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Improving flax one allele at a time

Rust hasn’t affected Canadian flax for more than 40 years, but new varieties must still incorporate resistance

On the surface, you’d think that a research project seeking to locate and sequence specific rust-resistance genes, then find ways to quickly identify the presence of these genes in plant breeding material is ultimately about preventing crop loss to rust.

But we’re talking about flax here, so think again.

Flax is a one million-acre crop in Western Canada, which doesn’t seem like a lot when you consider that canola is seeded to over 20 million acres and even upstart soybean is within spitting distance of three million. Still, a million acres means Canada is the biggest global producer of flax, most of which is exported.

That makes breeding of new flax varieties for higher yields and improved quality characteristics extremely important. But in order to do that, says Helen Booker, a professor and flax breeder at the University of Saskatchewan, your first focus has to be on flax rust.

Booker explains there hasn’t been a rust infection in Canadian flax crops since the early 1970s, but in order to register a new flax variety, it must carry resistance to rust — specifically to rust race 371. There are good reasons for this requirement, but it can slow the breeding process.

With funding from WGRF, Booker and colleagues from the U of S and Agriculture and Agri-Food Canada, have just launched a three-year project to find quicker, surer ways to identify rust-resistance genes in new flax lines for a faster, better breeding program.

On the shoulders of giants

“There are decades of research on rust resistance in flax and we’re trying to capitalize on that,” says Booker.

It begins, she says, with Harold Flor, an American plant pathologist who first discovered the genetic relationship between disease and host, i.e. that a plant’s resistance or sensitivity to a disease is caused by matching genes, one in the plant, one in the pathogen. Flor happened to be working on flax and flax rust in the late 1940s when he discovered this gene-to-gene relationship, which to this day is a foundational concept in all plant breeding programs, not just flax.

At the time of Flor’s discovery, flax rust was causing devastating crop losses across North America. Breeders worked tirelessly over the next three decades to develop resistant varieties, sometimes succeeding only to have the pathogen mutate and cause another collapse. By the 1970s though, they’d cracked it and since that time, all North American flax cultivars have been resistant to flax rust.

“We haven’t had a rust infection in Canada since the early ’70s, so that early breeding work was very efficient,” says Booker. “But when I want to make some advances in that material, I need to bring in ‘exotic’ material, which doesn’t have the R rating to North American rust pathogens.”

“Exotic” simply refers to breeding material from other parts of the world where flax rust strains are different from those in Canada. So while genetic diversity is the bedrock of any breeding program (it’s the reason breeders look worldwide for desirable traits such as yield, oil quality, harvestability, drought tolerance and more), if Booker wants to incorporate plant material from, say, Belgium, into her breeding program, she has to screen all the new lines developed with that material for resistance to North American flax rust.

Right now, that means growing out-crosses and exposing them to the disease to see which ones survive and which don’t.

“With this research, we’re hoping to increase the efficiency of breeding,” says Booker. The first step is to complete the genetic map of rust-resistance genes on the flax genome.

“Some of them are linked, meaning they are on the same chromosome,” says Booker, adding that there are five rust-resistance genes in flax and they are known to reside in five different locations in the flax genome: K, L, M, N and P.

Genes are just part of the equation. Booker and her colleagues are looking for alleles, which are variations of any given gene. A gene can have multiple alleles and each one can result in a different expression within the plant. For example, researchers know that there is one rust-resistance gene at the L locus (RL) and that it has 13 known alleles (RL1, RL2, and so on). Conversely, they know of the existence of alleles RK and RK1, but don’t know exactly where the K locus is on the genome.

The initial phases of the research project will be finding and sequencing the RK resistance gene, completing the sequencing of the RM gene and then building a data library for alleles related to all known flax rust-resistance genes.

The goal is to develop effective molecular marker assays so that breeders like Booker can quickly test all new flax lines that they develop using exotic plant material for the presence of alleles known to confer resistance to North American rust. It will let breeders know far earlier in the breeding process what to discard and what to keep.

Says Booker: “My goal is to have a diversified pipeline so I can respond to improve the yield and agronomic characteristics that growers want,” says Booker.


Characterization of Rust Resistance Genes of Flax is funded by:

  • Western Grains Research Foundation (WGRF)
  • SaskFlax Development Commission (SFDC)
  • Agriculture Development Fund (ADF)

WGRF is a farmer-funded and directed non-profit organization investing in agricultural research that benefits producers in Western Canada. For over 30 years the WGRF board has given producers a voice in agricultural research funding decisions. WGRF manages an Endowment Fund and the wheat and barley variety development checkoff funds, investing over $14 million annually into variety development and field crop research. WGRF brings the research spending power of all farmers in Western Canada together, maximizing the returns they see from crop research.

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