Meat and Livestock Australia has lost a legal battle to block a US company's cattle genome patent.

After a series of amendments, the Federal Court has decided to allow a patent application filed by a US company, which Australia's peak livestock research body says will have a chilling effect on genomic research for Australian cattle.

Meat and Livestock Australia (MLA) launched legal action against Branhaven LLC in 2016, appealing a decision by IP Australia to grant a patent which describes methods for identifying important traits in cattle, such as growth rates, milk production and fat marbling.

MLA, which has spent millions of its levy payers' money on genomic research, said the patent was so broad it potentially covered two thirds of the bovine genome, and nearly every valuable trait.

They attacked the patent application on nearly every legal ground possible in week-long hearing in late 2017.

In early 2018, Justice Jonathan Beach rejected most of MLA's arguments, save for three, and granted Branhaven a period of time to amend it.

But MLA did not give up its fight to block the patent application, according to Clayton Utz partner Richard Hoad.

"Effectively the first 30 pages of the decision address MLA's arguments that the judge didn't have the power to allow the amendments, because the judge had already decided the issues for determination in the case," he told the ABC via email.

"Arguing that a judge doesn't have the power to decide something tends to be an ambitious approach, and it was roundly rejected in this case by Justice Beach."

On Wednesday morning, Justice Beach said he would allow the amended patent.

The court ordered Branhaven to pay 10 per cent of MLA's legal fees, because MLA had "modest success" on its appeal of the patent application.

The court rejected Branhaven's request for MLA to pay the cost of preparing the amended patent application, saying "it obtained an indulgence" by being allowed to amend it in the first place.

MLA has 14 days to decide whether or not it will appeal the decision outlined in the full judgement.

If an appeal is granted, it would be heard by a full bench of the Federal Court.

If no appeal is made, then the amended patent application will go back to IP Australia, and it can proceed to grant.

Both sides can use the 14 day period to appeal the court's decision on costs as well.

What was in the original patent application?

Australian farmers use genomic testing on their herd to identify the best breeding stock, to speed up the adoption of desirable traits.

But it is expensive, costing about $65 per cow, and stud breeders have told the ABC previously they are worried this patent, if granted, could increase the cost.

MLA argued before the court the broadest claim in the patent potentially extends to nearly two thirds of the cattle genome.

It was originally filed by Cargill USA and Branhaven LLC, but in 2017 Cargill withdrew from the matter, assigning its rights to another US firm SelectGenetics LLC.

The patent, first written in 2003 and filed in Australia in 2010, describes a method for identifying genetic traits in cattle through the use of genetic markers called SNPs (single nucleotide polymorphisms and pronounced 'snips').

Genomic testing is increasingly used in the livestock sector to select animals with superior genetic traits. ( ABC News: Roxanne Taylor )

It identifies 2,510 specific SNPs (there are billions through the genome), but it also lays claims to a large region (500,000 base pairs of DNA) either side of each of the 2,510 identified SNPs.

Much of the concern about the patent comes from the secondary claim because, although the field of genetics has advanced rapidly since 2003, and many millions more SNPs have been located since then, researchers believe their current work could still infringe on the patent.

This is because it includes the 500,000 base pairs of DNA either side of the SNPs actually identified in the patent.

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"If this patent was concerned with human genes, there would be a public outcry," MLA's senior council Katrina Howard SC told the court in June 2017.

"There's no good reason it should apply to cattle."

While MLA attacked the patent on almost every legal ground, a central pillar of its argument was that the method described for identifying the genetic markers was common knowledge before the patent was written in 2003.

They argued that work being done on the human genome, as well as scientific papers published before 2003, meant methods described in the patent was obvious to skilled geneticist.

But Branhaven said that work to map the bovine genome had just started, and was not finished until 2009 so therefore, the patent describes a significant and noteworthy achievement and invention.