Episode 141      26 min 44 sec
Cash crop crusaders: Genomic approaches to fighting fungus in canola

Plant geneticist Professor Barbara Howlett explains how genetics research is helping to fight fungal pests that confront canola farmers. With science host Dr Shane Huntington.

"The important disease related genes are in that repetitive junk DNA. By nature of them being there they can be easily lost or gained or even mutated." -- Professor Barbara Howlett




           



Prof Barbara Howlett
Professor Barbara Howlett

Professor Barbara Howlett's research interests are fungal genetics and fungal diseases of plants. Most of the research involves Leptosphaeria maculans, the fungus that causes blackleg disease of canola. Her approach ranges from developing plant disease management strategies to jointly leading an initiative with French scientists to sequence and annotate the 16,000 genes of this fungus. Prof Howlett's research team has pioneered the development of genetic and molecular techniques for the blackleg fungus to understand how the fungus causes disease. The team uses molecular markers to monitor populations of the blackleg fungus for changes of virulence, and also study sclerotinia stem rot of canola. Many findings are of major significance to fungal biology and plant disease.

Prof Howlett is also analyzing genes involved in the biosynthesis of an important class of toxins (epipolythiodioxopiperazines) in a range of filamentous fungi, including animal and plant pathogens. These toxins include sirodesmin in L.maculans and gliotoxin in Aspergillus fumigatus. We are analysing regulation and evolution of toxin gene clusters in fungi.

Prof Barbara Howlett has a B.Sc (Hons) in Biochemistry and a Ph.D in Botany from University of Melbourne and a M.Sc from the Australian National University, Canberra. She has also spent time at the University of California, Berkeley and at Stanford University. During her career she has worked in disparate research areas including tapeworms of dogs, immunoglobulin A in mice, bacterial chemotaxis, nitrogen fixation and most recently fungal diseases of plants. During a sabbatical visit to Stanford University she studied the genetics of the model bread mould, Neurospora crassa and this laid the foundation for her current research on blackleg disease of canola.

Credits

Host: Dr Shane Huntington
Producers: Kelvin Param, Eric van Bemmel
Audio Engineer: Russell Evans
Episode Research: Dr Dyani Lewis
Voiceover: Dr Nerissa Hannink
Series Creators: Eric van Bemmel and Kelvin Param

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VOICEOVER
Welcome to Up Close, the research, opinion and analysis podcast from the University of Melbourne, Australia.

SHANE HUNTINGTON
I’m Shane Huntington.  Thanks for joining us.  The farming of any crop on a large scale tends to attract significant plant-based diseases or pests.  In some cases a successful harvest and even the livelihood of farmers is put in jeopardy by such problems with little or no way to respond.  Recently however a more detailed understanding of plant disease and pest genetics has enabled farming communities to fight back, armed with detailed knowledge and techniques to keep plant pestilence and disease at bay. 
On Up Close today molecular plant pathologist, Professor Barbara Howlett, joins us to explain how an understanding of the genetics of plant diseases can enable successful agricultural responses to protect crops and in particular the major cash crop canola, an important source of edible oil.  Professor Howlett is head of the Molecular Plant Pathology lab in the School of Botany here at the University of Melbourne Australia.  Welcome to Up Close Barbara.

BARBARA HOWLETT
Thanks so much Shane.

SHANE HUNTINGTON
Now an area of work that you have had a lot of focus on is canola.  Can you give us an idea first up what is canola and why is it so important to humanity?

BARBARA HOWLETT
Canola is an edible oil. So you may have recognised it as margarine and as a cooking oil.  It’s very important in Australia.  In 2010 there were a million tonnes and this is worth about $500 per tonne, so it’s a very important cash crop.  Not only is it a cash crop it confers a significant benefit to a subsequent wheat crop.  So farmers grow these crops in rotation.  The wheat crop following a canola crop has a 15 per cent yield benefit because of glucosinolates, gasses in the roots that kill soil borne fungi that would attack the wheat.  So wheat farmers certainly benefit as well.

SHANE HUNTINGTON
You mentioned that it’s grown in Australia.  Where else in the world do we find Canola?

