Abstract
Advancements in the field of epigenetics has initiated discussions into the mechanisms by which the environment modulates genetic effects. DNA methylation is an important epigenetic mark, essential for genomic stability and maintenance throughout development. In addition, it serves as a biomarker of chronological age and a biological fingerprint of the stress response. To successfully incorporate DNA methylation data into current genetic merit predictions for livestock, the approaches used need to be high throughput, robust and cost-effective. The first aspect of this study reviews four DNA methylation profiling assays (1) whole-genome bisulphite sequencing (WGBS), (2) reduced-representational bisulphite sequencing (RRBS), (3) Oxford Nanopore Technology (ONT) long-read sequencing, and (4) methylation microarray technology via the recently released custom mammalian methylation array “HorvathMammalMethyl40”. The relative accuracy of each assay is benchmarked against the WGBS dataset, the gold standard methodology, and the cost benefits are discussed with particular consideration for industry application.
While high-quality reference genomes are now available for the majority of livestock species, comparatively little is known about the regulatory elements that drive functional phenotypic variation. Toward understanding the molecular link between livestock genomes and phenotypic outcomes, the functional annotation of animal genomes (FAANG) project was launched in a coordinated effort to generate a comprehensive record of regulatory elements in the genomes of important agricultural species. The second element of this study is aligned with the ovine FAANG project to elucidate the complex interplay between regulatory elements, chromatin configuration, and epigenetic modifications in sheep. It involved the development of comprehensive, tissue-specific DNA methylation profiles, including WGBS of eight tissues and RRBS of an extended set of 50 tissues. The DNA methylation profiles were analysed in parallel with a high-resolution map of transcription start sites, chromatin accessibility and functional state profiles, and RNA-seq expression data generated for the same set of tissues. This work contributes to the comprehensive annotation of the ovine genome as a resource to advance our understanding of the genetic control of economically important traits in livestock.
DNA methylation has been widely used as a robust biomarker of chronological age in humans and model mammalian species such as rat and mouse, implemented via so-called “epigenetic clocks”. The concept of epigenetic clocks has emerged from a large body of literature describing the correlation between genome-wide methylation levels and age. Epigenetic clocks exploit this phenomenon and use small panels of differentially methylated cytosines to make accurate predictions of chronological age, independent of tissue type. The final facet of this research presents the first of its kind epigenetic clock for domesticated goat (Capra hircus), as well as cattle (Bos taurus), Red (Cervus elaphus) and Wapiti deer (Cervus canadensis), and composite-breed sheep. In addition to the species-specific clocks, a New Zealand livestock “farm animal epigenetic clock” was constructed for all animals included in the study, which will enable robust predictions to be extended to various breeds, species, and environments. The farm animal clock shows similarly high accuracies to the individual species’ clocks (r>0.97), utilising only 217 cytosines to estimate age (relative to the maximum lifespan of the species) with a single mathematical model.
Importantly, in human research, estimates using epigenetic clocks are not only predictive of chronological age but also indicate biological age, such that accelerated epigenetic ageing is related to environmental pressures, including past and/or present health status and historical stress exposure. Translating this concept into livestock research presents opportunities for selection. For example, deviation of biological age from chronological age could be used as a molecular phenotype for age-related pathologies or as an indicator of longevity to facilitate the selection of biologically robust animals that are resilient to environmental perturbation. Therefore, there is potential to utilise a livestock epigenetic clock in breeding programs as a predictor of age-related production traits.
Overall, this research is directed toward discovering individual methylation markers or marker combinations that may be useful in the selection and breeding of livestock for continued improvement.