Sheep's genome at last reveals its secrets

Scientists have published the complete DNA code of the sheep. Despite some industry indifference, there is much that could help farmers breed more productive animals. Elizabeth Finkel and Yi-Di Ng report.

Two Texel sheep like this one were chosen to reveal their species' genome. – iStock

The sheep may be one of the first animals to be domesticated, but it is one of the last to have its genome read. Now it has finally joined the ranks of 80 mammals, including the goat, cow, pig and horse. Its complete DNA code was published on 6 June in Science magazine.

The publication marks the end of a challenging eight-year quest. “At times I thought it was all going to fall apart,” admits Brian Dalrymple, the leader of the project at CSIRO Animal, Food and Health Sciences in St Lucia, Queensland. “It’s not just about science, it’s also about diplomacy and politics.”

Compared to cattle or pig farming, there was less international industry support to help fund it. “There are only two places in the world where there is a significant sheep export industry and that’s Australia and New Zealand,” explains Hutton Oddy, a former manager at Meat and Livestock Australia (MLA), who in 2003 helped lay the groundwork for the sheep sequencing project. But it has not always been easy to get the Australian industry on board.

“I don't believe in … picking a ram off a computer,” Wal Merriman, then chairman of the Australian Wool Innovation Corporation, told the Australian newspaper in 2012. He had just blocked a $5 million research grant for sheep genetics.

“It's an art, not a science. There's been nothing developed in sheep genetics in the last 10 years that is a tool I would use that I can't see already with my eye," Victorian fine wool breeder John Crawford said in the Australian article.

Despite this discouragement, Australian scientists formed a consortium with colleagues from New Zealand, US, Europe and, later, China to read the genome of two Texel sheep – a breed named for the island in the Netherlands where they originated. The genome has revealed new secrets of this hardy animal on whose back much of human civilization – and certainly Australia’s fortunes – were built.

Originating in the Middle East, sheep thrive in harsh, dry conditions. Thanks to their rumen, a four-chambered stomach, they can eat tough herbage like Australian saltbush or wallaby grass. It is a fermentation vat for microbes, which provide the enzymes to break down tough plant fibres.

The ancestors of sheep evolved a rumen 50 million years ago to exploit the grasslands that were spreading at the time. The difference between ruminants – such as yaks, antelopes, deer, cows and goats – and non-ruminants, such as horses, is obvious in their manure. The horse’s manure is full of undigested plant matter and seeds, unlike the sheep’s, which looks like it’s been ground to a pulp. The sheep does particularly well at surviving on marginal grasslands due to the relatively large size of its rumen compared to its body size.

The Science paper examines the genes that make up this highly successful organ. The researchers identified a gene called "trichohyalin-like type 2" (TCHHL2) that accounts for the toughness or “cornification” of the rumen wall. What scientists hadn’t realised is that sheep may use the gene to interweave strands of keratin, a fibrous protein also found in skin, hooves and hair into the rumen wall.

Genes might also help explain why modern sheep are
so woolly, whereas their ancestors were not.

The findings may also help breed animals that belch less methane, a by-product of fermentation and a major greenhouse gas. Livestock contribute around 14.5% of global man-made greenhouse gases, and in Australia more than 60% of all agricultural greenhouse gases.

As for genes that might play a role in these emissions, it’s still early days. But Oddy is now principal scientist on a project to breed sheep that produce less methane, based at the University of New England at Armidale. Sheep emissions, measured by placing a transparent plastic box over the sheep for 30 minutes or so, show that the difference between high and low emitters can vary by 20%. Genetic testing to identify low-emissions sheep will be much easier than trying to catch sheep-burps in a plastic box. “Genome technology is useful for any difficult-to-measure trait. And there’s no doubt about it – methane fits into the category of difficult to measure,” Oddy says.

Genes might also help explain why modern sheep are so woolly, whereas their ancestors were not. They were more like the endangered wild European Mouflon sheep, which are hairy with a short downy undercoat. Some time during the domestication of sheep over the past 10,000 years, that downy undercoat became the now-familiar long woolly coat.

The sheep's ancestor, like the Mouflon,was hairy rather than woolly. – Erich Kuchling/Getty Images

What genes were breeders unwittingly selecting when they chose the woolliest sheep? One candidate is a gene that has been duplicated five times in the modern sheep – MOGAT 2, and its partner, MOGAT 3, which has tripled. These genes are involved in metabolising fat and, in most mammals, are active in the liver and intestine. But in sheep they are most active in the skin. Fat is an important component of wool. Up to 25% of the weight of the fleece is made of fats, mostly lanolin, that helps make it waterproof, though how these fats are produced may also affect whether you end up with hair or wool.

Notwithstanding the reservations of some breeders, information trickling in from the early stages of exploiting the sheep genome has already been used by Australia’s Sheep Cooperative Research Centre of the Department of Industry. The centre is now breeding sheep that grow more efficiently than their forebears, while consistently producing tastier, more tender meat.

“That’s huge,” says James Rowe, CEO of the Sheep CRC. He points out that having the full genome will improve the ability to predict traits and speed up genetic improvement. “Once you improve the accuracy of estimating traits, the rest will follow.”

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