Tree Genetics and Molecular Breeding 2025, Vol.15, No.3, 128-137 http://genbreedpublisher.com/index.php/tgmb 132 6.2 Expression changes in oil-related genes mediated by epigenetic variation In addition to DNA methylation, histone modification can also affect lipid synthesis. Epigenetic modifications can control the synthesis and accumulation of fats by regulating the expression of important transcription factors and metabolic enzymes. For instance, histone H3 lysine 4 trimethylation (H3K4me3) is associated with some regulatory factors of fatty acid synthesis, including WRINKLED1, ABI3 and FUS3, which regulate glycolysis and fatty acid synthesis pathways and thereby affect lipid accumulation (Moreno-Pérez et al., 2021). In addition, fatty acids themselves can in turn regulate the epigenetic state of genes, thus forming the mutual influence between metabolism and epigenetics (Chung and Kim, 2024; Ediriweera and Sandamalika, 2024). 6.3 Integration of methylome, transcriptome, and lipidome data To gain a comprehensive understanding of the relationship between epigenetics and lipid traits, a combined multi-omics analysis is highly effective. Combining the data of the methylome, transcriptome and lipidome can more systematically identify the key methylation regions, differentially expressed genes and metabolites related to lipid accumulation (Moreno-Pérez et al., 2021; Wang and Yamaguchi, 2024). For instance, through the joint analysis of the methylome and transcriptome, the relationship between the methylation status of certain fatty acid synthesis genes and their expression levels can be directly observed. Lipidome data, on the other hand, can reveal the final accumulation of lipids. This integrated analysis method provides a new idea for studying the molecular mechanism of oil differences in Camellia oleifera under different altitude conditions. 7 Techniques for Studying Epigenetics in Woody Oil Crops 7.1 Bisulfite sequencing and whole-genome methylome profiling Bisulfite sequencing (BS-seq for short) is currently one of the most commonly used and highest-resolution methods for studying DNA methylation. After treatment with bisulfite, the unmethylated cytosine will transform into uracil, while the methylated cytosine will remain unchanged. This method can help us detect the changes at every methylation site across the entire genome. Using it to analyze the methylation patterns of oil woody plants in different environments (such as high altitude and low altitude) can provide valuable data to study the relationship between epigenetic regulation and oil accumulation (Mladenov et al., 2021; Agius et al., 2023; Singh et al., 2023). In addition to BS-seq, there are also methods such as MSAP (methylation-sensitive amplification polymorphism) that can be used to detect methylation differences between different populations or families (Albaladejo et al., 2019). 7.2 ATAC-seq, ChIP-seq and their limitations in tree species ATAC-seq and ChIP-seq are two other commonly used high-throughput technologies. ATAC-seq can quickly determine where the chromatin is open. ChIP-seq can be used to locate specific histone modification regions or identify the positions where transcription factors bind to DNA. These techniques are widely used in model plants and some crops. However, in woody oil crops, experiments and data analysis have become more difficult because samples are not easy to obtain, and there are many cell types and complex tissues (Chachar et al., 2022; Xue et al., 2025). Furthermore, the cell walls of woody plants are very thick, making it difficult to extract cell nuclei and perform chromatin immunoprecipitation, which also affects the promotion of these techniques. 7.3 Emerging single-cell and third-generation epigenomic tools In recent years, single-cell omics (such as single-cell transcriptomics and single-cell epigenomics) and third-generation sequencing technologies (such as nanopore sequencing and single-molecule real-time sequencing) have begun to be used in the epigenetic research of woody plants. Single-cell technology can clearly observe the differences among different cells in the same tissue and is helpful for understanding how complex traits such as lipid accumulation are regulated at the cellular level (Figure 2) (Liang et al., 2023; Xue et al., 2025). The third-generation sequencing technology can directly read the methylation information of long DNA fragments, making up for the drawback that the second-generation sequencing can only view short fragments. This provides a new tool for studying the epigenetic mechanisms in the complex genomes of woody plants (Yang et al., 2022). Although these technologies are not yet mature, their application prospects in woody oil crops like Camellia oleifera are worth looking forward to.
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