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The Multinational Arabidopsis Thaliana Functional Genomics Project

The Multinational Arabidopsis Thaliana Functional Genomics Project

The Multinational Coordinated thaliana Functional Project

Natural Variation

The Multinational Arabidopsis Steering Committee June 2006

MASC 2006 Cover R1.indd 1 6/8/2006 5:58:59 PM The Multinational Coordinated Functional Genomics Project Annual Report 2006

Philip Benfey [email protected] Chair

Ian Small [email protected] Co-chair

Thomas Altmann [email protected] David Bouchez [email protected] Jorge Casal [email protected] Bill Crosby [email protected] Ian Furner [email protected] Mary Lou Guerinot [email protected] Pierre Hilson [email protected] Heribert Hirt [email protected] Gerd Jürgens [email protected] Jaakko Kangasjärvi [email protected] Keith Lindsey [email protected] Sean May [email protected] Andrew Millar [email protected] Peter McCourt mccourt@.utoronto.ca Barry Pogson [email protected] Ben Scheres [email protected] Kazuo Shinozaki [email protected] Willem Stiekema [email protected] Paola Vittorioso [email protected] Yang Weicai wcyang@.ac.cn

Joanna Friesner [email protected] Coordinator and Executive Secretary

The Multinational Arabidopsis Steering Committee – June 2006

Cover: A number of diverse Arabidopsis thaliana accessions overlay a map of the world demonstrating the wide genetic variation that exists in this refer- ence . A recent analysis of twenty natural accessions resulted in the identification of over 500,000 unique single-nucleotide polymorphisms (SNPs) making Arabidopsis the organism with the highest SNP density relative to size. Studies of natural variation and comparative genomics, current areas of focus for the MASC, will be enabled by the availability of these data. Cover image concept: Philip Benfey, Duke University. Cover image design: , Max Planck Institute.



Table of Contents

Foreword to the Report...... 5

Executive Summary...... 6

Progress and Activities of the Multinational Arabidopsis Steering Committee (MASC)...... 8 Highlights of the Past Year Measuring Function Knowledge

Reports of the MASC Subcommittees...... 13 cDNA and Clone-based Functional Proteomics (ORFeomics) Natural Variation and Comparative Genomics Phenomics Proteomics

Analysis and Recommendations...... 19 Current Status of the Program Recommendations

The International Arabidopsis Functional Genomics Community...... 23 Argentina Australia and New Zealand Austria Belgium Canada China Germany Italy Japan The Netherlands Nordic Arabidopsis Network United Kingdom United States

Members of the Multinational Arabidopsis Steering Committee...... 50

Members of the MASC Subcommittees...... 51  Foreword to the Report

This is the 2005/2006 annual report of the Multinational Establishing and maintaining world-wide collaboration is Arabidopsis Steering Committee (MASC) on the status of the critical to the success of the Arabidopsis Functional Genomics Multinational Coordinated Arabidopsis thaliana Functional Project. The nature and volume of the proposed work necessi- Genomics Project. This 10-year program, initiated in 2001 tates that global resources be coordinated to attain a maximum following publication of the complete Arabidopsis thaliana ge- level of synergy as well as to avoid duplication of effort. Only nome sequence, was described fully in the 2002 MASC report. sustained and earnest collaborations will enable the Arabidopsis The primary project goal is to determine the function of every community to achieve its ambitious goals. The Multinational Arabidopsis gene and thus obtain a detailed and comprehensive Arabidopsis Steering Committee, supported by a full-time staff understanding of a . The value of this tractable member, plays a key role in supporting this international coor- plant system is immediately apparent and the intent is that the dination by collecting and disseminating information from the knowledge gained on this experimental will various initiatives and projects on technology development and serve as the central reference and conceptual framework for all functional analyses and by giving specific recommendations for of plant . further directions. The availability of the complete genome sequence was an This report highlights the progress made over the last year invaluable step towards the goal of understanding the function by the international Arabidopsis functional genomics communi- of every Arabidopsis gene. Using this knowledge, researchers ty. It also demonstrates the continued high level of cooperation around the world were newly equipped to investigate numer- that exists throughout the global community and the impor- ous facets of Arabidopsis biology. However, as the considerable tance of the support by funding agencies in producing impor- scale of the proposed project became clear, the necessity for tant and exciting results in plant biology. The continuing rapid newly developed high-throughput technologies, novel experi- progress in Arabidopsis functional genomics emphasizes the mental tools and comprehensive collections of plant resources central role that work on this reference plant has for further- as well as powerful procedures for data analysis, storage and ing our understanding of all . display, became apparent. In addition, it was realized that the complexity of even such a “simple” flowering plant as Arabi- The Multinational Arabidopsis Steering Committee dopsis requires continuous evaluation of the goals and needs of June 2006 the research community in order to adeptly respond to progress and bottlenecks.

 Executive Summary

The publication of the Arabidopsis thaliana genome just branches5. Another developmental puzzle involves the timing over five years ago marked the release of the first complete plant of plant flowering which has been shown to be under the influ- sequence. As the third multicellular organism to have its en- ence of a mysterious graft-transmissible substance known as tire genome sequenced, following C. elegans and D. melanogas- "." Two studies, one in Arabidopsis, the other in tomato, ter, Arabidopsis thaliana not only is the most important model revealed the long-sought identity of florigen as the - system for plant biology but is also an invaluable resource for ING TIME (FT) gene. How the signal is transmitted is still the study of other multicellular organisms. Increasingly com- controversial - in Arabidopsis the claim is that the FT RNA prehensive and sophisticated knowledge of Arabidopsis biology moves, while in tomato, it seems that only the moves6,7. allows researchers from both inside and outside the plant com- Finally, a report that over-expressing a yeast chromatin-remod- munity to leverage Arabidopsis resources and data for compara- eling protein in Arabidopsis dramatically increased the rate of tive genomics and complex systems modeling. Following the may point the way for precisely reshaping the success of the international collaborative genome of plants to enhance specific traits8. project the Arabidopsis community continues to strengthen The specific aims of the multinational Arabidopsis thaliana and grow; according to The Arabidopsis Information Resource functional genomics project comprise short-term, mid-term, (TAIR) there are currently more than 15,000 Arabidopsis re- and long-term goals. Many of the short-term goals have been searchers in nearly 6,000 laboratories worldwide. While much achieved and mid-term goals initiated including: has been accomplished it is clear that there is even more that can • Improved genome annotation through the use of ex- and should be done. It is only through continued widespread pressed sequences and expert knowledge and curation. research funding and international collaboration, particularly • Generation of comprehensive sets of sequence-indexed through timely sharing of data, stocks, and other resources, that mutants that are listed in an integrated database and we will fully realize the utility of Arabidopsis thaliana as a refer- available as stocks. This highly-utilized resource ef- ence plant and model organism. ficiently allows researchers to ascertain knowledge of gene Arabidopsis continues to play a dominant role in plant sci- function. ence research. In the past year alone a number of major break- • The production of genome-wide sets of gene-specific throughs were reported. While it has been known for many probes for expression analysis and the establishment of years that plant hormones are key regulators of a variety of pro- reference . cesses with high agronomic importance, including growth rate • Full-length cDNA sequence information has been deter- and flowering time, none of the hormone receptors had previ- mined for much of the genome and many cDNAs are sys- ously been identified. Starting with , two groups identified tematically being cloned into expression vectors that will the in Arabidopsis as a protein involved in targeting enable a variety of functional genomics and proteomics other for degradation1,2. Next, a receptor studies. was identified in rice, and its identity confirmed through its • Development of standardized vocabularies including interactions with the DELLA proteins, first identified in Ara- (GO) and , Attribute, and bidopsis as transducers of gibberellin signaling3. Most recently, a Trait Ontology (PATO), and the Plant Ontology Con- receptor for was identified as a gene in Arabidopsis sortium for plant structure, growth and developmental known to be directly involved in controlling flowering time4. stages. Hormones also regulate the number of branches on a shoot. • The development of numerous combinations of Recom- While it was known that auxin is partially responsible, a new binant Inbred Lines (RILs) to enable analysis of natural family of regulators known as MAX was shown this year variation. to control the flow of auxin in the shoot and thus the number of

 • The identification of species for survey genomic sequenc- The MASC’s (Multinational Arabidopsis Steering ing to enable studies of comparative genomics and natural Committee) short-term plan for the next year includes variation. • Ensure the successful establishment of recently formed • The establishment of metabolic profiling facilities for MASC subcommittees including Metabolomics, Natural global metabolite analysis. Variation and Comparative Genomics, Phenomics, and • Facilitation of international collaboration through the Proteomics. appointment of a full-time MASC coordinator to foster • Update and improve the Project’s webpages at TAIR. information flow and monitor progress of the program. • Work toward completion of genetic resources projects This past year’s progress included the following including collections of homozygous insertion mutants (SALK) and RNAi clones (AGRIKOLA). achievements • • Develop resources for studying protein interactions and The first Arabidopsis genome release by TAIR (The Ara- localization, including complete cloning of full-length bidopsis Information Resource, November, 2005): version cDNAs into expression vectors. 6.0 includes 26,751 protein coding genes, 3818 pseudo- • Expand data integration and interoperability efforts for genes, and 838 non-coding RNAs (31,407 genes in the optimal use of data resources. entire genome). • • Facilitate and encourage submission of data and stocks Identification of insertion mutations for 28,607 of 31,128 into public repositories. (92%) nuclear-encoded genes with approximately 75% of • Implement a Systems Biology working group. the insertions located in . • 2,729 homozygous mutant insertion lines (representing Past success of the Multinational Coordinated Arabidopsis 2,227 genes) have been identified from the newly-initi- thaliana Functional Genomics Project can be attributed to the ated project (Ecker/Salk Institute) to identify two homo- strength of both international collaborations and funding sup- zygous mutants for 25,000 Arabidopsis genes. port within the Arabidopsis community. Future successes will • Availability of nearly 22,000 RNAi clones targeting require that we continue to share information and resources so 19,202 genes. Completion of the AGRIKOLA project that our efforts are synergistic, not redundant, and that we ef- (expected mid-2006) will involve more than 25,000 fectively convey to funding agencies, decision-makers, and the clones targeting over 20,000 genes. public, our progress and the importance and relevance to society • Over 500,000 unique single-nucleotide polymorphisms of studying and understanding this reference plant. The MASC (SNPs) were identified for 20 natural accessions making will continue to monitor the Project’s progress and coordinate Arabidopsis the organism with the highest density of high activities of the global Arabidopsis research community. quality SNPs per kilobase of genomic sequence. (D. Wei- gel, Max Planck Institute). References • Fully-supported release of the Affymetrix Tiling 1.0 R 1. Dharmasiri N, Dharmasiri S, Estelle M, The F-box protein TIR1 full genome (April, 2006). • is an auxin receptor. Nature, 435 (441-445), May, 2005. Isolation of full-length cDNAs for nearly 75% of the 2. Kepinski S, Leyser O, The F-box protein TIR1 is an auxin recep- nuclear protein-coding genes (approximately 19,500 of tor. Nature, 435 (446-451), May, 2005. 26,541); clones of 14,216 are currently being distributed 3. Ueguchi-Tanaka M, Ashikari M, Nakajima M, Itoh H, Katoh E, Kobayashi M, Chow T, Hsing Y, Kitano H, Yamaguchi I, Mat- and an additional 9,058 are targeted for cloning. • suoka M, GIBBERELLIN INSENSITIVE DWARF1 encodes a An AT2010 Midcourse evaluation workshop to evaluate soluble receptor for gibberellin. Nature, 437 (693-698), September, the progress made toward the specific goals of the pro- 2005. gram and to recommend directions for the next five years 4. Razem F, El-Kereamy A, Abrahms S, Hill R, The RNA-binding protein FCA is an abscisic acid receptor. Nature, 439 (290-294), (Virginia, U.S., August, 2005). January, 2006. • A workshop on the needs and goals for a plant cyberin- 5. Bennett T, Sieberer T, Willett B, Booker J, Luschnig C, Leyser, O. frastructure for facilitating the synthesis of new biological The Arabidopsis MAX pathway controls shoot branching by regu- insights from all available functional genomics data (Vir- lating auxin transport. Current Biology, 16 (553-563), March, 2006. 6. Huang T, Bohlenius H, Eriksson S, Parcy F, Nilsson O. The ginia, U.S., October, 2005). mRNA of the Arabidopsis gene FT moves from to shoot apex • BioMoby pilot project workshops on web services for and induces flowering. Science, 309 (1694-1696), September, 2005. data integration were held in Germany (March, 2006) 7. Lifschitz E, Eviatar T, Shalit R, Goldshmidt A, Amsellem Z, Al- and the U.S. (April, 2006). Demonstrations will be made varez J, Eshed Y. The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse envi- to the wider Arabidopsis community at the Annual Inter- ronmental stimuli. Proc. Natl. Acad. Sci., 103 (6398-63403), April, national Conference on Arabidopsis Research (Madison, 2006. WI, June/July, 2006). 8. Shaked H, Melamed-Bessude C, Levy A. High-frequency gene • targeting in Arabidopsis plants expressing the yeast RAD54 gene. Establishment of a Metabolomics working group. Proc. Natl. Acad. Sci., 102 (12265-12269), August, 2005. • Establishment of a Phenomics working group.

 Progress and Activities of the Multinational Arabidopsis Steering Committee (MASC)

MASC Activities in 2005/2006 in place for demonstrations at the annual Arabidopsis meeting in Madison in June, 2006. The Bioinformatics Subcommittee In 2005/2006, Philip Benfey (Duke University) and Ian section of this report contains a more detailed description of Small (University of Western Australia) continued as MASC the program. chair and co-chair, respectively. Dr. Small will become the new A full-time MASC coordinator position was established MASC chair when Dr. Benfey steps down following the annual in 2002, initially funded for two years by the NSF (U.S.), then International Conference on Arabidopsis Research (ICAR) in for one year by the DFG (Germany), followed by another two- June, 2006. At this time, Xing-Wang Deng (Yale University) year grant from the NSF with current funding expiring at the will become the new MASC co-chair. th end of 2006. The MASC coordinator functions to provide help MASC subcommittees, proposed at the 13 ICAR held in and coordination to the MASC, the North American Arabi- Seville, in 2002, were established to help track progress dopsis Steering Committee (NAASC), and the larger Arabidop- towards the goals outlined in the 2002 Multinational Coordi- sis functional genomics research community. Specific duties nated Arabidopsis thaliana Functional Genomics Project. As the include (1) serving as the executive secretary of the MASC, field progresses, changes in needs and priorities require reas- (2) organizing and raising funds for the annual ICAR, (3) sessment of each MASC subcommittee. A major revision of producing and editing the annual MASC progress report and the MASC subcommittee structure was initiated at the annual th other MASC documents, (4) serving as a liaison between the MASC meeting held in conjunction with the 16 ICAR in MASC, the international research community, funding agen- Madison, Wisconsin (U.S.) June, 2005. Two new subcommit- cies, and databases and stock centers, and (5) maintaining and tees were proposed, two were dissolved, and the need for two updating the functional genomics MASC website together initiated at the 2004 annual meeting was re-emphasized. Newly with TAIR (Stanford, California) to inform the global research proposed groups include the Phenome subcommittee and the community about various opportunities, collaborations, large- Natural Variation and Comparative Genomics subcommittee. scale activities and research progress. Isabell Witt served from The Multiparallel Tools and Forward/Reverse Genetic Stocks 2004 to November, 2005 before returning to Germany to take subcommittees were dissolved, although some responsibilities up a position as Graduate Coordinator at the University of of the Genetic Stocks subcommittee will be assumed by the Cologne. In January 2006 the coordinator position relocated Natural Variation and Comparative Genomics groups. Finally, to TAIR and Joanna Friesner, a post-doctoral fellow from the Proteomics and Metabolomics subcommittees, originally pro- University of California at Davis, became the third MASC co- posed in 2004, were given renewed emphasis to form and chairs ordinator. The position was strategically affiliated with TAIR recently have been identified. These four new groups will join in order to provide for continuity in coordinator location and the original Bioinformatics and ORFeome subcommittees. also to facilitate the critical revision of the MASC functional In April, 2005, an NSF-funded workshop on “Data Inte- genomics webpages located at TAIR. Updating and modifying gration” was held at TIGR, followed by a workshop at the an- the MASC webpages are among the highest priorities for the nual Arabidopsis meeting in Madison in June, 2005. The goals coordinator during the second half of 2006. of the workshops were to assess needs, gather community input and exchange ideas about improving data integration in the Highlights of the Past Year Arabidopsis research community. Based on these workshops, Chris Town (TIGR) and Heiko Schoof (Max Planck) submit- Arabidopsis continues to play a dominant role in plant sci- ted successfully-funded proposals to establish an integrated ence research. In the past year alone a number of major break- pilot project to NSF and DFG, respectively. The pilot pro- throughs were reported. While it has been known for many gram includes workshops in Germany and the U.S., held in years that plant hormones are key regulators of a variety of pro- March and April, 2006, as well as plans to have web services cesses with high agronomic importance, including growth rate

