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. tention. They work with The workshop was hosted by the Plant Ontology students from primary and the Trait Ontology, and co-organised by school up to when they TransPlant, European Bioinformatics Institute, leave school at 18. GARNet, Generation Challenge Program, Sol SAPS: www.saps.org.uk Genomics Network, and SoyBase.

The goal of the workshop was to engage re- Plant Pathology Audit searchers associated with major cultivated crops worldwide, widen their awareness and showcase The British Society of Plant Pathology (BSPP) the latest developments in ontologies for plants. Audit of Plant Pathology Training and Educa- In addition to hearing presentations, participants tion in the UK was published in November. It re- engaged in hands-on activities, learning to use ports a major decline in teaching and research the ontology editor OBO-Edit and working in on plant diseases in British Universities. Fewer small groups to classify plant trait terms which than half the institutions that teach biology, agri- had been submitted in advance. 5 GARNish News and Views culture, or forestry offer plant pathology courses. Diary President of the BSPP Professor James Brown said, “These job losses are severe. Britain is not UK PlantSci 2013: 16–17 April, producing graduates with the expertise needed Dundee, Scotland to identify and control plant diseases in our farms GARNet Synthetic Biology workshop: 21-22 and woodlands. One of the most worrying find- May, Nottingham, England ings is the decline in practical training in plant pathology.” 31st New Phytologist Symposium (Orchid sym- bioses: models for evolutionary ecology): 14-16 ERA-CAPS: First Joint Call May, Calabria, Italy. Paul Wiley International Symposium on Plant Photobiology: BBSRC 3-6 June, Edinburgh, Scotland. The ERA-Net for Coordinating Action in Plant ICAR 2013: 24 – 28 June, Sydney, Australia Sciences (ERA-CAPS) launched its first joint call SEB Annual Main Meeting 2013: 3–6 July, for proposals on November 19th. The call, “Ex- Valencia, Spain panding the European Research Area in Molecu- lar Plant Sciences”, covers all areas of molecular ASPB Plant Biology 2013: 20–24 July, plant science. Four themes have been highlight- Providence RI, USA ed as areas of particular interest: Food Security, th Non-Food Crops, Adaptation to a Changing Cli- 7 EPSO Conference: 1–4 September, mate, and Biotic/Abiotic Stress. Applications out- Peloponnese, Greece side of these themes are also welcomed. Plant Genome Evolution: 8-10 September, Fifteen countries are contributing funds to the Amsterdam, The Netherlands. call: Austria, Belgium, Denmark, France, Germa- 32nd New Phytologist Symposium (Plant inter- ny, Ireland, Israel, Latvia, The Netherlands, New actions with other organisms): 20-23 November, Zealand, Norway, Poland, Portugal, Serbia, and Buenos Aires, Argentina. the UK. The NSF in the USA is running a par- allel call through their Plant Genome Research Program that will allow US researchers to join Funding deadlines in 2013 consortia. BBSRC: 9 January; 21-22 May; June (TBC). The call has a one-stage application process, and consortia must comprise research groups EPSRC: Outline proposal batch meetings 11 from a minimum of three different countries. The February; 15 April; 16 June. closing date is February 15th 2013, and the total FP7 KBBE theme: 5 Febuary budget is around €20M. Marie Curie Actions: Researchers’ Night, IAPP, Full details of the application process, funding IRSES, all in January; CIG,18 September. organisations and contacts are available on the ERA-CAPS website (www.era-caps.org). NERC Standard Research and New Investiga- tor Grants: 1 July; 1 December. Contact: Paul Wiley ([email protected]) For regular updates about open calls for re- search grant and fellowship applications, out- reach grants, and other opportunities, see the GARNet blog.

6 GARNish News and Views

Expanding plant science expertise vironment rooms, and new greenhouses on the at a new facility in Bristol roof. The growing strength and size of the plant science base in Bristol is recognised through Gary Foster, Claire Grierson, Antony Dodd, Ker- these new facilities and provides significant new ry Franklin, and Heather Witney opportunities not only in science but also in re- The University of Bristol, Woodland Road, Bristol cruitment. The School has a strong track-record BS8 1UG. For email addresses, see pg. 22. of developing and supporting independently- funded Research Fellows, recently appointing Biological Sciences at the University of Bristol will three (Dr Kerry Franklin, Dr Antony Dodd and Dr be moving into a new iconic £54 million state-of- Heather Whitney) to permanent academic posi- the-art Life Sciences Building in 2013. Clustered tions. around a central atrium will be teaching and re- search laboratories, seminar rooms, computer In addition to completing the new building, there facilities, staff offices and a café. The building will also be a new public realm works and exten- will be fully equipped to become one of the UK’s sive landscaping which will link St Michael’s Hill leading facilities for the advancement of Biologi- and Tyndall Avenue to Royal Fort House and its cal Sciences and a range of related disciplines. adjoining gardens. The building and surrounding area has been rated BREEAM Excellent, being Gary Foster, Professor of Molecular Plant Pathol- highly sustainable and environmental friendly. ogy, said: “This investment in Life Sciences is a The building will incorporate Green Living Walls major move by the University of Bristol, showing and areas to contain plants which will promote strength and ambition, with Bristol being an ex- wildlife within the area. citing and ideal place to carry out research over the coming years. GARNet Advisory Committee “The new building will also provide outstanding elections 2013: Voting now open laboratories for science teaching and will en- hance the undergraduate experience by facilitat- The GARNet Advisory Committee is the link be- ing research-led study and staff-student interac- tween GARNet and the Arabidopsis research tion, making Bristol University the first choice for community, steering GARNet’s activities to en- research and teaching. sure we best support UK plant scientists. Com- mittee members are volenteers elected from and by the research community. They serve three year terms. At the end of 2012, three committee members are stepping down, and the process of electing three new members is in progress. There are eight candidates for three vacancies on the committee: Dr Antony Dodd (University of Bristol); Prof. Nicholas Harberd (University of Oxford); Dr Paula Kover (University of Bath); Dr Vinod Kumar (John Innes Centre); Dr Sarah McKim (University of Dundee); Dr Steve Penfield An artist’s impression of the new Life Sciences (University of Exeter); Prof. David Salt (Univer- building, which will open in 2013. sity of Aberdeen); and Dr Carol Wagstaff (Univer- The Life Sciences building will be split into three sity of Reading). zones, including a five-storey laboratory wing complete with acoustic chambers, spectroscopy If you want to vote, please email charis@garnet- and microscope rooms, clean rooms, and a dou- community.org.uk with the names of your three ble height plant room. The new building provides preffered candidates, in order of preference. expanded state of the art laboratories for Bristol For the names of current committee members plant science research as well as extensive plant and their terms, see page 2. growth facilities through suites of controlled en- 7 GARNish Funding

Both BBSRC responsive mode Com- sive mode grants in that year. This means that mittees B and C are now available for research funding from the BBSRC for plants was roughly £30M, out of a £387M budget for plant science proposals research and capital grants. An additional £51M Charis Cook was allocated to maintenance of BBSRC re- [email protected] search institutes. What can realistically be done to improve the number of grants being awarded Plant scientists largely depend upon the BB- to plant science? At the September GARNet ad- SRC for funding, and the bulk of that funding is visory committee meeting, two conclusions were from responsive mode funding calls. An analysis drawn: of grants awarded in BBSRC responsive mode showed that plant science does very well from 1. As the age-old adage goes, ‘You have to be in Committee B, the only avenue obviously avail- it to win it!’ More proposals from the plant science able to plant science grant proposals. A good community will lead to more grants awarded to proportion of the plant science funded was Ara- the plant science community, because that is bidopsis research: in both 2009/10 and 2010/11, how responsive mode works. If the community more than half of the total money (£25M and maintains a high level of grant applications, if you £31M respectively) allocated by Committee B are unlucky in one round you may have a good went to plant science research, of which roughly chance in the next. half was for work on Arabidopsis (Figure 1). 2. Put yourself forward for appointment to a When looking at Committee B alone, plant sci- BBSRC Committee, and be supportive of good entists appear to be good at winning responsive plant science grants. If there are no plant sci- mode grants. However, in the two academic years ence experts on the Committees, plant research looked at only 11% of total committee-based re- is likely to get passed over as a matter of course. sponsive mode funding was allocated to plant There was good news for the 2011/12 calls and research. Committees A and D both dispensed beyond. It is now much easier for plant scientists roughly 15% more money in responsive mode to apply to Committee C, which is taking over than Committee B. This is because the same primary responsibility for genetics and develop- percentage of grants from each committee are ment instead of dealing only with development funded, so Committees A and D, which receive and methodologies, which had previously often more grant proposals, award more grants than been re-assigned, according to their context, to the other committees. other committees. There is a plant scientist on In 2010/11, the total number of grants award- Committee C, so be sure to consider sending a ed by the committees in responsive mode was proposal through it because if this year goes by 386, of which 48 were to plant science research with very few plant proposals, the next Commit- projects. Plant scientists won 24 non-respon- tee C may not be so plant-friendly.

