Podcast: Genetic progress in saving ash trees
1 October 2013 by Richard Hollingham
This week in the Planet Earth podcast, Richard Buggs and Lizzy Sollars of Queen Mary University of London describe the latest UK efforts to breed ash trees that are resistant to the dieback disease that's currently ravaging East Anglia and the south east of England.
To assist those who find text-based content more accessible than audio, a transcript of this recording is available below.
Richard Hollingham: This time in the Planet Earth podcast, the latest on UK efforts to save the ash tree. I'm Richard Hollingham and I'm on the roof of Queen Mary University of London in the east end of the City. I've got the towers of the City of London over to my left, the Olympic park to my right, Canary Wharf behind me and looking down on some residential houses and gardens, and the leaves on the trees around here are just starting to turn to their autumn reds, yellows and oranges, but some are showing more permanent signs of change. I'm with Richard Buggs who is leading the British Ash Tree Genome Project. Richard, there's already evidence, particularly in the south end of the country, of ash dieback.
Richard Buggs: There is. The Forestry Commission has been collating evidence for Chalara for ash dieback throughout Britain and there's a huge concentration in the south east, particularly in East Anglia where it was first discovered.
Richard Hollingham: What is it? It's a fungi, some sort of fungi?
Richard Buggs: It's a fungus called Hymenoscyphus pseudoalbidus, also known as Chalara fraxinea or just ash dieback and it grows within the wood of ash trees and it blocks up their xylem vessels that carry water and basically causes them to eventually die through lack of water.
Richard Hollingham: This isn't a sudden death, it's a long drawn out process?
Richard Buggs: No, once the tree has been infected and if it's an old tree a battle will ensue between the tree and the fungus over potentially many years, even decades, there will be this war back and forth between the fungus and the tree and eventually the tree will die.
Richard Hollingham: And we have to accept a significant loss do we of ash trees? There is no reversing of that?
Richard Buggs: At the moment we don't know any way of reversing it not on the scale that we would need to treat 80 million ash trees - that's the number we have in Britain. So our best hopes for the ash in the very long term are to try to breed trees that have resistance to ash dieback.
Richard Hollingham: That's your approach? That's the purpose of the project here. What's the overall aim then of what you're doing?
Richard Buggs: We're hoping that by sequencing as ash tree genome we can produce a foundational resource for genetic studies on ash trees and hopefully, eventually, pinpoint the genes that are involved in giving resistance to ash dieback.
Richard Hollingham: Now, you've made quite a lot of progress with that and last winter we were with you when you took samples from ash trees managed by the Earth Trust in Oxfordshire, on probably the coldest recording we've ever made for the Planet Earth Podcast, but let's head into the lab here at the university and see what you've been doing.
Richard Buggs: Here we are in our lab at Queen Mary where we do our molecular genetics work on ash trees.
Richard Hollingham: And you start off with those cuttings that we saw you take a few months ago?
Richard Buggs: That's right. So we brought that cutting here while it was still fresh and then we ground up the materials in the grinding equipment here.
Richard Hollingham: This looks like a very sophisticated scientific version of a kitchen grinder.
Richard Hollingham: It is very much like a kitchen mixer and that just grinds up the sample for us. We have it cooled with liquid nitrogen so that the DNA doesn't degrade as we're grinding it, and then we add various buffers and using columns that contain fibres that bind the DNA, we extract the DNA and then we can send it off for sequencing.
Richard Hollingham: So you send it off and it goes through a sequencing machine, what does it come back with, what, just a list of latter, the base pairs?
Richard Buggs: It comes back as billions of short reads. Each of them a hundred base pairs long, so just a hundred letters long and then we have to jigsaw all of that together to work out the actual genome sequence.
Richard Hollingham: Now, you're not doing most of that but the person who is is Lizzy Sollars, a PhD student here. Was does that involve? What, you have A, C, G, T, lots and lots of little fragments, little lists, you've got to put into one to make an entire sequence of DNA?
Lizzy Sollars: Yeah, that's right. So we get these reads of the A, C, G and Ts and some of them overlap so we can use computer algorithms to work out the over lap and piece them together into one genome.
