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1001 Genomes Project 2 Garnish Editorial and Contents GARNish December 2012 Edition 18 1001 Genomes Project 2 GARNish Editorial and contents Welcome to the December 2012 issue based in 42 institutions, grant success would av- of GARNish erage to just over one BBSRC award per institu- tion. I am sure that, like me, you will be shocked It’s a great pleasure to write the Editorial for this to learn about these figures. They are a serious edition of GARNish. I’ve been a member of the cause for concern for many reasons. Arguably the GARNet committee for just over a year now and most damaging effect in the long term will be its it’s great to see a number of issues that have impact on plant science research and teaching in been discussed at our meetings starting to de- university departments due to the increased dif- liver benefits to members of the community. ficulty of convincing our Heads of Schools to re- This includes the ‘hot topic’ Next Generation Se- cruit academic staff in this area, and our ability to quencing (NGS) that is impacting (and in numer- attract and/or retain the next generation of plant ous cases revolutionizing) many of our research researchers to a UK institute. projects. Gaining access to an NGS service is You are probably asking, why has plant science becoming increasingly important to Arabidopsis research funding become so limited when the (and other plant) researchers in order to perform Government and the current UK Chief Scientist whole genome sequencing to identify nucleotide are pushing the area of Global Food Security so changes causing a mutant phenotype, for ex- hard? Part of the reason for the squeeze on UK ample. Ian Moore and Smita Kurup’s article in plant research funding in recent years has been this edition (pg. 10) covers potential services at the negative effect of reducing the number of re- TGAC for the Arabidopsis community and we sponsive mode committees our community are encourage you to take a look. It also reveals able to apply to; in the majority of cases plant sci- that a surprising number of University, Institute entists are restricted to committee B. Thankfully, and commercial NGS services are available to help is at hand. BBSRC has recently made the UK researchers. Until very recently researchers decision to open up Committee C (Genes, De- submitting BBSRC grants requesting funding for veopment and STEM approaches to biology) to NGS services had to exclusively employ TGAC, plant applications (effectively recreating the Plant- the new BBSRC Genome Institute in Norwich. Microbial Science [PMS] and Genes and De- For many reasons, Arabidopsis researchers velopmental Biology [GDB] themed committees would prefer to have the choice to employ a wide successfully employed over from the last several range of NGS service providers. Thankfully, BB- decades). By effectively doubling the number of SRC have recently agreed that researchers are committees we are all able to apply to, BBSRC now free to employ any NGS service provider. has (in the short term) thrown a lifeline to many Research funding remains the single greatest UK plant research groups and may (in the longer area of concern for almost every UK group work- term) ensure many of our Universities continue ing on Arabidopsis or any other plant or crop to appoint academic staff and teach in this area. species. The effective loss of Defra as a source Whilst a very welcome decision by BBSRC, we of large scale research funding has resulted in must not forget that this remains an administrative BBSRC becoming the primary source of support fix; ultimately the only way to increase the number to the UK plant community. In this issue of GAR- of grants available to plant researchers is to in- Nish Charis Cook (GARNet) describes exactly crease the number of grants submitted. Given the how much funding is going to UK Arabidopsis impact of global food shortages, energy costs and and plant research groups (pg. 7). For example, climate change in the coming decades, significant in 2010/11, more than half of the total BBSRC increases in plant, crop and soil science research responsive mode grant funding (£31M) to com- funding are required to help mitigate their effects. mittee B went to plant science research, half of Increased Government investment into UK Ag which went to Arabidopsis research. Over the R&D staff, facilities and breeding programmes whole of the BBSRC budget, this translates to needs to happen now since the lead-time to de- 48 plant science research projects (plus 24 non- velop new, better adapted crop varieties will take responsive mode grants to plant researchers in at least 15 years. The clock is ticking….. 