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Novel drought-responsive regulatory coding and non-coding transcripts from Oryza Sativa L.

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Abstract

Drought-stress can cause major economic loss and is a serious issue to address in agriculture. Defining the molecular pathways in how a plant responds to drought-stress may prove valuable in developing new drought-resistant plants. In this study, we identified several novel drought-responsive regulatory coding and noncoding transcripts in rice, Oryza sativa L., using the next generation sequencing (NGS) technique and bioinformatics analyses. We produced comprehensive NGS RNA sequencing data for mRNA, small RNA, and long noncoding RNA at the experimental conditions of aeration without watering for 1 and 6 h in compared with the 0 h control. We performed bioinformatics analysis to identify novel drought-responsive transcription factors (TFs), novel drought-responsive micro RNA (miRNA), and novel drought-responsive long noncoding RNAs (lncRNAs). These transcripts were validated by quantitative real-time PCR (qRT-PCR). We identified 18 TFs, ten lncRNAs and one miRNA as being novel drought-responsive regulatory transcripts. Computational analysis using a gene regulatory network showed that these transcripts were related to regulation of response to drought-stress.

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Acknowledgments

This work was supported by grants from the Next Generation BioGreen 21 Program (No. PJ01121101) funded by the Rural Development Administration, Korea.

Funding

This study was funded by Grants from the Next Generation BioGreen 21 Program (No. PJ01121101) funded by the Rural Development Administration, Korea.

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Authors and Affiliations

  1. Department of Biomedical Sciences, Sunmoon University, Asan, 336-708, Korea

    Seon-Ju Shin & Hawk-Bin Kwon

  2. Department of Computer Science and Engineering, Seoul National University, Gwanak-Gu, Seoul, 151-744, Republic of Korea

    Hongryul Ahn, Sungmin Rhee & Sun Kim

  3. Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-Gu, Seoul, 151-747, Republic of Korea

    Inuk Jung & Sun Kim

  4. Bioinformatics Institute, Seoul National University, Gwanak-Gu, Seoul, 151-747, Republic of Korea

    Sun Kim

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  1. Seon-Ju Shin
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  2. Hongryul Ahn
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  4. Sungmin Rhee
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  5. Sun Kim
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Correspondence to Hawk-Bin Kwon.

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Shin, SJ., Ahn, H., Jung, I. et al. Novel drought-responsive regulatory coding and non-coding transcripts from Oryza Sativa L.. Genes Genom 38, 949–960 (2016). https://doi.org/10.1007/s13258-016-0439-x

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