How to Differentiate Soybean Phytophthora Root and Stem Rot and Stem Canker

Phytophthora root and stem rot and stem canker are soybean diseases found throughout the soybean growing areas of the United States that can reduce yield potential. Because both diseases share similar symptomology, one can easily be misidentified as the other. This spotlight concentrates on the identification and symptom differentiation between the two diseases.

What are the causal pathogens for Phytophthora root and stem rot and stem canker soybean diseases?

Phytophthora root and stem rot (PRR) is primarily caused by Phytophthora sojae, a non-fungal water mold also known as an oomycete. A less common oomycete, Phytophthora sansomeana, can also cause PRR.^1,2 Oomycetes produce two types of spores, mobile zoospores that can swim in water and thick-walled, immobile oospores that persist in soil. Both types of specialized spore contribute to Phytophthora root and stem rot infections.¹

Stem canker is caused by the fungal pathogens Diaporthe caulivora and Diaporthe aspalathi. These pathogens were originally found infecting plants in different geographic regions, so stem canker was previously treated as two diseases: northern stem canker (caused by D. caulivora) and southern stem canker (caused by D. aspalathi). However, both pathogens are now commonly found throughout the soybean growing area and their symptoms are very similar, so stem canker is now discussed as one disease with two causal pathogens.³

What are the disease cycle, optimum infection timing, and favored growing conditions for Phytophthora root and stem rot and stem canker in soybean?

• Phytophthora root and stem rot: Oospores, the thick-walled resting spores of P. sojae and P. sansomeana, can survive in soil for several years. Moisture saturated soils and soil temperatures above 60 °F favor oospore germination. Once soils are saturated, mobile zoospores—produced by oospores—swim to soybean roots, germinate, and infect the plants through the roots. Optimum timing for infection occurs as soybean seedlings emerge (VE growth stage), although infection can occur throughout the growing season.¹
• Stem canker: The causal fungi survive for several years on infested crop residue and release spores that splash onto soybean stems during rainy weather. Infection occurs during early vegetative growth stages (V1 to V7) with V3 being the most critical; however, even after infection, cankers do not appear until reproductive growth stages.^3,4 Extended periods (24 to 96 hours) of moderate temperatures (72 to 86 °F), with high humidity (80% or higher), and wet weather favors stem canker infection.⁴

What soil type is associated with Phytophthora root and stem root and stem canker?

• Phytophthora root and stem rot: Clay, compacted, and poorly drained soils.¹
• Stem canker: High organic matter soils and high fertility fields.⁵

What are the symptoms of Phytophthora root and stem rot and stem canker?

• Phytophthora root and stem rot:
  • Seedling
    • Infection occurs through the roots and moves up the stem.
    • Roots become brown and rotted causing death from damping-off (Figure 1).
    • Laboratory analysis is required to distinguish PRR from Pythium root rot.¹
  • Late vegetative stages
    • Infected stems appear bruised and are soft.
    • Secondary roots are rotted.
    • Leaves become yellow and then turn brown.
    • Plants wilt and die.¹
  • Mid to late season
    • Leaves turn yellow, wilt, and usually remain attached after death (Figure 2). Interveinal chlorosis may occur.
    • Brown lesions form on roots, then roots rot.
    • Dark chocolate-brown discoloration of the stem typically extends from the roots below the soil line upward into lower plant parts (Figure 3).
    • Field patches or row sections may be impacted.
    • Tolerant plants may be stunted but not killed with symptoms restricted to roots.¹
• Stem canker:
  • Early symptoms include small reddish-brown lesions at the base of branches or leaf petioles.
  • The lesions become elongated, sunken, dark brown, and extend up and down the stem.
  • Stems are girdled where lesions appear.
  • Green stem tissue is usually present above and below the cankers (Figure 4).
  • Plant parts above lesions may die.
  • Tiny black dots (perithecia) may appear on the stem singly or in clustered groups on plants killed by stem canker.
  • Reddish-brown discoloration may also occur inside the stem, and pods may abort.
  • Stem canker lesions do not impact the root, in contrast to Phytophthora root and stem rot lesions which do.
  • Leaves of stem canker–infected plants may develop necrosis and chlorosis between the veins and may remain attached after death.
  • Plants can snap easily at canker locations.
  • Plants can have healthy and infected stem branches if girdling does not occur on main stem (Figure 5).
  • Symptoms caused by D. caulivora and D. aspalathi are very similar.^6,7

What other soybean diseases can be misidentified as Phytophthora root and stem rot or stem canker?

