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Integrated Pest & Crop Management


Laura Sweets
University of Missouri
Plant Science & Technology
(573) 884-7307

SDS and Other Late Season Soybean Diseases

Laura Sweets
University of Missouri
(573) 884-7307

Published: September 11, 2014

After a challenging start to the season with numerous reports of damping-off, seedling blights and root rots as well as herbicide injury, the soybean crop finally took off and looked good for much of the season. Now the overwhelming disease problem is sudden death syndrome or SDS. Several of the other late season diseases such as late season Phytophthora and Cercospora leaf spot and blight are making minor appearances. There have been more samples with stem canker than we typically see. And there have been a few samples with brown stem rot and one or two with charcoal rot. Foliage diseases were not widespread or severe for most of the season although some are making a last minute appearance. Septoria brown spot, downy mildew and bacterial blight may be evident on green leaves still in the upper canopy. Very early symptoms of soybean vein necrosis virus may also be evident on green leaves in the upper canopy. Losses from soybean cyst nematode continue to be a problem and this would be a good year to sample fields for SCN. This is also the time of year when anthracnose and pod and stem blight may show up on maturing soybean plants.

Yield losses from these various late season diseases will vary depending on when symptoms began to occur, number of plants infected, severity of disease in infected plants and weather conditions from now to harvest.In some cases although yellowing of the upper canopy may be quite widespread and spectacular in a field, damage is limited to the uppermost leaves and pods so yield loss should be minimal. In other cases, especially with sudden death syndrome, the entire plant may have been killed prematurely. If large areas of a field are thus affected, yield losses will be greater. Although it is too late in the season to do much to control these diseases this year, management strategies to prevent or minimize these diseases next season are also given below.

Sudden Death Syndrome

Symptoms of sudden death syndrome (SDS), caused by a strain of Fusarium virguliforme, may appear several weeks before flowering but are more pronounced after flowering.Foliage symptoms begin as scattered yellow blotches in the interveinal leaf tissue. These yellow blotches may increase in size and merge to affect larger areas of leaf tissue. Yellow areas may turn brown but veins remain green giving the leaves a striking appearance. Severely affected leaflets may drop off the plant leaving the petiole attached or may curl upward and remain attached to the plant. Infected plants may die prematurely. Root systems may show deterioration and discoloration of lateral roots and taproot. When split open, internal tissues of the taproot and stem may show a light gray to light brown discoloration from the soil line several inches up the stem. If plants are carefully dug up, bluish-white, powdery masses of spores of the SDS fungus may be seen on the roots or taproot.

Figure 1. Foliage symptoms of SDS

Figure 2. Severe necrosis due to SDS

Figure 3. Defoliation at upper nodes due to SDS

Figure 4. Bluish mold growth on roots of plants with SDS

Figure 5. SDS causing widespread yellowing across field

Management options for SDS are somewhat limited but should include planting varieties which have performed well where SDS has been a problem, improving drainage in poorly drained fields, avoiding compaction, staggering planting dates, delaying planting until soils are warm and dry, avoiding continuous crop soybean, maintaining good crop vigor, avoiding crop stress including stress from soybean cyst nematode and harvesting fields with SDS in a timely fashion.

Late Season Phytophthora Root Rot

Figure 6.Single plant showing yellowing and wilting due to Phytophthora root rot

Figure 7. Discoloration of stem and out side branches caused by Phytophthroa

Wet conditions after planting regardless of planting date increase the likelihood of Phytophthora root rot. Phytophthora may cause seed decay and seedling blight but it can also cause symptoms later in the season as plants move into reproductive stages of growth. Infected older plants show reduced vigor through the growing season or die gradually over the season. Lower leaves may show a yellowing between the veins and along the margins. Upper leaves may yellow. The stems show a characteristic brown discoloration that extends from below the soil line upward and even out the side branches. Eventually the entire plant may wilt and die. Withered leaves remain attached even after the plant dies. Preventive measures are the main means for managing Phytophthora root rot. Select varieties with race-specific resistance, tolerance or a combination of the two, plant in good seedbed conditions, tile to improve drainage, take steps to reduce compaction, rotate crops and use an appropriate fungicide seed treatment.

