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Identification of drought stress-responsive genes in rice (Oryza sativa) by meta-analysis of microarray data

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Abstract

Meta-analysis provides a systematic access to the previously studied microarray datasets that can recognize several common signatures of stresses. Three different datasets of abiotic stresses on rice were used for meta-analysis. These microarray datasets were normalized to regulate data for technical variation, as opposed to biological differences between the samples. A t-test was performed to recognize the differentially-expressed genes (DEGs) between stressed and normal samples. Gene ontology enrichment analysis revealed the functional distribution of DEGs in different stressed conditions. Further analysis was carried out using software RICE NET DB and divided into three different categories: biological process (homoiothermy and protein amino acid phosphorylation), cellular component (nucleus and membrane), and molecular function (zinc ion binding ad DNA binding). The study revealed that 5686 genes were constantly expressed differentially in Oryza sativa (2089 upregulated and 3597 downregulated). The lowest P value (P = 0.003756) among upregulated DEGs was observed for naringenin, 2-oxoglutrate 3-dioxygenase protein. The lowest P value (P = 0.002866816) among the downregulated DEGs was also recorded for retrotransposon protein. The network constructed from 48 genes revealed 10 hub genes that are connected with topological genes. These hub genes are stress responsive genes that may also be regarded as the marker genes for drought stress response. Our study reported a new set of hub genes (reference genes) that have potentially significant role in development of stress tolerant rice.

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Acknowledgments

Authors are thankful to the Director, Motilal Nehru National Institute of Technology Allahabad, for providing research lab and financial support for performing this experiment. The author is thankful to the Ministry of Human Resource and Development, Govt. of India, New Delhi, India for providing scholarship during this tenure. Authors also sincerely thank Mr Manish P. Singh, MNNIT Allahabad for his help in manuscript correction.

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Author notes

  1. Conceived and designed the experiment, NKS and AM; performed the experiments, PS and BSY; analysed the data; PS and SA; wrote the paper, PS.

Authors and Affiliations

  1. Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, 211 004, India

    Preeti Sirohi, Birendra S. Yadav, Shadma Afzal, Ashutosh Mani & Nand K. Singh

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  1. Preeti Sirohi
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  2. Birendra S. Yadav
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  3. Shadma Afzal
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  4. Ashutosh Mani
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  5. Nand K. Singh
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Correspondence to Nand K. Singh.

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Corresponding editor: H. A. Ranganath

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Sirohi, P., Yadav, B.S., Afzal, S. et al. Identification of drought stress-responsive genes in rice (Oryza sativa) by meta-analysis of microarray data. J Genet 99, 35 (2020). https://doi.org/10.1007/s12041-020-01195-w

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  • DOI: https://doi.org/10.1007/s12041-020-01195-w

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