Forest genetics

Acknowledgments

Preface

ch. 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 1 : Basic principles

ch. 2. Molecular basis of inheritance : genome organization, gene structure and regulation

Genome organization

The DNA molecule

Cellular organization of genomes

Genome size

Chromosomes and polyploidy

Karyotype analysis

Repetitive DNA

Gene structure and regulation

The central dogma and the genetic code

Transcription and translation

Structural organization of a gene

Regulation of gene expression

Summary and conclusions

ch. 3. Transmission genetics : chromosomes, recombination and linkage

Mendelian genetics

Mendel's crossing experiments with peas

Mendelian inheritance of traits in forest trees

Statistical tests for Mendelian inheritance

Transmission and inheritance of chromosomes

Mitosis and cell division

Meiosis and sexual reproduction

Extensions to Mendel's laws

Partial dominance

Codominance

Epistasis

Genetic linkage

Organelle genome inheritance

Summary and conclusions

ch. 4. Genetic markers : morphological, biochemical and molecular markers

Uses and characteristics of genetic markers

Morphological markers

Biochemical markers

Monoterpenes

Allozymes

Other protein markers

Molecular markers

DNA-DNA hybridization : restriction fragment length polymorphism

Molecular markers based on the polymerase chain reaction

Summary and conclusions

ch. 5. Population genetics : gene frequencies, inbreeding and forces of evolution

Quantifying the genetic composition of populations

Genotype and allele frequencies

Hardy-Weinberg principle

Mating systems and inbreeding

Influence of inbreeding on genotypic frequencies

Inbreeding coefficient and regular systems of inbreeding

Inbreeding depression

Forces that change allele frequencies

Mutation

Migration

Selection

Genetic drift

Joint effects of evolutionary forces

Summary and conclusions

ch. 6. Quantitative genetics : polygenic traits, heritabilities and genetic correlations

The nature and study of polygenic traits

Characteristics of polygenic traits

Studying polygenic traits

Modeling phenotypes of parents and offspring

Clonal value and breeding value

Estimating the average performance of offspring

Genetic variances and heritabilities

Definitions and concepts

Estimates of heritabilities for forest trees

Uses and importance of heritability estimates in forest tree populations

Genetic correlations

Definitions and concepts

Trait-trait correlations

Age-age correlations

Genotype x environment interaction

Definitions and concepts

Importance of G x E interaction in forest trees

Estimating genetic parameters

Mating design

Field design

Study implementation, data cleaning and standardization

Data analyses

Parameter estimation and interpretation

Summary and conclusions

Section 2 : Genetic variation in natural populations

ch. 7. Within-population variation : genetic diversity, mating systems and stand structure

Quantifying genetic variation

Measures of genetic variation based on genetic markers

Measures of genetic variation based on quantitative traits

Genetic diversity in forest trees

Estimates of genetic diversity from genetic markers

Estimates of genetic diversity from quantitative traits

Factors promoting genetic diversity within populations

Large population size

Longevity

High levels of outcrossing

Strong migration between populations

Balancing selection

Mating system dynamics in forest trees

Mechanisms promoting high levels of outcrossing

Factors leading to unusually low levels of outcrossing

Patterns of cross-fertilization within populations

Spatial and temporal genetic structure within populations

Spatial genetic structure

Temporal genetic structure

Practical implications of within-population genetic diversity

Genetic improvements under natural regeneration systems

Seed collections in natural populations

Summary and conclusions

ch. 8. Geographic variation : races, clines and ecotypes

Definitions and concepts related to geographic variation

Provenances, seed sources and races

Clines and ecotypes

Varieties and subspecies

Provenance x environment interaction

Experimental methods used to study geographic variation

Genetic markers for studying geographic variation

Short-term seedling tests in artificial environments

Long-term provenance trials in field experiments

Patterns of geographic variation in forest trees

Racial variation associated with environmental differences

Racial variation not associated with environmental differences

Species with little or no racial variation

Geographic patterns of genetic diversity

Implications of geographic variation for seed transfer

Setting explicit objectives of provenance selection

Lessons learned from previous provenance studies

A decision tree to guide seed transfer decisions

Types of seed transfer guidelines and logistics of implementation

Summary and conclusions

ch. 9. Evolutionary genetics : divergence, speciation and hybridization

Divergence, speciation and hybridization

Species concepts

Mechanisms of speciation

Hybridization and introgression

Evolutionary history and phylogeny

Evolutionary history

Phylogenetics

Molecular mechanisms of genome evolution

Mutation and nucleotide diversity

Gene duplication and gene families

Polyploidy

Coevolution

Pines and rust fungi

White pines and corvids

Summary and conclusions

ch. 10. Gene conservation : in situ, ex situ and sampling strategies

Threats to genetic diversity

Habitat loss, deforestation, and fragmentation

Pathogens, insects, exotic species and movement of genetic material - Pollution and global climate change

Strategies to conserve genetic diversity

In situ gene conservation

Ex situ gene conservation

Population sizes for gene conservation

Number and location of populations for gene conservation

Effects of forest management practices and domestication of genetic diversity

Summary and conclusions

Section 3 : Tree improvement

ch. 11. Tree improvement programs : structure, concepts and importance

Scope and structure of tree improvement programs

The breeding cycle of forest tree improvement programs

Base population

Selected population

Breeding population

Propagation population

Infusions from external populations

Genetic testing

Genetic gains and economic value of tree improvement programs

Genetic gain concepts and types of gains estimates

Genetic gains achieved for different traits

Economic analysis of tree improvement programs

Summary and conclusions

ch. 12. Base populations : species, hybrids, seed sources and breeding zones

Types of taxa and their attributes for plantations

Species and interspecific hybrids

Subspecies, varieties, provenances and land races

Choosing species, hybrids and seed sources for plantation forestry

Identifying candidate species, hybrids and seed sources for plantation forestry

Multiphase field trials for testing species, hybrids and seed sources

Using available information to make taxa decisions for plantation forestry

Defining base populations for tree improvement programs

Number and size of breeding units

Composition of base populations

Summary and conclusions

ch. 13. Phenotypic mass selection : genetic gain, choice of traits and indirect response

