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Intro: This is a GRDC podcast.

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Shannon Beattie: Sclerotinia stem rot is a canola disease that is challenging to manage using rotation due to the wide range of crops that play host to the fungus that causes it. Hi, I'm Shannon Beattie. Since there are no Australian canola cultivars with sclerotinia resistance, the disease is usually managed with preventative fungicide sprays at flowering. However, fungicides can be costly, and their return on investment is difficult to predict. In an ideal world, Australian growers would have access to canola cultivars with resistance to sclerotinia stem rot, and that's exactly what researchers at GRDC and Curtin University's Centre for Crop and Disease Management are trying to develop. On today's episode, I'm joined by senior research fellow and project lead Mark Derbyshire to find out how.

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Mark Derbyshire: Sclerotinia stem rot of canola is a disease caused by a fungus which is called sclerotinia sclerotium. And this fungus, it produces resting structures called sclerotia, which live in the soil, and they lay there dormant, often for a number of years. So it's quite persistent in the soil. And it typically causes an issue in canola during flowering when these fruiting bodies called apothecia and the apothecia spread these spores, called ascospore, which spread via the wind and they land on the petals of the canola. And then when these land on the leaves, the fungus grows into the stem. And when you get significant infections, when it's normally quite humid, that stem damage can really reduce development of the grain in the crop and that's where you get yield loss.

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Shannon Beattie: Can you tell me how this disease is currently managed within our farming systems? What are the current tools that growers are using to try and control it?

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Mark Derbyshire: Sclerotinia is a broad host range pathogen, so in fact pretty much all rotation crops or broadleaf crops in general. So it's quite difficult to manage with rotation. I don't know that much about rotation in particular as a management tool for sclerotinia, but my understanding is that it's quite ineffective often, and I think most people just rely on fungicides for sclerotinia. So that would be a fungicide spray at 30 to 50 per cent flowering. And it can be challenging often, especially in places where you don't have consistent rainfall, to actually predict whether a fungicide spray is going to give you a good return on investment, whether or not there's going to be a significant outbreak of the disease.

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Shannon Beattie: Can you tell me where we are at with rotations being a management strategy for this particular disease? I understand it's not a great option. Can you tell me why?

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Mark Derbyshire: Sclerotinia as a host generalist species, it doesn't infect cereals, wheat and barley, oats, things like that. But it infects broadleaf species canola, chickpea, lupins, anything like that. We don't research rotation, but in general it's considered quite difficult to manage with rotation because of the fact that it can infect so many different species, and it persists in the soil for such a long time. So unless you have very, very long rotations of several years, it's going to be difficult to reduce the pathogen in the soil.

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Shannon Beattie: With the varieties of the cultivars of canola that we currently have available. What is their level of resistance at the moment to this disease?

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Mark Derbyshire: That's an interesting question. Most people would say that all cultivars that we have are completely susceptible to sclerotinia. I think from a management or grower decision perspective, I think that's a pretty safe assumption to make. But having said that, there hasn't been a really big and comprehensive assessment of every single canola variety currently being planted, and I think it would be interesting to do that to see if there is any difference in relative susceptibility. But in general, there's no evidence at the moment that there are any cultivars that have significant resistance. That would be a really good management option for sclerotinia.

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Shannon Beattie: Can you tell me what it is that yourself and the CCDM is actually looking into? At the moment, give us the broad overview and then we'll go into some more detail.

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Mark Derbyshire: Broadly we are researching ways of breeding for sclerotinia resistance in canola. So part of what we're doing is looking for varieties of brassica napus, so that's the species that canola is, which can be used in breeding for sclerotinia resistance. But we're also looking at kind of new modern breeding methods that might really improve the efficiency of the breeding process and make it easier for breeders to bring some of that resistance into cultivars.

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Shannon Beattie: I believe that there's been a little bit of work done in this space overseas, particularly in Canada and the UK. Can you talk to me about what's been done there? And I guess why it's not necessarily applicable to Australia.

