Development of novel species-specific primers for the specific identification of Colletotrichum nymphaeae based on conventional PCR and LAMP techniques

  • Kaivan KarimiEmail author
  • Mahdi Arzanlou
  • Ilaria Pertot


Colletotrichum nymphaeae is the primary causal agent of strawberry anthracnose in Iran resulting in epidemics in strawberry fields in recent years. Due to the hemibiotrophic nature of the pathogen, early detection in symptomless, infected plants, especially in nurseries could be advantageous for disease management. Assessing inter-species variation by rep-PCR fingerprinting of Colletotrichum spp. within the C. acutatum species complex causing strawberry anthracnose revealed a specific genomic segment amplified with only C. nymphaeae. The amplicon was extracted, purified and novel primer sets were developed based on conventional PCR and loop-mediated isothermal amplification (LAMP) techniques. The genus and species-specific PCR primers were able to discriminate the genus Colletotrichum and C. nymphaeae from other fungal species in pure culture and in assays of diseased, detached leaves. Similar results were observed for LAMP, but it was more sensitive compared to the PCR assay. Using both assays, asymptomatic strawberry plants infected with C. nymphaeae strain CCTUCch32 were readily detected. These results show that the primer sets developed in this study based on conventional PCR and LAMP techniques can be effective for early detection of C. nymphaeae, which can contribute to improved control strategies for strawberry anthracnose.


Fragaria × ananassa Anthracnose Latent infection LAMP and PCR techniques Accurate recognition 



We are grateful to Iran National Science Foundation (INSF) and University of Tabriz, Iran for financial support. The research reported here is also partially funded by the Autonomous Province of Trento.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animals rights

No human and/or animal participants were involved in this research.

Informed consent

All authors are consent to this submission.

Supplementary material

10658_2019_1895_MOESM1_ESM.docx (195 kb)
ESM 1 (DOCX 195 kb)


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Copyright information

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2019

Authors and Affiliations

  1. 1.Department of Plant Protection, Faculty of AgricultureUniversity of TabrizTabrizIran
  2. 2.Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation CentreFondazione Edmund Mach (FEM)San Michele all’AdigeItaly
  3. 3.Center Agriculture Food Environment (C3A)University of TrentoSan Michele all’AdigeItaly

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