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Healthy seed, healthy start: The importance of seed testing in preventing diseases of pulse crops

Montana has seen a spike in pulse crop acres in the last 10 to 20 years. When I started 10 years ago, my crop responsibilities included spring wheat, winter wheat, durum, and maybe a little barley. Now wheat is becoming a rotational crop for pulse production.

June 23, 2017  By Mary Burrows

Prevention of plant diseases is key to management. Most growers did not spray fungicides until about five to six years ago, after the stripe rust epidemic in wheat in 2011. I recommend seed treatments to keep out root rots and prevent seedborne diseases, but growers are reluctant to invest in seed treatments because it is an additional input cost. Pest populations build up over time, and seed treatments are a key to preventing that buildup. They are a good long-term investment, although they may not be directly profitable every year.

In Montana in 2016, we started to see quite a bit of Fusarium root rot, especially in the northeast corner of the state, which is our traditional pulse production area. We identified Aphanomyces root rot for the first time this year, and found it in three of 21 fields that we surveyed. We’re seeing very few nematodes, and none are known to be pathogenic on pulses. We saw widespread white mould of lentils for the first time in 2016 due to a cool, wet season around flowering. Ascochyta blight caused problems in chickpea where it was not managed early. Viruses of peas are being increasingly observed because of the mild fall and winters three years in a row, which encourages aphid populations, as well as a lack of seed testing for seed-borne viruses.

Prevention a key to IPM
You all know the principles of integrated pest management (IPM) and the disease triangle for management of plant diseases. One key to IPM is prevention. We’d rather prevent a problem than have to cope with it. A critical aspect of prevention is accurate identification of the pest. What is your most powerful tool for accurate identification of a plant disease or an insect or anything? It’s your cell phone. You can take a picture and send it to an expert; you can look up apps to help identify plant diseases, you can look up fact sheets. Getting proper identification and going to reputable sources of information is very, very important.


In Montana, we have the Schutter Diagnostic Lab, which is the diagnostic lab I supervise. This last year, we did 3,500 diagnoses, which is extremely high for us. The diagnostic laboratory is a member of the National Plant Diagnostic Network. There are 174 diagnostic labs that are members of the National Plant Diagnostic Network.

We use AgAlerts by email or fax to educate growers about pests. Extension specialists include pictures of the pest problem, how to recognize it, how to treat it, what varieties are recommended, and all kinds of information about pest management. Growers and consultants find AgAlerts are a valuable tool for early detection and response to plant pest problems.

I also run the Regional Pulse Crop Diagnostic Laboratory. This started in 2014 with Farm Bill funding from our Animal and Plant Health Inspection Service. In the United States, we didn’t have a diagnostic lab for detection of seed-borne pathogens on pulse crops, and getting information or tests done was relatively difficult. Since seed-borne plant diseases are especially critical in pulses due to high disease susceptibility and the amount of the crop exported overseas, having a lab that could respond rapidly to plant disease problems and educate growers is crucial to the sustainability of the industry. After the establishment of this lab, we can test for multiple pathogens.

Preventing introduction of new pathogens
We’re also concerned about monitoring and preventing the introduction of new pathogens, including preventing the development of fungicide resistance by providing detection services, and protecting our industry from phytosanitary regulations by providing information to the industry and regulators about what diseases are seed-borne on pulse crops in our area.

Information from the lab up to November 2016 shows the level of seed-borne disease that we were seeing in 2016 on chickpea, field pea and lentil. In field pea, 91 per cent of the seed lots are contaminated with Alternaria, but fortunately that disease is not very aggressive.

Twenty-four per cent of chickpea seed samples had Ascochyta, which is extremely high. Eighty per cent of our field peas had at least one seed per sample with Ascochyta blight, and lentils were a bit lower at about 23 per cent. This tells me that we have a pretty high risk of developing an epidemic in field pea. We have a susceptible host, we have a high level of the pathogen present and all we need is that last corner of that triangle – a favourable environment.

