From late September through early October, some areas in Pennsylvania experienced 10 or more days of constant rain that kept already mature soybean fields wet. These conditions led to soybean pre-harvest sprouting and also provided the perfect conditions for the growth of pathogens already present in the plant, often limited by the moisture content in the substrate. Precocious germination reduces the quality of grain lots, and fungal colonization further contributes to grain degradation through the breakdown of seed protein, oil, and fatty acids (1).

Several saprophytic (opportunistic) and pathogenic (disease-causing) microorganisms are present in soybean pods and seeds before harvest (2,3). Seed-pathogenic fungi infect plants before or during the reproductive stages and are favored by warm temperatures and wet conditions later in the season. Common fungal pathogens isolated from soybean pods and seeds include Diaporthe, Alternaria, Cercospora, and Colletotrichum (3). In the field, it is common to find seeds and pods colonized by a mix of these pathogens.

What are the different symptoms of soybean seed diseases?

Purple seed stain: The fungus (Cercospora kikuchii) survives in infected seed and crop debris. Infection may occur early in the season, causing stem brick-red lesions on petioles (4) and a dark brown/bronze discoloration of the leaves, known as Cercospora leaf blight. The fungus is also the causal agent of purple seed stain. Infected seeds have a discoloration that ranges from light pink to dark purple and from specks to large blotches that cover the entire seed and may lead to downgrading (Figure 1). Warm and wet weather conditions favor seed infection during reproductive stages (4). Purple seed stain does not reduce yield; however, it reduces grain quality, may delay germination, and impairs seedling growth.

Figure 1. Soybean seeds with purple seed stain. Photo credit: Adriana Murillo-Williams. Penn State.

Pod, stem blight, and Diaporthe seed decay: This disease, previously known as Phomopsis seed decay, is caused by Diaporthe longicolla and other Diaporthe species and reduces yield, seed viability, and vigor. Infection occurs early in the season without causing symptoms. Small black reproductive structures (pycnidia) on stems and pods are signs of the disease. On the stems, pycnidia form linear patterns (Figure 2). Infected seeds are lightweight and shriveled, elongated, white or chalky in appearance, and have cracked seed coats (2,5) (Figure 3). Diaporthe seed decay is favored by hot and humid weather from R5 (beginning seed) to R8 (full maturity) (4).

Figure 2. Linear arrangement of pycnidia on soybean stems with Diaporthe spp. Photo credit: Adriana Murillo-Williams. Penn State.

Figure 3. Diaporthe seed decay. Photo credit: Adriana Murillo-Williams. Penn State.

Anthracnose: The pathogen (Colletotrichum truncatum) survives in seed, crop debris, and soil as microsclerotia (6) and can infect plants anytime during the season when conditions are warm and humid. Symptoms are typically visible during reproductive stages on stems (Figure 5), petioles, and pods, and include brown irregular lesions that grow in size, coalesce, and become covered with black reproductive structures called acervuli. Anthracnose may lead to barren pods (4). Infected seeds may be asymptomatic or small, shriveled, with a brown or gray discoloration with black specks (7) that might be difficult to tell apart from other diseases or weather-related issues.

Figure 4. Stem symptoms of soybean anthracnose. Photo credit: Adriana Murillo-Williams. Penn State.

Sclerotinia stem rot (White mold): The fungus, Sclerotinia sclerotiorum, affects yield and seed quality. In addition to infected seed, seed lots may contain sclerotia, fungal survival structures that serve as the pathogen source for the next growing season and as long-distance dispersal units. Sclerotia will germinate to form apothecia when environmental conditions are favorable. Thousands of spores are released from apothecia and will infect stems through senescing flowers. Lesions develop on the stem, branches, and pods, forming new sclerotia. The premature death of the plants leads to barren pods or seeds that are small, shriveled, or covered with white cottony fungal growth (Figure 5).

Figure 5. Sclerotinia white mold on soybean seeds. Photo credit: Adriana Murillo-Williams. Penn State.

Although some diseases are easily identified, the presence of opportunistic fungi and mixed infections makes identification challenging. Scouting prior to harvest and identifying diseases early provides much better results than attempting diagnosis following maturity and harvest. If you need help identifying seed diseases, contact your local Penn State Extension Educator or send samples to the Penn State Disease Clinic.