functional genomics at the arabidopsis meeting

Meeting Review

Functional genomics at the Arabidopsismeeting

The 11th International Conference on Arabidopsis Research, University of Wisconsin,Madison, USA. June 2000

Karin van de Sande* and Ottoline LeyserDepartment of Biology, University of York, Heslington, York YO10 5DD, UK

*Correspondence to:Karin van de Sande,Department of Biology,University of York, Heslington,York YO10 5DD, UK.E-mail: [email protected]

Keywords: Arabidopsis; meeting overview; functional genomics; microarray; expression

pro®ling

The 11th International Conference on ArabidopsisResearch (June 24±28) took place at the Universityof Wisconsin in Madison. A wide range of topicswas covered in 18 sessions, ranging from `genomics'to `¯oral' induction, and `patterning and organo-genesis'. In the evenings, several very populargenomics workshops took place. Chuck Gasser(University of California) led the workshop, `Dis-cussion of the 2010 Project', and workshops anddrop-in sessions were organized by TAIR (TheArabidopsis Information Resource) and AFGC(Arabidopsis Functional Genomics Consortium).Invariably, even after rescheduling to a largerroom, the rooms were crowded with many peoplestanding or sitting on the ¯oor.

Starting with the Keynote Address, RichardJefferson spoke on the global impact of plantbiology. He stimulated people to `harness thecreative force in Arabidopsis biology for the publicgood' and passionately pleaded for a reduction ofrestrictions to the application of biotechnology inagriculture. Cambia, Jefferson's Australia-based bio-tech company, is developing new methods to usebiotechnology in plant breeding. He has started atransgenomics initiative using expression pro®lingfor genetic diversity analysis of uncharacterizedgermplasm and fast building of genetic maps.Using transcriptional activator facilitated enhancertrapping (TAFET), targeted evolution of novel

plant traits is addressed. More than 4000 TAFETrice lines have been developed thus far.

An overview of the progress on various genomegrants was given in the ®rst session, chaired by JeffDangl (University of North Carolina). Shortreports on NSF (National Science Foundation)grants gave an update on different projects provid-ing tools for the Arabidopsis community.

Judith Bender (Johns Hopkins University)described a project on the functional genomics ofchromatin, which is now mid-way through the ®rstyear. Database mining and reverse genetics, withemphasis on gene silencing, will be used for maizeand Arabidopsis. At http://ag.arizona.edu/chromatin/

chromatin.html information can be found on tar-geted chromatin genes, the dsRNA vector systemused and on chromatin mutant strains.

Andrew Brent (University of Wisconsin) pre-sented the use of functional and comparativegenomics in plant pathogen interactions. Roughly1% of Arabidopsis genes encode NBS±LRR (nucleo-tide binding site±leucine-rich repeat) proteins, acombination that to date has only been found inplant disease resistance genes (R genes). To resolvethe complex signal transduction involved, expres-sion pro®ling is being used, using the Affymetrixchip. In this way it is checked, for instance, whatgenes are induced by the action of different R geneproducts or by pathogens or their proteins. This

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Copyright # 2000 John Wiley & Sons, Ltd.

approach will be complemented by overexpressionstudies.

Ray Bressan (Purdue University) talked aboutthe Stress Functional Genomics Consortium (Uni-versity of Arizona, Oklahoma State University,Purdue University). 25 000 ESTs of salt-inducedgenes are generated in Arabidopsis, 40% of whichwere not yet in the database. An 18 000 spotmicroarray is being made using 3000 ESTs fromsodium chloride-treated material and 15 000 ESTsmade available by Tom Newman (MSU±DOEPlant Research Laboratory, Michigan State Uni-versity). T-DNA mutants are being made usinginsertion vectors and activation tagging vectors, andseeds will be pooled for reverse genetics. Thesemutants are being screened for different stressresponses and thus far, among others, two salt-sensitive and ®ve salt-resistant mutants have beenfound. Ultimately all the lines will go to the stockcentre, together with DNA pools.

Pam Green (Michigan State University) reportedon AFGC, which has two services, microarray andT-DNA knockout. The project consists of technol-ogy development, but also carries out research. Theknockout service opened in October 1999 for USusers and in January 2000 for international users.The microarray service produces slides with 11 000clones, of which an estimated 8500 are uniqueESTs. The second cycle of proposals has just beenaccepted and data from the ®rst experiments areavailable at the AFCG website.

John Quackenbush presented TIGR's wholechromosome gene expression analysis in Arabidop-sis, using DNA microarray. TIGR ®nished sequen-cing chromosome 2 and is now working onvalidation of gene predictions. The 3k ends of thepredicted genes of chromosome 2 were ampli®edwith a very impressive success rate and used for themicroarray. In parallel a clone-based array strategyis carried out. Information on optimalization of themicroarray methods used will soon be available onthe TIGR website and the software that wasdeveloped is already available. From chromosome2 only 25% of the genes were represented in theESTs thus far.

Sakis Theologis (Plant Gene Expression Center,PGEC) represented the SSP consortium (StanfordUniversity, Salk Institute and PGEC) that is work-ing together with Affymetrix on a chip containingall full-length Arabidopsis genes. This will allow the®nding of new, expressed genes that are not among

the ESTs, the experimental veri®cation of annota-tion, and the use of the chip in expression studies.

John Walker (University of Missouri) discussedfunctional genomics of kinases, with extensivebioinformatics and insertion mutagenesis; informa-tion available on http://plantsp.sdsc.edu.

