Climate change is intensifying environmental stresses, including drought, high temperature, and salinity, posing increasing challenges to plant growth and development. In addition to genetic variation, DNA methylation is an important epigenetic mechanism that regulates gene expression without altering the underlying DNA sequence through the addition of methyl groups to the fifth carbon of cytosine. Genome-wide dynamic changes in DNA methylation and demethylation at CG, CHG, and CHH sites contribute to the regulation of stress-responsive transcriptional networks, thereby shaping plant phenotypes and facilitating the establishment of stress memory. In recent years, advances in methylome profiling and molecular validation have shifted research from describing DNA methylation changes to elucidating their regulatory mechanisms. In this review, we summarize the molecular mechanisms underlying the establishment, maintenance, and removal of DNA methylation, with a particular focus on its dynamic changes and regulatory roles in plant responses to cold, heat, drought, and salt stresses. It also compares the characteristics of DNA methylation responses across different types of stress and discusses their potential molecular mechanisms. Overall, DNA methylation represents an important regulatory layer in plant responses to abiotic challenges, and its dynamic changes are closely associated with plant adaptation, providing new insights into the mechanisms underlying stress adaptation.

Background: Tomato growth is severely constrained by saline-alkali stress. Although the mitigating effects of exogenous selenium on various abiotic stresses have been documented, its physiological and molecular regulatory mechanisms in tomato seedlings under saline-alkali stress remain insufficiently understood. Results: In this study, the tomato inbred line Solanum lycopersicum cv. Ailsa Craig was selected as the experimental material. Saline-alkali conditions were established by supplementing 1/4 Hoagland nutrient solution with a complex saline-alkali mixture, and sodium selenite was used for exogenous selenium application. Growth phenotypes and physiological parameters were evaluated, and transcriptome sequencing was conducted to examine the associated molecular regulatory mechanisms. This treatment reduced chlorophyll degradation, increased the activities of superoxide dismutase (SOD by 377.37%), catalase (CAT by 145.67%), peroxidase (POD by 3.39%), and phenylalanine ammonia-lyase (PAL by 340.30%), and promoted the accumulation of salicylic acid and jasmonic acid. Concurrently, malondialdehyde content and reactive oxygen species accumulation were reduced. Transcriptomic profiling indicated that phenylalanine metabolism, carotenoid biosynthesis, galactose metabolism, and related pathways were activated, which supported the improved saline-alkali tolerance of tomato seedlings. Conclusions: In summary, exogenous Se synergistically enhances saline-alkali tolerance in tomato seedlings through multiple pathways, including the enhancement of antioxidant system activity, protection of photosynthetic function, maintenance of cell membrane homeostasis, and modulation of metabolic pathways such as phenylalanine and galactose metabolism. This study provides a theoretical basis and genetic resource support for the stress-tolerant cultivation of tomato and the genetic improvement of elite saline-alkali-tolerant germplasm under saline-alkali stress.