Figure 1: BBSRC Committee B responsive mode funding breakdown in 2009/10 and 2010/11 8 GARNish Making Data Accessible

GARNet workshop: Making Data perimental techniques are simply too modern for Accessible to All suitable data sharing outlets to have been es- tablished. Other datasets present the problem Charis Cook and Ruth Bastow of simply being too large to currently store and share, e.g. imaging data. Researchers, publish- In July 2012, GARNet held a workshop entitled es and funding bodies all have a responsibility ‘Making Data Accessible to All’. Together, work- and a role to play in finding effective solutions to shop speakers and delegates discussed the cur- make such data accessible. rent challenges in data storage, which data are ‘valuable’ and which may reasonably be left be- In many cases the solutions will be driven by the hind, and who should have the responsibility of user/researcher who, in the absence of a useful sharing, storing, and curating data. database, tool or resource will create their own. In fact a number of researchers utilise purpose The challenges of data sharing are more sig- built in house repositories to store their research nificant then ever due to the demand from UK data and share it with colleagues and collabo- funding bodies for open access to the results of rators in advance of publication. Such activities research they fund, and the rise of data driven are beneficial to building a culture of data shar- science such as systems biology which depends ing, and generally result in producing data that is upon well curated and publicly available data. carefully annotated and curated. Although most journals require that large-scale data sets are deposited in the appropriate repos- In order for data sharing to take hold and bear itory, the extent to which these requirements are fruit in plant science and biology as a whole, enforced appears to be unclear. In some cases, the workshop concluded that incentives for re- for example for high throughput plant phenotype searchers to store and share data, effective po- data, depositing data is not possible as appro- licing measures, and shifts in attitudes towards priate central repositories do not currently exist. an open access philosophy at all levels are ur- In addition to these problems the workshop also gently needed. Funding bodies, universities, and highlighted that there is no requirement for re- publishers and journals can provide important searchers to make the data underlying a table ‘sticks and carrots’ by shifting priorities and at- or graph in a publication publicly available. This titudes to support the practice of data sharing, makes it very difficult for those wishing to com- with all its demands. At the same time, research- bine or reuse data sets. ers need to seriously commit to data sharing by making it part of their principal aims and outputs. Not all data are created equal. Certain data types In most cases, community involvement matters (often based on DNA/RNA sequence) can be much more than the availability of technology. easily stored in well-established online central Recent initiatives to encourage data publica- repositories. They are clear guidelines on the tion such as data only journals and data sharing minimal information that a researcher is required platforms, principally Dryad and Figshare, are to collect and deposit data. For example GEO acknowledged as important drivers of the shift and Array express are well-utilised repositories toward an ethos of data sharing. and the MIAME guidelines for trancriptomics are used by a number of funders and journals. Shar- Workshop presentations can be found online at ing and re-use of sequence-based data is equal- http://www.plantsci.org.uk/news/workshop-talks- ly well supported via user-friendly web based in- now-available-making-data-accessible-all. The terfaces and associated analysis tools such as full list of speakers at the workshop was: Sabi- Genevestigator and NASC arrays. However this na Leonelli (Exeter), Andrew Millar (Edinburgh), is not the case for all data types. Nick Smirnoff (Exeter), Jay Moore (Warwick), Jacob Newman (UEA), Mary Traynor (J. Ex. The dominance of high-throughput data genera- Bot.), Giles Jonker (Elsevier), Ruth Wilson (Na- tion methods for datasets as varied as protein ture Publishing Group), Mark Hahnel (Figshare), interactions and phenotypic information means Claire Bird (Oxford University Press), Sean May there are many datasets for which current data (NASC), David Swarbreck (TGAC), and Paul sharing platforms are not appropriate. Some ex- Burlinson (BBSRC). 9 GARNish Making Data Accessible

A collection of standard repositories to for various large-scale datasets, including ‘main’ share and access data repositories and plant-specific resources. As data sharing is dependant on consistent methods, for- One of the outcomes of GARNet’s July Making mat and quality, the table also includes minimum Data Accessible workshop was the recognition of information guidelines where available. a need for standard practices in data generation, sharing, and usage. To encourage this, GARNet For a version including links to the online resourc- put together a list of important data repositories es, go to the GARNet blog.

Data type Main Plant Minimum General Other repository repository information journal repositories guidelines requirement Genes and gene Genbank TAIR Genbank, Submission to nomenclature TAIR Genbank or TAIR Genome Genbank TAIR sequence MIGS (Field et Submission EMBL al., 2008) to Genbank DNA barcodes EMBL Barcode of Life BOLD Systems standards RNA EMBL BCB RNA-seq RefSeq sequences Chip GEO Minseq (draft), Submission to NCBI Sequence sequencing GEO guide- GEO read archive, lines International Regulome Con- sortium Transcriptomics GEO, NASC MIAME from Submission to Array Express, ArrayExpress NCBI GEO or Array PLEXdb, EFP Express Browser Protein structure Protein Data Plant PDB Submission to NCBI Protein, and sequence Bank PDB, PIR PIR Proteomics GEO MASCP- MIAPE (Taylor Submission to EBI PRIDE, Gator et al., 2007) GEO, Swiss- NCBI Protein, Prot Plant PDB, EMBL Metabolomics BRMB Plant Me- Metabolomics Submission to Metabolome iHub (Ionom- tabolomic Standards BMRB Express ics) Network Initiative Epigenomics NCBI Epig- FGED Society Chromatin.csl enomics MINSEQ Interactions IMEX TAIR IntAct guide- Submission to IntAct nbrowse lines IMEX Mathematical Biomodels. PLASMO MIRIAM from Biomodels models net Biomodels.net Pathway infor- BioCyc AraCyc mation Synthetic biology Parts registry Parts registry SBOL Standard 10 GARNish Next Generation Sequencing