 and flowering time, none of the hormone receptors had previ- evaluation, please refer to the United States submission in the ously been identified. Starting with auxin, two groups identified International Arabidopsis Functional Genomics Community the receptor in Arabidopsis as a protein involved in targeting section of this report. The full report is also available at www. other proteins for degradation1,2. Next, a gibberellin receptor nsf.gov/pubs/2006/bio0601/bio0601.pdf was identified in rice, and its identity confirmed through its interactions with the DELLA proteins, first identified in Ara- Tiling Chips 3 bidopsis as transducers of gibberellin signaling . Most recently, a Whole genome tiling chips covering the entire Arabidop- receptor for abscisic acid was identified as a gene in Arabidopsis sis thaliana genome sequence (designed by Joe Ecker and Af- 4 known to be directly involved in controlling flowering time . fymetrix) were made available last year through an early ac- Hormones also regulate the number of branches on a shoot. cess program; the fully supported array was officially released While it was known that auxin is partially responsible, a new in April, 2006. The Arabidopsis Tiling 1.0R array is a single family of regulators known as MAX genes was shown this year chip comprised of over 3.2 million probe pairs tiled through to control the flow of auxin in the shoot and thus the number of the complete non-repetitive Arabidopsis genome (1 probe pair 5 branches . Another developmental puzzle involves the timing PerfectMatch/MisMatch every 38 bases) and includes nuclear, of plant flowering which has been shown to be under the influ- , and mitochondrial sequences. Through the early ence of a mysterious graft-transmissible substance known as access program the array has been used in a number of current- "florigen." Two studies, one in Arabidopsis, the other in tomato, ly unpublished experiments including transcript mapping and revealed the long-sought identity of florigen as the FLOWER- chromatin immunoprecipitation (ChIP/chip) (Ecker), analysis ING TIME (FT) gene. How the signal is transmitted is still of DNA methylation (Ecker/ Steve Jacobsen labs), and poly- controversial - in Arabidopsis the claim is that the FT RNA morphism discovery in different Arabidopsis accessions ( Justin 6,7 moves, while in tomato, it seems that only the protein moves . Borevitz). A second public-private project, initiated by Detlef Finally, a report that over-expressing a yeast chromatin-remod- Weigel (Max Planck Institute) and Joe Ecker (Salk Institute), eling protein in Arabidopsis dramatically increased the rate of and funded by a grant from the Max Planck Institute, involves gene targeting may point the way for precisely reshaping the whole genome study of natural variation in twenty Arabidopsis 8 genomes of plants to enhance specific traits . thaliana accessions using tiling arrays with Watson and Crick strands on independent chips. In collaboration with Perle- AT2010 Midcourse Evaluation gen Sciences, Weigel recently completed the data acquisition 2005 marked the halfway point of the NSF-sponsored phase, identifying over 500,000 unique single-nucleotide poly- AT2010 program which has funded 86 projects in its first morphisms (SNPs), making Arabidopsis the organism with the five years (U.S.). The program’s primary goal is to determine highest density of high quality common SNPs per kilobase of the function of every Arabidopsis gene by 2010 and ultimately genomic sequence. of the 20 accessions used in the study achieve a complete understanding of the biology of a flower- have been deposited with the Arabidopsis Biological Resource ing plant, using Arabidopsis thaliana as an experimental model Center (ABRC, stocks CS22676-22695), and all data will be system. Scientific objectives of this long-range plan include released upon publication, expected this year. (1) development of an expanded genetic toolkit, including new technology development that enables the broad commu- Mutant Biological Resources nity to conduct Arabidopsis functional genomics, (2) whole-sys- A number of international projects have developed and tems identification of gene function, including global analyses catalogued plant lines containing insertion elements. The Salk of gene expression, the plant proteome, metabolite dynamics, Institute Genomic Analysis Laboratory (SIGnAL, Joe Ecker, molecular interactions, and comparative genomics, (3) expan- http://signal.salk.edu/cgi-bin/tdnaexpress) has integrated data sion of the role for bioinformatics, (4) development of commu- from many of these sources including SALK, SAIL, Wiscon- nity and human resources, and (5) promotion of international sin knockout facility, FLAG, RIKEN, JIC suppressor-mutator cooperation. The NAASC organized a workshop in Virginia transposons, IMA Ds collection, GABI-KAT, and CSHL into (U.S.) on Aug. 25 and 26, 2005, to evaluate the progress made an online searchable database, essentially providing “one-stop” toward the specific goals of the program and to recommend access to almost all available information on insertions within directions for the next five years. Workshop participants felt a given locus. According to the SIGnAL website there are T- that the majority of the initial program goals had been met DNA and transposon mutants with insertions in nearly 92% or surpassed, and that high-throughput and/or bioinformatics (28,607) of the 31,128 nuclear-encoded Arabidopsis genes (re- approaches have particularly been useful for functional analysis annotated by TAIR in November, 2005.) Approximately 75% of biological processes. The participants developed a number of these loci contain insertions within exons and about 83% of specific recommendations for the project’s remaining five contain insertions in either introns or exons. In addition, a proj- years and looked towards the future and a possible Arabidopsis ect was initiated last year to experimentally identity two homo- 2020 project. For a more detailed description of the midterm zygous insertion mutants for 25,000 Arabidopsis genes (Ecker).

 Project data can be found at the SIGnAL website, and seed • Biological processes (e.g., , amino acid stocks will be distributed through the ABRC (http://signal. , cell wall biosynthesis, DNA repair) salk.edu/gabout.html). Currently, there are 2,729 homozygous 2. For non protein-encoding genes mutant insertion lines representing 2,227 genes, and about 60% • Activity of RNA/gene product of the lines contain insertions in exons and introns. The project • Expression pattern at cell and tissue level was designed to produce mutant plant lines in a high-through- • Structure of RNA/gene product put manner, however, some homozygous lines are difficult to • Subcellular location for RNA/gene product grow and mutants that require specialized growth conditions • Phenotype of genetic knockout/other loss-of-function often die before producing seeds. This makes it more important alleles than ever that the Arabidopsis community deposits homozygous • Interaction data lines for published mutants in publicly-accessible stock centers. The ultimate goal for functional characterization of a gene Recently, a “Portal of Mutants and Mapping Resources” has is to have full information for each of these categories. At the been incorporated into the TAIR website which summarizes opposite end of the knowledge spectrum is complete lack of and provides links to and information about available Arabi- characterizing features: dopsis forward and reverse genetics resources. Of particular note • Sequence has no homology to any sequence that we are tables that summarize available mapped mutation lines and know the function of seed resources (www.arabidopsis.org/portals/mutants/). This • ORF has no expression useful site provides a chart of, and links to, the major interna- • No cDNA has been isolated, just predicted tional reverse genetic projects and the corresponding genome browsers in which the Arabidopsis sequence coordinates can be In the next five years it should be possible to collect at least viewed. Furthermore, the site provides links to germplasm and one category for every gene in the genome. As shown in the seed stock catalogs, allows users to use BLAST, order stocks, thermometers below, there are functional data for nearly one- and request EMS-induced mutations in a gene of interest third of Arabidopsis genes, full-length cDNA information is through the TILLING project. known for nearly 70%, and at least some expression information is available for more than 90% (excluding pseudogenes). Most Measuring Gene Function Knowledge remarkably, just over 95% of all genes (excluding pseudogenes) are reported to be currently under study, or proposed for future At the MASC annual meeting held during the 2003 Inter- study. With continued funding and international collaboration national Conference on Arabidopsis Research members agreed we can look forward to numerous insights and discoveries from that it would be useful to establish a better way to update gene the community over the next five years, substantiating the value function knowledge and quantify the number of genes with of Arabidopsis as the foremost reference plant. known function. In the 2004 and 2005 MASC annual reports For this year’s report, Eva Huala and colleagues from this was illustrated by thermometers to provide a visual illustra- TAIR, and Hank Wu from TIGR provided the numbers of tion of the progress in Arabidopsis functional genomics efforts. genes that fall into different evidence codes, genes for which This year the thermometers are updated with data available at there are full-length cDNAs, genes that have been detected in the middle of April 2006. various expression profiling experiments, and genes for which Functional categories have been defined for easier there was experimental evidence in the literature for a function. quantification Information regarding genes with existing and targeted ORF clones was provided by Joe Ecker (Salk Institute) and includes 1. For protein-encoding genes data from a number of projects including Salk, CESG, Wis- • Protein activity/molecular function (catalytic or other- consin, ORPHEUS, Atome, and TIGR. Information for the wise: e.g., kinase, chaperone, phosphatase, proteinase) thermometers was also obtained through the Arabidopsis com- Gene and trait ontologies should be used for func- munity. A questionnaire was sent to 2010/AFGN researchers tional categorizations by the MASC coordinator about the categories listed under • Tertiary structure section 1: functional categories for protein-coding genes. Fify- • Post-translational modification data seven 2010/AFGN projects supplied data which were forward- • Expression pattern at cell and tissue level ed to TAIR and filtered for redundancy with other data. New • Subcellular localization non-redundant information was integrated into the Function • Protein interaction data thermometer and called community input (CIP). • Phenotype of genetic knockout/ other loss-of-func- tion alleles

10 Expression Function

27,608 27,608 25,515 26,218 23,855 21,818 19,248

8,514

4.171

Loci with cDNAs IDA Inferred by direct assay:...... 2,433

Loci with cDNAs or ESTs IGI Inferred from genetic interaction:...... 2,661

Loci with cDNAs, ESTs or mpss or sage IMP Inferred from mutant phenotype: ...... 3,130 Loci with cDNAs, ESTs, mpss, sage or microarray exp IPI Inferred from physical interaction:...... 3,202 CIP Community input 2010/AFGN category 3:...... 4,171 CIP Community input 2010/AFGN category 2:...... 8,514 CIP Community input 2010/AFGN category 1:...... 26,218

ORF Unknown

27,608 27,608

22,890

14,113

388

Loci with existing ORF clones Sequence has no homology to any sequence that we know the function of. +Loci with targeted ORF clones ORF has no expression No cDNA has been isolated, just predicted

Figure 1: Measuring Arabidopsis Gene Function Knowledge. Each thermometer measures against the total number of genes anno- tated in the most recent TAIR Arabidopsis genome release, including organellar genes (279) and excluding pseudogenes (3,818). Exact numbers for the different categories are as follows: Gene Expression: genes with full-length cDNA (19,248), additional genes with ex- pressed sequence tags (ESTs; 2,570), additional genes from massively parallel signature sequencing or serial analysis of gene expression (MPSS/SAGE; 2,037), additional genes from microarray data (1,660). Gene Function (includes loci annotated to Gene Ontology (GO) function, process or component with the listed evidence codes): IDA/inferred by direct assay (2,433), additional IGI/inferred by genetic interaction (228), additional IMP/inferred from mutant phenotype (469), additional IPI/inferred from physical interaction (72), CIP/ community input class 3- genes for which characterization in one or more functional categories is finished, or nearly finished (969), CIP class 2- additional genes for which characterization in one or more functional categories is partly finished (4,343), CIP class 1- additional genes selected for study but have not yet been characterized (17,704). Genes with existing ORF clones (14,113), additional genes with targeted ORFs for cloning (8,777). The total number of genes where the sequence has no homology to any sequence that we know the function of, ORF has no expression, or no cDNA has been isolated, just predicted (388). Please note that gene accessions were compared for redundancies; the numbers in each thermometer refer to non-redundant gene accessions.

11 References

1. Dharmasiri N, Dharmasiri S, Estelle M, The F-box protein TIR1 is an auxin receptor. Nature, 435 (441-445), May, 2005. 2. Kepinski S, Leyser O, The F-box protein TIR1 is an auxin recep- tor. Nature, 435 (446-451), May, 2005. 3. Ueguchi-Tanaka M, Ashikari M, Nakajima M, Itoh H, Katoh E, Kobayashi M, Chow T, Hsing Y, Kitano H, Yamaguchi I, Mat- suoka M, GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin. Nature, 437 (693-698), September, 2005. 4. Razem F, El-Kereamy A, Abrahms S, Hill R, The RNA-binding protein FCA is an abscisic acid receptor. Nature, 439 (290-294), January, 2006. 5. Bennett T, Sieberer T, Willett B, Booker J, Luschnig C, Leyser, O. The Arabidopsis MAX pathway controls shoot branching by regu- lating auxin transport. Current Biology, 16 (553-563), March, 2006. 6. Huang T, Bohlenius H, Eriksson S, Parcy F, Nilsson O. The mRNA of the Arabidopsis gene FT moves from leaf to shoot apex and induces flowering. Science, 309 (1694-1696), September, 2005. 7. Lifschitz E, Eviatar T, Shalit R, Goldshmidt A, Amsellem Z, Al- varez J, Eshed Y. The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse envi- ronmental stimuli. Proc. Natl. Acad. Sci., 103 (6398-63403), April, 2006. 8. Shaked H, Melamed-Bessude C, Levy A. High-frequency gene targeting in Arabidopsis plants expressing the yeast RAD54 gene. Proc. Natl. Acad. Sci., 102 (12265-12269), August, 2005.

12 Reports of the MASC Subcommittees

Bioinformatics The first workshop was held at the Max Planck Institute (Cologne, Germany) from March 14-18, 2006 and was attend- Prepared by Chris Town (Chair, [email protected]) and Heiko ed by representatives of MIPS, MPIEB-Tuebingen, MPIMP- Schoof ([email protected]) Golm, RZPD-Berlin, University of Cologne, VIB/PSB-Ghent and Centre for Biotechnology in Turku, Finland as well as the Last year’s report described the first major step towards TIGR partners. In addition to instruction and demonstration improved data integration in the Arabidopsis community in the of the core elements of BioMoby web services technology, top- form of an NSF-funded Workshop on “Data Integration” at ics covered included ontologies, data standards, and types of TIGR in April, 2005. This was followed by a workshop at the data that might be served. Although many areas requiring a International Arabidopsis Meeting in Madison, Wisconsin in significant amount of work were identified, the group was op- June 2005 at which the results of the TIGR workshop were timistic about having new services in place by the summer. The presented to the research community. The Madison workshop parallel U.S. workshop took place at TIGR (Maryland, U.S.) was well attended and there was considerable enthusiasm for from April 24-28, 2006 and built upon the experiences of the the prospects of Web Services to help solve some of the issues Cologne meeting. of data integration. Based upon this community response, both In August, 2005 the NSF convened a meeting of promi- the Deutsche Forschungsgemeinschaft (DFG) and the Na- nent researchers from both within and outside the Arabidopsis tional Science Foundation (NSF) indicated their willingness community to assess the progress of the 2010 project at the to consider a pilot project to begin to develop web services. In mid-point of its 10-year period. Embedded in the report (www. the Fall of 2005, proposals were submitted to DFG (by Heiko arabidopsis.org/info/2010_projects/AT2010WorkshopFinal. Schoof) and to NSF (by Chris Town) and both were funded pdf) are a significant number of comments and recommenda- (see http://bioinfo.mpiz-koeln.mpg.de/araws). Each proposal tions relating to perceived bioinformatics needs. Some of these aims to implement web services that will provide and facilitate had already been voiced and discussed at the TIGR workshop the integration of data that is not part of existing data ware- in April 2005. Practical steps towards accomplishing some of houses like TAIR, NASC or MIPS. In addition to developer's the goals were again discussed at the Cologne workshop and workshops to be held both in Germany and the U.S., each group will continue to be the focus of the BioMoby pilot project. A will provide a "flying geek" service to provide on-site assistance successful outcome of this project, including the enabling of to clients with limited informatics expertise. web services in the broader Arabidopsis community, will go a The goals of this integrated pilot project are twofold. The long way towards satisfying the recommendations of the mid- first is to educate a limited number of groups in web services term report. technology, to define the IT requirements necessary to deploy web services at any site and to develop a set of Standard Operat- cDNAs and Clone-based Proteomics ing Procedures that can be widely used by the Arabidopsis com- munity. The second is to actually have some more web services (ORFeomics) and workflows up and running in time for demonstrations at Prepared by Pierre Hilson (Chair, [email protected]. the International Arabidopsis meeting in Madison in the sum- be) mer of 2006. At this point, participation in the pilot project has, for logistical reasons, been limited to relatively small groups of Clone-based functional genomics is gradually picking up people in the EU and U.S. However, this is not meant to be an among Arabidopsis scientists (reviewed in Hilson, 2006). Large- exclusive process and we hope that these initial trials will allow scale screens based on the systematic introduction of constructs us to more rapidly propagate web services throughout the Ara- designed for ectopic expression or silencing of Arabidopsis bidopsis community in the months and years to come.

13 genes are underway. The first limited yeast two-hybrid protein- terminal fusions - as well as expression clones have been made protein interaction matrices have been published, and several available recently (See Table 1 on the next page.) groups have reported in vivo analyses of subcellular location The Arabidopsis community has done an excellent job at for hundreds of proteins carrying fluorescent tags. Biochemical promoting stock centers, supported by long-term funding, that assays and protein arrays have been described that take advan- curate and distribute clone collections for very low fees and tage of ORF and cDNA clone collections. But, in comparison with no material transfer agreements. These centers are key to to other eukaryotic model species, no Arabidopsis genome-scale the efficient use of resources and should be maintained for the dataset has yet been published in this area of research. benefit of all plant researchers. The steady increase in the number of cloned gene sequenc- es is for the most part due to large-scale initiatives, but also to Reference a few projects focusing on the systematic analysis of particular Hilson, P. (2006) Cloned sequence repertoires for small- and mechanisms that have generously donated their materials to large-scale biology. Trends Plant Sci. 11, 133-141. stock centers (Table 1). Importantly, the publicly available re- sources enable systematic approaches but are also used by sci- entists interested in the functional characterization of only a few genes. Material dissemination via stock centers is beneficial because it prevents duplication of efforts and promotes the use of well-documented reference materials across multiple experi- ments conducted by independent laboratories. Any functional genomics projects generating clone resources should be encour- aged by funding bodies to donate their materials for public re- lease or to include long term dissemination plans in their activ- ity. Forward looking, our community must understand the need to record the results obtained with these shared clone collec- tions using standard procedures and formats that facilitate the integration of diverse data types. When possible, these stan- dards should be borrowed from well-established initiatives, for example, the European Bioinformatics Institute (EBI)-funded IntAct (open-source database system and analysis tools for pro- tein interaction data.) Arabidopsis cloning efforts have been increasingly coor- dinated with the publication of target sequence lists at early stages of planning. Such advance notice should be implemented whenever possible. But, there is still substantial overlap between certain collections, generally resulting from different format choice or validation policies. Today, various entities distribute Arabidopsis clones (ABRC, NASC, RZPD, BRC, CNRGV and individual labo- ratories) and there is unfortunately no straightforward proce- dure to interrogate at once all relevant databases for constructs of interest. A system should be implemented to display the location(s) of available clones based on queries by sequence ho- mology searches or by AGI code names. Several groups are cur- rently investigating how to create a unique information system for Arabidopsis clones that will unite dispersed databases using webservices. Ideally, such a system should be extended beyond cDNA, ORF and silencing clones, to include repertoires with promoter and other non-protein coding sequence collections, as well as recipient plasmids (e.g. Gateway destination vectors) designed for particular functional assays. Interestingly, the first large sets of ORF entry clones from which the native stop co- don was removed – and therefore compatible with carboxyl-

