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A wake-up call for resistance stewardship

The phytophthora root rot pathogen is overcoming commonly used resistance genes in soybean varieties.

November 20, 2023  By Carolyn King

A strip trial comparing the yields of two soybean varieties with and without the correct resistance gene against éPhytophthora sojae. Photo courtesy of Jérôme Boissonneault, AYOS Technologies.

Resistant varieties are a critical tool for managing phytophthora root rot (PRR) in soybean. However, a recent PRR survey in Canadian soybean fields revealed troubling news: 84 per cent of the growers were using soybean varieties with resistance genes that were no longer effective against the PRR variants in their fields.

Fortunately, the new diagnostic method used in this survey is now available to soybean growers, breeders and seed suppliers so they can find out which resistance genes still work. That information can help everyone to more effectively fight this major disease.

A bit about PRR resistance
Richard Bélanger, a professor at Université Laval in Quebec, led the development of the diagnostic method and the survey. He explains that PRR is a destructive stem and root disease of soybean that results in about $50 million in yield losses per year in Canada. It is caused by Phytophthora sojae, a persistent, soil-borne pathogen called an oomycete. PRR can infect soybeans at any growth stage.


Although some seed treatments can help reduce this disease and practices like field drainage can help alleviate disease damage, genetic resistance is the cornerstone of PRR management. 

Crop breeders make use of two types of genetic resistance. One is horizontal resistance, also known as partial resistance or field resistance. It is not specific to the pathogen’s strain or race. It involves multiple minor genes which together give the plant some tolerance to the disease, but not complete resistance. 

The other type is vertical resistance, also known as total resistance or race-specific resistance. This involves single genes that provide complete resistance to specific variants of the pathogen. For PRR, such genes are called ‘Rps’, which stands for ‘Resistance to Phytophthora sojae.’ For instance, in Canadian soybean varieties, commonly used Rps genes include Rps1a, Rps1c and Rps1k. 

Beélanger explains that the effectiveness of a particular Rps gene actually depends on the presence of the corresponding avirulence (Avr) gene in the pathogen. This avirulence gene triggers a resistance response in the plant, enabling the plant to fight off the pathogen. 

So, if growers use a soybean variety with an Rps gene that matches the Avr variants in their field, they’ll get complete control of the disease – at least, in the short term. 

However, repeated use of the same Rps gene in a field selects for Phytophthora sojae variants that have some difference in the corresponding Avr gene which allows the pathogen to evade detection and infect the plant. With ongoing selection pressure, more and more of the pathogen’s population becomes virulent on soybean varieties with that Rps gene. 

Over the years, continued selection pressure has resulted in so many Phytophthora sojae races that plant pathologists now name the variants based on the Rps genes that they can overcome. For example, ‘pathotype 1a’ is virulent on Rps1a; ‘pathotype 1a, 1c’ is virulent on both Rps1a and Rps1c; and so on. These days, many variants can defeat more than one Rps gene.

A much better test
The traditional procedure to identify PRR pathotypes is called the hypocotyl method. Bélanger explains that this method requires culturing the pathogen in the lab and growing a set of different soybean lines that carry the different Rps genes. Then, for each isolate of the pathogen, you inoculate the hypocotyl of every soybean line. Then, you measure the reactions of the different lines and score the response to identify the pathotype. 

According to Bélanger, the hypocotyl method can take two to three months, and it is prone to errors like false-positives and false-negatives. “It is very cumbersome, time-consuming and imprecise,” he says. 

“With the advent of new genomic tools, we saw the opportunity to exploit them to get a faster and more accurate diagnosis.” 

The researchers have developed a molecular method that is based on identifying Phytophthora sojae’s Avr genes – the first time such an approach has been used for pathotyping a plant pathogen.

They have created genetic markers that distinguish between virulent and avirulent isolates for the most common Avr genes in Canadian soybean fields. These markers are used with a technique called multiplex PCR, which gives a response for all the different Avr genes simultaneously.

 Bélanger says, “Once you set things up, this method takes only two to three hours, so it has significant time savings. And in terms of accuracy, it is unmatched.”

Key survey findings
After confirming the accuracy of their new method, the researchers used it to analyze almost 300 Phytophthora sojae isolates from soil samples collected in Quebec, Ontario and Manitoba soybean fields. These three provinces together account for over 95 per cent of Canada’s soybean-growing area. 

The survey was conducted between 2016 and 2019, and the samples were analyzed for Avr1a, 1b, 1c, 1d, 1k, 3a, and 6. 

“We found a clear trend toward pathotypes that were overcoming the main Rps genes used in soybeans,” Bélanger notes. 

“For instance, almost all isolates carried the pathotype 1a. Rps1a was the first Rps gene released commercially in Canada, and because it has been used and over-used, it is now completely overcome. 

Rps1c, which came after 1a, is also basically overcome. Currently, Rps1c is by far the most used Rps gene in Canada. This is worrying because this gene is basically obsolete at this stage.” 

For the Quebec samples, 96 per cent of the isolates could overcome Rps1a, and 77 per cent could overcome Rps1c. For Ontario, 94 per cent could overcome Rps1a, and 75 per cent could overcome Rps1c. And for Manitoba, 100 per cent could overcome both Rps1a and Rps1c.