General concepts and their application to mass selection

The process of selection

Mass selection in first-generation tree improvement programs

Methods of mass selection

predicting genetic gain from mass selection

Equations for predicting genetic gain

Selection intensity

Factors affecting genetic gain from mass selection

Indirect mass selection

Definition and uses of indirect selection

Comparison of indirect and direct selection

Selection methods for multiple traits

Defining the breeding objective

Choosing which traits to measure

Index selection

Independent culling, tandem selection and two-stage selection

Summary and conclusions

ch. 14. Genetic testing : mating designs, field designs and test implementation

Types, objectives and functions of genetic tests

Defining genetic architecture

Progeny testing

Establishing advanced-generation base populations

Quantifying realized gains

Mating designs

Incomplete-pedigree mating designs

Complete pedigree (full-sib) family mating designs

Variations of classical mating designs

Field designs

Plot conformation

Statistical design (field layout) at each location

Selection of sites

Including additional trees (borders, fillers and controls)

Test implementation

Breeding and nursery, phases of test implementation

Site preparation and test establishment

Test maintenance and measurement

Summary and conclusions

ch. 15. Data analysis : mixed models, variance components and breeding values

Preliminary steps prior to data analysis

Editing and cleaning of data

Transformations and standardization

Exploratory data analysis

Linear statistical models

Parental versus individual tree models

Multivariate linear models

Concepts and applications of mixed model methods

Estimation of fixed effects

Estimation of variance components and genetic parameters

Prediction of genetic values

Implementation and limitations of mixed model analyses

Selection indices : combining information across relatives and traits

Concepts of selection indices

Calculating selection indices

Making selections and calculating genetic gain

Spatial variation and spatial analysis in genetic trials

Concepts of spatial variation

Methods of spatial analysis

Summary and conclusions

ch. 16. Deployment : open-pollinated varieties, full-sib families and clones

Interim options for meeting immediate seed needs

Seed production areas

Directed seed collections

Seed orchards

Clonal seed orchards

Seedling seed orchards

Considerations common to both clonal and seedling seed orchards

Family forestry

Family forestry based on control-pollinated (CP) seedlings

Family forestry using plantlets from vegetative multiplication

Clonal forestry

Advantages of clonal forestry

Issues and concerns about clonal forestry

Operational deployment of clones

Genetic diversity considerations in deployment options

Summary and conclusions

ch. 17. Advanced-generation breeding strategies : breeding population size, structure and management

General concepts of advanced-generation breeding strategies

Organization of a breeding strategy

Principles of recurrent selection

Management of genetic diversity and inbreeding

Placing more emphasis on better material

Breeding population size

Guidelines for breeding population sizes from theoretical studies

Further considerations about size of breeding populations

Recommendations for sizes of breeding populations

Breeding population structure

Structures that promote emphasis on superior material

Multiple populations

Sublines or breeding groups

Examples of breeding population structures

Mating designs for advanced-generation breeding

Open-pollinated (OP) management of the breeding population

Full-sib (FS) and complementary mating designs for managing the breeding population

Making advanced-generation selections

Within-family selection

Cloning the base population

Selections from overlapping generations

Selection indices and other methods of selection

Balancing genetic gain and genetic diversity

Optimum selection age

Summary and conclusions

Section 4 : Biotechnology

ch. 18. Genomics : discovery and functional analysis of genes

Structural genomics

Gene discovery

Genetic mapping

Gene mapping by bulked segregant analysis

Functional genomics

Comparative sequencing

Gene expression analysis

Forward and reverse genetic approaches

Quantitative trait locus (QTL) mapping

Positional cloning of QTLs

Association genetics

Comparative genomics

Bioinformatics and databases

Summary and conclusions

ch. 19. Marker-assisted selection and breeding : indirect selection, direct selection and breeding applications

concepts of marker-assisted selection (MAS)

Definitions and concepts related to MAS

Benefits, limitations and challenges of MAS

Indirect selection based on markers linked to QTLs

Marker-assisted early selection (MAES) versus mature phenotypic selection

Marker-assisted early selection (MAES) versus early phenotype selection

Combined phenotypic and marker-assisted early index selection versus early phenotypic selection

Marker-assisted selection and combined within-family and family selection versus combined within-family and family selection alone

Direct selection based on genes coding for target traits

Marker-assisted breeding

Quality control in tree improvement programs

Breeding and mating designs

Propagation populations and deployment

Hybrid breeding

Smart and ideotype breeding

Summary and conclusions

ch. 20. Genetic engineering : target traits, transformation and regeneration

Target traits for genetic engineering

Methods for gene transfer

Indirect gene transfer

Direct gene transfer

Vector design and selectable markers

Regeneration methods

Organogenesis

Somatic embryogenesis

Applications of genetic engineering in forest trees

Lignin modification

Herbicide tolerance

Pest and disease resistance

Flowering control

Transgene expression and stability

Commercialization, regulation and biosafety

Summary and conclusions

References

Index.