Soilborne Diseases and Disorders of Soybean: Is it Sudden Death Syndrome (SDS) or is Something Else Responsible?

Tom Allen, Extension Plant Pathologist
By Tom Allen, Extension Plant Pathologist September 3, 2012 17:19 Updated

Not all plants encountered in the field that exhibit interveinal chlorosis are the result of sudden death syndrome (SDS). However, telling the diseases and disorders apart throughout the growing season can be difficult.

Over the past few months I’ve observed numerous soybean fields throughout the state with interveinal chlorosis prevalent in several scattered plants throughout the field, or small to large areas of a field.  In some situations the symptoms of chlorosis appear indicative of sudden death syndrome (SDS).  However, there are several diseases as well as abiotic and biotic disorders that can result in the development of interveinal chlorosis.  The mere presence of interveinal chlorosis does not deem the problem to be SDS.  Several key characteristics (outlined below) can help determine the cause of the issue.

First and foremost the appearance of interveinal chlorosis (or a yellowing of the leaves in between the veins where the vein remains green) can be the result of factors that affect the root health.  In addition, interveinal chlorosis is mostly (but not always) the result of something that limits the flow of moisture and/or nutrients to the uppermost leaves on the plant.  In most of the situations outlined below, by cutting into the main stem of the soybean plant a darkening of the vascular tissues can help determine what has caused the leaves to become chlorotic.  Diagnostically speaking, soybean roots and stems should be white when you cut into the plant with a knife.  However, keep in mind that several diseases will discolor the inside of the vascular tissues and also produce a discoloration immediately beneath the outermost layer of plant tissue (e.g. charcoal root rot).

Some of the key diseases and disorders that can impact root health and ultimately result in observable interveinal chlorosis are outlined below.  One thing is certain about the list outlined below: once observed there are no management practices, such as a fungicide application, that can be performed at that time to rectify the issue save for making note of the particular problem (after proper diagnosis) and attempting to alleviate the concern in the subsequent season.


Foliar and root symptoms of a soybean plant in a stressed/shocked situation. Not the mild interveinal chlorosis accompanied with mild interveinal staining.

Shock or Stress Induced Leaf Chlorosis

More often than not, environmental stresses are classified as plant diseases and it can be difficult to determine the cause of the problem.  As mentioned above, irrigation induced stress or drought stress in general followed by excessive rainfall can act to shock a soybean plant.  In general, the chlorosis associated with this particular disorder can be less severe than some of the others listed below.  In cases I’ve observed during 2012, a slight yellowing occurred between the veins of soybean plants that ranged in age from late vegetative stages to R3/R4.  However, roots can show minimal symptoms and in some cases a light discoloration can be observed in the vascular tissue.  During 2012 I have also observed some pink discoloration of roots in certain situations.  The pink discoloration is likely a secondary fungal infection due to the stressed situation.  In almost every situation that I’ve observed this season, the fields contained heavier soil types and clear evidence of drought stress was present even following the rainfall.  In addition, in some of the situations, leaves also had some more generalized yellowing that would be more indicative of a nutritional problem or some other soil-based and/or root-based issue encountered in the particular field.


Fungicide phytotocity

Most notably, this is the one particular topic that is not a root-borne issue.  On the rare occasion that a fungicide application produces phytotocity the foliar symptoms can appear similar to SDS.  Several plots in my fungicide trials in Stoneville developed phytotoxicity in response to an R5 fungicide application, though I haven’t looked at the particular products.  I have not seen this issue in commercial fields in MS save for a single time but have seen this in fungicide trial plots when:

-the fungicide was applied during a hot time of the day

-a particular active ingredient burned the leaves (e.g. Folicur)

-an inert ingredient in the fungicide produced a leaf burn (e.g. certain additives in Caramba, hence the product no longer being labeled in soybean)

-the addition of an adjuvant with a particular fungicide resulted in a leaf burn

-or a high rate of a particular fungicide produced a leaf burn

However, one key component of this particular scenario will become clear.  The symptoms would likely be present across the entire field following the fungicide application.  In addition, plants removed from the soil would likely not have stained vascular tissue and aside from the leaf symptoms the plant would appear remarkably healthy.


Brown stem rot

For the past few seasons I’ve heard several people mention brown stem rot having been observed/diagnosed in MS.  I have never seen brown stem rot in MS, nor have any of my predecessors at MSU.  In fact, most of the reports of this particular disease, and the causal fungus (Phialophora gregata) on soybean, have been from well outside of our region (IA, IL, IN, MN, OH, WI).  The closest report of brown stem rot was from North Carolina in the 1980s.  I’m inclined to think that the fungus can’t handle our specific environment, especially the high temperatures, which in this case is a good thing.  As opposed to the other diseases and disorders listed in this blog update, brown stem rot causes the pith of infected plants to become brown.  The brown pith inside the plant as well as leaves exhibiting interveinal chlorosis are the main diagnostic characteristics of brown stem rot.


