Every year, root rot is a major threat to yield and quality of pulse crops. In regions where root rot is severe, growers must dramatically reduce acres or stop growing pulse crops entirely. Any decline of acres in the US and Canada is unfortunate because pulse crops provide extensive benefits in the field and at the table.

In the field, pulse crops provide alternatives to fallow (unplanted) acres, increase soil health, crop rotation diversity, and reduce input of synthetic nitrogen fertilizers. All of these can lead to more sustainable farming practices and increased profitability.

At the table, pulse crops provide a plant-based protein source that includes important vitamins and minerals, enhancing diet diversity and quality. In fact, eating more pulses has been associated with reductions in cholesterol, lower cancer risk, and helps with diabetes management.

what causes root rot
Yellowing plants and bare soil indicate areas with root rot issues.
Photo Credit: Dr. Carmen Murphy, Montana State University

What Is Root Rot Disease?

Root rot disease is caused by a collection of pathogens that span multiple genera of fungi and oomycetes. The major pathogens are found within several genera, including Aphanomyces, Fusarium, Pythium, and Rhizoctonia. 

Generally, there are pathogens found within each genus that can infect multiple pulse crops. All pulse crops, including chickpea, faba bean, field pea, lentil, and dry beans are susceptible to root rot pathogens.

Pulse crop root rot disease is more frequent during cooler and wetter weather, but it can still appear during dry weather. Symptoms are first observed above ground as stunted or yellowing plants in the field. 

Examining roots from these plants can help confirm root rot, where diseased roots are discolored (yellow, instead of white) with noticeably smaller root system and no nodules present. Aphanomyces root rot tends to be the most serious because of its ability to survive across multiple seasons as dormant, resting spores.

It is possible that multiple rot root pathogens are contributing to the disease within the same field. For example, both Fusarium and Aphanomyces species can be commonly found in the same field and within the same plant. Since different root rot pathogens cause identical symptoms and co-infections may also occur, visual-based diagnosis cannot accurately identify the pathogen species causing the root rot. 

Why is Accurate Root Rot Pathogen Identification Important?

Symptoms are indirect indicators of an underlying issue, and both pathogens and non-pathogen related issues can cause similar symptoms. For example, yellowing and stunted plants can be caused by nutrient deficiencies such as the lack of nitrogen or inefficient iron uptake. 

Distinguishing between a nutrient or pathogen issue can help determine the next action to help the growing crop. If root rot is misdiagnosed as a nutrient deficiency, this can lead to ineffective, unnecessary, and expensive application of fertilizers.

For confirmed root rot issues, the first step to effective root rot management is species-level identification. The numerous pathogens that lead to root rot have different lifecycles and biology that must be considered during management. Knowing the specific root rot pathogens within a field can help with pre-planting decisions. 

For example, fields that had Aphanomyces root rot issues in the recent past likely contain resting spores and should not be considered for peas or lentils for up to eight years. If other root rot pathogens, like Fusarium, were present in previous years, more tolerant pulse crops or varieties with known resistance could still be planted in the field. 

From a plant breeding and research perspective, developing new strategies (varieties, treatments) to combat root rot disease should be shaped by the prevalence and distribution of specific pathogens. Therefore, soil or root testing surveys that identify the root rot species can be highly informative for the start of long-term research programs.

root rot pathogen test
Healthy (left two) and diseased plants showing symptoms of root rot.
Photo Credit: Dr. Carmen Murphy, Montana State University

How to Identify Root Rot Pathogens 

DNA-based tests offer the fastest and most accurate method to identify root rot pathogens. A major advantage of DNA-based testing is its versatility for detecting pathogens from different sample types.

For example, soil samples collected across fields can be tested before planting to identify specific pathogens lurking within the soil. A positive root rot pathogen test from soil does not signify that root rot will occur later in the season – there are other factors (weather, host resistance) at play – but it does let growers know to keep an eye out for root rot during the early season or consider another field for their pulses. A subsample of the same soil collected for fertility testing can be used for pathogen tests.

Certain DNA-based tests not only detect but also quantify the pathogens within a sample, providing estimates on the levels of pathogens within the soil. With more research, it is thought that pathogen quantities from DNA-based tests of soil can be used as a predictive tool to estimate the risk of root rot disease before planting occurs.

Pulse crop DNA tests can also be used on root samples to help identify the pathogen that is causing root rot in the field. Roots can be collected from diseased plants across the field to evaluate whether the same root rot pathogen is causing disease within and across pulse crop fields of a farming operation.

While research continues to investigate how pathogen quantities relate to root rot disease risk, using a DNA-based test provides the best methods to identify the current drivers of root rot disease in pulse crops at local and regional scales.

NAGC’s Role n Root Rot Pathogen Surveillance 

To assist the pulse crop industry, the National Agricultural Genotyping Center (NAGC) continues to create root rot DNA-based tests for pathogen detection in soil and root samples.  

Our first validated test, Pulse Root Rot-1 (PRR1-Q), has been used by pathologists, agronomists, and growers to detect and quantify the three most concerning pathogens in North Dakota and Montana: Aphanomyces euteiches, Fusarium avenaceum, and Fusarium oxysporum.

NAGC is also actively working to validate additional tests to detect six (6) more pathogens, including Fusarium species, Pythium species, and Phytophthora medicaginis. In collaboration with pathologists in the National Predictive Modeling Tool Initiative, NAGC testing services will be used to investigate how DNA-based tests can help predict root rot risk in pulse crops.

NAGC is a practical choice as a testing facility because of our extensive industry connections, ISO-accreditation, and fast turnaround time. The test and sample extraction protocols can detect root rot pathogens in soil, residue, and root samples. To our knowledge, NAGC is the first private diagnostic facility to offer a DNA test for root rot pathogens to the U.S. pulse industry.   

Contact NAGC today to discuss how our root rot pathogen DNA testing services can assist you.