Improving sheep genetics with CT scanning

In the continuous drive to improve farm animal genetics and meat quality, agricultural researchers and farmers have often adapted medical imaging and diagnostic tools used in human health. CT scanning came to New Zealand in the 1990s when ultrasound scanning was already widespread.

Thanks to a ground-breaking joint venture between AgResearch and Pāmu, farmers now have a new tool for refining the genetics of their sheep.

The origin of INNERVISION

Pāmu, a state-owned farming enterprise involved in a variety of sheep, beef and deer farms, was looking for new ways to improve the genetics of its sheep flocks.

The Pāmu sheep operations are vertically integrated – it breeds genetically improved rams in its stud flocks for use in its commercial flocks. This means it’s able to capture all the benefits and financial profits of that genetic improvement when the lambs are sent to the meat plant. Pāmu used ultrasound to determine meat quality and yield in terminal sire stud flocks. Terminal sires are rams bred primarily to produce quality lambs – they grow quickly and efficiently to provide quality meat for the market.

Ultrasound had been beneficial for progressing genetics, with 40–50% accuracy for predicting the weight of meat on a live animal and around 70% accuracy for fat content. Pāmu wanted to better the odds in a way that didn’t involve large slaughter trials. It approached AgResearch, expressing an interest in exploring the use of CT scanning. By chance, agricultural scientist Dr Neville Jopson had been working on the application of CT scanners for measuring livestock.

It was from this initial approach that the INNERVISION joint venture began, and a CT scanner dedicated to agricultural science was installed at AgResearch Invermay in Mosgiel.

CT scanning versus ultrasound

A CT scanner produces detailed cross-sectional images through an animal by rotating an X-ray tube 360°, and the scanner software reconstructs the two-dimensional image at that specific location. Images can be collected throughout the entire body, which contributes to a high level of accuracy. CT images show muscle, fat and soft tissues, blood vessels and bone. It is able to determine with accuracy the fat and lean in a carcass or meat cut and does not require the slaughter of animals for the collection of the data.

A standard ultrasound is a blunter tool. It’s used only at one measurement site on an animal, which limits its accuracy. However, ultrasound costs a few dollars per animal compared to a few hundred dollars for CT scanning. Ultrasound is also a mobile operation. With CT scanning, there’s no leaping in the truck and heading out to the farm – the farm needs to come to the CT scanner, which is bolted to the floor at AgResearch.

A faster scanner

The original INNERVISION scanner took up to 2 hours to scan a whole animal. In order to scan an animal efficiently, a method was developed based on a six-image set from various points on the animal which could be scanned in around 10 minutes. Technicians then undertook a time-intensive analysis of the images to estimate the weight of meat, fat and bone in the hindleg, loin and shoulder cuts.

In 2014, a new CT scanner was installed at Invermay. This machine can image the entire sheep in a few minutes. However, the sticking point remained the time needed by technicians to analyse the images.

Dr Jopson had for some time been thinking about using the CT scans AgResearch had collected over many years to create a automated application to process the images. The 2020 COVID-19 lockdown was somewhat fortunate for Dr Jopson, who finally had the time to sit down with an open-source machine-learning platform and 20 years of data. He was able to set up an application to do the image analysis and was surprised at how well the programming worked, accurately analysing 95% plus of scans. The application has also been used to output data on earlier scans that were not able to be processed by the technicians. These can then be analysed and end data returned to the application to further refine the end completion rate.

The use of an open-source platform means the application is not protected by IP, but the 20 years of analysed scans are.

The success of CT scanning

Today, Pāmu continues to use ultrasound on its farms but now as a diagnostic tool for genetic ranking to screen which rams should be CT scanned. Alongside genomic and weight datasets, it selects the top 10% of the young rams to truck into AgResearch for CT scanning. Around 200–250 rams are scanned in the CT scanner to identify the top 2% to be used as sires in each stud. Pāmu says the economic benefit of CT scanning in its operation greatly outweighs the cost and logistical issues of trucking animals to the scanner.

INNERVISION provides the technology to other farms, vets and researchers across New Zealand. CT scanning is being used in a variety of primary industry research beyond meat yields. For example, in one research programme, pregnant ewes have been CT scanned to collect data on the effects on a developing lamb of shearing during mid-pregnancy.

The applications for research are exciting. A project has looked at methane production of individual sheep in order to aid genetic selection of low-methane sheep. The CT scanner is able to image the rumen in situ and measure the volume of gases, liquid and churned up grass inside it. In the past, it would have to be removed from the animal, which involved both the loss of the animal and distortion of the rumen shape affecting accuracy of measurement.