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DNA methylation is a conserved epigenetic modification influencing various biological processes, including fruit development and ripening. Previous research has shown that methylation changes affect ripening in fruits like tomato, strawberry, and sweet orange, but its role in grape development remained unclear. 'Fengzao', an early-ripening mutant of 'Kyoho', provided an ideal model to study these effects. Based on these challenges, there is a pressing need to explore the epigenetic factors driving grape ripening dynamics.

A research team from the College of Horticulture and Plant Protection at Henan University of Science and Technology published a on October 14, 2024, in . By comparing the DNA methylome of 'Kyoho' and 'Fengzao' grapes, the study identified key epigenetic modifications responsible for the early ripening of 'Fengzao'. Their findings highlight the role of CHH methylation and point to specific gene targets regulating ripening timing.

The team performed whole-genome bisulfite sequencing across multiple developmental stages in both 'Kyoho' and 'Fengzao' berries. They found that transposons and gene-flanking regions, particularly promoters, showed higher methylation levels in 'Fengzao', especially in CHH contexts. Unlike 'Kyoho', which displayed a gradual increase in methylation during ripening, 'Fengzao' exhibited erratic methylation dynamics. Among 38 candidate genes identified, JOX1—a jasmonate-induced oxygenase—stood out. Functional studies showed that overexpressing JOX1 delayed ripening in Arabidopsis, while knocking down JOX1 in grapes accelerated ripening. These results suggest that hypermethylation of the JOX1 promoter reduces its expression, facilitating earlier ripening in 'Fengzao'.

"Our study provides strong evidence that CHH promoter hypermethylation, particularly of key regulatory genes like JOX1, can significantly shift the timing of grape ripening," said Dr. Da-Long Guo, corresponding author of the study. "These findings not only deepen our understanding of epigenetic regulation in fruit development but also offer potential targets for breeding and cultivation strategies."

This discovery opens new avenues for manipulating grape ripening through epigenetic modifications, offering practical benefits for growers facing market demands for earlier harvests. Beyond grapes, these insights could apply to other non-climacteric fruits, enabling better control over fruit quality, shelf life, and resilience. Future research may further explore how modifying promoter methylation patterns could be harnessed to fine-tune fruit development across diverse crop species.

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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).

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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.