HIGH FLYERS THINK TANK

Emerging diseases – Ready and waiting?

The Shine Dome, Canberra, 19 October 2004

Emerging diseases: The plant health perspective

Dr John Manners
Program Leader, Crop Physiology and Genetic Improvement, CSIRO Plant Industry; Deputy Chief Executive Officer, CRC for Tropical Plant Protection

One of the difficulties with plants is that I can't put the fear of God into you with various human diseases, and I also can't get great votes of sympathy with piles of burning cattle. The most I can do, probably, is to get some sympathy around some burning trees or some wheat chaff or something like that. The issue of plant diseases is an issue for primary production, for natural ecosystems. It is not a metro-issue and it is probably an issue that illustrates the division between city people and country people. A plant disease that cuts production in half, say in the banana industry or in the sugarcane industry, has major economic impacts on regional towns in Queensland; we might get a ripple here in Brisbane. So it is a different type of impact.

Before I get going – I am likely to get a little bit carried away at the end of this in some of the technical stuff – I would just like to leave a couple of messages: the diversity of diseases, and also the diversity of hosts. Our human colleagues work with one host, our veterinary colleagues work with a handful of hosts. If you think of all the plants that you eat in your breakfast cereal now or in your dinner (if you eat any vegetables, that is), a multiplicity of plants in our food chain, a multiplicity of plants in our environment, each one of those plant species has a multiplicity of pathogens.

So trying to actually manage the diversity of challenges is one of the major differences that we would have between a plant protection strategy and maybe the animal and clinical.

Talk
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These (Slide 1) are the issues that I am going to talk about, just to give you a little bit of a taste for the types of diseases and, initially, some issues as to why we are dealing with emerging diseases in plants, some of the challenges I have just alluded to, what we might want to do about it and how we might structure ourselves – and how we are doing so, I suppose – to do something about it and then a few science perspectives. I do think, going back to the introduction and the mission that we were given here, that some of the future science and the pace of development in our understanding of plant diseases makes us very optimistic about understanding generic principles that underpin them and therefore maybe coming across some generic tools and generic approaches to managing them.

Plant diseases
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Here are just a few disease types. These are the sorts of categories that I have seen plant diseases put into these days, in terms of their emergence or threat.

‘New diseases', where you have a previously unrecognised disease on a host: I will just point out High Plains Virus here, which is a disease of wheat and corn in the US, discovered in Dakota in the mid-1990s. It is very unusual to find a new disease in crops like wheat and corn, which are so highly researched and also so highly monitored in the field because they are grown so widely. This is still currently localised in the US.

‘Threatening diseases' are diseases which are not in your region at the moment. I have put two in here. Sugarcane smut is present in every single sugarcane growing area in the world. Until about five years ago it was absent from Australia; it is now present in the Ord River, in north-western Australia. It is absent from the eastern seaboard production centres of sugarcane in Queensland, and therefore there is a strict quarantine maintenance now between the two regions in Australia. There is also a very, very frantic breeding for resistance, because every single variety five years ago that was grown in eastern Australia was susceptible to smut.

Karnal bunt is a pathogen that affects wheat quality and would have major impact on our trading of wheat. Wheat is worth about $4.5 billion a year to the Australian economy, so this is an important issue. It is absent in Australia. America used to use karnal bunt as a reason for maintaining very strict quarantine on trade barriers but now it has it, and of course now it is looking for a great liberalisation globally in respect of that disease.

‘Emerging diseases' are diseases that we have always had but are becoming more important. What happens in farming practice these days is that there is a lot of emphasis put on soil conservation, maintaining organic matter in the soil. And of course if you are going to maintain organic matter in the soil, through practices like retaining plant stubble, then you are going to actually have to deal with pathogens that can grow and prosper and proliferate in that organic material and then infect plants. These are two examples in wheat: head blight and yellow spot.

‘Re-emerging diseases' are diseases that we had under control and all of a sudden they are becoming a major problem. I will be talking a little bit about this one.

Potato late blight is a very well-known disease in the plant area. It is responsible for the Irish potato famine in 1845. The disease originates from South America. It moved around the world but then was pretty much under control until the late 1980s and early 1990s, and a little bit later I will get to why that has actually proliferated. It is to do, essentially, with genetic change in the population.