BARBARA HOWLETT
Well Canada is the world’s biggest exporter.  China probably produces the most but that’s for their domestic use and of course depending on the weather conditions in various countries of the world, the ranking of exporters varies.  But we’re a very important player - maybe in 2010 second or third exporter.

SHANE HUNTINGTON
Barbara what sort of conditions are required for successful canola crops?

BARBARA HOWLETT
Well in Australia we grow canola over the winter period, maybe over six months or so.  We need rain before the farmer plants the crop.  But during the season there are a lot of inputs of nitrogen, sulphur et cetera.  It’s a much more difficult crop for farmers to sow than say barley, but it’s a lot more profitable.

SHANE HUNTINGTON
There are a range of pests and diseases that attack most crops that we find in the world.  What specifically do we find with canola as a problem?

BARBARA HOWLETT
In all countries of the world the blackleg fungus is the most important pathogen.  We also have pests, but by far the most important fungus worldwide is the blackleg fungus.

SHANE HUNTINGTON
How would the farmer go about identifying this particular problem?  How does it present itself in a crop?

BARBARA HOWLETT
The disease is called blackleg.  There is a blackened canker at the leg of the plant.  That’s at the crown where the soil and the air are.  The farmer would go through the paddock and at harvest would see the plant had fallen over and he or she may also see these cankers.  The fungus is growing in the conducting material of the plant and so the plant is unable to take moisture up from the soil.  In the early months of the crop where you’ve still got a tiny seedling the farmer would see black necrotic lesions with fruiting bodies that have billions of spores.

SHANE HUNTINGTON
How long has blackleg been around?  What’s the scientific term for this particular fungus?

BARBARA HOWLETT
It’s scientific name is leptosphaeria maculans.  The fungus was identified in the last century and it’s been a problem in countries that have developed a canola industry.  So in the 1970s we began in Australia to plant canola.  Within two years the crop was wiped out and it wasn’t until the late 80s that plant breeders were able to bring in resistance germ plasm into their breeding programme so that we could then, since the late 80s, establish a really viable, vibrant canola industry.

SHANE HUNTINGTON
I guess many people would be aware that in the farming of certain particular crops you can either select specific plants to avoid these sorts of problems or you can spray for them.  There’s a variety of responses.  Do any of these standard responses work for blackleg and if so how long can you apply those particular responses before they become ineffective?

BARBARA HOWLETT
The farmer does three major things.  The farmer first manages the stubble from previous year’s crop.  Because the stubble, that’s the trash of the crop, has the sexual fruiting bodies that release billions and billions of spore inoculums.  They can move in the air up to 20-30 kilometres.  So managing the stubble is incredibly important.  The second thing is that the farmer can put fungicide on the seed.  It’s really important that its applied at this early stage because later on in the plant’s growth the fungus is growing very quickly down to the root.  We’ve done some experiments to show that after the plant has eight leaves, it’s no good using foliar fungicide. 
The third thing which is most important is to grow varieties that have particular resistance genes.  But this in itself presents a problem, because there is an evolutionary arms race between the fungus and the plant.  This is because the fungus has the ability to produce billions of individual genetic spores.  They can then be selected.  So if the farmer grows a particular plant with a resistance gene there will be selection on the populations of the spores such that ones that can attack the plant will be selected for.  So it’s a dynamic population and the farmer has to rotate the resistance genes in the cultivars that are planted.

SHANE HUNTINGTON
How dependent is the spread of this condition on, I guess, your neighbours farm or the farm down the road.  You mentioned how far some of these things have travelled. Presumably entire districts have to coordinate their management of this particular fungus, is that right?

BARBARA HOWLETT
It is.  For instance on a farm it’s important to grow the crop in a block so that you don’t have all the different boundaries.  We have shown that one needs to plant next year’s crop at least 500 metres from last year’s crop because the closer you are obviously the higher amount of inoculum you will have for next year.  So that’s right.  You really need to look at paddock history of your paddocks and also of those of your neighbours. 

SHANE HUNTINGTON
You mentioned this arms race that’s going on here between the plants and the fungi.  Is there a scenario where we’re approaching fewer and fewer resistant forms of canola?  Are we reaching an end point where we simply won’t be able to do that to the crop rotation to get us out of trouble?

