Molecular Dissection of Complex Traits

292 Pages·1997·4.561 MB·English

by  Andrew H. Paterson

M
OLECULAR
D
ISSECTION
OF
C T
OMPLEX RAITS
Edited by
Andrew H. Paterson, Ph.D.
Christine Richardson Professor of Agriculture
Department of Soil and Crop Science
Texas A&M University
College Station, Texas
CRC Press
Boca Raton New York London Tokyo
© 1998 by CRC Press LLC
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Library of Congress Cataloging-in-Publication Data
Molecular dissection of complex traits / edited by Andrew H. Paterson.
p. cm.
Includes bibliographical references and index.
ISBN 0-8493-7686-6 (alk. paper)
1. Molecular genetics. 2. Phenotype. 3. Gene mapping.
I. Paterson, Andrew H., 1960- .
QH442.M645 1997
572.8--dc21 97-12278
CIP
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© 1998 by CRC Press LLC
Preface
One of the great conflicts in the history of genetics was reconciled with the realization that
continuous variation in phenotype could reflect the net effects of a large number of genes. In the
past ten years, contemporary geneticists using new molecular tools have been able to resolve
complex traits into individual genetic components and describe each such component in much
detail. This volume summarizes the state of the art in molecular analysis of complex traits (QTL
mapping), placing new developments in this field within the context of their historical origins.
Leading authorities address central themes in analysis of complex phenotypes, and case histories
of seminal work in this burgeoning field are presented by the principal investigators.
Through this volume the authors strive to convey their excitement about a new experimental
approach that has empowered us to ask precise questions about complex phenomena. We and our
colleagues have, in the past few years, been fortunate to participate in a rare era in the evolution
of a field of science — an era in which ne w technology confers the rare opportunity to reinvestigate
both classical dogma and speculative proposals that are deeply entrenched in the history of a field.
Results to date have begun to clarify ambiguity, in a few cases resolve dichotomy, and in many
cases point to the need for still more detailed study. Now is an exciting time to be a geneticist,
with unprecedented new opportunities unfolding that we could only dream of a few short years ago.
The volume is written primarily for an audience of biologists familiar with genetics and is
intended to be useful both to senior scientists in a wide range of biotic disciplines and to entry-
level pre- or postdoctoral scientists. Lay people with a scientific bent can readily master the topics
presented herein, but it is recommended that they first become more familiar with the underlying
methods and principles of genome analysis by reviewing any of several recent reviews. The efficacy
with which QTL mapping is done in plants tends to bias the examples chosen; however, several
chapters address issues unique to animal systems, including humans.
The specific scope and objectives of this volume are:
1. To provide a complete, well-focused volume in the field of molecular genetic analysis
of complex phenotypes, including case histories written by leading practitioners in the
field. Such a volume will be intended to quickly bring the scientist or student up to the
state of the art in an important and rapidly-growing field and to introduce the layman
with a scientific bent to a new approach for investigating fundamental questions in the
life sciences.
2. To place contemporary technological developments in “molecular quantitative genetics”
within the context of their historical origins. Moreover, consider how recent advances in
the study of genetics are being applied to better understanding of classical questions.
3. To highlight future needs and directions in utilization of “molecular quantitative genetics”
across the biological sciences. The modern capability for molecular dissection of complex
phenotypes is capable of addressing a plethora of questions and issues in genetics,
breeding, and other areas of the life sciences. This volume will seek to explore efficient
approaches to addressing these issues which maximize return on investment of public
or private resources.
The book is divided into three parts:
Chapters 1–12, “Fundamental Principles” are intended to quickly bring the scientist or
student up to the state of the art in an important and rapidly-growing field and to introduce
© 1998 by CRC Press LLC
the layman with a scientific bent to a new approach for investigating fundamental questions
in the life sciences.
Chapters 13–19, “Case Histories” of seminal work in QTL mapping are intended to show
the utility of this new research approach in detailed investigation of a wide range of
biological questions. Leading practitioners of molecular dissection reveal the thought
processes which led to their seminal results.
Chapters 20–21, “Social Impact.” The modern capability for molecular dissection of complex
phenotypes is capable of addressing a plethora of questions and issues in genetics, breed-
ing, and other areas of the life sciences. These chapters will seek to explore possible long-
term impacts of these new research capabilities on agriculture and medicine, respectively.
We, the authors, hope that you, the readers, gain a sense of the excitement we enjoy about the
possibility of using these new tools and techniques to better describe our own experiments and
more generally to better understand the biological world around us. Further, we hope that the
contents of this volume are helpful to those of you who seek to join us in this endeavor, and we
welcome you into the dynamic field of “molecular quantitative genetics.”
Andrew H. Paterson
© 1998 by CRC Press LLC
Editor
Andrew H. Paterson, Ph.D., is the Christine Richardson Professor of Agriculture in the Department
of Soil and Crop Sciences and a full member of the Graduate Fields of Genetics and Plant
Physiology & Plant Biotechnology at Texas A&M University in College Station, Texas.