Sugarcane orange rust has always been a very minor disease of sugarcane except in 2000, when there was a major epidemic. This illustrates the dangers of monoculture. I flew into Mackay during this epidemic. Normally when you fly into Mackay it is a beautiful green colour and you get that big tropical warm feeling as you come down to land, but as you looked across the canefields at this time they were literally orange. Production out of that region slumped to below 50 per cent of its previous figures.

Why might plant diseases emerge?
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Why do we get diseases? They come from incursions – very similarly to what our previous colleagues have described, we get incursions through alleged quarantine breach, such as the citrus canker issue that has just broken out; quarantine breakdown, where something comes in inadvertently; or quarantine relaxation. There is also discussion about weather-mediated incursion. Sugarcane smut is thought to have actually come through cyclonic conditions from Indonesia to the Ord River.

Practice, for example soil conservation and monoculture, I have talked about.

Pathogen evolution or genetic change in a pathogen is a major issue. One of our major tools for controlling plant pathogens is host resistance, and pathogens therefore change in virulence. Fungicides or chemical control leads to fungicide resistance, in the same way as antibiotic resistance in clinical situations. And the genetics of the pathogen is very important in understanding this.

Sometimes what was acceptable yesterday is not acceptable today, and now we have a problem. Food standards for things like mycotoxins are becoming stricter and stricter, and now if you actually want to meet a certain level you have to get under the lower-level standards and therefore fungal diseases that create these toxins are becoming more and more important.

I can't give you an example of bio-terrorism, but it is very big in the American literature and, as the previous speaker said, it is driving a lot of the plant protection agenda. There are terrific fears in America of, for example, pathogens such as soya bean rust, which could have economic effects.

Challenges for plant systems
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To come back to some of the challenges: the diversity of pathogens, plants, pests and the vectors of these pathogens is a major issue, as I have indicated. We are not only dealing with farms, we are dealing with food security and natural ecosystems. Just to spend a minute on this: trade barriers and politics play a big role.

Diversity of banana diseases
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I will just deal with one issue here, such as banana diseases. Some of you may have read in the press that there has been a lot of debate about whether we should allow importation of bananas from the Philippines. I should indicate that the Australian banana industry is probably one of the cleanest in terms of pesticide use in the world. In Australia we spray probably 12 to 14 times a year to control this disease, yellow sigatoka. The rest of the world, particularly Central America, has this disease, black sigatoka, and there is weekly spraying, say 40 to 44 times a year, during the production growth period.

Because of politics we may want to import bananas from the Philippines, but of course the banana industry is very concerned about the impact that may have on its disease status and its green image.

As other speakers have said, what we are trying to do is manage what we have at the moment, be prepared for what might come and try to prevent it from coming, and juggle the emerging, the exotic, the predicted. But usually we end up with the unpredicted, and that means that you really need to have a generic preparedness, not so much a targeted preparedness unless, of course, your target is very, very important and you can clearly identify it.

New plant diseases and pests recorded in Australia since 2000 (DAFF)
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We do get lots and lots of entries for plant diseases. This is the DAFF (Department of Agriculture, Fisheries and Forests) list since 2000. I won't go into it, but a lot of them come through the northern regions. So half of these entries came through either Queensland or the Northern Territory, primarily I think due to the weather issues and travel patterns from the northern borders.

A coordinated approach
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Let's get a little bit onto how we might actually approach managing diseases. The pillar stones of managing plant diseases are strict quarantine, with monitoring and surveillance, and host resistance. Usually we don't get involved much in pre-emptive resistance, which means that we actually breed for resistance to a disease that isn't here. There is a lot of emphasis on breeding for diseases that are already here, and I think generally it has been very hard to get funds to breed for things that are not here. I think that is an issue that will become more and more a part of our biosecurity strategy.

Quarantine without monitoring is of no value, so you have to be monitoring locally and globally what is happening in the disease systems, and your monitoring really should include information on virulence, the genetics and also the development of diagnostics, so that they are appropriate. There have been some very good instances of the use of diagnostics in Queensland for managing incursions. The black sigatoka incursion in Tully a few years ago, where essentially a PCR based diagnostic monitored the success of eradication, is a very good example.

