Apple skin color is a key factor in determining the fruit's quality, with anthocyanins responsible for its red and purple hues. However, certain apple varieties, such as 'Daihong,' exhibit significant color fading as they mature—shifting from vibrant red to green. This change not only impacts the visual appeal of the fruit but also its marketability. To better understand the underlying molecular processes, particularly the role of DNA methylation in color fading, is crucial for enhancing fruit quality and addressing these challenges.
In a study (DOI: 10.1093/hr/uhae031) published in Horticulture Research on February 15, 2024, researchers from Qingdao Agricultural University delve into the role of DNA methylation in apple skin color fading. The team focused on the 'Daihong' apple variety, which shows substantial color loss during development. By examining methylation patterns and gene expression profiles, the study identifies critical epigenetic factors involved in this process.
Utilizing a combination of whole-genome bisulfite sequencing (WGBS) and transcriptomic analysis, the research team analyzed the molecular mechanisms at play in 'Daihong' apples at three developmental stages (S1, S4, and S7). The findings revealed a significant increase in DNA methylation levels, particularly in the promoter regions of genes involved in the flavonoid biosynthesis pathway, such as MdCHS, MdCHI, MdANS, and MdUFGT. This hypermethylation corresponded to decreased gene expression and lower levels of anthocyanins and other flavonoids. The study also highlighted a downregulation of DNA demethylase genes MdDME1, MdROS1, and MdROS2 during fruit development, further contributing to the elevated methylation levels. To confirm these results, the researchers treated mature 'Daihong' apples with the DNA demethylation agent 5-aza-2'-deoxycytidine. This intervention significantly boosted anthocyanin levels and the expression of key flavonoid genes, providing direct evidence of the negative correlation between DNA methylation and gene expression. Additionally, a notable enrichment of differentially methylated regions (DMRs) was found in the intergenic and promoter regions, underscoring the role of DNA methylation in regulating gene activity during fruit maturation.
Dr. Yugang Zhang, the study's corresponding author, underscored the importance of these findings, stating, "Our research highlights the critical role of DNA methylation in regulating fruit coloration. Understanding these epigenetic mechanisms can help us develop strategies to enhance fruit quality and prevent color fading in apple varieties."
These insights hold significant promise for the future of horticulture and fruit breeding. By targeting DNA methylation pathways, researchers may be able to breed new apple varieties with more stable and desirable color traits. Moreover, this study opens the door to exploring similar epigenetic processes in other fruit crops, paving the way for advancements in agricultural practices that can lead to improved fruit quality and greater consumer satisfaction.
###
References
DOI
10.1093/hr/uhae031
Original Source URL
https://doi.org/10.1093/hr/uhae031
Funding information
This work was supported by the Natural Science Foundation of Shandong Province (ZR2023MC169), the Taishan Scholar Foundation of Shandong Province (tstp20221134), the Agricultural Variety Improvement Project of Shandong Province (2023LZGCQY007; 2021LZGC024; 2022LZGC010), the China Agriculture Research System Foundation (CARS-27), and Science and Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta (2022SZX34).
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, 2022. 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.