Molecular Plant Breeding 2025, Vol.16, No.5, 261-267 http://genbreedpublisher.com/index.php/mpb 261 Research Insight Open Access Epigenetic Mechanisms Regulating Lycopene Accumulation in Solanum lycopersicum Jiong Fu , Zhongmei Hong Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China Corresponding email: jiong.fu@hibio.org Molecular Plant Breeding, 2025, Vol.16, No.5 doi: 10.5376/mpb.2025.16.0026 Received: 01 Aug., 2025 Accepted: 06 Sep., 2025 Published: 14 Sep., 2025 Copyright © 2025 Fu and Hong, This is an open access article published under the terms of the creative commons attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Fu J., and Hong Z.M., 2025, Epigenetic mechanisms regulating lycopene accumulation in Solanum lycopersicum, Molecular Plant Breeding, 16(5): 261-267 (doi: 10.5376/mpb.2025.16.0026) Abstract This study summarizes the role of epigenetic mechanisms in regulating lycopene accumulation in tomatoes, with a focus on DNA methylation, histone modification, and non-coding RNA, etc. It introduces the latest progress in their regulation of fruit development, ripening, and metabolism, and discusses the interactions between these epigenetic modifications and environmental factors as well as hormone signals. The potential mechanisms of their role in metabolic pathway regulation and fruit quality improvement were explained. By integrating new technologies such as high-throughput sequencing, multi-omics integration, and CRISPR/dCas9, the application prospects of epigenetic information in tomato molecular breeding, metabolic engineering, and precision agriculture were evaluated. This study aims to provide a theoretical basis and molecular strategies for increasing lycopene content and the nutritional quality of fruits. Keywords Tomato (Solanum lycopersicum); Lycopene; Epigenetic regulation; DNA methylation; Histone modifications 1 Introduction Lycopene is one of the most common carotenoids in the fruit of tomatoes (Solanum lycopersicum). It not only gives the fruit a bright red color, but also is regarded as very important for human health due to its strong antioxidant activity. As the main source of lycopene in human diet, it is closely related to health benefits such as reducing the risk of cardiovascular diseases and some cancers. The accumulation of lycopene is also a key process for fruit ripening and quality formation, which is regulated by many endogenous and exogenous factors (Luo et al., 2013; McQuinn et al., 2017; Ming et al., 2023). Epigenetics regulates gene expression through heritable means without altering the DNA sequence, including DNA methylation, histone modification, regulation of non-coding RNA, etc. (Wu and Li, 2024). Recent studies have found that these mechanisms play an important role in the development and ripening of tomato fruits. DNA methylation and histone deacetylation can affect the expression of genes related to carotenoid synthesis and regulate the accumulation of lycopene. The research by He et al. (2024) and Nazari et al. (2025) indicates that non-coding RNAs are involved in the regulatory network of fruit ripening and pigment accumulation. This study summarizes the epigenetic mechanisms regulating lycopene accumulation, introduces the roles of DNA methylation, histone modification, etc. in fruit development and ripening, and reveals how these mechanisms jointly regulate the expression of carotenoid synthesis genes by combining the latest molecular biology and epigenetic research. This study aims to provide a theoretical basis and new methods for precisely regulating lycopene content and improving fruit quality. 2 Lycopene Biosynthesis inSolanum lycopersicum 2.1 Carotenoid biosynthetic pathway: key enzymes and regulation points Lycopene belongs to the carotenoid family. Its synthetic pathway starts with isoprenyl pyrophosphate (IPP) and is completed through the action of a series of enzymes. The key enzymes include PSY1, PDS, ZDS, ZISO and CRTISO. PSY1 is a rate-limiting enzyme that controls the flow of the entire pathway. CRTISO converts the precursor prolycopene into lycopene. If this enzyme is lacking, prolycopene will accumulate and the fruit will turn orange instead of red (Zhang et al., 2018; Prashanth et al., 2023).
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