Cercospora Leaf Spot, Leaf Blight and Purple Seed Stain

Cercospora kikuchii can infect soybean seeds, pods, stems and leaves but is most commonly found on the seed. However, this year we are seeing some cases of leaf spot caused by this fungus. Infection is primarily occurring on the uppermost leaves and begins as reddish purple to reddish brown, angular to somewhat circular lesions on the soybean leaves. These lesions may coalesce to kill larger areas of leaf tissue. The uppermost trifoliolate leaf and petiole may be blighted and brown. One striking symptom of this disease may be the premature yellowing and then blighting of the youngest, upper leaves over large areas of affected fields. In most fields, the symptoms have not progressed down the plants more than one to two nodes.Pods at the uppermost node may develop round, reddish purple to reddish brown lesions.

Initial symptoms of Cercospora blight may appear as plants are beginning to set seed. Upper leaves in the canopy that are exposed to sun start to show a pink to red to purple discoloration from the leaf tip extending back toward the base of the leaflet. The discoloration may darken and eventually cover the entire upper surface of the leaflet.Leaflets may have a leathery texture and a dark, reddish purple color highlighted with bronze.

This pathogen may also infect seed causing purple seed stain.Infected seed show a conspicuous discoloration ranging in color from pink to pale purple to dark purple. The discoloration may range from small specks to large blotches which cover the entire surface of the seed coat. Temperatures of 82-86°F with extended periods of high humidity favor disease development.

At this point in the season control of Cercospora leaf spot and purple seed stain is not feasible. It is important to remember that since this fungus can infect the seed, seed from heavily infected fields should not be used for seed.If infected seed must be planted, seed lots should be thoroughly cleaned and an appropriate seed treatment fungicide used.Rotating soybean with crops other than legumes will also help reduce Cercospora leaf spot and blight in future soybean crops.

Figure 8. Stem canker lesion on stem

Stem Canker

Although stem canker can occur in Missouri, this disease is usually not widespread or serious in the state.With the cooler than normal temperatures for much of the growing season, there have been scattered cases of stem canker this season. At first glance the affected plants might be mistaken for ones infected with Phytophthora as the plants are off-color or gray green and wilting. Examining the stems for the pattern of discoloration should help distinguish between the two diseases.

Initial symptoms of stem canker are small reddish brown lesions on stems near a leaf node. Over time the lesions expand to form larger, sunken cankers that are brown to black in color. Since the lesions tend to develop around leaf nodes, the discoloration of the stem is not continuous over the entire stem. The stem near the soil line may be green with bands of discolored tissue at infected leaf nodes separated by green healthy tissue at healthy nodes or intermodal regions of the stem.Foliage symptoms of yellowing or browning of leaf tissue may also develop.

Diaporthe phaseolina, the fungus that causes stem canker, survives in infested residues. Infection by the stem canker pathogen is favored by extended periods of rainy weather and cooler temperatures during early vegetative stages of soybean growth.However, symptoms may not be evident until later in the season.

Charcoal Rot

Symptoms typically begin to develop as plants move into reproductive stages of growth.Infected plants are less vigorous and have smaller leaves.Leaves may turn yellow and wilt.Leaves eventually turn brown and have a dry appearance. The taproot and lower stem develop a silvery gray to light-gray discoloration of the epidermis (outer layer of the soybean stem). The epidermis may flake or shred away from the stem, giving the stems a tattered appearance.Fine black specks or microsclerotia may be evident in tissues below the epidermis and eventually in epidermal tissues. Symptoms may develop on scattered plants, in circular to oval patches in a field, in drier areas of a field or across much of a field. Charcoal rot is favored by drought conditions so may not be a problem in much of Missouri this season. Management options for charcoal rot include rotating crops, maintaining good crop vigor to help reduce losses from charcoal rot and irrigating properly from just before bloom to pod fill.

Figure 9. Foliage symptoms that may occur with brown stem rot


Figure 10. Discoloration of center pith due to brown stem rot

Brown Stem Rot

Brown stem rot is another soybean disease which is not usually a problem in most of the state. When brown stem rot is found in Missouri soybeans it tends to be in the northern part of the state and in years with cooler temperatures through the growing season. Brown stem rot is caused by the fungus Cadophora gregata (formerly Phialophora gregata) which survives in infested crop residues and in the soil.

When foliage symptoms occur, they usually develop as plants are beginning to set pods. Light green to yellow blotches develop in the interveinal leaf tissue. The blotches may increase in size and merge to affect larger areas of leaf tissue. Over time, the yellow areas may turn brown with the veins typically staying green. These foliage symptoms resemble those of sudden death syndrome.

