Molecular Plant Breeding 2025, Vol.16, No.5, 261-267 http://genbreedpublisher.com/index.php/mpb 265 Figure 2 Schematic of the CRISPR/dCas9 regulatory target gene (Adopted from Cai et al., 2023) Image caption: The expression vector expresses the dCas9 fusion protein in cells, which binds the transcribed sgRNA to form the CRISPR/dCas9 regulatory tool, resulting in the recruitment of the effector domain to the promoter or enhancer region of the target gene under the guidance of sgRNA. Effector domains act on promoters or enhancers of target genes to modify these regions, regulating target gene expression (Adopted from Cai et al., 2023) 6.3 Potential for integrating epigenomic data into tomato improvement programs With the development of high-throughput epigenomic sequencing technology, integrating multi-faceted epigenetic data such as DNA methylation, histone modification and non-coding RNA can more comprehensively analyze the regulatory network of lycopene accumulation (Moradpour and Abdulah, 2019). Combining epigenomic information with traditional genotype and phenotypic data can establish more accurate trait prediction models to assist in tomato variety improvement decisions (Karlson et al., 2021; Tiwari et al., 2023). In the future, the integration of epigenomic data is expected to promote molecular design breeding of lycopene high accumulation varieties and achieve targeted improvement of nutritional quality (Moradpour and Abdulah, 2019; Karlson et al., 2021). 7 Research Gaps and Future Perspectives 7.1 Limitations in current epigenomic studies on tomato carotenoids At present, there are still many deficiencies in the research on the epigenetic regulation of tomato carotenoids, especially lycopene. Although mechanisms such as DNA methylation, histone modification and non-coding RNA have been demonstrated to be related to fruit ripening and metabolic pathways, a complete regulatory network targeting key genes for lycopene synthesis has not been established, and systematic identification of related regulatory factors is also insufficient (Ming et al., 2023). Many studies only focus on a single epigenetic level and fail to delve into the interactions among different epigenetic modifications and their comprehensive regulatory effects on the entire carotenoid metabolic pathway. The mechanism by which environmental stress affects the epigenetic status and lycopene accumulation of tomatoes has not been systematically studied yet (Nazari et al., 2025).
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