3 Biotech

, 9:249 | Cite as

noxB-based marker for Alternaria spp.: a new diagnostic marker for specific and early detection in crop plants

  • Hillol Chakdar
  • Sanjay Kumar GoswamiEmail author
  • Ekta Singh
  • Prassan Choudhary
  • Jagriti Yadav
  • Prem Lal Kashyap
  • Alok Kumar Srivastava
  • Anil Kumar Saxena
Original Article


Alternaria species are a major plant pathogen and their precise detection and identification is crucial for effective management. In the present study, a polymerase chain reaction (PCR)-based diagnostic technique has been developed for detection of Alternaria species. Four primers were designed for four genes viz. noxB, AMK1, AKT3 and NIK1. In gradient PCR, only the primer sets for noxB gene showed specific amplicon of ~ 200 bp in all the isolates of Alternaria, while no amplification was observed in related fungal species such as Ulocladium botrytis, Ulocladium consortiale, Stemphylium vesicarium, Cochliobolus tuberculatus, Curvularia prasadii, and Bipolaris sorokiniana. The noxB primer set was used as diagnostic marker to discriminate and diagnose Alternaria species in nine different crop plants. Real-time assay revealed that the primer set was able to detect Alternaria noxB genes in leaves with no characteristic visible symptoms. Through real-time PCR, the noxB gene of Alternaria could be detected even in 0.5 ng of host DNA. This is the first report of noxB gene for molecular detection of Alternaria spp.


Alternaria Diagnostic marker Molecular detection noxPCR Real-time PCR 



The authors gratefully acknowledge the financial assistance under project ‘Development of gene chip for detection of major fungal plant pathogens’ from Indian Council of Agricultural Research (ICAR), India. The authors acknowledge National Agriculturally Important Microbial Culture Collection (NAIMCC) for providing the microbial cultures. The authors are grateful to Dr. Udai Bhan Singh, Plant Microbe Interaction and Rhizosphere Biology, ICAR-NBAIM, Mau for providing the culture of Bipolaris sorokiniana.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest. All the authors contributed equally in this work.


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Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  • Hillol Chakdar
    • 1
  • Sanjay Kumar Goswami
    • 1
    Email author
  • Ekta Singh
    • 1
  • Prassan Choudhary
    • 1
  • Jagriti Yadav
    • 1
  • Prem Lal Kashyap
    • 2
  • Alok Kumar Srivastava
    • 1
  • Anil Kumar Saxena
    • 1
  1. 1.ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM)MauIndia
  2. 2.ICAR-Indian Institute of Wheat and Barley Research (IIWBR)KarnalIndia

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