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Clubroot strikes back

Clubroot-resistant varieties are the cornerstone of clubroot management in Alberta canola. But the pathogen is actively chipping away at that cornerstone. In the past two years, 10 new variants of the pathogen have been found that are each able to defeat the resistance genetics in currently available canola varieties.

This is a warning bell signalling growers to do as much as possible to prevent and control clubroot, including stewardship of clubroot resistance. Otherwise, their most effective tool for clubroot management could be at risk.

Clubroot is a devastating disease caused by Plasmodiophora brassicae. This soil-borne pathogen produces irregular swellings (galls) on the roots of canola and other cruciferous plants such as mustard, cabbage and stinkweed. The galls hinder the movement of water and nutrients into the top parts of the plant, resulting in severe yield losses in susceptible cultivars. The galls on a single infected root can produce billions of resting spores. And those billions of tiny spores can survive in the soil for many years, poised to attack when the next host crop comes along.

Back in 2003, clubroot was discovered in a canola field near Edmonton. Annual surveys since then show this disease has continually spread to new fields. As of the 2014 survey, a total of 1,868 clubroot-infested fields had been confirmed in the province, mostly in central Alberta.

Clubroot pathotypes, or strains, are identified based on whether or not they cause disease in a standardized set of host plants, referred to as “differential hosts.” Pathotype 3, a very virulent type, is the most common one in Alberta canola. Other pathotypes found in the province include pathotypes 2, 5, 6 and 8. Breeders have developed canola varieties with excellent resistance to all of these pathotypes.

In 2013, a new pathotype was found that behaved like pathotype 5 on the differential hosts, but was different in a very important way – it could cause disease on clubroot-resistant canola. “A field in central Alberta was found to have a strain of the pathogen that was capable of overcoming the resistance in nearly all of the clubroot-resistant canola cultivars that we have on the market,” says clubroot-expert Stephen Strelkov, a professor of plant pathology at the University of Alberta. As a temporary measure, he named this new variant “pathotype 5x.”

Much more than one isolated case
“We wanted to find out whether this problem was localized to one field or whether there was a wider issue, and whether there was just a single new strain or multiple ones. So in August and September 2014, we conducted our regular clubroot survey, but we also worked with Alberta Agriculture and Forestry, some of the agricultural fieldmen and Canola Council agronomists to conduct a targeted survey to look at the performance of clubroot-resistant canola cultivars,” Strelkov says.

They identified a number of fields with clubroot-resistant canola and scouted them for possible clubroot symptoms. If they suspected clubroot, then they sampled the affected area of the field. “Most of the surveyed fields were in the Edmonton region because that is the part of Alberta with the longest history of clubroot in commercial fields and where the new pathotype was identified. There was a lot of surveillance around that first case to see if the variant had spread locally. As well, there were fields scouted across the province,” explains Michael Harding, a research scientist in plant pathology at Alberta Agriculture and Forestry (AAF).

They collected samples from 27 fields that had been planted to resistant varieties, but showed higher than expected levels of clubroot. Then they tested each pathogen sample in a three-step process, requiring months of work in the greenhouse.

“First, we re-inoculated the strain onto the same resistant variety that was in the field where the sample was found. That was to make sure the strain definitely was able to overcome that variety’s resistance and that the problem wasn’t due to some other factor, such as volunteer susceptible plants,” Strelkov explains. “Then if the strain was confirmed to really be causing increased virulence, we tested it on a whole set of clubroot-resistant canola varieties. And finally, we also obtained the pathotype identification by testing it on the differential hosts. The differential hosts included not just the ones that have historically been used, but also additional hosts that we are evaluating for a Canadian clubroot differential system.”

The survey’s findings were serious – multiple fields were affected, not just one. “Of the 27 fields, 16 were confirmed to have a clubroot strain that was able to overcome the resistance,” Strelkov says.

The affected fields were found in multiple counties, not just one area. “In 2013, we thought possibly just a single field was affected, and if we found new strains they might have come from that one specific field. In that case, the fields with new strains would have been clustered tightly together. Most of these new fields were in central Alberta, but some were quite geographically separated; there was up to about 600 km between some of the fields,” Strelkov explains.

There were nine new variants, in addition to 5x. And multiple varieties of clubroot-resistant canola were involved. Most of the new clubroot variants were highly virulent in all the clubroot-resistant varieties.

Strelkov notes, “The characteristic that most of the 16 fields had in common was they had seen a number of crops of clubroot-resistant canola planted over the last four or five years. So, probably one of the major factors was that these new strains had been selected for [by growing] resistant varieties. [The distance between the fields and the multiple strains indicate that] independent selection events were responsible for development of the new strains. In different fields, the selection pressure selected for different rare pathotypes.”

Proliferation of pathotypes
The first canola varieties with excellent clubroot resistance to Alberta’s pathotypes became available in 2009 and 2010. Although resistance breakdown within four or five years seems fast, it wasn’t unexpected by clubroot scientists and specialists.

