Transcriptomic Analysis Reveals the Role of Long Non-Coding RNAs in Response to Drought Stress in Tibetan Hull-less Barley

Long noncoding RNAs (lncRNAs), which are a type of RNA exceeding 200 nucleotides and lack representative open reading frames (ORFs), have emerged as crucial regulatory molecules that modulate numerous growth processes in plants. While substantial progress has been made in understanding the functions and regulatory mechanisms of coding RNAs, the study of lncRNAs in Tibetan hulless barley (Hordeum vulgare L. var. nudum) still remain incompletely understood. To elucidate the coordination of drought stress responses by long non-coding RNAs (lncRNAs), a study analyzed previously published RNA sequencing (RNA-seq) data from two cultivars of hulless barley, Z772 (drought-tolerant) and Z013 (drought-sensitive), subjected to varying durations of drought treatment (0, 1, and 5 h). The objective was to determine the expression profiles of long non-coding RNAs (lncRNAs) in hulless barley. Initially, we identified a total of 2,877 lncRNAs, of which 2,179 were co-expressed in both cultivars. Additionally, 331 and 367 lncRNAs showed cultivar-specific expression patterns in Z772 and Z013, respectively. Given the trans-regulatory functions of lncRNAs, we uncovered 11 modules that were enriched in drought-responsive pathways. Within these modules, lncRNAs and neighboring protein-coding genes (PCGs) were co-clustered in key regulatory modules. The GO enrichment analysis of potential lncRNA-PCG pairs primarily involved processes related to the response to water deprivation, regulation of abiotic stress, and RNA metabolic processes. Notably, 12 high-confidence lncRNA-PCG pairs displayed concordant expression profiles, with some annotated as acting as transcription factors (TFs). Two of these pairs were validated by qRT-PCR in the hulless barley cultivar Kunlun 14. These findings suggest that lncRNAs may participate in regulatory networks involved in drought adaptation in hulless barley, offering novel insights into the drought resistance mechanisms of Poaceae crops and potential targets for breeding drought-resistant varieties.