2010/11; data not shown in article). Given that Malcolm Bennet there are 350 plant research groups in the UK 3 GARNish Editorial Contents The GARNet Committee News and Views Pg 4 Malcolm Bennett Funding news Pg 7 University of Nottingham Term on committee Jan 2010 - Dec 2013 Making Data Accessible Pg 8 Jim Beynon Next Generation Sequencing Pg 10 University of Warwick Teaching Tools in Plant Biology Pg 14 GARNet PI 1001 Genomes Resource Pg 16 Juliet Coates University of Birmingham Spotlight on the University of Bath Pg 18 Term on committee Jan 2010 - Dec 2012 Spotlight on the University of Bristol Pg 22 John Doonan Many thanks to all who contributed to this issue, University of Aberyswyth especially Arthur Korte, Paula Kover, Claire Term on Committee Jan 2012 - Dec 2014 Grierson, Antony Dodd, Kerry Franklin, Heather Anthony Hall Whitney, Ian Moore, Smita Kurup, Mimi Tani- University of Liverpool moto, Paul Wiley, Malcolm Bennet, and Mary Term on committee Jan 2012 - Dec 2014 Williams. Cover image credit: Envel Kerdaffrec, Gregor Smita Kurup Rothamsted Research Mendel Institute. Term on committee Jan 2010 - Dec 2013 UK Plant Science Federation Sabina Leonelli Update University of Exeter Ex-Offico Member Mimi Tanimoto UK Plant Sciences Federation Sean May NASC Registration and abstract submission are now Ex-Offico Member open for UK PlantSci 2013, which will be held in Dundee from 16th-17th April 2013. We are Ian Moore pleased to announce that the keynote speakers University of Oxford will be Professor Sir David Baulcombe (Universi- Term on committee Jan 2010 - Dec 2012 ty of Cambridge) and Professor Charles Godfray (University of Oxford). Jim Murray University of Cardiff For the full programme, to submit an abstract, GARNet Chair Jan 2011 - Dec 2013 and to register, go to http://www.plantsci2013. org.uk/. For students, there will be a poster com- Heather Knight peition with an iPod Nano as the first prize. Durham University Term on committee Jan 2012 - Dec 2014 The 2nd International Fascination of Plants Day will be on 18th May 2013. Botanic gardens, re- Nick Smirnoff search labs, schools and farmers will open their University of Exeter doors to provide engaging activities for the pub- Term on committee Jan 2010 - Dec 2012 lic. We encourage anyone who works with or is interested in plants, to get involved and inspire Cyril Zipfel others by organising an event for Fascination The Sainsbury Laboratoy Norwich of Plants Day. For further details please contact Term on committee Jan 2012 - Dec 2014 [email protected] 4 GARNish News and Views Tweets and blog from GARNet The delegates concluded that there is a need for a broad, coordinated effort to create a semantic GARNet has entered the world of social media. framework for meaningful cross-species queries Our major new venture is the GARNet blog, which using a Common Reference Ontology for Plants. is updated regularly with posts on new methods, This Reference Ontology will encompass all spotlighted journal articles, key highlights from green plants and will facilitate queries for related workshops and conferences, advice on specific gene expression and phenotype data from plant grant calls, and round-ups of events and funding genomics, genetics experiments from the vari- opportunities. The most well received posts this ous species- and clade-specific databases, and year have been a piece on the β-carotene rich describe accessions in the various international orange sweet potato project; a collection of key crop germplasm collections. By creating a Com- resources for sharing and accessing large-scale mon Reference Trait Ontology for Plants, we can data; and funding updates. Where possible, posts achieve the goal of facilitating plant genetic and include links to relevant teaching resources trans- phenotypic data discovery and exchange. lating the cutting edge plant research highlighted on the blog to the classroom or lecture-theatre. For further information, list of participants and sponsors, links to presentations and more de- Follow Ruth and Charis on Twitter on tails, please visit the workshop wiki page at: @GARNetweets and @weedinggems for http://tinyurl.com/Trait-Ontology. updates on research papers, fund- ing, jobs, plant science in the me- dia, and live updates from confer- Science and Plants for Schools ences. You can also find GARNet on Google+. Science and Plants for Schools (SAPS) is a GARNet: www.garnetcommunity.org.uk Gatsby Foundation-sponsored initiative that aims Blog: http://blog.garnetcommunity.org.uk to get plant science into classrooms. The SAPS website features many practical plant science experiments for teachers to run in their classes, Crop Plant Trait Ontology Work- and the team want help from the research com- shop, Oregon State University munity to develop more. Plant breeders, biologists If you have run an undergraduate practical or and bioinformatics spe- outreach event that you think would translate cialists from ten countries, well to a classroom, please get in touch. SAPS seven US states, and two are particuarly interested in practical ways of plant agribusinesses gath- teaching photosynthesis, systems biology, and ered in Corvallis, Oregon in fast 10-minute dem- on September 13th-15th onstrations that grab at- 2012 for a Crop Plant Trait Ontology Workshop.
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