Identification and analysis of long non-coding RNAs response to quinclorac stress in tobacco

Quinclorac is a widely used herbicide known to inhibit tobacco growth, yet its molecular impact remains poorly understood. To elucidate tobacco's response mechanisms, we profiled long non-coding RNAs (lncRNAs) under quinclorac stress. A total of 1867 lncRNAs were identified, including 1337 novel transcripts. Differential expression analysis revealed 672 lncRNAs significantly altered by quinclorac treatment. Co-expression clustering grouped these into 20 distinct expression profiles. Target prediction indicated that 415 lncRNAs potentially regulate mRNAs via cis- and/or trans-acting interactions. Functional enrichment of their targets highlighted overrepresentation of photosynthesis and stress-response pathways. Moreover, we constructed regulatory networks linking lncRNAs to quinclorac-resistance-associated genes involved in hormone biosynthesis and signaling, molecular transport, and xenobiotic metabolism. These findings uncover a repertoire of lncRNAs responsive to quinclorac and suggest their roles in mediating herbicide tolerance in tobacco.