ALBERT

Note: Contents 1 The Conifers Conifer Taxonomy Geographic Distribution and Biogeography Life History Ecological Tolerance Conifer Mating System, Life Cycle, and Reproduction The Largest, Tallest, and Oldest Organisms on the Planet Genetic Diversity Summary Part I Genomes 2 Genomes: Classical Era The Beginnings of Genome Research in Conifers Chromosome Number and Polyploidy Genome Size Karyotype Analysis Genome Content Organelle Genomes: Chloroplast and Mitochondria Size and Structure Gene Content Inheritance Variation Summary 3 Gene and Genome Sequencing in Conifers: Modern Era A Short History of DNA Sequencing in Conifers Expressed Sequence Tag Sequencing Gene Discovery Using Next-Generation Sequencing Conifer Reference Genome Sequences Sequencing, Assembly, and Annotation Strategies Summary Statistics of Published Conifer Genome Sequences Discovery of the Noncoding DNA Content of Conifer Genomes Discovery of the Number and Types of Coding Genes in Conifers Chloroplast and Mitochondrial Genome Sequencing Summary 4 Noncoding and Repetitive DNA Introduction Ribosomal DNA Tandem Repeats: Satellite, Minisatellite, and Microsatellite DNA Transposons and Retrotransposons Pseudogenes Summary 5 Gene Structure and Gene Families A Short History of Early Conifer Gene Sequencing Wood-Forming Genes Vegetative Growth Genes Floral Genes Light-Regulated Genes Defense-Related Genes Disease-Resistant Genes Summary 6 Gene Expression and the Transcriptome A Short History of Gene Expression Studies in Conifers Wood Formation Biotic Factors Abiotic Factors Seasonal Patterns Epigenetic Control of Gene Expression Summary 7 Proteomics and Metabolomics A Short History of Proteomic and Metabolomic Research in Conifers Wood Formation Biotic Factors Abiotic Factors Seed Development and Somatic Embryogenesis Summary Part II Variation 8 Phenotypic Variation in Natural Populations Introduction Definitions Terms for Describing the Identity of Experimental Plant Materials: Provenance, Population, Seed Source, and Accession Terms for Describing Patterns of Genetic Variation on the Natural Landscape: Cline, Race, and Ecotype Historical Perspectives Application of Common Garden Experiments Experimental Approaches and Analytical Methods Experimental Approaches Analytical Methods Dependent and Independent Variables Common Garden Testing Literature Amount, Distribution, and Pattern of Genetic Variation in Phenotypic Traits of Conifers Amount and Distribution of Genetic Variation Patterns of Variation Are Local Sources Best? Case Studies Pseudotsuga menziesii (Douglas-fir) Pinus Summary 9 Neutral Genetic Variation Introduction and Background Molecular Markers Used in the Study of Neutral Variation Three Conifer Genomes Purpose and Applications of Neutral Genetic Variation Studies General Diversity Results: Allozymes Variation Within Species Variation Within Populations Distribution of Variation Among Populations (Based on Polymorphic Loci only) Differences in Measures of Diversity Among Conifer Genera and Families Allozyme Summary General Diversity Results: Molecular Markers Organelle Markers Nuclear Markers Population Differentiation Factors Affecting Amount and Distribution of Genetic Variation Mating Systems Gene Flow Genetic Drift Case Studies Diversity, Population Structure, and Biogeography Conservation and Mating Systems Effects of Forest Management and Tree Improvement on Genetic Diversity Summary 10 Adaptive Genetic Variation A Short History of Adaptive Genetic Variation in Conifers General Trends in Patterns of Adaptive Genetic Diversity in Conifers Observed from Neutrality and FST Outlier Tests Detection of Nonneutral Genes in a Few Conifer Species Pinus taeda Pinus sylvestris Pinus mugo, P. uncinata, and P. uliginosa Pinus pinaster and P. halepensis Pinus radiata Pinus contorta Pinus massoniana and P. hwangshanensis Pinus lambertiana and Other Subgenus Strobus Species Pseudotsuga menziesii Larix Species Abies Species Picea Species Cryptomeria japonica and Taxodium distichum Summary 11 Quantitative Trait Dissection A Short History of Complex Trait Dissection in Conifers Pinus taeda Pinus elliottii Pinus radiata Pinus sylvestris Pinus pinaster Pinus contorta Pseudotsuga menziesii Picea ssp. Larix ssp. Cryptomeria japonica Summary 12 Landscape Genomics A Short History of Landscape Genomics Studies in Conifers Pinus Subgenus Pinus Pinus Subgenus Strobus Picea Abies and Larix Summary 13 Conservation Genetics A Brief Introduction to Conservation Genetics in Forestry Fragmentation Habitat Loss Forest Practice Disease Insects Climate Change Summary 14 Forest Health Introduction The Growing Relevance of Forest Health Genetic Variation in Forest Health Traits Insects and Disease Abiotic Stress Mechanisms of Resistance and Tolerance Case Studies Resistance to Pissodes strobi (White Pine Weevil) Found in Picea sitchensis (Sitka spruce) Resistance to an Introduced Pathogen (Phytophthora lateralis) in Chamaecyparis lawsoniana (Port-Orford-cedar) Resistance to Stem Rusts in North American White Pines and Southern Yellow Pines Summary Part III Evolution 15 Hybridization and Introgression Introduction Definitions and Background Definitions Background Approaches to Identifying Hybrids and Quantifying Levels of Introgression Evolving Insights Case Studies of Introgressive Hybridization in Conifers Pinus contorta (Lodgepole Pine) x P. banksiana (Jack Pine) Picea sitchensis (Sitka Spruce) x P. glauca (White Spruce) and P. engelmannii (Engelmann Spruce) x P. glauca Pinus taeda (Loblolly Pine) x P. echinata (Shortleaf Pine) Hybrid Speciation Artificial Hybrids Summary 16 Paleobotany, Taxonomic Classification, and Phylogenetics Introduction Paleobotany Taxonomic Classification Cupressus Pinus Phylogenetics Character Selection The Conifers and Related Gymnosperms Araucariaceae Cupressaceae Pinaceae Podocarpaceae Sciadopityaceae Taxaceae Summary 17 Comparative Genomics Introduction to Comparative Genomics Comparative Mapping Comparative Gene Content and Transcriptomics Comparative Genome Sequences Summary 18 Historical Perspective and Future Directions in Forest Genetics and Genomics Historical Perspective Current Situation Future Directions Primary Commercial Species (Group A) Appendix 1 Appendix 2 References Index