Transcriptome analysis revealed lncRNA-mRNA modules responsive to low temperature stress in Qingke

Background Qingke (hull-less barley), a staple crop on the Qinghai-Xizang Plateau, has evolved unique stress tolerance mechanisms. Cold stress damages plants through ice formation and oxidative stress, triggering antioxidant systems and stress-related gene expression. Long non-coding RNAs (lncRNAs) are known to regulate these responses. Results Physiological analysis revealed a dynamic defense strategy: antioxidant systems (SOD/POD) activated early (12 h), shifting to osmotic regulation (soluble protein) later (48 h). Membrane damage (MDA/conductivity) increased under stress but showed repair during recovery. Transcriptome profiling identified a core set of 317 differentially expressed genes enriched in catalytic and stress-response functions. Early stress (12h) predominantly involved hormone (jasmonate) and pathogen defense pathways. Later (48h), protein synthesis (ribosome) and secondary metabolism (phenylpropanoid) were upregulated. Recovery (24h) activated carbon metabolism and fatty acid degradation. Furthermore, specific lncRNAs (e.g., LNC_003210) were identified as potential regulators of photosynthesis-related genes. Conclusions Qingke adapts to cold through phased physiological responses (antioxidant defense, osmoregulation) and dynamic metabolic reprogramming. LNC_003210 may play a key role in cold adaptation by regulating photosynthesis.