14 Stock center ABRC ABRC ABRC ABRC CESG RZPD ABRC ABRC CNRGV BRC BRC RZPD NASC NASC ABRC

URL signal.salk.edu www.tigr.org/tdb/hypos/ TargetGeneList.shtml plantsubq.genomics.purdue.edu www.uwstructuralgenomics. org/cloning.htm www.gabi.rzpd.de/materials/ http://www.evry.inra.fr/ ublic/projects/orfeome/orfeome. html http://www.brc.riken.go.jp/lab/ epd/Eng/order/order.shtml same www.gabi.rzpd.de/materials/ www.agrikola.org www.agrikola.org www.chromdb.org 111 768 155 144 1,283 1,100 4,500 13,854 16,913 21,903 19,640 ~ 1,500 ~ 1,000 ~ 2,000 ~ 3,500 Count 246,640 Validation 5' and 3' end seq. Full sequence Full sequence Full single pass seq. 5' and 3' end seq. Full sequence 5' and 3' end seq. 5' and 3' end seq. Full sequence Single pass 5' end seq. PCR sized insert PCR sized insert Single pass seq. clone collections Focus Random factors Transcription Hypothetical genes Protein ubiquitination Potential new fold factors Transcription transcription TAP-tagged factor fusion for subcellular GFP location Random Random (from SSP) Random Random Random Random Random Chromatin remodel. Arabidopsis PS PS λ λ ZAP or ZAP ZAP or ZAP Format Gateway entry Gateway entry Gateway entry Gateway entry Gateway entry Expression (from JC) Peking-Yale Univector pUNI51 and Gateway entry Expression (from SSP) Gateway entry no Gateway entry, stop λ λ Gateway expression Gateway entry hp RNA expression ds RNA ds RNA expression . Publicly available 1 Creator clones ORF SSP consortium SSP & Salk Institute Peking-Yale Joint Center TIGR J. Callis et al. CESG REGIA Dinesh-Kumar et al. Doonan et al. 1 ATOME 2 ATOME clones cDNA RIKEN RIKEN MPI-MG RNAi clones AGRIKOLA AGRIKOLA CFGC Table Table

15 Metabolomics The Phenome subcommittee is meant to track the progress of efforts including development and availability of biological Prepared by Ian Graham (Chair, [email protected]) materials for phenotyping, efforts to develop and use standard- ized phenotype descriptions including ontologies, and the avail- A continuous goal and monitoring operation will be to ability of materials and data in stock centers and databases. ensure full integration of Arabidopsis-based Metabolomics re- search with the Metabolomics Standards Initiative that is cur- Biological resources for phenotyping rently being coordinated by the Metabolomics Society (www. Insertion lines: A total of 28,607 genes (92%) have been metabolomicssociety.org). In this initiative five working groups tagged with insertions in the combined set of all insertion col- have already been formed and documents are being finalized lections, and 23,509 (76%) of these genes contain insertions into covering (a) Biological Sample Context; (b) Chemical Analy- the coding region, according to the SIGnAL website (http://sig- sis; (c) Data Analysis; (d) Ontology and (e) Data Exchange. nal.salk.edu/cgi-bin/tdnaexpress). A list of projects with brief Several members of the MASC Metabolomics subcommittee descriptions, location of data and links can be found at TAIR: are involved in drawing up the plant biology specific documen- http://arabidopsis.org/portals/mutants/worldwide.jsp. tation for the Metabolomics society. In addition this committee Homozygous mutant lines: The Salk “phenome-ready” will aim to establish a mechanism that allows the dissemination project to produce homozygous mutant T-DNA lines is in the of metabolomics datasets to the wider Arabidopsis community process of generating homozygous mutants for 24,357 Arabi- and encourage and facilitate initiatives for the integration of dopis protein-coding genes. Currently (as of March 31 2006), metabolomic datasets with other ‘omic datasets. This will in- seeds for 1989 lines (affecting 1740 genes) are available from volve depositing Metabolomic data in a usable format for data the Arabidopsis Biological Resource Center (ABRC) and will integration. also be available from NASC. The remainder of the Salk ho- Natural Variation and Comparative Genomics mozygous lines should be completed in 2007, and seeds will be available in quantities sufficient to allow partial or full sets of Prepared by Tom Mitchell-Olds (Chair, [email protected]) lines, or pools of lines, to be utilized by researchers for research projects and/or screening. A second large project at RIKEN is The newly-restructured subcommittee on Natural Varia- now preparing homozygous mutant transposon-tagged lines for tion and Comparative Genomics includes two working groups. approximately 5,000 Arabidopsis genes. RIKEN BRC (http:// The Natural Variation Working Group has been established www.brc.riken.jp/lab/epd/Eng/) will start the distribution of to identify technological and resource issues which are needed homozygous seeds by the end of this year. In addition to these for progress in analysis of Arabidopsis natural variation. In ad- two large collections, 642 Salk and SAIL homozygous inser- dition, conceptual opportunities for improved understanding of tion lines from the community have been donated to ABRC as fundamental processes in plant biology will be considered. of April 2006 and are available for ordering. The Comparative Genomics Working Group has been RNAi lines: The AGRIKOLA project (http://www. established to consider priorities for future research in Arabi- agrikola.org/) has cloned 21,862 gene-specific tags into binary dopsis Comparative Genomics in order to identify conceptual hairpin RNA vectors and made them available to the public and technical goals as well as recommend species which will through NASC. These lines target a total of 19,202 genes. The optimize progress towards these research goals. final targets to be achieved in mid-2006 will be over 25,000 Finally, this subcommittee also inherits responsibilities of tags for over 20,000 genes. In addition, 786 sets of transformed the former subcommittee on Genetic Resources which dealt lines and 6755 individual transformed lines are currently avail- with forward and reverse genetics, natural variation, and com- able for ordering from NASC, out of a final target of around parative genomics. Although much progress has been made by 3,000 sets of transformed lines. The AGRIKOLA lines are also the International Arabidopsis 2010 Initiative on many of these being made available by ABRC (200 lines currently in-house). issues, further consultation regarding possible future needs is ongoing. Members of each working group are in contact by e- Ontology development mail and aim to produce recommendations and summary docu- Several efforts are underway to provide the controlled vo- ments before the end of 2006. cabulary needed to describe in a standardized way.

Phenomics POC: The goal of the POC (Plant Ontology Consortium, http://www.plantontology.org/) is to provide a standardized Prepared by Eva Huala (Chair, [email protected]) and vocabulary to describe anatomy, morphology, and growth and Sean May (co-chair, [email protected]) developmental stages in Arabidopsis, , rice, Fabaceae and Solanaceae, with future plans to extend the vocabularies to other

16 plant families. This standardized vocabulary will serve as a ba- not been made publicly available. A group at INRA (Granier sis for cross-species queries for phenotype and gene expression et al., New Phytol. 2006;169:623-35) has described a robotic information, an essential capability that will permit researchers setup for large scale phenotyping of general morphological working with crop species to leverage Arabidopsis research re- traits but no large data releases to the community have resulted sults into agricultural advances. POC has released ontologies to date. covering plant structure (release date July 2004, currently 753 Examples of recent efforts aimed at phenotyping for spe- terms) and growth and developmental stages (release date July cific traits include ion profiling of large numbers of mutants 2005, currently 274 terms). These ontologies are now in use at (Salt, Plant Physiol. 2004;136:2451-6) and searching for cell TAIR and NASC as well as several other databases including wall mutants using MALDI-TOF MS to detect structural Gramene, MaizeGDB, SGN, BRENDA, Genevestigator and changes in cell wall polymers (Lerouxel et al., Plant Physiol. ArrayExpress. Requests for additional terms can be made by 2002;130:1754-63). using the Feedback button on the POC website. Efforts to identify large numbers of natural variants in- PATO: The Phenotype, Attribute and Trait Ontology clude a project in Detlef Weigel’s group to phenotype about (PATO) is currently under development as part of the NIH- 15 F2 populations from crosses among the “Nordborg 96” eco- funded cBiO project (http://www.bioontology.org/). The pur- type sets, examining 500 plants of each population for a variety pose of this ontology is to facilitate description of phenotypes of morphological traits including flowering time. Individual using controlled vocabulary terms arranged in a syntax line plants will be phenotyped and also genotyped at about 80 loci referred to as the Entity, Attribute and Value (EAV) model. each, to produce a large number of QTL maps. It is planned Entity terms describe physical entities such as body part, cell to store the phenotypes in a genotype-phenotype database, as type, subcellular structure, developmental stage or biological a prototype for the future integration of phenotyping data sets process affected, and can be drawn from other ontologies such from many different sources. as PO (Plant Ontology) and GO (Gene Ontology). Attribute Phenotyping at the level of individual genes or small sets terms describe the trait that is altered, and Value terms describe is ongoing, and this information is primarily captured in the the nature of the alteration in the mutant or natural variant literature. Phenotype descriptions have been published for ap- (For example Entity:leaf, Attribute:color, Value:yellow could proximately 3000 loci, estimated from the number of loci at be used to describe a mutant with yellow ). The core TAIR that are associated to published papers containing the participants in development of PATO include Monte West- word “mutant” in the abstract. TAIR is working to extract this erfield at ZFIN (the database), information from the literature. at Flybase (the database) and Ida Sim of UCSF, leader of a group that will use the ontology to describe the Storage and display of phenotype data results of human clinical trials, with Georgios Gkoutos in the NASC currently displays PO and PATO controlled vocab- UK serving as the main PATO curator. The POC organizer ulary phenotype annotations for 1,897 mutant lines and natural (Katica Ilic) has been in contact with the project organizers variants, and will continue to add additional annotations in the and there is a shared opinion that the plant community should future. participate more actively in PATO development to ensure that POC currently displays NASC’s PO annotations for 1,897 this ontology becomes more suitable for description of plant mutant and natural variant lines. The consortium is working on mutants and natural variants. To facilitate the development displaying plant phenotype descriptions on the POC website as of PATO for use in plant biology, curators from plant data- a combination of controlled vocabulary terms and free text (us- bases are encouraged to request new PATO terms through the ing PO terms to describing the affected part (entity), and using SourceForge website (http://sourceforge.net/tracker/?group_ free text for attribute and value). id=76834&atid=595654). TAIR is planning to participate in a TAIR contains phenotype descriptions for mutants in ap- PATO content development workshop in mid-May 2006. proximately 1100 AGI loci, collected from the literature and from ABRC stock data. TAIR is currently working to separate Phenotyping efforts free text phenotype descriptions from other descriptive infor- No public domain effort to date has released data system- mation relating to germplasms and add search and display ca- atically describing the overall phenotype of large numbers of pabilities specific to phenotype. In the next 12 months TAIR Arabidopsis gene knockouts. Rather, the emphasis has been on expects to begin adding PO and PATO controlled vocabulary investigating specific traits and on describing natural variants phenotype annotations through literature curation and com- and QTLs. Large scale phenotyping of knockouts has been munity submissions. carried out in the past by the private sector (for example at Paradigm genetics – see Boyes et al. 2001, 13:1499– (Additional report contributors: Ian Small, Randy Scholl, Detlef 1510). However, the phenotype data from these projects have Weigel, Minami Matsui and Katica Ilic)

17 Proteomics • Develop a master list of the Arabidopsis gene loci that have been identified at the proteomic level by mass Prepared by Wolfram Weckwerth (Chair, weckwerth@mpimp- spectrometry. golm.mpg.de) • Work towards a central international database of MS/ MS spectra derived from Arabidopsis samples. Proteomics using Arabidopsis thaliana as a model system • Collaborate with TAIR and other interested parties on has made great progress in recent years. The throughput and Arabidopsis proteomic data storage. accuracy of protein identification techniques such as shotgun proteomics based on liquid chromatography coupled to mass spectrometry (LC/MS) or two-dimensional gel-electrophore- sis (2DE) relies strongly on the availability of whole genome sequences. The availability of both a complete genome sequence and high quality genome annotation makes Arabidopsis thali- ana an ideal system to develop new technologies and identify candidate genes. Furthermore, Arabidopsis thaliana proteomics research will give direction to future plant proteomics develop- ments and can serve as a unique database resource, especially when coordinated with the metabolomics and bioinformatics initiatives. However, in light of the enormous complexity of a dynamic proteome, different approaches have to be combined to measure protein expression and dynamics, stress- and de- velopmental responses, posttranslational protein modifications and protein interaction. Therefore, it is a very opportune mo- ment to establish a working group devoted to Arabidopsis pro- teomics, and combine the efforts of different research groups to develop programs which will consolidate databases, technique standards and experimentally validated candidate genes and functions.

Subcommittee goals and priorities • Organization of a common webpage including stan- dards for different proteomic techniques, databases, procedures, meetings, proteome labs, etc. • Meet at Arabidopsis International Conference each year. • Discuss international network grant proposals for plant proteomics. • Develop standards for two-dimensional gel-electro- phoresis, shotgun proteomics, and quantitative pro- teomics. • Write guidelines for minimal requirements for differ- ent types of proteomic studies and distribute these to plant journals (especially: Plant , , Plant Cell, and the Plant Journal) for their consideration of publication standards – is- sues include experiments, data analysis and call of identifications. These activities will be coordinated with the MASC metabolomics subcommittee chaired by Ian Graham, the subcommittee for bioinformatics and the Proteomics Standard Initiative (PSI). • Hold a workshop each year at the International Ara- bidopsis Conference on the methods/practice of pro- teomics to inform the community, make new contacts, and to develop initiatives for proposals.

18 Analysis and Recommendations

The Multinational CoordinatedArabidopsis thaliana Func- all.) These data are integrated into the TAIR database and tional Genomics Project has now completed its fifth year. In are available from NCBI. 2005/2006 there was a continued increase in publicly acces- 2. Generation of comprehensive sets of sequence-indexed sible data and resources including SNPs, MPSS, microarray, mutants listed in an integrated database and made avail- full length-cDNA information as well as full-length cDNA able as seed stocks. Currently the mutant collection clones, ORF clones, RNAi clones and insertion mutants. In- includes insertions in nearly 92% of the 31,128 nuclear- tensive international efforts have made a large number of bio- encoded Arabidopsis genes with approximately 75% of logical resources available to the Arabidopsis community and all loci containing insertions within exons. Recently, a the ease of access to these materials is particularly noteworthy. “Portal of Mutants and Mapping Resources” has been While there is still much to discover in the Arabidopsis genome incorporated into the TAIR website which summarizes and particularly using systems approaches, new and provides links to and information about avail- frontiers include proteomics and metabolomics. In addition, able Arabidopsis forward and reverse genetics resources. information gathering between genomes, i.e. comparative ge- Of particular note are tables that summarize available nomics and natural variation, is increasingly enabled by genome mapped mutation lines and seed resources (www.arabi- resequencing and reannotation, and the development of more dopsis.org/portals/mutants/). Joe Ecker's lab at the Salk sophisticated genome surveying tools and bioinformatics and Institute began a project last year to isolate two homo- data integration approaches. Subcommittees focusing on Sys- tems Biology, Metabolomics, Proteomics, and Natural Varia- zygous insertion mutants for each of 25,000 Arabidopsis tion and Comparative Genomics recently formed to evaluate genes (http://signal.salk.edu/gabout.html). Currently current knowledge, identify needs and bottlenecks, and estab- there are 2,729 homozygous mutant insertion lines rep- lish appropriate courses of action. International cooperation by resenting 2,227 genes, and about 60% of the lines contain motivated researchers, a high level of coordination, and suffi- insertions in exons and introns. As of March, 2006, 1,000 cient funding remain critical to the success of this ambitious confirmed homozygous mutants from Joe Ecker and 600 project. confirmed lines from additional laboratories have been deposited with the ABRC. It is expected that 50,000 con- Current status of the program firmed lines, searchable in the TAIR germplasm resource, will be deposited within the next two years. In addition, Strong international collaboration within the Arabidopsis the EU-funded AGRIKOLA project has produced nearly community has contributed to the attainment of many of the 22,000 RNAi Gateway clones, targeting 19,202 genes, for short-term goals of the Functional Genomics Project, as well the creation of ‘knock-down’ lines. The final targets (ex- as the initiation of mid- and long-range goals. In the first five years the major accomplishments included: pected to be achieved in mid-2006) will be over 25,000 1. The release of improved whole genome annotations, the clones for more than 20,000 genes. The development of most recent versions supported by full-length cDNA artificial (miRNAs) as a new ‘knock-out’ tool sequences and expert input. In 2004, TAIR took over the shows particular promise for closely related genes (Weigel task of maintaining and improving genome annotation; lab, Schwab et al, The Plant Cell, 2006). their first release (version 6.0) took place in November, 3. Steady progress in characterizing Arabidopsis gene func- 2005. This release contains 26,751 protein coding genes, tion. Currently there are functional data for nearly one- 3818 pseudogenes, and 838 non-coding RNAs (31,407 in third of Arabidopsis genes. Most remarkably, just over 95% of all genes are reported to be currently under study, or proposed for future study (excluding pseudogenes.) For

