Is the answer to methane in the genome?

Selective breeding of livestock is a craft millennia old. The ability to fully decode DNA only arrived with the 21st Century.

Together, these two widely separated innovations make possible the breeding of ruminant livestock that produce negligible amounts of methane, which is a potent greenhouse gas and a source of much bad press for the red meat industries.

Two University of New England (UNE) projects in Armidale, NSW, aim to use the burgeoning science of genomics to reduce the methane output of cattle and sheep. The goal is for each new generation of these species to produce 1 per cent less methane than the preceding generation.

The projects (see Box) are driven by genomics: the study of genes and their interactions. Livestock breeders will still use the ancient craft of selective breeding to develop low-emissions cattle and sheep, but instead of selecting for a trait that can be paraded around a show ring, like muscling, breeders will select for a trait – low methane production – that can only be accessed through reading the double helix of DNA.

The word “trait” is singular, so it’s natural to assume that a trait is a product of a single gene. That was the belief in the 1990s, when researchers thought that targeting one or two genes would influence a trait like meat tenderness. But it turns out that organisms are more like ecosystems than machines.

Now, says livestock genetics expert Dr Rob Banks, scientists understand that for most traits of interest, “almost without exception, there are at least hundreds, if not more, genes that are affecting those traits. So any one gene has pretty small effect”.

There is no single “low methane emissions” gene. There are, however, animals that produce significantly less methane than their peers without any apparent loss of prosperity, and that characteristic is likely encoded in their genetic make-up.

The UNE projects will read the DNA of animals which have been measured for methane output (and other traits) and use the resulting genomic reference – the “DNA library” – to identify patterns in the DNA of other animals associated with lower emissions in each breed. 

“One of the beautiful things about genomic selection is it is unbelievably simple,”

Rob Banks, UNE

This approach to low-emissions livestock doesn’t use invasive genetic engineering or gene editing. It just gives a leg-up to evolution.

Banks, who until earlier this year was director of the Animal Genetics and Breeding Unit (AGBU), is fond of evolutionary biologist Leslie Orgel’s “Second Rule”: “Evolution is cleverer than you are.”

“One of the beautiful things about genomic selection is it is unbelievably simple,” he says. “If you want to improve a trait, you simply measure it on enough individuals to calculate reasonable genomic breeding values, and you’ll be able to breed for that trait.

“You won’t have really any idea how the body makes it; you won’t have found a gene for whatever it might happen to be. But you will breed animals that have the thing you want.”

Breeding for lower methane production is also a permanent solution that will forever define the breeds pursued for this approach. Banks has reservations about a parallel push to find dietary supplements which tame the methane-producing tendencies of rumen bacteria. “Whatever their merits, supplements will be a cost to the livestock sectors – forever,” says Banks.

Banks also knows, better than anyone, that if the principles of breeding for low-emissions livestock are straightforward, the science is not.

Livestock genomics is younger than the iPhone. The cattle genome was first sequenced in 2009, the sheep genome in 2014. Researchers working on the genetic improvement of these species have since used genomics to enhance understanding of how relationships between animals can be used to breed for certain traits. The current work on methane highlights the power of the genomic approach.

Some context: From prehistory, livestock owners have chosen animals to mate based on visible characteristics. Over the past 300 years, the process began to be enhanced by record keeping that was used to map pedigrees and codify species into breeds, like Hereford cattle or Merino sheep.

Livestock genomics is younger than the iPhone.

In the 1960s, Australian cattle breeders began to enhance shared pedigree records with the sharing of performance records. In the early 1970s, at UNE, a visionary named Arthur Rickards began feeding all these pedigree and performance records into a primeval punch-card computer. Using statistical tools developed by another set of visionaries at UNE – a team of geneticists led by Dr Keith Hammond – the computer returned statistical probabilities of how reliably a bull’s offspring would manifest certain traits like muscle, growth, or fertility in female offspring, compared with all other bulls in the database.

These probabilities are called “estimated breeding values” (EBVs). An EBV distils into a single figure years of pedigree and performance records and their relationship to related records of other individuals in the breed. EBVs have become a staple of modern livestock breeding.

