Tomato ripening is a complex physiological process governed by genetic networks and epigenetic modifications. Ethylene, a key plant hormone, orchestrates ripening by activating gene expression cascades. Recent research emphasizes the importance of epigenetic regulators such as DNA methylation and histone modifications in fine-tuning this process. Histone deacetylases (HDACs), which remove acetyl groups from histones to silence gene expression, have been linked to developmental control in various plant organs, but their specific roles in tomato fruit maturation remain unclear. Based on these challenges, there is a growing need to explore how HDACs, particularly SlHDA7, contribute to the regulation of ripening-associated genes through histone modification.
A research team from the South China Botanical Garden and Guangdong AIB Polytechnic published a study (DOI: 10.1093/hr/uhae234) on August 14, 2024, in Horticulture Research, revealing the regulatory function of histone deacetylase SlHDA7 in tomato fruit ripening. The study demonstrates that SlHDA7 acts by reducing acetylation at specific gene promoters, thereby repressing ripening-related genes. Using CRISPR/Cas9-mediated gene editing and overexpression strategies, the researchers systematically investigated how SlHDA7 modulates ethylene biosynthesis, carotenoid accumulation, and cell wall metabolism.
SlHDA7, a member of the RPD3/HDA1 histone deacetylase family, was found to exhibit increased expression during early tomato fruit ripening. Functional experiments showed that SlHDA7 knockout mutants ripened earlier and exhibited increased ethylene production and carotenoid accumulation, while overexpression delayed ripening and preserved firmness during storage. Transcriptomic analyses revealed over 6,400 differentially expressed genes between wild-type and slhda7 fruits, including key players in ethylene synthesis (ACO1, ACS2), carotenoid biosynthesis (GGPPS2, ZISO), and transcriptional regulation (RIN, FUL1). ChIP-qPCR assays confirmed that SlHDA7 selectively deacetylates histone H4ac at the promoters of these genes, thus reducing their expression. This epigenetic suppression curtails ripening-related changes in fruit physiology, such as pigment accumulation and cell wall softening. Additionally, storage tests showed that SlHDA7-overexpressing tomatoes maintained weight and texture significantly longer than controls, while knockout fruits exhibited accelerated shriveling. These results suggest that SlHDA7 plays a central role in chromatin-based regulation of ripening and has potential as a target for breeding longer-lasting fruits.
“SlHDA7 represents a compelling example of how plants use epigenetic machinery to fine-tune developmental processes like fruit ripening,” said Dr. Guoxiang Jiang, corresponding author of the study. “By manipulating histone acetylation, we can directly impact the expression of genes involved in ethylene production and pigment accumulation. This not only deepens our understanding of fruit biology but also provides valuable insights for developing crop varieties with improved postharvest qualities.”
The discovery of SlHDA7 as a negative regulator of tomato fruit ripening has significant implications for agricultural biotechnology and postharvest management. By targeting SlHDA7 through gene editing or expression modulation, breeders could potentially delay ripening, extend shelf life, and reduce postharvest losses—benefits that are particularly critical for fresh produce supply chains. Moreover, understanding the role of histone acetylation in regulating ripening-associated gene networks opens the door to broader applications in other climacteric fruits like bananas and apples. This study offers a promising direction for enhancing fruit quality through epigenetic engineering.
###
References
DOI
10.1093/hr/uhae234
Original Source URL
https://doi.org/10.1093/hr/uhae234
Funding information
This work was funded by the National Natural Science Foundation of China (Nos. 32272782, 32302625, and 32101567), Guangdong Basic and Applied Basic Research Foundation (Nos. 2023A1515010369 and 2022A1515010518), South China Botanical Garden, Chinese Academy of Sciences (Granted No: QNXM-202306), and Innovative Team Project of Guangdong Universities (Nos. 2022KCXTD051), Guangdong Science and Technology Plan Project (Grant No: 2023B1212060046).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.