Handbook of Quantitative Forest Genetics

FORESTRY SCIENCES

Volume 39

The titles published in this series are listed at the end o/this volume.

Handbook of

Quantitative Forest Genetics

Edited by

LAUREN FINS University of Idaho, Moscow, lD, U.S.A.

SHARON T. FRIEDMAN USDA Forest Service, Washington, DC, U.S.A.

and

JANET V. BROTSCHOL USDA Forest Service, Olympia, WA, U.S.A .

Production Editor

LAUREN FINS University of Idaho, Moscow, lD, U.S.A.

Springer-Science+Business Media, B.V

ISBN 978-90-481-4112-8 ISBN 978-94-015-7987-2 (eBook) DOI 10.1007/978-94-015-7987-2

Printed on acid-free paper

All Rights Reserved © 1992 Springer Science+Business Media Dordrecht

Originally published by Kluwer Academic Publishers in 1992.

No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording or by any information storage and retrieval system, without written permission from the copyright owner.

To

David and Tracy B.,

Steve and Alex,

Ernie, Amanda and Benjamin.

Contents

Preface xi

Acknowledgements xvi

Chapter 1 Quantitative Genetics: Why Bother? 1 C. B. Talbert

Everyone's a geneticist! 1 Decision-making in today's environment 2 The origin and basis of quantitative genetics 5 Making decisions based on quantitative genetics 8 The care and feeding of data 23 Where quantitative approaches leave off 26

Chapter 2 Fundamental Genetic Principles 29

1. P. van Buijtenen

Mendelian genetics 29 Population genetics 39 Quantitative genetics 50

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Chapter 3 Mating Designs 69 F. Bridgwater

Bases for comparing mating designs 70 Evaluation of mating designs 72 Variations and combinations of mating designs 89

Chapter 4 Field Test Design 96 1. Loo-Dinkins

Importance of field test design 96 What is a field test design 99 Matching design with situation 115 A posteriori data adjustment for local variation 123 Symbols used in this chapter 134

Chapter 5 Concepts of Selection and Gain Prediction 140 G. R. Hodge and T. L. White

Chapter organization 141 Derivation of general prediction formula 142 Mass selection 147 Parental selection: Both parents selected 153 Parental selection: One parent selected 160 Indirect selection 161 Multiple traits 164 Family and within family selection 168 Multiple tests of the 'same' trait 178 Summary 188

Chapter 6 Computational Methods R. W. Stonecypher

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195

The analysis of variance (ANOVA) 196 Analyses of forest genetics experiments: Some examples 201

Chapter 7 Estimating Yield: Beyond Breeding Values 229

G. S. Foster

Introduction Genetic tests

229 230

Part-record selection 237 Deployment strategy 239 Growth and yield modeling to predict genetic gain 251 Verifying realized genetic gain 260 Conclusion 262

Chapter 8 Quantitative Approaches to Decision-Making

in Forest Genetics Programs 270

S. T. Friedman

Uses for economic criteria 272 Economic analysis Example 274 Choices of GRM alternatives under constraits 298 Risk and uncertainty in GRM decisions 302

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Chapter 9 Developing Seed Transfer Zones 313

R. D. Westfall

Chapter organization 314 Development of seed (procurement) zones 315 Transfers within breeding zones 361 Future directions and needs 377 Appendix 9.1 388 Appendix 9.2 395

Subject Index 399

Preface This book has been four years in the making. Its inception logically dates back to the 1987 meeting of the Western Forest Genetics Association, when several of us suggested that WFGA sponsor a shortcourse that would emphasize quantitative methods. There was some discussion, but it didn't take much convincing. The members of WFGA agreed to provide both financial support and their enthusiastic professional support.

In the fall of 1987, during our first planning meeting, we realized that none of the textbooks that were currently available would meet our needs for the shortcourse. That's when we conceived the idea of compiling our instructors' lecture notes into a handbook that would serve both as a text for current and future students and as an important reference tool for professional forest geneticists and tree breeders.

In March of 1989, 10 of the most highly qualified instructors in the United States and Canada presented the week-long "Shortcourse in Quantitative Forest Genetics" to 67 participants. Although we had described our target audience as "forest geneticists, tree improvement specialists and breeding specialists holding an MS degree or a bachelor's degree with experience in forest tree improvement", our participants ran the gamut of tree improvement personnel. At the end of the week, most of them told us that the course had been very much worth their time and had provided useful information at many

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different levels. Even our most veteran instructors said they learned some "new tricks".

We have spent the last two-and-a-half years compiling and editing this "Handbook". Each of its chapters comes from the instructors' notes from the shortcourse. We've tried to ensure their readability and

consistency by reviewing and editing all of the chapters ourselves and having them reviewed by one or several other scientists. Our reviewers were tough and thorough ... our authors (bless their hearts!) were patient and cooperative.

Some of the chapters have been expanded beyond the instructors' presentations to include information that the authors would have liked to present but simply didn't have the time. Other chapters have been re-arranged to improve their flow. They follow a logical sequence and each contains information that has a special and important place in any tree improvement program.

In the first chapter by Cheryl Talbert, we begin with a justification for why one should even bother with quantitative forest genetics. Talbert ''focuses on quantitative genetics in support of six different kinds and levels of decision-making, and nicely develops the concept of a genetic­process model as providing the theoretical underpinning of quantitative genetics. ,,1

1 Editors' note: This quote and those that follow in the preface are from W J. Libby's review of the manuscript.

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Although we assume that our readers will be well-schooled in basic genetics, we felt compelled to present clear definitions and fundamental principles to help ensure a consistent basis of understanding among our readers. In Chapter 2 then, Hans van Buijtenen concisely and elegantly reviews the fundamental principles that are the basis of all of quantitative genetics. This chapter is not intended as the student's sole introduction to the field, but rather, as "a good text to accompany additional formal or informal instruction in

genetics".