We’re also monitoring Stemphylium spp and Colletotrichum spp (anthracnose), which were at relatively low levels. We are finding a lot of Fusarium spp on the seed, from 14 to 31 per cent. The Botrytis spp and Sclerotinia spp pathogens are very important for our new acres. I don’t want those pathogens moving into the new acres because they have not been problems before. This is particularly important for organic growers and new acres, I don’t want people buying seed with Botrytis and Sclerotina. These diseases have very long-lived survival structures in the soil and stubble and can be difficult to manage. Since organic growers do not have synthetic fungicide options, disease management really comes down to prevention.

Slide 26The point I want to emphasize is that seed testing is really important. Getting a good, representative sample is very, very important, especially for a seed transmission event. For example, if you find one seed infected in a 400-seed sample, that’s 0.25 per cent transmission. If you calculate the pathogen transmission based on targeted seeding rate, for pea, you would have 80,000 seeds per hectare. If you had a 0.25 per cent transmission rate, that means you have 200 seeds per hectare with a seed-borne pathogen. So even a tiny amount of a pathogen in a seed sample is quite a bit when you think about distribution in a field. Diseases are transmitted to a small proportion of the plants growing from infected seed.

If you’re looking at a seed lot and the disease level is low, what’s the next question you’re going to ask? “Well, what’s the threshold?” Well, pathologists hate thresholds because we have that triangle – the host, the pathogen, and the environment – but added into that is the crop variety, the strain of the pathogen, the fungicide resistance status, the environmental conditions, the crop growth stage, the thickness of the canopy – it gets really complicated really quickly. For Montana we have borrowed some thresholds from the Canadians and the Australians, but I still don’t like using thresholds due to the complexity of the system

If you have any amount of pathogen in the seed, you need to be aware that it may be a problem in your crop. That’s the important lesson. I think these seed tests allow us to get rid of the poor quality seed and they allow us also to know what could be a problem. If you are planting white mould into your field, you should learn how to recognize white mould and maybe, if the environmental conditions are favourable, prepare a fungicide application or choose a resistant variety if you know there is a disease risk.

I ran the data since we started testing for Ascochyta blight in Montana starting in 2000. From 2000 to 2003 there were a lot of chickpea being planted. Then it plunged. We had a big Ascochyta blight epidemic. Nobody wanted to plant it. Then 2011, prices increased, people had kind of forgotten about the epidemic, and we started planting it again. So we once again have a high level of Ascochyta in chickpea, which we’re obviously very concerned about.

But when we look at pea, you’ll see, when we first started testing pea, there was zero Ascochyta in those seed samples, 38 per cent in 2004, and then pretty low levels until 2010. In 2010, we had 65 per cent of the seed lots becoming infected with Ascochyta blight.

So we’re planting more acres of peas and we are getting more rain. We have a susceptible host, the pathogen is present, so we are set up for an epidemic if we get rain.

Fungicide resistance
We are very concerned about management and fungicide resistance of Ascochyta blight. In 2013, we had 145 detections of Ascochyta in pea, lentil, and chickpea. Of the eight isolates infecting chickpea, four were resistant to Headline (pyraclostrobin). That was a wake-up call for us and was also the first year Priaxor (pyraclostrobin + fluxapyroxad), so Xemium plus Headline, was available. One of those fields had a field failure of Priaxor the first year it was available in Montana in chickpea.

We did not find any insensitivity in 2014 or 2015. Last year, we did find one seed lot that was resistant to Headline. Again, the grower did not plant the seed. We have not found any thus far in 2016.

The other thing that’s happened to the QoI fungicides is that around 2009, Headline got a label for a plant health benefit. As a pathologist, I only recommend fungicides when there’s an actual disease. This plant health benefit encouraged growers to spray Headline prophylactically when there was no disease present, which in chickpea may make some sense because this is an extremely susceptible host, but in wheat it does not make as much sense to me.

We’re also using Headline as a seed treatment and a foliar application. That increases our risk for resistance development. A study from Van Den Bosch in 2016 found that if you apply fungicides as a seed treatment and as a foliar, you’re going to increase your risk of resistance development. So the recommendation is that if you are applying a seed treatment, you should rotate to another FRAC group fungicide if you apply a foliar fungicide.

