‘HETEROZYGOSITY’ PROBLEM – Genome sequence for mother of ash dieback survival [16Jun13]

The genetic insights could eventually be used to cross Tree 35 with breeding stock from our native ash population. Tree 35 is predominantly female and the genetic make-up could help identify a predominantly male UK tree with resistance to make a breeding pair. Or it could be used to identify both female and male UK trees with similarly low susceptibility to the fungus. A combination of crosses might be needed for a lasting comeback from the epidemic.

Ash trees are almost always fertilised by pollen from another ash tree rather than by self-pollination. This generates two copies of each chromosome in the resulting seeds. Although very similar, the chromosomes tend to have many differences when you look at the detail. This ‘heterozygosity’ makes it difficult to generate a genome sequence because in effect you have to put two genomes together at the same time.

Tree 35 has been identified as highly heterozygous.

http://www.tgac.ac.uk/home/news/54/68/Genome-sequence-for-mother-of-ash-dieback-survival/

 

“BREAKTHROUGH” – Genetic secrets of resistant tree gives new hope over ash dieback disease [16Jun13]

The scientists are extremely hopeful that, having determined the tree’s complete set of genetic material – through a process known as genome sequencing – they have paved the way to identify those genes which might be connected to its ability to withstand the fungus.

Although the breakthroughs have raised hopes that a new breed of ash will be able to grow and survive in the face of the fungus, they will do nothing to protect Britain’s 80m existing ash trees, which are all under threat.

Adult clones of tree 35 grown from cuttings taken from the original trees in the 1930s were recently discovered on the Danish island of Sealand. [However] just planting this variety of Ash in the UK would result in a narrow genetic base making the species vulnerable to future diseases, experts said, adding that the latest breakthroughs still represented a giant step forward for the long-term prospects of the tree in this country.

http://www.independent.co.uk/news/uk/home-news/genetic-secrets-of-resistant-tree-gives-new-hope-over-ash-dieback-disease-8660992.html

 

STARTING WITH TREE 35 – Ash genome reveals fungus resistance [16Jun13]

Scientists have sequenced the genome of a type of ash tree with resistance to the deadly fungal disease sweeping the UK.

The development could be the starting point for breeding a strain of ash to replace thousands expected to succumb to ash die-back in the next few years.

All the data is being put on a crowd sourcing website OpenAshDieBack to enable experts from around the world to help identify genes that might be connected to the trees’ ability to withstand the fungus.

These genes could then be part of a breeding programme for resistant trees.

The samples for the latest research came from so-called “tree 35”, a strain of ash from Denmark originally bred nearly 100 years ago, which has shown an ability to tolerate the fungal disease, when virtually all its Danish relatives were wiped out.

Prof Allan Downie of the John Innes Centre believes this genetic understanding of both the lethal fungal infection and the surviving strain could help fill the impending gap in the canopy.

“We’re trying to give nature a bit of a helping hand by identifying the right kind of (native) trees to do the appropriate crosses,” he said.

http://www.bbc.co.uk/news/science-environment-22913111

 

NORNEX – Unravelling the genetic code of the Ash Dieback survivor “tree 35” [14May13]

The Genome Analysis Centre (TGAC) has worked fast to sequence and assemble the valuable genome of the survivor “tree 35” from the recent Ash Dieback outbreak that have caused devastating damage to the Danish Ash woodlands and that now threatens the UK trees.

This information will be useful to those that are trying to find the trees that would offer at least a partial resistance and can be used to replace the now empty woodlands and remediate the damage.

This work contributes to the Nornex consortium, part of the Biotechnology and Biological Sciences Research Council (BBSRC) and Defra funded bioscience response to ash dieback (Chalara fraxinea). Prof. Erik Dahl Kjær and his group have been instrumental in the success of this project, read more about his work on this here.

“The genome sequence of this ash will be an essential tool that can help us to follow the inheritance of the ability of some ash trees to tolerate and to inhibit the growth of the Chalara fraxinea pathogen. Such knowledge will help generate new varieties of ash trees that can withstand attack by the fungus,” said Prof. Allan Downie at the John Innes Centre.

http://www.tgac.ac.uk/news/52/68/Unravelling-the-genetic-code-of-the-Ash-Dieback-survivor-tree-35/

 

“CRYO SCANNING” – First close up images of #Chalara fraxinea growing on the leaf stem of infected ash [14May13]

The images were obtained using cryo scanning electron microscopy, where the sample is plunged into liquid nitrogen to freeze it and imaged using the electron microscope.

The benefit of this method is that the sample is imaged in as close to its natural state as possible, providing the best quality 3D view of an organism.

http://news.jic.ac.uk/2013/05/close-up-images-of-chalara-fraxinea/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+NewsFromTheJohnInnesCentre+%28News+from+the+John+Innes+Centre%29

 

 

“POWER TO THE PEOPLE” – #Crowdsourcing genomic analyses of ash and ash dieback [12Feb13]

To kick start genomic analyses of the pathogen and host, we took the unconventional step of rapidly generating and releasing genomic sequence data. We released the data through our new ash and ash dieback website, oadb.tsl.ac.uk, which we launched in December 2012. Speed is essential in responses to rapidly appearing and threatening diseases and with this initiative we aim to make it possible for experts from around the world to access the data and analyse it immediately, speeding up the process of discovery. We hope that by providing data as soon as possible we will stimulate crowdsourcing and open community engagement to tackle this devastating pathogen.

