Journal of Plant Molecular Breeding

Identification of drought stress-responsive long non-coding RNAs (lncRNAs) in root tip region of rice (Oryza sativa)

Document Type : Original research paper

Authors

1 Institute of Biotechnology, Shiraz University, Shiraz, Iran.

2 Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran.

3 Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, Shiraz

Abstract

Drought is a severe abiotic stress factor that significantly impacts rice production globally. The investigation of drought stress response components, particularly in plant roots, holds great importance. Recent evidence highlights the critical role played by long non-coding RNAs (lncRNAs) in the response to abiotic stress. In this study, we identified drought stress-induced lncRNAs in the root tip region of rice using transcriptome sequencing analysis performed on seedlings of a sensitive rice genotype (IR64) under drought and control conditions. We identified a total of 358 differentially expressed lncRNAs (DElncRNA), more than 60% of which were in intergenic regions. Our results demonstrated that DElncRNAs can directly or indirectly regulate 710 and 7535 mRNAs in cis and trans, respectively. Additionally, the target genes of DElncRNAs were involved in drought resistance genes, lateral root growth, and genes affecting auxin transport. We also identified 24 conserved sequence motifs in the upstream regions of DElncRNAs and differentially expressed mRNAs (DEmRNAs) motifs through a search and functional analysis of these motifs indicated their involvement in regulation of transcription, translation, and the transmembrane receptor protein tyrosine kinase signaling pathway. Finally, we constructed a network of DElncRNAs and DEmRNAs. Our functional analysis of the top 10 hub lncRNAs in the network demonstrated their involvement in growth processes, cellular responses to stimuli, and signaling pathways. These results offer a comprehensive perspective on potentially functional lncRNAs and provide insight into the molecular mechanisms underlying drought resistance in the root tip region of rice.

Keywords

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Journal of Plant Molecular Breeding
Volume 10, Issue 2
December 2022
Pages 31-45
  • Receive Date: 25 July 2023
  • Revise Date: 05 September 2023
  • Accept Date: 19 November 2023
  • First Publish Date: 19 November 2023