19 a more detailed summary of gene function knowledge, see uted, with an additional 9,058 ORFs targeted for clon- ‘Measuring Gene Function Knowledge’ in the Progress ing. Last summer, the Ecker lab, in collaboration with and Activities of the MASC section of this report. Invitrogen, began creating a parallel set of Gateway vector 4. Development of new tools for comparative genomics. ORF clones to complement the existing pUNI vector Data acquisition in a whole genome study of natural system. As of February, 2006, 3,329 SSP/SALK pUNI variation in twenty Arabidopsis accessions was recently ORF clones have been transferred to Gateway vectors, completed. Over 500,000 unique single-nucleotide poly- and will be deposited into the ABRC upon completion of morphisms (SNPs) were identified making Arabidopsis sequence validation (estimated to occur in summer, 2006). the organism with the highest density of high quality This set, when combined with previously deposited ORFs, common SNPs per kilobase of genomic sequence (Detlef will bring the total number of fully sequenced and error Weigel). The decision last year by the Department of free SSP/SALK/Invitrogen clones to 5,126. Energy (DOE) Joint Genome Initiative (JGI) to se- 7. Development and investment in tools for standardized quence the closely related species and vocabulary. Several efforts are underway to provide con- the more distantly related rubella will contribute trolled vocabularies for genes, gene products, and pheno- to comparative genomics efforts; sequencing of A. lyrata types. The goal of the National Human Genome Research is underway while C. rubella sequencing is expected to Institute (NHGRI)-funded Gene Ontology Consortium begin shortly. Another JGI project involving sequencing is to produce dynamic controlled vocabularies that can be of the lycophyte Selaginella moellendorfii, which represents used to describe the roles of genes and gene products in an intermediate between nonvascular and vascular plants, all organisms. There are currently more than 100,000 GO will provide a reference genome for bridging large-scale annotations searchable in TAIR (provided by TAIR and genome comparisons and contribute to defining evo- TIGR.) The goal of the NSF-funded Plant Ontology lutionary relationships. Portions of the S. moellendorfii Consortium (POC) is to provide standardized vocabu- genome sequence have been submitted to the GenBank lary to describe anatomy, morphology, and growth and Trace Archives. developmental stages of Arabidopsis and other plants. This 5. The production of genome-wide sets of gene-specific vocabulary will provide a resource for researchers working probes for expression analysis and the establishment of with crop species to leverage Arabidopsis research results reference transcriptomes. The amount of freely available into agricultural advances. Phenotype, Attribute and Trait genome-wide transcriptome data continues to increase Ontology (PATO), funded by the National Institutes of through a number of initiatives: AtGenExpress, an in- Health (NIH), is currently under development. The pur- ternational project initiated in 2004, generated a gene pose of this ontology is to facilitate description of phe- expression profiling database; NASCArrays, the array notypes using controlled vocabulary terms arranged in a facility and expression profile repository of the GARNet standard syntax, and while researchers studying zebrafish, program, allows free access to microarray data; AREXdb drosophila and humans are the core organizers, the plant is a tissue-specific expression database focusing on the community is becoming involved via the POC. (Philip Benfey lab). All three projects use the Af- 8. Initiation of working groups to establish multinational fymetrix ATH1 full genome chip. In addition, there are consortia for target Arabidopsis research areas including a number of web-based tools and programs designed to natural variation and comparative genomics, proteomics, analyze microarray data; TAIR has summarized and pro- phenomics, systems biology, database interoperability, and vided links to many of these (http://arabidopsis.org/info/ metabolomics. expression). An Affymetrix tiling chip covering the entire 9. Appointment of a full-time MASC coordinator to foster Arabidopsis genome sequence became available last year information exchange, international collaboration and via an early access program; the fully supported array was coordination and to monitor progress of the program. officially released in April, 2006. The Arabidopsis Tiling 1.0R array is a single chip comprised of over 3.2 million Areas that lag behind initial plans or are probe pairs tiled through the complete non-repetitive currently underrepresented Arabidopsis genome. 6. Isolation of full-length cDNAs for nearly 75% of the 1. As the Arabidopsis community generates an increas- nuclear protein coding genes. Collectively, there is full- ing amount of data and develops more resources and length (fl) cDNA sequence information for about 19,498 tools, the improvement of database integration is criti- of the 26,541 nuclear protein-encoding Arabidopsis genes, cal. Last year Chris Town (TIGR) and Heiko Schoof and fl-cDNA clones of 14,216 genes are being distrib- (DFG) submitted proposals for “BioMoby” pilot projects

20 to begin to develop web services for data integration. opment of tools for functional genomics (antibody production Workshops funded by the pilot projects were held in against Arabidopsis proteins, assays to rapidly detect, quantify March and April, 2006, and a Bioinformatics workshop and determine the activities of large numbers of metabolites, to demonstrate the project to the broader community high throughput sequencing to enable evaluation of natu- will take place at the 2006 annual Arabidopsis meeting ral variation and discovery of low-abundance transcripts, and (Madison,WI). It is hoped that success in these pilot improved in vitro and in vivo approaches for macromolecular programs will translate into more broad-reaching data interactions.) Intensive efforts should continue to determine a integration efforts throughout the Arabidopsis community. basic set of characteristics about all Arabidopsis genes including 2. Proteomics, metabolomics and natural variation and (1) temporal and spatial gene expression data under different comparative genomics are all areas that need more em- environmental conditions and in specified accessions, and (2) for protein-coding genes, identification of interacting protein phasis. Working groups for each of these areas have been partners via comprehensive and cost effective high-through- established in the last few months and in 2005, the NSF put protein-protein interaction studies. Importantly, we must funded two AT2010 proposals involving metabolomics, capitalize on previous efforts and encourage the international and a third to design an Arabidopsis proteome chip. Ara- Arabidopsis community to submit datasets and resources to Cyc, a database containing biochemical pathways of Ara- publicly-accessible repositories and stock centers. bidopsis, was developed at TAIR to represent Arabidopsis It is critical that we improve database integration and de- metabolism as completely as possible with a user-friendly velop new modeling and computational tools. Synchronization Web-based interface. Proteomics resources, including of data syntax and semantics within different Arabidopsis de- production of antibodies against, or epitope tags on all rived data types and also with formats from other model or- deduced proteins are needed, as well as proteomic profil- ganisms is urgently needed. An acutely needed resource is a ing. straightforward way to query all relevant databases at once for 3. Tools for Arabidopsis functional research such as methods clones, constructs, mutants, and other resources. It is important for inactivating redundant genes, homologous recombina- to improve genome annotation and tool development for visu- tion, methods for analyzing posttranslational modifica- alization, annotation and curation. The frequency of whole ge- tions, protein profiling, analyzing protein-small molecule nome annotation updates should increase and should consist of interactions, subcellular localization, both semi-automated and manual curation and use controlled binding and epigenetic phenomena. syntax consistent with efforts of other model organisms. Priori- 4. Development of networks and systems biology is needed. ties include development of standardized protocols and tools The long-range Arabidopsis research plan, developed in to allow for submission of common data types for genome an- 2000, had the overall goal of determining the function of notation and development or adoption of visualization tools for every Arabidopsis gene. It is becoming increasingly clear viewing and linking the sequence annotations, in addition to that many genes have more than one function and many new means of data integration. genes work together in biological processes making an We must build on the knowledge gained from completing understanding of genes in the context of networks critical. the Arabidopsis genome and apply our resources to other ‘-omics’ 5. Temporal and spatial gene expression data are still needed areas; we must establish a reference proteome and metabolome, and support metabolomics and ionomics through studies of the under varied conditions, in specific tissues, and in differ- production, regulation and function(s) of small molecules such ent genotypes. Expression profiles of single cell or popu- as metabolites as well as the transport and activities of ions. We lations of sorted cells are needed. must also further the mapping of the ‘’ network by 6. Analysis of non-protein coding genes is still lagging. systematically obtaining information on where (in what cells There is increasing understanding of the importance of or tissues) and when (at what stage(s) of development and/or non-protein coding RNAs such as miRNAs, siRNAs, under what conditions) large numbers of genes are expressed, stRNAs, and snoRNAs, however, the genes encoding and where and when their products are localized at the subcel- these RNAs have been underrepresented in expression lular level. analysis, functional research, and annotation. In order to leverage the vast amount of genetic informa- Recommendations for the coming year tion available for Arabidopsis thaliana and apply these data to crops and other useful plants we need to improve natural varia- There are a number of goals remaining for the Multina- tion and comparative genomics studies within and between in- tional Coordinated Project including completion of resource formative and develop tools for whole-genome popu- collections (homozygous insertion lines, RNAi lines, con- lation biology. Informative sets of RILs and ecotypes need to ditional mutants, full-length cDNA and ORF clones for ex- be developed and made easily accessible to the community for pressed genes, recombination inbred lines or RILs,) and devel- functional studies, and genome sequencing within and between

21 appropriately chosen ecotypes or natural populations is needed Based on the analysis above as well as through feedback for population studies and SNP development. by the community and the MASC subcommittees, and from As a community, we need to effectively communicate our recommendations described in the AT2010 midterm evalua- successes as well as our needs, and convey the value of Arabi- tion, the MASC makes the following recommendations for the dopsis research. We must engage the broader community by next year: providing resources and tools and develop cyberinfrastructure for the dispersed network of resources. The Arabidopsis com- • Ensure the successful establishment of recently munity is encouraged to reach out to all educational levels and formed MASC subcommittees including Metabolo- the general public, and in particular, to policy decision-making mics, Natural Variation and Comparative Genomics, arenas and underrepresented groups. Finally, we must enhance Phenomics, and Proteomics. international collaboration. A major reason for success in the • Update and improve the Project’s webpages at TAIR. establishment of Arabidopsis as the reference plant is the strong • Work toward completion of genetic resources projects international collaboration that has developed over the last de- including the collection of homozygous insertion mu- cade. International collaboration is particularly important in tants (SALK) and RNAi clones (AGRIKOLA). genomics research as this scientific revolution requires costly • Develop resources for studying protein interactions efforts to generate resources and tools for genome-wide analy- and localization, including complete cloning of full- ses. Mechanisms should be sought to avoid unnecessary dupli- length cDNAs into expression vectors. cation of work and collaboration should be further stimulated • Expand data integration and interoperability efforts so that researchers share resources. These should be maintained for optimal use of data resources. in public stock centers making Arabidopsis research readily ac- • Facilitate and encourage submission of data and stocks cessible to the worldwide community. Equally important is the into public repositories. need for international collaboration on the development of a • Implement a Systems Biology working group. common database or a confederated database system, which stores and makes accessible the vast array of genomic and phe- notypic data on Arabidopsis.

22 The International Arabidopsis Functional Genomics Community Argentina

http://www.Arabidopsis.org/info/2010_projects/Argentina.jsp Instituto Leloir. Buenos Aires Contact: Jorge J. Casal • Functional analysis of oxidative stress-regulated genes. IFEVA, University of Buenos Aires Estela M. Valle, [email protected] Email: [email protected] Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario. Prov- Current Research Projects ince of Santa Fe • Identification of key components for retrograde signaling • Transcriptome analysis in plant- interactions: between mitochondria and nucleus in higher plants by plant genes required for susceptibility to fungal infection. transcriptomic, proteomic and functional analyses of re- Malena Alvarez, [email protected] spiratory complex mutants in Arabidopsis. CIQUIBIC-CONICET, Facultad Ciencias Quimicas, Eduardo Zabaleta ([email protected]) Universidad Nacional de Cordoba. Province of Córdoba Universidad de Mar del Plata. Province of Buenos Aires http://www.ciquibic.gov.ar/ • Regulatory genes involved in the biogenesis of mitochon- • The genetic network involved in plant responses to the drial Fe-S proteins. Metabolic analysis of Arabidopsis mu- light environment: transcriptome analysis in tants deficient in enzymes involved in carbon metabolism. and mutants. Diego Gómez-Casati ([email protected]) Jorge J. Casal, [email protected] Instituto de Investigaciones Bioteconológicas, Universi- IFEVA, Facultad de Agronomía, Universidad de Buenos dad Nacional de San Martin, Province of Buenos Aires Aires. Buenos Aires http://www.ifeva.edu.ar/en/staff/casal.htm • Functional analysis of genes involved in the biogenesis of Arabidopsis Genomics Tools and Resources the cytochrome c-dependent respiratory chain. • Recombinant inbred lines (RILs) between Landsberg Daniel H. Gonzalez, [email protected] erecta and Nossen produced by Jorge J. Casal in col- Facultad de Bioquímica y Ciencias Biológicas. Universi- laboration with the groups of Allan Lloyd (University of dad Nacional del Litoral. Province of Santa Fe Texas) and Javier Botto (University of Buenos Aires), are • Role of senescence associated genes in the formation of available at the Arabidopsis Biological Resource Center lytic vacuoles during senescence. (ABRC), Ohio State University, USA. Juan José Guiamet, [email protected] • The first Affymetrix workstation in Latin America has Instituto de Fisiología Vegetal, Universidad de La Plata. gone to Arabidopsis research groups. ANPCYT has Province of Buenos Aires granted an Affymetrix workstation to a consortium inte- • Genes involved in Potassium and Sodium transport. grated mainly by research groups listed above. The equip- Guillermo E. Santa-Maria, [email protected] ment has been installed at IFEVA. Instituto de Investigaciones Bioteconológicas, Universi- dad Nacional de San Martin. Province of Buenos Aires • Regulatory genes involved in the control of transcription of genes of the photosynthetic antenna. Roberto J. Staneloni, [email protected]

23 Major Funding Sources for Arabidopsis Functional Genomics

• ANPCYT (Agencia Nacional de Promoción Científica y Técnológica), http://www.agencia.secyt.gov.ar/ • CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), http://www.conicet.gov.ar/ • FIRCA (NIH), http://www.fic.nih.gov/programs/firca. html • TWAS (Third World Academy of Sciences), http://www. twas.org/

24 Australia & New Zealand

http://www.Arabidopsis.org/info/2010_projects/Australia.jsp Genomics Companies Contact: Barry Pogson • CAMBIA (www.cambia.org) The Australian National University, Canberra • Email: [email protected] Diversity Arrays Technology Pty Ltd (www.diversityar- rays.com). Examples of Australian Universities with Australia has a strong tradition in plant scientific research with most institutions across all states of Australia having some substantial research on Arabidopsis research involved Arabidopsis as a model system. Major areas • of Arabidopsis research and functional genomics are Canberra, Monash University (www.biolsci.monash.edu.au/) • University of Melbourne (www.unimelb.edu.au/) Melbourne and Perth. Major sites of plant science with foci on • crops such as grains, grapes and legumes include Queensland, The Australian National University (www.anu.edu. Tasmania, South Australia and New South Wales. au/bambi/; www.rsbs.anu.edu.au/) • The University of Queensland (www.uq.edu.au/) • The University of Adelaide (www.adelaide.edu.au/) Major Research Institutions involved in Examples of Research Projects Using Functional Genomics of Arabidopsis Functional Genomics Approaches • Australian Research Council (ARC) Centre of Excel- • lence in Plant Energy Biology (www.plantenergy.uwa. Aluminum and manganese stress tolerance- Peter Ryan • edu.au/). The focus of the Centre is Arabidopsis functional Arabinogalactan proteins - Carolyn Schultz and Tony genomics as it pertains to the roles of the chloroplast, Bacic • mitochondria and peroxisome in energy and Boron tolerance- Robert Reid • . This new knowledge will aid improve- CesA- related genes and cellulose synthesis- Richard ment of plants by enabling better management of: (1) the Williamson • timing and rate of plant growth and development; (2) Chloroplast development and function, oxidative stress biomass and yield; (3) efficient use of water and mineral and photoprotection - Barry Pogson • nutrients; (4) tolerance of plants to environmental stresses Dehydrin genes - Roger W. Parish • such as excess light and drought; and (5) synthesis of gene family - David McCurdy • plant metabolites important for human nutrition. Inves- Flowering time control - Alan Neale and John Hamill • tigators are: Ian Small, Murray Badger, David Day, Barry Heterotrimeric G-proteins - Jimmy Botello • Pogson , Harvey Millar, Jim Whelan. Mechanical impedance in - Josette Masle • • CSIRO Plant Industry (www.pi.csiro.au). Liz Dennis Microtubule associated proteins - Geoffrey Wasteneys • leads a major Program on Genomics and Plant Develop- Mitochondria - Jim Whelan David Day, Harvey Millar • ment. This program investigates several aspects of plant Myb gene function - Roger W. Parish • function and, importantly, is developing major facilities Nodulation related control mechanisms - Peter Gresshoff • for Arabidopsis functional genomics work. Gene Discov- Phosphorus-use efficiency - Peter Ryan • ery by Functional Genomics (Peter Waterhouse) has a Photosynthetic capacity regulation - Murray Badger • 10,000-plus non-redundant cDNA microarray facility Plant Natriuretic Peptide immunoanalogues (PNPs) - (Iain Wilson) and activation tagging (Chris Helliwell). Helen R. Irving and David Cahill • These facilities are being used intensively in CSIRO's Plasmodesmata functional proteomics - Robyn Overall • subprograms in reproductive development (Abed Chaud- Respiration: non-phosphorylating pathways of associated hury), floral initiation ( Jean Finnegan), Genetic Engi- with the mitochondrial electron transport chain - Kath- neering for Plant Improvement (Jeff Ellis), and Hormon- leen Soole • al Control of Gene Expression (Frank Gubler). Sodium efflux systems in the plasma membrane - Ian A. Newman • Defense gene expression - Karam Singh

25 Major Funding Sources For Arabidopsis New Zealand

Functional Genomics Increasing numbers of New Zealand plant scientists are incorporating Arabidopsis thaliana into their research, and sev- Funding is mainly available through the Australian Re- eral are using functional genomics approaches. Funding is prin- search Council's (ARC's) Discovery and Linkage Grant cipally available through the Royal Society of New Zealand's Schemes and its Centre of Excellence Scheme (www.arc.gov. Marsden Fund and the New Zealand Foundation for Research, au). Science and Technology. In addition to the projects being con- • Discovery Grants and Fellowships - supporting funda- ducted at the universities, research programs are carried out at mental research the Government-owned Crown Research Institutes, includ- • Linkage Grants - supporting projects between academic ing Horticulture and Food Research Institute of New Zealand institutions and industry (HortResearch), and the New Zealand Institute for Crop & • Linkage-International - In the context of the Interna- Food Research Limited (Crop & Food Research). tional Arabidopsis Research Community, the Linkage- International Scheme is particularly relevant. It provides Major Funding Sources for Arabidopsis funding for movement of researchers at both senior and junior levels between Australian research institutions Functional Genomics and centers of research excellence overseas. Two types • Royal Society of New Zealand Marsden Fund: (www. of awards include (1) Fellowships, under international rsnz.org/funding/marsden_fund/) agreements for the reciprocal exchange of postdoctoral • New Zealand Foundation for Research, Science and researchers, (2) Awards, to build links between research Technology: (www.frst.govt.nz/) centres of excellence in Australia and overseas by funding extended collaborations. Major Locations involved in Functional • The Genome-Phenome Link is one of 4 Priority Area Research Programs for ARC funding in 2003. Under the Genomics of Arabidopsis direction of the Minister responsible for the ARC, these • University of Auckland: (www.auckland.ac.nz/) program areas are to receive no less than 33% of the total • Association of Crown Research Institutes, including funds allocated under the National Competitive Grants AgResearch and HortResearch: (www.acri.cri.nz/) Scheme in the 2003 funding round. • University of Otago: (www.otago.ac.nz/) Other major sources of funding for Plant Science are the Research Development Councils. The funding for these orga- nizations is based to a substantial degree on Industry levies and therefore the research is targeted to particular industries. The largest is the Grains Research and Development Corporation of Australia (GRDC). A list of the RDCs is given at www.grdc. com.au/sites/rdcorp.htm.