“The organism that causes clubroot can be quite diverse, so in a population of resting spores, these variants can already exist. If we put a lot of selection pressure on them by growing a resistant cultivar, then only a small fraction of the population can cause disease. So we essentially select for those variants to become common in the population because they are the only ones that can survive,” Harding explains.

“Let’s say we have a population that is predominantly pathotype 3. Then we introduce clubroot-resistant varieties that are resistant to, for instance, pathotypes 3, 5, 6 and 8. Any of the spores in the soil that are of those pathotypes are no longer able to cause the disease at any significant level. But there are other variants at very, very low frequencies that maybe can cause the disease. So over time, by growing the resistant varieties, we select for those variants, until they start showing up as dead patches in what was a resistant canola variety.”

Harding adds, “In other parts of the world that have had clubroot longer than we have, this is not uncommon. Because clubroot produces so many spores and is so genetically diverse, experiencing the resistance two or three times is enough to allow variants that can overcome the resistance to start showing up.”

Strelkov has found the same type of result in greenhouse experiments. The experiments showed that, for some resistant cultivars, growing the cultivar just twice in a row under high disease pressure produced pathogen strains that caused high disease levels on the cultivar.

“We weren’t surprised that the survey found a shift in pathotype. Results from other countries and other crops, such as cabbage, suggest a shift in pathotype after two to three exposures [to a resistant cultivar],” says Dan Orchard, agronomy specialist with the Canola Council of Canada (CCC).

“But one surprise was finding nine new ones all at once. And the second surprise was the geographic distribution of the new pathotypes. I think we anticipated seeing the pathotype shift occur in the heavily infested areas around Edmonton. Although fields in that area were identified, other fields were scattered from north to south across Alberta’s clubroot-affected region.”

Implications for monitoring, research and breeding
To monitor for clubroot pathotype shifts, AAF is again collaborating with Strelkov, the CCC and others to conduct a targeted pathotype survey in 2015, with the results expected in early 2016.

For researchers, one of the immediate hurdles is to develop a better way to differentiate and name pathotypes for the Canadian situation, since the current set of differential hosts doesn’t cover the new Alberta pathotypes. Strelkov is leading this work.

Strelkov and his collaborators have also started to work on developing DNA markers for distinguishing between the various strains of the pathogen. If they can develop such markers, strain identification would be much quicker and easier than the current method of having to isolate the pathogen from the sample, then grow it in the greenhouse, then inoculate all the differential hosts, and then evaluate each of the hosts for the presence of the disease.

Breeders have already been working on adding resistance to pathotype 5x into their resistant varieties. “A lot of work has been done in the past couple of years in breeding resistance against pathotype 5x. There is some talk in the industry already of varieties that will be tested in 2016 that appear to have resistance to this new strain,” Orchard says. (Canterra’s clubroot-resistant canola CS2000 has an intermediate level of resistance to 5x, partway between a resistant and a susceptible response.)

Adding resistance to the other nine pathotypes could be challenging. “With these nine additional pathotypes, the questions for breeders will be: Do their varieties need to have resistance to all nine of these new strains? If they don’t have resistance to all of them, would the varieties need to be regionally deployed? For that, we’ll have to get a better understanding of what strains are most prevalent in what areas,” Orchard says.

“In the vast majority of Alberta canola fields, the resistance in our current varieties seems to be holding up well,” Strelkov notes. “But if the resistance starts to be defeated in a more widespread area, then it becomes more and more of a challenge for breeders to find effective sources of resistance, bring those resistance sources into our canola varieties, and have a registered product. It really highlights the need for resistance stewardship. The genetics is the most important tool we have to manage clubroot. If we’re not careful, we could end up jeopardizing that.”

Strelkov and his colleagues are conducting research to answer a number of questions about the new pathotypes, such as which ones are the most virulent and which ones should be a focus for breeding efforts in terms of resistance screening. For instance, it may be that if a breeding line’s resistance holds up against a particular variant, then there’s no need to test it against certain other variants.

The researchers also want to delve into the evolutionary relationships of the new variants, for instance, to figure out how the variants relate to the pre-existing strains. Strelkov explains, “That can help us understand what characteristics are allowing some variants to emerge more quickly than others.”

Implications for growers
“This is a really serious issue. We shouldn’t underestimate the clubroot pathogen. This is a real threat to canola production. We don’t really know how soon we’re going to be able to have resistance to these new variants because most of the new variants haven’t even been tested against any germplasm,” Harding explains.

“Having said that, I don’t want to give the impression that this is the apocalypse. The resistant varieties we have right now are still resistant to pathotypes 3, 5 and 6, and in most of the fields in Alberta those are the most common ones. The second thing is we are hopeful that canola companies will be able to come up with varieties that can help manage these new pathotypes. So we think that the clubroot management practices that we have in place are still the growers’ best chance to be successful.”

