THE NATIONAL PLANT GENOME INITIATIVE
OBJECTIVES FOR 2003–2008
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NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropriate balance.
This study was supported by Contract/Grant No. DBI-0215024 between the National Academy of Sciences and the National Science Foundation, Contract/Grant No. 59-0790-2-089 from the Department of Agriculture, and AP02-02C001575.000 of the Department of Energy. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the organizations or agencies that provided support for the project.
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THE NATIONAL ACADEMIES
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COMMITTEE ON OBJECTIVES FOR THE NATIONAL PLANT GENOME INITIATIVE: 2003–2008
JEFF DANGL (Chair),
University of North Carolina, Chapel Hill, North Carolina
University of California, Davis, California
University of Chicago, Chicago, Illinois
ELIZABETH (TOBY) KELLOGG,
University of Missouri-St. Louis, St. Louis, Missouri
formerly at Cereon Genomics, Cambridge, Massachusetts
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Cornell University, Ithaca, New York
University of Minnesota, Minneapolis, Minnesota
Carnegie Institution and Stanford University, Stanford, California
University of Georgia, Athens, Georgia
Scripps Research Institute and Syngenta, La Jolla, California
ROBIN A.SCHOEN, Study Director
CLARA COHEN, Staff Officer
BRIDGET K.B.AVILA, Senior Project Assistant
NORMAN GROSSBLATT, Editor
BOARD ON LIFE SCIENCES
COREY S.GOODMAN (Chair),
University of California, Berkeley, California
University of Wisconsin, Madison, Wisconsin
Salk Institute for Biological Studies, La Jolla, California
The University of Chicago, Chicago, Illinois
Keck Graduate Institute of Applied Life Science, Claremont, California
Texas A&M University, College Station, Texas
Hope College, Holland, Michigan
Natural Resources Defense Council, Washington, DC
Harvard Medical School, Cambridge, Massachusetts
California Institute of Technology, Pasadena, California
University of Washington, Seattle, Washington
Brandeis University, Waltham, Massachusetts
Columbia University, New York, New York
University of South Florida, St. Petersburg, Florida
Howard Hughes Biomedical Research, Chevy Chase, Maryland
Washington University, St. Louis, Missouri
DNA Sciences, Inc., Fremont, California
FRANCES SHARPLES, Director
BOARD ON AGRICULTURE AND NATURAL RESOURCES
HARLEY W.MOON, (Chair),
Iowa State University, Ames
Quaker Oats Company, Barrington, Illinois
University of Wisconsin, Madison
University of California, Davis
Federation of Animal Science Societies, Bethesda, Maryland
National Consumers League, Washington, D.C.
University of California, Oakland
Institute for Forest Analysis, Planning, and Policy, Wayland, Massachusetts
Harvard University, Cambridge, Massachusetts
University of California, Davis, California
Cargill, Inc., Minneapolis, Minnesota (retired)
DuPont BioSolutions Enterprise, Wilmington, Delaware
Cornell University, Ithaca, New York
Montana State University, Bozeman, Montana
Novigen Sciences, Inc., Washington, D.C.
University of Illinois, Urbana-Champaign, Urbana, Illinois
University of Minnesota, Minneapolis
University of California, Berkeley
JACK WARD THOMAS,
University of Montana, Missoula, Montana
Agriculture Research Service, U.S. Department of Agriculture, Gainesville, Florida
Clark University, Worcester, Massachusetts
CHARLOTTE KIRK BAER, Director
STEPHANIE PADGHAM, Administrative Assistant
This report is the product of many people. First, we would like to thank all those who participated in the workshop on the National Plant Genome Initiative: 2003–2008 on June 6–7, 2002. Their input played an important role in the committee’s deliberations.
Philip Benfey, New York University, New York
Jeffrey Bennetzen, Purdue University, West Lafayette, Indiana
Toby Bradshaw, University of Washington, Seattle, Washington
Gloria Coruzzi, New York University, New York
Rebecca Doerge, Purdue University, West Lafayette, Indiana
Michael Donoghue, Yale University, New Haven, Connecticut
Joe Ecker, The Salk Institute, La Jolla, California
Philip Hieter, University of British Columbia, Vancouver, British Columbia
Joseph Hirschberg, Alexander Silberman Institute of Life Sciences, Jerusalem, Israel
Randal Linder, University of Texas, Austin
Joseph Noel, The Salk Institute, La Jolla, California
Jim Ostell, National Center for Biotechnology Information, Bethesda, Maryland
Ron Phillips, University of Minnesota, St. Paul, Minnesota
Michael Purugganan, North Carolina State University, Raleigh, North Carolina
Marc Vidal, Harvard University, Boston, Massachusetts
Sue Rhee, Carnegie Institution of Washington, Stanford University, Stanford, California
Michael Snyder, Yale University, New Haven, Connecticut
Brian Staskawicz, University of California, Berkeley, California
James Tumlinson III, University of Florida, Gainesville, Florida
Richard Young, Massachusetts Institute of Technology, Cambridge, Massachusetts
Robert Waterston, Washington University, St. Louis, Missouri
Second, this report has been reviewed in draft form by people chosen for their diverse perspectives and technical expertise in accordance with procedures approved by the National Research Council’s Report Review Committee. The purpose of this independent review is to provide candid and critical comments that will assist the institution in making its published report as sound as possible and to ensure that the report meets institutional standards of objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We wish to thank the following for their review of this report:
Robin Buell, The Institute for Genomic Research, Rockville, Maryland
Vicki Chandler, University of Arizona, Tucson, Arizona
John Doebley, University of Wisconsin, Madison, Wisconsin
Michael Freeling, University of California, Berkeley, California
Vivek Kapur, University of Minnesota, St. Paul, Minnesota
Gill Kulvinder, University of Nebraska, Lincoln, Nebraska
Hei Leung, International Rice Research Institute, Makati City, The Philippines
Elliot Meyerowitz, California Institute of Technology, Pasadena, California
Steven Rounsley, formerly of Cereon Genomics, Cambridge, Massachusetts
David Stern, Boyce Thompson Institute, Cornell University, Ithaca, New York
Lila Vodkin, University of Illinois, Urbana, Illinois
Although the reviewers listed above have provided constructive comments and suggestions, they were not asked to endorse the conclusions or recommendations, nor did they see the final draft of the report before its release. The review of this report was overseen by R.James Cook of Washington State University. Appointed by the National Research Council, Dr. Cook was responsible for making certain that an independent examination of this report was carried out in accordance with institutional procedures and that all review comments were carefully considered. Responsibility for the final content of this report rests entirely with the authoring committee and the institution.
