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Attack on seedling diseases

Researchers are gaining the upper hand in a battle that is much more complex than anyone expected

A cultured phytophthora sojae sample (on the white pad) is inserted into a naturally resistant soybean seedling. Scott Bauer photo courtesy ARS/USDA.

When it comes to production problems in soybeans, growers have grown used to hearing that with soybean cyst nematode, once you’ve got it, it’s in your fields to stay. Only diverse rotations and SCN-resistant varieties can reduce the damage to future crops.

But nematodes are far from the only threat. Surveys in the U.S. have estimated the lost yield due to seedling diseases in American soybean fields at 37 million bushels a year.

There are at least four different seedling diseases in this complex, including phytophthora, pythium, fusarium and rhizoctonia. But it’s the first two that are the focus of research now being conducted in the U.S.

Times are changing for in-depth disease research, so the battle with seedling diseases can benefit from more detailed surveys as well as from new technological tools to help determine the presence of different species of phytophthora and pythium.

Martin Chilvers, an assistant professor at Michigan State University, is part of a team of researchers across 12 soybean-growing states and Ontario, looking to build a more detailed analysis of the disease pathogens involved, including what effect they can have on soybean seedlings and roots.

The funding in the U.S. comes from the U.S. Department of Agriculture’s National Institute of Food and Agriculture, with matching funds from the United Soybean Board and the North Central Soybean Research Program, while Canadian research was funded primarily by Agriculture and Agri-Food Canada through the Agricultural Adaptation Council and the Grain Farmers of Ontario.

“Up until now, we haven’t had a national survey to figure out what species are out there, and we haven’t really had the molecular tools that we have now, either,” says Chilvers, who is originally from Australia and has studied disease pathogens around the world.

“We now have a pretty good snapshot of what pythium species are actually out there and in soybeans in particular. With the isolates that we’ve collected, we’re now trying to determine which ones are pathogenic and are truly causing disease.”

It’s one thing to isolate an organism in the soil environment, and to determine whether it is infecting a plant or is associated with the disease in seedlings. It’s quite another to prove that it’s the cause of the disease. And that’s what Chilvers and others in the U.S. Midwest and Ontario are trying to understand.

As with any research into plant diseases, the more they can understand about the species that are present, including their activity and their disease transmission capabilities, the more researchers can target suitable responses, be it improved seed treatments or fungicide applications, or passing along the information to plant breeders for enhanced germplasm and improved varieties.

There’s also the notion that phytophthora and pythium, like soybean cyst nematode, have been a part of the soybean disease landscape in the Midwest and in Ontario for years, if not decades. And with pythium in particular, a surprise turned up when scientists tallied the number of different species that were collected in this regional survey.

In 2011, 55 species of pythium were identified, plus 40 more in 2012. The same survey identified only two phytophthora species in 2011 and two more in 2012.

What also turned up in the research was the possibility that environmental conditions including temperature, precipitation and soil texture might play a role in this developing story.

“The study has opened our eyes to the number of pythium species that are out there,” says Chilvers, acknowledging the importance of phytophthora, which is already recognized as a significant cause of disease. “But with pythium, it’s much more difficult for these seedling diseases, in terms of identification. If you bring in a diseased seedling, it’s very difficult for me to tell you exactly what’s causing that disease because the symptoms on the plant are hard to distinguish. You often can’t differentiate pythium, phytophthora, fusarium and rhizoctonia from each other — they just produce very similar symptoms.”

From the Grainews website: Managing soybean seedling diseases can cut production costs

In addition to identifying the species, Chilvers and the other researchers are trying to develop molecular tools to speed the identification process. That way, growers will be able to get quicker diagnosis, with improved identification leading to more precise recommendations to combat the disease, including better targeted fungicide seed treatments.

The benefit of this type of research also includes the long-term potential to build some sort of diagnostic tool that helps a plant breeder incorporate this information for the purpose of improving new or existing germplasm. Chilvers is quick to point out that although he can come up with newer diagnostic tools based on his work to identify the specific causes, incorporating this information into new soybean varieties is not an overnight development.

“That’s a difficult process, where incorporating different resistance genes is concerned, but they’re going to be able to combine different resistances much more quickly than what they have in the past,” says Chilvers.

Here in Canada

From Albert Tenuta’s perspective, the seedling disease complex is second only to soybean cyst nematodes in Canada. “We’re seeing the same thing in Ontario,” says Tenuta, the field crops pathologist for Ontario Ministry of Agriculture and Food (OMAF). “We’re seeing shifts in populations, particularly when you look at pythium.”

Tenuta says disease watchers are also seeing pythium species with more diversity, and some are becoming better able to adapt to the changing environmental conditions. That’s a concern because, while pythium is usually considered a cool-weather, early-spring problem, there’s evidence that some pythium species can tolerate warmer temperatures and hurt crops further into the season.

The impact of that shift cannot be ignored, and Tenuta adds that these trends are occurring in the U.S. just as they are in Ontario, which is why he’s helping out in the survey and is part of the process of developing a regional distribution map of the pathogens that are out there. That makes it much more beneficial for public and private breeding programs as well, because there is now the capacity to target genetics to the specific issues profiled in various regions. If Ontario finds that there’s a unique situation with pythium or phytophthora, there is the opportunity to breed varieties for those specific needs in the different regions.

“It’s a challenge, because we’ve been breeding soybeans for how long?” says Tenuta. “And other than phytophthora, where we have good race resistance and race-specific resistance as well as partial resistance, when we think of fusarium, rhizoctonia and pythium, we don’t have the same level of genetic resistance or tolerance in a commercial variety. So we’re dependent on things such as seed treatments and management to reduce the risk to producers from these diseases. The result is that we’re seeing more of what I call ‘nibbling’ — a little bit more every year of these diseases. And some years more so than others, a lot of it will depend on the environmental conditions early on in the spring.”

So in a year such as 2013, with a cool, wet spring, there was a substantial increase in pythium, phytophthora, rhizoctonia and fusarium seedling disease injury in Ontario in areas that are more prone to them, such as the heavy clay soils, or areas that had saturated soil conditions. And just as Chilvers cautions against making too many conclusions based on current research, Tenuta notes that under current conditions in Ontario, there is still considerable work to be done to determine the specific capabilities of the pathogens involved. Finding and identifying a species doesn’t mean it’s the cause of the disease.

“One of the evolutionary strategies of any of the best disease-causing pathogens is their ability to find a little niche or a little opening or a crack in our wall of protection,” Tenuta says. “And when they find that little crack, they’re able to then get in and start to do their thing.”

What Tenuta sees is the development of resistance by some pythium species against the current fungicide treatments that are based on metalaxyl. It isn’t that the products have lost their efficacy completely — they haven’t, says Tenuta. But using this information could lead to the incorporation of other seed treatment fungicides to compensate for these new developing soybean issues.

“Now, you’re going to see at least one, maybe two new products that are targeting the oomycetes for pythium and phytophthora,” adds Tenuta. “So by combining the two actives, you’re able to manage both groups of oomycetes that are maybe becoming less sensitive to the metalaxyl, but the new active in these new seed treatment fungicides can control them.”

Again, the word of caution is that these developments take time. It’s one thing to identify the species and how they can affect your soybean crop. That’s the stage at which Chilvers and Tenuta are working. But it’s another branch of science that figures out how a new seed treatment is developed, or how a new variety is bred. And typically, that process can take between five and 10 years.

Stay tuned!

— Ralph Pearce is a production editor for Country Guide at St. Marys, Ont. This article appeared in the October 2013 edition of Soybean Guide (pages 24-26).

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CG Production Editor

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