THE NATIONAL PLANT GENOME INITIATIVE

OBJECTIVES FOR 2003–2008

COMMITTEE ON OBJECTIVES FOR THE NATIONAL PLANT GENOME INITIATIVE: 2003–2008

BOARD ON LIFE SCIENCES

BOARD ON AGRICULTURE AND NATURAL RESOURCES

DIVISION ON EARTH AND LIFE STUDIES

NATIONAL RESEARCH COUNCIL OF THE NATIONAL ACADEMIES

THE NATIONAL ACADEMIES PRESS
Washington, D.C. www.nap.edu



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The National Plant Genome Initiative: Objectives for 2003–2008 THE NATIONAL PLANT GENOME INITIATIVE OBJECTIVES FOR 2003–2008 COMMITTEE ON OBJECTIVES FOR THE NATIONAL PLANT GENOME INITIATIVE: 2003–2008 BOARD ON LIFE SCIENCES BOARD ON AGRICULTURE AND NATURAL RESOURCES DIVISION ON EARTH AND LIFE STUDIES NATIONAL RESEARCH COUNCIL OF THE NATIONAL ACADEMIES THE NATIONAL ACADEMIES PRESS Washington, D.C. www.nap.edu

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The National Plant Genome Initiative: Objectives for 2003–2008 THE NATIONAL ACADEMIES PRESS 500 Fifth Street, NW Washington, DC 20001 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. International Standard Book Number 0-309-08521-7 Additional copies of this report are available from the Board on Life Sciences, 500 Fifth Street, N.W., Washington, D.C. 20001; (202) 334–2236 or the National Academies Press, 500 Fifth Street, N.W., Lockbox 285, Washington, D.C. 20055; (800) 624–6242 or (202) 334–3313 (in the Washington metropolitan area); Internet, http://www.nap.edu Printed in the United States of America Copyright 2002 by the National Academy of Sciences. All rights reserved.

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The National Plant Genome Initiative: Objectives for 2003–2008 THE NATIONAL ACADEMIES Advisers to the Nation on Science, Engineering, and Medicine The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the Congress in 1863, the Academy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Bruce M.Alberts is president of the National Academy of Sciences. The National Academy of Engineering was established in 1964, under the charter of the National Academy of Sciences, as a parallel organization of outstanding engineers. It is autonomous in its administration and in the selection of its members, sharing with the National Academy of Sciences the responsibility for advising the federal government. The National Academy of Engineering also sponsors engineering programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Wm.A.Wulf is president of the National Academy of Engineering. The Institute of Medicine was established in 1970 by the National Academy of Sciences to secure the services of eminent members of appropriate professions in the examination of policy matters pertaining to the health of the public. The Institute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government and, upon its own initiative, to identify issues of medical care, research, and education. Dr. Harvey V.Fineberg is president of the Institute of Medicine. The National Research Council was organized by the National Academy of Sciences in 1916 to associate the broad community of science and technology with the Academy’s purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Bruce M.Alberts and Dr. Wm.A.Wulf are chair and vice chair, respectively, of the National Research Council. www.national-academies.org

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The National Plant Genome Initiative: Objectives for 2003–2008 COMMITTEE ON OBJECTIVES FOR THE NATIONAL PLANT GENOME INITIATIVE: 2003–2008 JEFF DANGL (Chair), University of North Carolina, Chapel Hill, North Carolina DOUGLAS COOK, University of California, Davis, California ROBERT HASELKORN, University of Chicago, Chicago, Illinois ELIZABETH (TOBY) KELLOGG, University of Missouri-St. Louis, St. Louis, Missouri ROBERT L.LAST, formerly at Cereon Genomics, Cambridge, Massachusetts ROBERT MARTIENSSEN, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York SUSAN MCCOUCH, Cornell University, Ithaca, New York ERNEST F.RETZEL, University of Minnesota, Minneapolis, Minnesota CHRIS R.SOMERVILLE, Carnegie Institution and Stanford University, Stanford, California SUSAN WESSLER, University of Georgia, Athens, Georgia JOHN YATES, Scripps Research Institute and Syngenta, La Jolla, California Project Staff ROBIN A.SCHOEN, Study Director CLARA COHEN, Staff Officer BRIDGET K.B.AVILA, Senior Project Assistant NORMAN GROSSBLATT, Editor