Red crown rot of soybean. Notice the red pycnidia around the base of the plant at the soil line. The interveinal chlorosis that can be attributed to this particular disease is noted with the inset photo at the bottom right.

Red crown rot and Neocosmospora root and stem rot

Annually I’m asked about the appearance of red crown rot in MS.  Firstly, red crown rot has only been observed in 3 counties in MS to date: Chickasaw (1 field diagnosed in 2007), Clay (1 field diagnosed in 2012), and Noxubee counties.  Red crown rot is most easily recognized when the red fungal structures (pycnidia) are observed at the base of the plant near the soil line (see attached photo).  The red structures appear similar to a tiny red pin cushion.  Interveinal chlorosis as well as vascular staining of the internal plant parts also occur with red crown rot.  But, keep in mind that not all red discoloration at the base of the soil line is caused by red crown rot.  Other factors can contribute to a red discoloration at the soil line.

In addition, one other less common disease can produce a similar, orange to red structure (a perithecium….so a different fungal structure) at the base of the plant, Neocosmospora root rot.  The red structure produced on infected plants will look more vase-shaped, rather than a pin cushion, and appear more violet to almost purple in color.  In the 5 years I’ve been in MS I have only seen what I thought was Neocosmospora root rot twice: once in a field in Adams County of R5.5 soybean plants, and once from a field in northeast MS and the soybean plants were at R8.   Neocosmospora root rot can result in interveinal chlorosis as well as a general discoloration of the vascular tissues of the soybean plant.  In fact, I’ve seen Neocosmospora root rot so infrequently (and haven’t properly diagnosed the issue in the laboratory) that I don’t even have a photograph of the disease in the field.



Phytophthora root rot, note the gray lesion on the stem. Interveinal chlorosis as well as vascular staining can also occur as a result of Phytopthora root rot.

Phytophtora root and stem rot

I’ve listed this particular disease as a rare occurrence in MS.  In most field cases this season (2012), where the above described symptoms have occurred (interveinal chlorosis), an initial misdiagnosis of Phytophthora root rot was made.  In the 5 years I’ve been with the Extension Service I have only encountered this particular disease once, in a small isolated area of a field in western Bolivar County during 2008 in a heavy gumbo soil that was heavily irrigated and saturated following several days of rain.

Firstly, the organism that causes Phytophthora root and stem rot is water-loving so would be more of a concern in areas of a field that remained saturated for an elongated period of time.  Typically, the disease will be observed on heavier soils but requires an extremely conducive environment (typically 77 to 86F) with excessive moisture present.  Phytophthora root rot would not be presumed to be a problem in a pivot irrigated field outside of the area that received moisture.  In addition, Phytophthora root rot will occur in a clump of plants and would not likely be an issue in random plants scattered throughout a field.

Diagnostically, a grey lesion that extends up from the base of the plant along the stem from the soil line is one of the key characteristics of Phytophthora root rot.  In addition, a rotted root system can cause the plant to completely wilt.  Lateral roots as well as the tap root will rot off the plant due to the saturated soil situation and the presence of the fungus.  Phytophthora can cause a “soft rot” situation where the root system and/or lesion growing up the main stem will be soft and mushy.  But, again, Phytophthora root rot has not been a common occurrence over the past 5 years in MS.


Fusarium wilt, note how light the interveinal chlorosis can appear where the veins remain dark green. The blackened and rotted roots as well as vascular staining appear in the photos in the top left and right inset.

Fusarium wilt (?)

I have a question mark next to Fusarium wilt since the disease is poorly described especially in the southern United States.  I have many friends that work at other universities who have spent the majority of their career working with the diseases caused by Fusarium and they struggle to identify this particular disease.  Over the past 5 seasons we have observed an increased number of fields with scattered plants throughout the field that have interveinal chlorosis that is incredibly similar to SDS.  However, when plants are removed from the soil the root is almost always rotted away or a portion of the taproot breaks off of the plant and remains in the soil.  In addition, the portion of the root that remains is black from the root rot.  Every time I take plants back to the laboratory and isolate fungi from the roots I almost always end up with several different isolates of Fusarium.   Over the past 5 seasons we have begun to encounter a disease that I’ll begin to refer to as Fusarium wilt (in the past we have also referred to this as Black root rot, but have not been able to positively identify this in the laboratory as we have never extracted the correct fungus from the roots).  Diagnostically speaking, this particular disease can be observed more often in fields with lighter soil types, on scattered plants throughout the field, or in some situations on adjacent plants.  If you pull the plant out of the soil and expose a black root, leave a portion of the tap root in the soil, strip the bark back to expose a heavily stained vascular tissue, then you more than likely have Fusarium wilt.


Southern blight of soybean. Note the white fungal matte growing on the stem as well as the subtle interveinal chlorosis associated with the disease. Typicaly sclerotia are included in the inset photo.

