Exploring Horizons for Domestic Animal Genomics

Workshop Summary

BOARD ON AGRICULTURE AND NATURAL RESOURCES

BOARD ON LIFE SCIENCES

DIVISION ON EARTH AND LIFE STUDIES

National Research Council

By

Robert Pool

and

Kim Waddell

National Academy Press
Washington, D.C.



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Exploring Horizons for Domestic Animal Genomics: Workshop Summary Exploring Horizons for Domestic Animal Genomics Workshop Summary BOARD ON AGRICULTURE AND NATURAL RESOURCES BOARD ON LIFE SCIENCES DIVISION ON EARTH AND LIFE STUDIES National Research Council By Robert Pool and Kim Waddell National Academy Press Washington, D.C.

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Exploring Horizons for Domestic Animal Genomics: Workshop Summary NATIONAL ACADEMY PRESS 2101 Constitution Avenue, NW Washington, DC 20418 NOTICE: The project that is the subject of this summary 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 planning group responsible for the planning of the workshop were chosen for their special competences and with regard for appropriate balance. This workshop was supported by agreement numbers 59-0790-1-137, 2001-38831-11434, 263-MD-203182, DE-FG02-02ER63368, and IBN-0136019 between the National Academy of Sciences and the U.S. Department of Agriculture (ARS and CSREES), the National Institutes of Health, the Department of Energy, and the National Science Foundation (any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation). 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 0-309-08505-5 Additional copies of this summary are available from National Academy Press, 2101 Constitution Avenue, NW, Lockbox 285, Washington, DC 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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Exploring Horizons for Domestic Animal Genomics: Workshop Summary THE NATIONAL ACADEMIES National Academy of Sciences National Academy of Engineering Institute of Medicine National Research Council 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 chairman and vice chairman, respectively, of the National Research Council.

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Exploring Horizons for Domestic Animal Genomics: Workshop Summary PLANNING GROUP FOR THE WORKSHOP ON EXPLORING HORIZONS FOR DOMESTIC ANIMAL GENOMICS CLAIRE M. FRASER, Chair, The Institute for Genomic Research, Rockville, Maryland RONALD L. PHILLIPS, University of Minnesota, St. Paul, Minnesota ELAINE A. OSTRANDER, Fred Hutchinson Cancer Research Center, Seattle, Washington LAWRENCE B. SCHOOK, University of Illinois, Urbana, Illinois JAMES E. WOMACK, Texas A&M University, College Station, Texas STAFF KIM WADDELL, Senior Program Officer JOAN ESNAYRA, Program Officer MICHAEL R. KISIELEWSKI, Research Assistant CINDY LOCHHEAD, Project Assistant ROBERT POOL, Science Writer

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Exploring Horizons for Domestic Animal Genomics: Workshop Summary BOARD ON AGRICULTURE AND NATURAL RESOURCES HARLEY W. MOON, Chair, Iowa State University, Ames, Iowa SANDRA BARTHOLMEY, Quaker Oats Company, Barrington, Illinois DEBORAH BLUM, University of Wisconsin, Madison, Wisconsin ROBERT B. FRIDLEY, University of California, Davis, California BARBARA P. GLENN, Federation of Animal Science Societies, Bethesda, Maryland LINDA F. GOLODNER, National Consumers League, Washington, DC W. R. (REG) GOMES, University of California, Oakland, California 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, Michigan PAMELA A. MATSON, Stanford University, California TERRY L. MEDLEY, DuPont BioSolutions Enterprise, Wilmington, Delaware JAMES A. MERCHANT, University of Iowa, Iowa City, Iowa ALICE N. PELL, Cornell University, Ithaca, New York SHARRON S. QUISENBERRY, Montana State University, Bozeman, Montana NANCY J. RACHMAN, Exponent, Inc., Washington, DC SONYA B. SALAMON, University of Illinois at Urbana-Champaign, Urbana, Illinois G. EDWARD SCHUH, University of Minnesota, Minneapolis, Minnesota BRIAN J. STASKAWICZ, University of California, Berkeley, California JACK WARD THOMAS, University of Montana, Missoula, Montana JAMES H. TUMLINSON, U.S. Department of Agriculture, ARS, Gainseville, Florida B. L. TURNER, Clark University, Worcester, Massachusetts STAFF CHARLOTTE KIRK BAER, Director JOE ESPARZA, Project Assistant

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Exploring Horizons for Domestic Animal Genomics: Workshop Summary BOARD ON LIFE SCIENCES COREY S. GOODMAN, Chair University of California, Berkeley, California R. ALTA CHARO, University of Wisconsin, Madison, Wisconsin JOANNE CHORY, The Salk Institute for Biological Studies, La Jolla, California 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 E. GREER, Natural Resources Defense Council, Washington, DC ED HARLOW, Harvard Medical School, Boston, Massachusetts ELLIOT M. MEYEROWITZ, California Institute of Technology, Pasadena, California ROBERT T. PAINE, University of Washington, Seattle, Washington GREGORYA. 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 BRIDGET AVILA, Administrative Assistant

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Exploring Horizons for Domestic Animal Genomics: Workshop Summary Acknowledgments This workshop summary was enhanced by the contributions of many individuals who graciously offered their time, expertise, and knowledge. The committee thanks all who attended and/or participated in the public workshop (Appendixes B and C). This summary has been reviewed in draft form by individuals 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 for 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 thank the following individuals for their review of this summary: Pieter de Jong of the Children’s Hospital Oakland Research Institute, Oakland, CA; Vivek Kapur of the University of Minnesota, St. Paul, MN; and Bruce A. Roe of the University of Oklahoma, Norman, OK.

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Exploring Horizons for Domestic Animal Genomics: Workshop Summary Contents 1   INTRODUCTION   1 2   THE VALUE OF SEQUENCING DOMESTIC ANIMAL GENOMES   3     Sequencing for Agriculture   3     Sequencing for Enhanced Basic Scientific Understanding   4     Sequencing for Human Health and Medical Research   5     Advantages of Domestic Animals for Comparative Genomics   8 3   IDENTIFYING PRIORITIES   9     Finding the Balance Between Scientific Interest and Practical Needs   10     Which Animal Genomes Should Be Considered for Sequencing?   17 4   ROLES OF PUBLIC, PRIVATE, AND NONGOVERNMENTAL ORGANIZATIONS IN ADVANCING GENOMICS RESEARCH   20     Partnership Is Essential for Advancing Animal Genomic Research   20     The Role of Federal Agencies   21     The Role of the Private Sector   22     The Role of a Public-Private Partnership   23     Allocating Work in Animal Genomic Research   24

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Exploring Horizons for Domestic Animal Genomics: Workshop Summary 5   DATA ACCESS   26     Appropriate Tools and the Importance of Data Access   26     The Challenge of Scaling Up in Response to Increases in Data   27     Structuring Genome Databases   28     Allocation of Resources for Bioinformatics   29 6   LOOKING FORWARD   30     A Strategy for an Animal Genome Initiative   30     APPENDIXES     A   Workshop Agenda   33 B   Workshop Participant List   35 C   Workshop Speaker Biographies   41

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Exploring Horizons for Domestic Animal Genomics: Workshop Summary Boxes Box 1-1   Goals of the Workshop   2 Box 3-1   Phylogenetic Relationships Among Modern Orders of Placental Mammals   12 Box 3-2   Targeted Sequencing   15 Box 6-1   Factors That Contributed to the Establishment of the Plant Genome Initiative   31

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