26 Austria

http://www.Arabidopsis.org/info/2010_projects/Austria.jsp 2. Lasting effects of abiotic stress in plant genomes and Contact: Heribert Hirt their potential for breeding strategies, funded through University of Vienna the Austrian Genome Research Program GEN-AU: Email: [email protected] Plants are especially required to withstand external stress conditions due to their sessile life-style. The project addresses mechanisms by which plants overcome unfa- Current Research Projects vourable environmental conditions on long terms. In a Three consortia are presently performing active genome research systematic approach, combining the expertise of seven on Arabidopsis in Austria: Austrian research groups, the genetic and epigenetic plas- 1. APAR (Austrian Platform of Arabidopsis Research) is ticity of plants is going to be explored under well-defined funded by the Austrian Science Fund FWF: stress conditions. Using Arabidopsis as a model organism, The APAR consortium is a research platform that coor- the effect of stress on genomic variability and its potential dinates and promotes science on Arabidopsis in Austria. It use for plant breeding is elucidated. currently consists of the following members: Consortium members • Marie-Theres Hauser • Functional characterization of gene families involved in root mor- Werner Aufsatz, GMI Vienna phogenesis Role of histone deacetylation in gene silencing and gene Institute for Applied Genetics and Cell Biology (IAGZ), Uni- regulation (www.gmi.oeaw.ac.at/waufsatz.htm) • versity of Natural Resources and Applied Life Science (BOKU), Marie-Theres Hauser, IAGZ Vienna • Vienna (www.boku.ac.at/zag/AG_hauser.htm) Heribert Hirt, MFPL Vienna • Claudia Jonak, GMI Vienna • • Heribert Hirt Christian Luschnig, IAGZ Vienna, Coordinator • Stress Ortrun Mittelsten Scheid, GMI Vienna Department of Plant Molecular Biology, Max F. Perutz Labo- Epigenetic changes in polyploid plants (www.gmi.oeaw. ratories (MFPL), University of Vienna (www.heribert-hirt.at) ac.at/oms.htm) • Karel Riha, GMI Vienna • Claudia Jonak Analysis of glycogen synthase kinase/shaggy-like kinases 3. Integrative analysis of stress response mechanisms to Gregor-Mendel Institute of Molecular Plant Biology (GMI) improve plant performance, funded by the Vienna Sci- Vienna (www.gmi.oeaw.ac.at/cjonak.htm) ence and Technology Fund WWTF: The network combines expertise in the fields of protein • Irute Meskiene kinases, viral-interacting host factors and micro RNAs Specificity and functional analysis of a PP2C protein phosphatase to elucidate their roles in response to abiotic and biotic gene subfamily stresses. The research specifically focuses on integrative Department of Plant Molecular Biology, MFPL Vienna (www. responses when plants are challenged with a combination mfpl.ac.at/index.php?cid=53) of stresses. The aim of these studies is to provide the mo- lecular basis for breeding novel sustainable crop varieties • Karel Riha of broad resistance against abiotic and biotic stresses. Functional study of the complex at Arabidopsis GMI Vienna (www.gmi.oeaw.ac.at/rkriha.htm) Consortium members • • Markus Teige Andrea Barta, Department of Medical Biochemistry, Calcium-dependent protein kinases in Arabidopsis signal transduc- MFPL, Medical University of Vienna tion Modes of interaction of SR splicing factors in Arabidopsis (www.mfpl.ac.at/index.php?cid=68) Department of Biochemistry, MFPL Vienna (www.mfpl.ac.at/ • index.php?cid=55) Heribert Hirt, MFPL, University of Vienna

27 • Claudia Jonak, GMI Vienna Major Funding Sources for Arabidopsis • Elisabeth Waigmann, Department of Medical Bio- Functional Genomics chemistry, MFPL, Medical University of Vienna Plant as a model system for intra- and intercellular • Basic research only: FWF (Fonds zur Förderung der wis- spread (www.mfpl.ac.at/index.php?cid=57) senschaftlichen Forschung) (www.fwf.ac.at) • Vienna region: WWTF (Wiener Wisenschafts-, Forsc- Other activites on an individual basis hungs- und Technologiefonds) www.wwtf.at • Thomas Greb, GMI Vienna • Specific programs: Bundesministerium für Wissen- Development of vascular tissue schaft, Bildung und Kultur, (www.bmbwk.gv.at/start. (www.gmi.oeaw.ac.at/tgreb.htm) asp?bereich=5) • Austrian Research Promotion Agence, Ltd. (FFG) (www. • Fritz Kragler, Department of Biochemistry, MFPL fff.co.at) Vienna Nature and function of systemic non-coding RNAs (www.mfpl.ac.at/index.php?cid=52)

• Peter Schlögelhofer, Department of Biology, MFPL Vienna Analysis of meiotic recombination (www.mfpl.ac.at/index.php?cid=54)

• Gerhard Adam, IAGZ, BOKU Vienna Detoxification of Fusarium mycotoxins (www.dapp.boku.ac.at/5499.html?&&L=1)

• Marjorie and Antonius Matzke, GMI Vienna Epigenetics (www.gmi.oeaw.ac.at/amatzke.htm )

28 Belgium

http://www.Arabidopsis.org/info/2010_projects/Belgium.jsp Major Funding Sources for Arabidopsis Contact: Pierre Hilson Functional Genomics Department of Plant Systems Biology, VIB, Ghent University Email: [email protected] • Flanders Interuniversity Institute for Biotechnology (VIB; www.vib.be) • European Union Framework Programmes (www.cordis. Belgian Arabidopsis projects are funded via university-, re- lu/) gional- or federal-level grants, but not within calls specifically • Belgian Federal Science Policy Office (www.belspo.be) targeting this model plant species or plants. In addition, the • Institute for the Promotion of Innovation by Science and Flanders Interuniversity Institute for Biotechnology provides Technology in Flanders (IWT; www.iwt.be) significant support to the Department of Plant Systems Biology • European ERA-Plant Genomics initiative (www.erapg. (PSB) (about 5 million Euro per year) in which the Functional org) Genomics Division (P. Hilson) mainly carries out Arabidopsis research. Finally, the Flanders government participates in the Arabidopsis Genomics Tools and Resources European ERA-Plant Genomics initiative and has earmarked • Gateway-compatible destination vectors (www.psb.ugent. funding specifically supporting research in that framework. be/gateway) Furthermore, PSB continuously develops and disseminates an • Large generic ongoing programs include: exhaustive collection of destination vectors, designed for the functional analysis of genes in plant cells and compatible with 1. CATMA (www.catma.org; database hosted at PSB) the recombinational cloning Gateway technology (www.psb. maintaining a repertoire of >30,000 gene-specific se- ugent.be/gateway). Finally, PSB participates in efforts to con- quence tags for transcription profiling and RNAi, avail- federate database systems and aims at providing information able from NASC; about clone resources and phenotypes via integrated webser- 2. AGRIKOLA (www.agrikola.org; database hosted at PSB) vices. creating and exploiting genome-scale resources for target- ed hairpin RNA gene silencing, available from NASC; in Current Research Projects collaboration with the Belgian Coordinated Collections of Microorganisms (BCCM/LMBP), PSB is also setting • A Belgian national research project (IAP) focuses on the up a service for the sequence validation and dissemination study of the molecular mechanisms regulating the devel- of AGRIKOLA resources (http://www.belspo.be/belspo/ opment of plant roots and the interaction of roots with fedra/proj.asp?l=en&COD=C3/020) their environment. 3. SAP (www.psb.ugent.be/SAP) creating and exploiting a • Other current Arabidopsis research topics in Belgium include the cell cycle (D. Inzé, L. De Veylder), root and genome-scale promoter amplicon collection for the analy- leaf growth and development (T. Beeckman, G. Beemster, sis of transcriptional networks. M. Van Lijsebettens), abiotic stress (F. Van Breusegem), genome annotation and (Y. Van de Peer, P. Rouzé), (M. Kuiper), proteomics (G. De Jaegher), transcriptional networks and heterosis (M. Vuylsteke), lignin biosynthesis (W. Boerjan), ethylene signaling (D. Van Der Straeten), hormone biology (Harry Van Onckelen), membrane proteins (M. Boutry), salt stress and tolerance to heavy metal (N. Verbruggen), and plant pathogen interaction (B. Cammue).

29 Canada

http://www.Arabidopsis.org/info/2010_projects/Canada.jsp The Crosby lab investigates the role of E3 ubiquitin ligase Contact: W.L. Crosby (E3) complexes in the regulation of patterning and devel- University of Windsor, Ontario, Canada opment in Arabidopsis. • Email: [email protected] Raju Datla – NRC Plant Biotechnology Institute (raju. [email protected]) The Datla lab investigates gene expression dynamics dur- In March of 2006, 57 laboratory groups known to be con- ing embryo development, currently focusing on genes in ducting research with Arabidopsis were polled by Email for con- Arabidopsis as well as the closely related Brassica napus. tributions to the MASC report. Of these, approximately 30 re- • Michael Deyholos – University of Alberta (deyholos@ sponded and their contributions are summarized in this report. ualberta.ca) The past two years have witnessed a period of rapid turnover The Deyholos lab applies genetic analysis and functional and new hires among University Faculty in Canada – in part genomics of Arabidopsis to two areas of research: vascular due to the retirement of those Faculty hired in the late 1960’s development, and abiotic stress responses. and early 70’s. As a result, a number of new and exciting young • Sonia Gazzarrini – University of Toronto, Scarborough, scientists have joined the plant science research cadre, includ- ([email protected]) ing a significant number of Arabidopsis researchers. The Gazzarrini group uses functional genomic, molecular and chemical genetic approaches to study the molecular Reports mechanisms that regulate early developmental phase transitions and plant resistance to abiotic stresses in Ara- • François Belzile- l’Université Laval ([email protected]. bidopsis. ca) • Vojislava Grbic – University of Western Ontario (vgrbic@ The Belzile lab studies Arabidopsis DNA mismatch repair uwo.ca) (MMR) in regards to both microsatellite instability and The Grbic lab investigates the diversification of plant homoeologous recombination. forms by studying a set of late-flowering Arabidopsis ac- • Thomas Berleth – University of Toronto (thomas.ber- cessions with naturally occurring variant morphology. [email protected]) • George Haughn – University of British Columbia The Berleth lab developed approximately 4,000 indirect ([email protected]) enhancer trap lines, together with ~ 70,000 indirect acti- The Haughn laboratory studies regulation of plant mor- vation tags (among them ~30,000 conditional activation phogenesis and seed coat differentiation in Arabidopsis tags) for use in the study of very early vascular genes. In and oversees the Canadian reverse genetic TILLING addition, they are conducting a study to map QTLs de- facility, CAN-TILL (http://www.botany.ubc.ca/can-till/). fining Arabidopsis fibre properties. • Shelley Hepworth – Carleton University (shelley_hep- • Malcolm Campbell – University of Toronto (campbell@ [email protected]) botany.utoronto.ca) The Hepworth lab focuses on determining how positional The Campbell lab investigates (1) the perception of information is translated into morphological asymme- sugars, amino acids and water, and how this affects the try, an important aspect of developmental patterning in allocation of resources to key facets of metabolism and plants. development, (2) comparative genomic analyses with the • Robert Hill –University of Manitoba (Rob_Hill@umani- model woody perennial Populus. toba.ca) • Jin-Gui Chen – University of British Columbia (jingui@ The focus of the research in the Hill laboratory is interchange.ubc.ca) on ABA receptors and their mechanism of interaction The Chen lab investigates signal transduction networks with other signaling components. using both forward- and reverse-genetic, molecular and • Kenton Ko – Queens University ([email protected]. cellular biological, and biochemical approaches. ca) • William Crosby – University of Windsor (bcrosby@ uwindsor.ca)

30 The Ko lab uses Arabidopsis as a model for studying the The Regan lab investigates the role of ethylene in regulat- relationship between plastid protein delivery, adaptation, ing developmental processes such as seed dormancy, flow- and organelle biogenesis. ering time, development, and secondary growth. • Igor Kovalchuk –University of Lethbridge (igor.koval- • Dan Riggs – University of Toronto at Scarborough [email protected]) ([email protected]) The Kovalchuk lab uses Arabidopsis to study genetic and Research in the Riggs laboratory focuses on two distinct epigenetic aspects of plant genome stability and plant but interrelated processes: factors which affect plant ar- stress response. chitecture and factors that regulate chromatin condensa- • Ljerka Kunst – University of British Columbia (kunst@ tion. interchange.ubc.ca) • Owen Roland – Carleton University (owen_roland@ The Kunst laboratory studies lipid metabolic pathways in carleton.ca) higher plants, focusing on two specific areas of lipid me- The Roland lab studies the synthesis of cuticular waxes tabolism: cuticular wax biosynthesis and secretion. and their deposition onto plant surfaces via map-based • Xin Li – University of British Columbia (xinli@inter- cloning and reverse genetic and biochemical approaches. change.ubc.ca) • Kevin Rozwadowski – Agriculture and Agri-Food Cana- The Li group is studying R-protein signaling pathways da, Saskatoon ([email protected]) that play central roles in recognizing and initi- The Rozwadowski group is interested in DNA double- ating downstream defense cascades. strand break repair in vegetative and meiotic cells. The • Jaideep Mathur – University of Guelph (jmathur@ lab uses Arabidopsis as a model to characterize the details uoguelph.ca) of the repair process and evaluate plant responses to The Mathur lab studies subcellular dynamics and organ- genotoxic stress. elle interactions in order to understand the early respons- • Lacey Samuels – University of British Columbia (lsamu- es of plants to various abiotic / biotic stimuli. [email protected]) • Doug Muench – University of Calgary (dmuench@ucal- The Samuels lab is conducting a multi-disciplinary re- gary.ca) search project to study the plant cuticle. The project in- Research in the Muench laboratory is aimed at under- volves characterizing biosynthetic mutants (Kunst Lab), standing the role of the plant cytoskeleton, specifically studying wax export and the cell structure of these mu- microtubules, in subcellular mRNA localization, protein tants (Samuels Lab) and analyzing the chemical composi- sorting, and low temperature stress signaling. tion and biosynthetic pathways of cuticular lipids (Jetter • Roger Lew – York University, Toronto (planters@yorku. Lab). ca) • Dana Schroeder – University of Manitoba (schroed3@@ The Lew lab is interested in the electrical properties of cc.umanitoba.ca) Arabidopsis root hairs. Current studies involve ion trans- The Schroeder group works on the regulation of light sig- port in cellular expansion and plant cell stress response. naling and DNA repair by DET1, DDB1A, and DDB2 • Nicholas Provart – University of Toronto (nicholas.pr- in Arabidopsis. [email protected]) • Elizabeth Schultz – University of Lethbridge (schultz@ The Provart lab oversees the Botany Array Resource (see uleth.ca) Functional Tools at the end of this section.) In addition, The Schultz lab studies the regulation of leaf vein pattern the wider Arabidopsis research group at the University of and its relation to leaf shape. Toronto has generated 10,000 DEX inducible random • Geoffrey Wasteneys- University of British Columbia in insertion lines which will be deposited to the stock center Vancouver ([email protected]) His laboratory in the future. uses Arabidopsis thaliana as a model system to understand • Przemyslaw Prusinkiewicz – University of Calgary how microtubule function is regulated in eukaryotic cells. ([email protected]) • Randall Weselake – University of Alberta (randall.wese- The Prusinkiewicz group focuses on simulation modeling [email protected]) of Arabidopsis, including the multiple roles of auxin in The Weselake group is (1) assessing the functionality (in plant morphogenesis, general methods of modeling plants this case the ability to impart tolerance to abiotic stress) across multiple scales of organization, and further devel- of a number of oilseed rape genes using Arabidopsis, and opment of simulation software. (2) researching novel methods for modifying the fatty • Sharon Regan – Queens University (regans@biology. acid composition of seed oils. queensu.ca) • Tamara Western – McGill University (tamara.western@ mcgill.ca)

31 The Western lab uses a combination of forward genetics Arabidopsis Genomics Tools and Resources screens for mutants affected in mucilage production and • reverse genetics identification of knockouts in genes pre- Canadian reverse genetic TILLING facility, CAN-TILL (http://www.botany.ubc.ca/can-till/). dicted to act in cell wall synthesis and modification. • • Stephen Wright – York University ([email protected]) Botany Array Resource (http://bbc.botany.utoronto. The Wright lab is interested in (1) understanding the ca): Contains more than 1000 gene expression data sets forces driving gene and genome evolution in the genus consisting of more than 24.6 million data points. Tools Arabidopsis, (2) testing for the accumulation and increased available for the exploration of these data include: [1] an activity of transposable elements in the allopolyploid Expression Browser for performing electronic Northerns genome of Arabidopsis suecica, and (3) sequencing of the [2] a new Fluorescent Protein Browser tool, which paints genomes of Arabidopsis lyrata and . gene expression information from the Gene Expression • Jitao Zou – NRC Plant Biotechnology Institute (jitao. Map of Arabidopsis Development onto a diagrammatic [email protected]) representation of the developmental series used, [3] Ex- The Zou lab is primarily interested in lipid and carbon pression Angler, to identify genes that are co-expressed metabolism. They study enzymatic components of the with gene of interest in a specified data set, and [4] lipid metabolic network and are also interested in explor- Promomer for the identification of potential cis-regula- ing natural variation in wild type accessions to dissect tory elements in the promoter of a given gene, or in the regulatory components of seed oil deposition. promoters of a set of co-regulated genes. Additional tools include a database of genome-wide predicted CAPS markers across 96 accessions, based on sequence data from Magnus Nordborg and colleagues (2005, PLoS Biol. 3:e196).

32 China

http://www.Arabidopsis.org/info/2010_projects/China.jsp • the genetic control on growth by Dr. De Ye’s Contact: Wei-Cai Yang group on VGD1 and TPD1 genes and gametogenesis by Institute of Genetics and , Chinese Dr. Wei-Cai Yang’s group on SWA1 gene function; and Academy of Sciences • the role of blue light receptor in stomata opening by Dr. Email: [email protected] Hong-Quan Yang’s group. • In addition, progress has been made in understanding plant responses to stresses, includes functional studies on Arabidopsis research takes place mainly in the Beijing AtNAC2 by Shou-Yi Chen’s group, LOS4 by Dr. Zhi- and Shanghai areas, including Peking University, China Zhong Gong’s group, AtERF7 by Dr. Chun-Peng Song’s Agricultural University, Tsinghua Univeristy, and Chinese group, and NHO1 by Dr. Jianmin Zhou’s group. Academy of Sciences (CAS). Funding for Arabidopsis research • Finally, large scale whole genome profiling on 18 is improving in China as the National Science Foundation of different organs and/or tissues was performed using China (NSFC), the main funding agency for basic research, will 70mer oligomer microarrays by Dr. Xing-Wang Deng double its budget in the next five years. A new Center for Signal and coworkers at the Peking-Yale Joint Center for Plant Transduction & Metabolomics (C-STM) using model plants Molecular Genetics and Agro-biotechnology was established at the Institute of Botany, CAS in 2005. This center will focus on hormone and peptide signaling, secondary Major Funding Sources for Arabidopsis metabolites, and plant toxins. On November 30, 2005, more Functional Genomics than 300 participants attended the annual Workshop on Arabi- dopsis Research, held at Peking University. National Science Foundation of China: (www.nsfc.gov.cn/) 83 Shuangqing Road, Haidian District, Beijing Current Research Projects

• In 2005, NSFC funded Dr. De Ye at China Agricultural University and Dr. Zhong-Nan Yang at Shanghai Normal University to support two key projects on sexual plant reproduction focusing on male sterility in Arabidopsis. • To facilitate international collaboration on research in epigenetics, the Chinese Academy of Sciences (CAS) funded a team project headed by Dr. Xiao-Feng Cao at the Institute of Genetics and Developmental Biology, Beijing.

