Soybean Diseases

Stem Diseases

Stem and root diseases can have a greater impact on soybean yield and quality than foliar diseases. Symptoms typically arrive later in the growing season during reproductive stages, which can directly impact pod and seed production. The most prevalent and economically important diseases in this category are white mould (Sclerotinia) and Phytophthora root rot. For more information and images of all diseases listed here, visit the Crop Protection Network web page.

Source: Crop Protection Network – Scouting for Soybean Stem Diseases publication.

White Mould

White mould in soybeans. Inset: Sclerotia body within the stem.

White mould can cause 2-5 bu/ac of yield loss for every 10% increase in incidence (% of plants affected). Cool, wet conditions throughout July and August and a dense crop canopy favour disease development. Infection begins low in the canopy at nodes along the stem.

Symptoms may first be noticed from afar as lodged plants or wilted, drying leaves at the top of the canopy. Inside the canopy, symptoms may appear as white mycelium (mouldy growth) along the stem, with black sclerotia bodies inside the stem.

Phytophthora Root Rot (Phytopthora sojae)

Phytophthora root rot on soybean stems, extending to the roots.

Phytophthora root rot (PRR) is considered both a root and stem disease. It was detected in 35% of surveyed soybean fields in Manitoba in 2017, and 30% in 2018. This disease can affect plants at all stages, but it is easier to identify at reproductive stages when a distinct brown lesion girdles the stem.

PRR progresses from the base of the plant upwards and wilted leaves remain attached to the plant. Foliar fungicide will not salvage infected plant tissue.

Stem Canker (Diaporthe caulivora, D. aspalathi)

Two different stages of stem canker, including initial (left) and advanced (right) stem lesions. Roots appear healthier than they would on a Phytophthora-infected plant.

Initial symptoms typically appear on the lower third of the stem shortly after flowering. The disease begins as small, reddish-brown lesions at the base of a branch or leaf petiole, and then expand to form slightly sunken cankers that are reddish-brown with reddish margins. Cankers may span several nodes on the main stem. Stem canker may at first resemble Phytophthora, where lesions wrap around the stem and extend to the soil line. However, the main difference is that the root will appear healthier overall compared to PRR, in which roots will be obviously rotten.

Stem canker incidence remains low overall in Manitoba, but this disease is one to watch over time.

Pod and Stem Blight (Diaporthe phaseolorum var. sojae)

Pod and stem blight pycnidia on a soybean pod and stems.

Pod and stem blight is present in Manitoba, but at low levels. It is identified by distinct lines of raised, black dots (pycnidia) on infected stems, pods and petioles.

Seed infection (Phomopsis seed decay) only occurs if pods are affected, reducing seed quality. Symptoms may be easier to detect in August through September.

Anthracnose (Colletotrichum truncatum)

Anthracnose symptoms on soybean stems.

Anthracnose is less common in Manitoba-grown soybeans. It appears as reddish-brown irregularly-shaped blotches on the leaves, stems and petioles. Black fungal bodies develop in these blotches later in the season. Leaf symptoms include reddish veins and petioles may become twisted and bent into a Shepherd’s crook, resulting in early defoliation.

New Potential Threats


Below is a list of diseases that are not yet confirmed in Manitoba. However, early detection and preventative management can slow the spread of these pests. If you suspect one of these diseases in your crop, geo-reference the location and contact MPSG Production Specialists Cassandra Tkachuk (eastern Manitoba) or Serena Klippenstein (western Manitoba) to facilitate lab verification. Note that foliar fungicides will not offer control of these pests.

Charcoal Rot

Charcoal rot appears as a light-grey or silver-coloured lower stem and taproot. When stems are split, black streaks will be present in the woody portion of the stem. This disease also produces tiny, black fungal structures (microsclerotia) throughout affected areas of the plant, giving the tissue a charcoal-like appearance.

Soybean Cyst Nematode

Soybean cyst nematode (SCN) is an inconspicuous pest that may first be identified by a steady yield decline over time. Once foliar symptoms of SCN appear in the field (yellowing and stunting) soybeans could already be losing >30% of yield. Scout for SCN during July and August by carefully digging up roots and inspecting them for cysts. The tiny, lemon-shaped cysts are much smaller than root nodules and may require a magnifying lens for identification. Look for SCN in high-risk areas of the field such as field entrances, depressions and headlands. Fields located near the Canada-United States border are also at greater risk.

Sudden Death Syndrome

Sudden death syndrome (SDS) infects roots early in the growing season, but foliar symptoms usually appear after flowering. Interveinal leaf chlorosis becomes necrotic, then leaves eventually die and prematurely fall from the plant leaving the petiole attached. Fields infested with SCN can increase the severity of SDS symptoms.