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Resisting a devastating duo

Breeding soybean varieties for Ontario with resistance to two major disease threats.

May 13, 2024  By Carolyn King

SDS-susceptible soybean lines compared to resistant lines in one of Eskandari’s field locations. Photo courtesy of Eskandari’s research group, University of Guelph-Ridgetown.

Both soybean cyst nematode (SCN) and soybean sudden death syndrome (SDS) are able to take big bites out of soybean yields. And both pests have been spreading almost hand-in-hand across Ontario’s soybean-growing areas. To develop soybean varieties able to withstand this double threat, breeder Milad Eskandari is working to stack SCN and SDS resistance genes and to diversify SCN resistance sources in his breeding lines.

His soybean breeding program at the University of Guelph’s Ridgetown Campus focuses on high-yielding, Ontario-adapted varieties with a range of quality traits that appeal to various markets. Resistance to SCN and SDS are key breeding objectives for his program.

“SCN and SDS rank as the primary and secondary threats to soybean cultivation in southwestern Ontario, causing substantial economic losses amounting to millions of dollars. The development of cultivars equipped with resistance to SCN and SDS stands as the most effective management strategy currently available to farmers,” says Eskandari.


“Consequently, the development and utilization of high-yielding commercial soybean varieties resistant to these diseases are imperative for ensuring sustainable soybean production in Ontario. By prioritizing the cultivation of resistant varieties, farmers can mitigate the economic impact of these destructive pests, maintain their yields, and contribute to the long-term viability of soybean farming in the region.”

Funding for Eskandari’s current studies related to SCN and SDS is from Grain Farmers of Ontario, SeCan, Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA), the Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Guelph (both Ridgetown and the main campus). Collaborators on the SCN research include Owen Wally with Agriculture and Agri-Food Canada in Harrow and Albert Tenuta with OMAFRA. SDS research collaborators include Istvan Rajcan with the University of Guelph as well as Wally and Tenuta.

A quick look at the pathogens
SCN was first detected in Ontario in 1988 in the Chatham area and has been spreading through the province ever since. This soil-dwelling, microscopic roundworm attacks a host plant’s roots, stealing nutrients from the roots and reproducing on them. The nematode’s name refers to pinhead-sized cysts found on infested roots, which contain its eggs. 

SDS, first observed in the Chatham area in the mid 1990s, appears to be spreading in SCN’s wake. It is a soil-borne fungal disease caused by Fusarium virguliforme. SDS can cause root rot as well as leaf damage and defoliation. 

Each disease on its own can cause very high yield losses when conditions favour the pest. Plus, the two diseases often occur together. Although researchers are still looking into exactly how the two pathogens interact, SDS tends to be more severe if SCN is present. Research indicates that root damage by the nematode can provide entry points into the root for pathogens like F. virguliforme. Also, this fungus is found in SCN cysts so the nematode may be helping to spread SDS. 

Diversifying SCN resistance
SCN resistance genes are named based on the soybean line, or plant introduction (PI), that was the original source of the genes. For example, PI 88788 is the name of the resistance source used in more than 95 per cent of North American SCN-resistant soybean varieties. 

Breeders have been relying heavily on PI 88788 for about three decades, which is worrisome. Growing a particular resistance source in a field selects for the few natural variants in the nematode’s population that are able to survive and reproduce on those plants. Repeatedly using the same resistance in the field shifts more and more of the nematode’s population to those variants. Eventually that resistance source will no longer be effective in that field.

As in the rest of North America, PI 88788 predominates in Ontario. Almost all the SCN-resistant varieties in the 2023 Ontario Soybean Variety Trials use PI 88788. Only a handful have a different source, which is PI 548402, also known as Peking. 

“The prolonged reliance on SCN-resistant soybeans exclusively carrying the PI 88788 source in the Midwest U.S. has led to the emergence of SCN types capable of overcoming this resistance,” says Eskandari. He notes that this concerning trend is already appearing in southwestern Ontario, where PI 88788 is starting to lose its effectiveness in some fields, resulting in yield declines in those fields.

