Comparative Physiological and Transcriptome Analysis of Salt Stress Responses in Tolerant and Susceptible Grapevine Rootstocks

Grapevine is one of the most extensively cultivated and economically important fruit crops, renowned for its nutritional and health benefits. However, salt stress severely impairs its growth, development, and yield. Rootstocks play a crucial role in enhancing salt stress tolerance in grafted grapevines, however the underlying mechanisms particularly at morphophysiological and transcriptomic study remain poorly understood and require further investigation. Therefore, in the present study, morphophysiological and transcriptomic sequencing was performed on tolerant grapevine rootstock ‘SO4’ and susceptible ‘Beida’ in response to salt stress and control group. Morphophysiological results showed that the plant height, stem diameter, root length, root weight, number of roots, root surface area, malondialdehyde, soluble sugar, proline, antioxidants enzymes after 12 days of salt stress boosted more significantly in ‘SO4’ than ‘Beida’. Furthermore, transcriptomic analysis studies showed that a total of 2268, 1066, and 1135 differentially expressed genes (DEGs) were identified in ‘SO4’, and ‘Beida’ rootstock after 0, 6, and 12 days. The metabolic pathways, pyruvate metabolism, plant hormone signal transduction, biosynthesis of secondary metabolites, and osmotic adjustment were the primary response systems in both grapevine rootstock under salt stress. Different transcription factors involving bHLH, AP2, ERF, HSF, WRKY, MYB, and MYB-related had more annotated in ‘SO4’ than ‘Beida’ rootstock under salt stress. In addition, using weighted gene coexpression analysis (WGCNA), five modules (MEblack, MEblue, MEyellow, MEgreen, and MEgrey) were highly associated with salinity stress tolerance. Among them, MEblack was the most positive (upregulated) module color in ‘SO4’, while it was negatively correlated with ‘Beida’ rootstocks under salt stress. Furthermore, 10 DEGs related to the tolerance response were selected and validated based on transcriptomic data and RT-qPCR. Our findings outline a tolerance mechanism model for rootstocks under abiotic stress, providing necessary information for improving the tolerance of grapevine genotypes.