Dr. Paterson received his B.S. in Plant Science from the University of Delaware, Newark
Delaware, in 1982, under the direction of Professors James A. Hawk and Donald L. Sparks. He
obtained his M.S. in 1985 and Ph.D. in 1988 from the Department of Plant Breeding and Biometry,
Cornell University, Ithaca, New York, under the direction of Professor Mark E. Sorrells. After doing
postdoctoral work with Professor Steven D. Tanksley at Cornell University, he joined the Agricul-
tural Biotechnology program of E.I. duPont de Nemours as a Research Biologist, and simulta-
neously held an Adjunct Assistant Professorship in Plant Molecular Biology at the University of
Delaware. In 1991, he joined the Department of Soil and Crop Sciences at Texas A&M University
as an Assistant Professor. He received tenure and promotion to Associate Professor in 1995 and
was appointed the holder of the Christine Richardson Endowment in 1996.
Dr. Paterson is a member of the American Association for the Advancement of Science, the
Genetics Society of America, the Crop Science Society of America, the Brazilian Society of
Genetics, and the honorary societies Sigma Xi, Phi Kappa Phi, and Gamma Sigma Delta. In 1996,
he was named the Young Crop Scientist of the Year by the Crop Science Society of America. He
was recently named the Faculty Lecturer of 1997 by Texas A&M University.
Dr. Paterson has delivered many invited seminars and symposium talks. He has regularly
lectured at the International Plant and Animal Genome Conference, Keystone Symposia, Gordon
Conference, Beltwide Cotton Conference, and at many universities and research institutions.
Dr. Paterson is currently the recipient of research grants from the United States Department of
Agriculture, International Consortium for Sugarcane Biotechnology, Pioneer Hibred International,
Texas Higher Education Coordinating Board, and Texas State Support Committee of Cotton, Inc.
He has published about 40 refereed papers, contributed chapters to several books, and edited one
other volume. His current research interests focus on genome organization and evolution in several
higher plant taxa, with particular emphasis on gene manipulation in crop improvement.
© 1998 by CRC Press LLC
Contributors
Kjell Andersson Lon R. Cardon
Department of Animal Breeding and Genetics Sequana Therapeutics, Inc.
Swedish University of Agricultural Sciences La Jolla, California
Uppsala, Sweden
Gary A. Churchill
Leif Andersson
Department of Plant Breeding and Biometry
Department of Animal Breeding and Genetics
Cornell University
Swedish University of Agricultural Sciences
Ithaca, New York
Uppsala, Sweden
John C. Crabbe
Lena Andersson-Eklund
Portland Alcohol Research Center
Department of Animal Breeding and Genetics
Department of Veterans Affairs Medical Center
Swedish University of Agricultural Sciences
and
Uppsala, Sweden
Department of Behavioral Neuroscience
William D. Beavis Oregon Heath Sciences University
Quantitative Genetics Group Portland, Oregon
Trait and Technology Integration
Rebecca W. Doerge
Pioneer Hi-Bred International, Inc.
Johnston, Iowa Departments of Agronomy and Statistics
Purdue University
John K. Belknap West Lafayette, Indiana
Portland Alcohol Research Center
Department of Veterans Affairs Medical Center Inger Edfors-Lilja
and Department of Engineering and Natural Sciences
Department of Behavioral Neuroscience University of Växjö
Oregon Heath Sciences University Växjö, Sweden
Portland, Oregon
Hans Ellegren
Douglas W. Bigwood
Department of Animal Breeding and Genetics
Department of Plant Biology Swedish University of Agricultural Sciences
University of Maryland Uppsala, Sweden
College Park, Maryland
Yuval Eshed
Thomas K. Blake
Faculty of Agriculture
Department of Plant and Soil Sciences
The Hebrew University of Jerusalem
Montana State University
Rehovot, Israel
Bozeman, Montana
H. D. Bradshaw, Jr. Michel Georges
College of Forest Resources Department of Genetics
University of Washington Faculty of Veterinary Medicine
Seattle, Washington University of Liege
Liege, Belgium
Mark D. Burow
Department of Soil and Crop Sciences Chris S. Haley
Texas A&M University Roslin Institute
College Station, Texas Edinburgh, UK
© 1998 by CRC Press LLC
Ingemar Hansson Susan R. McCouch
Department of Food Science Department of Plant Breeding and Biometry
Swedish University of Agricultural Sciences Cornell University
Uppsala, Sweden Ithaca, New York
James E. Irvine Andrew H. Paterson
Department of Soil and Crop Science Department of Soil and Crop Sciences
Texas A&M Research and Extension Center Texas A&M University
Weslaco, Texas College Station, Texas
Sara A. Knott Joao L. Rocha
Institute of Cell, Animal and Department of Animal Science
Population Biology Texas A&M University
University of Edinburgh College Station, Texas
Edinburgh, UK
Hakan Sakul
Zhikang Li Sequana Therapeutics, Inc.