Southern blight

Prior to 2012 I had only seen 5 plants with southern blight symptoms since I was employed by MSU.  One of those plants was on a trip to Louisiana.  Southern blight can also produce an interveinal chlorosis.  However, as opposed to having to dig up the plant, in most cases the fungus that causes southern blight (Sclerotium rolfsii, that also causes white mold of peanut) will produce a thick, heavy matte of white fungus at or just below the soil line.  The interveinal chlorosis that I’ve observed with southern blight has generally been mild.  In addition to the thick white fungal matte, in situations where dead plants are present, or the fungus has run its course, white to cream to brown sclerotia will be present either on the plant or on dead organic matter around the base of the plant.





Stem canker, note the red-brown lesion extending up the main stem of the plant. Leaves with the characteristic interveinal chlorosis as well as a close-up of the canker are included in the inset photos.

Stem canker

With the advanced breeding programs that have been conducted to develop soybean cultivars with tolerance/resistance to stem canker the occurrence of this particular disease has been infrequent over the past 5 years in MS.  To date, I’ve seen 3 fields with recognizable stem canker: a field in Coahoma County, a field outside of Verona, MS, and a field on the AL/MS line.  In most cases, stem canker is a disease that if a field has a history of the disease the best choice is to select a variety with tolerance to the disease.  Interveinal chlorosis will be one of the more notable symptoms in the leaves.  However, the canker that will either be along one side of the plant starting at the soil line and moving upwards or girdling the entire stem of the plant will be red-brown in color and quite evident.  In addition, staining of the vascular tissues will be associated with this particular disease.  Plants infected can tend to be in a small clump, or, if a susceptible variety is planted across a large area of a field.  The difference between stem canker and some of the diseases listed above will be the color of the canker along the stem and the field history.  One other important diagnostic feature has to do with leaves remaining attached to the plant after death of the entire plant.


Root-knot nematode on soybean. Typically, fields with sandier soil characteristics will be more prone to a root-knot nematode problem, especially in situations where either continuous soybean has been grown or soybean following cotton.


I have encountered more fields with nematode disorders this year than in all of my years prior to 2012 combined.  As I’ve stated above, anything that impacts the roots of a soybean plant can ultimately result in the occurrence of interveinal chlorosis.


The main nematodes affecting soybean include:

-reniform nematode (prefers soils with more silt characteristics)

-root-knot nematode (prefers soils with more sand characteristics)

-soybean cyst nematode (SCN)

In addition to stunted plants, nematodes can produce symptoms of interveinal chlorosis on the leaves.  In most cases it is not enough to simply remove the plant from the soil and observe the roots since only the root-knot nematode will produce galling that can be observed with the naked eye.

To properly determine the particular nematode component in any field submit a soil sample to the Plant Disease and Nematode Diagnostic Laboratory in Starkville, MS.  Observing galls on roots is the easiest way to distinguish a root-knot nematode problem.  However, both reniform and soybean cyst nematode are difficult to observe on the root with the naked eye and require increased magnification from a laboratory microscope to properly identify the causal organism.  In addition, in some cases the soybean cyst nematode can enhance sudden death syndrome.  If you are observing field situations with large, oval areas of plants with leaves that have interveinal chlorosis then SDS could have been caused by the presence of high populations of SCN.  But, as I’ve stated below, the soil characteristics are one of the biggest features of whether or not SDS is present or not.  Nematodes are generally not a problem in heavy soils but can reach large populations in light to sandy soil types.  However, SCN has not been a big issue in MS since the 1970s when a natural soilborne fungus wiped out most of the SCN populations in the state.  But, with that said, I’ve observed 3-5 field situations in MS where SCN has been present and resulted in plant stunting early in the season.

Severe sudden death syndrome (SDS) in a field of soybean near Marks, MS. The field was also diagnosed to have a heavy soybean cyst nematode infestaton.

Sudden Death Syndrome (SDS)

I’ll close with SDS.  Telling SDS apart from many of the other disease causing organisms that can produce interveinal chlorosis can be difficult.  However, there are a few key characteristics that will discern SDS from the other maladies that result in interveinal symptoms.

1)      SDS is more typical on light soils.  If you are detecting interveinal chlorosis on heavy clay or buckshot soils then you can rule SDS out.

2)      In all instances where I’ve identified SDS you can almost always (but I’m sure there are exceptions) pull the entire tap root out of the soil.  If you start to pull the plant up by holding onto the base of the plant near the soil line and the tap root breaks off below the soil line then it is likely not SDS.

3)      In the most advanced cases of the disease the area between the vein will fall out of the leaf.

4)      SDS will typically not be observed until the R5 growth stages or beyond.  For some reason pod set seems to predispose infected plants to the expression of the disease symptoms on leaves.




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Tom Allen, Extension Plant Pathologist
By Tom Allen, Extension Plant Pathologist September 3, 2012 17:19 Updated
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