Temporal transcriptome analysis under salt stress reveals disrupted rhythmic expression and altered homoeolog usage in allopolyploid cotton

Excessive soil salinity poses a significant threat to plant growth and agricultural production. However, the dynamic transcriptional processes underlying plant salt stress response, particularly the transition from transient to steady-state responses and the involvement of rhythmic regulation, remain poorly understood. Here we conducted phenotypic and transcriptomic analyses of upland cotton ( Gossypium hirsutum ) under salt stress, generating a high-resolution temporal expression profile. Our results identified distinct stress perception and homeostasis responsive phases of gene regulation and revealed a substantial disruption of rhythmic gene expression under stress. A large proportion of rhythmically expressed genes (REGs) lost rhythmicity, with significant alterations in expression phase, period and amplitude. Furthermore, we found that salt stress induced notable shifts in homoeolog expression bias (HEB), suggesting a role for subgenome regulation in environmental plasticity. Collectively, our findings distinguish short-term from long-term adaptive changes and underscore the interplay between stress-induced and rhythmic-regulated transcription. This work provides valuable insights into the temporal and regulatory complexity of salt stress in cotton. Salt stress reprograms transcriptional dynamics in cotton, disrupting rhythmic gene expression and reshaping homoeolog expression bias to facilitate environmental adaptation. • Three distinct phases were revealed: stress perception (0.5–1 h), stress response (3–18 h), and stabilization (24–168 h). • Salt stress reprograms rhythmic gene expression patterns in cotton, leading to widespread loss of rhythmicity. • Salt stress induces notable shifts in homoeolog expression bias (HEB), highlighting subgenome regulation in environmental plasticity.