A special issue of the Journal of Integrative Plant Biology dedicated to Arabidopsis research in China was published in January 2006. Significant progress achieved by Chinese Arabi- dopsis researchers in broad aspects of plant sciences was reviewed by Prof. Zhihong Xu of Peking University. Areas include: • the epigenetic control in leaf development by Dr. Hai Huang’s group on RDR6 gene and in root development by Dr. Xiaoya Chen’s and Dr. Huishan Guo’s group on miRNA160 and miRNA164 respectively, and by Dr. Shunong Bai and coworkers on histone modification; • the role of hormone signaling in leaf development by Dr. Lijia Qu’s group on the functional study of IAMT1 gene and MSBP1 by Dr. Hong-Wei Xue’s group;

33 France

http://www.Arabidopsis.org/info/2010_projects/France.jsp • The role of abscisic acid and reversible protein phosphor- Contact: David Bouchez ylation in drought adaptive responses. PI: Annie Marion- Institut Jean-Pierre Bourgin, SGAP-INRA Centre de Ver- Poll, Versailles sailles, Versailles • Characterization and control of meiotic recombination in Email: [email protected] plants. PI: Mathilde Grelon, Versailles • Structural and functional study of oil and protein storage bodies in A. thaliana and in B. napus: towards environ- The major source of funding in France forArabidopsis func- mentally friendly oil and protein extraction process? PI: tional genomics projects is Génoplante, a federative program Thierry Chardot, (Grignon) for plant genomics research created by public institutions and • of redox interactions and their role in stress several French ag-biotech companies. Created in 1999, it has responses using insertion mutants and metabolomics. PI: supported research on the genomes of crop plants, and also has Graham Noctor (Orsay) directed over €62 million of research on Arabidopsis, supporting • Functional and structural characterization of the Arabi- creation of high throughput genomics tools and resources as dopsis APC/cyclosome. PI: Pascal Genschik (Strasbourg). well as functional genomics studies. Over a hundred projects • Identification of plant components involved in the per- have been funded by the ministries of research and agriculture. ception by Arabidopsis of Ralstonia solanacearum, a bacte- A new initiative was launched in April 2005 to sustain re- rial pathogen. PI: Yves Marco (Toulouse) search in plant genomics to the year 2010: "GENOPLANTE 2010" is a 6 year initiative involving seven partners from the Ongoing Research Projects public sector (INRA, CNRS, CIRAD, IRD) and private com- • panies (Biogemma, Arvalis, Sofiproteol). This program is now A short description of ongoing Génoplante projects can administered by the French National Research Agency (ANR: be found at: (www.genoplante.com/doc/File/pdf/Projets Agence Nationale de la Recherche). The annual budget for en cours.pdf) the program for the next few years is planned to be around Arabidopsis Génoplante projects funded in 2004 included 12 million Euros per year. Although a large part is devoted to efforts on (D Roby, I Jupin, P Saindrenan, L crop plants, several Arabidopsis projects are funded through the Jouanin), epigenetics (V Colot, O Vionnet), seed devel- "Functional Analysis" and "New Tools" committees. The ANR opment and eQTLs (M Caboche, L Lepiniec) and new also contributes to funding Arabidopsis research through its methods for purifying TAP-tagged protein complexes (H "white programs" for fundamental research. Mireau). • French-Spanish-German projects and ERA-PG: Sev- Examples of Newly Funded Research Projects eral Génoplante projects are jointly funded with similar (2005) German and Spanish initiatives in the frame of bi- and tri-lateral collaborations. (www.genoplante.com/doc/File/ (http://www.genoplante.com/doc/File/pdf/Projets 2005.pdf) pdf/Projets collaboratifs.pdf ) • (http://www.agence-nationale-recherche.fr/documents/ Génoplante and ANR are participating in ERA-PG, aap/2005/finances/financeBLANCSAE2005.pdf) a European network of research funding organizations responsible for the development of national or regional • Improving homologous recombination and gene target- plant genomics research programs. The network concen- ing, a three species confrontation. PI : Marie-Pascale trates on creating a stimulating and fruitful environment Doutriaux, Gif for European plant genomics. ERA-PG started in 2004 • Repair mechanisms of oxidized proteins in chloroplast of with twelve member organizations from eleven countries Arabidopsis thaliana, PI : Pascal Rey, Cadarache funded through the EU’s 6th Framework Program. In • Arabidopsis functions involved in disease susceptibility, PI 2005, four new countries have joined. : Bruno Favery, Antibes

34 Major Funding Sources for Arabidopsis • ATOME: Arabidopsis thaliana ORFeome whose goal is to Functional Genomics create expression vectors. ATOME, in collaboration with Invitrogen, aims to clone up to 5000 Arabidopsis ORFs • Génoplante : (http://www.genoplante.com/) into Gateway entry vectors. (www.evry.inra.fr/public/ • French National Research Agency (ANR): (www.gip-anr. projects/orfeome/orfeome.html) fr/) • ERA-PG: (www.erapg.org/) The Institut Jean Pierre Bourgin (INRA Versailles, www- ijpb.versailles.inra.fr/en/) houses the French Resource Centre Arabidopsis Genomics Tools and Resources for Arabidopsis (www-ijpb.versailles.inra.fr/en/sgap/equipes/ variabilite/crg) which distributes insertion lines and several The Plant Genomics Unit (URGV, Evry), runs large ge- populations of recombinant inbred lines and contains: neric programs on Arabidopsis functional genomics (www.evry. • VNAT: A database on Arabidopsis natural variation inra.fr/public/scientific/functional.html), including • (http://dbsgap.versailles.inra.fr/vnat/ FLAGdb++: an Arabidopsis genomics database includ- • Agrobact +: A database for the Versailles T-DNA lines ing amongst many other things an inventory of flanking (http://dbsgap.versailles.inra.fr/agrobactplus/English/Ac- sequence tags from the Versailles Arabidopsis T-DNA col- cueil_eng.jsp) lection. Also includes the rice genome and its annotation. (www.evry.inra.fr/public/projects/bioinfo/flagdb.html) The recently created "National Resources Centre for Plant • CATMA: A complete Arabidopsis thaliana microarray Genomics" (CNRGV) in Toulouse distributes Arabidopsis containing more than 24000 gene-specific tags. This pro- cDNA and BAC clones. They also provide services including gram involves several EU countries. (www.catma.org) high density colony arrays, genomic pools, custom screening, • CAGE: A reference expression database using the CAT- robotic services and large scale PCR amplification. MA microarray chip. Involves a consortium of European • CNRGV: (http://cnrgv.toulouse.inra.fr/ENG/) researchers. (www.cagecompendium.org/objectives.htm)

35 Germany

http://www.Arabidopsis.org/info/2010_projects/Germany.jsp In 2003, AFGN initiated the largest international Ara- Contacts: bidopsis transcriptome project entitled AtGenExpress. It con- 1) MASC, German representative: Thomas Altmann; Uni- sists of 497 data sets almost all of which cover duplicate or versity of Potsdam; E-Mail: [email protected] triplicate experiments. The AFGN part of the project includes 2) AFGN (Arabidopsis Functional Genomics Network, DFG 310 data sets for Arabidopsis development and responses to the funded): Klaus Harter; University of Tuebingen; E-Mail: biotic and abiotic environment (photomorphogenic light, dif- [email protected] ferent stresses, pathogens) and for several natural accessions. 3) GABI (Genome Analysis of the Plant Biological System, Further major contributions to AtGenExpress were provided by colleagues from RIKEN (mainly hormone and inhibitor re- BMBF funded): Bernd Weisshaar; Bielefeld University; sponses), from the 2010 Project (responses to pathogens) and E-Mail: [email protected] from ETH Zürich (cell cycle). The overall database, which is open to the scientific public, provides the experimental base for Research on Arabidopsis thaliana has a long history in Ger- many open access bioinformatics tools such as Genevestigator many, and many individual research groups have used this refer- and MapMan. ence plant for analysing different aspects of plant biology. Two AFGN Programs and Funding independent programs support research on plant functional genomics in Germany, namely the Arabidopsis Functional Ge- • In collaboration with the 2010 Project, AFGN founded nomics Network (AFGN), supported by the German Research the Young Researcher Exchange Program. This program Foundation (DFG), and the more crop, and therefore applica- financially supports short term research visits (up to three tion oriented plant genomics research program, GABI, funded months) of young German scientists in cooperating US by the Federal Ministry of Education and Research (BMBF). laboratories and vice versa. Both programs work together in close cooperation, with inten- • Together with colleagues from Austria and Switzerland, sive links at both the scientific and the contributor level. AFGN initiated an international conference on Arabidop- The DFG-supported AFGN was founded by a bottom- sis functional genomics which is recognized and attended up approach of the German Arabidopsis research community by many European and US scientists. in 2001 as a basic research program. AFGN currently funds • The second funding period of the AFGN will end in the 25 projects in Germany and has, almost from the start, been fall of 2007. Discussions about the structure and the main organized in close coordination with the 2010 Project of the goals for future funding periods are presently underway. United States National Science Foundation (NSF). Together In any event, AFGN will maintain the basic character with many other research programs throughout the world, these of its research and will continue to concentrate on the programs aim to elucidate the function of all Arabidopsis genes reference plant Arabidopsis. The future direction of the by the year 2010. A coordinated and unique reviewing process research in AFGN will aim to get in-depth predictions of the jointly submitted proposals from US and German re- of how certain plant processes and pathways take place search groups was organized for the first time for the projects under given endogenous or environmental conditions. currently running between the 2010 Project and the AFGN. This approach requires the analysis of gene networks and a strongly integrated view of gene functions. AFGN Current Research Projects GABI Funding and Programs The main activities of the ongoing research projects con- centrate on the analyses of members of selected multiprotein GABI, a BMBF funded German plant genome research families and cover the elucidation of their structure, activity, program is now in its seventh year. With an annual budget of interaction partners, gene expression, intracellular localisation, 10 million Euros plus an additional 20% from industrial part- post-translational regulation and function. From the methodi- ners GABI is the biggest research program in plant genomics cal point of view, the AFGN members utilize many techniques in Germany. Approximately 30% of the total budget supports and methods of the functional genomics approach. research on A. thaliana. In its second program period transla- tional research was introduced: topic-oriented research clusters

36 combine basic research on A. thaliana with research activities Major Funding Sources for Arabidopsis on crops. Since the start of GABI, A. thaliana has also served Functional Genomics to deepen international cooperation through bilateral as well as trilateral research projects between France (Génoplante), Spain • AFGN: (www.uni-tuebingen.de/plantphys/AFGN/) 2 and GABI. million €/year budget from the German Research Foun- Within GABI, important resources such as the GABI- dation (DFG) (www.dfg.de) KAT lines, the world’s second largest T-DNA insertion line • GABI: (www.gabi.de) 12 million €/year from the Federal population, were generated and are available to the global re- Ministry of Education and Research (www.bmbf.de) and search community. The transfer of the confirmed insertion a Business Platform promoting GABI Plant Genome lines from Cologne to the Nottingham Stock Center (U.K.) Research e.V. (WPG) (www.wirtschaftsverbund-gabi.de) began in 2005 and will continue until the conclusion of the GABI-KAT project. The generation of plant resources for the Arabidopsis Genomics Tools and Resources analysis of natural diversity (natural accessions and experi- • AtGenExpress: (web.uni-frankfurt.de/fb15/botanik/mcb/ mental populations such as F1's, F2's, RIL's, NIL's), as well as AFGN/atgenex.htm) their geno- and phenotyping to provide characterized biologi- • GABI-KAT: (www.gabi-kat.de/) cal material for researchers, is coordinated between colleagues • GABI-Matrix: (http://mips.gsf.de/projects/plants/) from Génoplante (France) and GABI. A database summarising • GABI-PD: (http://gabi.rzpd.de/) genetic and experimental data is under construction, and data • GABI-ARAMEMNON: (www.uni-koeln.de/math-nat- warehousing, management and visualisation are primary foci fak/botanik/bot2/agflue/HOME/projects/GABI_rkunze/ for bioinformatics activities in GABI. GABI-Matrix at MIPS index.html) (GSF Munich) and the GABI-Primary Database (RZPD • GABI-TILLING: (www.gabi-till.de/index.de.html) Berlin) are the two big centres for bioinformatics in GABI, flanked by many decentralized bioinformatics groups within the research institutions. ARAMEMNON, one of the world largest databases on Arabidopsis thaliana membrane transport proteins, was generated to aid in the identification, classifi- cation and characterization of novel transporters. The GABI TILLING facility is an example of a coordinated technological development that expands the worldwide capacity for TILL- ING screens in Arabidopsis. Discussions have also started within the GABI commu- nity on how to continue research and development activities. GABI-FUTURE (2007-2013), the third funding phase of the national plant genomics program, is underway and is expected to increase the research budget significantly. GABI-FUTURE will continue to bundle fundamental and applied, but still pre- competitive, research activities within a single program. Public- private-partnerships, the backbone of the program, will con- tinue and more partners will be needed for the gradual creation of a knowledge based bio-industry. Furthermore, basic research on crops will be improved to close the gaps in knowledge and to ease the technology transfer from A. thaliana to important crop plants. GABI and the AFGN played an important role during the establishment of the European Research Area network on Plant Genomics (ERA PG). Out of the total annual budget of approximately 10 million Euros for the first joint call of the ERA PG, the two German funding agencies support German research groups with more than 3 million Euros per year.

37 Italy

http://www.Arabidopsis.org/info/2010_projects/Italy.jsp • Another Italian group (B. Mattei) is one of the partners Contact: Paola Vittorioso involved in the project "Functional Genomics for Biogen- University of Rome "La Sapienza", Dept. Genetics and Mo- esis of the Plant Cell Wall" using Arabidopsis as a model lecular Biology, Rome system, and funded by the UE Marie Curie Training Net- Email: [email protected] work. • Italy (L. Colombo) is also participating in the EU FP6 Marie Curie Training Project “TRANSISTOR” (Trans- Most of the Italian groups actively engaged in Arabidopsis cis element regulating key switches in plant develop- research are involved in national and international plant func- ment). tional genomic network projects. In the last few years, devel- opment of a common technological platform has allowed for Major Funding Sources for Arabidopsis creation of a network among groups of the highest qualification Functional Genomics in Italian universities, public research institutes and the most relevant plant biotechnology companies. This national network, • MIUR (www.miur.it) will support the First Call for Pro- funded by the Italian Ministry of Research (MIUR), repre- posal of the ERA-NET Plant Genomics as part of its sents a first step towards the establishment of a National Plant institutional activities. National Call Coordination: Dr.

Biotechnology Center. Post-genomic technologies and other M. Massulli, [email protected]. The Ministry has existing technologies will be made available to all partners of also funded many national projects (PRIN 2005-2007). the network. The network has developed technologies for (1) • The UE Marie Curie Training Network is funding the gene functional analysis (i.e., RNA interference, negative and projects: "Functional Genomics for Biogenesis of the positive dominant transformants, Tilling), (2) the analysis of Plant Cell Wall" (2005-2009), and “Transistor” (Trans-cis interactions between genes (i.e., Arabidopsis macro- and mi- Regulatory Element regulating key switches in plant de- cro-arrays, real-time PCR) and (3) the identification of pro- velopment). tein partners and targets (i.e., TAP-TAG analysis, two hybrid • The Italian Space Agency (www.asi.it) analysis in yeast and plants, and stable antibodies phage display • The European space Agency (www.esa.int/esaCP/index. libraries). html) • The Insitut Pasteur (www.pasteur.fr/pasteur/internation- Current Research Projects al/Dai_en/lines.html) • Italy will participate in the ERA-NET program, a novel feature of the European Union’s 6th Framework Program that provides support for transnational networking and coordination of national research programs. • The Italian Ministry of Research has funded several col- laborations between Arabidopsis groups from two differ- ent countries. One such collaboration involving Italy (P. Costantino) and Spain (R. Solano) aims to contribute to transcriptional regulation analysis of two important processes of higher plants: seed and the re- sponses to necrotrophic fungi, respectively. This project is based on the joint exploitation of complementary tech- nologies for the identification of TF targets available in the two proposing laboratories: (1) TAP-TAG and ChIP technologies, being developed in Rome for Arabidopsis (MIUR funded), and (2) microarray analysis, with tech- nology fully established in Madrid.

