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Resisting soybean cyst nematode

Soybean cyst nematode (SCN) is a tiny plant parasite that is causing big problems for Ontario soybean growers. SCN-resistant varieties are key to managing this yield-robbing pest. However, almost all the resistant varieties for 

Ontario rely on a single source of resistance genes. That increases the risk that new SCN variants will emerge that are able to defeat those resistance genes. So a project is underway to bring different sources of SCN resistance into high-yielding, high-quality soybean varieties for Ontario.

“Soybean cyst nematode is one of the most damaging pathogens of soybean in the world, including Ontario. Damage by SCN costs Ontario soybean growers more than $30 million each year, and it is estimated to be more than $10 million in southwestern Ontario,” notes Milad Eskandari, a soybean breeder at the University of Guelph’s Ridgetown Campus, who is leading the project.

SCN was first found in Ontario in 1988 in the Chatham area and has been spreading across Ontario’s soybean growing area ever since. This soil-dwelling, microscopic roundworm moves from field to field through the movement of infested soil, for example, on field equipment or by soil erosion. Its population in a field increases when a susceptible host crop is grown and decreases when a non-host or a resistant host is grown.

The nematode attacks a host plant’s root, pulls nutrients from the root, and reproduces on it. The root damage also provides entry points for other types of root pathogens. The nematode’s name comes from the lemon-shaped cyst that protects its eggs. These cysts are about the size of a pinhead and change from white to yellow to brown over time.

“Soybean cyst nematode can have a significant impact on crop health and yields,” says Albert Tenuta, a plant pathologist with the Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA). “Yield losses can range from a minimum of about five to 10 per cent all the way to total failures in many parts of a field. A general rule is that when growers start to see aboveground SCN symptoms – which are yellowed, stunted or dead plants in patches in a field – you’re probably looking at a 25 per cent yield loss by that point. Those symptoms often indicate that the nematode’s population in the field has built up significantly.”

Resistant varieties are a cornerstone of SCN management. SCN resistance genes are identified by the name of the soybean line that was the original source of the genes. For instance, in Ontario soybean varieties, SCN resistance genes are from plant introduction (PI) 88788 and from PI 548402, also known as “Peking.”

“In Ontario, more than 98 per cent of our SCN-resistant soybeans have their resistance genes from PI 88788,” Eskandari notes. “We believe that our farmers are too much dependent on this specific resistance source.” Growing a particular resistance source in a field selects for those few variants in the nematode’s population that can overcome the resistance genes because those variants survive and reproduce. Repeatedly growing the same resistance genes 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.

According to Tenuta, soybean growers in areas with a relatively long history of SCN, such as Missouri and Illinois, are starting to see significant SCN populations that can bypass PI 88788 resistance. Tenuta and Tom Welacky, who is with Agriculture and Agri-Food Canada at Harrow, have been looking at this issue in Ontario.

With funding support from the Grain Farmers of Ontario, they conducted SCN sampling over 10 years at various Ontario locations. Welacky’s lab tested the samples to determine the SCN variants, or HG types. “HG” refers to Heterodera glycines, the scientific name for the nematode. “In HG type testing, an SCN population from a field is grown on a susceptible check variety and seven different resistance sources,” Tenuta explains. “SCN reproduction on the check is compared to the reproduction on the resistance sources. If the population grows quite well on a particular resistance source, then it is identified as the associated HG type. For example, HG type 1 reproduces on Peking, HG type 2 reproduces on PI 88788, and HG type 1.2 reproduces on both.”

Tenuta and Welacky have found some SCN populations that can reproduce on PI 88788 and Peking. Fortunately, such populations are very low overall in Ontario, so both PI 88788 and Peking are still effective resistance sources for the province.

Developing varieties with new resistance sources for Ontario would help growers where the SCN population has started shifting. Plus it would allow growers to rotate between different resistance sources. So, it would help lower SCN populations, reduce the selection pressure pushing the population toward particular variants, and decrease the risk of yield loss due to SCN.  

