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Arabidopsis Thaliana Functional Genomics Project Annual Report 2008

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The Multinational Coordinated Arabidopsis thaliana Functional Genomics Project Annual Report 2008 Xing Wang Deng [email protected] Chair Joe Kieber [email protected] Co-chair Joanna Friesner [email protected] MASC Coordinator and Executive Secretary Thomas Altmann [email protected] Sacha Baginsky [email protected] Ruth Bastow [email protected] Philip Benfey [email protected] David Bouchez [email protected] Jorge Casal [email protected] Danny Chamovitz [email protected] Bill Crosby [email protected] Joe Ecker [email protected] Klaus Harter [email protected] Marie-Theres Hauser [email protected] Pierre Hilson [email protected] Eva Huala [email protected] Jaakko Kangasjärvi [email protected] Julin Maloof [email protected] Sean May [email protected] Peter McCourt [email protected] Harvey Millar [email protected] Ortrun Mittelsten- Scheid [email protected] Basil Nikolau [email protected] Javier Paz-Ares [email protected] Chris Pires [email protected] Barry Pogson [email protected] Ben Scheres [email protected] Randy Scholl [email protected] Heiko Schoof [email protected] Kazuo Shinozaki [email protected] Klaas van Wijk [email protected] Paola Vittorioso [email protected] Wolfram Weckwerth [email protected] Weicai Yang [email protected] The Multinational Arabidopsis Steering Committee—July 2008 Front Cover Design Philippe Lamesch, Curator at TAIR/Carnegie Institute for Science, and Joanna Friesner, MASC Coordinator at the University of California, Davis, USA Images Map of geographical distribution of ecotypes of Arabidopsis thaliana Updated representation contributed by Philippe Lamesch, adapted from Jonathon Clarke, UK (1993). The distribution map of J. Clarke was re- drawn from an original by George Redei, USA (1969). World map: courtesy of Kingston University London, UK. Arabidopsis thaliana natural accessions overlaying DNA sequences Contributed by Korbinian Schneeberger, Kirsten Bomblies, and Detlef Weigel, Max Planck Institute for Developmental Biology, Germany. The newly-proposed 1,001 Genomes project (http://1001genomes.org) aims to discover sequence variation, such as the single-nucleotide polymorphisms (SNPs) at G/C and A/T base pairs highlighted in blue, in 1,001 natural Arabidopsis thaliana accessions. Back Cover Arabidopsis plant from the ‘Vårhallarna’ population collected in Skåne, Sweden (Latitude: 55.70187, Longitude: 13.51756). Image contributed by Alison Anastasio in the lab of Joy Bergelson, Department of Ecology and Evolution, University of Chicago, USA. Table of Contents Foreword to the Report . 5. Executive Summary . 6. Progress and Updates of Multinational Arabidopsis Functional Genomics Projects . 9. Progress and Activities of the MASC Scientific Highlights Including Arabidopsis Publications Graph and Science/Nature Publications Tables Community Arabidopsis Projects and Resources Measuring Gene Function Knowledge Including ‘Tracking’ Thermometers Broader Impacts of Arabidopsis Research . 22 Impacts on Industry Including Graph of US Utility Patents Referencing Arabidopsis Translational Research Examples Using Arabidopsis Reports of the MASC Subcommittees . 26 Bioinformatics cDNA and Clone-based Functional Proteomics (ORFeomics) Natural Variation and Comparative Genomics Phenomics Proteomics Systems Biology Analysis and Recommendations . .34 The International Arabidopsis Functional Genomics Community . .37 Country Highlights Argentina Australia and New Zealand Austria Belgium China France Germany Israel Italy Japan The Netherlands Nordic Arabidopsis Network United Kingdom United States MASC Country Representatives . .61 MASC Subcommittee Members . 62 Foreword to the Report This is the 2007/2008 annual report of the Multinational studying other organisms was revealed in a recent survey of users Arabidopsis Steering Committee (MASC) on the status of the of TAIR (The Arabidopsis Information Resource). It was found Multinational Coordinated Arabidopsis thaliana Functional that only 34% of respondents focus their research exclusively Genomics Project. The project was proposed as a follow-up to on Arabidopsis, 62% focus on other species including crops the Multinational Coordinated Arabidopsis thaliana Genome and other model organisms in addition to Arabidopsis, and 3% Research Project that concluded with the release of the reference work exclusively on other species (see page 16 for survey details.) genome sequence in 2000. The success of the genome sequencing The results from this small sample is a positive reflection on effort motivated researchers to propose an even more ambitious the Arabidopsis community and the investment by government goal: