Transcriptomic and Physiological Profiling Elucidates Differential Salt Stress Responses in Tolerant 'SO4' and...

Soil salinity severely limits grapevine (Vitis spp.) growth and productivity, yet the mechanisms distinguishing tolerant and sensitive rootstocks remain incompletely understood. We compared the salt-tolerant rootstock 'SO4' with the salt-sensitive 'Beida' under 100 mmol L^-1 NaCl for 0, 6, and 12 days. Salinity progressively reduced photosynthetic pigments in both genotypes, although 'SO4' retained higher levels. Salt treatment also increased hydrogen peroxide, malondialdehyde, soluble sugars, soluble proteins, proline, and antioxidant enzyme activities. Compared with 'Beida', 'SO4' showed stronger osmotic adjustment and greater activation of superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase. RNA-seq analysis revealed extensive genotype- and time-dependent transcriptional reprogramming, with differentially expressed genes mainly associated with hormone signalling, secondary metabolism, carbon fixation, protein processing, and lipid metabolism. Weighted gene co-expression network analysis identified the MEblack module as positively associated with salt tolerance in 'SO4' but negatively associated with 'Beida'. Within this module, Vitvi01g00735/VvBCA2 and Vitvi07g02043/VvLCB1 were prioritized as candidate hubs based on high module membership, gene significance, and intramodular connectivity. Hub-centred networks linked VvBCA2 to redox regulation, protein homeostasis, defense, and osmotic signalling, whereas VvLCB1 was associated with cell-wall remodelling, methyl metabolism, membrane signalling, and lipid turnover. Transcription-factor families, including MYB, WRKY, AP2/ERF, bHLH, and HSF, were more strongly represented in 'SO4'. Collectively, these findings identify coordinated physiological and transcriptional mechanisms underlying salt tolerance and provide candidate genes for grapevine improvement.