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Comparative transcriptome profiling of contrasting finger millet (Eleusine coracana (L.) Gaertn) genotypes under heat stress

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Abstract

Background

Eleusine coracana (L.) Gaertn is a crucial C4 species renowned for its stress robustness and nutritional significance. Because of its adaptability traits, finger millet (ragi) is a storehouse of critical genomic resources for crop improvement. However, more knowledge about this crop’s molecular responses to heat stress needs to be gained.

Methods and results

In the present study, a comparative RNA sequencing analysis was done in the leaf tissue of the finger millet, between the heat-sensitive (KJNS-46) and heat-tolerant (PES-110) cultivars of Ragi, in response to high temperatures. On average, each sample generated about 24 million reads. Interestingly, a comparison of transcriptomic profiling identified 684 transcripts which were significantly differentially expressed genes (DEGs) examined between the heat-stressed samples of both genotypes. The heat-induced change in the transcriptome was confirmed by qRT-PCR using a set of randomly selected genes. Pathway analysis and functional annotation analysis revealed the activation of various genes involved in response to stress specifically heat, oxidation-reduction process, water deprivation, and changes in heat shock protein (HSP) and transcription factors, calcium signaling, and kinase signaling. The basal regulatory genes, such as bZIP, were involved in response to heat stress, indicating that heat stress activates genes involved in housekeeping or related to basal regulatory processes. A substantial percentage of the DEGs belonged to proteins of unknown functions (PUFs), i.e., not yet characterized.

Conclusion

These findings highlight the importance of candidate genes, such as HSPs and pathways that can confer tolerance towards heat stress in ragi. These results will provide valuable information to improve the heat tolerance in heat-susceptible agronomically important varieties of ragi and other crops.

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Data availability

All the datasets used are online available.

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Acknowledgements

This financial support from the Department of Biotechnology, New Delhi, under the project “Phenomics and Genomics of Ragi (Eleusine coracana)” is acknowledged. The authors are grateful to Prof. Y.A. Nanja Reddy, Project Coordinator, AICP on Small Millets, UAS, GKVK Campus, Bangalore, for providing seeds of KJNS-46 and PES-110 and for their valuable suggestions.

Funding

This financial support is from the Department of Biotechnology, New Delhi, under the project “Phenomics and Genomics of Ragi (Eleusine coracana)”.

Author information

Authors and Affiliations

  1. Biotechnology and Climate Change Laboratory, National Institute for Plant Biotechnology, New Delhi, India

    Etika Goyal, Amit Kumar Singh, Mahesh Mohanrao Mahajan & Kumar Kanika

Authors
  1. Etika Goyal
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  2. Amit Kumar Singh
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Contributions

E.G. grew the plants and carried out the experiment. E.G., A.K.M., and M.M.M. performed RNA isolation. K.K. conceived the study, designed the experiment, was associated with wet lab work, and coordinated the study. E.G., A.K.S., M.M.M, and K.K. were involved in result interpretation, analysis, and integration of results, besides associating with drafting and finalizing the manuscript. All authors have read and approved the manuscript.

Corresponding author

Correspondence to Kumar Kanika.

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Supplementary Fig 1

: Physiological analysis under heat stress. Membrane Stability Index

Supplementary Fig. 2

: Transcriptome assembly information. (a) Length distribution of fully assembled transcripts. (b) Proteome analysis of total transcripts of E. coracana

Supplementary Table 1

: Primers used in the study

Supplementary Table 2

: FPKM value from the in-silico analysis

Supplementary Table 3

: GO classification of 684 differentially expressed unigenes

Supplementary Table 4

: KEGG classification of 684 differentially expressed unigenes

Supplementary Table 5

: Distribution of Transcription factor family of 684 differentially expressed unigenes

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Goyal, E., Singh, A.K., Mahajan, M.M. et al. Comparative transcriptome profiling of contrasting finger millet (Eleusine coracana (L.) Gaertn) genotypes under heat stress. Mol Biol Rep 51, 283 (2024). https://doi.org/10.1007/s11033-024-09233-x

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