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

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.