Jansson / Bhalerao / Groover Genetics and Genomics of Populus

2010
ISBN: 978-1-4419-1541-2
Verlag: Springer US
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 8, 384 Seiten

Reihe: Plant Genetics and Genomics: Crops and Models

Genetics and Genomics of Populus provides an indepth description of the genetic and genomic tools and approaches for Populus, examines the biology that has been elucidated using genomics, and looks to the future of this unique model plant. This volume is designed to serve both experienced Populus researchers and newcomers to the field. Contributors to the volume are a blend of researchers, some who have spent most of their research career on Populus and others that have moved to Populus from other model systems. Research on Populus forms a useful complement to research on Arabidopsis. In fact, many plant species found in nature are - in terms of the life history and genetics - more similar to Populus than to Arabidopsis. Thus, the genetic and genomic strategies and tools developed by the Populus community, and showcased in this volume, will hopefully provide inspiration for researchers working in other, less well developed, systems.

Stefan Jansson is Professor at Umeå Plant Science Centre, Department of Plant Physiology, Umeå University. He was the European coordinator during the Populus genome sequencing initiative, and has a research focus on natural variation and autumn senescence. Andrew T. Groover studies the developmental biology of forest trees, with a primary focus on secondary growth and wood formation. He is a Geneticist and Director of the Institute of Forest Genetics, US Forest Service, in Davis California. Rishikesh P. Bhalarao is Professor at Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences. His primary research interests are auxin signaling and seasonal activity/dormancy transitions of the cambium.

Autoren/Hrsg.