The Genome Analysis Centre and the Multiplexing will most probably come at the cost Arabidopsis Community of delayed delivery as samples will wait until Il- lumina flow cells can be filled, which will depend Ian Moore1 and Smita Kurup2 on demand. Recent quotes have specified deliv- ery within 6-8 weeks of receiving DNA samples. 1 Department of Plant Sciences, Univer- More rapid turn-around can be offered through sity of Oxford, South Parks Road, Oxford. use of the Illumina MiSeq (10x, £805 +VAT based [email protected] on pooling with up to 1 other sample; 30x, £1500 2 Plant Biology and Crop Science, +VAT based on running a single sample). TGAC Rothamsted Research, Harpenden. has a budget to replace and upgrade facilities [email protected] and will shortly be able to offer faster sequenc- ing of lower numbers of samples on the Illumina The power and scope of genetic research is be- HiSeq 2500 platform. ing rapidly expanded by Next-Generation Se- quencing (NGS). The speed of this change is Sequence Samples per Cost per sam- matched by the rate of change in sequencing depth per HiSeq lane ple technologies, services, and costs. Many proce- sample dures that were specialist applications only a few > 10x 16 £220 years ago, such as mutant identification, are now > 20x 8 £330 essentially routine contract services. In 2009, > 30x 6 £400 BBSRC established TGAC, The Genome Analy- sis Centre, in the Norwich Research Park to pro- > 40x 4 £545 vide a commercial contract NGS service as well > 80x 2 £970 as a collaborative partner for innovative de novo > 160x 1 £1,826 sequencing and bioinformatics. TGAC augments *These are exclusive of VAT, which would be charged if other academic and commercial service provid- the work is undertaken on a contract rather than on a grant ers in the UK and internationally, and here we set funded / research collaboration basis (see below). out the facilities and services that it provides to In addition to genome re-sequencing, for organ- the Arabidopsis community. isms such as Arabidopsis thaliana with a fully Sequencing Technologies and Indicative annotated reference genome, TGAC offers tran- Pricing scriptome analysis based on Illumina RNASeq or Roche 454 cDNA sequencing (RNASeq is typi- TGAC has Illumina, Roche 454, and SOLiD se- cally based on a minimum of 25 million reads per quencing technologies (http://www.tgac.ac.uk/ sample with 50 base single or paired end reads). about/technology/). Arabidopsis genome re- Further information about the services and analy- sequencing is currently offered on the Illumina ses available can be obtained from TGAC project HiSeq 2000 platform. A single lane on this plat- managers. form will generate enough data from nuclear DNA samples to yield over 150-fold coverage of Working with TGAC the Arabidopsis genome. This is far greater than Researchers can interact with TGAC via two is required for simple re-sequencing, SNP detec- routes. BBSRC funded projects that involve col- tion, or mutant mapping (10-20x). By bar-coding laboration with TGAC, for example in de novo se- individual samples, several can be run at once to quencing or novel bioinformatic projects, require reduce costs for each sequencing project. Prices a completed Technical Assessment form (TAF) are liable to change (usually downwards) and at the time of application (http://www.tgac.ac.uk/ need to be discussed with TGAC project manag- projects/bbsrc-grant-submissions/).The TAF will ers so the costs supplied below should be con- set out the aims of the NGS and bioinformatics sidered indicative at the time of going to press. work, plus include advice and input from TGAC These costs are based on multiplexing specified staff on feasibility, experimental design, appro- numbers of samples per lane and on 100 base priate methodologies, and costs. A completed paired-end sequencing (100 nucleotides from TAF will form part of the supporting information each end of each sequenced library fragment). for the BBSRC grant application. Four weeks are 11 GARNish Next Generation Sequencing

required for the consideration of an applicant’s less than 3μg of total DNA isolated from flower completed TAF by TGAC. BBSRC originally gave buds. It may be possible in the near future to as- TGAC preferred supplier status for ‘large-scale’ sess organellar genomic content during the QC NGS but guidelines have been relaxed, now ac- stage to agree on an acceptable sequencing cepting any UK academic partner and even over- strategy. seas and commercial partners, but require ap- plicants to justify their choice of service provider TGAC will perform a quality control of all DNA/ and collaborator with some proof of competence RNA samples upon arrival and will assess the (BBSRC Research grants guidance notes 5.27). suitability of such samples for library construc- tion and subsequent sequencing. If the sam- It is also possible to gain access to TGAC facili- ples pass QC then they are deemed suitable for ties on a contract research basis via their sub- downstream work. If the library then fails TGAC sidiary, Genome Enterprises Ltd (GEL). This av- will undertake one attempt to re-make the library enue may serve much of the community’s needs, at its own cost. Similarly if problems arise in se- given that much NGS of Arabidopsis will involve quencing libraries that have passed QC, TGAC relatively routine procedures for sequencing, will inform the client and re-sequence as soon read-mapping, SNP detection, and SNP frequen- as possible. Repeated failures will be discussed cy calling. The specific requirements and costs of with the client. a project can be discussed with one of TGAC’s Project Managers and a quotation will normally Sequencing data is subject to quality control be- be received within 2-3 working days of an en- fore being supplied via electronic download. As quiry being received. Enquiries can be made by a general rule, 97% of data for samples of 100 e-mail ([email protected]), telephone (+44 million bases is delivered at Q20 or better (99% 1603 450861) or via the website (http://www. probability of correct base call) and these qual- tgac.ac.uk/contact-us/). It is unclear that a TAF ity scores are substantiated in our subsequent is required for BBSRC applicants who undertake analyses. This compares favourably with data contract research with GEL and the relatively low from other commercial suppliers that have been costs involved may be included as a directly in- used by colleagues in this Department (Dr. Ste- curred cost along with other contract services. ven Kelly, University of Oxford, pers. comm.). For RNASeq data, analysis is via a Bowtie – We understand that collaborative sequencing Tophat – Cufflinks pipeline (FPKM values, pair- at TGAC can be funded by BBSRC at 80% fEC wise differential expression) and visualisation is without incurring VAT, whereas sequencing at in G-Browse, Ensembl or TGAC Browser). Bio- GEL can be funded at 100% fEC (Guidance note informatic tools, computing facilities, and serv- 2.59) but will attract VAT. ices are also offered at various levels (http:// www.genome-enterprise.com/services/detail/url/ Sample submission and data delivery. bioinformatics). For contract services, costs will TGAC requires 1-5μg of genomic DNA or total be quoted for individual projects depending on RNA per sample for paired-end genomic se- the degree of TGAC involvement. In October quencing or RNASeq on the Illumina platform 2012, an basic analysis involving read-mapping and approximately 10-fold more for 454 tran- to reference genome, SNP detection, and SNP scriptome analysis. A document setting out rec- frequency calling was costed at approximately ommended methods for sample preparation, £900+VAT for up to 16 samples. More involved quality-control, and shipment is available at: or novel bioinformatic projects can be entered http://www.genome-enterprise.com/content/files/ into as collaborations with TGAC’s bioinformati- services/TGAC+sample+guidelines.pdf and an cians. update was planned at the time of writing. For genomic DNA samples, nuclear DNA prepara- tions are recommended to minimise organellar DNA contamination. Total genomic DNA samples are accepted but may require a greater depth of coverage and, in practice, it is possible to optain 40x-fold coverage of the nuclear genome from 12 GARNish Next Generation Sequencing

NGS Sequencing Services offered in the UK

Name Services offered Platform/Other comments

University-based / publicly funded services Biosciences, University De novo genome sequencing; HiSeq 2500 of Exeter Genome resequencing; RNA-Seq; Small RNA; ChIP-Seq; Meth-Seq; Bioinformatics analysis and support (by special arrangement) TGAC, The Genome Genome sequencing; RNA-Seq; HiSEQ2000; Illumina GAIIx; Analysis Centre Bioinformatics analysis Abi- SOLiD4; Roche 454 FLX Titanium NBAF, Liverpool Genome sequencing; ABi-SOLiD5500xl; De novo sequencing; RNA-Seq; Roche 454 FLX; ChIP-Seq; Epigenomics; Metagenomics IonTorrent sequencer School of Biological Genome sequencing; Illumina GAIIx; Sciences, University of De novo sequencing; RNA-Seq; IonPGMTM sequencer Bristol ChIP-Seq; MeDIP-Seq Commercial services BGI De novo genome sequencing; Illumina HiSeq; Genome resequencing; AB SOLiD system; RNA-Seq; Small RNA; Metagenomics; IonTorrent Epigenomics; ChIP-Seq; Bioinformatics analysis and software. GATC- Biotech, De novo genome sequencing; PacBio RS; Germany Genome resequencing; RNA-seq; HiSeq 2000; Small RNA; ChIP-seq; Meth-seq; Roche GS FLX+ System PacBio RS; metagenomics LGC genomics De novo genome sequencing; HiSeq 2000; Genome resequencing; RNA-seq; Roche 454 FLX Titanium Small RNA; ChIP-seq; Meth-seq; metagenomics Source BioSciences, Genome sequencing; RNA-Seq; Illumina GAIIx HiSeq 2000; Nottingham ChIP-Seq; Bioinformatics solutions Roche 454 FLX

Acknowledgements. comparisons between service providers. Ian Moore thanks Chris Watkins (TGAC) Thanks to Cyril Zipfel and Heather Knight for and Mike Ball (BBSRC) for information and comments on the article. comments during the preparation of this article, and Dr. Steven Kelly (Deptartment of Plant Sci- ences, University of Oxford) for sequence quality 13 14 GARNish Inspiring the Next Generation

