A review of the advances and perspectives in sequencing technologies for analysing plant epigenetic responses to abiotic stress

• Multilayer sequencing to capture dynamic epigenetic landscapes in plants under abiotic stress. • Multi-omics integration, single-cell/spatial epigenomics & AI-assisted multi-omics: challenges and perspectives in plant stress epigenetics. Abiotic stresses, such as drought, salinity, heat, and cold constrain plant growth and productivity by influence plant internal regulatory networks. Transcriptional/epigenetic regulation, which encompasses mechanisms such as DNA methylation, histone modifications, chromatin accessibility, non-coding RNAs, and RNA modifications, orchestrates rapid transcriptional reprogramming and stress memory and provides key adaptive capacity for plants to resist stress. Recent sequencing breakthrough system-level mapping of these layers, including ATAC-seq (accessibility), CUT&Tag/ChIP-seq (histone marks), Hi-C (3D genome), WGBS (methylomes), lncRNA/small-RNA profiling (regulatory RNAs), and Nanopore direct RNA sequencing (RNA modification). This review summarizes the application of these methods to capture the landscape of dynamic DNA methylation, chromatin conformation changes, non-coding RNA regulation, and RNA modification under abiotic stress conditions, and addresses current technical challenges in multi-omics research and explores future perspectives.