We have generated and released Illumina sequence data of both the transcriptome and genome of Chalara and the transcriptome of infected and uninfected ash trees. We took the unusual first step of directly sequencing the “interaction transcriptome” [2] of a lesion dissected from an infected ash twig collected in the field. This enabled us to respond quickly, generating useful information without time-consuming standard laboratory culturing; the shortest route from the wood to the sequencer to the compute

Most importantly, crowdsourcing allows for a new form of potentially effective live peer-review, many sets of eyes interrogating and reviewing data and analyses mean that unusual results are quickly highlighted and can be assessed and dealt with appropriately. Whether they are eventually found to be inconsistencies in analysis or more exciting genuine new discoveries, the end product is brought to the scientific community many times faster than the usual peer-review by a small number of reviewers and crucially it all happens out in the open with maximum transparency. The cornerstone of our crowdsourcing is our repository on GitHub [4], a versioning system designed for collaboration in software development that automatically maintains attribution of contribution, meaning that whoever contributes will get full credit for the difference that they made. We are certain that the data will prove useful to anyone who wishes to be involved in the fightback against ash dieback and that concerted, early data-sharing and open analysis is a crucial step in a productive and timely response to emergent pathogen threats.

Our initiative is an early step towards developing the crucial function of the digital immune system for response to plant pathogens; the thing we cannot upload to a repository is the people with the expertise and the will to contribute, and that is why we need the scientific community to download our data and provide analyses.

http://www.gigasciencejournal.com/content/2/1/2

 

HAPPY COUPLE – How trees 35 and 18 could enable fight back against ash dieback [31Mar13]

Scientists are now breeding the two ash trees together in the hope that they will be able to create a new generation of saplings able to survive infection by the Chalara fraxinea fungus, which causes ash dieback.

Experts have found two trees – known as tree 35 and tree 18 – among Denmark’s ruined woodland that show the highest levels of resistance to the fungus ever seen.

British scientists have teamed up with Danish researchers in a bid to find the genes responsible for protecting these plants from ash dieback.

They hope to develop a test that will allow them to find similar trees in Britain’s woodland so they can begin breeding new saplings to replace those that die as a result of the fungus.

While other ash trees in the plot withered and died as the fungus slowly spread along their branches and through their leaves, the plants grown from tree 35 and tree 18 remained strong and healthy.

The pair also were found to be a viable breeding pair – with tree 35 being predominantly female and tree 18 being predominantly male.

 

FERA FEARS – Government ash dieback ‘management plan’ criticised for failing to stop disease [26Mar13]

Landowners have accused the Government of ignoring scientists’ efforts to develop a cure for ash dieback and instead relying on cheaper ‘management’ of the disease.

Sir Richard Storey, who owns 300 acres of mature ash trees on his Settrington Estate in Yorkshire, pointed out that Britain has far more ash trees than Continental Europe as it is more difficult to grow other species like beech and oak in the UK because of grey squirrels.

Harriet Tupper, Chairwoman of the International Dendrology Society, accused the Government agency in charge of tackling the disease, the Food and Environment Research Agency (FERA) of rejecting projects working on cures and antidotes.

“It is pessimistic not to try to find a cure/antidote. Over the centuries, scientists have discovered cures for many diseases, of humans, animals and plants. There is no reason why this cannot also happen for Chalara fraxinea. No antidote was found in Poland or Denmark, but of the trees in those countries, ash represented only a tiny fraction unlike the situation in the UK.”

http://www.telegraph.co.uk/earth/earthnews/9948411/Government-ash-dieback-management-plan-criticised-for-failing-to-stop-disease.html

 

GENOME MAPPING – Major cash for ash [08Mar13]

“We won’t be able to solve the whole problem in the life of this collaboration. However, we aim to use new technologies to help tree breeders select the best trees to cross-fertilise. We hope to generate the knowledge needed to understand why this fungus has become such a problem. That knowledge will catalyse further research around the world.”

It will be the first time that some advanced genetic techniques such as ‘associative transcriptomics’ are used in trees. This is where the expressed genes of plant varieties are compared to identify markers for traits. These can be used to speed up marker assisted breeding.

The scientists will focus part of their ash research on ‘Tree 35’, a tree in Denmark that has stayed healthy during the epidemic that has damaged most ash trees in the country. By mapping the genomes of ‘Tree 35’ and other trees with low susceptibility, they will be able to establish the genetic basis of resistance.

Ash is highly variable because mother trees can have multiple partners. If, within this variation, different types of ash show some resistance, the scientists will be able to recommend building stronger resistance based on multiple crosses. Different crosses for different environments will also need to be suggested, to breed resistant trees adapted to specific conditions.

http://news.jic.ac.uk/2013/03/major-cash-for-ash/

 

BANKING ON SCIENCE – Major funding to fight back against ash dieback [01Mar13]

Forest Research’s principal pathologist, Dr Joan Webber is a key player in a new consortium of researchers awarded £2.4M of fast-track research funding from BBSRC and DEFRA for a two-year project to gather an in-depth understanding of the ash dieback fungus and provide genetic clues about some ash trees’ natural resistance to attack. Computer models will also be built to develop monitoring plans of the distribution and spread of the fungus as well as chart how the disease might progress. This knowledge will help to fight the fungus and replace lost trees with those able to survive.

The Nornex consortium (named for the three Norns who tend the ash tree of life Yggdrasil in Norse mythology) brings together tree health and forestry specialists with scientists working with state-of-the-art genetic sequencing, biological data and imaging technologies to investigate the molecular and cellular basis of interactions between the fungus and ash trees. Data from the project will be uploaded to an open-access website. This crowd-sourced, data-sharing approach will share the genetic data to exploit the expertise of plant and fungal research communities internationally.

http://www.forestry.gov.uk/website/forestresearch.nsf/byunique/INFD-95LFXJ