Teaching Tools in Plant Biology, to tal reading to augment their textbooks, or the inspire the next generation instructor can incorporate selected slides into a formal lecture. Alternatively, the materials can be Mary Williams used as resources and offer the foundation for Features Editor, The Plant Cell. in-depth classroom discussions of primary litera- [email protected] ture. Each topic is conveyed in two sets of slides; a full set of about 100 slides, and an abridged set University faculty are squeezed between the of 24 slides that highlight the major topic themes need to teach and a system that evaluates them and are intended for use in introductory courses. primarily by their research accomplishments. Years of preparation and training support their Ultimately, Teaching Tools in Plant Biology will research endeavors, but there is little support for cover all the major topics in plant biology at a their role as teacher. A major objective of Teach- level suitable for advanced undergraduates. A ing Tools in Plant Biology, a feature of the Ameri- set of ten lectures that covers each of the ma- can Society of Plant Biologists’ premier plant bi- jor plant hormones was completed in 2011, and ology journal The Plant Cell, is to help instructors these lectures have been updated since their teach. The project was initiated by TPC Editor- initial publication to incorporate the most recent in-Chief Cathie Martin of the John Innes Centre breakthroughs. For example, putative receptors and is edited by Mary Williams, an experienced for salicylate and strigolactone hormones were teacher of plant science, researcher, and win- identified after the corresponding Tools were first ner of the 2011 ASPB Excellence in Education published, but this new information was included Award. Teaching Tools are designed to bridge when the Tools were revised. Several lectures on the gap between textbooks and the research the theme of biotic interactions of plants (includ- literature, by providing up-to-date, hyperlinked, ing microsymbionts, arthropods, and pathogens) online content, sometimes described as a “living have been published, and more, are coming textbook”. Instructors and students can access soon. Lectures on the theme of plant physiology materials electronically and use them as launch will be published during 2013 and will include points for further study and inquiry. Importantly, Teaching Tools on water uptake and movement, Teaching Tools are revised and updated regular- mineral assimilation, photosynthesis, and so ly by scientists so that instructors can be confi- forth. dent that they are presenting the most important, An important objective of biology education is to current information to their students. teach students the processes of scientific data Each Teaching Tool covers a key topic in plant gathering and interpretation. Biology is an em- biology through a review article written for un- pirical science, in which knowledge and under- dergraduates with links to primary literature and standing come from experiments and models are review articles, PowerPoint slides (examples can continually refined and modified to incorporate be seen in Figure 1) that provide both introducto- new data. Students need to learn how to design ry and advanced material arranged into a coher- and analyze experiments and interpret this infor- ent narrative, and a teaching guide that includes mation. To support this objective, Teaching Tools learning objectives and questions for discussion in Plant Biology slides include summary models or assessment. The information in each Teach- as well as explanations of key experiments, and ing Tool is drawn from the primary literature, and figures from research papers and descriptions of the content is peer reviewed. One of our users classic and groundbreaking experiments. Each remarked, “It saves time I would’ve spent search- Tool points out unanswered questions and areas ing the literature,” and another appreciates that of current and future research, to help students these materials are “current, up-to-date, and all recognize the importance of the future contri- in one place.” butions that they might make. Another user re- marked, “Students really appreciate and like the Teaching Tools can support a wide variety of way the information has been presented.” teaching styles. For example, the lecture notes or slides can be used by students as supplemen- Periodically we publish Tools on topics of broad societal interest, such as human nutrition, medic- 15 GARNish Inspiring the Next Generation

inal plants, and biofuels. Whether they become Teaching Tools in Plant Biology is available by researchers or not, the students we are educat- institutional or personal subscription to The Plant ing now are going to be faced with social and en- Cell and to ASPB members; a pay-per-view op- vironmental challenges that demand a solid un- tion has just been added. Access to the first six derstanding of the roles of plants in ecosystems Teaching Tools, including the highly accessed and human endeavors. Teaching Tools in Plant “Why Study Plants?” is unrestricted. Have a look Biology highlights the applications of plant sci- and tell us what you think, and please inform ence to improving agriculture, the environment your students and colleagues about this innova- and human health, with the objective of enlight- tive educational resource. ening and inspiring students.

Figure 1: Teaching Tools slides are designed to convey information visually, as illustrated by this set that highlights societal and environmental issues being addressed by plant scientists. 16 GARNish 1001 Genomes Resource

1001 Arabidopsis thaliana genomes 10% difference in genome size between different 8 and GWAS A.thaliana accessions, the source of this varia- tion being far from clear. It is clear, however, that Arthur Korte massive genomic differences, including chromo- somal fusions and large translocations, exist be- Gregor Mendel Institute of Molecular Plant Biol- tween A.lyrata and A.thaliana; these two species ogy, Vienna, Austria. diverged only about 10 million years ago.9 The [email protected] Brassica genomes may be more flexible than To understand the causal relationship between a naïve glimpse at their DNA sequence would genomic variation and phenotypic variation, imply. The above argues that even though the genome-wide association studies (GWA) have A.thaliana genome might be one of the best un- become the general approach.1 These analy- derstood genomes at the moment, there is still ses have become routine in A.thaliana, and the much that we do not understand. The hope is number of published GWA studies is still increas- that once a thousand or more genomes of the ing dramatically. Although most analyses to date same species are available, we can really start have been conducted with a relatively small tackling these questions. sample size, the recent release of dense (250k) In regard to first point association mapping, it is SNP data for over 1,300 accessions2 will enable important to be aware that it is unlikely for the ac- much larger studies. In addition, online tools that tual causal variant(s) - for any given phenotype enable GWA analyses on the fly have been de- - to be present in the 250k data (they only repre- veloped (see Fig.1), which will further facilitate sent ~ 2-4 % of the SNPs that are still segregat- the use of GWA. Recently, over one hundred ing). Although these data may show significant Arabidopsis genomes collected from around associations in the GWA analysis, linkage dis- the world have been released.4-6 Their analysis equilibrium (LD) with causative variants will often reveals several differences within the thaliana be the driving force behind these associations. lineage, including millions of single nucleotide That is, although the resolution in GWA is bet- polymorphism (SNPs), structural variants (SVs), ter than in classical QTL studies (using recom- and copy-number variants (CNVs). These data binant inbred lines from single crosses), it is still already enable evolutionary and functional stud- coarser than single-base-pair resolution. Having ies but do not completely match the data used full sequence data – and therefore potentially the in GWA. Efforts are presently under way to causative polymorphism (meaning both SNPs as completely sequence more than 1,000 acces- well as SVs, which are as likely to cause phe- sions,7 and this raises a question: to what extent notypic differences) in the dataset – should help will these additional sequences add to our un- in theory. But there are still many reasons (e.g. derstanding of the genotype-phenotype map in epistasis and allelic heterogeneity) why a non- A.thaliana? causative marker may still be a better descrip- The answer has two parts: one regards the use tor of the phenotype, than the causative one.10 In of this data for GWA; and the other concerns the these cases, use of more sophisticated models general picture of the A.thaliana genome. might be necessary. In this respect, extensions to classical GWA models, analyzing multiple phe- Starting with the latter, it is noteworthy that even notypes or loci together, have been proposed.11,12 though we are speaking of full genome sequenc- The combination of both, higher marker density es, the current data are in fact far from complete and specific GWA models, should increase the genome sequences. We are able to call SNPs power of the analysis. To add an extra layer of (and to a lesser degree SVs) with relatively low complication, it is increasingly clear that addi- error rates in the unique part of the genome, but tional data, such as expression and methylation we have only a basic idea about the remaining data, influence the relationship between - geno parts of the genome. We have very little idea of type and phenotype. Efforts are underway to pro- the amount of large structural variants, although duce these data as well.13 some examples have already been seen. Exper- iments using Flow Cytometry suggest a nearly The vision is that all of these data and tools will 17 GARNish 1001 Genomes Resource