Also important for resistance management is the ability to rapidly detect whether your fungus is fungicide-resistant. With Ascochyta blight, we now have a real-time PCR assay for chickpea. Within a couple hours, we can tell you whether it’s resistant or susceptible to Headline. That test will hopefully be available semi-commercially soon through the Regional Pulse Crop Diagnostic Laboratory. Then any other diagnostic laboratory that’d be interested, we’d be happy to share the method.

We have conducted a pea disease survey so that we know what diseases are occurring. We started in June [2016] and found quite a bit of Fusarium root rot. We also identified Aphanomyces in three locations of the 21 tested.

The other important result is that we finally found pinodes. Up to this point, we’ve been getting Ascochyta pisi out of our seed tests. We are working on what conditions are different for these different fungi. It’s my understanding that pinodella is more aggressive than pisi, so it’s something we’re watching.

Extension activities
The other important thing that we’re doing as part of the Pulse Diagnostic Lab is developing recommendations. We’re starting with seed treatments to find out the most effective fungicides on the different pathogens. We tested seven different fungi – Fusarium, Botrytis, Stemphylium, Alternaria, Diaporthe, Ascochyta, and Ulocladium – with the SDHIs, QoIs and other active ingredients. Preliminary results show there is some variation in the effectiveness of these fungicides, but all of them are fairly effective. However, one strobilurin and one triazole are not as effective as the others. You really do the need this in-depth information about the effectiveness of the individual products. Make sure that your fungicide is registered for the disease that you have in your field, make sure that you accurately identify the disease and that you don’t confuse it with nutrient deficiency or something else.

We’re also looking at germination of sclerotia, because we have a lot of seed-transmitted Sclerotinia, especially in our lentils this year. We tested Maxim, Mertect, and Thiram. Maxim and Mertect were much better.

What can organic growers do? We have very limited data. Lyndon Porter has done some work in Washington on some of the biocontrols. He said that most of the products that showed efficacy are no longer available on the market. In the U.S., most of the biocontrols were developed for soybeans and don’t perform well in cool soils. There are foliar products like sulphur, copper, oils, and bicarbonates.

Slide 41The IR-4 Project has a biopesticide and organic support database. Products in the database would be labelled in the U.S., not internationally, but it’s a good place to start. You can search for your crop and what type of product you are looking for. In January 2017, there were 45 products for wheat, two on dry pea, six for chickpea, and 66 on alfalfa, so there’s quite a bit of development that needs to be done for the pulse market.

The Northcentral Regional IPM Center funded Pulse Crop Working Group has developed a Pea Disease Diagnostic Series, available from North Dakota State University. This is a series of flip cards, which give symptoms, how to recognize the disease and important facts about the disease. We have also put out a Diseases of Cool Season Legumes, which is a good place to start for disease recognition.

Another important product for growers is a chart of registered foliar fungicides and seed-treatment tables. These are separated by FRAC group so you can tell growers where it fits and where the blends are. We don’t have any efficacy data to add to this table.

Slide 47 crop

We put out a calendar for the pulse industry, and our next step will be to put together a series of playing cards with diseases of peas, lentils, and chickpeas; and then the insects or abiotic disorders on the different suits.

Another interesting tool is a mobile website that I call a “fungicide calculator.” This was developed for wheat, but you can also use it for peas. The calculator lets you put in a cost for a fungicide application, the yield loss due to tires travelling on the field, the yield gain from the application and the crop price. It tells you if the fungicide application would pay for itself. It’s a good little tool to think about what your application will cost and what your gain will be.

The other thing I want to develop is a table of crop rotations and diseases. So, if you have white mould, should you plant canola? Or what are your management options as far as crop rotation?

Part of pest prevention is planning. We hosted a Pest Management Strategic Planning meeting in Montana in 2016. We had agronomists and entomologists, pathologists, weed scientists, consultants and a representative of the organic industry and the Environmental Protection Agency (EPA). Priorities for research and education were developed. The U.S. Dry Pea & Lentil group used it as their priority list in their last round of grants. The EPA will use the priorities when they’re looking at registration of products.


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