Upper trifoliolates may become brown and dry out. Brown stem rot causes a brown discoloration of the vascular tissues and center pith of the soybean stem that is evident when the stem is split open. Initially the brown discoloration may be found in stem tissues close to the soil line and near nodes higher up on the plant. Later in the season, the brown discoloration may be almost continuous within the stem.

Development of brown stem rot is favored by temperatures in the range of 59-81 degrees F. As air temperatures increase above 81 degrees F, both incidence and severity of brown stem rot decrease. Leaf symptoms are most pronounced if cool weather occurs as the crop enters the reproductive stages of growth. Management of brown stem rot is primarily through the use of resistant varieties and crop rotation.

Soybean Vein Necrosis

In 2012, a relatively new virus disease of soybean, soybean vein necrosis, showed up in many soybean fields in various regions of the state. Initially, small light-green to yellow patches develop near main leaf veins. These patches then develop a mottled light green-yellow-brown pattern. The veins in these areas of the leaflet may become clear to almost translucent which is referred to as vein clearing. As the disease progresses these areas turn reddish-brown with a browning of the veins. The reddish-brown areas may have a scaly or scabby appearance. On more susceptible varieties the brown areas may expand killing larger areas of leaf tissue and giving a scorched appearance to the leaves.

The virus which causes soybean vein necrosis belongs to a group of viruses called tospoviruses which are spread by thrips. Under the drought conditions of 2012 thrips were present at high levels in many areas of the state and soybean vein necrosis virus was also widespread. With more normal conditions in 2013 and cooler conditions in 2014, this virus disease has not been nearly as prevalent.

At this point the disease is still a relatively new disease and there are more questions about it than answers. It appears that the virus is spread from soybean to soybean by thrips but which species(s) of thrips is unknown. Other hosts, especially weed hosts, have not been confirmed. And there are many questions related to the disease cycle, possible yield losses and appropriate management strategies. Varieties seem to vary in their susceptibility to this virus disease and symptoms may vary with varieties.

At this time there isn’t enough known about the virus and disease to make effective management recommendations. As more information becomes available on this disease, management strategies can be formulated and recommendations made. Overall, disease symptoms of soybean vein necrosis have been low to moderate across fields in all states in which the disease has been reported this season. So for this season no control measures are recommended

Septoria Brown Spot

Septoria brown spot causes small brown spots on the unifoliolate and lower trifoliolate leaves. The individual spots may run together forming irregularly shaped brown blotches on the leaves. Infected leaves may yellow and drop prematurely. Brown spot usually starts on the lower portion of the plant. Under favorable weather conditions (warm, wet weather), the disease may move up through the plant. Brown spot was evident in many Missouri soybean fields earlier this season. But late season rains can trigger a reoccurrence of Septoria brown spot. Symptoms move up through the canopy of soybean plants. Lower leaves may show heavy spotting, yellowing and dropping prematurely. Upper leaves may also show spotting and yellowing. Some fields which have a yellow cast from the road may be showing symptoms of Septoria brown spot rather than SDS.

The fungus which causes this disease, Septoria glycines, survives in infested residues left on the soil surface. Fields with continuous soybean production are more likely to show damage. Planting disease-free, good quality seed of resistant varieties, rotating crops with at least one year between soybean crops and maintaining good plant vigor should reduce losses from Septoria brown spot.

Downy Mildew

Downy mildew, caused by the fungus Peronospora manshurica, is reported wherever soybeans are grown. The downy mildew fungus survives as oospores in infected leaf residues and on seeds. Spores produced in diseased areas on lower leaf surfaces are wind-blown and serve to infect additional leaves on that plant or other plants.

Initial symptoms of downy mildew are pale green to light yellow spots or blotches on the upper leaf surface of young leaves. These areas enlarge into pale to bright yellow blotches of indefinite size and shape. Eventually lesions turn grayish brown to dark brown with a yellow margin. During periods of heavy dew or wet weather, a gray to purple fuzz that is visible growth of the downy mildew fungus develops on the lower leaf surface beneath the diseased areas on the upper leaf surface. Severely infected leaves turn yellow and then brown. Downy mildew is favored by high humidity and temperatures of 68-72 degrees F.

Management options for downy mildew include planting disease-free seed and rotating crops with at least one year between soybean crops.

Bacterial Blight

Bacterial blight, caused by the bacterium Pseudomnas savastanoi pv glycinea, can occur on soybeans anywhere in the state and is common during cool, wet weather. The causal bacterium may be carried on the seed or can survive in crop residues. It is spread by wind driven rains or splashing rain.

