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Identification and Validation of Functional miRNAs and Their Main Targets in Sorghum bicolor

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Abstract

MicroRNAs (miRNAs) are typically non-coding RNAs of 18–26 nucleotides (nts) that are produced endogenously and regulated post-transcriptionally through degradation or translational repression. Since miRNAs are evolutionarily conserved, their preservation is essential for important regulatory functions in plant development, growth, and responses to environmental stress. Sorghum bicolor (sbi) is a valuable food and fodder crop which is grown worldwide. A range of sbi miRNAs were identified so far as being connected to plant development and stress responses. Herein, we employed a variety of bioinformatics tools for miRNA profiling in sbi and a PCR-based platform for the validation of these miRNAs. In total, 74 new conserved sbi miRNAs from 52 miRNA families have been predicted. Using the psRNA Target method, 10613 different protein targets of these predicted miRNAs have been attained. These targets include 54 GO-terms which have substantial targets in the biological, molecular, and cellular processes. We particularly found that the sbi-miR1861c and sbi-miR5050 are involved to regulate sulphur compound biosynthetic process, while the significant spliceosomal complex is regulated by sbi-miR815b and sbi-miR7768b. Also, we report that the pre-ribosome, electron transport chain, cell communication, cellular respiration, protein localization, and photosynthesis are controlled by sbi-miR2907b, sbi-miR530, sbi-miR7749, sbi-miR1858a, sbi-mi7729a, and sbi-miR417, respectively. The identification and validation of these novel sbi miRNAs shall contribute a lot in improving the crop yield and ensure sustainable agriculture.

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Acknowledgements

The authors are particularly grateful to University of Balochistan, Quetta, Pakistan, and Hazara University, Mansehra, Pakistan for approving this project and facilitating the core facilities.

Funding

This research work was supported by Hazara University (HU), Mansehra, Pakistan, under number HU/699/2021.

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Authors and Affiliations

  1. Department of Chemistry, University of Balochistan, Quetta, 87300, Pakistan

    Abdul Baqi &  Samiullah

  2. Department of Chemistry, Hazara University Mansehra, Mansehra, Pakistan

    Wajid Rehman & Iram Bibi

  3. Department of Biomedical and Environmental Engineering (BEE), California Innovations Corporation (CIC), San Diego, CA, 92037, USA

    Farid Menaa

  4. Department of Chemistry, COMSATS University Islamabad, Islamabad, 45550, Pakistan

    Yousaf Khan & Abdul Sattar

  5. Department of Biology, Faculty of Science, University of Tabuk, 71491, Tabuk, Saudi Arabia

    Doha A. Albalawi

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  1. Abdul Baqi
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Contributions

Conceptualization: WR, FM; writing-original draft preparation: WR, and IR; methodology, software, validation, formal analysis, investigation, and data curation: AB, FM, YK, AS; visualization, supervision, and project administration: AS; resources, writing-review, editing, funding acquisition, and submission: WR, DAA, ASA, SMA, FM. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Wajid Rehman or Farid Menaa.

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Baqi, A., Samiullah, Rehman, W. et al. Identification and Validation of Functional miRNAs and Their Main Targets in Sorghum bicolor. Mol Biotechnol (2023). https://doi.org/10.1007/s12033-023-00988-5

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