Network-guided transcriptomic insights into tissue-specific and temporal salt stress responses in broccoli (Brassica oleracea L. var. italica)

Salinity is a major constraint on global crop productivity, particularly affecting moderately tolerant species such as broccoli. To elucidate the molecular basis of salt stress adaptation, we performed an untargeted transcriptomic analysis in broccoli roots and aerial tissues at three time points after treatments (6 h, 3 days, and 10 days). Our results revealed a complex, biphasic response involving an early transcriptional shock, followed by a sustained adjustment phase marked by transcriptional reprogramming. Tissue-specific differences were observed, as each organ exhibiting distinct strategies shaped by its developmental context. ABA signalling (synthesis, catabolism and receptors, PYR/PYL) could be a central regulator, modulating not only individual gene expression but entire metabolic pathways. Also, induction of P5CS1, involved in proline biosynthesis, further suggests prolonged activation of ABA-dependent osmoprotective pathways. Roots, while showing pronounced salt-specific responses, also retained developmentally driven expression profiles as cell wall reinforcement. While in aerial tissues, global transcriptomic patterns largely followed intrinsic developmental trajectories. Overall, our study highlights the importance of coordinated regulation between stress adaptation mechanisms and ongoing developmental programs. Maintaining this balance, particularly through ABA signalling, osmotic adjustment, and cell wall remodelling, is essential for long-term survival under chronic salinity.