Richard Hollingham: And so you've now got, what, the third version of that. Does that mean you're getting a pretty accurate idea of this particular ash genome?
Lizzy Sollars: Yeah. As we've received more data from the sequencing company we've been able to get a better quality genome assembly.
Richard Hollingham: And ultimately, Richard, you're looking for resistance? You're looking for variations between different ash trees?
Richard Buggs: Yeah. The resistance genes aren't going to pop out of just one genome sequence you need studies of many, many individuals and in particular of trees in Denmark which have been shown to have lower susceptibility to ash dieback, and a group called Nornex which are based in Norwich are sequencing an ash tree from Denmark which does have low susceptibility to Chalara.
Richard Hollingham: And, Lizzy, you're about to head off to Denmark to do more work on this because they've had, what, ash back for quite a while.
Lizzy Sollars: Yeah, the ash dieback disease spread to Denmark in 2003, so they've had ten years of this disease and approximately 95% of the trees have been affected by the disease, so about 5% appear to be resistant.
Richard Hollingham: And this is the key really to this isn't it Richard, is working together with people who have had the disease, people who are also working on the resistance genes rather than everyone working in isolation.
Richard Buggs: That's right. So there's a European-wide effort to work on ash dieback. The UK has put a lot of funding into this very large consortium who is working in this problem. In addition we're beginning to work with scientists in the USA because over there they have a problem called Emerald Ash Borer, which is a beetle that is attacking ash trees and really devastating their populations there and we're beginning to link up with them as well because they can benefit from the genomic data that we're generating here.
Richard Hollingham: Ultimately you're looking for resistant varieties, but these aren't going to benefit the ash trees that are around right now, the ones we can perhaps see from the rooftop here.
Richard Buggs: No, unfortunately. Unless surprising did crop up in the genomic studies which helped us to understand the biochemical basis of what's going on between the tree and the fungus in some way that we could design a chemical to interfere with that but, you know, when we're talking about 80 million ash trees that's not a population that you can easily treat with any fungicide.
Richard Hollingham:So, ultimately what you're looking for is to re-grow another generation of ash trees with, hopefully, some resistant genes in them?
Richard Buggs: That's right. Ideally we want British ash trees that are resistant to ash dieback and ultimately also resistant to the Emerald Ash Borer, because this beetle that's in America is also found near Moscow in Russia and could be moving westwards, and so we don't want to be in a situation where we've just spread a tree that is resistant to ash dieback and then the Emerald Ash Borer comes in and gobbles all of them up. We probably need a tree that is resistant to both of them and that's why we need to collaborate with the Americans.
Richard Hollingham: And the predications are there will be more diseases particularly with climate change that they will spread and the UK will see more of these sorts of threats, not just in ash but in other species?
Richard Buggs: Yeah, I think this is a real case study here in ash because it's come at a time when genome sequencing has become much cheaper than before, so very rapidly we've sequenced the genome with a host to the tree, we sequenced the the genome of the fungus, in Norwich a group has done that, and we will be able to find out can our new technologies actually help us to tackle these problems, and we're doing our best to show that they can and hopefully they will and if they do we will be able to roll that out in other cases of tree disease and indeed in other diseases in animals and plants.
Richard Hollingham: So although the majority of ash trees in the UK are going to get this. They are going to die over 10, 20, 30 years or so, you are making some progress and there's may be a reason to be optimistic for the long term future.
Richard Buggs: We would like to think so. We have some of the foundational resources that we need now in place but there's a huge research programme that needs to go ahead based on these before we can be even close to trees that we've bred that are resistant to ash dieback.
Richard Hollingham: Richard Buggs and Lizzy Sollars, thank you both very much. We referred to podcasts that we recorded earlier this year in the freezing cold Oxfordshire countryside, you can listen again to that by visiting Planet Earth online. You can also find us on Facebook and Twitter. That's the Planet Earth podcast from the Natural Environment Research Council. I'm Richard Hollingham, thanks for listening.