be combined with the amazing phenotypic re- 7. The 1001 Genomes Consortim. http:// sources in A.thaliana, and hosted in one com- www.1001genomes.org. mon location, thus becoming an unparalleled re- 8. Schmuths, H., Meister, A., Horres, R. & Bachmann, source for the entire Arabidopsis community. K. (2004) Genome size variation among accessions of Arabidopsis thaliana. Ann. Bot. 93, 317-21. References 9. Hu, T.T. et al. (2011) The Arabidopsis lyrata ge- 1. Atwell, S. et al. (2010) Genome-wide association nome sequence and the basis of rapid genome size study of 107 phenotypes in Arabidopsis thaliana in- change. Nat. Genet. 43, 476-81. bred lines. Nature 465, 627-31. 10. Platt, A., Vilhjalmsson, B.J. & Nordborg, M. (2010) 2. Horton, M.W. et al. (2012) Genome-wide patterns Conditions under which genome-wide association of genetic variation in worldwide Arabidopsis thaliana studies will be positively misleading. Genetics 186, accessions from the RegMap panel. Nat. Genet. 44, 1045-52. 212-6. 11. Korte, A. et al. (2012) A mixed-model approach for 3. GWAPP. http://gwas.gmi.oeaw.ac.at. genome-wide association studies of correlated traits 4. Cao, J. et al. (2011) Whole-genome sequencing of in structured populations. Nat Genet 44, 1066-71. multiple Arabidopsis thaliana populations. Nat. Genet. 12. Segura, V. et al. (2012) An efficient multi-locus 43, 956-63. mixed-model approach for genome-wide associa- 5. Gan, X. et al. (2011) Multiple reference genomes tion studies in structured populations. Nat. Genet. and transcriptomes for Arabidopsis thaliana. Nature 44, 825-30. 477, 419-23. 13. Arabidopsis 1001 Epigenomes Project. 6. Schneeberger, K. et al. (2011) Reference-guided http://www.nsf.gov/awardsearch/showAward. assembly of four diverse Arabidopsis thaliana genom- do?AwardNumber=1122246. es. Proc. Natl. Acad. Sci. USA 108, 10249-54.

Fig1: Screenshot of GWAPP. A tool, to perform GWA analysis on the fly. The tool is hosted at htpp://gwas.gmi.oeaw.ac.at. 18 GARNish Spotlight on the University of Bath

There are over 350 plant research groups in the Richard M. Cooper UK, in 42 institutions scattered from Aberdeen to [email protected] Exeter. Many of these groups are international http://www.bath.ac.uk/bio-sci/contacts/ leaders in their field. To promote the breadth of academics/richard_cooper/ plant science throughout the UK, and increase Plant-pathogen interactions awareness of the different types of research being undertaken, GARNet is focusing on geo- Innate Immunity: how plants recognize patho- graphical areas and institutions across the UK. In gens. Microbial pathogens release conserved this issue we continue our tour around the coun- molecules which elicit host defences. These try highlighting the outstanding research being MAMPs (Microbial Associated Molecular Pat- undertaken at the University of Bath and the Uni- terns) include chitin from fungi, flagellin and li- versity of Bristol. popolysaccharide (LPS) from bacteria. MAMPs are recognized by PRR receptors, trigger calcium Spotlight on the University of Bath ion influx, signalling pathways and subsequently myriad defences. The Cooper lab was the first to show: bacterial peptidoglycan (PGN) is recog- nized by plant cells; Arabidopsis cells recognize simultaneously multiple MAMPs to avoid patho- gen camouflage; Large MAMPs (PGN, LPS) need first to be degraded to pass through the The plant research groups at the University of plant cell wall matrix. Bath include a wide diversity of researchers Microbial Pathogenicity: suppression of host in- involved in many aspects of plant biology. Re- nate immunity. Pathogens have evolved arsenals search themes encompass reproduction, evo- of suppressive molecules in order to counteract lution and conservation of plants, tropical plant MAMP-induced defences. Bacterial extracellular biotechnology and pathology, plant-microbe in- polysaccharides (EPS) are required for full viru- teractions, defence and hormone signalling, and lence, and provide protection from desiccation algae as an alternative fuel. More detail of each and antimicrobials. It was revealed that chelation PI’s research can be found below, or by visiting of calcium ions by polyanionic EPS of diverse www.plantresearch-bath.org/. pathogens, prevents calcium influx in plants to the cytosol from the apoplast. Defence signalling The plant group is housed within the Biology and is suppressed in this way. Biochemistry department, which has recently been ranked second in the country by The Sun- Plant defences and sustainable control of tropical day Times University guide, reflecting the high diseases: The Cooper lab also undertakes ap- satisfaction of our students and the quality of plied research on diseases of some major tropi- both staff and outgoing students. The diversity cal crops including cassava, cacao and oil palm. of research groups within the department allows Methods of screening disease resistant lines to valuable collaborations with bioinformaticians, the major pathogens of oil palm, Fusarium ox- biochemists, protein structure specialists, etc. ysporum and Ganoderma, have been improved or developed. The lab’s method of eradicating We have a large number of plant growing fa- Fusarium from oil palm seed is in commercial cilities, including a dedicated GM house, glass- use. DNA probes for rapid and specific detection houses, walk-in chambers, and growth cabinets, of Fusarium for seed quarantine are being devel- and we offer undergraduate, masters and PhD oped. Ganoderma infection and epidemiology is courses for students interested in pursuing plant ongoing; genetic studies show the importance of sciences (www.bath.ac.uk/bio-sci/admissions/). basidiospores in its spread. The group is keen to support prospective inde- pendent research fellows and informal enquiries are very welcome. 19 GARNish Spotlight on the University of Bath

James Doughty suite of β 1,3 and β 1,4 glucanase enzymes. A [email protected] combination of molecular genetic and proteomic http://www.bath.ac.uk/bio-sci/contacts/ approaches are being deployed to dissect this academics/james_doughty/ crucial phase of reproductive development. Cell-cell communication during plant repro- duction; reproductive development Research in the Doughty group is centred on as- Paula X. Kover pects of plant reproductive biology, with a par- [email protected] ticular focus on understanding how cells commu- http://www.plantresearch-bath.org/dr- nicate with one another at various stages of this paula-kover/ exquisitely regulated process. In recent years Evolutionary genetics, complex trait evolu- much progress has been made in elucidating the tion, ecological adaptation molecular basis for recognition events that lead to the rejection of ‘self’ or closely related pollen The Kover lab is interested in the genetic basis by classic self-incompatibility (SI) systems, how- and evolution of complex traits such as flowering ever, comparatively little is known about the reg- time, seed size, germination rate, and response ulators of compatible interactions. to drought and temperature, etc. The aim of this research is to understand how genetics inter- Work in the lab is addressing this gap in our acts with an organism’s ecology to determine knowledge by examining the role of pollen-borne the evolution of traits under natural selection. To proteins that are involved in the earliest steps of reach this goal the lab has developed a number the pollen-stigma interaction. Compatible inter- of resources that allows improved mapping of actions must activate processes that initially per- quantitative traits in A.thaliana, which includes mit effective hydration of pollen and this is likely the densely genotyped set of MAGIC lines (Mul- to be established by protein interactions at highly tiparent Advanced Genetic InterCross); and re- focussed regions of the stigmatic plasma mem- sequencing the 19 parental accessions that were brane. Small cysteine-rich proteins (CRPs) are used to produce the MAGIC lines. The group of particular interest as not only are they impor- continues to develop more resources for these tant components of the pollen coat but they are lines to improve mapping efficiency and accura- firmly established as important regulators of vari- cy. They also use a direct approach to determine ous steps in the reproductive process. A range of the adaptive value of candidate genes, using ex- molecular genetic approaches are being utilised perimental evolution. This approach allows the to gain a full understanding of the role of pollen lab to investigate what genes underlie response CRPs in early pollination events and to identify to selection, and what are the pleiotropic conse- their stigmatic targets. quences of genetic changes. Finally, the Kover group is also interested in investigating gene by In collaboration with the Scott Lab at Bath, the environment interactions, as well the genetic ba- group aims at understanding how seed size is sis of plasticity, under both field and laboratory regulated in Arabidopsis. Early stages of seed settings. development involve endosperm proliferation without the formation of cell walls, followed by cellularisation of the endosperm later in develop- ment. It is now clear that the timing of this cellular- Rod J. Scott isation event is a crucial determinant of seed size [email protected] and work is focusing on factors that potentially interrupt cell-cell signalling which bring about this http://www.bath.ac.uk/bio-sci/contacts/ important developmental process. The group are academics/rod_scott/ also investigating the regulation and mechanism Seed development, plant reproduction, and of tetrad dissolution during pollen development. algae biotechnology This step, which separates the developing mi- crospores of the tetrad, involves that action of a Seeds are the most important agricultural prod- 20 GARNish Spotlight on the University of Bath

