Delaying decay: Epigenetic repressor extends tomato freshness
image: SlHDA7 represses tomato fruit maturation.
Credit: Horticulture Research
Understanding the molecular basis of fruit ripening is essential for improving shelf life and quality. In this study, researchers uncovered a critical role of the histone deacetylase gene SlHDA7 in regulating tomato fruit ripening. The deletion of SlHDA7 accelerated ripening and reduced shelf life, while its overexpression delayed ripening and prolonged fruit storage. Mechanistically, SlHDA7 suppresses ripening by removing acetyl groups from histone H4 (H4ac), thereby reducing expression of key ripening-related genes. These findings highlight SlHDA7 as a central epigenetic regulator that fine-tunes ripening processes, opening new opportunities for agricultural strategies that target fruit quality and postharvest longevity.
Tomato fruit ripening is a tightly regulated process involving hormonal signaling, metabolic reprogramming, and epigenetic modulation. Ethylene plays a pivotal role in climacteric fruit ripening, but the transcriptional regulation of ethylene-responsive and ripening-associated genes remains incompletely understood. While DNA methylation and histone modifications are known to affect chromatin structure and gene expression, the specific role of histone deacetylases (HDACs) in fruit ripening has been underexplored. Previous studies suggest that other HDACs may repress ripening, but their target genes and mechanisms remain unclear. Due to these knowledge gaps, it is necessary to investigate the epigenetic functions of subclass II HDACs in regulating ripening-related pathways.
A research team from the South China Botanical Garden of the Chinese Academy of Sciences published (DOI: 10.1093/hr/uhae234) a study on August 14, 2024, in Horticulture Research, identifying a novel epigenetic regulator of tomato fruit ripening. The study revealed that the histone deacetylase SlHDA7 delays ripening by modulating gene expression through histone H4 deacetylation. Using CRISPR/Cas9 gene editing, RNA-seq, and ChIP-qPCR, the team demonstrated how SlHDA7 acts as a transcriptional repressor to control fruit maturation and shelf life. Their findings offer a promising molecular tool for enhancing postharvest storage in tomatoes.
The researchers first analyzed the expression of SlHDA7 and observed a ripening-associated pattern, with a peak at the turning stage. Using CRISPR/Cas9, they generated knockout lines (slhda7) and overexpression lines (SlHDA7-OE), finding that slhda7 mutants ripened faster and showed increased ethylene production, carotenoid biosynthesis, and softening. In contrast, SlHDA7-OE lines exhibited delayed ripening and reduced physiological changes. RNA-seq identified over 6,000 differentially expressed genes between wild-type and slhda7 fruits, notably involving ethylene signaling, carotenoid metabolism, and cell wall modification. RT-qPCR and ChIP-qPCR validated that SlHDA7 represses expression of key ripening genes such as ACO1, ERF.E1, ZISO, and transcription factors like RIN and FUL1 by removing H4ac at their promoter regions. Furthermore, fruit shelf life was markedly extended in SlHDA7-OE tomatoes due to reduced water loss and slowed ripening, while slhda7 fruits showed rapid deterioration. Together, these findings position SlHDA7 as a key epigenetic suppressor of fruit maturation.
“This study provides compelling evidence that histone deacetylation is not just a passive chromatin mark but an active regulatory mechanism for fruit development,” said Dr. Guoxiang Jiang, co-corresponding author of the study. “By uncovering the role of SlHDA7 in modulating ethylene synthesis and transcription factor activity, we can now consider novel breeding strategies that exploit epigenetic control to improve postharvest fruit quality.”
The discovery of SlHDA7 as a histone H4ac deacetylase that represses fruit ripening offers a valuable genetic target for breeding tomatoes with extended shelf life and improved transportability. By manipulating SlHDA7 expression, producers could develop cultivars tailored for delayed ripening, reducing postharvest losses and enhancing global food supply chains. Beyond tomatoes, this mechanism may be conserved across other climacteric fruits, offering broader agricultural potential. Future research could explore the interactions between SlHDA7 and additional chromatin regulators or apply CRISPR-based precision editing to fine-tune fruit ripening schedules in commercial crops.
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References
DOI
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.