Genomics helps ease regulatory burden for Canadian soybean growers

From humble beginnings as little more than a novelty crop in the 1930s and 1940s, soybeans have grown into Canada's fifth most-valuable agricultural crop.Footnote 1 In 2013, Canadian growers produced close to 5.2 million tonnes of soybeans,Footnote 2 generating more than $1.5 billion in farm cash receipts.Footnote 3 Exports of Canadian soybeans to Japan, China, the European Union and elsewhere are now worth more than $1 billion a year.Footnote 4

Cysts of soybean cyst nematode taken from roots of an infested plant. The cysts are less than a millimetre in diameter and may contain 200 eggs.  
(Photo credit: AAFC)

Like any crop, soybeans are susceptible to a variety of diseases and pests. One of the important damaging parasites is called the soybean cyst nematode (SCN), heterodera glycines, a microscopic roundworm that attacks the roots of the plant.

The pest arrives in Canada

Even with import requirements in place aimed at keeping it out, SCN was detected in Canada in 1987, in Ontario. At that time, soybean producers in affected areas became subject to regulations to prevent the movement of soil and plants that could be infested with SCN. The rules were strict—if a farmer drove a tractor through a field where SCN was present and did not wash potentially contaminated soil off the tractor before driving to another field, it could be considered a violation of the regulations.

In spite of these precautions, SCN continued to spread in soybean production areas, infesting large parts of Ontario, where losses caused by the tiny invader have been measured in the tens-of-millions of dollars annually.Footnote 5 As the SCN expanded its range, so did the area covered by the regulations, including into Manitoba after SCN was detected there in 2012.

Early detection is key

Once established in a particular area, SCN is difficult to control. At the same time, experience has shown that the damage caused by SCN can be limited through careful and innovative management, such as crop rotation and planting different, newly developed SCN-resistant varieties of soybeans from one year to the next.

For these measures to be effective, SCN must be detected at the earliest stages of infestation. By the time soybean plants start to show visible signs of SCN damage, it is too late. If resistant or tolerant varieties are not available to the producer, the affected field may have to be taken out of production for years to bring the SCN population down to a manageable level.

Improving early detection

With early detection in mind, Agriculture and Agri-Food Canada research scientist and nematode specialist Dr. Qing Yu and his team have developed a test for the presence of SCN in soil that is faster and more accurate than anything available in the past.

"Before this, the only sure way to know if SCN was present in a field was to examine large soil samples under a microscope, searching for adult nematodes," says Dr. Yu. "With this genomics-based test, we are looking for the DNA of the nematode in the soil sample. This allows us to see if SCN is present, in even the smallest quantity and at any stage of its development, from egg to adult."

Dr. Yu says the test he has developed for SCN would not have been possible without the new applications for next generation genomic sequencing pioneered by researchers funded through the Government of Canada's Genomics Research and Development Initiative (GRDI). "Other genetic tests for SCN are available," says Dr. Yu, "But using the techniques coming from GRDI researchers, we have been able to develop a test method that is both faster and more precise."

Canada lifts regulations for SCN

In 2013, Dr. Yu used his test to confirm the presence of SCN in Quebec for the first time, a finding that played a part in the Canadian Food Inspection Agency (CFIA) decision to lift the regulations that had been imposed on soybean growers in Ontario and Manitoba.

Cameron Duff, Executive Director of Plant Health Science Directorate at the CFIA, says the detection of SCN in Quebec could have led to the imposition of regulations on growers in that province. however based on a number of factors—including population distribution, impact of the regulatory control measures and availability of resistant varieties—the decision was made to eliminate the regulations for all Canadian soybean growers in November 2013.

"Dr. Yu's test gives us the ability to detect SCN earlier and with precision," says Mr. Duff. "This early detection capability was a key factor in making an informed decision, knowing growers can now implement techniques to control SCN at the earliest stage of infestation and manage their production effectively without regulatory controls."

A welcome decision

At the Grain Farmers of Ontario, Research Coordinator Meghan Moran says soybean growers welcome the decision to lift the regulations. "Instead of making sure they meet every detail of the regulations, growers can focus on following good management practices," says Ms. Moran. "And now that the presence of SCN can be detected earlier, growers can take action earlier, when it is most effective."


Footnote 1

Statistics Canada, The soybean, agriculture's jack-of-all-trades, is gaining ground across Canada (2007 report)

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Footnote 2

Canadian Soybean Council, Industry Statistics

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Footnote 3

Statistics Canada, Farm Cash Receipts (November 2011), data from 2010 crop year, accessed at:

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Footnote 4

AAFC, Harper Government Creates Export Opportunities for Canadian Soybean Industry (news release), 19 Dec. 2013

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Footnote 5

Albert Tenuta, plant pathologist, Ontario Ministry of Agriculture, Food and Rural Affairs, Watch for soybean cyst nematodes in Manitoba, Manitoba Co-operator, 14 March 2012. accessed at:

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