The NAC (for NAM, ATAF1,2, and CUC2) proteins family are plant-specific transcription factors, which play important roles in leaf development and response to environmental stresses. In this study, an NAC gene, DRL1, isolated from grapevine Vitis vinifera L. “Yatomi Rose”, was shown to be involved in leaf senescence. The quantity of DRL1 transcripts decreased with advancing leaf senescence in grapevine. Overexpressing the DRL1 gene in tobacco plants significantly delayed leaf senescence with respect to chlorophyll concentration, potential quantum efficiency of photosystem II (Fv/Fm), and ion leakage. Moreover, exogenous abscisic acid (ABA) markedly reduced the expression of DRL1, and the ABA and salicylic acid (SA) concentration was lower in the DRL1-overexpressing transgenic plants than in the wild-type plants. The DRL1 transgenic plants exhibited reduced sensitivity to ABA-induced senescence but no significant change in the sensitivity to jasmonic acid-, SA- or ethylene-induced senescence. Transcriptomic analysis and RNA expression studies also indicated that the transcript abundance of genes associated with ABA biosynthesis and regulation, including 9-cis-epoxycarotenoid dioxygenase (NCED1), NCED5, zeaxanthin epoxidase1 (ZEP1), ABA DEFICIENT2 (ABA2), ABA4, and ABA INSENSITIVE 2 (ABI2), was markedly reduced in the DRL1-overexpressing plants. These results suggested that DRL1 plays a role as a negative regulator of leaf senescence by regulating ABA synthesis.

In plant cells, multiple paralogs from ribosomal protein (RP) families are always synchronously expressed, which is likely contributing to ribosome heterogeneity or functional specialization. However, previous studies have shown that most RP mutants share common phenotypes. Consequently, it is difficult to distinguish whether the phenotypes of the mutants have resulted from the loss of specific genes or a global ribosome deficiency. Here, to investigate the role of a specific RP gene, we employed a gene overexpression strategy. We found that Arabidopsis lines overexpressing RPL16D (L16D-OEs) display short and curled rosette leaves. Microscopic observations reveal that both the cell size and cell arrangement are affected in L16D-OEs. The severity of the defect is positively correlated with RPL16D dosage. By combining transcriptomic and proteomic profiling, we found that overexpressing RPL16D decreases the expression of genes involved in plant growth, but increases the expression of genes involved in immune response. Overall, our results suggest that RPL16D is involved in the balance between plant growth and immune response.

DNA methylation is a key epigenetic regulator in plant development. However, the changes in methylation patterns between the early and late stages of grape berry development, the two phases with the most pronounced morphological differences, and the respective roles of methylation at these stages remain largely unexplored. To investigate the dynamic DNA methylation changes during this stage and their regulatory role in fruit development, we constructed genome-wide methylation maps of grape at two key time points: the early development stage (7 days after flowering, 7DAF; hereafter referred to as S1) and the late development stages (78 days after flowering, 78DAF; hereafter referred to as S2). Global cytosine methylation increased from 12.57% (S1) to 14.16% (S2), driven primarily by a substantial increase in CHH methylation (from 5.88% to 7.92%; p < 0.001), whereas CG and CHG methylation showed no statistically significant change. Most differentially methylated regions (DMRs) were hypermethylated in S2, predominantly in the CHH context. Integrative methylome and transcriptome analysis revealed that CHH hypermethylation was associated with the downregulation of YABBY5 (a berry size repressor) and upregulation of UGPase (a cell wall biosynthesis gene), suggesting a potential regulatory role in fruit expansion. Because our study compares only two time points, it cannot distinguish between gradual and stage-specific methylation changes, and functional validation of the identified genes is required. Nevertheless, these findings provides a valuable resource for understanding stage-specific DNA methylation dynamics and their association with gene expression during grape berry development.

Soil salinity severely restricts grapevine growth and development. Here, we integrated whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) to investigate DNA methylation changes and their relationship with gene expression under salt stress in Vitis vinifera L. ‘Shine Muscat’ grapevine. Salt stress altered genome-wide DNA methylation patterns, reducing methylation levels in CG, CHG, and CHH contexts following NaCl treatment. We identified 8606 differentially methylated regions (DMRs) and 3106 DMR-associated genes (DMGs) under salt stress. RNA-seq analysis revealed 2691 differentially expressed genes (DEGs), including multiple stress-related transcription factors (e.g., MYB, NAC, WRKY) and hormone-related genes strongly induced by salinity. Integrative analysis identified 171 genes that were both differentially methylated and differentially expressed, primarily enriched in metabolic pathways, fructose and mannose metabolism, and fatty acid biosynthesis. Notably, several key stress-responsive genes (e.g., VvNAC72, VvBAK1, VvMYBS3) showed coordinated changes between methylation status and transcript abundance. Collectively, this study provides a comprehensive integrative analysis of DNA methylation and transcriptome reprogramming in ‘Shine Muscat’ grapevine under salt stress, revealing potential epigenetic mechanisms involved in transcriptional regulation and salt adaptation. The identified candidate genes provide valuable targets for further functional validation and genetic improvement of grapevine salt tolerance.