These are essentially managed at the science level by state departments, CSIRO, universities, CRCs et cetera, but what concerns me is the dialogue here (Slide 7) in this arrow between dealing with the science and dealing with government and implementation. I think that we really do need to have a clear dialogue across this arrow, and that policy in fact is based on clear science.

Science perspectives
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I will just get a little bit more into the science, and I would like to indicate that these are some of the things that we actually have to have in place. You need deep knowledge of your most threatening pathogens, and you need deep knowledge of general principles that underpin pathogenesis. This is what we are really talking about here, in pathogen knowledge and host resistance, genetics et cetera. To do that you have to work globally, but you also need the infrastructure of delivering that information to our industries and to our communities and, I suppose, ensuring that we actually have an educative process so that we can actually surveill diseases properly.

I won't go through these (Slide 8) in a lot of detail. There are many areas of interest that we need to increase our knowledge of, but I think I would just like to be a little bit optimistic by indicating some lessons that have been learned, that I think we have learned and are actually dealing with now in terms of how we understand pathogens.

Potato late blight — a lesson in being unprepared for genotypic invasion
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I will just use this example, very quickly: potato late blight. It is caused by a pathogen called Phytophthera, which is an oomycete fungus. As I said, this was essentially under control up to about 1970, after its emergence in the 1800s, primarily through use of fungicides and partial resistance. Then all of a sudden, in the 1980s and 1990s, it went berserk. As we can see here on Slide 9 this is actually the spread of the disease through the US, in terms of outbreaks over a certain level. Some of these can actually be quite substantial, so you can see here the yield in tonnes per hectare that is marketable. Once this region in north-eastern America was hit with this disease, basically profitability plummeted and people were going broke at a very rapid rate. And this is not only in the US; this happened in Europe as well.

Once one got into actually looking at the pathogen, it was discovered that in fact we had a replacement of one pathotype with another pathotype – a different genotype. Interestingly, up to this time it appeared that the pathogen was almost clonal, genetically uniform. What had happened was that a new genotype of the fungus had been introduced from Mexico but, more importantly, that was a genotype that could mate with the existing genotype and it brought sexual genetics into the pathogen population. So you had the ability then to actually adapt to the fungicide application, and levels of virulence were raised dramatically.

Transgenic resistance — powerful stuff if you can take it
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Solutions: we do have solutions to some emerging diseases. Using genetic modification, which I suppose is a luxury that we have in plants that perhaps humans and many of our animal colleagues don't have so readily, it is possible to manipulate disease resistance. It is now generally accepted that almost every virus could be controlled in a plant system through existing gene technology – absolutely no question that there is a generic tool to provide protection against any virus, usually by expressing small pieces of the actual viral genome itself. This has been used in Hawaii to control papaya ring spot virus, and basically in Hawaii now involves genetically modified papayas, or pawpaws, which are exported to the mainland in the US.

Many developing countries could use this technology – pawpaw is in fact the major source of vitamin A – but basically it is not getting accepted because of the politics of marketing GM produce. So again you can run into all sorts of different types of politics.

Global village — for plant diseases
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Because I am getting the hurry-on I think I will just finish here. I think the potato leaf blight example, a very well documented one, illustrates the importance of actually, if we are taking an Australian view of plant disease management and threatening and emerging diseases, we have to do that in the context of the global situation and therefore any of our research or policy has to be coordinated not only nationally but also globally.

Discussion

Serge Corbeil – What is the mechanism of protection in plants when you express a gene from a virus?

John Manners – The mechanism is based on an innate system that is present in the plant which degrades and recognises double-stranded RNA. It is essentially the same mechanism as is used in antisense gene suppression, or what is now called hairpin or RNAi based gene suppression. The mechanism essentially is a system of defence that is based on the specific degradation of specific messenger RNA sequences – which is involved in endogenous gene regulation and also protection against invading nucleic acids.

Serge Corbeil – What about resistance?

John Manners – You can get resistance through expressing viral proteins or you can get resistance through expressing parts of the sequence that are only, say, 22 base pairs long.