Predicting age of livestock from DNA samples Final Report

Summary

Accurately recording age of animals is a major challenge in the Northern Beef industry, where animals are mustered infrequently. This limits the uptake of genetic evaluation and has adverse implications for herd management and meat quality for Northern beef producers. In this project, a “methylation clock” has been derived, such that beef producers can take a tail hair from their animals, and age can be predicted from the DNA in this sample.

Objectives

1. Deliver a DNA test to predict age of animals, that uses the same sample as for taken for genotyping, and can be integrated into the workflows currently used to genotype animals on a large scale.

2. Deliver DNA based predictions of ossification, that can be integrated into a prediction of MSA grade in live animals.

Key findings

Using Nanopore sequencing to derive methylation profiles (with 50 animals with known birthdates as reference population) a methylation clock was derived for predicting age. In an independent validation, age was predicted with an accuracy of 0.65. This was for both sites with 80% of animals called, and a much smaller set of sites that were shown to be predictive both in human and dog. The average difference in predicted age and actual age for animals less than three years old was one year, for animals between 3 years and 10 years it was 1.5 years.

Benefits to industry

• Allow selection of heifers that fell pregnant as yearlings, and culling of heifers that fell pregnant much later in life, improving the fertility of the herd over time.
• For meat quality, the ability to discriminate between animals that are in the range 6 and 10 years would have some value.
• As the reference population for deriving the methylation clock grows, the prediction of age will become more accurate. This will open up new opportunities for the northern beef industry.

MLA action

To look at the on-going development of a reference population for methylation across species.

Future research

• An additional 50 animals with known ages with the Nanopore technology – adding this information to the reference population will increase the accuracy of the methylation clock to months rather than ~ 1 year. The reference population should continue to be expanded until birth month can be accurately predicted.
• Adaptive sequencing, a new extension to the Nanopore technology that was developed in response to the COVID-19 pandemic, would allow only the human-dog methylation sites to be targeted, which would reduce the cost of obtaining the necessary sequence for the methylation clock for each animal by a factor of ~ 10.