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The National Plant Genome Initiative: Objectives for 2003–2008 BOARD ON LIFE SCIENCES COREY S.GOODMAN (Chair), University of California, Berkeley, California R.ALTA CHARO, University of Wisconsin, Madison, Wisconsin JOANNE CHORY, Salk Institute for Biological Studies, La Jolla, California ELAINE FUCHS, The University of Chicago, Chicago, Illinois DAVID J.GALAS, Keck Graduate Institute of Applied Life Science, Claremont, California BARBARA GASTEL, Texas A&M University, College Station, Texas JAMES M.GENTILE, Hope College, Holland, Michigan LINDA GREER, Natural Resources Defense Council, Washington, DC ED HARLOW, Harvard Medical School, Cambridge, Massachusetts ELLIOT M.MEYEROWITZ, California Institute of Technology, Pasadena, California ROBERT T.PAINE, University of Washington, Seattle, Washington GREGORY A.PETSKO, Brandeis University, Waltham, Massachusetts STUART L.PIMM, Columbia University, New York, New York JOAN B.ROSE, University of South Florida, St. Petersburg, Florida GERALD M.RUBIN, Howard Hughes Biomedical Research, Chevy Chase, Maryland BARBARA A.SCHAAL, Washington University, St. Louis, Missouri RAYMOND L.WHITE, DNA Sciences, Inc., Fremont, California Staff FRANCES SHARPLES, Director

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The National Plant Genome Initiative: Objectives for 2003–2008 BOARD ON AGRICULTURE AND NATURAL RESOURCES HARLEY W.MOON, (Chair), Iowa State University, Ames SANDRA BARTHOLMEY, Quaker Oats Company, Barrington, Illinois DEBORAH BLUM, University of Wisconsin, Madison ROBERT B.FRIDLEY, University of California, Davis BARBARA GLENN, Federation of Animal Science Societies, Bethesda, Maryland LINDA GOLODNER, National Consumers League, Washington, D.C. W.R.GOMES, University of California, Oakland PERRY R.HAGENSTEIN, Institute for Forest Analysis, Planning, and Policy, Wayland, Massachusetts CALESTOUS JUMA, Harvard University, Cambridge, Massachusetts JANET C.KING, University of California, Davis, California WHITNEY MACMILLAN, Cargill, Inc., Minneapolis, Minnesota (retired) TERRY L.MEDLEY, DuPont BioSolutions Enterprise, Wilmington, Delaware ALICE PELL, Cornell University, Ithaca, New York SHARON QUISENBERRY, Montana State University, Bozeman, Montana NANCY J.RACHMAN, Novigen Sciences, Inc., Washington, D.C. SONYA SALAMON, University of Illinois, Urbana-Champaign, Urbana, Illinois G.EDWARD SCHUH, University of Minnesota, Minneapolis BRIAN STASKAWICZ, University of California, Berkeley JACK WARD THOMAS, University of Montana, Missoula, Montana JAMES TUMLINSON, Agriculture Research Service, U.S. Department of Agriculture, Gainesville, Florida B.L.TURNER, Clark University, Worcester, Massachusetts Staff CHARLOTTE KIRK BAER, Director STEPHANIE PADGHAM, Administrative Assistant

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The National Plant Genome Initiative: Objectives for 2003–2008 Acknowledgments 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

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The National Plant Genome Initiative: Objectives for 2003–2008 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

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The National Plant Genome Initiative: Objectives for 2003–2008 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.

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The National Plant Genome Initiative: Objectives for 2003–2008 Preface 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

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The National Plant Genome Initiative: Objectives for 2003–2008 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.

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The National Plant Genome Initiative: Objectives for 2003–2008 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.

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The National Plant Genome Initiative: Objectives for 2003–2008 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. Jeff Dangl Chairman

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The National Plant Genome Initiative: Objectives for 2003–2008 Contents     EXECUTIVE SUMMARY   1 1   INTRODUCTION   9 2   SEQUENCING: GENERATING THE RAW MATERIAL   15 3   MAXIMIZING THE RETURN FROM REFERENCE SEQUENCING: TRANSLATIONAL AGRICULTURE   23 4   FUNCTIONAL EXPLOITATION OF GENOME SEQUENCES   31 5   GENOMICS AND THE MAJOR TRANSITIONS IN PLANT EVOLUTION   37 6   DEVELOPMENT OF A NATIONAL STRATEGY FOR PLANT BIOINFORMATICS   41 7   ACHIEVING INTERDISCIPLINARY TRAINING   51     REFERENCES   53

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The National Plant Genome Initiative: Objectives for 2003–2008     APPENDIXES     A   June 6–7, 2002 Workshop Agenda   55 B   Committee Biographies   59 C   Number of Publications in 2000–01 of 50 Most Cultivated Species   65     GLOSSARY   69