38 Japan

http://www.Arabidopsis.org/info/2010_projects/Japan.jsp • The PFGRG and Genome Exploration Research Group Contact: Kazuo Shinozaki of the RIKEN Genome Sciences Center and the Experi- RIKEN Plant Science Center mental Plant Division of the BRC produced the Arabi- Email: [email protected] dopsis DNABookTM containing 1,069 RIKEN Arabidop- sis Full-Length (RAFL) cDNAs for transcription factors (http://pfgweb.gsc.riken.jp/DNA-Book/). In Japan, ongoing programs for Arabidopsis functional ge- nomics are mainly found at RIKEN (www.riken.go.jp/engn/in- Kazusa DNA Research Institute dex.html) and Kazusa DNA Research Institute (www.kazusa. • At the Kazusa DNA Research Institute (Satoshi Tabata), or.jp/eng/index.html). Other programs are supported by the ongoing projects include a collection of T-DNA tagged CREST program of the Japan Science & Technology Corpo- lines and Arabidopsis and Lotus japonicas ESTs. A major ration, the Program of Promotion of Basic Research Activities project is the genomic sequencing of Lotus japonicas and for Innovative Biosciences (BRAIN), the NEDO project, and tomato. Grants-in-Aid for Science from the Ministry of Education, • Arabidopsis T87 cultured cells have been transformed with Science, Culture and Sports (MEXT). A joint meeting on Ara- th th RAFL cDNAs and other cDNAs for metabolic profiling bidopsis and rice research was held on July 6 and 7 , 2005 in of primary and secondary metabolites (Daisuke Shibata). Nara; more than 300 attendants discussed systematic analyses • New websites include KaPPA-View: Integration of tran- of gene functions and networks. scriptome and metabolome data in plant metabolic path- RIKEN ways (Dr. Toshiaki Tokimatsu), and KATANA, Kazusa Annotation Abstract: Integration of major database sites RIKEN groups involved in Arabidopsis functional genom- of Arabidopsis genome annotation (Dr. Kentaro Yano). ics include the Plant Functional Genomics Research Group (PFGRG), the Plant Science Center (PSC) and the BioRe- Other Arabidopsis Functional Genomics source Center (BRC). Activities • In 2005, the PSC (Director: Kazuo Shinozaki) started a new project entitled “Understanding metabolic systems Several groups at other centers and universities are also for plant productivity” to integrate metabolomics with involved in Arabidopsis functional genomics. transcriptomics. The Metabolomics Research Group • The Plant Gene Function Research Team of AIST (Group Director: Kazuki Saito) was established at the (http://unit.aist.go.jp/gfrc/pgrt/) is systematically analyz- PSC (http://prime.psc.riken.jp/) in 2005, while the PF- ing various functions of transcription factors using repres- GRG (Group Director Minami Matsui) joined in April, sor domain (CRES-T system) (Masaru Ohme-Takagi, 2006. Agency of Industrial Science & Technology in Tsukuba). • Since 2004, PSC has contributed to AtGenExpress • Genome-wide analysis of the two-component system is (Yukihisa Shimada and Shigeo Yoshida) (www.arabidop- performed in Nagoya University (Takeshi Mizuno). sis.org/info/expression/ATGenExpress.jsp). • A database on metabolites, KNApSacK, is available from • The BRC is supported by the National Bio-Resource NAIST (Shigehiko Kanaya). Project and distributes plant materials developed in Ja- pan. More than 18,000 plant materials including RAFL Major Funding Sources for Arabidopsis clones, Ds-tagged lines and Activation (T-DNA)-tagged Functional Genomics: lines (see below for more information) have been provid- ed to approximately 730 laboratories located in 38 coun- • CREST of Japan Science and Technology Corporation tries. Homozygous seeds of Ds-tagged mutants are under (www.jst.go.jp/EN/) preparation, and some of them will be publicly available • Program of Promotion of Basic Research Activities for this year. Masatomo Kobayashi ([email protected]) is Innovative Biosciences (http://brain.naro.affrc.go.jp/in- in charge of distributing Arabidopsis resources at the BRC dex-e.html) (www.brc.riken.jp/lab/epd/Eng/).

39 • NEDO (www.nedo.go.jp/english/activities/1_sangyo/1/ 6. Transcriptome analysis of genes expression in re- pro-sangi2e.html) sponse to both abiotic and biotic stress using RAFL • Grants-in-Aid for Science from the Ministry of Educa- full-length cDNA microarray analysis (Motoaki Seki) tion, Science, Culture and Sports (MEXT) (www.jsps. (http://pfgweb.gsc.riken.go.jp/pjCdma.html) 7. go.jp/english/e-grants/grants.html) Homozygous Ds-insertional lines in gene-coding re- gions (Takashi Kuromori, Fumiyoshi Myouga) (http:// Arabidopsis Genomics Tools and Resources pfgweb.gsc.riken.go.jp/pjAcds.html) 8. Reverse proteomics for functional analysis of in vitro • Plant Functional Genomics Research Group in The RIK- expressed proteins using the wheat germ cell-free pro- EN PSC (PIs of the PFGRG are Minami Matsui and tein synthesis system in collaboration with a group at Kazuo Shinozaki) (http://pfgweb.gsc.riken.go.jp/index. Ehime University (Yaeta Endo, Principal Investigator html) & Motoaki Seki) (www.ehime-u.ac.jp/English/facul- 1. A collection of full-length cDNAs (RAFL clones: ties/cell.html) Motoaki Seki) (http://rarge.gsc.riken.go.jp/) • RIKEN Plant Science Center (www.psc.riken.go.jp/in- 2. A collection and phenotype analysis of Ds-tagged dexE.html) lines (Takashi Kuromori), (http://rarge.gsc.riken. • RIKEN Genome Sciences Center (www.gsc.riken.jp/in- go.jp/) dexE.html) 3. A collection and phenotype analysis of activation tag- • Kazusa DNA Research Institute (www.kazusa.or.jp/eng/ ging lines (Miki Nakazawa), (http://amber.gsc.riken. index.html) jp/act/top.php) • BioResource Center (www.brc.riken.jp/lab/epd/Eng/) 4. Full-length-cDNA-overexpressing (FOX) transgenic • KaPPA-View (http://kpv.kazusa.or.jp/kappa-view/) lines (Takanari Ichikawa) • KATANA (Kazusa Annotation Abstract: www.kazusa. 5. Structural proteomics of plant regulatory proteins or.jp/katana/) with novel structures in collaboration with the GSC • KNApSacK (http://kanaya.aist-nara.ac.jp/KNApSAcK/) Protein Research Group (PI: Dr. Shigeyuki Yo- • The Metabolomics database at the PSC (http://prime.psc. koyama) (http://protein.gsc.riken.go.jp/Research/in- riken.jp/) dex_at.html)

40 The Netherlands

http://www.Arabidopsis.org/info/2010_projects/Netherlands.jsp Wageningen University–Current Projects Contacts: Willem Stiekema, • QTL express: identification of plant performance traits in Centre for BioSystems Genomics, Wageningen Arabidopsis by combining high-throughput mapping and Email: [email protected] expression profiling (funded to 2008; M. Koornneef, D. Ben Scheres Vreugdenhil). Department of Molecular Cell Biology, University of Utrecht • Controlling phytate and micronutrients as determinants Email: [email protected] of food quality (funded to 2007; Jianjun Zhao, M. Koorn- neef, G. Bonnema, D. Vreugdenhil) Center for BioSystems Genomics, the • Heavy metal tolerance and accumulation in Thlaspi caer- Netherlands Plant Genomics Network ulescens, a heavy metal hyper-accumulating plant species (M. Aarts, J. van de Mortel, S. Talukdar; 2002-2007). • Arabidopsis research within this national plant genomics Do plants love heavy metals? (A. Assunção, M. Aarts; research program focuses on the analysis of the regulatory net- 2005-2008) • work of genetic, biochemical, physiological and environmental Functional genomics of secondary metabolite biosynthe- interactions that control plant performance and the complex sis: the Arabidopsis model (W. van Leeuwen, traits involved in plant- interactions and adaptation M. Aarts; 2004-2006) • to stresses. The Center strives for fully integrated large-scale Natural variation for Arabidopsis mineral content (A. activation tag screening, gene expression, proteome and me- Ghandilyan, M. Aarts; 2003-2007) • tabolite profiling based on the full exploration of the available Brassica vegetable nutrigenomics (G. Bonnema, M. Aarts; genetic variation with emphasis on control of metabolic com- 2005-2010) • position. Additional projects involve understanding the adap- The role of tomato serine and cysteine proteases in de- tive traits relevant for research in and tomato and the fense signaling (R. van der Hoorn) • development of concepts and technologies based on Arabidopsis A molecular genetic approach to chemical ecology and genetics and genomics. Four current projects funded through community ecology (M. Dicke) • 2008 focus on: Cross-talk between signal-transduction pathways in in- • Arabidopsis quality: the genetic and genomic analysis of duced defense of Arabidopsis against microbial pathogens metabolic composition (Koornneef/Vreugdenhil, Wa- and herbivorous insects. M. Dicke (joint projects with C. geningen University; Pereira, Plant Research Interna- Pieterse, Utrecht University) • tional, Wageningen; Smeekens, Utrecht University) Development of a method for breeding of cucumber • The analysis of -receptor interaction networks in for improved attraction of biological control agents (M. Arabidopsis (Liu, Plant Research International, Wagenin- Dicke, H. Bouwmeester) • gen; Heidstra, Utrecht University; De Vries, Wageningen From genetic code to ecological interactions: molecular, University) phytochemical and ecological aspects of a glucosinolate • The role of chromatin structure in gene expression of polymorphism in Barbarea vulgaris (N. van Dam) • Arabidopsis and tomato (Bisseling/de Jong, Wageningen Arabidopsis: the system to study structure and function of University) heterochromatin (T. Bisseling) • • Priming of defense gene expression in plant-oomycete in- Chromatin genomics: functional analysis of Arabidopsis teractions (Pieterse/van Ackervecken, Utrecht University) chromatin remodeling genes in development (T. Bissel- ing) • Arabidopsis projects funded by other sources such as first Wageningen Phytoinformatics: the added value from flow university funds, second flow Netherlands Organization plants (funded to 2008; W. Stiekema) for Scientific Research, EU etc. and third flow contract re- search:

41 Plant Research International, Wageningen– control of cell division; Chromatin dynamics; Ubiqui- Current Projects tination and cell cycle control; dissection of retinoblas- toma-mediated control of cell differentiation; in silico • Identification and characterization of genes for drought modeling of developmental pathways, with an emphasis tolerance (2006; A. Pereira) on emergent properties of feedback loops between auxin • Identification of plant genes for abiotic stress resistance transport, cell polarity and transcription factor networks (2006; A. Pereira) (B. Scheres) • • Isolation and characterization of key-genes in the for- Genomics for multicellular development: Function of the mation of germination stimulants of the parasitic weeds quiescent center in regulation of pattern formation and Striga and Orobanche (H. Bouwmeester) differentiation within the Arabidopsis thaliana root meri- • LRR receptor-like proteins and their functions in plant stem (R. Heidstra) • signaling (2004-2008; G.C. Angenent) Analysis of the hyponastic and differential growth re- • MADS box transcription factor functioning, their signal- sponse of Arabidopsis thaliana petioles induced by sub- ing and protein interaction (2004-2008; G. Angenent) mergence and low light conditions (funded to 2010; T. • Cis-Trans regulation in floral (G. Ange- Peeters, R. Voesenek) nent; 2005-2008) • Signaling pathways controlling embryogenic cell develop- Leiden University–Current Projects ment in Arabidopsis (funded to 2008; K. Boutilier) • Auxin-mediated orientation of plant development di- • Signaling in the shoot apical : A question of rected by plant protein kinases (R.Offringa) determinate or indeterminate growth (funded to 2007; R. • The role of ubiquitination in auxin and jasmonic acid Immink) signaling (funded to 2008; R.Offringa; J.Memelink) • Utrecht University–Current Projects Characterization of a novel regulator of plant secondary metabolism (funded to 2008; J. Memelink) • • Sugar signaling pathways in plants (funded to 2010; J. Regulation of jasmonate-responsive gene expression in Smeekens) Arabidopsis (funded to 2007; J. Memelink) • • Trehalose-6-phosphate as a regulatory molecule in plants Novel approach for dissection of jasmonate signaling in (funded to 2010; H. Schlüpmann) Arabidopsis (funded to 2006; J. Memelink) • • Control of plant architecture (funded to 2010; M. Prove- T-DNA activation tagging: an approach to isolate com- niers) ponents in jasmonate-dependent defense responses in • Dormancy as survival mechanism in plants (funded to Arabidopsis (funded to 2009; J. Memelink) • 2010; L. Bentsink) Plant stress resistance: jasmonate-responsive defense sig- • Induced disease resistance signaling in Arabidopsis (fund- nalling (funded to 2008; J. Memelink) • ed to 2010; C. Pieterse) Analysis of the ORA47 transcription factor involved in • Cross-talk between signal-transduction pathways in in- jasmonic acid signal transduction in Arabidopsis thaliana duced defense of Arabidopsis against microbial pathogens (funded to 2008; J. Memelink) • and herbivorous insects (funded to 2006; C. Pieterse, Analysis of the transcription factor ORA59, which plays joint projects with M. Dicke, Wageningen University) a crucial role in the jasmonate- and ethylene-medi- • Plant innate immunity: cross-talk between signaling ated defense response in Arabidopsis (funded to 2010; J. pathways to fine tune defense (funded to 2009; C. Piet- Memelink) • erse) Jasmonate-mediated changes in the modification and • Controlled regulation of broad spectrum pathogen resis- protein interaction status of AP2/ERF-domain transcrip- tance in plants (C. Pieterse; 2004-2008) tion factors in Arabidopsis (funded to 2006; J. Memelink) • • A functional proteomics approach to identify phospho- How do plants discriminate between specialist and gener- proteins involved in plant innate immunity; the relation alist insects (funded to 2010; H. Linthorst, P. Klinkhamer, between innate immunity signal transduction and plant R.Verpoorte) • development. (F. Menke) Changes in the Arabidopsis metabolome after stress, using • Priming in plant-pathogen interactions: the molecular NMR-metabolomics and targeted analyses of secondary mechanism of the alarmed state (2005-2008; J. Ton) metabolites (R. Verpoorte, H.Linthorst, P.Klinkhamer, • Signaling at the host-microbe interface: pathogen-in- C.van den Hondel) • duced modulation of the plant plasma membrane (A. van Effect of Non-homologous recombination mutations den Ackerveken) on genome stability and development in Arabidopsis (P. • Genetic networks in root development: Interplay between Hooykaas) cell polarity information, pattern formation cues, and

42 • Targeted integration in plants (funded to 2009; Vrije Universiteit, Amsterdam–Current S. de Pater, P.Hooykaas) Projects • Cre-lox mediated cassette exchange in the Arabidopsis genome (funded to 2007; J. Louwerse, P.Hooykaas) • Function of meristem identity in flower and • Development of artificial zinc finger transcription factors development (R. Koes) as regulators of plant function (funded to 2009; E. van • Genetic control and evolution of inflorescence architec- der Zaal, P.Hooykaas) ture (R. Koes) • Phospho-fingerprinting Arabidopsis development (R.Offringa) University of Groningen–Current Projects • The role of auxin in initiation (funded to 2009; • Molecular biology of in higher A.Vivian-Smith, R.Offringa) plants (Dijkwel, J. Hille) University of Amsterdam–Current Projects Major Funding Sources for Arabidopsis • Role of PA kinase in plant stress signaling (funded to Functional Genomics 2007, B. van Schooten, T. Munnik) • Sensing the lipid second messenger, phosphatidic acid • Netherlands Organization for Scientific Research (www. (funded to 2011, T. Munnik) nwo.nl) • Targets for the novel lipid second messenger, phospha- • The Netherlands Genomics Initiative (www.genomics.nl) tidic acid (funded to 2006; C. Testerink, T. Munnik) • The Netherlands Plant Genomics Network (www.cbsg.nl) • Role of phospholipase C signaling in plant defense (fund- • Foundation for Technology funded by Ministries of Eco- ed to 2007; S. van Wees, Munnik) nomic Affairs and Education (www.stw.nl) • SUMO-signaling in plants (H. van den Burg)

43 Nordic Arabidopsis Network

http://www.Arabidopsis.org/info/2010_projects/Nordic.jsp conserved counterpart in Arabidopsis. Research topics include: Contact: Jaakko Kangasjärvi plant development, flower development and hormone physi- University of Helsinki, Finland ology; photosynthesis and metabolism with a special interest Email: [email protected] for stress responses (low temperature in particular); ecophysi- ology studying C- and N- assimilation. The research groups are supported by technical platforms in genomics, proteomics, Norway metabolomics, production of transgenic plants, . The UPSC is also a partner in the European CATMA-project. The Norwegian Plant Functional Genomics Program (NARC) started in 2003 and is fully operative. NARC is 1 of Arabidopsis Resources and Funding 11 genomics technology platforms forming the national func- • UPSC (www.upsc.se/) tional genomics program (FUGE). The plant platform includes • service activities within transcriptional profiling (full genome Wallenberg Consortium North (WCN)- Funding (www. arrays and custom designed arrays) and bioinformatics (Atle wcn.se/) Bones, NTNU) genotyping and clone collection (Odd-Arne Finland Rognli, UMB), in situ hybridization and yeast two-hybrid screening (Reidunn Aalen, UIO). Most of the activity involves The Finnish groups involved in Arabidopsis research are Arabidopsis thaliana. Norway is a partner of the EU Plant Ge- concentrating on stress-physiology and functional genomics nomics network ERA-PG and hosted the Nordic Arabidopsis of plant stress responses, developmental and hormone biology, meeting 2004. and in photosynthesis. They are using genomics, proteomics, and metabolomics to determine plant defense and adaptation Arabidopsis Resources and Funding to biotic and abiotic stresses and the functions of the proteins • Norwegian Arabidopsis Research Centre (NARC): The in chloroplast membranes. Arabidopsis genomic in- Norwegian service facilities are open for all scientists at formation is also used in functional and comparative genomics equal conditions. The program is coordinated by Atle M. of the lower plants as a template for the eurosids. Information Bones (NTNU) and information about the services can is stored and made available at openSputnik- the comparative be found at www.narc.no or by request to [email protected]. genomics platform. The outcrossing relative Arabidopsis lyrata no . is being used in studies of population genetics of adaptation to • University of Oslo: in situ hybridization and yeast-two- abiotic conditions. The eight of the species differ hybrid analyses (http://www.imbv.uio.no/mol/groups/ from the A. thaliana genome mainly by a small number fusions narc/) and reciprocal translocations. The Finnish Plant Functional • UMB: Arabidospsis transformation, T-DNA genotyping, Genomics Project Program was created in the spring of 2003 in seed collection: (www.umb.no/?viewID=2552) order to increase collaboration in functional genomics between • Research Council of Norway (www.forskningsradet.no): the participating groups. It is also member in the European Functional Genomics in Norway (FUGE)- Funding plant functional genomics network ERA-PG.

