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 --