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Tracking soybean pathogens

 Symptoms of root rot complex in a commercial field. Photo courtesy of Allen Xue. 

In order to control diseases in the infamous seedling disease complex – including seed rot, root rot, seedling blight and damping off – you have to track the pathogens responsible.

Allen Xue, a plant pathologist at the Ottawa Research and Development Centre, has been attempting to do just that since he started working as a soybean pathologist at the centre in 2009.

“I did some checking for the diseases in the field that spring, and I got a lot of reports from Albert Tenuta, field crop pathologist for the Ontario Ministry of Agriculture, Food and Rural Affairs, saying that lots of farmers had seedling disease problems in the newer areas,” he says.

Xue investigated and found patches of plants that were soft and rotting. He suspected pythium or its close relative, phytophthora, and found that, in one case, the disease was in fact caused by pythium in the early stages. But in dry areas, Fusarium or rhizoctonia are often responsible for rot.

“We decided we needed to sort out what are the pathogens that are involved,” he said.

In 2014, Xue wrapped up a project identifying sources of resistance to the pathogens that cause some of Ontario’s most devastating diseases in soybean.

“There are some similarities between the diseases, but plant research for different pathogens is quite different, so you have to look at the diseases one by one,” he explains.

“Each pathogen is controlled by specific genes. You can’t
apply Fusarium research to pythium. The most effective way to control disease is to use genetic controls for resistance. But you have to know where the target is and how to screen for the pathogen.”

The goal of Xue’s research: to identify resistant germplasms to assist breeding programs in developing stronger hybrids – plants that can stand up to pathogens in the field.

Results
The study paid off.

Xue and his team identified six different pythium species responsible for seed rot and damping-off, four of which had not previously been reported on soybean in Canada.

It’s an important discovery, but a sobering one. “These species are not new to the rest of the world,” Xue says. “In the past, soybean production was only a rumour in southwestern Ontario, but now that soybean has been growing in short-season areas in Prince Edward Island, Ontario and Manitoba – in cold climates – now pythium has become a problem,” he says.

Through analyzing the effects of changing temperatures, the team zeroed in on the changing pathogenicity of pythium. “We discovered for the first time that P. ultimum var. ultimum was the most pathogenic species to soybean in Canada,” Xue says.

But the study’s results were not confined to pythium. Xue also identified 22 races of Phythophthora sojae, the causal agent of Phytophthora root rot—“the most destructive and widespread disease in Canada”—17 of which, Xue claims, had not yet been detected in the country.

“This new information was crucial to appropriately target deployment of resistance genes in new cultivars by soybean breeding programs,” he says.

Finally, the team identified nine Fusarium species responsible for Fusarium root rot in Ontario.

Xue says the results provide improved knowledge of the pathogen complexes, which is essential for developing better controls.

Next steps
Now, breeders can use this information on the predominant races, or races with specific virulence genes, when screening their breeding lines. The goal is cultivars with resistance genes to the most devastating races; they’ll have a longer lifespan, but they’ll also form a foundation for future cultivar development.

Elroy Cober, a research scientist involved in soybean breeding and genetics at the Ottawa Research and Development Centre, was Xue’s collaborator in the project.

Plant breeding is a long process, Cober says. Once the parents are chosen, breeding, start to finish, takes seven to 10 years.

“The first phases of breeding involve making a cross. Then you do inbreeding to get pure lines and then you test the pure lines. Right now we’re in the inbreeding phase,” he says.

Cober says that yield is always the priority in soybean breeding programs, but disease is also a major focus. He says the long-term nature of plant breeding is a reality everyone in the industry needs to keep in mind, but there are payoffs in the end. “There’s not an immediate payback, but there is a payback,” he says.

While Xue’s project yielded important results, he emphasizes that the work is not over yet. “There is lots to do in terms of monitoring pathogen dynamics and monitoring techniques and then breeding and studying the inheritance of resistance,” he says.

May 3, 2016  By Julienne Isaacs