Unlocking grape ripening: How CHH hypermethylation accelerates ‘Fengzao’ berries

Fruit ripening is a tightly regulated process influenced by genetic and epigenetic factors. In grapes, the timing of ripening has major implications for quality, flavor, and commercial value. Researchers have uncovered that CHH-type DNA hypermethylation in promoter regions is a key factor accelerating berry development in the early-ripening grape bud mutant ‘Fengzao’. Through a genome-wide methylation and transcriptome analysis, they identified 38 candidate genes linked to berry development, with the jasmonate-induced oxygenase gene (JOX1) emerging as a negative regulator of ripening. Hypermethylation of JOX1 appears to suppress its expression, thereby promoting early fruit maturation. These insights expand understanding of epigenetic control in non-climacteric fruit crops.

DNA methylation is a conserved epigenetic mechanism that regulates gene expression, genome stability, and developmental processes across plants. Studies in tomato, strawberry, and sweet orange have revealed contrasting methylation dynamics in fruit ripening, highlighting its species-specific complexity. Grapes, as globally important non-climacteric fruits, show unusually high levels of DNA methylation compared with other crops. While hormones and reactive oxygen species have been implicated in grape ripening, the direct role of methylation in early versus standard ripening varieties remained unclear. Fengzao, a natural bud mutant of ‘Kyoho’ grapes, ripens about 30 days earlier, providing an ideal model to explore epigenetic drivers. Based on these challenges, there is a pressing need to investigate DNA methylation during grape berry development.

A research team from Henan University of Science and Technology has revealed how promoter hypermethylation shapes grape berry development. Their findings, published (DOI: 10.1093/hr/uhae285) online on October 14, 2024, in Horticulture Research, describe genome-wide DNA methylation landscapes in the widely grown ‘Kyoho’ grape and its early-ripening bud mutant ‘Fengzao’. By integrating whole-genome bisulfite sequencing with transcriptomic data, the study uncovers CHH-type methylation patterns and identifies jasmonate-induced oxygenase gene (JOX1) as a pivotal regulator, offering new insights into the molecular basis of fruit ripening.

The team conducted whole-genome bisulfite sequencing across six developmental stages of ‘Kyoho’ and five of ‘Fengzao’, generating high-quality methylomes with >110 million clean reads per sample. Comparative analysis revealed striking differences in methylation dynamics. While ‘Kyoho’ berries showed a gradual rise in methylation during ripening, ‘Fengzao’ displayed irregular changes, with promoter regions consistently more hypermethylated. This hypermethylation was especially prominent at CHH sequence sites, known to influence transcriptional regulation. Integrating methylome data with transcriptome profiles, the researchers identified 38 candidate genes whose expression correlated with methylation shifts. These genes are involved in secondary metabolite biosynthesis, hormone signaling, and cell wall modification—processes central to fruit quality and maturation. Notably, JOX1 emerged as a negative regulator: overexpression delayed ripening in Arabidopsis, while knockdown in grape berries accelerated ripening. The findings propose a model in which promoter CHH hypermethylation silences JOX1, reducing jasmonic acid turnover and thereby advancing ripening in ‘Fengzao’. This study not only defines methylation’s role in grape development but also points to epigenetic breeding strategies.

“Our study highlights the pivotal role of epigenetics in shaping fruit development timelines,” said Dr. Da-Long Guo, the corresponding author. “The discovery that promoter CHH hypermethylation accelerates ripening by repressing JOX1 provides a new mechanistic understanding of grape biology. Importantly, this demonstrates how subtle epigenetic modifications can have profound effects on crop phenotypes. Such knowledge opens opportunities for precision breeding and epigenetic interventions to tailor fruit ripening schedules, potentially improving both agricultural productivity and consumer satisfaction.”

The identification of DNA methylation as a key driver of early grape ripening has significant implications for horticultural science and viticulture. Understanding how promoter hypermethylation regulates ripening genes could help breeders design varieties with optimized harvest times, better flavor, and improved resistance to storage-related quality loss. Beyond grapes, the findings contribute to the broader understanding of epigenetic control in non-climacteric fruits, suggesting that targeted manipulation of methylation patterns could become a powerful tool in crop improvement. Future work may explore applying epigenome editing or demethylation treatments to fine-tune ripening across different fruit crops.

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References

DOI

10.1093/hr/uhae285

Original Source URL

https://doi.org/10.1093/hr/uhae285

Funding information

This work was financially supported by National Natural Science Foundation of China (NSFC: 32472662, 32202409), Natural Science Foundation of Henan Province (232300421112), and Ph.D. Research Startup Foundation of Henan University of Science and Technology (13480066).

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.