Since its inception, the National Plant Genome Initiative has become both a national and international focal point for plant biologists, creating excitement for genome scientists, crop breeders and plant physiologists alike. The diverse interests of the plant biology community, whose members work on more than 100 different plant species of economic, agricultural, or purely scientific concern, have converged on the enabling potential of plant genomics. Both the Arabidopsis genome project and the NPGI have leveraged important ties to the international plant biology community to further the field as a whole.
This community needs now to exploit the power of “complete” genome sequences, such as the finished sequence of Arabidopsis thaliana, and more recently, the draft sequence of Oryza spp. (rice) to make basic discoveries about plant biology, and to translate these into agricultural use. Additionally, we are poised to determine the genomic DNA sequence of several judiciously chosen additional species, as detailed in this report. There are several reasons why complete genome sequences are powerful enabling tools for discovering how genes, cells, organisms and populations function: First, because all plants have basic similarities, one can use “model” and “reference plants” with well-documented genetic features to make educated assumptions about similar features in many other species. That gives all plant biologists a head start on
understanding any application in their particular crop or plant of interest. Second, the ability to specifically manipulate a plant’s genetic building blocks permits us to make directed changes in its physiology. While that detailed knowledge is essential, genomics gives us a different perspective with which to obtain it—that of the big picture—because we can access and describe the activity of all the genes simultaneously. Finally, because genomic sequence is a record of a plant’s evolutionary history, we can, using comparative methods, unravel what has occurred in the past, understand how the great diversity of plant form and function arose, and begin to direct that evolution to beneficial and ecologically sound uses in the future.
As the second phase of the NPGI gets under way, it will be important to keep in mind the interdependent nature of genomics research. Complete and partial genomic sequences and their attendant genomics tools are critical resources on which community members rely for individual research projects. If everyone is to make progress, funding needs to be distributed competitively in the light of stringent peer review, and the results and resources delivered need to be of the highest-quality possible, accessible without restrictions, and provided on schedule. In other words, for the sake of all of the plant biology community, the NGPI needs to fund the best science and the most qualified representatives to undertake the work. In addition, in the rush to apply genomic approaches to uncover information in many different plants, we need to remember that rapid discovery using easily manipulated model and reference species is the most efficient tool to convey knowledge to an application-oriented user community. It is thus vital that we continue to efficiently mine the model for all of plant biology—Arabidopsis thaliana— while building our knowledge base outward from there, through the sequencing of carefully selected reference species that we define herein, and onward to all the major crop species over time. To do otherwise is to diffuse the fundamental value of genomics as a science and as an applied tool, and does not do justice to the progress made under the first round of the NPGI.
This argument is not only supported solidly on both scientific grounds (including experience from other genome projects leading up to the Human Genome Project), it is also an economic reality. Plant genomics has made remarkable progress in a short time period with a cumulative amount of funding that simply pales in comparison to that currently available for human, mouse, invertebrate, and microbial genomics efforts. Obviously if more money were to be made available, the Initiative could accommodate a more wide-ranging set of projects to the satisfaction of many more research and commodity groups anxious to use genomics. In fact, I would argue that the competitive, peer-reviewed plant biology research funded by the NSF, DOE, USDA, and NIH is one of the best investments made by the federal government in terms of “bang for the buck,” given the importance of plant biology to our society. But, given financial constraints, it makes sense to exploit the data from the model and reference species to their fullest, recruit techniques developed in non-plant genomics projects into plant biology, capitalize on falling sequencing costs when appropriate, and continue to make careful decisions on how to build the resources that the plant biology community uses collectively.
In this report, the committee on Objectives for the National Plant Genome Initiative: 2003–2008 which I chaired, makes suggestions for the next phase of the Initiative that adhere to these realities. The committee was established by the National Research Council in response to a request from the sponsors of the Initiative (OSTP, NSF, DOE, and USDA) for guidance in crafting future objectives for the program.
To assist its deliberations, the committee organized a workshop at the National Academy of Sciences on June 6–7, 2002. (The agenda is attached as Appendix A). The group that participated included plant geneticists and biochemists, evolutionary biologists, bioinformaticists, and investigators who study yeast, C. elegans and human pathogens. We are particularly grateful for the time they spent in both the panel sessions and working groups. Their insights added significantly to the breadth of our thinking, and are reflected in the report.
We hope that the report’s recommendations, if implemented, will help the Initiative carry out its mission, launched just 5 years ago, of bringing the power of plant genomics to bear on efforts to meet the nation’s needs for innovation in agriculture and energy, and in the vitally important journey towards understanding the plant world to which we, as humans, owe our very existence.