Hordeum vulgare

The study shows DNA methylation dynamically decreases during barley callus induction, with promoter methylation of regeneration genes like HvKRP4 and HvWOX5 negatively correlating with their expression. 5-Aza-dC treatment inhibits callus formation by affecting cell cycle and ABA pathways, indicating DNA methylation regulates transcription for callus development and regeneration.

Hordeum vulgare

The study finds that androgenesis-induced barley regenerants show increased global DNA methylation and sequence variation (SV) linked to transposable elements (TEs). Different TE families contribute variably to SV, with CACTA and TRIM elements showing higher activity and LARD/Ty1-copia lower. DNA methylation changes (demethylation and de novo methylation) in CG, CHG, and CHH contexts partially explain SV, but TE surrounding sequences and other factors also influence variation, highlighting epigenetic dynamics in TE activation during in vitro regeneration.

Hordeum vulgare

Barley exhibits high and generally stable genome-wide DNA methylation under water deficiency. However, stress induces numerous differentially methylated sites (DMSs) in leaves and roots. Within genes, leaves show equal proportions of novel methylation and demethylation events, while novel methylation dominates in roots. Repetitive elements preferentially undergo demethylation in leaves and novel methylation in roots. Rewatering reverses most stress-induced methylation events, but this reversibility is more efficient in leaves than roots. DMSs within genic regions are enriched for distinct biological processes in leaves versus roots. This organ specificity of methylome changes suggests an important regulatory mechanism for multi-level stress tolerance in barley.

Hordeum vulgare

Barley plants under Fe deficiency showed reduced growth, decreased root-to-shoot Fe translocation, and increased phytosiderophores release. DNA methylation analysis revealed significant differences in fully/hemy-methylated sequences versus Fe-sufficient plants. Eleven differentially methylated DNA bands were identified in Fe-starved plants. Five sequences aligned to barley genes encoding: glucosyltransferase, putative acyl carrier protein, peroxidase, β-glucosidase, and a Homeodomain-containing transcription factor. Fe resupply at 13 DAS failed to restore plant recovery: Fe absorption and translocation capacities remained impaired. Resupplied plants maintained DNA methylation/demethylation patterns similar to Fe-deprived barley. This suggests potential heritability of these epigenetic modifications.

Hordeum vulgare

Mature barley (cv. Zafer-160) embryos cultured on callus induction medium (MS + 4 mg l⁻¹ Dicamba) for 30 days produced embryogenic calli, transferred to regeneration medium (MS + 0.5 mg l⁻¹ trans-zeatin riboside). Retrotransposon movements and methylation alterations in 15-day-old calli, 30-day-old calli, and 4-day-old seedlings (control) were analyzed using IRAP and MSRF. IRAP patterns were monomorphic. MSRF indicated increased cytosine methylation during callus formation. Changes in retroelement movements and methylation alterations were assessed against literature.

Hordeum vulgare

Barley microspore embryogenesis utilized nine induction media variants differing in CuSO₄ (0.1, 5, 10 µM), AgNO₃ (0, 10, 60 µM), and anther incubation time (21, 28, 35 days). Green plant regeneration efficiency (GPRE), DNA demethylation (DM), and de novo methylation (DNM) were assessed using DArTseqMet. Biochemical levels (GSH, SAM, β-glucan) were estimated via ATR-FTIR spectroscopy. In vitro conditions significantly affected biochemical levels, DNA methylation changes (DM, DNM), and GPRE. Increasing Cu(II) concentration in the induction media (IM) impacted metabolism and DNA methylation, elevating GPRE. Samples formed groups linked to factors contributing to two main components explaining 55.05% of variance: DNM and DM (first component); GSH, β-glucan, Cu(II), and GPRE (second component). The experiment involved spring barley regenerants obtained through anther culture. Nine variants (trials) of induction media were created by adding copper (CuSO4: 0.1; 5; 10 µM) and silver salts (AgNO3: 0; 10; 60 µM), with varying incubation times for the anthers (21, 28, and 35 days). Changes in DNA methylation were estimated using the DArTseqMet molecular marker method, which also detects cytosine methylation. Phenotype variability in β-glucans, SAM and GSH induced by the nutrient treatments was assessed using tentative assignments based on the Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy. The effectiveness of green plant regeneration ranged from 0.1 to 2.91 plants per 100 plated anthers. The level of demethylation ranged from 7.61 to 32.29, while de novo methylation reached values ranging from 6.83 to 32.27. The paper demonstrates that the samples from specific in vitro conditions (trials) formed tight groups linked to the factors contributing to the two main components responsible for 55.05% of the variance (to the first component DNM, DM, to the second component GSH, β-glucans, Cu(II), GPRE).

Hordeum vulgare

The barley senescence-associated gene HvS40 shows altered histone modifications during leaf senescence: euchromatic H3K9ac increases near its promoter and coding sequence, while heterochromatic H3K9me2 decreases. Bisulfite sequencing revealed no DNA methylation in this region, but a heavily methylated DNA island upstream of the translational start site in both mature and senescent leaves. DNA methylation decreased at one specific CpG motif in senescing leaves. Immunocytology showed senescence-associated changes in spatial distribution of heterochromatic H3K9me2 patterns in nuclei. These results demonstrate a senescence-specific mechanism altering histone modifications at HvS40 and heterochromatin distribution.

Hordeum vulgare

The authors developed Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq), replacing conventional MSAP's gel-based separation with Next Generation Sequencing (NGS) and automated analysis. The authors validated MSAP-Seq in Hordeum vulgare, enabling global sequence-based identification of DNA methylation changes. The authors confirmed this technique allows parallel analysis across hundreds of thousands of genomic sites, provides direct genomic localization and quantitative evaluation, and specifically targets gene-containing regions (covering three-quarters of all genes in large genomes per analysis). The authors demonstrated MSAP-Seq's simplicity, cost-effectiveness, and high-multiplexing capability make it affordable for DNA methylation analysis in crops with large, complex genomes.