uct, accounting for at least 70% of the world’s maternal effects, epigenetic effects, indirect ge- food supply. With rising population and diminish- netic effects, and gene interactions. The lab in- ing availability of agricultural land, it is increas- tegrates theoretical, computation, and empirical ingly urgent to improve crop yields; increasing approaches to understand how these sources seed size is one route to this goal. A major inter- of variation structure the genotype-phenotype est in the lab is the mechanism of seed growth and influence evolutionary dynamics. They use regulation. The Scott group is investigating this several different model organisms to achieve from several angles by looking at the effect of their goals, including plant, animal, and micro- crossing A.thaliana plants of different ploidies on bial models. Plant based research has mainly fo- alterations to the cell cycle in endosperm, altera- cused on the genetic basis of interactions (e.g., tion of gene expression, and changes in pattern competition) between plants, using primarily QTL of imprinting. mapping and candidate gene approaches in Ara- The lab also collaborates with Drs James Dough- bidopsis thaliana. ty and Susan Crennell (University of Bath) to solve a long-standing issue in plant reproductive biology – the identity and regulation of the glu- canases responsible for releasing microspores Richard Hooley from the post-meiotic male tetrad. The callosic [email protected] ‘barrier’ around the tetrad separates the walls of http://www.bath.ac.uk/bio-sci/contacts/ adjacent microspores, allowing them to develop academics/richard_hooley/ individually. In order for pollen development to The molecular basis of signal transduction in proceed, the tetrad walls must be dissolved to plants release the microspores. The immediate aim of this project is to identify the genes encoding the S-acylation of eukaryotic proteins is the revers- enzymes responsible for degrading the tetrad ible attachment of palmitic or stearic acid to walls. cysteine residues, catalysed by protein S-acyl The lab is also interested in several aspects of transferases (PATs) that share an Asp-His-His- algal biotechnology including: isolating thermo- Cys (DHHC) motif. Previous evidence suggests tolerant species from the hot waters of the Ro- that in Arabidopsis S-acylation is involved in the man Baths; reducing product recovery costs by control of cell size, polarity and the growth of pol- weakening the algal cell wall via mutagenesis len tubes and root hairs. Using a combination and selection; combining wastewater cleaning of yeast genetics, biochemistry, cell biology and and algae biomass production to reduce input loss of function genetics, the roles of a member costs. These projects are in collaboration with Dr of the PAT family, AtPAT10, have been explored. Chris Chuck (Chem. Eng) and Dr Chris Bannis- In keeping with its role as a PAT, AtPAT10 auto- ter (Mech. Eng), both of the University of Bath. S-acylates, partially complements the yeast akr1 PAT mutant, and this requires Cys192 of the DHHC motif. In Arabidopsis AtPAT10 is localised in Golgi and tonoplast. Loss-of-function mutants Jason Wolf have a pleiotropic phenotype involving cell ex- [email protected] pansion and division, vascular patterning, and fertility that is rescued by wild-type AtPAT10 but www.evolutionarygenetics.org not by catalytically inactive AtPAT10C192A. This Genetic architecture, quantitative genetics, supports the hypothesis that AtPAT10 is function- ally independent of the other Arabidopsis PATs. evolutionary theory Our findings demonstrate a growing importance The Wolf lab focuses on the genetic architec- of protein S-acylation in plants, and reveal a Gol- ture of complex traits. The research emphasis gi and tonoplast located S-acylation mechanism is mainly on components of genetic variation that affects a range of events during growth and that tend to be ignored or under-appreciated in development in Arabidopsis. analyses of genetic architecture. These include Mathematics in the Plant Sciences Study Group VI

25-­28 March 2013 Nottingham

If you are a plant or crop scientist who would like a willing team of mathematicians to work on your research problem at this meeting, please contact Susie Lydon ([email protected]).

For more information about how study groups work and previous successful problems, visit www.cpib.ac.uk/events/mpssg/

CPIB training courses in 2013: 4-­6 September: Image Analysis for Biologists 9-­12 September: Mathematical Modelling for Biologists

Contact: [email protected] @cpib_news www.cpib.ac.uk/events-­activities/ 22 GARNish Spotlight on the University of Bristol

Spotlight on the University of Bristol Bailey, Gary Foster), ecology (Jane Memmott, Heather Whitney, Marion Yallop), and evolution (Simon Hiscock and Jon Bridle), all within a lively and highly collegiate environment. The theme of Evolution is at the heart of the mis- sion for the new Life Sciences building, and will Plant Science research and teaching in Bristol incorporate expertise from Chemistry (Steve are on a rapid upward trajectory. Two out of five Mann, investigating proto-life), Earth Sciences new academic appointments are plant scientists (palaeobiology, Mike Benton, Phil Donoghue, (Heather Whitney and Antony Dodd). In addition, Emily Rayfield), Computer Science (protein Bristol has a fundamental role in the BBSRC structure databases, Julian Gough) and Social wheat genome project, driven by Keith Edwards Medicine (human genome analysis, Ian Day), and Gary Barker. The University is committed to plus three new appointments in phylogenomics the future of plant science, becoming the first UK (Davide Pisani, Seirian Sumner, Jakob Vinther). University in nearly 50 years to create a new bo- Bristol aspires to be a world centre for evolution- tanic garden. The University incorporates Fens- ary biology and Omics technologies will be at the wood Farm, which houses additional plant growth heart of this. facilities and field trial facilities. Plant sciences in The final theme “Ecology and Environmental Bristol interconnects with the Food Security and Change” focusses on climate and environmen- Land Research Alliance (Bristol, Exeter, Roth- tal change (NERC strategic theme) and links amsted http://www.fslra.ac.uk/), including access strongly with the newly formed University of to North Wyke experimental farm platform in Bristol Cabot Institute (http://www.bristol.ac.uk/ Devon. Doctoral Training in the School includes cabot/), a hub of interdisciplinary research activ- World Class Bioscience and Food Security PhD ity to address how humanity might live sustain- studentships within the BBSRC-funded South ably in the face of environmental uncertainty. West Doctoral Training Partnership (http://www. bris.ac.uk/swdtp/). Overall, plant science in Bris- tol is on the up – literally too – we move in 2013 to the top floor of the new Life Sciences building! Andy Bailey The strength of Bristol’s research and teach- [email protected] ing lies in its breadth. The unifying theme is our http://www.bris.ac.uk/biology/research/ desire to understand biological complexity at all plant/pathology/ scales - from molecules to ecosystems. Research Fungal plant pathology and fungal biotech- at Bristol is in four interwoven themes: 1) Evolu- nology tion, 2) Animal Behaviour and Sensory Biology, 3) Plant and Agricultural Sciences, 4) Ecology Andy’s research interests are based around the and Environmental Change. “Animal Behaviour biology of fungi. Several different areas are re- and Sensory Biology” is the ‘brand’ that Bristol searched including; the biology of plant patho- is best known for, described as ‘world leading’ at genic fungi, fungal viruses, transformation and the last RAE, with two members of the University manipulation of basidiomycetes and fungal bio- Centre for Behavioural Biology, Alasdair Houston technology including natural product production and John MacNamara, recently elected FRS. by fungi. These areas often overlap, for instance in the case where a secondary metabolite is also The new grouping “Plant and Agricultural Sci- used as a virulence factor for establishing dis- ences” reflects growing strengths and the global ease. need for research in Food Security (a BBSRC strategic theme). Plant scientists at Bristol per- Andy also has interests in genome analysis and form a wide range of research from model organ- has been involved in the generation and anal- ism molecular, cell and systems biology (Antony ysis of genome data for species such as My- Dodd, Kerry Franklin, Claire Grierson, Alistair cosphaerella graminicola, responsible for Sep- Hetherington) to biotechnology, pathology (Andy toria tritici leaf blotch on wheat and Agaricus 23 GARNish Spotlight on the University of Bristol

