An Innovative Technology for Early Detection of Foliar Soybean Diseases in Manitoba Soybean

By Gustavo Díaz Cruz, BSc, MSc
Graduate Student, Brandon University
Bryan Cassone, BSc, MSc, PhD
Assistant Professor, Brandon University

August 2, 2018

The Rural Development Institute’s investigation of the strengths and weaknesses of the soybean supply chain in Manitoba has highlighted the great work of a Brandon University research team working on soybean pathogens.

Soybean production in Manitoba has been going strong since the year 2005. A major contributor to Manitoba’s success so far is that many of the economically important pathogens found in more established soybean regions of North America have not yet made it to the province. While this is certainly good news, the threat of their emergence looms large.

Most disease surveys rely on visual inspection of symptom development or lab culturing of the pathogen. However, these tools are limited and can be unreliable. More recently, surveillance has used serological or nucleic acid-based approaches. While sensitive and accurate, both approaches only validate existing diseases, and they are therefore impractical for detecting emerging pathogens. However, a novel diagnostic approach overcomes all of these obstacles by harnessing a relatively new technology called “Next-Generation Sequencing.” First we collect a single leaf from a diseased plant and take it back to the lab to be fully sequenced. Then, we extract DNA from any kind of disease that the soybean plant could be harbouring. We then go through multiple stages of lab work to generate the data — billions of pieces of DNA from the plant and the pathogens. These are pieced together for each plant, and the result is an accurate and comprehensive catalogue of all of the surveyed pathogens — including reliable identification of some that have never before been detected in Manitoba.

Our surveillance efforts were a collaboration between Brandon University; Manitoba Pulse & Soybean Growers; and Manitoba Agriculture, Food and Rural Development. A total of 81 fields located throughout Manitoba’s soybean-growing region were surveyed in late June (V2/3) and/or in late August (V6). In each field, samples were collected from any plant exhibiting foliar disease symptoms, resulting in nearly 700 leaf collections. Wet conditions in eastern Manitoba limited the number of V2/3 collections in that region.

Our survey uncovered a myriad of foliar disease-causing pathogens in all regions surveyed. As expected, we identified several pathogens of common soybean diseases — Septoria brown spot, bacterial blight, leaf spots, downy mildew, and Cercospora blight (Figure 1). Most of these were distributed throughout the growing region but are not considered to be of major economic importance.

Figure 1. Typical symptoms for Downy Mildew (A), Brown spot (B) and Bacterial Blight (C).

Additionally, we identified disease-causing pathogens that have not yet been reported in Manitoba soybean. This includes widespread incidence of two Xanthomonas species that cause soybean bacterial pustule. Another important diagnosis is the fungus Cercospora sojina, which causes frogeye leaf spot of soybeans. Both pathogens are most damaging in hot and wet conditions and can result in significant yield losses on susceptible soybean varieties. The prevalence of both diseases suggests their respective pathogens were present in Manitoba in previous years but went unreported.

Our survey also uncovered two previously unreported but relatively common soybean viruses: Bean yellow mosaic virus and Tobacco necrosis virus strain D. The good news is neither virus is considered to be economically important. Their presence in the province, however, suggests we should be on the lookout for other common soybean viruses that could cause appreciable damage, such as Soybean mosaic virus, Bean pod mottle virus, and Tobacco ringspot virus.

Foliar pathogens are responsible for economic losses in different levels across the world. Based on data from 2006, 52% of the worldwide yield reduction was due to foliar diseases (Wrather et al. 2010)[1]. Two of the most commonly found diseases in Manitoba, Brown spot and Cercospora leaf blight, were responsible for an estimated reduction of 2 million metric tonnes in Argentina; a similar loss was estimated for Chinese production due to Downy Mildew, also present in Manitoba. In the US, Tennessee has reported more than 100 thousand tonnes lost due to Frogeye Leaf Spot in 2003, whereas Illinois reported a similar number due to Anthracnose (Wrather and Koenning, 2006)[2]. Information about losses in Manitoba has not been reported yet.


A second survey was carried out during the 2017 growing season, following a similar procedure, in order to determine the presence of new pathogens that could have a significant impact in soybean production. The results have been partially analyzed, showing similar trend to the results of 2016.

[1] Wrather, A., Shannon, G., Balardin, R., Carregal, L., Escobar, R., Gupta, G.K., Ma, Z., Morel, W., Ploper, D., Tenuta, A., 2010. Effect of Diseases on Soybean Yield in the Top Eight Producing Countries in 2006. Plant Heal. Prog. 10, 2008–2013. doi:10.1094/PHP-2010–0125–01-RS

[2] Wrather, J.A., Koenning, S.R., 2006. Estimates of Disease Effects on Soybean Yields in the United States 2003 to 2005. J. Nematol. 38, 173–180.

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