SREL Reprint #3741

Development of DNA methylation-based epigenetic age predictors in loblolly pine (Pinus taeda)

Steven T. Gardner1, Emily M. Bertucci1,2, Randall Sutton3, Andy Horcher3, Doug Aubrey1,4,
and Benjamin B. Parrott1,2

1Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA
2Odum School of Ecology, University of Georgia, Athens, Georgia, USA
3US Forest Service Savannah River, New Ellenton, South Carolina, USA
4Warnell School of Forestry, University of Georgia, Athens, Georgia, USA

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.

Keywords: biological age, chronological age, DNA methylation, epigenetic clock, Pinus taeda

SREL Reprint #3741

Gardner, S. T., E. M. Bertucci, R. Sutton, A. Horcher, D. P. Aubrey, and B. B. Parrott. 2023. Development of DNA methylation-based epigenetic age predictors in loblolly pine (Pinus taeda). Molecular Ecology Resources 23(1): 131-144.

This information was provided by the University of Georgia's Savannah River Ecology Laboratory (srel.uga.edu).