Sequence of oat genome a major step forward

In a province dominated by corn, soybeans and wheat, oat production can be undervalued. But those who grow it for food markets, work in the seed trade or feed it to livestock defend the crop’s production and value.

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That is why the recent sequencing of the oat genome is viewed with anticipation. Creation of the world’s first reference genome for oats is a huge step in generating a more targeted approach to improving yield, disease tolerance and other characteristics.

Why it matters: Greater knowledge of oat genomics may offer more opportunities for growers in Eastern Canada.

Oats are one of the better-known “super-foods,” capable of reducing cholesterol and improving heart health. Yet production in Ontario lags behind the big three: corn, soybeans and wheat. Only 60,600 acres of oats were planted in 2023 and 77,900 acres harvested in 2022, according to the Ontario Ministry of Agriculture, Food and Rural Affairs.

Sequencing the oat genome is cause for optimism within the research community. Wubishet Bekele and Nicholas Tinker are two Canadian team members who are part of this work, alongside 31 researchers from 20 institutions in five countries.

It took years to fully unravel the oat genome, in part because it is a unique and complex fusion of three sub-genomes. The work has both scientific and practical applications.

“We sequenced, characterized and compared two oat genomes, plus two of their wild ancestors,” says Tinker, a research scientist from Agriculture and Agri-Food Canada’s Ottawa Research and Development Centre.

“We found parts of the chromosomes have been inverted or jumped over to other chromosomes and also that different oat varieties have different chromosome arrangements.”

These rearrangements are a natural process but oats seem to have tolerated it more than other species, which explains why the genome is so complicated. It also provides a roadmap to tame that complexity.

“Crosses between oats with different chromosome arrangements can have good or bad surprises,” says Tinker. “We now have tools and knowledge to avoid or anticipate those surprises.”

“We apply tools to assist in selection by predicting things that we can’t see,” adds Bekele, who is also a research scientist at AAFC in Ottawa.

“Breeding is painstakingly detailed work that distills tens of thousands of lines down to one or two cultivars over a 10- to 12-year cycle. We combine genomic information with performance data to develop predictive models that improve the speed and accuracy of that selection process.”

Having complete genome sequences allows them to better pinpoint scientific traits and characteristics and begin to understand and predict the underlying genes and molecular processes.

“In addition to selecting progeny, we’re now trying to predict better parental combinations based on gene content and chromosomal configurations,” says Bekele. “This is the next level of improvement in genomics-assisted breeding, made possible by this new genomic resource.”

Good news for oats

The sequencing provides well-timed good news for public sector breeding in Ontario and Eastern Canada.

“To my way of thinking, having a viable oat breeding program within Eastern Canada is as critical to those value-added processes as having a battery plant in St. Thomas for the auto industry,” says Jeff Reid, general manager of SeCan.

“This is foundational to where we’re trying to go as a country. There should be no question as to whether oat breeding needs to be maintained or growing in terms of capacity in Eastern Canada.”

Reid refers to the “complicated puzzle” between government and producer funding groups, to figure out who will take responsibility for upstream foundational research versus closer-to-market testing. Will it be AAFC, the universities, industry or producers?

Who will participate in research for smaller and regional crops? And who will take responsibility for ensuring products reach the market in a way that’s available to every farmer in each region?

“When we talk about mapping the genome, that’s awesome,” says Reid. “That should help us to make much more rapid progress when we’re looking at introducing tools like gene editing.

“But that’s only going to help to tweak specific traits within a variety. In order to get the overall yield and general agronomic adaptation, there is no replacement for boots-on-the-ground testing and multi-location variety testing.”

Without making selections in the environment where a crop will be grown, it’s difficult to make progress.

“That’s really a key message that we’ve been trying to hammer home as we look to solve this puzzle,” says Reid. “This needs to happen on the ground where the crop is grown. And across Eastern Canada, I don’t see that capacity filling that void if we were to lose our public funding.”

Disease tolerance an issue

Quentin Martin believes in the need to balance optimism with the reality of growing the crop. Ontario deserves to have more than three crops, he says, without any slight against corn, soybeans or wheat. But his concern surrounding any new technology is that it’s often perceived as a panacea instead of a tool.

“We need varieties that have resistance to crown rust, which is the enemy of oats in this part of Ontario,” says Martin, co-owner of Cribit Seeds and Wintermar Farms near Kitchener.

“I don’t think we know enough about the disease, and there’s another risk we’re not talking about and it’s that we only have a couple of fungicides. If crown rust develops resistance to those, then we are really challenged, and we’re using some of the same chemistry in seed treatments as we are in full-year applications.”

Martin cautions against becoming complacent about use of fungicides and notes the inevitability that new varieties will lose tolerance to rust. Until a new line is exposed to the disease, it’s difficult to know whether it has tolerance.

In theory, that’s the advantage of working at the genetic level.

One trend that Martin sees as a benefit to oat production, over and above genome mapping or growing it for food manufacturers like PepsiCo, is its use as a cover crop.

Ontario may have harvested only 77,900 acres for grain in 2022 but there are usually more than a million acres of winter wheat that would benefit from an oat cover crop.

“To me, that’s where the real importance is going forward,” he says. “There’s certainly a place for oats in the whole cover crop repertoire, and we’re nowhere near saturating that opportunity. That’s where our future focus, energy and thought should be, is those acres as well.”