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International Wheat Genome Sequencing Consortium (IWGSC) Workshop, the 22nd International Triticeae Mapping Initiative (ITMI) Workshop and the 4th US National Wheat Genomics Workshop, North Dakota, USA 24th – 29th June 2012
This conference brought together researchers working on cereal genetics and genomics from across the world. I was invited to present my work on resistance to eyespot disease in wheat as part of the “Young Triticeae Researchers” session. The conference provided a combination of presentations; some detailing progress on the collaborative wheat genome sequencing effort, some presenting genome level analyses based on the data generated as part of this consortium, and others (like myself) presenting how they are using the genomic tools rapidly being developed in the Triticeae to map and understand traits of interest.
A number of presenters reported on progress in generating and sequencing physical maps of individual wheat chromosomes.
However, one of the major developments from the wheat sequencing effort, presented by Jane Rogers from The Genome Analysis Centre, Norwich, is the release of the wheat chromosome survey sequences on the IWGSC website. This project has used next-generation sequencing methods on flow-sorted wheat chromosomes to generate a database of sequences from each of the 21 wheat chromosomes.
This has provided an invaluable tool for anyone working in wheat genetics. Similarly Sasha Allen from the University of Bristol reported on the extensive sequencing and single nucleotide polymorphism (SNP) identification work that has been undertaken in the UK. This information has been made publically available throughout the project and is already being heavily utilised by plant breeders and researchers alike.
Despite the significant efforts in wheat sequencing, due the extreme size and complexity of the hexaploid wheat genome there is still a long way to go until we have an assembled and annotated wheat genome sequence, as is available in grasses such as rice and Brachypodium.
However, the conference left me in no doubt that this would be achieved.
In the absence of a finished wheat sequence a number of researchers presented work utilising synteny between Brachypodium, rice, and Sorghum to develop scaffolds to predict the genes present within a region in wheat to finemap and clone agronomically important genes. During the conference, some useful tools were outlined to aid this process, such as the wheat ‘zapper’ presented by Filippo Bassi from North Dakota State University.
There were also a number of presentations on work to fine-map and functionally characterise genes of interest in cereals. These covered a wide range of traits, but pathology was extensively represented with work presented on resistance to powdery mildew, leaf rust, stem rust, leaf stripe, tan spot, Stagonospora, eyespot, Fusarium, Russian wheat aphid and Hessian fly. It is noticeable how genomic resources and SNP tools such as KASPar and the iSelect wheat SNP chips are helping plant pathologists to understand the genetics of resistance to these pathogens and to speed up the introgression of novel resistances into cereal varieties.
The conference excursion was a field trip to Bagg Farm. This was a Bonanza Farm, one of many large farms created in the late 1800’s when the Northern Pacific Railroad allowed stockholders to buy large tracts of land at a competitive rate to raise the necessary capital to continue building the railroad that was crossing North Dakota. Much of the land was farmed too intensively and many of the farms fell out of use. The Bagg farm buildings have been restored, and we were given a very entertaining tour from some very enthusiastic local guides. I particularly enjoyed the old agricultural machinery and found some equipment (see picture) to help irrigate our Fusarium head blight field plots at the John Innes Centre!
The conference was extremely useful to keep up to date with the wheat genomic resources that are available and to hear progress on a number of cereal mapping projects. It was also very interesting to meet a number of plant breeders and researchers from the USA, and to hear their perspectives on agriculture and plant breeding. I am grateful to the BSPP and the ITMI organising committee for providing funds for me to attend the meeting.
Chris Burt John Innes Centre 5th Sudden Oak Death Science Symposium and study trip, California, USA June 2012 This study trip started at the 5th Sudden Oak Death Science Symposium (SOD 5), held in Petaluma, California, June 19th – 22nd. This symposium occurs every 2 or 3 years and is organised by the University of California. It brings together around 150 researchers, regulators, land managers and industry representatives from the US, Canada, Europe and Australia working on Phytophthora ramorum. 52 talks and 25 posters where presented on a number of aspects of P. ramorum research including genetic diversity, fire ecology and diagnostics. Initially field trips to Quarryhill Botanical Garden and Bouverie Wildflower Preserve took place on the 19th June where a discussion was initiated by Clive Brasier on the biosecurity risks posed by the international trade in plants and of plant hunting. Local woodland restoration efforts following SOD outbreaks were also shown at Bouverie Wildflower Preserve.
