How Epigenetic Changes Speed Up Pear Ripening

Jenn Hoskins
8th April, 2024

How Epigenetic Changes Speed Up Pear Ripening

Genomic analysis reveals that DNA methylation levels progressively increased during pear domestication and improvement (a–d), a trend that inversely correlates with the significant downregulation of PpyDML demethylase genes (e).

Image adapted from: Song et al. / CC BY (Source)

Key Findings

  • Researchers at Nanjing Agricultural University found that domesticated pear trees have more DNA methylation compared to wild types
  • Increased methylation is linked to less activity of the DML1 gene, which is involved in removing methyl groups from DNA
  • Methylation changes affect fruit ripening, with the CAMTA2 gene inhibiting early ripening when overexpressed
DNA methylation is a crucial biological process where a methyl group, a small chemical fragment, is added to DNA. This can control how genes are turned on or off without changing the DNA sequence itself, a concept known as epigenetics. In the context of plant biology, DNA methylation has been shown to be vital for normal development and response to environmental stress[2][3]. However, until recently, the role of DNA methylation in the domestication of perennial fruit trees, like pear, was not well understood. A team from Nanjing Agricultural University has shed light on this mystery through their research[1]. They examined how DNA methylation has changed in pear trees throughout the process of domestication and improvement. By comparing 41 pear accessions, or genetically distinct lines, they found an overall increase in DNA methylation, which contrasts with the decrease observed in domesticated rice, suggesting a unique pattern in fruit trees. The researchers discovered that the increase in methylation in pears was significantly associated with the reduced activity of a gene called Demeter-like1 (DML1), which is responsible for removing methyl groups from DNA. This reduction in DML1 activity appears to be a result of human selection during the domestication process. They identified 5,591 differentially methylated regions (DMRs)—parts of the genome where the methylation status differs significantly between domesticated and wild pears. Interestingly, these DMRs showed more genetic diversity than regions of the genome under selection for specific traits, and most were not associated with changes in the DNA sequence itself. The study also explored the relationship between methylation and gene function. The researchers found that genes near regions of increased methylation were often involved in fruit ripening. In particular, they studied a gene associated with a hypermethylated DMR called CAMTA2. By overexpressing CAMTA2 in tomato plants and pear callus (a type of plant tissue culture), they demonstrated that this gene's activity can inhibit fruit ripening. This suggests that DNA methylation, through its effect on genes like CAMTA2, plays a critical role in the early ripening of pear fruits, which is a desirable trait selected during domestication. The findings from Nanjing Agricultural University build upon earlier studies that have outlined the importance of DNA methylation in plant development and stress responses[2][3][4]. The pear study expands our understanding by highlighting the role of methylation in the domestication process, showing that it can lead to trait changes over time. Moreover, it emphasizes that DNA methylation is a dynamic and complex mechanism, influenced by both genetic and epigenetic factors, that contributes to the diversity of plant traits. In conclusion, the research indicates that the increase in DNA methylation observed in domesticated pear trees is an essential factor in the development of traits favored by humans, such as early fruit ripening. These insights not only enhance our understanding of plant domestication but also may inform future agricultural practices and breeding programs for perennial fruit trees. The study serves as an example of how subtle epigenetic modifications can have significant impacts on the traits of cultivated plants, potentially paving the way for new approaches to crop improvement.

AgricultureGeneticsPlant Science

References

Main Study

1) Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement.

Published 5th April, 2024

https://doi.org/10.1186/s13059-024-03220-y

Related Studies

2) Dynamics and function of DNA methylation in plants.

https://doi.org/10.1038/s41580-018-0016-z

3) Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution.

https://doi.org/10.3390/ijms23158299

4) Programming of DNA methylation patterns.

https://doi.org/10.1146/annurev-biochem-052610-091920


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