROPEAN JOURNAL OF PLANT PATHOLOGY
Eur. J. Plant Pathol.
volume
143
issue
2
pages
305 - 316
Web of Science type
Article
Web of Science id
000360770600007
JCR category
HORTICULTURE
JCR impact factor
1.494 (2015)
JCR rank
9/34 (2015)
JCR quartile
2 (2015)
ISSN
0929-1873
DOI
10.1007/s10658-015-0681-0
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
6842380
handle
http://hdl.handle.net/1854/LU-6842380
date created
2015-06-23 09:16:10
date last changed
2017-01-23 13:39:51
@article{6842380,
  abstract     = {Twelve Heterodera species are considered of major economic significance in cereals, of which Heterodera avenae, H. latipons and H. filipjevi are the most important. Precise identification and quantification of these nematodes are necessary to develop effective integrated pest control. This study reports on the use of the mitochondrial cytochrome oxidase subunit 1 (COI) gene to develop qPCR assays that could be used for the identification and quantification of H. avenae and H. latipons. Two qPCR primer sets, each comprising two primers and a probe, were designed for each of both species. After optimization, the qPCR assays using a single second-stage juvenile (J2) were able to identify and quantify H. avenae and H. latipons. Their specificity was confirmed by the lack of amplification of J2 of 14 other Heterodera species. A qPCR using DNA extracted from 120 J2 + eggs of H. avenae and H. latipons resulted in steady Ct-values (Ct = 22.33 +/- 0.1 and Ct = 21.83 +/- 0.12, respectively). Dilution series of DNA extracted from 120 J2 + eggs of the two species were made. The assays for both species resulted in a standard curve showing a highly significant linearity between the Ct-values and the dilution rates (R-2 = 0.99; slope = -3.03 and R-2 = 0.99; slope = -3.28 for H. avenae and H. latipons, respectively). The two qPCR assays provide a sensitive and valid tool for rapid detection and quantification of the two species whether they occur alone or in mixtures with other species.},
  author       = {Toumi, Fateh and Waeyenberge, Lieven and Viaene, Nicole and Dababat, Abdelfattah Amer and Nicol, Julie M and Ogbonnaya, Francis C and Moens, Maurice},
  issn         = {0929-1873},
  journal      = {EUROPEAN JOURNAL OF PLANT PATHOLOGY},
  keyword      = {H. avenae,H. latipons,quantification.,qPCR,cytochrome oxidase subunit 1 (COI) gene,REAL-TIME PCR,EVOLUTION,IDENTIFICATION,SOIL,FILIPJEVI,POTATO CYST,QUANTIFICATION,CYST-NEMATODE,RIBOSOMAL DNA,ROOT-LESION NEMATODE},
  language     = {eng},
  number       = {2},
  pages        = {305--316},
  title        = {Development of qPCR assays for quantitative detection of Heterodera avenae and H. latipons},
  url          = {http://dx.doi.org/10.1007/s10658-015-0681-0},
  volume       = {143},
  year         = {2015},
}

Chicago
Toumi, Fateh, Lieven Waeyenberge, Nicole Viaene, Abdelfattah Amer Dababat, Julie M Nicol, Francis C Ogbonnaya, and Maurice Moens. 2015. “Development of qPCR Assays for Quantitative Detection of Heterodera Avenae and H. Latipons.” European Journal of Plant Pathology 143 (2): 305–316.
APA
Toumi, F., Waeyenberge, L., Viaene, N., Dababat, A. A., Nicol, J. M., Ogbonnaya, F. C., & Moens, M. (2015). Development of qPCR assays for quantitative detection of Heterodera avenae and H. latipons. EUROPEAN JOURNAL OF PLANT PATHOLOGY, 143(2), 305–316.
Vancouver
1.
Toumi F, Waeyenberge L, Viaene N, Dababat AA, Nicol JM, Ogbonnaya FC, et al. Development of qPCR assays for quantitative detection of Heterodera avenae and H. latipons. EUROPEAN JOURNAL OF PLANT PATHOLOGY. 2015;143(2):305–16.
MLA
Toumi, Fateh, Lieven Waeyenberge, Nicole Viaene, et al. “Development of qPCR Assays for Quantitative Detection of Heterodera Avenae and H. Latipons.” EUROPEAN JOURNAL OF PLANT PATHOLOGY 143.2 (2015): 305–316. Print.