Jansson, Stefan

Bhalerao, Rishikesh

Groover, Andrew

Inhaltsverzeichnis

1;Preface;6
2;Contents;10
3;Contributors;12
4;Author Biographies;16
5;Part I Overview and an Introduction to the Biology of Populus ;17
5.1;Why and How Populus Became a Model Tree;18
5.1.1;1 Model Systems Within Biological Research;18
5.1.2;2 Key Events That Led to Adoption of Populus as the Prime Tree Model System ;20
5.1.3;3 The Populus Genome Sequencing ;22
5.1.4;4 Populus Biotechnology and Breeding Past and Future Visions ;27
5.2;References;28
5.3;Salient Biological Features, Systematics, and Genetic Variation of Populus;30
5.3.1;1 Dendrological Overview;31
5.3.1.1;1.1 Morphology;31
5.3.1.2;1.2 Habitat;32
5.3.1.3;1.3 Life History;32
5.3.1.3.1;1.3.1 Sexual Reproduction;32
5.3.1.3.2;1.3.2 Asexual Reproduction;35
5.3.2;2 Systematics and Evolution;36
5.3.2.1;2.1 Fossil Record;36
5.3.2.2;2.2 Relationships to Salix and Other Families;36
5.3.2.3;2.3 Classification;36
5.3.2.4;2.4 Natural Hybridization;37
5.3.3;3 Genetic Variation;38
5.3.3.1;3.1 Molecular Markers;38
5.3.3.1.1;3.1.1 Allozymes and RFLP;38
5.3.3.1.2;3.1.2 Microsatellites;44
5.3.3.1.3;3.1.3 Nucleotide Diversity;44
5.3.3.2;3.2 Adaptive Traits;45
5.3.4;4 Conclusions;46
5.4;References;47
5.5;Growth and Physiology;54
5.5.1;1 Growth and Biomass Production;54
5.5.1.1;1.1 Biomass Yields;54
5.5.1.2;1.2 Root Growth and Physiology;59
5.5.1.3;1.3 Hybridization and Heterosis;60
5.5.1.4;1.4 Allocation Patterns;61
5.5.2;2 Allometric Relationships;62
5.5.3;3 Productivity Determinants;63
5.5.3.1;3.1 Gas Exchange;64
5.5.3.2;3.2 Leaf Traits;65
5.5.3.3;3.3 Branching Pattern: Syllepsis versus Prolepsis;66
5.5.3.4;3.4 Phenology;68
5.5.4;4 Water Relations and Productivity;69
5.5.4.1;4.1 Water Requirements;69
5.5.4.2;4.2 Stomata;70
5.5.5;5 Phytohormones and Growth Regulation;71
5.5.6;6 Conclusion;72
5.6;References;72
6;Part II Populus Genetics and Genomics;79
6.1;The Populus Genome and Comparative Genomics;80
6.1.1;1 Overview;80
6.1.1.1;1.1 Significance of the Populus Genome Sequence;80
6.1.1.2;1.2 Background to the Genome Sequencing Effort;81
6.1.2;2 Summary of Whole Genome Shotgun Results;82
6.1.2.1;2.1 Sequencing Strategy;82
6.1.2.2;2.2 Selection of a Populus Genotype for Sequencing ;82
6.1.2.3;2.3 Preparation of Sequencing Template and Shotgun Sequencing;83
6.1.2.4;2.4 Sequence Assembly;84
6.1.2.5;2.5 Contamination of the Sequencing Template;84
6.1.2.6;2.6 BAC-Based Physical Map;85
6.1.2.7;2.7 Map-Based Assembly;87
6.1.3;3 Populus Genome Structure;89
6.1.3.1;3.1 Overview;89
6.1.3.2;3.2 Comparison of the Populus and Grape Genomes;91
6.1.3.3;3.3 Repeat Composition Compared to Other Sequenced Genomes;92
6.1.4;4 Gene Content and Comparative Genomics;94
6.1.4.1;4.1 Overview of Gene Prediction Methods and Gene Content;94
6.1.4.2;4.2 Retention of Duplicate Genes;95
6.1.4.3;4.3 Synteny with Other Species;96
6.1.4.4;4.4 Comparison of Select Gene Family Composition Between Sequenced Genomes;97
6.2;References;99
6.3;Nucleotide Polymorphism, Linkage Disequilibriumand Complex Trait Dissection in Populus;104
6.3.1;1 Genetic Diversity in Populus ;104
6.3.2;2 Nucleotide Polymorphism in Populus ;105
6.3.3;3 Linkage Disequilibrium in Populus ;109
6.3.4;4 Patterns of Sequence Divergence in Populus ;111
6.3.5;5 Complex Trait Dissection in Populus ;114
6.3.5.1;5.1 Linkage Mapping and Genome Dynamics in Populus ;114
6.3.5.2;5.2 Association Mapping and the Dissection of Complex Traits in Populus ;115
6.3.6;6 Genetic Control of Bud Phenology and Dormancy;116
6.3.7;7 Perspective;119
6.4;References;120
6.5;Transformation as a Tool for Genetic Analysis in Populus;125
6.5.1;1 Introduction;125
6.5.2;2 Value of Transformation as a Genetic Tool;126
6.5.3;3 Postgenomic Challenges and Opportunities;127
6.5.4;4 Transformation and Poplars;128
6.5.5;5 Approaches for Transgenic Modifications of Gene Function;129