• Sudden death syndrome, brown stem rot, and soybean white mold develop similar interveinal leaf chlorosis; therefore, diagnosis should not be made exclusively by leaf symptoms.
• The diagnostic symptom of brown stem rot is the brown pith, which stem canker may develop but Phytophthora does not.

What is the management strategy for Phytophthora root and stem rot and stem canker soybean diseases?

• Phytophthora root and stem rot
  • Select soybean products that include Rps gene(s) and good field tolerance in conjunction with a seed treatment labelled for PRR.
  • Plant soybean products with specific Rps resistance genes effective against the particular Phytophthora populations identified within a field. Many Phytophthora sojae pathotypes exist, so pathotype identification is necessary to help select soybean products with the specific race resistance required for each field.
  • Available resistance genes include Rps1a, Rps1c, Rps1k, Rps3a, and Rps 1k+ 3a.
  • Plant products with partial resistance or “root rot resistance” have different levels of resistance to the different races. Soybean products with good partial resistance may still develop symptoms but yield impact is greatly reduced (Figure 6).
  • Improve soil drainage and manage compaction.
  • Labeled seed treatments containing metalaxyl or mefenoxam can help manage seedling PRR.^1,8
• Stem canker
  • Plant resistant soybean seed products.
  • Rotate crops and incorporate residue to help reduce inoculum. Corn, wheat, and sorghum are alternative non-host crops.
  • University research trials have shown inconsistent foliar fungicide efficacy and only a few may be labeled for stem canker management.
  • Weed management is important as many weeds are stem canker hosts, including black nightshade, curly dock, and morning glory.
  • Planting later when weather conditions are less favorable for disease development may help deter early infection.^3,4

Sources

¹Webster, R., Becton, H., Mathew, F., and Baldwin, S.A. 2025. Phytophthora root and stem rot of soybean. North Dakota State University. PP2251. https://www.ndsu.edu/agriculture/extension/publications/phytophthora-root-and-stem-rot-soybean
²Detranaltes, C.E., Ma, J., and Cai, G. 2022. Phytophthora sansomeana, an emerging threat to soybean production. Agronomy. 12(8): 1769. https://doi.org/10.3390/agronomy12081769
³Wise, K., Bradley, C., Chilvers, M., et al. 2025. An overview of stem canker. Crop Protection Network, A Product of Land Grant Universities. CPN-1006. https://cropprotectionnetwork.org/publications/an-overview-of-stem-canker
⁴Hershman, D.E. 2013. Stem canker of soybean. University of Kentucky – College of Agriculture, UK Cooperative Extension Service. PPFS-AG-S-07. https://plantpathology.mgcafe.uky.edu/files/ppfs-ag-s-07.pdf
⁵Jardine, D.J. 2020. Stem canker. Soybean Research & Information Network, Soybean Diseases. https://soybeanresearchinfo.com/soybean-disease/stem-canker/
⁶Giesler, L.J. Stem canker. In Soybean diseases. University of Nebraska–Lincoln, CropWatch. https://cropwatch.unl.edu/plantdisease/soybean/stem-canker
⁷Olson, T.R., Gebreil, A., Micijevic, A., Bradley, C.A., Wise, K.A., Mueller, D.S., Chilvers, M.I., and Mathew, F.M. 2015. Association of Diaporthe longicolla with black zone lines on mature soybean plants. Plant Health Progress. 16(3): 188–122. https://doi.org/10.1094/PHP-RS-15-0020
⁸Giesler, L.J. and Miller, J.J. 2017. Seed treatment fungicides for soybeans. Nebraska Extension, NebGuide. G1852. https://extensionpubs.unl.edu/publication/g1852/na/html/view
Web sources verified 7/28/26. 1311_142869