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Transcriptome analysis identifies novel gene(s) and pathways for salt stress responses in Dandi cultivar

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Abstract

Salinity tolerance has been documented as one of the main abiotic stresses, disapprovingly impeding the growth and fertility of core food crops including rice in the ecosphere. We have evaluated 24 varieties exposed to salt stress (150–300 mM NaCl; for 48–72 h) at the vegetative stage. The cellular-level physiological response was observed by assessing the morphophysiological parameters and significant differences were observed in the rice varieties of the Gujarat region of the Indian continent. Additionally, we have performed a comparative transcriptome analysis of the shoots and roots of rice varieties at the vegetative stage (Dandi, salinity-tolerant; and GR-11, Salinity-sensitive) in response to salinity. Based on transcriptome analysis, the genes specifically activated and differentially over-expressed during salinity stress belong to different functional categories mostly located on chromosomes 1, 2, 3, 4, 8, and 11 in both cultivars. A total of 617 and 676 significant DEGs with log2-fold change in the range of ≥  + 2.0 to ≤  − 2.0 were identified from the comparative analysis of the two data sets DS (Dandi Shoot) and GS (GR-11Shoot) (Dandi vs. Control, GR-11 vs. Control) in the shoot sample. Similarly, a total of 510 and 508 significant DEGs DR (Dandi Root) and GR (GR-11 Root) (Dandi vs. Control, GR-11 vs. Control) in the root samples. The DEGs were examined against the KEGG database to explore the biological pathways of Dandi (226) and GR-11 (397) in the shoot as well as root (218,285) samples. Further PageMan analysis showed that there was a significantly higher number of DEGs (p < 0.05, ≥  ± 2.0-fold) involved in signalling pathways including secondary metabolism, hormone metabolism, abiotic stresses, and development which have significant regulatory functions in shoot and root of Dandi and GR-11 variety of rice.

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All the supplementary data is available in the supplementary data section. The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.

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Acknowledgements

Authors are thankful to The Department of Agri. Biotechnology, Anand Agriculture University, Anand, Gujarat (India) for providing the experimental facility.

Funding

No potential funding is involved to carry out this study.

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Authors and Affiliations

  1. Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, 362001, India

    Ashish Kumar G. Vala & Rukam Singh Tomar

  2. Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India

    Nasreen Bano

  3. CSIR-CIMAP, Lucknow, India

    Yogita Deshmukh

  4. Department of Science & Technology Government of Gujarat, Gujarat Biotechnology Research Centre (GBRC), Block-B & D, 6Th Floor, M. S. Building, Sector 11, Gandhinagar, Gujarat, 382011, India

    C.G. Joshi

  5. Department of Biotechnology, Anand Agricultural University, Anand, Gujarat, India

    N. Subhash

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  1. Ashish Kumar G. Vala
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Contributions

A.V. did the overall execution of the experiment, analytical work, and collection of data after morpho-physiological and biochemical analysis of leaves, organization of resulting data, and writing up and revision of the manuscript. Y.D. and N.B. contributed to the planning, designing, and finalization of the basic idea of the experiment and overall supervision during analytical work carried out the statistical analysis of data using XL-STAT software did the presentation of the resulting data in the form of graphs, and revised and finalized the manuscript. R.T., C.J., and S.N. the arrangement and provision of rice seeds contributed to the study's basic idea and planning of the glasshouse experiment and revised and finalized the manuscript. All authors contributed to the article and approved the submitted version.

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Correspondence to Ashish Kumar G. Vala.

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Communicated by Tommaso Martinelli.

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Vala, A.K.G., Bano, N., Deshmukh, Y. et al. Transcriptome analysis identifies novel gene(s) and pathways for salt stress responses in Dandi cultivar. CEREAL RESEARCH COMMUNICATIONS 51, 351–365 (2023). https://doi.org/10.1007/s42976-022-00319-5

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