On the 20th June the International Updates session of the symposium took place where the current situation regarding the upsurge of sudden larch death in the UK was presented by Joan Webber and where I gave my talk: The epidemiology of Phytophthora ramorum and P. kernoviae at two historic gardens in Scotland. The discovery of the new P. ramorum EU2 lineage, present in Northern Ireland and SW Scotland, was also announced during this session by Clive Brasier.
A chronology of P. ramorum invasion into California in the 1990s was outlined by Matteo Garbelotto (University of California). They used genotyping to conclude that there were eight concurrent introductions of P. ramorum into Californian nurseries from where local spread further occurred into forests; although they noted that forest infection were not as severe, suggesting that P. ramorum shows less fitness in forests than in nurseries. They also suggested a dispersal distance of 1 to 4 km in forests, a conclusion reached by findings of identical alleles in forests at this distance from nursery outbreaks.
Over the past 10 years, forests in California have been severely impacted by P. ramorum infection resulting in an investment in research of approximately $10 million. This therefore seemed an ideal opportunity to spent time in California after the conference in order to gain a better understanding of the impact of P. ramorum in natural forests.
I travelled from Petaluma on the 22nd June to Humboldt County with Ben Jones (Forestry Commission) and Sabine Werres (Julius Kuehn Institute, Germany) to meet with the forest advisor for Humboldt and Del Norte, Yana Valachovic. Yana showed us first hand the devastating affect of P. ramorum infection of tanoak (Notholithocarpus densiflorus) in local forests and explained some of the issues around disease management in Humboldt County. It was noticeable that the forests were largely unmanaged and heterogeneous and that P. ramorum was killing the tanoak but leaving the other species unaffected. It was a stark contrast to the current larch situation in the UK where large areas are clear felled leaving no trees behind at all.
The following day we met with Maia Beh and Lenya Quinn-Davidson (UC Davis) to see an area in Redwood Valley where they are trying a novel P. ramorum management technique. Upon the initial discovery of infected trees in this area in spring 2011, local landowners, funders and other collaborators were quickly brought together to start eradication measures. Eradication involved the complete removal of California bay laurel and tanoak trees and seedlings within 100 meters of known infected trees using chainsaws or herbicides thereby creating a host free buffer within the forest. Over 300 acres were treated by the end of the year. A study is now in place to monitor the long term benefits to forests that have been exposed to this management practice, it is hoped that the spread of P. ramorum locally will be reduced or stopped by creating these buffer zones.
We traveled through the redwood groves north into Oregon on the 24th June. The next day we were shown P. ramorum outbreak sites within the 212 mile square quarantine zone around the town of Brookings in the south west of the state by Ellen Goheen (USDA Forest Service) and Alan Kanaskie (Oregon Dept. of Forestry). There has been a severe escalation in P. ramorum findings in this area recently with the identification of 83 new infested sites in 2010 and 172 in 2011. Some of these findings were outside of the quarantine zone and some distance from known infected sites. This has led to a revision in management objectives because the initial goal of containment and complete eradication in this county is now deemed to be unachievable so efforts will be concentrated on early detection, rapid eradication, reduction in inoculum levels and more public outreach to prevent spread within the local horticultural industry.
After the excursion to Northern California and Oregon I drove to UC Davis to meet with Jessica Wright (USDA Forest Service) and other scientists involved in P. ramorum research. Jessica is a conservation geneticist working on the conservation of tanoak which is an important ethnobotanical species because of its traditional uses by Native Americans, as well as for a number of insect pollinators. On June 29th and 30th I travelled to UC Berkeley to assist Catherine Eyre, a post doc in the Garbelotto lab. We conducted field work in the San Francisco Public Utilities Commission watershed at Crystal Springs, collecting soil samples for P. ramorum quantification in soil in infected areas. This was an interesting parallel with my field work in Scotland where I had quantified inoculum in soil in gardens and forests.
I returned from Berkeley to Davis in order to assist in aerial surveys with the USDA Forest Service. Aerial surveys have become an important tool in the UK, particularly during the larch outbreaks, so this was a good opportunity to experience how surveys are conducted in the US. We flew west and then north from Davis in a light aircraft, as opposed to the helicopters used in the UK, to survey the Mendocino coast area of California.
During these surveys the crews note all forest problems during a flight, including factors such as bear damage and herbicide use, not just P. ramorum damage as tends to happen in the UK.
This trip, funded by the BSPP travel bursary and the University of St. Andrews, provided me with an enjoyable and invaluable experience which has furthered my understanding of P. ramorum infection in forests and allowed me to share my knowledge with colleagues in the US.
Matthew Elliot Forest Research