In our third chapter, Floyd Bridgwater develops the use of alternative mating designs to achieve specific program objectives. The chapter outlines "the main kinds of mating designs available, and compares them

on the basis of backward selection (progeny testing), forward selection

(gain), parameter estimation, long-term breeding, and cost", providing the reader with the critical information necessary to decide which mating design will support various program objectives.

Once the families of interest are generated (either through controlled crosses or through open-pollinated collections) the progeny must be evaluated in well-planned, well-designed genetic tests. In Chapter 4 on field test designs, Judy Loo-Dinkins explores the various objectives of testing, the designs that can best meet those objectives and potential design flaws that may hamper one's ability to analyze data from them. According to Libby, "Chapter 4 alone is worth the price of

the book. Loo-Dinkins thoroughly covers most aspects of field-test

design, layout and deployment ... [providing] valuable readingfor beginners

and abundant food for thought for experts. "

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Chapter 5 contains a beautifully condensed version of Gary Hodge and Tim White's book on predicting breeding values. In this chapter the authors describe powerful analytical tools that can link genetic entries over time and/or space by using multiple sets of data to calculate a single breeding value for each entry. "Hodge and White at

first seem to make some simple ideas difficult, but they then use these carefully constructed approaches to make some difficult analyses possible, if not simple ... This is a useful chapter, both with respect to ways of looking at traits and experiments, and with respect to ways to analyze them for the purposes of selection. "

No book on quantitative forest genetics would be complete without a presentation and discussion of the use of analysis of variance. "In Chapter 6, the reader is given excerpts based on 2 + decades of experience and accumulated wisdom by Roy Stonecypher. [This chapter J. .. gives the reader hope that big studies with missing data and bent assumptions really can be analyzed both effectively and honestly. Several examples of real analyses, some done in several alternative ways, are provided for study and evaluation."

In Chapter 7, Sam Foster takes the analytical process beyond the theoretical models and tackles some of the most pesky practical problems in predicting and achieving gains from tree improvement programs. He "nicely covers the theory and practice of testing,

deploymen~ and gain predictions ... [The chapter J complements and

extends the earlier chapters by focusing on how present data can be used

not only to predict future growth and yield, but also on how such

knowledge affects deployment of selected clones and families. This

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thoughtful chapter is backed by a substantial review of the literature, with abundant entries to primary references. II

With changing technologies and changing markets, tree breeders are often required to present economic justifications for continuing existing programs and/or developing new· or expanded programs. In Chapter 8, Sharon Friedman nicely presents a variety of economic tools for decision-making in breeding programs. This chapter IIleads

most forest geneticists and many tree improvers into new topics of proper

concern. For some, it provides the framework for thinking about such topics. For those who actually need to do such analyses, it provides

theory, examples, and appropriate references to the relevant

literature ... [The 1 methods of calculating the annual planting area needed

to justify an improvement program, and the contrasts of methods ... [were 1 particularly useful and insightful II

In our last and probably most complex chapter, Bob Westfall presents some sophisticated and elegant analytical tools for developing seed transfer guidelines. This chapter logically closes our book in that it explores in depth some of issues introduced in van Buijtenen's chapter on fundamentals, namely the determination of seed procurement zones for the first generation and seed deployment zones for advanced generation programs. Much of the focus of Westfall's chapter is on dealing with genotype by environment interactions and the issues surrounding genotypic stability across environments. IIFor the beginner,

Westfall raises a number of important questions and suggests good ways

to go about answering them. For more advanced readers, he provides

useful insights and details with respect to some complex techniques. It

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is not a chapter where novices can find cookbook routes to advanced analyses, however. His caution about not allowing computer analyses and multivariate techniques to distance the investigator from the data is well taken."

That's it...nine chapters of excellent information and advice from experts in the field. New and more efficient analytical tools continue to be developed. As they come to light, new workshops and shortcourses will be offered and new books will supplant the old ones. In the meantime, we enjoyed working on this book and the shortcourse that preceded it. They were both challenges for us and took more time than we'd originally anticipated. But we expanded our own professional knowledge and expertise in the process. Our objective now is to help others do the same.

Lauren Fins Sharon Friedman

Janet Brotschol June 1991

Acknowledgements The editors acknowledge and thank the members of the Western Forest Genetics Association for providing their professional and financial support for the original shortcourse on which this book is based. We also thank our chapter authors for their patience and professionalism in writing and revising their manuscripts and responding to questions and critiques from us and reviewers. They did a magnificent job of condensing, into single chapters, bodies of information that might each constitute an entire book. Our chapter reviewers, in alphabetical order, were: Floyd Bridgwater, Bob Campbell, Jim Cathcart, Chris Hansen, Steve Knowe, Steen Magnussen, Barb McCutchan, Steve McKeand, Gene Namkoong, and Gerald Tuskan. Their individual and collective contributions to the readability and flow of the chapters were invaluable, and we thank them heartily. Our sincere appreciation and thank yous go to W.J. Libby who reviewed the entire manuscript. His watchful eye caught several remaining inconsistencies within and between chapters, and his

insightful comments helped us to maintain appropriate perspective throughout the book. And finally, a giant thank you to Deb Hornbuckle who helped pull all the pieces together. Without her knowledge of word processing and her eye for detail, we could not have produced this book.

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The Editors

June 1991