to determine the function for every Arabidopsis gene by agencies that focused funding on Arabidopsis, and suggests that the year 2010. The Functional Genomics Project, described by Arabidopsis resources are informing and benefiting a wide range some as ‘the second-phase of the far-reaching vision’ by those of basic and applied studies. who launched the Genome Project, was an ambitious and This report details progress made over the last year by the inspiring endeavor. Since the project was proposed in 2001, the international Arabidopsis functional genomics community. very definition of gene function has expanded, making it clear It demonstrates the continued high level of cooperation that that it is not trivial to determine the ‘function’ of a gene and exists throughout the global community and the impressive leading researchers into new and exciting avenues of discovery. returns that funding agencies gain from supporting Arabidopsis Over the last 8 years, international projects have generated vast research. Success in acquiring a fundamental understanding of datasets and resources and produced numerous breakthroughs plant biology, and indeed, for translating basic plant knowledge in understanding the fundamental processes underlying plant to other systems, relies on maintaining and strengthening growth and development. The benefits of focused efforts on funding streams and world-wide collaboration. Resources need Arabidopsis are increasingly being appreciated; it is widely to be coordinated to maximize synergy and only sustained recognized as the most suitable plant for experimentation in collaborations will enable the Arabidopsis community to achieve genetics and genomics and has gained almost universal support its ambitious goals. As the Functional Genomics Project nears as the central reference and conceptual framework for much of its conclusion, the research community and funding agencies plant biology, particularly for molecular studies. The value of must consider the future directions for Arabidopsis and plant Arabidopsis as a central reference is well justified by the huge research. The Multinational Arabidopsis Steering Committee strides forward in our understanding of basic plant science, has already begun facilitating the process of obtaining input efforts that are underscored by a strong publication record from important stakeholders, including members of the global whose trajectory sharply increased following the release of the Arabidopsis and plant communities, through workshops and reference genome sequence. The intent has always been that extended planning discussions at MASC Annual meetings. the knowledge gained from this reference plant would serve to It is clear that a thorough understanding of the basic advance understanding about other plant species, particularly biology and ecology of plants will be required to address crop species, and thus translate into new or improved plant many of the challenges facing the world today, including products and increased agricultural productivity. As highlighted greater food requirements of a rapidly increasing human in this year’s report, such ‘knowledge transfer’ is occurring at population, the need to develop renewable energy sources, many levels by many different routes. Furthermore, there are loss of habitat, and global climate instability. At this critical undoubtedly many more examples of research that has benefited juncture, fundamental studies using Arabidopsis are more from Arabidopsis resources and knowledge, such as work important than ever, and efforts to strengthen links between performed in private companies that have not yet made their researchers working with model and crop plants, and approaches and data publicly-known, or translational efforts that between basic and applied science are needed. result in crop improvement where the link to ‘proof-of-concept’ work performed in Arabidopsis is not always clear. In addition, it is difficult to quantify the frequency by which Arabidopsis The Multinational Arabidopsis Steering Committee resources are used by researchers from outside Arabidopsis, or July 2008 even outside plant systems. This is partly due to the collegiality of many researchers in the Arabidopsis community who make their resources freely available through data repositories such as TAIR and genetic repositories such as ABRC and NASC, and resource-sharing is often required by funding agencies. One indication of the utility of Arabidopsis resources to scientists 5 Executive Summary The need for detailed understanding of the basic biology Highlights in Arabidopsis research and ecology of plants has never been greater. The increasing The past year continued to be strong for Arabidopsis publications
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