During barley pollen development, vegetative and generative nuclei initially share identical chromatin modifications. Differential patterns emerge with nuclear differentiation. H3K27me3 enriches in subtelomeric euchromatin and becomes restricted to the vegetative nucleus, indicating a role in gene activation. Cytoplasmic H3K9ac in the generative cell suggests unknown functions.

HMT and HDM originate from Chromista and are highly conserved in green plants. Histone methylation modifications became complex and diverse during plant evolution, aiding adaptation to variable environments. In barley, HMT/HDM families show high conservation but differential variation in the Lasa Goumang SDG subfamily. HvHMTs/HvHDMs exhibit tissue-specific expression and complex patterns under multiple stresses. HMT/HDM amplification facilitates plant environmental adaptation while remaining conserved in barley development and stress responses.

In this study, HMs underwent purifying selection based on Ka/Ks ratios. Gene/genome duplications impacted HM evolution in wheat. TaHM expression changed during grain development under brassinosteroid, brassinazole, or activated charcoal treatments. ZmHMs responded to gibberellin and drought. TaHMs function in grain development, BR-/brassinazole-mediated root growth, activated charcoal-mediated root/leaf growth, and biotic/abiotic adaptations. ZmHMs function in seed development, GA-mediated leaf growth, and drought adaptation.

In this study, the senescence-associated barley gene HvS40 exhibits increased euchromatic H3K9ac at its promoter and coding sequence alongside decreased heterochromatic H3K9me2. A heavily methylated DNA island 664 bp upstream of the translational start site persists in mature and senescent leaves, with decreased DNA methylation at one specific CpG motif in senescing leaves. Senescence-associated redistribution of heterochromatic H3K9me2 patterns occurs in nuclei. These alterations demonstrate a senescence-specific mechanism modifying histone marks at HvS40 and heterochromatin organization.

Microspore embryogenesis involves epigenetic reprogramming, particularly histone H3K9 methylation dynamics. In Brassica napus and Hordeum vulgare, low H3K9 methylation promotes cell reprogramming and embryogenesis initiation. As embryogenesis progresses, H3K9 methylation increases, correlating with BnHKMT SUVR4-like and BnLSD1-like expression. Short-term BIX-01294 treatment enhances reprogramming and reduces H3K9 and DNA methylation, while long-term treatment inhibits embryo differentiation, indicating H3K9 methylation is essential for differentiation. Pharmacological modulation of histone methylation via BIX-01294 may improve microspore embryogenesis efficiency.

Epigenetic modifications during plant development are established by positional information and tissue specificity, determining cell fate and differentiation. The root apical meristem (RAM), generating radial tissue patterns, models the correlation between cell position and epigenetic modification patterns. Levels of histone and DNA modifications vary across RAM tissues. Crucially, histone H4 acetylation in the epidermis is not solely replication-dependent and likely functions in epidermal cell differentiation.

Drought triggers ABA-mediated gene expression reprogramming in barley (Hordeum vulgare cv. Morex). Epigenome analysis identified 129 genes gaining H3K4me3 and 2008 genes gaining H3K9ac under drought, indicating H3K9ac responds more sensitively than H3K4me3. Genes marked with these euchromatic modifications and induced by drought are predominantly involved in ABA signaling and related pathways. This includes two PP2C family members, key regulators of ABA signaling.

Multi-omics analysis of eight hulless barley varieties under abiotic stress identified 231,440 lowly methylated regions (LMRs), predominantly in intergenic regions. Correlation analysis revealed 97,909 enhancer-gene pairs. Transcription factor regulatory network inference for drought stress predicted the NAC transcription factor targets TCP, bHLH, and bZIP transcription factor genes. H3K27me3 modification regions overlapped with LMRs more than H3K4me3 regions. Single nucleotide polymorphism variation was more abundant in LMRs than in other genomic regions. Epigenetic regulation, involving DNA methylation and histone modifications, underpins hulless barley's adaptation to abiotic stress, with transcription factors like NAC playing significant roles.