NCM 2021: An epigenetic aging clock for cattle using portable sequencing technology

Loan’s first question is ‘Why predict the age of livestock?’ The birth date is essential to register the livestock breed and provides important information for ‘genomic selection for economically important traits: growth rate, calving intervals and age at puberty’. However, it’s very challenging to get this information in Australia, which can have ‘extensive livestock production systems’ and infrequent cattle mustering. DNA methylation can be used as a biomarker of ageing. Epigenetic clocks have been developed in humans and some animals: mouse, dog, wolf, elephant and cat. This led to their second question, ‘Can we build the Cattle Epigenetic clock’ using Oxford Nanopore technology? DNA from the hair of 66 female cattle, ranging from 5 days to 17 years of age, were isolated and libraries were prepared using the Ligation Sequencing Kit for sequencing on MinION. The analysis tool f5c was used to call methylation and samples were filtered in two ways: ‘sites that called in at least 80% of animals’, giving 56,673 sites, and ‘sites close to genes reported to human and dog’, which called 15,667 sites. The results were used to build ‘methylation relationship matrices’ and MeBLUP was applied before age prediction. A good correlation was achieved between predicted age and actual age: 0.71 for all sites and 0.6 when dog and human sites were used. In future studies, they aim to improve their ‘cow-hair- epigenetic clock’ using the PromethION device with Prowler, a recently developed novel filtering program.

Authors: Loan To Nguyen