New methods for detecting crop disease

Professor Linton Winder

 
*Protecting our crops

Here’s a scary thought: Each year around 30% of the world’s crops are lost to pests and diseases. But scientists from Unitec, Massey and Lincoln are investigating ways of detecting the presence of destructive fungal diseases in crops much earlier than ever before, giving farmers a powerful new tool in the fight against a pervasive enemy.

One way to help farmers in their on-going fight with disease and pests in their crops is to provide them with tools to nip problems in the bud, says Unitec’s Head of Natural Sciences Professor Linton Winder. An interdisciplinary research breakthrough by Winton and his research partners means a solution that could help the farming community could be at hand.

As with human health, early intervention is critical – and if you can’t get a speedy diagnosis, taking the appropriate measures to fix a problem can be difficult. In the case of many diseases that threaten crops, from avocados and apples to brassicas and tomatoes, as soon as you can see the problem, it’s probably too late. “You need to get in right at the start because it’s easier to control a problem when it isn’t widespread – you have a real opportunity to control it effectively early in the season,” says Winder. “The amount of crop loss globally caused by pests and diseases is frightening – roughly around 30% of crop yields around the world are lost in this way.

“The issue of food security and increasing world populations means we need to come up with ways of reducing the loss. One way to do that is to provide farmers with diagnostic tests that allow them to decide how best to manage their crops.”

Winder, an agro-ecologist specializing in entomology, has teamed up with Massey University evolutionary biologist Professor Pete  Lockhart (also an adjunct Professor for Natural Sciences at Unitec) and Lincoln University agricultural ecologist and statistician, Dr Simon Hodge.

Together, with help from $20,000-worth of Proof of Principle funding from the Agricultural and Marketing Research and Development Trust (AGMARDT), they have found a better way of detecting fungal diseases in crops before they can get a foothold. The project has also been supported by Dr Charles Merfield, based at the Biological Husbandry Unit’s Future Farming Centre (located on the Lincoln campus) where field trials are being conducted, and Lincoln’s Dr Eirian Jones and researchers from LandCare and Scion Research who provided the team with samples to test in their system.

Using DNA sequencing technology they have found a way to make rapid diagnoses of diseased crops – before the rot sets in. Once the research is fully tested and realised (field trials to prove the theoretical findings are underway) it will provide a tool that many farmers will be able to easily use.
According to Lockhart, their new method for applying existing technology is more effective and addresses more problems.

“The DNA technology we are using has its widest application in the diagnosis of infectious disease in humans. However the technology also has great potential for other areas,” he says. “We wanted to make it work for agriculture, in particular in the detection of fungi, which are a major problem for New Zealand’s agricultural sector.”



The process involves the extraction and high throughput sequencing of DNA from pathogens present in plant tissue, water or soil. Using novel laboratory protocols developed by the team this can be done very quickly. The sequencing provides a reference genome for the organism and the means to develop rapid diagnostic tests which take around 30 minutes. These simple tests can then be applied in the field to signal whether or not a disease is present, and whether the farmer needs to take action. If a clean bill of health comes back, an unnecessary ‘just in case’ spray can be avoided.

High throughput sequencing uses a small benchtop machine – made by biotechnology company Illumina – to analyse between 12 and 15 million pieces of DNA within 26 hours. The equipment for this is available in New Zealand thanks to a $35m investment by the government to establish a national infrastructure (www.nzgenomics.co.nz/) for New Zealand scientists.

The team’s methodology, which is under wraps pending potential commercialisation, can be used in two ways depending on what you are looking for, Lockhart says.

When evidence of a specific disease is needed they are able to make very rapid diagnostic tests which can identify the causative agent of a disease or a problem in around half an hour. A second, more comprehensive approach is also possible which is applied when it is not known exactly what to look for. The comprehensive test is not as fast as the rapid diagnostic test, says Lockhart, with a time frame of two to three weeks for the results. But from the larger test a series of targeted, rapid tests can be developed. “The way we think these two approaches might work in practice is at the beginning of a growing season or at different periods there might be a comprehensive assessment made and based on what you find, you would develop the rapid tests. That might mean surveying a few orchards or fields a couple of times during the year and developing the rapid tests based on those results.”

Winder says eventually the process will be as simple as a farmer heading into a field or crop, taking a sample of a seemingly healthy plant, mashing it up and putting it through a machine that will tell if a disease is present or not. “You could buy a little hand-held detector, walk out into a field and within 30 minutes it will tell you yes or no, is that disease there and do you need to spray or not? That gives farmers a huge competitive advantage because it means they can choose early on how to manage and control that disease by applying a fungicide or managing that crop in an appropriate way.”

Lockhart began looking at the high throughput technology in 2010, but in a more ‘blue sky’ research capacity. Combining his skills as an evolutionary biologist with Winder and Hodges’ experience in applied science meant they were able to take these findings and put them to practical use for the farming community. Results have come quickly since they started working together in late 2013.
 
And Winder says these methods will continue to progress at a similarly rapid rate. While the comprehensive test takes up to three weeks now, that is lightning speed considering where things were just three years ago.

 “Although the complete profiling will take two weeks at the moment, in two to three years it will take much less time than that. The rate of technological change is absolutely astonishing, especially in biology. “Over the next few years all this is going to become more efficient, more effective and more rapid. There is a lot of maths behind the sequencing; you’re trying to match up complicated data sets against publicly available ones, but the maths is becoming thousands of times quicker as well. And as the techniques become quicker and quicker they become more and more valuable to the farmer.

“The great thing about the AGMARDT grant is that it allows us to try and provide New Zealand farmers with a competitive advantage because we are developing these techniques now. It’s so valuable having these seeding grants.”

The speed of change so far is easily demonstrated. “Three years ago, the machine ran for a minimum of two weeks and up to four weeks before the data even came off it. And you’ve got to have 2-4 weeks of uninterrupted power. Sometimes little things would go wrong and you’d have to set up the machine again, and then wait again.”

It then took up to six months to get the data matched against the public reference sequences, a step made much faster when a colleague at a German university developed a method of matching the sequences 10-20,000 times faster than previously possible. “All of a sudden we could get results back quickly,” says Lockhart.

While this will present farmers with a tool that could boost productivity and reduce the spray bill, it will also help produce healthier crops. “I think a lot of good could come from this,” Lockhart adds. “Because the rapid tests are relatively low-tech there is the potential to put it in a lot of hands. If you could dramatically reduce the amount of sprays being used globally that would be huge.”

Winder says rapid diagnostic testing could drastically change the way farmers look after their crops. “Modern agriculture tends to over-use pesticides. It creates pests and diseases that are resistant to the very compounds we are using. We self-generate the problem in many respects.”

While fungal diseases have been the focus of the study so far, there is much greater potential for the technology. It could be used to test for the presence of insects, and also in border security where the arrival of soil and produce pose risks to New Zealand’s biosecurity. Being armed with a hand held, rapid diagnostic testing device means bio-security staff could better assess risks through routine monitoring of soil and plants brought into the country. “One of the biggest bio-security problems concerns the soil brought into New Zealand in ship containers. They’ve got no idea how much of a problem it is really but it’s something that could be assessed quite easily,” says Lockhart. “Anything you don’t immediately recognise you could have a test for.”

Having proved the theory and with field testing underway the time has come to take the project to the next level. “The question was, ‘Can we quickly and efficiently obtain the genetic information that is needed for making these tests?’, and we have shown that it can be done. We’re confident we can do it now. The next stage is to start engaging with the farming community to find some key diseases they really want to tackle.”