genes-13-00096.pdf (2 MB)

Development of epigenetic clocks for key ruminant species

Download (2 MB)
journal contribution
posted on 2023-05-03, 20:23 authored by Alex CaultonAlex Caulton, Ken Dodds, Kathryn McRaeKathryn McRae, Christine Couldrey, Steve Horvath, Shannon ClarkeShannon Clarke
Robust biomarkers of chronological age have been developed in humans and model mammalian species such as rats and mice using DNA methylation data. The concept of these so-called “epigenetic clocks” has emerged from a large body of literature describing the relationship between genome-wide methylation levels and age. Epigenetic clocks exploit this phenomenon and use small panels of differentially methylated cytosine (CpG) sites to make robust predictions of chronological age, independent of tissue type. Here, we present highly accurate livestock epigenetic clocks for which we have used the custom mammalian methylation array “HorvathMammalMethyl40” to construct the first epigenetic clock for domesticated goat (Capra hircus), cattle (Bos taurus), Red (Cervus elaphus) and Wapiti deer (Cervus canadensis) and composite-breed sheep (Ovis aries). Additionally, we have constructed a ‘farm animal clock’ for all species included in the study, which will allow for robust predictions to be extended to various breeds/strains. The farm animal clock shows similarly high accuracy to the individual species’ clocks (r > 0.97), utilizing only 217 CpG sites to estimate age (relative to the maximum lifespan of the species) with a single mathematical model. We hypothesise that the applications of this livestock clock could extend well beyond the scope of chronological age estimates. Many independent studies have demonstrated that a deviation between true age and clock derived molecular age is indicative of past and/or present health (including stress) status. There is, therefore, untapped potential to utilize livestock clocks in breeding programs as a predictor for age-related production traits.


Rights statement

Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// 4.0/).


  • English

Does this contain Māori information or data?

  • No



Journal title





Caulton, A., Dodds, K. G., McRae, K. M., Couldrey, C., Horvath, S., & Clarke, S. M. (2022). Development of epigenetic clocks for key ruminant species. Genes, 13(1), 96.

Usage metrics


    Ref. manager