Contents

Acknowledgments

Preface

Chapter 1: Forest Genetics – Concepts, Scope, History and Importance

Global Scope and Importance of Natural and Managed Forests

The Role of Plantations as Forest Ecosystems

Concepts and Sources of Variation in Forests

Separating Genotypic and Environmental Influences on Phenotypic Variation

Environmental Sources of Variation

Genetic Sources of Variation

Historical Perspective on Forest Genetics

General Genetics

Forest Genetics

Why Study Forest Genetics?

SECTION I: BASIC PRINCIPLES

Chapter 2: Molecular Basis of Inheritance – Genome Organization, Gene Structure and Regulation

Genome Organization

Gene Structure and Regulation

Summary and Conclusions

Chapter 3: Transmission Genetics – Chromosomes, Recombination and Linkage

Mendelian Genetics

Transmission and Inheritance of Chromosomes

Extensions to Mendel's Laws

Summary and Conclusions

Chapter 4: Genetic Markers – Morphological, Biochemical and Molecular Markers

Uses and Characteristics of Genetic Markers

Morphological Markers

Biochemical Markers

Molecular Markers

Summary and Conclusions

Chapter 5: Population Genetics – Gene Frequencies, Inbreeding and Forces of Evolution

Quantifying the Genetic Composition of Populations

Mating Systems and Inbreeding

Forces that Change Allele Frequencies

Joint Effects of Evolutionary Forces

Summary and Conclusions

Chapter 6: Quantitative Genetics – Polygenic Traits, Heritabilities and Genetic Correlations

The Nature and Study of Polygenic Traits

Modeling Phenotypes of Parents and Offspring

Genetic Variances and Heritabilities

Genetic Correlations

Genotype x Environment Interaction

Estimating Genetic Parameters

Summary and Conclusions

SECTION II: GENETIC VARIATION IN NATURAL POPULATIONS

Chapter 7: Within-population Variation – Genetic Diversity, Mating Systems and Stand Structure

Quantifying Genetic Variation

Genetic Diversity in Forest Trees

Factors Promoting Genetic Diversity within Populations

Mating System Dynamics in Forest Trees

Spatial and Temporal Genetic Structure within Populations

Practical Implications of Within-population Genetic Diversity

Summary and Conclusions

Chapter 8: Geographic Variation – Races, Clines and Ecotypes

Definitions and Concepts Related to Geographic Variation

Experimental Methods Used to Study Geographic Variation

Patterns of Geographic Variation in Forest Trees

Implications of Geographic Variation for Seed Transfer

Summary and Conclusions

Chapter 9: Evolutionary Genetics – Divergence, Speciation and Hybridization

Divergence, Speciation and Hybridization

Evolutionary History and Phylogeny

Molecular Mechanisms of Genome Evolution

Coevolution

Summary and Conclusions

Chapter 10: Gene Conservation – In Situ, Ex Situ and Sampling Strategies

Threats to Genetic Diversity

Strategies to Conserve Genetic Diversity

Effects of Forest Management Practices and Domestication on Genetic Diversity

Summary and Conclusions

SECTION III: TREE IMPROVEMENT

Chapter 11: Tree Improvement Programs – Structure, Concepts and Importance

Scope and Structure of Tree Improvement Programs

The Breeding Cycle of Forest Tree Improvement Programs

Genetic Gains and Economic Value of Tree Improvement Programs

Summary and Conclusions

Chapter 12: Base Populations – Species, Hybrids, Seed Sources and Breeding Zones

Types of Taxa and Their Attributes for Plantations

Choosing Species, Hybrids and Seed Sources for Plantation Forestry

Defining Base Populations for Tree Improvement Programs

Summary and Conclusions

Chapter 13: Phenotypic Mass Selection – Genetic Gain, Choice of Traits and Indirect Response

General Concepts and Their Application to Mass Selection

Predicting Genetic Gain from Mass Selection

Indirect Mass Selection

Selection Methods for Multiple Traits

Summary and Conclusions

Chapter 14: Genetic Testing – Mating Designs, Field Designs and Test Implementation

Types, Objectives and Functions of Genetic Tests

Mating Designs

Field Designs

Test Implementation

Summary and Conclusions

Chapter 15: Data Analysis – Mixed Models, Variance Components and Breeding Values

Preliminary Steps Prior to Data Analysis

Linear Statistical Models

Concepts and Applications of Mixed Model Methods

Selection Indices: Combining Information Across Relatives and Traits

Spatial Variation and Spatial Analysis in Genetic Trials

Summary and Conclusions

Chapter 16: Deployment – Open-pollinated Varieties, Full-sib Families and Clones

Interim Options for Meeting Immediate Seed Needs

Seed Orchards

Family Forestry

Clonal Forestry

Genetic Diversity Considerations in Deployment Options

Summary and Conclusions

Chapter 17: Advanced-generation Breeding Strategies – Breeding Population Size, Structure and Management

General Concepts of Advanced-generation Breeding Strategies

Breeding Population Size

Breeding Population Structure

Mating Designs for Advanced-generation Breeding

Making Advanced-generation Selections

Summary and Conclusions

SECTION IV: BIOTECHNOLOGY

Chapter 18: Genomics – Discovery and Functional Analysis of Genes

Structural Genomics

Functional Genomics

Comparative Genomics

Bioinformatics and Databases

Summary and Conclusions

Chapter 19: Marker-assisted Selection and Breeding – Indirect Selection, Direct Selection and Breeding Applications

Concepts of Marker-assisted Selection (MAS)

Indirect Selection Based on Markers Linked to QTLs

Direct Selection Based on Genes Coding for Target Traits

Marker-assisted Breeding

Summary and Conclusions

Chapter 20: Genetic Engineering – Target Traits, Transformation and Regeneration

Target Traits for Genetic Engineering

Methods for Gene Transfer

Vector Design and Selectable Markers

Regeneration Methods

Applications of Genetic Engineering in Forest Trees

Transgene Expression and Stability

Commercialization, Regulation and Biosafety

Summary and Conclusions

References

Index

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