Orchard recommends a multi-stage management strategy for clubroot, rather than relying exclusively on resistant varieties. “Growing a resistant variety is sort of a Band Aid. Although it won’t propagate the disease as much as a susceptible variety would and it allows you to successfully grow canola on an infested soil, it doesn’t cure the infestation.”

The first stage of the strategy is to prevent the pathogen from coming into your fields for as long as possible. Orchard explains, “Although you may eventually have uncontrolled exposure because clubroot goes anywhere that soil goes – on equipment, animals, seed, in the wind – a clubroot-free field is worth its weight in gold in the meantime. So do your best to stop dirty equipment from coming onto your farm, and keep traffic out as much as you can.”

Also, growers should continually scout their canola fields to identify any clubroot infestations as early as possible. Orchard says, “Typically the field’s entrance is the first spot you’ll find the disease because it tends to come in on equipment. But also look at areas where water will run across the field and where wind-blown soil gathers.”

The second stage is when you find some small clubroot-infested patches. Orchard recommends micromanaging those patches to try to slow down the disease. “In other countries, they lime those areas to raise the pH, doing a thorough job of incorporating the calcium properly at the right rate and the right depth. Liming doesn’t eliminate clubroot, but it can decrease clubroot’s impact on the crop.” However, he adds that liming may not have much impact on the pathogen if the conditions are really wet and warm.

Harding advises limiting traffic and soil movement in the infested patch and using equipment sanitation practices to slow the spread of clubroot within the field and between fields. He notes, “If the infested area is small, some growers have been seeding that patch to alfalfa or grass for an extended period of time. There has also been some work with soil fumigants to see if they can bring the number of resting spores per gram of soil down significantly.”

The next stage is when the disease has spread beyond a few small patches. “Once you have clubroot in your field, one of the key management practices is to not provide it with any host where it can complete its life cycle. When it completes its life cycle, it produces so many resting spores in a season that it can become a real problem in a hurry. So plant a non-host crop and control any weeds that could be hosts,” Harding says. “If you grow a canola crop, make sure it’s resistant, and be sure to use resistance stewardship, mainly a rotational break between canola crops of at least three years.”

Overcoming resistance is a numbers game, so a heavily infested field is at greater risk of resistance breakdown than a lightly infested field. Orchard explains that a four-year rotation won’t prevent the pathogen population from shifting to new virulent variants after two or three times of deploying a resistant cultivar in a moderately to heavily infested field. However, a four-year rotation does space out the selection pressure events and also prevents spore levels in the soil from increasing as quickly, allowing breeding programs a little more time to try to keep up with pathotype shifts.

According to Orchard, all the clubroot-resistant canola varieties currently available on the Prairies likely have the same major resistance mechanism, so rotating between the current resistant varieties will probably not stop the pathogen from overcoming the resistance.

Another key practice is to remain vigilant. “Don’t stop scouting for clubroot once you grow resistant varieties. In fact, you have to really be on the lookout for patches where the pathogen is evading the resistance,” Orchard emphasizes.

If you suspect a breakdown in clubroot resistance in your fields and would like a diagnosis, you could contact Orchard, or you could call AAF’s pest surveillance hot line at 310-PEST. ”If a grower chooses to report, that’s very helpful because it gives an idea of how common this problem is and how fast it is spreading,” Harding explains.

Using some additional practices, along with resistant varieties and longer rotations, could bolster your efforts to manage clubroot. “Things like liming and fumigation are very expensive, but canola is worth a lot of money, and this disease has major impacts,” Orchard says.

“Some countries are using bait crops, and I think this option should be explored, perhaps in combination with liming and possibly fumigation, for fields where the spore loads aren’t that high.” A bait crop involves planting a cruciferous crop to stimulate the resting spores to germinate, and then spraying out the bait crop before the pathogen completes its life cycle.

“Another factor that we’ve maybe overlooked is that clubroot is really affected by soil temperature. Canadian researchers found that clubroot doesn’t seem to be active at all until the soil temperature is about 15 to 17 C, and its peak growth occurs at 20 C and above,” Orchard notes. “So you may be better off seeding a heavily infested field as early as you can get on the land, and maybe seeding it a little heavy in case of frost and emergence issues. The idea is to get the crop established early in those fields, so the plants will have big, healthy roots by the time the soil warms up to 17 to 20 C. That will help reduce clubroot’s impact on the crop because bigger, healthier roots may withstand infection better, and because the infection comes at a later crop growth stage; an early infection really robs the yield and can kill the plant. Once you’ve seeded your heavily infested fields, you can wash your equipment, and then seed your less infested land when conditions are a little warmer.”

As more clubroot pathotype monitoring, research and testing are conducted, a clearer picture should emerge of the severity of the challenge facing canola growers in clubroot-affected areas.


November 2, 2015  By Carolyn King

A clubroot-infected canola root can produce billions of resting spores Clubroot-resistant varieties are the cornerstone of clubroot management in Alberta canola.


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