Sweden Arabidopsis Resources and Funding • The Umeå Plant Science Center (UPSC) is a center of ex- openSputnik: A comparative genomics platform (www. opensputnik.org) perimental plant biology in Umeå. It was created in 1999 by • moving plant groups from the Umeå University and Swedish The Finnish Project Program on Plant Genomics- Fund- University of Agricultural Sciences (Umeå) to the same build- ing (www.honeybee.helsinki.fi/esgemo/pg/eng_index. htm) ing. UPSC groups have also received National Center of Excel- • lence status and funding for functional genomics. Their activi- The Academy of Finland- Funding (www.aka.fi/index. ties are mainly concentrated in trees (hybrid poplar). However, asp?id=eb9a8e15a46244d989ac56c132e8d13a) Arabidopsis functional genomics is heavily utilized for the de- termination of the function of poplar genes that have a well-

44 Denmark

In Denmark, a number of groups at The Veterinary and Agricultural University, Copenhagen University, Risø National Laboratory, Danish Institute of Agricultural Sciences and Aal- borg University work on Arabidopsis. The research, which in most cases is funded by the national research councils, involves studies of several aspects of plant life. The activities are coor- dinated through the Plant Biotech Denmark-network (www. plant-biotech.dk).

45 United Kingdom

http://www.Arabidopsis.org/info/2010_projects/United_ Major Funding Sources for Arabidopsis Kingdom.jsp Functional Genomics Contacts: Andrew Millar (Coordinator) University of Edinburgh The Biotechnology and Biological Science Research Email: [email protected] Council, BBSRC (http://www.bbsrc.ac.uk/) is the major fund- Ruth Bastow (Administrator) ing agency for Arabidopsis functional genomics. BBSRC en- University of Bristol courages applications that use genomic technologies and has Email: [email protected] launched several initiatives to stimulate research in this area, (www.bbsrc.ac.uk/science/initiatives/) including: • Centers for Integrative and Systems Biology (www.bbsrc. If Arabidopsis researchers are to make the best possible ac.uk/science/initiatives/cisb_phase2.html) st progress as we move into the 21 century they will need to • The Crop Science Initiative; exploitation of Arabidopsis understand the contemporary questions in crop science in order Research for crop science (www.bbsrc.ac.uk/science/ini- to facilitate the translation of basic plant science into practical tiatives/crop_science.html) outcomes. Long-term funding, coordination and coherent data • Tools and Resources; (http://www.bbsrc.ac.uk/science/ policies will also need to be developed at both national and initiatives/trdf.html) international levels to provide the informatics, mathematical • E-science (www.bbsrc.ac.uk/science/initiatives/escience/ models and data required for a comprehensive framework of Welcome.html) Arabidopsis biology in silico. Other UK funding bodies supporting Arabidopsis research GARNet include • GARNet, the Genomic Arabidopsis Resource Network was NERC (Natural Environmental Research Council) (www. established in 2000 to provide publicly available functional ge- nerc.ac.uk/) • nomics resources for Arabidopsis research. Funding was extend- DEFRA (Department for Environment Food and Rural ed to move the services provided by GARNet to self-sustaining Affairs) (www.defra.gov.uk/) • cost recovery. Coordination activities are funded 2005-2010, SEERAD (Scottish Executive Environment and Rural to provide an information resource (http://garnet.arabidop- Affairs) (www.scotland.gov.uk/topics/agriculture) sis.info/, newsletter, annual meeting) and point of contact for International Genomics Funding other UK plant communities and international plant genomics programs. Plant systems biology and translational research are The BBSRC is one of 17 funding bodies involved in ERA- now important parts of GARNet’s activities. PG (European Research Area in Plant Genomics), allowing UK researchers to participate in the funding initiative; ‘Structuring UK Arabidopsis Meetings Plant Genomic Research in ’ http://www.erapg.org/. • GARNet hosts an annual meeting for plant scientists Arabidopsis Genomics Tools and Resources across the UK and Europe to disseminate information about new technologies and resources. GARNet 2006, Resources initiated by GARNet include transcriptomics, “Plant Networks – How to integrate data” will be held at proteomics and metabolomics, insert clone libraries and inser- the University of Bristol 11-12th September (http://gar- tional populations. Data from GARNet-funded net.arabidopsis.info/garnet_meeting.htm). Affymetrix and proteomics projects are available at NASC, and • The Genetical Society hosts an annual one-day meeting metabolomics results at Rothamsted http://www.metabolo- on Arabidopsis, which in 2006 will be held at Cambridge mics.bbsrc.ac.uk/. Many leading universities and institutes in on May 20th (http://www.genetics.org.uk). the UK have established their own functional genomics centers • GARNet is also involved in the organization of Plant- and resources including METRO and ProtLocDB. GEMS 2006, 11-14 October, Venice (http://www.plant- gems.org/)

46 European Stock Centre

NASC (http://arabidopsis.info/) is an international re- source for seed, DNA amplicons, clones and data. The UK BBSRC government funding body currently subsidizes all of NASC services. • Phenotype data is held according to both plant ontology (PO) and Phenotype (PATO) standards (http://arabidop- sis.info/bioinformatics/Ontology_details.html). • The NASC genome browser (http://atensembl.arabidop- sis.info) brings together MIPS and TIGR annotation; germplasm; Affymetrix GeneChip data; comprehensive insertion line coverage; and RNA-i knockdown clone resources. • NASC provides a not-for-profit international GeneChip hybridization service and database and currently holds data from 3,000 GeneChips (http://affy.arabidopsis.info). • NASCs resources are available as BioMOBY web services (70+) for automated data-mining engines and desktop workflow GRID applications such as Taverna.

47 United States

http://www.Arabidopsis.org/info/2010_projects/United_ 8. Localizing gene products at the cellular and subcellular States.jsp level Contacts: Philip Benfey 9. Facilitating metabolomics and ionomics Duke University 10. Engaging the broader community Email: [email protected] 11. Enhancing international collaboration Mary Lou Guerinot Looking beyond 2010, the panel foresaw a program that Dartmouth College "enables the international community of plant biologists to an- Email: Mary.Lou [email protected] alyze, understand, and manipulate the full spectrum of biologi- cal processes required to make a plant that functions effectively and predictably under both standardized laboratory conditions AT2010 Midterm Progress and complex natural environments." A major event in the U.S. Arabidopsis functional genomics Plant Cyberinfrastructure Center Workshop community was the marking of the midpoint in the National Science Foundation Arabidopsis 2010 program (www.nsf.gov/ Recent progress in plant science has resulted in the de- bio/pubs/awards/2010awards.htm.) The North American Ara- velopment of a wide range of new tools and resources for re- bidopsis Steering Committee (NAASC) organized a two-day search and education. Optimal use of these resources requires workshop in August, 2005, to evaluate the progress made and combining the information represented among them in inno- provide guidance for the second half of the program. Workshop vative ways to achieve a better understanding of fundamental participants came from the U.S., Pacific Rim and Europe and principles in plant biology; and it also requires that individuals represented a wide range of subspecialties within the Arabidopsis from multiple fields and disciplines be able to find, understand genomics community. The final report is available in its entirety and effectively employ these resources in novel ways. at www.nsf.gov/pubs/2006/bio0601/bio0601.pdf. Prior to the To discuss the means by which to achieve such a synthesis workshop, a web-based survey was conducted to solicit input of resources, and to design the appropriate cyberinfrastructure from the broader community. In addition, data were collected for their best utilization, a workshop for a Plant Cyberinfra- on the impact of the 86 funded projects to date, including publi- structure Center was held at the National Science Foundation cations, stocks deposited and database submissions. The overall on October 17 and 18, 2005 (complete report at www.arabidop- assessment was that most of the initial goals set in 2000 for the sis.org/info/2010_projects/index.jsp.) Participants represented first five years had been met or surpassed. Of particular note was the widest possible range of plant and computational biolo- the utility of genome-wide resources such as insertion lines. In gists, with experts in plant genomics, development, metabolism, assessing the funded projects, the panel came to the conclusion ecology, and evolutionary biology, ecoinformatics and experts that those that used high throughput and/or computational ap- in computational modeling, databases, computer infrastructure, proaches to understanding biological processes had the highest software, and mathematics. The participants achieved consen- impact. For the upcoming five years of the program, the panel sus on the need for a center to provide the cyberinfrastructure recommended focusing on these 11 areas: for facilitating interdisciplinary research in plant science and 1. Benchmarking gene function for generating a new kind of plant biologist, and made a num- 2. Developing genome-wide tools and reagents for analyz- ber of recommendations and suggestions outlining their vision ing gene function and regulation for such a center. 3. Improving genome annotation and tools for visualization, annotation and curation Workshop recommendations 4. Improving database integration and developing new 1. There is a strong need to create a plant cyberinfrastruc- modeling and computational tools ture center to promote the integration of diverse and 5. Exploring exemplary networks and systems large-scale genomics and other data to address a few 6. Analyzing non-protein coding genes fundamental problems in plant biology using multi-disci- 7. Leveraging natural variation to understand gene function plinary approaches. in Arabidopsis thaliana

48 2. A core mission should be to train a new generation of viewed using the interactive SeqViewer tool. In addition, pag- scientists who can combine multi-disciplinary approaches es on news, information on the Arabidopsis Genome Initiative and utilize data in public repositories maximally. (AGI), Arabidopsis lab protocols, and useful links are provided. 3. The center should be composed of an entity that is con- TAIR's first genome release, version 6.0, has been inte- nected to a number of adjunct institutions with different grated into the TAIR database, SeqViewer, MapViewer and types of scientific expertise and facilities. sequence analysis datasets, and is also available from NCBI. 4. The core infrastructure and staffing should follow the suc- The TAIR6 release contains 26,751 protein coding genes, 3818 cessful models of NCEAS (National Center for Ecologi- pseudogenes and 838 non-coding RNA genes (31,407 genes in cal Analysis and Synthesis) and NESCent (National Evo- all). A total of 437 new genes were added and nine genes were lutionary Synthesis Center) and designate enough core made obsolete. Updates were made to 973 genes including 831 updates to coding sequences, 14 gene splits and 7 gene merges staff to facilitate the activities of the center efficiently. and the addition of 1200 new splice variants. A total of 3159 5. The center should provide an umbrella infrastructure to Arabidopsis genes (10%) now have annotated splice variants. No coordinate disparate outreach activities and train students changes were made to the chromosome sequences for this re- and faculty in achieving a comfort level in interacting lease. Access to the fully annotated chromosome sequences in with the public about plant science and its importance. TIGR xml format as well as FASTA files of cDNA, coding, 6. The center should maximally leverage existing databases genomic and protein sequences and lists of added, deleted and and standards to promote international integration of changed genes are available at the TAIR website. FASTA for- data. matted files for all sequence analysis datasets including sets of Young Researcher Exchange Program intron, intergenic, UTR, upstream and downstream sequences are also available. Access the new release using TAIR's genome In collaboration with the German Arabidopsis Functional browser (http://arabidopsis.org/servlets/sv). Genomics program, AFGN, an NSF-funded Young Researcher • Exchange Program was started. This program provides stipends ABRC (The Arabidopsis Biological Resource Center, www. and travel expenses for short-term research visits (up to three biosci.ohio-state.edu/pcmb/Facilities/abrc/abrchome.htm) months) for graduate students (and postdoctoral fellows in the distributes and is actively collecting stocks that are associated U.S.) to work in German laboratories and for German stu- with genomics and phenomics. The NSF grant which sup- dents to work in U.S. labs. For more information please see ports the Center was recently renewed for a five-year period, (www.arabidopsis.org/news/job_postings/friesner022806.doc) through March 2011. Relevant seed stocks include inser- and (www.uni-tuebingen.de/plantphys/AFGN/yrep.htm). tion lines (200,000+ from many major contributors as well as smaller sets of purified lines from individual researchers), Major Funding Sources for Arabidopsis the lines of the Arabidopsis TILLING service, 800+ distinct Functional Genomics natural accessions, 9 recombinant inbred populations, related species and RNAi lines including the AGRIKOLA lines. In • NSF: National Science Foundation (www.nsf.gov/) addition, 1,900 of the ca. 50,000 "Confirmed" (genetically • USDA: U.S.Department of Agriculture (www.usda.gov/ purified) T-DNA lines being produced by the J. Ecker labora- wps/portal/usdahome) tory have been received, and the remainder will be arriving • DOE: U.S. Department of Energy (www.energy.gov/) during the next two years. These will be made available as they • NIH: National Institutes of Health (www.nih.gov/) arrive, and distribution of these as large sets and sub-sets for phenotypic experimentation, etc, is planned. On the DNA side, Arabidopsis Genomics Tools and Resources ABRC presently houses full-length ORF and cDNA clones • for 15,000+ genes, BACs covering the entire genome, BACS of TAIR (The Arabidopsis Information Resource, http:// four related species, the AGRIKOLA RNAi clones and vari- arabidopsis.org) collects information and maintains a data- ous sets of Expression and Destination clones. The extensive base of genetic and molecular biology data for Arabidopsis Expression ORF collection from S. P. Dinesh Kumar is being thaliana, a widely used model plant. TAIR is produced by the received, with 1,100 of these currently in-house. It should be Carnegie Institution of Washington Department of Plant emphasized that donation of published mutants and clones, Biology, Stanford, California, and the National Center for including purified insertion mutants and expression clones Genome Resources (NCGR), Santa Fe, New Mexico. Fund- are very welcome. The annual distribution of seed and DNA ing is provided by the National Science Foundation, (Grant stocks continues to exceed 90,000 in total volume. No. DBI-9978564) and DBI-0417062. TAIR collaborates with the Arabidopsis Biological Resource Center (ABRC) to provide researchers with the ability to search and order stocks. The data in TAIR can be searched, analyzed, downloaded, and

49 Members of the Multinational Arabidopsis Steering Committee

Thomas Altmann Pierre Hilson Andrew Millar Randy Scholl Representing Germany Representing Belgium Representing the United Kingdom Representing the United States [email protected] [email protected] [email protected] ex officio Universitaet Potsdam Ghent University University of Edinburgh [email protected] Golm, Germany Ghent, Belgium Edinburgh, United Kingdom Arabidopsis Biological Resource Center Philip Benfey, Chair Heribert Hirt Lutz Nover Columbus, Ohio, USA Representing the United States of Representing Austria Representing Germany America [email protected] [email protected] Ian Small, Co-chair [email protected] University of Vienna Biozentrum Representing Australia Duke University Vienna, Austria Universitaet Frankfurt [email protected] Durham, NC, USA Frankfurt, Germany University of Western Australia Gerd Jürgens Perth, Australia David Bouchez Representing Germany Javier Paz-Ares Representing France [email protected] Representing Spain Willem Stiekema [email protected] University of Tübingen [email protected] Representing The Netherlands INRA Centre de Versailles Tübingen, Germany Centro National de Biotechnoligia [email protected] Versailles, Cedex, France Madrid, Spain Center for BioSystems Genomics Jaakko Kangasjärvi Wageningen, The Netherlands Jorge Casal Representing the Nordic Barry Pogson Representing Argentina Arabidopsis Network Representing Australia Paola Vittorioso [email protected] [email protected] and New Zealand Representing Italy University of Buenos Aires University of Helsinki [email protected] [email protected] Buenos Aires, Argentina Helsinki, Finland Australian National University University of Rome Canberra, Australia Rome, Italy Bill Crosby Keith Lindsey Representing Canada Representing the United Kingdom Ben Scheres Weicai Yang [email protected] [email protected] Representing the Netherlands Representing China University of Windsor University of Durham [email protected] [email protected] Ontario, Canada Durham, United Kingdom University of Utrecht Chinese Academy of Sciences Utrecht, The Netherlands Bejing, China Ian Furner Sean May Representing the United Kingdom Representing the United Kingdom Kazuo Shinozaki Joanna Friesner [email protected] [email protected] Representing Japan Coordinator and Executive University of Cambridge Nottingham Arabidopsis Stock [email protected] Secretary Cambridge, United Kingdom Center RIKEN Genomic Sciences Center [email protected] Loughborough, United Kingdom RIKEN Tsukuba Institute The Carnegie Institution Mary Lou Guerinot Tsukuba, Ibaraki, Japan Stanford, CA, USA Representing the United States Peter McCourt [email protected] Representing Canada Dartmouth College [email protected] Hanover, New Hampshire, USA University of Toronto Toronto, Ontario, Canada

50 Members of the MASC Subcommittees

Bioinformatics cDNAs and Clone- Metabolomics Natural Variation and Based Functional Comparative Genomics Proteomics (ORFeomics) Natural Variation

Chris Town (chair) Pierre Hilson (chair) Ian Graham (co-chair) Tom Mitchell-Olds (chair) [email protected] [email protected] [email protected] [email protected]

Fabrice Legeai Kazuo Shinozaki Basil Nikolau (co-chair) Carlos Alonso-Blanco [email protected] [email protected] [email protected] [email protected]

Sean May Ian Small Mike Beale Thomas Altmann [email protected] [email protected] [email protected] [email protected]

Klaus Mayer Oliver Fiehn Ian Bancroft [email protected] [email protected] [email protected]

Yasukazu Nakamura Alisdair Firnie Joy Bergelson [email protected] [email protected] [email protected]

Yves van de Peer Tony Larson Justin Borevitz [email protected] [email protected] [email protected]

Heiko Schoof Rob Last Kathleen Donohue [email protected] [email protected] [email protected]

Kazuki Saito Matthias Hoffmann [email protected] matthias.hoffmann@botanik. uni-halle.de Steven Smith [email protected] Olivier Loudet [email protected] Wolfram Weckwerth weckwerth@mpimp-golm. Julin Maloof mpg.de [email protected]

Annie Schmitt Johanna_Schmitt@brown. edu

51 Members of the MASC Subcommittees (continued)

Natural Variation and Phenomics Proteomics Comparative Genomics

Comparative Genomics

Tom Mitchell-Olds (chair) Eva Huala (co-chair) Wolfram Weckwerth (chair) [email protected] [email protected] weckwerth@mpimp-golm. mpg.de David Baum Sean May (co-chair) [email protected] [email protected] Harvey Millar (co-chair) [email protected] Hans Bohnert Joe Ecker [email protected] [email protected] Sacha Baginsky (co-chair) [email protected]. Sean Cutler Katica Ilic ethz.ch [email protected] [email protected] Hans-Peter Braun Graham King Minami Matsui [email protected]. [email protected] [email protected] de

Marcus Koch Randy Scholl Joshua Heazlewood [email protected] [email protected] [email protected]. berg.de au Detlef Weigel Kathryn S. Lilley Martin Lysak [email protected] [email protected] [email protected]

Chris Pires Hans-Peter Mock [email protected] [email protected]

Ming Ray Sigrun Reumann [email protected] [email protected]

Detlef Weigel Michel Rossignol [email protected] [email protected]

Klaas van Wijk [email protected]

Julian Whitelegge [email protected]

52

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