Bacterial blight produces small, angular yellow lesions on the leaves. Lesions usually have a translucent or water-soaked appearance that may be more easily seen if the leaves are held up to the light. Lesions progress in color from yellow to light brown and eventually to a dark reddish brown. Older lesions have a dark center surrounded by a water-soaked margin and a yellow halo. In cool, rainy weather the small, angular lesions may enlarge and merge, producing large, irregular dead areas in the leaf. With wind and rain, these large dead areas drop out or tear away, giving the leaf a ragged appearance.

Symptoms typically occur several days after a rain with driving winds or a hailstorm. If there are alternating periods of wet and dry weather, plants may show bands of leaves with symptoms. Leaves that were expanding during wet periods show bacterial blight symptoms and leaves that expanded during dry periods are free of disease.

Bacterial blight is favored by cool, rainy weather. During early to midseason, disease outbreaks usually occur five to seven days after wind driven rain storms or hailstorms. Hot, dry weather checks disease development.

Soybean Cyst Nematode

Symptoms of soybean cyst nematode (SCN) range from no obvious symptoms to subtle differences in plant height and vigor or unexpected decreases in yield to severe stunting and discoloration of plants or dead plants. Foliage symptoms may include a yellowing of leaves from the margin inward or a general yellowing of leaves. But such foliage symptoms are also caused by a number of other factors including root rot diseases, nutrient deficiencies, herbicide injury and compaction, so foliage symptoms should not be used to diagnose SCN. Plants with SCN may have poorly developed root systems, if plants are carefully dug up, females may be evident on the roots. The females appear as tiny (smaller than nitrogen-fixing nodules), whitish to yellow to brownish, lemon-shaped structures on the roots. Symptom expression may be more severe if plants are subjected to other stresses such as moisture stress, nutrient deficiencies, herbicide injury, insect damage or other diseases.

It is important to periodically sample fields and have SCN egg counts done to know population levels in the field and to understand how management practices are influencing those levels. Variety selection is still an important tool in managing SCN. Rotating crops, maintaining good plant vigor and maintaining good weed control are also important. Recently several seed treatment materials which may aid in the management of SCN have become available.


Colletotrichum truncatum and several other Colletotrichum species cause anthracnose of soybean. Typically, anthracnose is a late season stem and pod disease of soybean. Symptoms occur on stems, pods and petioles as irregularly shaped, light to dark brown spots, streaks or lesions. Eventually black fungal structures may be evident in these lesions. Anthracnose may also cause tip blight. The tip blight phase of anthracnose causes a yellowing or browning of the uppermost leaves and pods. The blighted tips may dry up and die prematurely. Anthracnose is favored by warm, wet weather, and the tip blight phase of anthracnose is most likely to occur after a rainy period.

Again, at this point in the season control of anthracnose is not feasible. This fungus may also infect seed so seed from heavily infected fields should not be used for seed. If infected seed must be planted, seed lots should be thoroughly cleaned and an appropriate seed treatment fungicide used. Rotating crops with at least one year out of soybean will also help reduce anthracnose.

Figure 11. Anthracnose (large black spots) and pod & stem blight ( small black specks)

Figure 12. Anthracnose and pod & stem blight

Pod and Stem Blight

Phomopsis longicolla and the other Diaporthe and Phomopsis species that cause pod and stem blight and Phomopsis seed decay can survive in infested crop residues, in the soil and in seed. Symptoms usually develop on stems of plants during later reproductive stages of growth.

Pod and stem blight infected plants may be stunted and their stems discolored. Black pycnidia or fruiting bodies of the cause fungi develop on the lower portion of the main stem, branches and pods as plants reach maturity. The pycnidia may be limited to small patches near the nodes or may cover dead stems and pods. On stems, pycnidia are usually arranged in linear rows while on pods they are scattered across the pods. The fungi may grow through the pod walls and infect the seed causing Phomopsis seed decay. Infected seed is usually oblong in shape, somewhat shrunken or shriveled and covered with a white mold growth.

Although prolonged periods of wet weather during flowering and pod fill favor the development of pod and stem blight, the rains since Labor Day have been enough to trigger low levels of this disease this year. If wet weather continues through harvest, levels of Phomopsis seed decay may increase.

At this point in the season control of pod and stem blight is not feasible. Management options include rotating crops with at least one year between soybean crops and planting disease-free seed.

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