Expression profiling of miRNAs indicates crosstalk between phytohormonal response and rhizobial infection in chickpea

  • Manish Tiwari
  • Sabhyata BhatiaEmail author
Original Article


Legumes develop root nodules in which bacteria fix nitrogen for plants. The phytohormones auxin and cytokinin regulate nodule organogenesis by recruiting various genes to effect symbiosis. Moreover, these genes are regulated by the action of microRNAs also. To understand the complex regulatory network involving miRNAs in response to phytohormones and rhizobial interactions in chickpea roots, a miRNA expression profiling was performed. Indole acetic acid and 6-benzylaminopurine at concentrations of 0.1, 1 and 10 µM were used for auxin and cytokinin exogenous treatment and Mesorhizobium ciceri to study rhizobial interaction with chickpea root. Expression profiling of a set of 11 miRNAs was performed. Further, the targets of the candidate miRNAs were identified, followed by functional annotation. This analysis revealed that cat-miR160, cat-miR164, cat-miR396 and cat-miR398 were responsive to auxin and cytokinin. cat-miR319 was found to be only auxin responsive and is known to regulate auxin signalling by targeting TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) which interacts with auxin inducible genes. Further, cytokinin elicited a response at very low concentration of 0.1 µM, and most of the miRNAs investigated were responsive to cytokinin. Interactome analysis revealed that cat-miR164 and cat-miR168 work in conjunction to regulate auxin signalling. Interestingly, cat-miR169 and cat-miR482 were low expressing during auxin treatment and M. ciceri infection but their expression spiked during cytokinin treatment, indicating a cytokinin mediated mode of action. The miRNA expression profiling in response to phytohormones and rhizobia and the reported function of their target genes suggested a crosstalk among the phytohormonal responses during chickpea nodulation.


Auxin Cytokinin miRNA Nodule qRT-PCR Rhizobia 



This work was supported by National Institute of Plant Genome Research (NIPGR) and grant (BT/PR3305/AGR/2/816/2011) from Department of Biotechnology, India ( We kindly acknowledge the University Grant Commission (UGC), Govt. of India for providing predoctoral fellowship to Manish Tiwari.

Author contributions

Conceived and designed the experiments: SB MT. Performed the experiments: MT. Analyzed the data: MT. Wrote the paper: SB MT.

Compliance with ethical standards

Conflict of interest

The authors declare no competing interest.

Supplementary material

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Supplementary material 1 (XLSX 9 kb)
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Supplementary Fig. 1 Secondary structures of 11 set of miRNAs. (A) cat-miR160, (B) cat-miR164, (C) cat-miR166, (D) cat-miR167, (E) cat-miR168, (F) cat-miR169, (G) cat-miR319, (H) cat-miR393, (I) cat-miR396, (J) cat-miR398 and (K) cat-miR482 (PPTX 540 kb)
13562_2019_545_MOESM6_ESM.pptx (369 kb)
Supplementary Fig. 2 Stemloop PCR validation of 11 miRNAs in chickpea nodule tissue (PPTX 369 kb)


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Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  1. 1.National Institute of Plant Genome ResearchJawaharlal Nehru University CampusNew DelhiIndia

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