Background: The global transcriptome reprogramming in grapevines in response to powdery mildew remains poorly understood, despite its economic implications, especially the new cultivars. Methods: Thus, this study aimed to elucidate these changes through RNA sequencing in ‘Yeniang No. 2’ grapevine leaves infected with powdery mildew compared to healthy ones. Results: A total of six samples were subjected to transcriptome sequencing, resulting in 36.85 Gb of clean data. A minimum of 5.89 Gb of clean data was generated for each sample, with at least 92.24% of the clean data attaining a quality score of Q30. Clean reads from each sample were aligned to the designated reference genome. The mapping ratio varied between 88.77% and 89.66%. The high-quality sequencing data revealed 1219 differentially expressed genes (DEGs), of which the infection upregulated 790 and downregulated 429. Functional enrichment analyses revealed a significant activation of key defense-related pathways. These included plant–pathogen interaction, phenylpropanoid and flavonoid biosynthesis for creating antimicrobial compounds, glutathione metabolism for reducing oxidative stress, and oxidative phosphorylation for enhanced energy production. This indicates a coordinated, multi-faceted defense strategy. The study also uncovered a complex layer of post-transcriptional regulation, identifying 1883 novel genes and 22,210 alternative splicing events, primarily skipped exons and intron retention. Key hub proteins identified within interaction networks, along with these splicing changes, underscore a sophisticated defense involving transcriptional reprogramming and metabolic shifts. Conclusions: The genes and molecular markers discovered are valuable resources for marker-assisted breeding. Leveraging these findings, particularly hub genes and favorable splice variants, can accelerate the development of new grapevine cultivars with durable resistance to powdery mildew.

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.