At most Australian bull sales, the sale catalogue’s list of EBVs is as necessary to buyers as a view of the animal striding around the sale ring. EBVs are represented in figures like birth weight: -1.5 kilograms or 400 days: +85 kilograms – meaning that this bull’s calves will be lighter at birth than the average of all bulls in the breed, but about 85kg heavier than the average by the time they are 400 days old (the bull contributes half of these attributes; the cow the other half).

The data sitting behind a growing number of EBVs now cumulatively contains billions of data points. It is managed by the BREEDPLAN software first developed by AGBU in the 1970s. BREEDPLAN, and the ecosystem of data collection around it, has given Australia one of the world’s best livestock genetic evaluation systems. AGBU later developed the Sheep Genetics evaluation software based on the BREEDPLAN model.

Genomics has added new power to these systems and new efficiencies. To develop a traditional EBV based on performance records, the methane production of every bull and cow associated with the breeding value would have to be measured.

“Let’s say each test costs $200 per cow,” Banks says, “and that in a prominent breed there are 75,000 seedstock cows that need to be tested: that’s $15 million per year. It’s not going to happen.

“But with genomics, we can test between 500-1000 cows in that breed, at a cost of $200,000. We then use the reference library – our knowledge of how patterns in the DNA are related to methane output – to very quickly and cost-effectively screen every individual in the breed, and find those with the most favourable DNA profiles for methane emissions.”

No trait is an island, though. Pull on one trait, and other traits come too.  For instance, wool producers pushing their flocks towards heavier fleece weights can expect an undesirable coarsening of wool fibres. Or breeding for heavier sheep can make lambs larger at birth, increasing the risk of birthing problems.

“We’re hoping that methane efficiency is favourably correlated with useful sheep production traits,” says Julius Van Der Werf, a UNE professor of animal breeding who is running the sheep methane project. “If they are positively correlated, and we can achieve production benefits and lower methane output, then sheep breeders will be willing to push for lower methane output in their breeding programs.”

“We’re hoping that methane efficiency is favourably correlated with useful sheep production traits,”

Julius Van Der Werf, UNE

If production and methane traits are not correlated, or pushing for lower methane output makes sheep less productive in certain ways, the job becomes more difficult. “Then we have to find the balance between how much of selection emphasis is on production traits, and how much selection emphasis is on methane,” Van Der Werf observes.

“In theory, that depends on the economic benefits of these traits: you put a price on methane, you put a price on productivity, and then you balance how much you push your breeding selection in one way or another. If there is a big cost placed on greenhouse gas emissions, breeders might choose to go faster towards methane at the expense of productivity.”

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Preliminary modelling holds out hope that there won’t be a large trade-off between lower methane output and sustained productivity. “It looks like we can achieve both,” he says.

However effective the genomic science, it would remain locked away on computers unless there is a conduit to get it into the real world – in the hands of the breeders who run the seedstock herds and flocks, and the livestock producers who buy that seedstock to improve their own productivity.

Fortunately, Australia began building that conduit more than 40 years ago.

BREEDPLAN and Sheep Genetics, built for an earlier era of data collection, have become vital for relaying the findings of genomics science into the paddock. The databases provide a trusted conduit through which the findings of genomics research can be communicated to livestock breeders in the simplest of exchanges: a single figure.

Box

Ruminant methane is a by-product of ruminant digestion, which is largely undertaken by microbes. An estimated 8500 species of rumen microbe work in complex collaborations to break down the tough cellulose of grass and other forages eaten by their host. Methane, a by-product of this process, is burped out (and in much lesser quantities, farted) by cattle, sheep and goats.

FAO calculates that this expelled gas makes up 39 per cent of the overall contribution of animal agriculture to global warming. Livestock globally produce about 14.5 per cent of anthropogenic greenhouse gas emissions.

Concern about the contribution of ruminant livestock to climate change is contributing to declining per-capita consumption of red meat in affluent countries, and climate change itself is denting farm profits. Australia’s red meat industries have committed to becoming carbon-neutral by 2030. As part of this initiative, Meat and Livestock Australia, the nation’s red meat R&D body, has marshalled $19 million for the UNE-led projects aimed at breeding towards more efficient digestion in cattle and sheep. NSW Department of Primary Industries and breed society Angus Australia are collaborators in the project.