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Forest genetics
Author
Publisher
CABI Pub
Publication Date
2007
Language
English
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Table of Contents
From the Book
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.
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ISBN
9780851993485
9780851990835
9781845932855
9781845932862
9780851990835
9781845932855
9781845932862
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