Abstract
Biological ageing is connected to life history variation across ecological scales and informs a basic understanding of age-related declines in organismal function. Altered DNA methylation dynamics are a conserved aspect of biological ageing and have recently been modelled to predict chronological age among vertebrate species. In addition to their utility in estimating individual age, differences between chronological and predicted ages arise due to acceleration or deceleration of epigenetic ageing, and these discrepancies are linked to disease risk and multiple life history traits. Although evidence suggests that patterns of DNA methylation can describe ageing in plants, predictions with epigenetic clocks have yet to be performed. Here, we resolve the DNA methylome across CpG, CHG, and CHH-methylation contexts in the loblolly pine tree (Pinus taeda) and construct epigenetic clocks capable of predicting ages in this species within 6% of its maximum lifespan. Although patterns of CHH-methylation showed little association with age, both CpG and CHG-methylation contexts were strongly associated with ageing, largely becoming hypomethylated with age. Among age-associated loci were those in close proximity to malate dehydrogenase, NADH dehydrogenase, and 18S and 26S ribosomal RNA genes. This study reports one of the first epigenetic clocks in plants and demonstrates the universality of age-associated DNA methylation dynamics which can inform conservation and management practices, as well as our ecological and evolutionary understanding of biological ageing in plants.
| Original language | English |
|---|---|
| Pages (from-to) | 131-144 |
| Number of pages | 14 |
| Journal | Molecular Ecology Resources |
| Volume | 23 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 2023 |
| Externally published | Yes |
Funding
We would like to thank Samantha Bock for her assistance with bioinformatic analyses, as well as the members of the Parrott laboratory at SREL for their feedback pertaining to the results of this study. We would also like to thank Dr Sibbett, the Subject Editor, and two anonymous reviewers for their efforts, which went above and beyond and substantially improved the manuscript. This study was supported in part by the USDA Forest Service-Savannah River, under Interagency DE-EM0003622 with the U.S. Department of Energy, the National Science Foundation (Award no. 2026210, BBP), and the U.S. Department of Energy Office of Environmental Management under award number DE-EM0004391 to the University of Georgia Research Foundation. We would like to thank Samantha Bock for her assistance with bioinformatic analyses, as well as the members of the Parrott laboratory at SREL for their feedback pertaining to the results of this study. We would also like to thank Dr Sibbett, the Subject Editor, and two anonymous reviewers for their efforts, which went above and beyond and substantially improved the manuscript. This study was supported in part by the USDA Forest Service‐Savannah River, under Interagency DE‐EM0003622 with the U.S. Department of Energy, the National Science Foundation (Award no. 2026210, BBP), and the U.S. Department of Energy Office of Environmental Management under award number DE‐EM0004391 to the University of Georgia Research Foundation.
| Funders | Funder number |
|---|---|
| National Science Foundation | 2026210 |
| U.S. Department of Energy | |
| U.S. Department of Agriculture | DE-EM0003622 |
| Office of Environmental Management | DE‐EM0004391 |
| University of Georgia Research Foundation |
Keywords
- DNA methylation
- Pinus taeda
- biological age
- chronological age
- epigenetic clock