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Differential Transcriptional Regulation of Drought Stress Revealed by Comparative RNA-seq Analysis of Contrasting indica Rice from North East India

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Abstract

Indica rice varieties especially from North East India show a broad variation in drought tolerance due to the rich biodiversity of the region. In this study, genome-wide analysis of drought-responsive regulons was performed by comparing the stress-tolerant, Tampha and stress-sensitive, Chandan, indica rice genotypes. The results showed that drought stress induces greater number of differentially expressed transcripts in the Tampha as compared to Chandan. Sixty-one drought-regulated transcripts showed higher expression level in Tampha and these included dehydrins, glycosyltransferases, DnaK molecular chaperones and several transcription factors. The drought-responsive transcripts formed co-expression gene modules and were majorly associated with redox pathways and carbohydrate metabolism. The gene regulation was coordinated by transcription factors and miRNAs. The Tampha transcriptome also exhibited significant changes in ASE under drought stress. Therefore, the results demonstrate that substantial differences in both transcriptional variations and post-transcriptional regulations determine the transcriptome profiles to regulate the plant response to drought stress in varieties.

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Data Availability

Accession

Sample_title

Cultivar

SAMN32723754

Ch-0_R1_RNAseq

Chandan

SAMN32723755

Ch-0_R2_RNAseq

Chandan

SAMN32723756

Ch-20_R1_RNAseq

Chandan

SAMN32723757

Ch-20_R2_RNAseq

Chandan

SAMN32723758

T-0_R1_RNAseq

Tampha

SAMN32723759

T-0_R2_RNAseq

Tampha

SAMN32723760

T-20_R1_RNAseq

Tampha

SAMN32723761

T-20_R2_RNAseq

Tampha

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Acknowledgements

This work was financially supported by the core grant from DBT, India.

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Authors and Affiliations

  1. Department of Life Science & Bioinformatics, Assam University, Silchar, Assam, India

    Smita Sahoo

  2. Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan

    Kazutaka Kusunoki & Hiroyuki Koyama

  3. Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India

    Kavita Goswami & Neeti Sanan-Mishra

  4. Department of Biochemistry, Central University of Rajasthan, Bandarsindri, Ajmer, India

    Sanjib Kumar Panda

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SKP, NSM and HK conceived and designed the study. SS performed the experiments. KK performed RNA-seq data processing, transcriptome analysis and interpretation of the data. KG performed the miRNA analysis. SS, KK and KG wrote the manuscript. NSM, HK and SKP edited the manuscript. All authors read and approved the final manuscript.

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Correspondence to Neeti Sanan-Mishra or Sanjib Kumar Panda.

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Sahoo, S., Kusunoki, K., Goswami, K. et al. Differential Transcriptional Regulation of Drought Stress Revealed by Comparative RNA-seq Analysis of Contrasting indica Rice from North East India. J Plant Growth Regul 42, 5780–5795 (2023). https://doi.org/10.1007/s00344-023-10964-7

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