Rps1k, which was the answer to the new pathotypes developing as a result of Rps1c being overcome, is slowly getting overcome as well,” Bélanger says. “The situation in Manitoba is particularly worrying because Manitoba started with Rps1k earlier than Ontario or Quebec did. Selection pressure has been doing its job and Rps1k is being overcome.” 

In Manitoba, 67 per cent of the isolates were able to defeat Rps1k, compared to 16 per cent in Quebec and 33 per cent in Ontario.

Fewer isolates were able to defeat newer genes like Rps3a and Rps6. He notes, “The options for Rps genes that are still widely effective are getting extremely limited.” 

The survey in Manitoba and Quebec also collected data on the soybean varieties grown in the sampled fields. The researchers’ analysis found that 84 per cent of the fields had varieties with Rps genes that were not resistant against the pathotypes in those fields.

As expected, the survey results showed that pathotype diversity has increased since two earlier Canadian PRR surveys, one conducted in the 1980s and the other from 2010 to 2012. For instance, pathotype 1a is now rare, and more complex pathotypes like pathotype 1a, 1b, 1c, 1d, 1k, 7 are on the rise. “As we grow more soybeans in Canada and we plant more resistance genes, the pathotype diversity increases,” says Bélanger.

He also points out that concerns about the stewardship of Rps genes are not limited to Canadian soybean production. He and his research group were involved in an international study published in 2023, which determined that the decreasing effectiveness of commonly used Rps genes is a global trend.

Implications for breeders and growers
“Our findings show that we really need to be more aware and have a better strategy to deploy Rps genes in line with the selection pressure on the different Phytophthora sojae isolates,” says Bélanger. 

“These Rps genes are very precious. We need to protect them and make them last longer.”

He stresses that breeders need to make greater use of more recent Rps genes like 3a and 6. “From what we saw, about 50 per cent of the [PRR-resistant soybean varieties available in Canada] are based on Rps1c, but we know this gene has been overcome. There is also a large portion of Rps1k varieties, and that gene is being overcome.”

Discovering new Rps genes is also crucial. He notes, “Corteva has reported a new Rps gene called Rps11, and we hope it will be deployed very soon.” 

Another option is to stack PRR resistance genes. At present, most Canadian PRR-resistant soybean varieties rely on a single Rps gene. A few varieties have two stacked Rps genes, but often one of the two is Rps1c or Rps1a. Stacking Rps genes with genes for partial PRR resistance also helps provide more durable resistance. 

“For growers, good resistance stewardship is being aware of which pathotypes are in your field and then planting soybeans with Rps genes based on that understanding,” says Bélanger. “You can also rotate your Rps genes to reduce the selection pressure on the pathogen.” 

Other practices that can help with on-farm Rps resistance stewardship include diversifying crop rotations, so soybean is grown less often, and using seed treatments. 

What’s in your field?
“You need to know what is in your field so you’ll know which Rps genes will work. That is why we developed our pathotyping technique,” Bélanger says. 

“We had an advisory committee of expert scientists and when we reported our results, they recommended making the test commercially available.” So, some of Bélanger’s students involved in the research have created AYOS Technologies, which offers this testing service.

The test can use either soil or plant samples to determine what PRR pathotypes are in your field, even if no soybeans are growing there right now. The test results will tell you which pathotypes are present and which Rps genes are effective against the main pathotypes in your field. Provincial soybean variety performance lists identify the Rps genes in the PRR-resistant varieties.

Bélanger’s team is continually updating and improving the molecular test. “For example, we have already discovered Avr11 for the new gene Rps11, even before Rps11 has been deployed. We have a bank of over 1,000 isolates, and as new Rps genes come along, we can go into our bank and find the avirulence genes that are needed for the testing,” he explains. “Also, we keep working to improve the test by developing even better markers and faster tests.” 

According to Bélanger, seed suppliers are currently the main Canadian users of the AYOS service because the test results enable the companies to make proper variety recommendations to their customers. As well, AYOS is receiving samples from other countries like the United States and Brazil. 

A few Canadian growers have also embraced the value of this test. Bélanger is hopeful that more growers will do so, since choosing a variety with the right Rps genes is a simple decision that can result in big yield benefits.

To demonstrate this, Bélanger’s research group has carried out strip trials with some interested growers. After determining the PRR pathotypes in the grower’s field, they set up a trial with half of the field seeded to the grower’s susceptible soybean variety and the other half seeded to a potentially resistant variety. 

“We have shown an increase in soybean yield by as much as 49 per cent just based on a good variety decision. So, I would like to say to the growers: give it a chance.” 

Collaborators working with Bélanger on the new molecular method and the PRR survey include researchers from Universiteé Laval, Agriculture and Agri-Food Canada and the University of Alberta. This research was funded by Genome Canada and Genome Québec, the Canadian Field Crop Research Alliance, and the Program Prime-Vert #2 #19-002-2.2-C-ULAV of Ministère de l’Agriculture, des Pêcheries et de l’Alimentation (MAPAQ). 


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