This study shows that barley tissue culture increases global DNA methylation in regenerants and their progeny, with transposable element (TE) activity higher in regenerants than progeny, suggesting sexual reproduction stabilizes TEs despite persistent methylation changes.

This protocol establishes whole-genome bisulfite sequencing (WGBS) as the optimal method for single-base resolution mapping of DNA methylation across plant genomes, enabling comprehensive analysis of context-specific methylation (CG/CHG/CHH). Validated in maize and barley, WGBS reveals genome-wide epigenetic patterns, identifies natural variation, and uncovers regulatory pathways. Coupling with sequence capture technology further allows targeted methylation profiling, advancing studies on gene regulation, transposon silencing, and environmental responses.

The study shows chromosomal rearrangements in barley alter DNA methylation patterns, affecting both rearranged and non-rearranged chromosomes, with homologues sometimes differing. Some regions like NORs are relatively constant, but translocation in T-30 induces satellite hypermethylation. Methylation correlates with heterochromatin and inversely with gene density, indicating it drives genome reorganization post-rearrangement, vital for chromatin assembly via maintaining 5-mCyt-rich heterochromatic regions.

MSAP-Seq enables cost-effective, high-throughput detection of tissue-specific DNA methylation changes at CCGG sites in barley under drought stress, revealing differential methylation patterns in roots versus leaves while efficiently targeting genic regions in large genomes.

he study shows that barley microspore reprogramming to embryogenesis via cold stress induces initial global DNA hypomethylation, contrasting with hypermethylation in generative/sperm nuclei during pollen maturation. Methylation levels are low in vacuolated microspores, rise during pollen development, drop in reprogrammed microspores/early embryos, then increase again in later embryogenesis, paralleling zygotic embryogenesis. This dynamic suggests DNA methylation regulates developmental switching, with hypomethylation aiding totipotency and subsequent hypermethylation supporting embryo differentiation.

Barley possesses an epigenetic surveillance system that discriminates against foreign DNA based on methylation patterns: CG methylation stabilizes introduced DNA, while bacterial-like N6-methyladenine triggers rapid elimination. This mechanism explains historical instability of transgenic DNA in cereals.

This review highlights epigenetic regulation of leaf senescence, including DNA methylation, histone modifications, and chromatin remodeling, which dynamically modulate gene expression. Barley dark-induced senescence shows distinct epigenetic patterns versus developmental senescence, implying an epigenetic switch for cell survival/death. Chromatin remodeling controls senescence progression, and leveraging epigenetic variation via "epibreeding" could enhance crop traits for sustainable agriculture.