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The search for oat rust resistance

Orange pustules on AC Morgan indicate crown rust. The black discoloration surrounding some pustules is called “telia,” which consists of the over-wintering structures of the fungus. Photos courtesy of Dr. Curt McCartney, Crop Development Centre, University of Saskatchewan.

Unseen but virulent, rust spores wait in the air whenever a new oat variety shoots up somewhere on the eastern Prairies. The region is home to milling oats, a member of the Avena family found worldwide in thousands of variations, and susceptible to rust infection.

By its nature, rust is highly adaptive. New races routinely defeat so-called “rust-resistant” genes. As a result, breeders and pathologists are always looking for a new “major gene” to move into the genetics for high-producing milling oats.

Simultaneously, spores wait, seemingly nearby, to defeat the new gene. A “major” gene gives a plant full season-long resistance to one or more rust races.

Initially, an effective major gene provides protection against the majority of the crown rust population. After five to 10 years of widespread use in an oat variety, crown rust adapts to the major gene. The process, called resistance breakdown, is similar to the buildup of herbicide resistance in weed populations.

Canada has an advantage, as winter shuts down the spore attack and development. “Crown rust is a huge problem for oat production in Argentina and Brazil because the rust cycles constantly all year long on the wild oats and the tame oats,” says Dr. Brian Rossnagel, oat breeder at the University of Saskatchewan’s Crop Development Centre (CDC) in Saskatoon. “When those folks find new single gene resistance, they’ll release it, and by the time they get the seed produced, it’s already breaking down. We’re not hammered quite that badly.”

One of the key gene-trackers aiming to shut down oat rust spores more effectively is a cereal and flax pathologist at the CDC, Dr. Curt McCartney.

Finding those “major” genes is relatively simple today, says McCartney. Less than 200 metres from his office is a world collection with more than 21,000 accessions of the Avena family. Many, tested and untested, contain a major gene for crown rust resistance. Thousands of accessions already have been grown specifically in crown rust nurseries to check for resistance.

Discovering resistance genetics was one aspect of research by Dr. James Chong, Agriculture and Agri-Food Canada (AAFC) pathologist, in Winnipeg. Before he retired in November 2009, Chong passed on his database and germplasm to McCartney. “We’re working now with around 50 accessions of Avena sterilis, the best of the larger set screened by Dr. James Chong,” McCartney says. “Avena sterilis is a winter wild oat. Accessions that I have are mainly from the Middle East. The species possesses a lot of effective crown rust resistance. It also has the same basic genome as cultivated oats, so you can cross-pollinate and move the resistance genes into adaptive material fairly easily. There are definitely more genes that could be brought over to cultivated oats.”

There is one drawback, however: the major genes are expected to break down again.

Field plots at the University of Saskatchewan on July 29, 2009.

Stacking genes
One new option involves stacking two major genes. In limited testing, it looks hopeful. According to Dr. Jennifer Mitchell Fetch, an AAFC oat breeder in Winnipeg, the oat program has a very promising milling oat: Summit. Marketed by FP Genetics in Regina, it is promoted as the “best crown rust resistance currently available on the market.” Mitchell Fetch says, “We believe Summit carries two major genes for crown rust resistance that were defeated. For now, it seems to be providing us with some resistance again. It’s interesting that putting two defeated genes together has brought us resistance.”

The older gene in Summit, Pc48, was carried by Triple Crown. The other gene in Summit, Pc68, was carried by AC Assiniboia, Ronald and other oat varieties. Mitchell Fetch estimates that at one point, up to 95 per cent of oat varieties grown in Manitoba carried the Pc68 gene. “For a few years, farmers grew these lines and they were clean. Then the rust started coming in slowly and defeated the resistance,” Mitchell Fetch says.

Stacking Pc48 and Pc68 in Summit oat was helpful but it did not completely solve the issue for growers.

Current major genes protecting the oat industry are Pc91and Pc94. The Pc91 gene, identified by North Dakota State University, is used in HiFi and Stainless oats. It also is in the CDC’s OT3044, which was supported for registration in February 2010.

The Pc94 gene, discovered in the Winnipeg oat breeding program, appears to be holding up very well as a major gene. It is one of two resistance genes stacked into the variety Leggett, from AAFC Winnipeg, and is in the CDC’s OT3037 (also supported for registration in February 2010).

Predictably, Mitchell Fetch says the Pc68 and Pc94 resistance stacked into Leggett also will be overcome in time.

Crown rust pathogens recombine sexually and make new genetic combinations, Mitchell Fetch says. The alternate host, buckthorn, is available throughout the growing region. “You might have one individual spore that can overcome Pc48 growing next to one that can overcome Pc68. Their offspring could produce an isolate that’s virulent on both genes. So, we’re always trying to stay one step ahead of the pathogens,” she says.

Partial resistance
The better, but much more challenging goal, is an oat that builds resistance to fungal attack with a stack of three to five genes, says McCartney. It will not be a stack of defeated major genes. Instead, partial resistance will derive from several genes that slow the development of a rust epidemic. The collective resistance is expressed during the course of a growing season, as they exhibit partial resistance at a level that eliminates the need for fungicide. To the grower, the crop will be infected, but it will not be serious.

It is a two-stage search. In the greenhouse, McCartney only selects lines that show susceptibility at an early stage. The few seedlings that are resistant will probably have a major gene.

A field test is the second stage, with each line reaching maturity. “We’re looking for material in the field that has relatively less crown rust than susceptible varieties.”

McCartney notes that a leaf rust resistance gene in wheat, known as Lr34, has been used for many years and remains effective. It is “undefeated” and still is used widely in breeding programs in Western Canada. “The pathogen has never adapted to it. We’re hoping to find something in oats that will have a similar effect to Lr34 in wheat. We definitely have material which has these partial resistance genes, no question. We have that identified already. Now we’re doing the genetic studies; trying to understand it.”

Marker genes
The discovery process for partial resistance genes needs to be pinpointed on oat chromosomes. The genes then need to be moved into existing high-performance lines of the cereal.

Pinpointing genes or pieces of DNA is becoming possible with the development of “genetic markers.” A genetic marker is a gene or DNA sequence with a known location on a chromosome. Markers beside a desirable trait make it easier to find. The more markers on the genome map, the easier is it to select characteristics. Major crops like wheat, canola, corn and soybeans now have many markers. Recently, a few have been found on oats. An international collaboration to map the oat genome and develop markers for it has been underway for the past few years. With patience, science and current techniques, eventually an equivalent to Lr34 should emerge for oat.

McCartney says, “In the near future, there will be varieties with combinations of Pc91 and Pc94. We’re also working with another major gene from a North Dakota variety, and on some DNA markers for resistance in that variety. Hopefully, we will prolong the effectiveness of these genes with some good gene combinations. ”

As for the “magic bullet” partial resistance package, he says, “It definitely won’t be in the next five years.”