Identification, genomic localization, and functional validation of salt-stress-related lncRNAs in Indian Mustard (Brassica juncea L.)

Indian Mustard ( Brassica juncea L.) is a globally cultivated winter oilseed crop of the rapeseed-mustard group. In India, it is mainly grown in the semi-arid northwest agroclimatic zone, known for high soil salinity. In this regard, enhancing salt stress tolerance in B . juncea is critical for sustaining its production in the region. Long non-coding RNAs (lncRNAs) play critical roles in coordinating gene expression under various abiotic stresses, including salt stress, but their involvement in salt stress response in B . juncea remains largely unknown. In this study, we conducted RNA-seq analysis on control, salt-stressed, and salt-shocked young leaves of the salt-tolerant B . juncea var. CS-52. We identified 3,602 differentially expressed transcripts between stress versus control and shock versus control samples. Among these, 61 were identified as potential lncRNAs, with 21 specific to salt stress and 40 specific to salt shock. Out of the 21 lncRNAs specific to salt stress, 15 were upregulated and six were downregulated, while all 40 lncRNAs unique to salt shock were downregulated. The chromosomal distribution analysis of lncRNAs revealed their uneven placement across 18 chromosomes in B . juncea . RNA-RNA interaction analysis identified 26 interactions between 10 lncRNAs and 23 miRNAs and predicted 13 interactions between six miRNAs and 13 mRNAs. Finally, six lncRNA-miRNA-mRNA interaction networks were established, involving five lncRNAs, 13 miRNAs, and 23 mRNAs. qRT-PCR analysis revealed the upregulation of four out of five lncRNAs along with their target mRNAs, supporting their involvement in the salt stress response in B . juncea .