Illumina uses genomics testing to improve livestock productivity

Biotechnology company Illumina is using genomic technology to detect the traits such as disease tolerance or milk production in livestock, and says the results could aid the resilience of sheep flocks and cattle herds.

Genomics, the study of an individual's genes, is used extensively in cancer and prenatal testing in humans, but researchers said some of the most practical gains were taking place in agriculture.

The Illumina demonstration laboratory is located in the Peter MacCallum Cancer Centre and researchers said they were keen to strengthen ties with the agriculture sector to fast-track outcomes for determining traits in livestock to bolster productivity.

Illumina applied genomics market development manager Evgeny Glazov, a senior manager for Asia Pacific, Japan, Africa and Middle East, said genomic testing could help the agriculture sector in many ways.

"It can improve productivity of agriculture production and increase value of agriculture production in Australia across livestock, crops, as well as aquaculture species," Dr Glazov said.

"In livestock, it can help eliminate detrimental genetic traits and diseases from the population because it now tests animals routinely to see if they carry genetic variances... and just eliminate it from breeding programs.

"It can help shrink the time of results and helps farmers to accelerate the breeding cycle by using the predicted genomic techniques."

Data is supplied by farmers to the laboratory through a tissue sample from the ear of an animal, and unlike selective breeding, researchers said the data could detect rare genetic diseases or individual production traits.

"One of the key differences between previous selective breeding methods and genomics is, first of all, with genomics you can start to select for things you don't easily see or can't easily measure," Dr Glazov said.

"You can start selecting for things like disease tolerance or milk production and make sure that neither of those traits are compromised.

"The focus now is shifting not just to look at genetic traits as such, but to look at overall farm economics and how can we make the herd more economically sustainable and profitable."

He said the aim of providing genomic data to farmers would help them assess the genetic traits of their livestock in a more timely manner.

"It allows farmers to customise those indexes so they can decide what they want to select for to make the herd more productive," he said.

"It can mean not just which cows produce more milk, but what does performance mean in terms of economic performance, in terms of overall health, and things like feed conversion efficiency, for example.

"When you look at all those factors, you can combine them to the one index and customise the index depending on your objective.

"A similar type of technology is being used to improve crops and pasture species as well."

Sheep Genetics Advisory Committee member and Nareen sheep producer Kate Dorahy, Cloven Hills, said genomic testing was an important tool for the industry, with the potential to more accurately and quickly select for emerging traits like methane production and feed conversion efficiency.

"The faster you can do that, the faster you're going to make genetic gain," Mrs Dorahy said.

"It gives you a higher baseline to start with because you're culling the animals that are not suited and not in the selection criteria for what the market wants.

"From a farming perspective, we get better animals that are more resilient and productive and have better animal welfare outcomes, plus selecting traits like meat eating quality that are important for the consumer."

Mrs Dorahy and her husband Chris join more than 4000 maternal stud ewes and a similar number of commercial ewes each year and select stock based on their fertility, growth, carcase and resilience to produce prime lambs.

"If you improve your fertility, growth and carcase along with your resilience traits like reduced worm egg counts and improve meat eating quality, those 1 and 2 percenters make a difference," she said.

"The cumulative gain is what we need and that is what will make the difference for commercial breeding operations.

"In the current economic climate, all those 1 and 2 percenters have never been more important."

She said genomics was used in the sheep industry primarily by seedstock producers to make more accurate decisions earlier in an animal's life for harder-to-measure traits like eating quality and reproduction.

"Since the introduction of genomics into Australian Sheep Breeding Values, we've seen the rate of genetic progress improve," she said.

"This means that the rams being delivered to industry are of a higher genetic merit."

Mrs Dorahy said the genomic technology used in agriculture, which was introduced to Australia in 2005, was continuing to develop, and as a result, costs were decreasing.

"Our rapid rate of genetic improvement means we have entire drops of industry-leading genetics, meaning all clients have access to elite rams," she said.

"So far, not as much work has been done with maternal breeds for the prime lamb industry and as ewes stay on farms for six-to-seven years, I believe the economic value of genetic gain in maternal sheep has been considerably underestimated.

"The stud industry still needs to do the hard work to validate genomics in the paddock, but it's a fantastic tool which will help move industry forward."