Aegilops tauschii
Omics
Epigenomics
| Species | Categorization | Article Overview | Tissue | Stress | Growth Stage | Source |
|---|---|---|---|---|---|---|
| Non-coding RNA | The miRNA loci of wheat's D-genome progenitor Aegilops tauschii are overwhelmingly associated with repetitive elements, particularly En/Spm and TcMar DNA transposons. Comparative analysis reveals dynamic reorganization of repeat-associated miRNA stem-loops during wheat domestication, with conserved miRNAs showing divergent repeat-binding patterns between ancestral and cultivated genomes. Crucially, while transcriptionally active pre-miR5523 is conserved in both species, its processing into mature miRNA is disrupted specifically in bread wheat—indicating a species-specific post-transcriptional regulatory alteration likely influenced by repetitive element divergence. | Whole seedlings | Shock dehydration | seedling | Akpinar et al., 2016 | |
Aegilops tauschii | Non-coding RNA | This study comparing miRNA prediction in *Aegilops tauschii* using raw NGS reads versus an assembly constructed from them revealed a clear trade-off: raw reads significantly increased sensitivity, identifying three times more miRNAs (62 vs 22), primarily capturing numerous "repeat-related" miRNAs associated with DNA transposons masked during assembly; however, prediction from the assembly offered greater specificity (55% vs 37% supported by prior evidence) and uniquely identified 6 miRNAs whose stem-loops required longer contiguous sequences. Therefore, raw reads optimize sensitivity especially for repeat-associated miRNAs, while assemblies enhance specificity and enable deeper structural analyses, indicating that the choice of input data should align with the specific goals of miRNA discovery. | Budak et al., 2015 | |||
Aegilops tauschii | Non-coding RNA | This study revealed that transposable elements (TEs) are a major evolutionary driver of microRNA (miRNA) diversity in wheat and its diploid relatives, with 73-85% of identified pre-miRNAs classified as TE-associated (TE-miRs). Comparative analysis demonstrated that polyploidization and domestication significantly shaped the miRNA repertoire, leading to lineage-specific expression patterns and losses (e.g., miR5050 in bread wheat). Critically, TE proliferation, particularly involving DNA transposons (En-Spm, MITE, TcMar), underpins the expansion of key miRNA families regulating development and stress responses. These findings highlight the profound impact of TE-mediated epigenetic mechanisms and genome evolution on miRNA regulatory networks in wheat. | root and shoots | seedling | Alptekin et al., 2017 | |
Aegilops tauschii | Non-coding RNA | In nascent hexaploid wheat, small RNAs orchestrate heterosis via epigenetic reprogramming: nonadditive miRNA expression dynamically regulates growth and stress-response pathways, while elevated siRNA density at D-subgenome transposable elements drives biased homeolog repression through epigenetic silencing—collectively establishing the molecular basis for enhanced vigor and adaptation. | spikes;seeds | seedling | Li et al., 2014 | |
Aegilops tauschii | Non-coding RNA | The massive invasion of transposable elements (TEs), constituting 85.9% of the Aegilops tauschii genome, drives elevated DNA methylation levels (particularly CG and CHG contexts) especially within genic regions; this hypermethylation, pronounced in the introns of nearly half of all genes containing TE insertions, strongly correlates with reduced gene expression compared to TE-free genes. The study also identified characteristic "mCHH islands" flanking genes, suggesting a potential role in insulating gene expression from TE silencing. Furthermore, the exceptionally high pseudogene content in Ae. tauschii, the highest reported in plants, is closely linked to historic bursts of TE activity, with TEs frequently disrupting pseudogene sequences. | Whole seedlings | seedling | Zhao et al., 2017 | |
Hordeum vulgare | DNA methylation | This study integrates DNA methylation and transcriptome data with genomics to predict complex traits in barley. Multi-omics models explained 0.72–0.91 of phenotypic variance, outperforming genomic-only models (0.55–0.86). While drought had little impact on DNA methylation, adding transcriptomic and methylation data improved prediction accuracy for nitrogen uptake and protein content, capturing environmental and non-additive genetic effects. Differentially expressed genes related to abiotic stress (e.g., Myb-like, dehydrin, AP2) mediated treatment effects, and the best models combined all three omics, demonstrating the value of multi-omics for complex trait prediction in barley. | leaf,root | Heat ；NaCl；drought | maturation | Hansen et al., 2022 |
Hordeum vulgare | DNA methylation | Sakai et al., 2022 | ||||
Hordeum vulgare | DNA methylation | This study shows that what was thought to be random DNA methylation in barley is actually affected by greenhouse microclimate variations. Using MSAP and phenotypic analysis on nine barley varieties under 0 and 75 mM NaCl, it found positional effects caused epigenetic differences that increased over development from the 4th leaf to anthesis. Environmental factors like humidity and light correlated with methylation and biomass/yield, and salt stress effects were mixed with microclimate impacts. The study concludes that microenvironmental factors must be considered in epigenetic research to separate real stress responses from positional effects. | leaf | drought | Konate et al., 2020 |
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