To help counter this trend, Eskandari’s program is actively working with PI 548402, PI 437654 (also known as Hartwig) and PI 89772. As more soybean varieties with different SCN resistance sources become available, Ontario growers will have more options for rotating their resistance sources to slow the development of SCN variants that can defeat the resistance genes. And growers will have more options in situations where PI 88788 is no longer as effective. 

Developing soybean lines with these alternative SCN resistance sources is complex and time-consuming, but Eskandari’s program is making progress.

“Currently, we have promising soybean lines in our pipeline carrying PI 437654 and PI 548402 resistance sources. These lines are undergoing thorough field evaluation for both yield and agronomic characteristics,” he says. 

“We are optimistic about their performance, and if they meet our criteria, we plan to release them to farms in the near future.” 

Developing molecular tools
Eskandari’s program is using and developing molecular markers to screen breeding materials for SCN resistance. “In the realm of plant breeding, success often hinges on numbers – the more lines evaluated, the higher the likelihood of success. Leveraging reliable molecular marker technologies enhances the efficiency of a breeding program,” he explains. 

“Moreover, using molecular markers in the development of SCN-resistant cultivars offers a distinct advantage. SCN infestations in fields are not uniform, leading to potential variability in field ratings. Molecular analyses and greenhouse bioassays provide a more consistent and reliable means of evaluating resistance, offering a valuable complement to field assessments. This dual approach, combining field evaluations with molecular marker analyses, strengthens our ability to develop soybean cultivars with robust resistance to SCN.” 

Some of his group’s work to develop better molecular tools for breeding SCN-resistant lines involves using RNA sequencing. Dual RNA sequencing shows which genes are being expressed; so, for example, researchers can determine which plant genes are involved as a soybean line responds to the nematode’s attack and which nematode genes are involved in overcoming the plant’s defences. This helps to increase understanding of the complexities of SCN resistance in soybeans.

“In our recent study, led by my research associate Sepideh Torabi, utilizing RNA sequencing, we identified candidate genes integral to the defence mechanisms associated with SCN resistance in various sources including PI 437654, PI 548402 and PI 88788,” Eskandari says. Their results indicate that the different PIs use different genes to fight off the nematode’s attack.

“While further analyses are required to validate these findings, the identified genes show promise as valuable indicators for discerning resistance mechanisms among different sources.” 

This discovery opens avenues for creating markers that could be used in developing varieties that have stacked SCN resistance genes from multiple sources, offering more durable resistance to the pest. 

Towards SDS resistance
Although SCN resistance is a longstanding focus for Eskandari’s group, their work on SDS resistance only started a few years ago. 

“Developing soybean lines with resistance to SDS presents several challenges within our program. Since SDS is relatively new in our research focus, that necessitates an initial step to establish a comprehensive understanding of how our Canadian germplasm responds to this disease,” Eskandari explains.

“Following this initial hurdle, the subsequent challenge involves the identification of suitable exotic donors. These donors not only need to align with our germplasm but also show great adaptability to our local climate. Currently, we are actively engaged in this phase, rigorously evaluating various SDS sources in Ontario to pinpoint the most promising lines for subsequent breeding crosses.” 

He adds, “SDS presents an additional challenge due to its complex genetics. A thorough understanding of the genetic factors associated with the disease is essential for effective breeding strategies.” 

At present, Eskandari is collaborating with Rajcan to evaluate the University of Guelph’s soybean germplasm for reactions and resistance to SDS. Their work so far has revealed a diverse range of reactions to SDS. 

Through further work, they hope to discover some of the genomic regions underlying the resistance to SDS. They can then use those findings to develop reliable markers for selecting SDS-resistant breeding lines. 

“Within another project in my program, we initiated crosses between our elite lines and exotic SDS-resistant lines. The progenies from these crosses are undergoing comprehensive evaluations for their resistance to SDS, along with assessments of important agronomic traits. Our goal is to develop germplasm with robust SDS resistance that can be either released to farmers directly or utilized in future breeding crosses for cultivar development,” he notes. 

“This multifaceted approach underscores our commitment to advancing the understanding and application of SDS resistance in soybean cultivation.”

All of these efforts to advance SCN and SDS resistance in soybeans contribute to achieving the overall aim of Eskandari’s breeding program to help ensure sustainable and resilient soybean production in Ontario. 


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