bisporus, the common cultivated button mush- Jane Memmott’s, and uses field experiments and room. molecular and quantitative genetics to explore how species’ interactions evolve in response to Much of the research has its basis in the estab- climate change, and the effects of local adapta- lishment of effective genetic transformation sys- tion and genetic diversity on the success of plant tems for the fungus, to allow investigations into translocations. gene function and providing a means to manipu- late gene content or gene expression and these The evolution of pollination networks in response tools and techniques have been developed for a to climate change may be critical for population large number of different ascomycete and basidi- persistence, as well as in stabilising networks af- omycete species. fected by species loss. At the same time, varia- tion in species’ responses may create mismatch- es between the timing of flowering and insect emergence. In collaboration with the Avon Wild- Gary Barker life Trust, the group are testing the role of local [email protected] adaptation in shaping biotic interactions in the http://www.bristol.ac.uk/biology/people/ cowslip Primula veris, a plant of UK conservation gary-l-barker.html interest, as well as the potential for its interac- tions with its pollinators to evolve in the future. Bioinformatics for wheat genetics. Plant translocation and reintroduction may be Gary Barker is a bioinformatician, with a primary crucial for ecosystem health and species conser- interest in the development and application of vation with rapid climate change. Should seed wheat genetic markers. be sourced from nearby sites to preserve local Wheat is one of the world’s, and certainly the adaptation, or combined across several popula- UK’s, most important crops. We need to be able tions to maximise genetic diversity, providing the to grow more wheat on less land with lower in- local environment with the widest range of plant puts to meet population growth predictions, and characteristics to favour following translocation? this comes at a time when many fear that yields Policy on reintroductions often specifies that ma- are plateauing. The UK wheat pre-breeding pro- terial used should be from local sites, but this gram funded by BBSRC aims to introduce novel may be counter-productive. The group are col- genetic diversity into modern UK wheat germ- laborating with the Somerset Wildlife Trust, and plasm by generating novel synthetic wheat varie- are using molecular genetic techniques to test ties and by bringing in novel alleles from non-cul- whether introducing appropriately adapted popu- tivated wheat and wild relatives. At Bristol we are lations improves the success of reintroductions using state-of-the-art sequencing, bioinformatics of a UK BAP species, Sium latifolium (Greater and genotyping to generate dense genetic maps Water Parsnip). for wheat. Marker-assisted selection is then used to speed up the lengthy process of generating stable, commercially viable new varieties with novel useful phenotypes. See www.cerealsdb. Antony Dodd uk.net for more information. [email protected] http://www.bristol.ac.uk/biology/people/ person/antony-n-dodd/ Circadian biology Jon Bridle [email protected] Antony Dodd investigates how the circadian clock http://www.bristol.ac.uk/biology/people/ controls cell physiology and signal transduction, group/lab/915 in order to understand how circadian regulation optimizes plant performance. The circadian clock Ecological and population genetics produces a biological estimate of the time of day. Jon’s research group collaborates closely with Circadian regulation is crucial because circadian 24 GARNish Spotlight on the University of Bristol

timekeeping increases photosynthesis, produc- wheat genome, data that was placed in the pub- tivity and seed production, and regulates plant lic domain in August 2010. Following on from water use, so contributes to crop yield and eco- the sequencing success, Keith, via the BBSRC system productivity. The Dodd lab investigates funded wheat improvement strategic program, the following questions: has focused his efforts on converting the infor- mation to SNP-based markers for use by wheat 1. How does the circadian clock control photo- breeding companies, work that has resulted in synthesis? There are circadian rhythms of pho- the release of over 100,000 wheat SNPs to the tosynthesis, but it is not known how the circadian wheat community. Keith was awarded the 2011 clock regulates the photosynthetic apparatus Royal Agricultural Society of England’s research within chloroplasts. The group are investigating medal for his contribution to UK agriculture. the nature of the signalling pathways that couple the circadian clock with the photosynthetic ap- Recently Keith has expanded his research pro- paratus. gram to include a study of homoeologous and homologous recombination, to achieve this he 2. Circadian organization of the proteome, phos- is currently developing a number of deletion and phoproteome and membrane transport. Little transgenic lines for genes known to be involved is known of how the circadian clock organizes in recombination. It is because of the problems in the proteome in terms of protein abundance and growing and crossing wheat within the university post-translational modification. The Dodd lab are system that Keith is now a big fan of the wheat using proteomics strategies to investigate this variety “Apogee”. Apogee is a rapid cycling wheat question with a particular focus on membrane (9-10 weeks) making it ideal for undergraduate systems, which are a crucial focus in plants for studies. Keith received his first transgenic Apo- abiotic stress responses, photosynthesis, water gee wheat from Rothamsted in September and fluxes and signal transduction. They are also in- he is looking forward to letting his level III practi- vestigating the role of specific protein kinases in cal project students loose on the material over circadian oscillator function and the coupling of the coming academic year. the circadian clock with circadian-regulated cell physiology. 3. How is the circadian clock tailored to physi- Gary D. Foster ologically-relevant cell types? A small number of cell types in plants have a disproportionately [email protected] large impact on water use and stress tolerance. http://www.bristol.ac.uk/biology/re- This includes the stomatal guard cell and root en- search/plant/pathology/ dodermis. The Dodd group are investigating how Molecular plant pathology and biotechnology circadian regulation in these cell types optimizes plant performance because the environment is Gary’s research is focused on investigating a characterized by 24 h cycles of water availability. range of interconnecting themes that include plant virology, plant pathology, plant molecular biology, molecular mycology and biotechnology. The interdisciplinary approach to this research is Keith Edwards one of the strong selling points, along with a vi- [email protected] brant lab community and the strong supervisory team, which has been supported by a range of http://www.cerealsdb.uk.net/ funding sources continuously since 1992. This Wheat genomics and pre-breeding has included funding from the BBSRC, DEFRA, LESARS, Royal Society, the Wellcome Trust, Keith’s research covers the board areas of wheat DfID/ODA, Rothamsted International, and col- genetic and genomics; he was the PI on the BB- laborative funding with agricultural industries and SRC funded project to generate, in collaboration institutes, such CSL-York, HRI-Wellesbourne, with Liverpool and the John Innes Centre, a 5 RHS-Wisley, PBI-Unilever. Funding has also fold sequence coverage of the Chinese Spring come from international partnerships and collab- 25 GARNish Spotlight on the University of Bristol

orations that have created research links/inter- perature and have identified a number of genes changes and visitors to the research group. The which are regulated by phytochrome in a tem- molecular mycology and biotechnology areas perature-dependent manner. These include the have also covered projects on drug discovery CBF regulon of genes involved in cold acclima- and manipulation including a major collabora- tion and freezing tolerance. The group have also tion with GSK on antibiotic discovery and devel- established that the phytochrome-interacting opment. This work continues through a large factor PIF4 functions as a key regulator of plant team exploring the potential of basidiomycetes architectural responses to elevated temperature, to produce compounds of interest to industry and thereby operating as a central hub of light and medicine. temperature signal integration. They are cur- rently investigating the parallels between shade Current research themes within the lab cover avoidance and high temperature signalling and a range of topics in plant pathology, including the fitness costs/benefits of such plasticity. plant pathogen-stomatal interactions, changes in leaf surface upon pathogen attack which is also linked to how insect vectors perceive plants. This in addition to more direct and molecular studies Claire Grierson on specific viruses which at present include the [email protected] serious diseases of Pepino mosaic virus which is http://www.bristol.ac.uk/biology/people/ causing significant losses in tomato, as well as claire-s-grierson.html Cassava brown streak virus, a cassava virus that is affecting large parts of East Africa and threat- Root development ening a staple food crop for much of the region Claire Grierson’s research has three linked and which is now reached epidemic proportions. strands: Root hair development, Theoretical ap- Work also continues on a range of fungal patho- proaches to biology; and Interactions between gens, including basidiomycete pathogens such roots and soils. By dissecting root hair growth as those in Armillaria, which links nicely with the in Arabidopsis, Grierson, her team, and interna- drug discovery team within the group. tional collaborators identified numerous genes with important roles, showed how auxin flows sustain root hair growth, and revealed how dy- Kerry Franklin namic interactions between molecules could establish polar growth in root hair cells. Funda- [email protected] mental theoretical collaborations include charac- http://www.bristol.ac.uk/biology/people/ terising the surprisingly wide range of behaviours keara-a-franklin.html of even very simple biochemical circuits, and Light and temperature-regulation of plant de- tackling how network structure might contribute velopment to function. Grierson is developing new research to discover what plants contribute to root-soil co- Light and temperature are two of the most im- hesion, addressing questions such as “why are portant environmental stimuli regulating plant plants so hard to uproot?”, “how can roots help development. Plants perceive light using spe- to prevent soil erosion?”, and “how might roots cialised information transducing photoreceptors be affected by climate change?”. She continues which include the red and far-red light-absorbing to use Arabidopsis for most of her experiments phytochrome family. The Franklin lab focuses on because of its unsurpassed power for empirical investigating the interactions between light and plant genetic research, but has ongoing research temperature signalling in Arabidopsis. A primary with Keith Edwards and others on root hair de- research interest of the group is the interaction velopment in cereals. between light quality and temperature signalling pathways in the regulation of plant architecture. We have shown that some shade avoidance responses of the model species, Arabidopsis thaliana, are modulated by ambient growth tem- 26 GARNish Spotlight on the University of Bristol

