Triticeae Genomics and Genetics, 2024, Vol.15, No.5, 255-265 http://cropscipublisher.com/index.php/tgg 256 key findings from recent studies and discuss the future prospects and challenges in this field. The study aims to offer insights into how epigenetic approaches can contribute to the sustainable intensification of wheat production, addressing global food security challenges. 2 Current Status of Wheat Epigenetics Research 2.1 Analysis of wheat epigenome and technological advances The analysis of the wheat epigenome has made significant strides, particularly with the advent of high-throughput sequencing technologies. These advancements have enabled researchers to overcome the challenges posed by the large and complex allohexaploid genome of wheat. Recent studies have provided comprehensive epigenomic maps that reveal the intricate regulatory networks governing wheat development and stress responses. For instance, a detailed comparison of epigenomes and transcriptomes across various developmental stages and environmental conditions has identified thousands of distal epigenetic regulatory elements (distal-epiREs) linked to their target promoters. This study highlighted the role of subgenome-divergent activity of homologous regulatory elements, influenced by specific epigenetic signatures such as H3K27me3, mediated by the Polycomb complex and demethylases (Wang et al., 2021). Technological advances have also facilitated the integration of epigenomic information into crop improvement strategies (Huang, 2024). The use of chromatin profiles to enhance the understanding of complex crop genomes has been a focal point. This approach, termed 'epigenome guided' improvement, leverages chromatin information to better annotate and decode plant genomes. It also aims to identify and select heritable epialleles that control crop traits independently of the underlying genotype. The integration of epigenomic data with CRISPR/Cas9 gene editing and precision genome engineering holds promise for future crop improvement endeavors (Zhang et al., 2022). 2.2 Epigenetic regulatory elements in the wheat genome Epigenetic regulatory elements play a crucial role in the regulation of gene expression in wheat. These elements, including DNA methylation, histone modifications, and non-coding RNAs, contribute to the dynamic regulation of the wheat genome. A comprehensive review of epigenetic mechanisms has highlighted the importance of these modifications in plant responses to biotic and abiotic stresses. DNA methylation, histone post-translational modifications, and RNA-directed DNA methylation create memory marks that help plants survive various stresses through physiological regulation based on their epigenetic history (Samantara et al., 2021). The coordinated regulation of early meiotic stages in wheat is dominated by non-coding RNAs and stage-specific transcription. A study focusing on the meiotic transcriptome revealed significant enrichment of non-coding RNAs during prophase I, which controlled the reprogramming of central metabolic pathways. This study identified 9,309 meiosis-specific transcripts and many known and novel non-coding RNAs differentially expressed at specific stages, providing new insights into the regulatory controls of meiosis in wheat (Jiang et al., 2023). 2.3 Application of epigenetic tools and techniques The application of epigenetic tools and techniques in wheat research has opened new avenues for crop improvement. Epigenetic modifications, such as DNA methylation and histone modifications, have been shown to play a role in developmental gene regulation, response to environmental stimuli, and natural variation of gene expression levels. These modifications can be harnessed to select for favorable epigenetic states, create novel epialleles, and regulate transgene expression, thereby contributing to crop improvement strategies (Springer, 2013). Recent research has focused on exploiting both induced and natural epigenetic variation for crop improvement. Understanding the sources of epigenetic variation and the stability of newly formed epigenetic variants over generations is crucial for fully utilizing the potential of epigenetic variation. The development and application of methods for widespread epigenome profiling and engineering are expected to generate new avenues for using the full potential of epigenetics in crop improvement. This includes the use of epigenetic diversity to predict plant performance and increase final crop production, particularly in response to climate change (Springer and Schmitz, 2017; Kakoulidou et al., 2021).
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