Genes Against Ash Dieback - Planet Earth

28 February 2013

Interview with

Richard Buggs, Queen Mary University of London; Jo Clark, Forestry Research Manager;

Eighty million trees in Britain are at risk of dying from ash dieback - a fungal disease that's gradually spreading across the country.

But there is a glimmer of hope, thanks to scientists at Queen Mary, University of London, who are decoding the ash tree's genetic sequence to discover how to produce a tree strain resistant to the disease.

Richard Hollingham spoke with the scientist leading the research, Richard Buggs, and Forestry Research Manager, Jo Clark...

Richard Hollingham - Jo, just set the scene for me here. We're in the middle of a field and surrounded by woodland...

Jo Clark - Well this is Paradise Wood which is the research woodland of the Bluebells woodlandEarth Trust. It was set up about 20 years ago and it is the largest collection of genetic broad leaf trials in the country dedicated to improving the quality of the timber of some of our most important timber trees.

Richard Hollingham - Now to get to the location we're at right now we've walked through some lovely woodland and we've passed a plantation of ash and there's woodland all around us, but where we are right now the trees are really quite small and stubby.

Jo Clark - The reason they're so small is partly an environmental effect - we're in a bit of a frost pocket here, so it's not a great place for planting trees but also all of the trees that we're looking at is especially bred line of ash trees that have been crossed within themselves so the material is much more homozygous and that is an actual impact on the growth, so that's another reason why they look so small.

Richard Hollingham - When I say they look small, they're really just coming up to my waist, that sort of height, but Richard these are of particular interest to you these trees despite their small size.

Richard Buggs - Yes, so for me to sequence a genome it is really important that these are in bred trees because every tree has one genome copy from its mum, one from its dad and they can be quite different and so when I sequence a genome it can be really hard to untangle those two. However in a plant that is the product of a self pollination it has the same mum and dad and so the two genomes are not very different and that will really help me as I sequence a genome to do the assembly of that genome in a way that is efficient and actually gives us really good results.

Richard Hollingham - And at the moment, Jo, there's that alarming statistic of 80 million trees likely to be affected by ash die back - how important are ash trees?

Woodland canopyJo Clark - Well ash is one of our most important trees, it's the third most common tree and the second most widely planted broad leaf tree. It performs a very important part of many valued ecosystems - a lot of British biodiversity is dependent on not so much the ash tree itself but on the structure of a woodland, a broad leaf woodland that is created through different species composition. So ash is very important and it's a very important timber tree. Ash is quite elastic, it's quite good at absorbing impact and it is used quite widely in things like flooring and door frames. Morgan cars are still made from ash trees - it is widely used.

Richard Hollingham - So, Richard, you are starting with the ash trees here, these small ash trees, these young ash trees, what are you actually going to do?

Richard Buggs - I will be collecting a sample here today from a self progeny of ash. I will be taking that back to my lab at Queen Mary University of London and my PhD student, Yasmin Zoren, is going to extract the DNA from the bark of that specimen. We will be sending that DNA sample to Eurofins in Germany and the data they will give back to me is a whole load of short reads from throughout the genome at random covering the genome 155 times over, and we have to put that all together using high performance computers to assemble the genome of ash.

Richard Hollingham - And essentially, what, you will get a list of all the Symptoms of Chalara ash dieback. A fungal disease affecting the ash trees of Europe. Picture shows wilting of leaves caused by necrosis of the rachis.bases in the ash DNA?

Richard Buggs - Exactly. The ash genome is 950 million bases long, so that's just under a third size of the human genome. Sequencing a genome is a bit like taking aerial photos of an unexplored island. Just imagine there is an island in the Pacific that hasn't been explored and all we know is how big it is and we want to know more about it, and so what we might do is send planes over it taking lots and lots of small aerial photos at random and then we have to take those little aerial photos that we have, which in our case are reads of DNA, and put them all together in a big jigsaw puzzle to recreate on the computer the whole genome code of the ash tree.

Richard Hollingham - Okay, you've got your secateurs in your hand and you're going to take a sample now - so you're actually going to chop off a little bit of this tree here.

Richard Buggs - I'm taking a sample here...

Richard Hollingham - There we go! You literally take that back and you've got to do all that work on it.

Richard Buggs - It's the start of a huge programme of research.

Richard Hollingham - So you have the sequence of DNA, how does that help you with looking at which trees are going to be resistant to the disease?

Richard Buggs - The gene spur resistance are not just going to pop out of the genome as soon as we sequence it, we're going to have to actually find them and the way we do that is to look at lots of trees and find ones that are resistant and ones that are susceptible and then genotype them.

Richard Hollingham - When you say genotype, look at the genetics of them and sequence them?

Richard Buggs - Yes. So we won't sequence the whole genome with them but we will look at a subset of the genome using a system of markers like, for example, there is a system called rad markers that look at thousands of points across the genome but not the whole of the genome but enough of it for us to pick out the genes that are associated with resistance or susceptibility to ash die back.

Jo Clark - The underlying genetics is absolutely of paramount importance, whether you're trying to produce robust populations to combat climate change, or in fact a novel disease like Charlara. The genetics is what underpins all our research work to produce productive timber trees for the future.

Richard Hollingham - Richard, how long is this going to take?

Richard Buggs - The sequencing of the genome should take less than a year and we should be releasing a draft assembly of the ash genome very quickly. Technologies have moved on really fast in the last five years and this is now quite a routine thing to do.

Richard Hollingham - And, Jo, how soon do you expect to be able to use this information?

Jo Clark - Well as soon as Richard gives us those individuals that are likely to be resistant we have very good techniques for bulking up material, so ash grafts very, very easily. You can graft it onto a root stock and then you can be producing seeds perhaps in five years time.

Richard Hollingham - So while ash trees are dying you would be hoping to breed resistant ash trees and almost starting to catch up.

Jo Clark - Absolutely. Just because most of the ash trees are dying hopefully we will find one or two individuals. I mean the public can even help here by identifying individuals and letting researchers know and they can do that on the Peach Trees Trust website, because those are the ones that will be resistant and those are the ones that we would like Richard to be screening and saying, yes they actually are resistant and then we can bred from them.

Richard Buggs - This is obviously a huge natural disaster for Britain and for our ash trees but one of the really encouraging things that has come out of it is that it has shown up how much the public cares about woodlands. And also within the scientific community I have seen a huge enthusiasm for lots of scientists to get involved with trying to combat this problem and different people with different research skills are coming together and saying, look here is something that I can bring to the table, let me work on this, and we're all looking to collaborate together to combat this as a scientific community within Britain.

Richard Hollingham - Richard Bugg and Jo Clark, thank you both very much.

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