Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA.
Odum School of Ecology, University of Georgia, Athens, Georgia, USA.
Mol Ecol Resour. 2023 Jan;23(1):131-144. doi: 10.1111/1755-0998.13698. Epub 2022 Aug 24.
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.
生物衰老与生态尺度上的生命史变化有关，并为理解与年龄相关的生物体功能下降提供了基础。改变的 DNA 甲基化动态是生物衰老的一个保守方面，最近已经被建模来预测脊椎动物物种的年龄。除了在估计个体年龄方面的实用性之外，由于表观遗传衰老的加速或减速，实际年龄和预测年龄之间存在差异，这些差异与疾病风险和多种生命史特征有关。尽管有证据表明 DNA 甲基化模式可以描述植物的衰老，但表观遗传钟的预测尚未进行。在这里，我们在火炬松（Pinus taeda）中解析了 CpG、CHG 和 CHH 甲基化环境中的 DNA 甲基组，并构建了能够在该物种的最大寿命内预测其年龄的表观遗传钟，误差在 6%以内。尽管 CHH 甲基化模式与年龄几乎没有关联，但 CpG 和 CHG 甲基化环境与衰老密切相关，随着年龄的增长，它们主要被去甲基化。与年龄相关的基因座包括靠近苹果酸脱氢酶、NADH 脱氢酶以及 18S 和 26S 核糖体 RNA 基因的基因座。本研究报告了植物中首批表观遗传钟之一，并证明了与年龄相关的 DNA 甲基化动态的普遍性，这可以为保护和管理实践提供信息，以及我们对植物生物衰老的生态和进化理解。
