Fast, on-farm genetic testing for cattle is practical and achievable for northern producers, according to University of Queensland research.
In partnership with Meat & Livestock Australia and the Department of Primary Industries, a team from UQ's Queensland Alliance for Agriculture and Food Innovation (QAAFI) tested low pass nanopore sequencing on 3 commercial farms.
Associate Professor Elizabeth Ross said the team produced reliable data for age, genomic breeding values (GBVs) and parentage for about 24 animals in less than 24 hours on each farm.
"The platform provides a practical solution for northern beef systems because it allows producers to obtain core genetic information on farm without multiple musters or lengthy lab turnaround times," Dr Ross said.
Low pass nanopore sequencing reads about 10 per cent of the total genome, or 300 million DNA positions.
It compares to SNP array-based genotyping, which has been used since the late 1990s and reads 30,000-100,000 DNA positions.
Dr Ross said it gives a good indication of an animal's overall genetic merit and also reads markers that attach to the DNA as the animal ages.
"This process solves the problems associated with long mustering intervals, imprecise birthdates, uncertain parentage and the lengthy turnaround time of traditional laboratory-based genotyping," she said.
The team completed DNA extraction, sample processing and library preparation in about 4 hours, with stable overnight sequencing conducted on farm.
Dr Loan Nguyen , an ARC Early Career Industry Fellow working in an applied genomics, said challenges remained before the technology could be commercialised, but the work showed what was possible.
"It achieved a breakthrough in age prediction, estimating the age of young cattle to within less than 6 months," Dr Nguyen said.
"We also confirmed that hair is an excellent sample type for this kind of work, as it is already routinely used by producers.
"This means producers can take samples when animals are put through a crush for routine management practises and on-farm genetic testing can begin straight away."
A producer survey carried out as part of the project found strong interest in rapid on-farm genomics, particularly for bull selection, culling decisions, identifying replacement females and strengthening pedigree accuracy.
More than 80 per cent of respondents said parentage verification would be very useful, while half valued the 24-hour turnaround times.
While cost remains a barrier, 40 per cent of those surveyed said they would be prepared to pay a premium for faster results.
"This is the first time we've shown that a single low-cost sequencing test can provide accurate age estimates, parentage values and GBVs," she said.
"This all-in-one approach dramatically improves the practicality of genomics in Australia's northern herds."
Collaboration and acknowledgements
This research was funded by Meat and Livestock Australia, The University of Queensland and the Department of Primary Industries.
The Queensland Alliance for Agriculture and Food Innovation is a research institute at The University of Queensland, established with and supported by the Department of Primary Industries.