BARBARA HOWLETT
We still not have a good handle on how many different resistant sources we have available in our canola germ plasm.  Over the years people have crossed wild varieties of brassicas.  Canola is a brassica, brassica napus.  So breeders have been able to introgress or breed in from other plants resistances.  But we’re still coming to terms as to how many we have and we think of it in terms of rotating the resistances we use. 
I’d like to give you an example of an epidemic that we had in part of Australia, in South Australia, in 2003.  The farmers were delighted to get a variety of canola that showed absolutely no disease.  Before that they had always planted varieties that showed some disease.  But after two years in that particular area there was a big yield crash.  So 90 per cent of the crop was lost.  This was because of the selection pressure put on the populations of the fungus.  But we’ve been monitoring these sites now for 10 years and now that that particular variety is not commercially sown - we still sow it in small trial plots - we can see that that resistance gene is effective again.  So we can rotate the resistance genes.  It doesn’t mean to say that we need to take them out of circulation forever.

SHANE HUNTINGTON
I’m curious about the reason for the fungus being there in the first place.  Is this sort of nature’s response to us over-farming a particular plant?  Is it as simple as that?  Do we know what’s going on?

BARBARA HOWLETT
Well firstly, agriculture does a lot of the time mean monoculture.  But if you go out to a natural environment, out into a eucalypt forest look at the leaves.  You will see fungi.  You will see all sorts of spots and blotches and whatever. So fungi, plants co-exist.  Most fungi do not cause disease but often in these particular situations, in agricultural situations, to grow the crop in a conducive way, high moisture et cetera you’re also providing a very good environment for a pathogen.

SHANE HUNTINGTON
I’m Shane Huntington and my guest today is Professor Barbara Howlett.  We’re talking about the genetics of plant diseases and efforts to fight crop failure here in Up Close, coming to you from the University of Melbourne, Australia. 
Barbara obviously one of the big changes that have occurred over the last decade is to start to address this problem from a genetic perspective.  Let’s start with canola.  How much do we know about the genetics of canola at this point in time?

BARBARA HOWLETT
Canola is brassica napus and the brassicas have been highly bred over centuries such that it’s really a composite of several genomes.  Canola is very closely related to cauliflower, broccoli, mustard, et cetera.  So we are learning about the genomes of these plants and as we are able to sequence genomes, we are finding the relationships between these particular plants.  What’s important, what is not.

SHANE HUNTINGTON
Now speaking of sequencing my understanding is you’ve sequenced the genome of the blackleg fungus itself.

BARBARA HOWLETT
Yes.  Forty per cent of the DNA of the blackleg fungus is repetitive sequences that do not code for genes.  Furthermore, the genome itself is compartmentalised.  We call it a patchwork genome where we have the junk DNA with very few genes and then another compartment where we have genes that are very, very close together.  So it’s gene rich regions, gene poor regions, right throughout the genome.

SHANE HUNTINGTON
When we look at this genome now what have we learned about the fungus that’s going to help us?

BARBARA HOWLETT
What we’ve learnt is how the fungus can change so quickly under selection pressure and make the resistance genes in our crops ineffective.  This is because the important disease related genes are in that repetitive junk DNA.  By nature of them being there they can be easily lost or gained or even mutated so that a G nucleotide base may become a T.  Once those sort of mutations occur then a protein isn’t made.  So in other words we can now explain by the location of the genes in this very dynamic unstable environment why we see such changes in the fungus in the field.

SHANE HUNTINGTON
Is blackleg unique in this scenario?  I mean it sounds like it’s an extremely adaptive organism in the way in which it can call on this junk DNA and just bits as required I guess due to selection pressures.  But are other fungi’s that we find around the world similar?

BARBARA HOWLETT
This has been the first example that we have seen.  However talking to my colleagues overseas, we are finding that this will probably be the case with other fungi.  But plant pathologists put diseases in particular risk categories and blackleg disease of canola is in the highest category.

SHANE HUNTINGTON
Now Barbara it’s all well and good to have all the genetics knowledge in the world in the lab, but sooner or later it has to get out to the farmers.  How are you going about doing that and what sort of effects are you seeing from any programmes with the farmers here in Australia?

