Molecular Plant Breeding 2025, Vol.16, No.5, 261-267 http://genbreedpublisher.com/index.php/mpb 266 7.2 Multi-omics approaches for integrative understanding Multi-omics integration is an important future direction for solving these problems. The combination of data from genomics, epigenomics, transcriptomics, metabolomics, etc. can be used to analyze the dynamic relationship among epigenetic modifications, gene expression and metabolite accumulation. The histone variant Sl_H2A.Z has been proven to regulate the expression of genes related to carotenoid synthesis (Ming et al., 2023), but its synergistic effects with mechanisms such as DNA methylation and non-coding RNA still require multi-omics data for explanation. The influence of epigenetic changes caused by environmental factors on lycopene accumulation can be tracked and analyzed by multi-omics methods (Nazari et al., 2025). 7.3 Prospects for precision agriculture and metabolic engineering With the continuous revelation of epigenetic regulatory mechanisms, precision agriculture and metabolic engineering will have great potential in the targeted regulation of lycopene. By regulating key epigenetic factors, it is possible to achieve precise control of the lycopene synthesis pathway and improve the nutritional quality of fruits (Ming et al., 2023). Molecular breeding and gene editing technologies based on epigenetic markers will also provide new theoretical foundations and technical support for the breeding of varieties with high lycopene content. In the future, it is necessary to study the plasticity of epigenetic regulation under environmental stress to improve the stress adaptability and fruit quality of tomatoes (Nazari et al., 2025). Acknowledgments The authors thank Professor Gai for his meticulous guidance and valuable modification suggestions during the process of writing the manuscript of this study. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Alba R., Cordonnier-Pratt M., and Pratt L., 2000, Fruit-localized phytochromes regulate lycopene accumulation independently of ethylene production in tomato, Plant Physiology, 123(1): 363-370. https://doi.org/10.1104/PP.123.1.363 Apel W., and Bock R., 2009, Enhancement of carotenoid biosynthesis in transplastomic tomatoes by induced lycopene-to-provitamin a conversion, Plant Physiology, 151: 59-66. https://doi.org/10.1104/pp.109.140533 Cai R., Lv R., Shi X., Yang G., and Jin J., 2023, CRISPR/dCas9 tools: epigenetic mechanism and application in gene transcriptional regulation, International Journal of Molecular Sciences, 24(19): 14865. https://doi.org/10.3390/ijms241914865 Chandrasekaran M., Boopathi T., and Paramasivan M., 2021, A status-quo review on CRISPR-Cas9 gene editing applications in tomato, International Journal of Biological Macromolecules, 190: 120-129. https://doi.org/10.1016/j.ijbiomac.2021.08.169 Chen L., Meng J., He X., Zhang M., and Luan Y., 2018, Solanum lycopersicum microRNA1916 targets multiple target genes and negatively regulates the immune response in tomato, Plant, Cell and Environment, 42(4): 1393-1407. https://doi.org/10.1111/pce.13468 He X., Liu K., Wu Y., Xu W., Wang R., Pirrello J., Bouzayen M., Wu M., and Liu M., 2024, A transcriptional cascade mediated by two APETALA2 family members orchestrates carotenoid biosynthesis in tomato, Journal of Integrative Plant Biology, 66(6): 1227-1241. https://doi.org/10.1111/jipb.13650 Jogam P., Sandhya D., Alok A., Peddaboina V., Allini V., and Zhang B., 2022, A review on CRISPR/Cas-based epigenetic regulation in plants, International Journal of Biological Macromolecules, 219: 1261-1271. https://doi.org/10.1016/j.ijbiomac.2022.08.182 Karlson C., Mohd-Noor S., Nolte N., and Tan B., 2021, CRISPR/dCas9-based systems: mechanisms and applications in plant sciences, Plants, 10(10): 2055. https://doi.org/10.3390/plants10102055 Leiva-Ampuero A., Agurto M., Matus J., Hoppe G., Huidobro C., Inostroza-Blancheteau C., Reyes-Díaz M., Stange C., Canessa P., and Vega A., 2020, Salinity impairs photosynthetic capacity and enhances carotenoid-related gene expression and biosynthesis in tomato (Solanum lycopersicumL. cv. Micro-Tom), PeerJ, 8: e9742. https://doi.org/10.7717/peerj.9742 Liu L., Wei J., Zhang M., Zhang L., Li C., and Wang Q., 2012, Ethylene independent induction of lycopene biosynthesis in tomato fruits by jasmonates, Journal of Experimental Botany, 63: 5751-5761.
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