Given the importance of having diverse resistance sources, why have breeders relied so heavily on PI 88788? “When breeders introgress SCN-resistance genes, or for that matter any gene of interest into elite soybean lines, there are potential yield reduction side effects. PI 88788 has less of these side effects than other SCN resistance sources, so it’s much easier for breeders to use,” Eskandari explains.

In his project to bring new resistance sources into superior Ontario varieties, Eskandari is working with resistance genes from PI 437654, or “Hartwig.” (In another project, his lab is working on Peking resistance sources.)

“Incorporating Hartwig into elite agronomic soybean varieties has been a challenge, so nobody likes to work with it,” notes Eskandari. “But Hartwig is the best source of SCN resistance; it is resistant to almost all of the existing SCN races in Ontario.”

Eskandari’s Hartwig project runs from 2014 to 2017 and is funded by OMAFRA, the University of Guelph and SeCan. His lab has crossed a Hartwig line with 12 elite soybean lines that are well adapted to Ontario conditions, to create 12 different breeding populations.

Fortunately, Eskandari didn’t have to start from scratch by crossing with the original Hartwig line. “We are using a line from Dr. Brian Diers’ lab at the University of Illinois. That line is a soybean cultivar with a relatively high seed yield and good agronomic traits and performance,” he says.

His lab already has F4 and F5 generation progeny for each of the 12 breeding populations. Eskandari notes, “We hope that in 2016 we will evaluate the progeny in the lab and field to select lines that have Hartwig SCN resistance genes for further breeding work. In the following years, we will evaluate those resistant lines for yield and other agronomic traits, to pick the best ones for commercial release in Ontario.”

In addition to developing superior Ontario varieties with Hartwig SCN resistance, the project is also examining the genetic control of these resistance genes in their Ontario breeding lines. Eskandari’s Master’s student Xin Lu is working on this aspect of the project.

The primary reason for this genetic work is to find DNA markers that are linked to the resistance genes. Such markers would allow soybean breeders to quickly screen breeding material for the presence of those resistance genes, rather than going through the labour-intensive, time-consuming and expensive process of greenhouse and field trials to evaluate the thousands of progeny in their breeding programs for SCN resistance.

Managing SCN
Tenuta provides some important SCN advice for Ontario soybean growers. “A key recommendation is to scout your fields and look for the cysts on the roots. It can be done any time during the growing season, and even after harvest. The earlier SCN is detected, the better; that is an important message where SCN is a relatively new problem. In southwestern Ontario, we have a long history of SCN, and growers know what it looks like and the significant
damage that can occur. But new areas – like central Ontario, eastern Ontario, the Ottawa Valley and into western Quebec – are seeing the nematode’s populations building up. Producers in those areas need to look for SCN and start dealing with it before those populations build up.”

If you find SCN in your fields, then choose SCN-resistant soybean varieties, use non-host crops such as corn, wheat and forage in the rotation, and rotate between different SCN-resistant varieties and if possible between resistance sources. The Go Soy website ( provides performance data on SCN-resistant varieties, as well as each variety’s resistance source.

Tenuta also suggests learning more about a variety’s SCN resistance package when you order seed for an SCN-infested field. “In cyst nematode resistance sources, there is no one specific gene that provides total resistance. Instead, a combination of major and minor genes produces the resistance. So, different soybean varieties that have SCN resistance from the same source may have differing combinations of those resistance genes,” explains
Tenuta. “For instance, one variety might have most of the resistance genes and as result have more effective resistance. Another variety might have only some of the resistance genes and may be only moderately resistant. So ask the company if the variety you’re interested in is highly resistant and what is the reproduction ability of the nematodes on the variety – low, medium or high. Go for the variety that is best for both yield and SCN resistance.” Because of the differences between resistance packages, rotating between different soybean varieties with the same resistance source may help reduce selection pressure on the nematodes.

Tenuta also notes that additional SCN management tools are coming soon. “A number of nematicides are being registered or will be available to producers in the near future. A two-way combination of SCN resistance and nematicide seed treatments will provide another level of protection for growers against SCN as well as soybean sudden death syndrome [a fungal disease associated with SCN].” 


January 19, 2016  By Carolyn King


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