BARBARA HOWLETT
Yes well what we do is we monitor the virulence of the populations of the fungus across Australia.  We do this by farmers and plant pathologists in the states of Australia where canola is grown.  They will send us the stubble.  The stubble is the part of the crop that will have the inoculum for the following year’s crop.  We look at the fungal populations there and using genetic markers in the fungus that we have developed to show us whether the disease related genes are mutated or present, we can predict whether the disease will be of great concern in those particular areas and whether farmers could and should plant a different variety where the fungus will not be able to attack in the short term.  But of course in the long term it’s a constant battle. We call it a boom and bust cycle.

SHANE HUNTINGTON
Obviously as we mentioned earlier canola is a very valuable crop.  But the research here has to be funded somehow.  Where is that funding coming from and what are the sort of longer term goals of the research?

BARBARA HOWLETT
In Australia we have a series of rural research and development corporations.  One of them is the Grains Research and Development Corporation.  So the farmer spends one percent of the farm gate value and that’s matched by one percent of commonwealth funds to each year have a budget of about 120 million dollars of farmer funds.  So this is farmer tax payer funds.  This is invested in a range of research and we in my lab receive such funding to develop management strategies for canola farmers.

SHANE HUNTINGTON
Do you have to go out to the farms themselves and train the farmers how to collect the material that you need to get the genetic information or is it just sort of so simple that they can just send it in, in an envelope as it were?

BARBARA HOWLETT
They can pick up stubble from a crop and send it to us in an envelope.  But because farmers are paying this one percent they’re extremely interested in what their money is being spent on.  So my group and the groups that I collaborate with spend a lot of time talking to farmers, going to farmer field days et cetera, talking about how we do our research and in fact how their money is being spent.  The funding of this research through the Grains Research and Development Corporation is a really impressive model worldwide. There aren’t other countries that have such a scheme.

SHANE HUNTINGTON
What sort of information are you supplying back to the farmers?  I mean obviously they don’t need detailed genetic knowledge of the particular crops that they’re working with, but I can imagine that they need some level of detail so they could forward plan, purchasing and so forth.

BARBARA HOWLETT
That’s right.  What they would like to know from us, the scientists and indeed we tell them this each year, is which varieties of canola are doing well even with large populations of the blackleg fungus around.  So in other words which ones are highly resistant at the moment, how the rankings are changing from year to year.  So we’ve put together with my colleague at Horsham, Dr Steve Marcroft and pathologists in various states - we’ve put together information which is giving them a risk assessment of what is your rainfall, what did you have in your paddocks last year, what varieties are you planning to grow, we think that these varieties may be at risk of becoming susceptible.  Using all of this information they can decide which paddocks to plant or maybe this year they might not even grow canola. 
The other thing to think about of course are the seed companies because quite often we would be saying to farmers, look you’ve grown this variety that this particular seed company has put out for a couple of years, but it’s going to crash, so don’t sow it.  So we’ve spent a lot of time - and I don’t necessarily mean me and my lab - but the whole team of us, taking to various seed companies et cetera.  Because when they breed a variety they can’t have it sitting on a shelf for five years and then give it to the farmers because the germination rate would be really low.  So our research and our recommendations not only impact on farmers but they impact on the seed companies and how they release and sell their seeds as well.  As well as seed companies, plant breeding companies as well.  They use our information for their benefit. 

SHANE HUNTINGTON
I’m Shane Huntington and my guest today is Professor Barbara Howlett.  We’re talking about the genetics of plant diseases and efforts to fight crop failure here on Up Close, coming to you from the University of Melbourne, Australia.
Barbara give us an idea, I guess what I’d like to hear is the real impact of this research is how much better these farms are doing compared to not having this information.  Are you able to quantify the sorts of improvement in crop yield that you’re seeing?

BARBARA HOWLETT
The identification of these markers for the disease related genes has really occurred in the last six to 12 months.  So we are applying this knowledge to the farmers.  We are impressed with the uptake.  We must remember though that canola is a part of their farming business.  So it’s a crop they grow in rotation with wheat, barley, peas, et cetera. They will also perhaps have fat lambs et cetera.  So one of the messages though that we’re able to get across to them is that they have to manage the disease really well, that they can’t and they will not get any magic cures. 

SHANE HUNTINGTON
Do you find the farmers are showing surprise at just how good this particular fungus is at changing and adapting?  Do they see that in anything else they deal with?