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Mark Derbyshire: Overseas, especially in Canada, there's been more of a research effort towards sclerotinia resistance. There are only a few sclerotinia resistant cultivars that I'm aware of commercially around the world, and they're all from the same company. And they were first released in Canada and then more recently, Europe. And they developed basically methods of screening plants in the field and selecting the most resistant plants. But this was all done through a commercial breeding program, and there's not a huge amount of public information on that. Although the disease resistance screening and all of that sort of stuff is applicable in Australia. The material from the breeding programs often is not applicable because it needs to be adapted to Australian conditions, which are quite different to those in Canada and Europe.

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Shannon Beattie: So talk to me through what it is that you guys are doing in a practical sense. I know that breeding can be a bit complicated when we're talking about screening, breeding lines and all this sort of thing, but can you talk me through the process and try and help me understand what it is you're doing, and then how it will be applied in the future, or how it will hopefully be applied in the future.

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Mark Derbyshire: We have already identified a number of varieties that have good resistance to sclerotinia relative to popular cultivars. And these are not cultivars, so they're not adapted to Australian conditions. These are varieties of brassica napus that have good levels of resistance to sclerotinia, but that resistance would have to be combined with other agricultural characteristics. And to do that, you'd have to take these resistant varieties and then cross them with other varieties that have good yield and good agronomy in Australia. And you would need to go through the breeding process of selecting plants over a number of years and then crossing them and maintaining the resistance and the agronomic performance. And to do that, you need to have a reliable system for evaluating plants in the field. And that's very challenging for sclerotinia because it's such a sporadic disease. So what we've been doing recently as well is testing different material that can potentially carry sclerotinia, and working out which material is the best for applying in the field across canola plots. And we found this quite a scalable and efficient technique for selecting the most resistant plants in the field. So that's where we're at at the moment.

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Shannon Beattie: Mark, you just mentioned in there that you'd been trialling methods for spreading the fungal pathogen on canola plots in the field. How are you going about doing that? And I guess making sure that growers’ crops are safe.

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Mark Derbyshire: In the experiments that we've done, we've inoculated plants in controlled plots, in experimental field stations or in Curtin University itself. So these are not in growers’ paddocks. But in any case, we're putting the inoculum on the plants in the controlled experimental plots and there's no risk of it spreading in that experiment to neighbouring crops in general. The only thing that we could risk doing is building up inoculum in the soil at a particular experimental site. That's probably desirable in the long term. You would call that perhaps a disease nursery. So somewhere where people routinely trial for disease susceptibility. And this is done for other diseases, but that's not likely to have an impact on cropping in the region, in the local area. It's just the sort of specific site where you do experiments. In our experiments as well, because often the people that are using the sites with other researchers, they don't want to have sclerotinia in the soil, so what we've ended up doing in our experiments so far, anyway, is pulling the plants out at the end of the experiment. So there's no sclerotinia left in the soil anyway. So there's really no spread of the disease anywhere outside of the experimental plots.

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Shannon Beattie: What's next Mark, what do you have coming up in this research?

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Mark Derbyshire: What we've got coming up is more research into methods for basically improving the efficiency of the breeding process. So one of those is looking into genomic data to try and find bits of the genome that have the biggest contribution to sclerotinia resistance. And then the other part is using a technique called speed breeding, where you basically expose the plants to very long day lengths, so they develop very quickly. And you can progress through lots of breeding cycles in a very short amount of time. So what we're hoping to do, once we've got all of those tools in place, along with our resistant material and our field screening approaches, we're hoping to be able to then start making populations and bringing some of the resistance into better adapted Australian varieties. But at the moment, that's kind of beyond the scope of the current project. But that's where we would really like to go to next once we have the tools in place.

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Shannon Beattie: So the long-term goal, I'm assuming, is to start combining those more resistant brassica napus with, as you said, the better agronomic, commercially available varieties of canola that we have, and breeding them together to try and create an actually resistant version of canola. That is the long-term goal?

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Mark Derbyshire: That would be the long-term goal. From our perspective as researchers, what we would want to do, although this is not within the scope of what we're doing right now. Once we have the tools in place, we'd want to create varieties for the Australian crop breeders. And these would be varieties that are suitable to their breeding programs that carry sclerotinia resistance but also have good agronomic traits so that they could incorporate all of that into their cultivars. So it's quite a long way to go, really, but I think we've made some pretty good advancements in terms of the tools and the resources that we've got. And if we can make the process much more efficient, then it becomes a lot more feasible and something that the breeders would hopefully get on board within the future.

