Identification and expression analysis of conserved microRNAs during short and prolonged chromium stress in rice (Oryza sativa)

  • Sonali DubeyEmail author
  • Sharad Saxena
  • Abhishek Singh Chauhan
  • Priyanka Mathur
  • Vibha RaniEmail author
  • Debasis Chakrabaroty
Research Article


MicroRNAs (miRNAs) are one of the most critical epigenetic regulators of gene expression which modulate a spectrum of development and defence response processes in plants. Chromium (Cr) contamination in rice imposes a serious concern to human health as rice is used as staple food throughout the world. Although several studies have established the differential response of miRNAs in rice during heavy metal (arsenic, cadmium) and heat or cold stress, no report is available about the response of miRNAs during Cr stress. In the present study, we identified 512 and 568 known miRNAs from Cr treated and untreated samples, respectively. Expression analysis revealed that 13 conserved miRNAs (miR156, miR159, miR160, miR166, miR169, miR171, miR396, miR397, miR408, miR444, miR1883, miR2877, miR5072) depicted preferential up- or down-regulation (> 4-fold change; P value < 0.05). Target gene prediction of differentially expressed miRNAs and their functional annotation suggested the important role of miRNAs in defence and detoxification of Cr though ATP-binding cassette transporters (ABC transporters), transcription factors, heat shock proteins, auxin response, and metal ion transport. Real-time PCR analysis validated the differential expression of selected miRNAs and their putative target genes. In conclusion, our study identifies and predicts miRNA-mediated regulation of signalling pathway in rice during Cr stress.


Oryza sativa MicroRNA Cr stress NGS Transcriptome Heavy metal toxicity 



This work was supported by SERB, Government of India, New Delhi (File No: YSS/2015/000742) and CSIR (File No: 09/1132 (0004)/18-EMR-I). The authors also acknowledge the Jaypee Institute of Information Technology (JIIT), Noida, for the infrastructural support.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Sonali Dubey
    • 1
    Email author
  • Sharad Saxena
    • 2
  • Abhishek Singh Chauhan
    • 3
  • Priyanka Mathur
    • 2
  • Vibha Rani
    • 2
    Email author
  • Debasis Chakrabaroty
    • 3
  1. 1.Amity Institute of BiotechnologyAmity UniversityNoidaIndia
  2. 2.Transcriptome Laboratory, Centre for Emerging Diseases, Department of BiotechnologyJaypee Institute of Information TechnologyNoidaIndia
  3. 3.Council of Scientific and Industrial Research—National Botanical Research Institute (CSIR-NBRI)LucknowIndia

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