BARBARA HOWLETT
The biggest export crop in Australia is wheat.  Wheat has rust which is another fungus. This fungus doesn’t undergo sexual crossing, but there are great changes in this.  So quite often in spite of spraying et cetera there will be heavy rust epidemics.  So the farmers certainly think about canola and blackleg. But also on their mind will be diseases of other crops such as wheat rust, stripe rust. 

SHANE HUNTINGTON
Now you just mentioned one of the differences there between that particular problem and the one faced by canola is sexual crossing.  I might get you to just unpack that a little bit for us.

BARBARA HOWLETT
Yes, I’m sorry I hadn’t explained it previously.  The fungus grows through the canola plant down into the roots and on the stubble of the stem and then mating occurs.  So two different individuals mate, sexual crossing occurs and when that happens there is recombinance.  So you’ve got genetically different individuals.  You then have billions of spores going out on the wind. So if we compare it to a rust fungus where we do not get sexual mating occurring, the billions of spores going out there are all genetically identical.  So if you put selection pressure on a population of genetically different individuals you can select for any particular one and so the selection pressure can operate much more effectively on a sexually crossing organism.

SHANE HUNTINGTON
Barbara do we find the sort of knowledge you’re gaining on the blackleg fungus is helping the scientific community deal with other fungi that we find around the world?

BARBARA HOWLETT
Absolutely.  The fungus is very closely related to some other very important pathogens of Australian crops and European crops called glume blotch and yellow spot.  These are the Australian terms.  The Americans would call this disease yellow spot, tan spot.  So we know that the genomes of these fungi are relatively similar but there are quite a lot of differences.  Similarly the barley net blotch, which is an important problem for us in Victoria, has a similar genome in terms of the genes present.  But not the presence of all this junk DNA.  So at the scientific level we’re working out not just these markers for those disease related genes that will help the farmers, but we’re looking at other parts of the genetic material that may be good fungicide targets.  We have a dearth of fungicides that we can use for crops, but there are some interesting targets that could be developed if we can find a gene that’s crucial to the fungus for its survival and find a way of attacking that, then that is an approach that fungicide companies are interested in.  But it’s very long term research.

SHANE HUNTINGTON
You mentioned towards the start of our discussion that canola is grown in other parts of the world.  Is there an intention for your lab to extend its influence in what it’s doing to other regions in the world to provide the same sort of assistance?

BARBARA HOWLETT
Yes there is.  We do talk a lot to our French and Canadian colleagues.  But our research is really of most benefit to Australian farmers because overseas we do not have the great amount of blackleg disease.  It’s the most important pathogen still, but it’s not as rampant as in Australia.  That’s because of the way we grow our crop.  We grow it over a temperate mild winter where lots of sexual crossing can occur.  In Europe there’s snow on the ground.  In Canada the season is really short.  There’s snow on the ground.  So you never get the high levels of inoculum and sexual crossing.  It’s much more important in Australia to have this information than in the other countries. When they see epidemics they’re nothing like what we see.  In fact breeders from other countries bring their germ plasm to Australia because they figure if it can survive an Australian blackleg winter it will do okay in Canada or France. And indeed that’s the case. 

SHANE HUNTINGTON
Professor Barbara Howlett, Head of the Molecular Plant Pathology Lab in the School of Botany here at the University of Melbourne.  Thank you for being our guest on Up Close today and giving us an understanding of the genetics of plant diseases and how it’s applied to enhancing agricultural output by minimising risk of crop failure.

BARBARA HOWLETT
Thanks very much Shane. 

SHANE HUNTINGTON
Relevant links, a full transcript and more info on this episode can be found at our website at upclose.unimelb.edu.au.  Up Close is a production of the University of Melbourne, Australia.  This episode was recorded on Thursday 21 April 2011.  Our producers for this episode were Kelvin Param and Eric van Bemmel.  Audio engineering by Ben Loveridge.  Background research by Dyani Lewis.  Up Close is created by Eric van Bemmel and Kelvin Param.  I’m Shane Huntington.  Until next time, goodbye.

VOICEOVER
You’ve been listening to Up Close.  For more information visit upclose.unimelb.edu.au.  Copyright 2011, The University of Melbourne.


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