You are reading: A COVID test for your diseased crop – now that’s cool!

A COVID test for your diseased crop – now that’s cool!

We've discovered a new gene in the pathogen causing ascochyta blight that triggers disease resistance in lentils, with potential to advise growers on which lentil varieties to grow for maximum resistance. Author: Megan Jones Sep 21, 2022 Read Time: 4 minutes

Let’s pretend you think you’ve got COVID-19. You get in your car and make your way to the COVID testing clinic, and get swabbed up the nose. This then goes through a PCR test, and you find out a day or so later whether you have the spicy flu. The staff behind the test can also detect which variant it is – Delta or Omicron.

Now, for the sake of it, let’s pretend you’re an ascochyta pathogen on a lentil leaf. Again you get swabbed, then taken through a similar PCR test to COVID-19. A day later, CCDM researchers behind the test can not only confirm that you are indeed an ascochyta pathogen that infects lentils, but, thanks to new CCDM research, they can also tell what variant of the lentil pathogen you are.

Why is this so amazing? Because CCDM researchers, in collaboration with SARDI, have developed a lab test that has potential to inform a grower which variety of lentil to grow for maximum resistance, based on whether pathotype 1 or pathotype 2 of ascochyta is present in their paddock.

CCDM researcher Bernadette Henares said the lab test, while still under development to become an in-field test, could make an excellent decision-support tool for growers selecting lentil varieties.

“From this research we now know there are two types of the ascochyta pathogen – pathotype 1 which doesn’t cause disease on PBA Hurricane XT, PBA Hallmark XT, PBA Bolt and other varieties that carry the same resistance, but does cause disease on Nipper,” she said.

“The other type, pathotype 2, is damaging to PBA Hurricane XT, PBA Hallmark XT and PBA Bolt, but not Nipper.

“If we can diagnose which pathotype of ascochyta is in the grower’s paddock or on stubble, then we can let them know, for example, if PBA Hurricane XT might be susceptible to the ascochyta pathotype that is present in their paddock, and suggest they choose a different variety.”

Listen directly to the researchers talking about this discovery on the latest episode of The Crop Disease Podcast

It’s all about triggering the defence response in lentils

Recently published in scientific journal Molecular Plant Pathology, the research team were able to flip their thinking on how this pulse pathogen goes about infecting lentils.

Rather than traditionally looking for a gene within the pathogen that produces toxic proteins that cause disease symptoms in lentils, they instead found a protein responsible for triggering a defence response in lentils, leaving certain lentil varieties asymptomatic.

There are two pathotypes of the pathogen causing ascochyta blight. Different lentil varieties are triggered by 1 or 2 or both. By determining which pathotype is present in the paddock, growers can choose varieties that have a defence response to that pathotype.


How pathotypes may change

CCDM researcher Lars Kamphuis said this discovery has helped to explain in part why certain lentil varieties have come and gone.

“We’ve been collecting samples of lentil ascochyta from across Australia since 2013. Analysis has shown that pathotype 1 was the predominant one at a time when variety Nipper was popular,” Lars said.

“Then other varieties were introduced, with varieties such as PBA Bolt, PBA Hallmark XT and PBA Hurricane XT gaining a lot of popularity from 2016 onwards, which resulted in pathotype 2 becoming the more dominant pathotype.

“Both pathotypes have been found across the lentil cropping regions of southern Australia, but one will dominate over the other when a certain lentil variety is grown.”


Managing ascochyta blight this season

SARDI pulse pathologist and co-author Sara Blake has been collaborating with CCDM on ascochyta blight research for seven years, and is the key contact for pulse pathology advice in South Australia.

She said growers dealing with ascochyta blight in their pulse crop need to continuously monitor their crop for disease at this time of year.

“Also, if disease is present, it’s really important to ensure fungicide sprays go out ahead of a rain front, because that will protect the uninfected plant foliage from spores dispersed by rain splash,” Sara said.

“If the weather is dry, then fungicide can be delayed, because the disease spreads by rain splash.

“Another critical management approach is ensuring that fungicide groups are rotated and that growers are adhering to their label recommendations, as this helps reduce the risk of fungicide resistance developing.

“And for next year, consider crop rotations, and choose a lentil cultivar with a good resistance to ascochyta, because the resistance prevents the disease from really taking hold and becoming a problem.”

Send us samples of your diseased leaves!

Have you spotted ascochyta blight in your paddock lately? We would love to get a sample! Samples of ascochyta blight infections help us monitor changes in the pathogen population and continue to develop new genetic tools to help breeders breed more resistant lentil varieties.

Send us a sample by contacting your local state pulse pathologist:

SA: Sara Blake, SARDI; Email:; Phone: 8429 2248

VIC: Josh Fanning, Agriculture Victoria; Email:  Phone: 0419 272 075

WA: Andrea Hills, DPIRD; Email:; Phone: 9083 1144

More information on sampling: Bernadette Henares, CCDM; Email:; Phone: 9266 3042

The Paper

The paper, The novel avirulence effector AlAvr1 from Ascochyta lentis mediates host cultivar specificity of ascochyta blight in lentil, can be found here

The Podcast

Listen to the Crop Disease Podcast where Bernadette, Lars and Sara talk about this work and the tool and how it can make a difference to lentil growers. Listen here


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