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Role of miRNAs in the host–pathogen interaction between sugarcane and Colletotrichum falcatum, the red rot pathogen

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Abstract

Key message

Sugarcane microRNAs specifically involved during compatible and incompatible interactions with red rot pathogen Colletotrichum falcatum were identified. We have identified how the miRNAs regulate their gene targets and elaborated evidently on the underlying molecular mechanism of sugarcane defense response to C. falcatum for the first time.

Abstract

Resistance against the fungal pathogen Colletotrichum falcatum causing red rot is one of the most desirable traits for sustainable crop cultivation in sugarcane. To gain new insight into the host defense mechanism against C. falcatum, we studied the role of sugarcane microRNAs during compatible and incompatible interactions by adopting the NGS platform. We have sequenced a total of 80 miRNA families that comprised 980 miRNAs, and the putative targets of the miRNAs include transcription factors, membrane-bound proteins, glutamate receptor proteins, lignin biosynthesis proteins, signaling cascade proteins, transporter proteins, mitochondrial proteins, ER proteins, defense-related, stress response proteins, translational regulation proteins, cell proliferation, and ubiquitination proteins. Further, qRT-PCR analyses of 8 differentially regulated miRNAs and 26 gene transcript targets expression indicated that these miRNAs have a regulatory effect on the expression of respective target genes in most of the cases. Also, the results suggest that certain miRNA regulates many target genes that are involved in inciting early responses to the pathogen infection, signaling pathways, endoplasmic reticulum stress, and resistance gene activation through feedback response from various cellular processes during the compatible and incompatible interaction with the red rot pathogen C. falcatum. The present study revealed the role of sugarcane miRNAs and their target genes during sugarcane—C. falcatum interaction and provided new insight into the miRNA-mediated defense mechanism in sugarcane for the first time.

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Availability of data and material

The transcriptomic data and associated analyzed data are available in the following NCBI links.

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Acknowledgements

The authors are thankful to the Directors of ICAR-Sugarcane Breeding Institute, Coimbatore for extending the necessary field and laboratory facilities to carry out this research work.

Funding

The financial support has been received from the Institute’s budget and no specific grants received from outside agencies.

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Authors and Affiliations

  1. ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India

    M. Nandakumar, P. Malathi, A. R. Sundar & R. Viswanathan

  2. AgriGenome Labs, Infopark-Smart City Short Rd, Kochi, Kerala, 682030, India

    C. P. Rajadurai & Manuel Philip

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  1. M. Nandakumar
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  2. P. Malathi
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  3. A. R. Sundar
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  4. C. P. Rajadurai
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  5. Manuel Philip
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  6. R. Viswanathan
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Contributions

RV conceived and designed research. MN conducted the experiments. PM and ARS analyzed the data. CPR and MP analyzed NGS data. MN and RV wrote the manuscript. All authors read and approved the manuscript.

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Correspondence to R. Viswanathan.

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The authors declare that they have no conflict of interest. The present research did not involve human participants and/or animals. Informed consent was obtained from all individual participants included in the study.

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Communicated by Marcelo Menossi.

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Nandakumar, M., Malathi, P., Sundar, A.R. et al. Role of miRNAs in the host–pathogen interaction between sugarcane and Colletotrichum falcatum, the red rot pathogen. Plant Cell Rep 40, 851–870 (2021). https://doi.org/10.1007/s00299-021-02682-9

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