Epigenetic regulation in tomato fruit ripening

Multi-omics analysis of non-pungent (Capsicum annuum) and fiery hot ghost chili (C. chinense) provides insights into proteins involved in fruit development and metabolites biosynthesis

Global omics offer extensive insights into the diversity of essential biomolecules across various plant developmental stages. Despite advancements in high-throughput technologies, the integrated analysis of global omics such as proteomics, transcriptomics, and metabolomics, is yet to be fully explored in fruits of Capsicum species. In this study, we used an integrated omics approach to identify proteins involved in fruit development, and metabolite biosynthesis in the placenta and pericarp tissues of two contrasting genotypes belonging to ghost chili (Capsicum chinense) and C. annuum. The mass spectrometry analysis identified a total of 4,473 and 2,012 proteins from the pericarp and placenta tissues of Capsicum fruits. We observed expression of developmental stage-specific proteins, such as kinases, transferases, ion transporters, F-box proteins, and transcription factors that were enriched in the biosynthesis of primary and secondary metabolites. The abundance of these proteins corresponded with RNAseq data. Key proteins related to capsaicinoids biosynthesis, such as Acyltransferase 3, 3-oxoacyl-[acyl-carrier protein], 4-coumaroyl co-A ligase, and 3-ketoacyl-coA synthase 3, were identified in placenta of highly pungent ghost chili, along with J-domain proteins and transcription factors such as MYB101, MYB 14-like, bHLH112, NAC, and Cyt p450 CYP82D47, suggesting their role in capsaicinoids and secondary metabolites biosynthesis. Further, we observed a correlation of the expression of genes and proteins with the abundance of primary and secondary metabolites, such as carbohydrates, alcohols, fatty acids, phenolics, glycerides, polyamines, and amino acids. Our findings provide a novel multiomics resources for future functional studies, with potential applications in breeding programs.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-025-01581-7.

Effect of histone modifications on fruit ripening

Histone modifications are canonical epigenetic modifications mediating plant growth and development. Specially, histone modifications play important regulatory roles in plant fruit ripening, directly affecting fruit color changes, soluble sugar accumulation, and fruit softening. In this review, we focus on the effects of histone acetylation and methylation during fruit ripening. In particular, histone acetylation at H3 and H4 accelerates fruit ripening, whereas removal of histone acetylation via histone deacetylases (HDACs) inhibits or delays ripening by regulating the expression of carotenoid and anthocyanin production, glycometabolism, cell wall degradation, ethylene synthesis and signalling, and cell expansin-related genes. In addition, histone methylation is also involved in fruit ripening, in which the emergence of H3K27me3 modifications represses fruit ripening and H3K4me3 modifications promote fruit ripening by affecting multiple ripening-related pathways. However, the relationship between other histone modifications and fruit ripening is currently unclear. Here, we point out that accurate and comprehensive studies concerning the regulatory mechanism of histone modifications in fruit ripening are needed to facilitate the design of high-quality and high-yield fruit.

Recent Insights into the Physio-Biochemical and Molecular Mechanisms of Low Temperature Stress in Tomato

Climate change has emerged as a crucial global issue that significantly threatens the survival of plants. In particular, low temperature (LT) is one of the critical environmental factors that influence plant morphological, physiological, and biochemical changes during both the vegetative and reproductive growth stages. LT, including abrupt drops in temperature, as well as winter conditions, can cause detrimental effects on the growth and development of tomato plants, ranging from sowing, transplanting, truss appearance, flowering, fertilization, flowering, fruit ripening, and yields. Therefore, it is imperative to understand the comprehensive mechanisms underlying the adaptation and acclimation of tomato plants to LT, from the morphological changes to the molecular levels. In this review, we discuss the previous and current knowledge of morphological, physiological, and biochemical changes, which contain vegetative and reproductive parameters involving the leaf length (LL), plant height (PH) stem diameter (SD), fruit set (FS), fruit ripening (FS), and fruit yield (FY), as well as photosynthetic parameters, cell membrane stability, osmolytes, and ROS homeostasis via antioxidants scavenging systems during LT stress in tomato plants. Moreover, we highlight recent advances in the understanding of molecular mechanisms, including LT perception, signaling transduction, gene regulation, and fruit ripening and epigenetic regulation. The comprehensive understanding of LT response provides a solid basis to develop the LT-resistant varieties for sustainable tomato production under the ever-changing temperature fluctuations.

Virus-Induced galactinol-sucrose galactosyltransferase 2 Silencing Delays Tomato Fruit Ripening

Tomato fruit ripening is an elaborate genetic trait correlating with significant changes at physiological and biochemical levels. Sugar metabolism plays an important role in this highly orchestrated process and ultimately determines the quality and nutritional value of fruit. However, the mode of molecular regulation is not well understood. Galactinoal-sucrose galactosyltransferase (GSGT), a key enzyme in the biosynthesis of raffinose family oligosaccharides (RFOs), can transfer the galactose unit from 1-α-D-galactosyl-myo-inositol to sucrose and yield raffinose, or catalyze the reverse reaction. In the present study, the expression of SlGSGT2 was decreased by Potato Virus X (PVX)-mediated gene silencing, which led to an unripe phenotype in tomato fruit. The physiological and biochemical changes induced by SlGSGT2 silencing suggested that the process of fruit ripening was delayed as well. SlGSGT2 silencing also led to significant changes in gene expression levels associated with ethylene production, pigment accumulation, and ripening-associated transcription factors (TFs). In addition, the interaction between SlGSGT2 and SlSPL-CNR indicated a possible regulatory mechanism via ripening-related TFs. These findings would contribute to illustrating the biological functions of GSGT2 in tomato fruit ripening and quality forming.

Recent Advances in Studying the Regulation of Fruit Ripening in Tomato Using Genetic Engineering Approaches

Tomato (Solanum lycopersicum L.) is one of the most commercially essential vegetable crops cultivated worldwide. In addition to the nutritional value, tomato is an excellent model for studying climacteric fruits' ripening processes. Despite this, the available natural pool of genes that allows expanding phenotypic diversity is limited, and the difficulties of crossing using classical selection methods when stacking traits increase proportionally with each additional feature. Modern methods of the genetic engineering of tomatoes have extensive potential applications, such as enhancing the expression of existing gene(s), integrating artificial and heterologous gene(s), pointing changes in target gene sequences while keeping allelic combinations characteristic of successful commercial varieties, and many others. However, it is necessary to understand the fundamental principles of the gene molecular regulation involved in tomato fruit ripening for its successful use in creating new varieties. Although the candidate genes mediate ripening have been identified, a complete picture of their relationship has yet to be formed. This review summarizes the latest (2017-2023) achievements related to studying the ripening processes of tomato fruits. This work attempts to systematize the results of various research articles and display the interaction pattern of genes regulating the process of tomato fruit ripening.