Nan Eckardt (Pennsylvania State University)discussed the use of PCR suppression subtractivehybridization libraries in the collection of stresscDNAs in different plant defence responses.Specialized cDNA microarrays, the stress chips,were prepared from these clones and from ESTsfrom several known stress-induced genes, andhybridized with RNA from plants harvested atdifferent times after various pathogen or stresstreatments. It was found that `simple and similarpatterns are observed in widely disparate systems'.Therefore, complex gene systems exhibit a simplecontinuous response to perturbation. There were afew posters from the same project, for instance onefrom Mali Mahalingam from Nina Fedoroff's lab,working on biotropic fungal pathogens such asPeronospora parasitica. http://sg102.biotec.psu.edu

gives more information on the project.In several other presentations and posters, the use

of microarrays was discussed. Steve Whitham(NADI) used the Affymetrix gene chip for theidenti®cation of genes induced by virus infection,®nding several genes involved in biotic and abioticstress responses, encoding metabolic proteins orheat shock proteins, kinases and receptor kinasesand several with unknown function. Their project ismoving on to targeting several of the found geneswith reverse genetics, to determine their role ininfection.

Doug Boyes (Paradigm Genetics) introduced ahigh-throughput functional genomics project com-bining detailed phenotype analysis with metabolitepro®ling and microarray analysis. Ultimately,growth stage-speci®c links will be made betweenthese data.

The multinational coordinated Arabidopsis pro-ject started as a follow-up to the Arabidopsisgenome sequencing efforts. It wants to give direc-tion to future Arabidopsis research and to stimulateand make full use of new developments in plantgenomics. The workshop on the multinational co-ordinated Arabidopsis 2010 project was a follow-upof two workshops on this subject that took placeearlier this year, for which reports can be found atthe TAIR website (http://www.arabidopsis.org).

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Copyright # 2000 John Wiley & Sons, Ltd. Yeast 2000; 17: 235±237.

Detlef Weigel presented an overview of the 10-yeargoals to be reached, and asked for input from thecommunity. With a ®nal aim of knowing everymolecule at any time in every cell, a virtual plantcan be created from which can be predicted whathappens when speci®c changes are introduced. The2010 project, which is even more ambitious than thegenome-sequencing project, is divided into short-(1±3 years), mid- (3±6 years) and long-term (6±10years) aims. Some of the goals for the short termare knockout mutants and full-length cDNAs of allgenes and subcellular localization for all proteins.For the mid-term, global metabolite pictures,expression patterns for all genes and developmentof methods for directed genetics are envisaged.Some long-term goals are construction of plantarti®cial chromosomes, knowing cis regulatorysequences for all genes and biochemical functionsfor all proteins. A large proportion of theseresources will be generated in centres that developthe technology and make it available for everybody.

Different European initiatives then were pre-sented, showing the worldwide importance offunctional genomics. Thomas Altmann (MPI-Golm) presented Genome Analysis in BiologicalSystem Plant (GABI). Initially funded for 3±4years, with research in Arabidopsis, barley, rape-seed, maize, rye, poplar and sugar beet, GABI isfunded partly governmentally, partly industrially.Apart from several resource centres, many researchgroups are part of the project. Proteomics, micro-arrays, protein arrays, yeast two-hybrid, an Arabi-dopsis knockout facility and bioinformatics willform part of the resources. Kiyotaka Okadaintroduced the Japanese functional genomics pro-jects. The Kazusa DNA research Institute, RikenGenomic Science Centre and the Riken PlantResearch Centre will be involved in microarrays,production of tDNA and transposon-tagged linesand collection and construction of mutants. LizDennis represented the Australian approach,explaining that several individual groups areinvolved in small projects, but that funding from

the government for national projects was lacking.CSIRO is involved in microarrays and developmentof new systems for gene silencing. Pierre Hilsonintroduced Genoplante. A 5 year French pro-gramme, it consists of different companies andpublic institutions. Genoplante will work on Arabi-dopsis and different crop plants, for instancedeveloping functional genomics on the modelgenomes rice and Arabidopsis, and analysing syn-teny between major crops and model genomes.Pierre stressed the importance of internationalstandards for data collection and access. Sean Mayintroduced the UK functional genomics project,called GARNet. GARNet, the Genomic Arabidop-sis Resource Network, will be funded for 3 years bythe BBSRC (Biology and Biotechnological SciencesResearch Council) and is aimed purely at creatingservices and resources. The GARNet projectconsists of the sequencing of transposon insertionsites, creating mutant lines with multiple transposoninsertions, screening of large insert cosmid libraries,proteomics, metabolomics and transcriptomics(macro- and microarray). Information onGARNet, and a meeting organized for potentialusers of the different services, can be found at http://

garnet.Arabidopsis.org.uk.The crowded AFGC workshops ®rst introduced

the AFGC microarray services, explaining theprocedures followed when one applies for service,quality controls and how to use the database ofmicroarray results that is now available. In thesecond workshop, several people presented dataobtained using microarrays, including the Stressmicroarray chip as used by Nina Fedorofs' lab,which involves clones from Monsanto, AFGC'sown `biological conditions' experiments with dataon their circadian rhythm experiments, the NADIprogramme involving Novartis, and the Affymetrixgene chip, which is available now. These presenta-tions show that the use of tools of functionalgenomics in Arabidopsis is increasing at a rapidpace. Undoubtedly, next year even more veryinteresting results will be available.

Functional genomics of Arabidopsis 237

Copyright # 2000 John Wiley & Sons, Ltd. Yeast 2000; 17: 235±237.

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