Department of Soil and Crop Sciences La Jolla, California
Texas A&M University
College Station, Texas Keith F. Schertz
U.S. Department of Agriculture
Yann-Rong Lin Agricultural Research Service
Department of Soil and Crop Sciences College Station, Texas
Texas A&M University
College Station, Texas Charles W. Stuber
U.S. Department of Agriculture
Ben-Hui Liu Agricultural Research Service
Department of Forestry Department of Genetics
North Carolina State University North Carolina State University
Raleigh, North Carolina Raleigh, North Carolina
Sin-Chieh Liu Jeremy F. Taylor
Department of Soil and Crop Sciences Department of Animal Science
Texas A&M University Texas A&M University
College Station, Texas College Station, Texas
Kerstin Lundström Claire G. Williams
Department of Food Science College of Agriculture and Life Sciences
Swedish University of Agricultural Sciences Texas A&M University
Uppsala, Sweden College Station, Texas
Lena Marklund Jinhua Xiao
Department of Animal Breeding and Genetics Department of Plant Breeding and Biometry
Swedish University of Agricultural Sciences Cornell University
Uppsala, Sweden Ithaca, New York
Maria Johansson Moller Dani Zamir
Department of Animal Breeding and Genetics Faculty of Agriculture
Swedish University of Agricultural Sciences The Hebrew University of Jerusalem
Uppsala, Sweden Rehovot, Israel
© 1998 by CRC Press LLC
Contents
INTRODUCTION
Chapter 1
Of Blending, Beans, and Bristles: The Foundations of QTL Mapping...........................................1
Andrew H. Paterson
PART I. FUNDAMENTAL PRINCIPLES
Chapter 2
Molecular Tools for the Study of Complex Traits..........................................................................13
Mark D. Burow and Thomas K. Blake
Chapter 3
Mapping Quantitative Trait Loci in Experimental Populations......................................................31
Gary A. Churchill and Rebecca W. Doerge
Chapter 4
Computational Tools for Study of Complex Traits.........................................................................43
Ben-Hui Liu
Chapter 5
QTL Mapping in Outbred Pedigrees...............................................................................................81
Claire G. Williams
Chapter 6
Mapping QTLs in Autopolyploids...................................................................................................95
Sin-Chieh Liu, Yann-Rong Lin, James E. Irvine, and Andrew H. Paterson
Chapter 7
QTL Analysis under Linkage Equilibrium....................................................................................103
Jeremy F. Taylor and Joao L. Rocha
Chapter 8
Molecular Analysis of Epistasis....................................................................................................119
Zhikang Li
Chapter 9
QTL Mapping in DNA Marker-Assisted Plant and Animal Improvement..................................131
Andrew H. Paterson
© 1998 by CRC Press LLC
Chapter 10
QTL Analyses: Power, Precision, and Accuracy...........................................................................145
William D. Beavis
Chapter 11
High-Resolution Mapping of QTLs..............................................................................................163
Andrew H. Paterson
Chapter 12
Compilation and Distribution of Data on Complex Traits............................................................175
Douglas W. Bigwood
PART II. CASE HISTORIES
Chapter 13
Case History in Plant Domestication: Sorghum, An Example of Cereal Evolution....................187
Andrew H. Paterson, Keith F. Schertz, Yann-rong Lin, and Zhikang Li
Chapter 14
Case History in Crop Improvement: Yield Heterosis in Maize....................................................197
Charles W. Stuber
Chapter 15
Case History in Germplasm Introgression: Tomato Genetics and Breeding Using
Nearly Isogenic Introgression Lines Derived from Wild Species................................................207
Dani Zamir and Yuval Eshed
Chapter 16
Case History in Genetics of Long-Lived Plants: Molecular Approaches to
Domestication of a Fast-Growing Forest Tree: Populus...............................................................219
H. D. Bradshaw, Jr.
Chapter 17
Case History in Animal Improvement: Mapping Complex Traits in Ruminants.........................229
Michel Georges
Chapter 18
Case History in Animal Improvement: Genetic Mapping of QTLs for Growth and
Fatness in the Pig...........................................................................................................................241
Leif Andersson, Kjell Andersson, Lena Andersson-Eklund, Inger Edfors-Lilja,
Hans Ellegren, Chris S. Haley, Ingemar Hansson, Maria Johansson Moller,
Sara A. Knott, Kerstin Lundström, and Lena Marklund
Chapter 19
Case History in Humans: Mapping QTLs for Complex Traits in Humans.................................255
Hakan Sakul and Lon R. Cardon
© 1998 by CRC Press LLC
PART III. SOCIAL IMPACT OF QTL MAPPING
Chapter 20
From Malthus to Mapping: Prospects for the Utilization of Genome Analysis to Enhance
the World Food Supply..................................................................................................................267
Jinhua Xiao and Susan R. McCouch
Chapter 21
Ethical Consequences of Mapping QTLs for Complex Human Traits........................................279
John C. Crabbe and John K. Belknap
EPILOGUE
Chapter 22
Prospects for Cloning the Genetic Determinants of QTLs...........................................................289
Andrew H. Paterson
© 1998 by CRC Press LLC