Alistair Hetherington Simon Hiscock [email protected] [email protected] http://www.bristol.ac.uk/biology/people/ http://www.bristol.ac.uk/biology/people/ alistair-m-hetherington/.html person/simon-j-hiscock Signal transduction pathways controlling sto- Plant ecological and evolutionary genetics matal function and development Research in Simon’s lab seeks to understand The research in Alistair Hetherington’s group fundamental processes in plant evolution, such centres on understanding, at the cellular level, as adaptation and speciation, using genetics and how plants respond to a changing environment. genomics to study the interacting forces of mat- Hetherington is interested in identifying the com- ing system, interspecific hybridization, and poly- ponents present in the intracellular signalling ploidy. Much of this work has focused on three pathways responsible for coupling extracellular taxonomically ‘difficult’ groups: Senecio (Aster- stimuli to their characteristic responses. To inves- aceae), Sorbus (Rosaceae), and Orobanche tigate this, his group focus on stomata, the pores (Orobancaceae). Current research projects in- found on the surfaces of leaves. Environmental clude: (i) the genomic basis of adaptation and signals regulate both stomatal development and speciation in the genus Senecio (Asteraceae), the aperture of the stomatal pore and current in- (ii) the molecular genetic basis of pollen-stigma terests lie in the regulation of stomatal aperture recognition and self-incompatibility in Senecio, and development by carbon dioxide, ABA and (iii) the genetic basis of mating system (self-in- changes in atmospheric relative humidity. At the compatibility) variation and evolution in Senecio, cellular level the group maintain a strong interest (iv) genetic divergence, mating systems, and on- in calcium-based intracellular signalling with on- going evolution in the genus Sorbus (Rosaceae), going research into long chain phosphorylated (v) local adaptation and genetic divergence in sphingoid base signalling and the mechanisms holoparasitic broomrapes (Orobanche). Funding responsible for encoding information in, and de- for this work has come from NERC, BBSRC, The coding information from, stimulus-induced cal- Leverhulme Trust, Royal Society, The Linnean cium elevations (calcium signatures). More re- Society (COSyst), and BSBI. Collaborators in- cently, through work on stomatal evolution, there clude: Richard Abbott (University of St Andrews), is an increasing interest in the evolution of sig- Dmitry Filatov and Stephen Harris (University of nalling pathways. Although most of the work is in Oxford), Mark Carine (NHM), Tim Rich (National Arabidopsis, recently research has involved the Museum of Wales). model lower plant Selaginella and the cereals barley and wheat. The cereal work, which is car- ried out with colleagues at Bristol and elsewhere, is in the context of Food Security and is focussed Professor Jane Memmott on investigating the potential of modifying sto- [email protected] matal behaviour and development with the aim http://www.bristol.ac.uk/biology/re- of improving water use efficiency. This later area search/ecological/community/ relates to Living With Environment Change re- search and in this context Alistair Hetherington’s Community ecology group are also interested, together with other Jane’s research interests in ecology include pol- colleagues in Geography at Bristol, in using crop lination ecology, invasion ecology, agro-ecology, albedo as a possible bio-geoengineering strat- biological control, urban ecology and restoration egy to combat global warming. ecology. A theme that runs through many of her projects is the use of ecological networks (food webs or pollination networks) as a tool to answer a variety of environmental questions. For exam- ple does restoration ecology restore ecological function, are ecosystem services affected by farming approach and how do aliens integrate 27 GARNish Spotlight on the University of Bristol

into ecological networks? assessing how many times they have adapted to extreme cold habitats during the Earth’s history, Jane works as both a pure and an applied ecolo- and 3) the use of molecular phylogenetics to un- gist and is particularly keen on working at the in- derstand the evolutionary processes that some terface between the two disciplines. A wide varie- plants groups have used (e.g. new morphologi- ty of techniques are used by her research group, cal traits) to adapt and colonise extreme high el- from field observation to field experiment, from evation ecosystems in Andean mountains. theory to molecular approaches. Plants form the bottom layer of all her food webs and one of the areas her group is particularly interested in is whether positive and negative effects can cas- Heather Whitney cade upwards from these plants, rippling through [email protected] the associated ecological network. For example, http://www.bristol.ac.uk/biology/people/ work recently published in Science, demonstrat- heather-m-whitney.html ed that some farmland plant species were dis- proportionately well-linked to many other species Interactions at the plant surface and these were the ones to target when conserv- Heather’s research focuses on how the structure ing biodiversity in agroecosystems. of the plant surface can influence both biotic and abiotic interactions. At the moment this includes a range of projects from how the plant surface in- Patricia Sanchez-Baracaldo teracts with water and temperature to how bees grip onto the petal surface. One major project [email protected] is an investigation how the plant surface inter- http://www.bristol.ac.uk/biology/people/ acts with light, in particular, how structural colour patricia-sanchez-baracaldo.html and iridescence is produced by the plant surface and how this be of benefit to the plant either The evolution of cyanobacteria and biogeo- through the light transmitted (for photosynthe- chemical cycles sis), or through the light reflected (photoprotec- Cyanobacteria have played a fundamental role tion, temperature control or, in flowers, attraction in the Earth’s history, enabling the rise of atmos- of pollinators). This is an interdisciplinary project pheric oxygen. Patricia’s work on the evolution looking at every aspect of iridescence from its of cyanobacteria uses phylogenomics, molecu- structure, development and occurrence to the lar clock analyses and ancestral character state impact it has on plant growth and interactions reconstruction. Her research has revealed that with other organisms such as insects. Heather cyanobacteria first evolved in freshwater envi- therefore uses a range of techniques to investi- ronments (2.7 Ga = billion years ago) and later gate these interactions including plant molecular they started colonising marine environments at biology, optical analysis, biomimetics and animal around the Great Oxygenation Event (2.3 Ga). behavioural assays. The origination and diversification of cyanobacte- ria had a profound impact on global biogeochem- ical cycling and the climate of the early Earth. Marian Yallop Her current research focuses on understanding how the colonisation of marine environments by [email protected] different groups of cyanobacteria has had an im- http://www.bristol.ac.uk/biology/people/ pact on biogeochemical cycles such as nitrogen, marian-l-yallop.html oxygen and carbon. Patricia’s interdisciplinary Ecosystem change approach combines evolutionary biology and an Earth system modelling. Other areas of research Marian’s work focuses on various aspects of the in her lab include: 1) the evolution of nitrogen structure and function of freshwater ecosystems fixation, 2) the generation of new genomic data in changing environments. One research area to study the evolution of glacial cyanobacteria by uses benthic diatoms as indicators of ecological 28 GARNish Spotlight on the University of Bristol

status in both rivers and lakes. The Yallop group work on a number of aspects of lake functioning with a key interest in lake state switching, growth of periphyton, phytoplankton and submerged macrophytes. In compliance with recent legisla- tion (Water Framework Directive) they have been involved in the development of predictive tools, using benthic diatoms, to assess the ecological status or rivers and lakes in the UK. These tools primarily detect eutrophication but ongoing work examines the impact from other agrochemical pressures. In addition to work in temperate envi- ronments the group is involved in an interdiscipli- nary collaboration to investigate how algal com- munities in extreme conditions, such as those growing within glaciers, may function and evolve in response to climate change. Critically, these algae may produce screening pigments to pro- tect them from UV or high irradiance, and these pigments in turn may potentially reduce albedo of snow and ice and actually promote surface melt, thereby promoting their growth in addition to melting the ice sheet. 29 GARNish Item