A hand-held device uses DNA extracted from tail hairs or tissue samples can deliver genetic data to identify issues with a beast or herd
Portable sequencing technology previously developed to track the spread of COVID-19 is now showing promise as a cost-effective way of determining breeding values for cattle income operations.
Scientists at The University of Queensland are trialling what’s called crush-side genotyping to predict important production traits.
Queensland Alliance for Agriculture and Food Innovation (QAAFI) PhD candidate Harry Lamb said the approach would mean producers no longer have to send tail hair samples to a laboratory for genotyping.
“There’s enormous potential for this to be used on any number of production traits QAAFI researchers are working on, including parasite resistance, growth rates, methane production from the gut and traits related to animal welfare,” Harry Lamb added.
“There are even opportunities for the on-farm diagnosis of diseases in cattle, such as Bovine respiratory disease.”
The samples are taken with a hand-held device called MinION, that then uses DNA extracted from tail hairs or tissue samples to deliver genetic data.
The device is smaller than a toaster and passes dozens of individual DNA molecules from a sample through a biological pore, disrupting the flow of ions in the process.
Mr Lamb said the device allowed the DNA sequence to be read, “We aren’t reading the entire genome but reading snippets of DNA and piecing the rest of the genome together using software.
“This helps us accelerate the process and test many animals at once.
“We’ve already demonstrated we can use this device to derive breeding values with the same accuracy as existing genomic prediction technology, so now we are tackling the logistics of doing this in on-farm settings.”
The work is part of the Northern Genomics project led by UQ Centre for Animal Science Director, Professor Ben Hayes, in partnership with Meat & Livestock Australia (MLA), which has established a reference population for genomic prediction in the northern cattle industry.
The project incorporated data from the herds of 54 northern beef producers and involved comparisons of genotypes against the animals’ performance characteristics.
Harry Lamb is now conducting proof-of-concept studies for crush-side genotyping in on-farm environments.
“It’s looking very promising, but we’re still trying to optimise the system to bring the cost down,” Harry added.
Recent trials indicated 100 animals could be genotyped in 24 hours at a little over $55 per sample.
MLA Program Manager, Genetics, Hamish Chandler, said the technology had significant potential for the extensive production systems of the northern cattle industry.
“In extensive systems in the North, cattle are often only handled once a year and this really limits our ability to capture information, analyse data and then make an informed selection decision without having to re-handle cattle at a later date,” Hamish Chandler expalined.
“The crush-side genotyping technology changes this.
“It allows us to make informed decisions about which animals carry the genes we want to keep in our breeding program and which animals should be culled while they are still in the yards.”
Meanwhile Harry Lamb confirmed further field work would occur in 2023, with a target of completing the technology in time to demonstrate it at Beef 2024 in Rockhampton.
“From all the producers I have spoken to the response has been very positive,” and Harry also added, “In future, this technology may also have applications in rapid diagnostics on-farm.
“We hope the technology will deliver additional benefits.
“Another recent study demonstrated we can detect bacteria and viruses associated with bovine respiratory disease while generating breeding values from the same test.
“There are also other researchers interested in exploring how they could use the MinION technology to monitor exotic disease outbreaks in northern Australia,” Harry concluded.
This research is funded by Meat & Livestock Australia (MLA), MLA Donor Company, the Queensland Department of Agriculture and Fisheries and The University of Queensland.
