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Genome-wide profiling of drought-tolerant Arabidopsis plants over-expressing chickpea MT1 gene reveals transcription factors implicated in stress modulation

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Abstract

Drought, a major abiotic limiting factor, could be modulated with in-built reprogramming of plants at molecular level by regulating the activity of plant developmental processes, stress endurance and adaptation. The transgenic Arabidopsis thaliana over-expressing metallothionein 1 (MT1) gene of desi chickpea (Cicer arietinum L.) was subjected to transcriptome analysis. We evaluated drought tolerance of 7 days old plants of Arabidopsis thaliana in both wild-type (WT) as well as transgenic plants and performed transcriptome analysis. Our analysis revealed 24,737 transcripts representing 24,594 genes out of which 5,816 were differentially expressed genes (DEGs) under drought conditions and 841 genes were common in both genotypes. A total of 1251 DEGs in WT and 2099 in MT1 were identified in comparison with control. Out of the significant DEGs, 432 and 944 were upregulated, whereas 819 and 1155 were downregulated in WT and MT1 plants, respectively. The physiological and molecular parameters involving germination assay, root length measurements under different stress treatments and quantitative expression analysis of transgenic plants in comparison to wild-type were found to be enhanced. CarMT1 plants also demonstrated modulation of various other stress-responsive genes that reprogrammed themselves for stress adaptation. Amongst various drought-responsive genes, 24 DEGs showed similar quantitative expression as obtained through RNA sequencing data. Hence, these modulatory genes could be used as a genetic tool for understanding and delineating the mechanisms for fine-tuning of stress responses in crop plants.

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Acknowledgements

The authors are highly thankful for the infrastructural support to the Director, CSIR-National Botanical Research Institute, Lucknow. We also express our gratitude to CSIR, New Delhi, for the funds under the project MLP0026. The authors are also thankful to CSIR, DST and UGC for providing research fellowships. CSIR-NBRI Manuscript Number: CSIR-NBRI_MS/2021/11/03.

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Authors and Affiliations

  1. Plant Transgenic Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Uttar Pradesh, Lucknow, 226001, India

    Sanoj Kumar, Ankita Yadav, Nasreen Bano, Rita Verma, Ankesh Pandey, Anil Kumar, Sumit Bag & Indraneel Sanyal

  2. Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, India

    Sanoj Kumar & Sudhakar Srivastava

  3. Laboratory of Morphogenesis, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India

    Ankita Yadav

  4. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India

    Nasreen Bano, Ankesh Pandey, Sumit Bag & Indraneel Sanyal

  5. Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Be’er Sheva, Israel

    Arvind Kumar Dubey

  6. Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India

    Rita Verma

  7. Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, 263136, India

    Anil Kumar

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Contributions

Sanoj Kumar conceptualized and performed experiments with formal analysis and investigation. Ankita Yadav wrote the original draft along with the data validation. Nasreen Bano was involved in software and writing—review and editing. Arvind Kumar Dubey, Rita Verma, Ankesh Pandey and Anil Kumar formally analysed and investigated the data. Sumit Bag critically reviewed the manuscript and provided guidance. Sudhakar Srivastava investigated and reviewed the manuscript. The whole work was designed and performed under the supervision of Indraneel Sanyal with funding acquisition, review and editing of manuscript. All authors have read and approved the manuscript.

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Correspondence to Indraneel Sanyal.

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Kumar, S., Yadav, A., Bano, N. et al. Genome-wide profiling of drought-tolerant Arabidopsis plants over-expressing chickpea MT1 gene reveals transcription factors implicated in stress modulation. Funct Integr Genomics 22, 153–170 (2022). https://doi.org/10.1007/s10142-021-00823-7

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