Jian-Ping Tao, Ting Huang, Zhi-Hang Hu, Chen Chen, Hui Liu, Xiong You, Ai-Sheng Xiong
Genome-wide analysis revealed pronounced context-specific methylation changes that differed markedly between genotypes. CHG methylation was broadly reduced under stress in both genotypes, with a stronger response in BGI, whereas CHH methylation showed a genome-wide increase in BGI but only modest changes in Azucena, indicating more extensive epigenomic perturbation in the susceptible background. At the local level, differentially methylated regions (DMRs) were predominantly hypomethylated across all cytosine contexts and, particularly within the CHG and CHH contexts, were significantly enriched within transposable elements and upstream regulatory regions relative to genomic background, suggesting that stress-induced relaxation of TE silencing and regulatory reprogramming of promoter regions are conserved features of the Al epigenetic response. Integration of DMR and differential expression data identified 71 and 93 genes with both methylation and transcriptional changes in Azucena and BGI, respectively, with only three genes shared between genotypes, all showing opposite transcriptional responses, underscoring the near-complete genotype specificity of the methylation-expression interface. In Azucena, the Al-tolerant genotype, methylation and expression changes were targeted in genes directly linked to Al exclusion, including organic acid and MATE transporters, whereas BGI showed a broader and less specific epigenomic response.
The integration of light and cold signaling is critical for cold acclimation in plants, but the regulatory complexity of the underlying transcriptional network remains poorly understood. To systematically dissect this interplay in tomato (Solanum lycopersicum), we constructed a computational model that merges the core cold-responsive inducer of CBF expression 1 (ICE1)-C-repeat binding factor (CBF)-cold regulated factors (COR) pathway with light-sensitive modules, including the constitutive photomorphogenic 1 (COP1)-elongated hypocotyl 5 (HY5)-MYB domain protein 15 (MYB15) cascade and the phytochrome-phytochrome interacting factor 4 (PIF4)-GA-INSENSITIVE 4 (GIA4) regulatory axis. Simulations successfully reproduced the experimentally observed gene expression dynamics across different photoperiods and revealed that phytochrome activity is co-modulated by both light quality and temperature. Our model predicts that a low red/far-red ratio enhances the expression of CBF, whereas cold treatment stabilizes phyA and phyB proteins, jointly promoting cold tolerance. Additionally, the PIF4-GAI4 negative feedback loop is shown to generate sustained oscillations in SlPIF4's expression, and the cold-responsive gene SlCOR413 is predicted to exhibit low-temperature-induced oscillatory behavior. This integrative framework provides a systems-level tool for dissecting light-cold crosstalk and offers a basis for rationally engineering cold tolerance in horticultural crops through targeted modulation of transcriptional networks.