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Shannon Beattie: I think it's important for us to make it clear, whenever we're talking about breeding, that this isn't a in two years we'll have a new canola variety available for you sort of situation. I'm assuming, as per usual, breeding, this is like a five, seven, ten-year sort of process that we're looking at.

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Mark Derbyshire: Yeah, it would be. I think it's kind of dependent in the end on the breeding companies, how they use the tools and the material, and I can't really comment for individual breeding companies, but usually going from a source of resistance or some other favourable trait all the way to a cultivar takes a number of years like you said.

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Shannon Beattie: You mentioned that you're wanting to develop it. This is a scalable technique. What does that actually mean when you say that? Is it just that you can apply it to a larger paddock more often? And you mentioned the speed breeding. What does a scalable technique mean and why is that important?

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Mark Derbyshire: So generally, in the scientific literature, most people screen plants in glasshouses, controlled environments, sometimes in the field as well. But the standard method is to attach an agar plug carrying sclerotinia to the stem and then measure the spread of the lesion up and down the stem over time. And that does work pretty well. I think it gives you a fairly reasonable assessment of what's very resistant and what's very susceptible. But it's not really applicable at the scale that would be needed in an applied breeding program for improving sclerotinia resistance, because in breeding program, typically you would have a number of trials across different environments with probably hundreds or thousands of breeding lines. And you basically need a way of developing large quantities of fungal inoculum and being able to just go out and easily spread it across a very, very large trial and then just go out and score the plants without having to go in and measure every single individual plant with a ruler. So it's scalable in the sense that it's a practical method that is aligned with really what people in the industry seem to be doing overseas that the breeders can use potentially in the field across very large plots with large number of varieties, which is sufficient for the breeding process.

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Shannon Beattie: And you mentioned that there's been sort of success in that scalability, and you have done some field inoculation sort of trials and used that method, I believe, over the past couple of years, and you have shown then the differences in stem rot.

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Mark Derbyshire: In the field, we were able to differentiate between varieties that we had shown had good levels of resistance using the stem infection method and varieties that look very susceptible using that method in previous studies. So we basically went from screening varieties in a controlled environment by infecting the stems and finding some candidates that had better resistance than the cultivars that we tested. And then we showed that using this technique, we could create consistent disease across a plot with just standard overhead irrigation. And we could actually see differences in the level of susceptibility between these varieties out in the field with broader inoculation methods as well.

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Shannon Beattie: To finish up, Mark, can you give us in really quick, easy to understand terminology, in what way the research that you're working on is going to impact growers and how it's going to help our growers. For those who are listening to it going yeah, that all sounds great, but what is it going to mean for those listening?

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Mark Derbyshire: I think that's always the key question. And from my perspective, what we do in pre-breeding research often depends on a lot of commercial factors and whether or not the companies themselves really engage with the particular thing that we're working on. But I'm hopeful that we can engage with the breeders, especially now that we've started to get some really good tools and resources in place to really go that next step and try and bring some of the resistance into cultivars. And I think in the longer term, if we could do that, that would really be a big benefit to the industry in Australia.

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Shannon Beattie: Mark, is there anything else that you want to add that I haven't asked you yet that you think is important for our listeners to know?

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Mark Derbyshire: I think that if you look at what's happening in the industry overseas, there is good commercial precedent for sclerotinia resistance in canola. There are companies that have improved sclerotinia resistance in canola cultivars. We don't have commercial resistance in Australia, but I think with that precedent, it's something that's worth continuing to try and develop. And the more we can improve the efficiency of the process and improve the feasibility of doing it, I think the better chance we'll be able to get there as an industry.

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Shannon Beattie: Mark, thank you so much for joining me on the podcast today. I really appreciate your time.

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Mark Derbyshire: Thank you very much.

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Shannon Beattie: That was Mark Derbyshire from CCDM talking about how researchers are developing sclerotinia stem rot resistant canola. More information on this topic can also be found in the description box of this podcast or online at grdc.com.au. I'm Shannon Beattie and this has been a GRDC podcast. Thanks for listening.