6.5.6;6 Other Approaches for Generation of Knock-Down Gene Modifications;130
6.5.6.1;6.1 Artificial miRNAs and Overexpression of siRNAs;130
6.5.6.2;6.2 Zinc-Finger Nucleases (ZFN);132
6.5.6.3;6.3 Virus Induced Gene Silencing (VIGS);132
6.5.7;7 Transformation Methods in Populus ;133
6.5.8;8 Using Transformation for Mutagenesis;136
6.5.9;9 Future Prospects and Challenges;137
6.6;References;140
6.7;Populus Resources and Bioinformatics;146
6.7.1;1 The Populus Genome;147
6.7.1.1;1.1 Genome Databases and Browsers;148
6.7.1.2;1.2 Expressed Sequence Tags;148
6.7.1.3;1.3 EST Databases;149
6.7.1.4;1.4 Transcription Factor Databases;150
6.7.1.5;1.5 Promoter Motif Analysis;150
6.7.1.6;1.6 Ortholog Prediction;151
6.7.1.7;1.7 miRNA Databases;151
6.7.1.8;1.8 QTL Databases and Browsers;152
6.7.2;2 Omics Methods ;152
6.7.2.1;2.1 Transcriptomics;152
6.7.2.2;2.2 High Throughput Sequencing;154
6.7.2.3;2.3 Metabolomics and Proteomics;155
6.7.3;3 Germplasm;156
6.7.4;4 Future Directions;158
6.8;References;159
7;Part III Genetics and Genomics of Key Populus Traits;164
7.1;Reproductive Development in Populus ;165
7.1.1;1 Introduction;165
7.1.2;2 Initiation of Flowering;166
7.1.2.1;2.1 Juvenility/Maturity;167
7.1.2.2;2.2 Transition to Flowering;170
7.1.3;3 Flower Development and Sex Determination;173
7.1.4;4 Perspectives;177
7.2;References;177
7.3;Perennial Life Style of Populus: Dormancy Cyclingand Overwintering;181
7.3.1;1 Defining Perenniality;181
7.3.1.1;1.1 Seasonal Growth;181
7.3.1.2;1.2 Meristems;182
7.3.1.3;1.3 Dormancy Concept;184
7.3.1.4;1.4 Dormancy Locus;185
7.3.2;2 Photoperiod Induced Priming of Overwintering;185
7.3.2.1;2.1 Sensing by the Leaves;185
7.3.2.2;2.2 Events at the Apex;188
7.3.2.3;2.3 Gibberellins in the Stem;189
7.3.2.4;2.4 Dormancy at the SAM;190
7.3.2.5;2.5 Dormancy at the Cambium;191
7.3.2.6;2.6 Events in Leaves and Stem;192
7.3.3;3 Freezing Tolerance;193
7.3.3.1;3.1 Environmental Regulation;193
7.3.3.2;3.2 Osmotic Adjustments and Dehydration;194
7.3.3.3;3.3 Regulation of Gene Expression;195
7.3.3.4;3.4 Dehydrins and Other Protective Proteins;196
7.3.3.5;3.5 Transcriptional Regulation;196
7.3.4;4 Release from Dormancy;197
7.3.4.1;4.1 Phenology;197
7.3.4.2;4.2 Cell Biology and Biochemistry;198
7.3.4.3;4.3 Gibberellins;200
7.3.4.4;4.4 Chilling and Vernalization;201
7.4;References;202
7.5;Wood Formation in Populus ;211
7.5.1;1 Biology and Salient Features of Populus Wood ;211
7.5.1.1;1.1 Introduction to Wood Formation;211
7.5.1.2;1.2 Wood Development in Populus;212
7.5.1.3;1.3 Populus Wood and Its Uses ;214
7.5.1.4;1.4 Environmental Influences on Wood Formation;217
7.5.2;2 Genetic and Genomic Methods for the Study of Wood Formation in Populus ;218
7.5.2.1;2.1 Traditional Breeding and Quantitative Genetics;218
7.5.2.2;2.2 Gene Discovery Using Gene Tagging;219
7.5.2.3;2.3 Determining Gene Function Using Transgenics;221
7.5.2.4;2.4 Gene Discovery Using Microarray Profiling of Gene Expression;221
7.5.2.5;2.5 Proteomic and Other ''Omic'' Approaches;222
7.5.3;3 Genetic Regulation of Cambium Functions and Wood Formation;222
7.5.3.1;3.1 Global Gene Expression Across Cambium and Wood Forming Tissues;222
7.5.3.2;3.2 Regulation of Tissue Patterning;225
7.5.4;4 Hormonal Control of Wood Formation;226
7.5.4.1;4.1 Introduction;226
7.5.4.2;4.2 Auxin;226
7.5.4.3;4.3 Gibberellin;228
7.5.4.4;4.4 Cytokinin;229
7.5.4.5;4.5 Ethylene;230
7.5.4.6;4.6 Other Hormones;230
7.6;References;231
7.7;Populus Responses to Abiotic Stress;235
7.7.1;1 Introduction;235
7.7.2;2 Stress Signaling and Responses at the Cellular and Tissue Level;236
7.7.2.1;2.1 Cellular Consequences of Water Shortage;236
7.7.2.2;2.2 Signaling Water Limitations;237
7.7.2.3;2.3 Activation of Cellular Defences;238
7.7.3;3 Tree-Specific Adaptation Measures;239
7.7.3.1;3.1 Growth Responses to Drought;239
7.7.3.2;3.2 Adaption of the Hydraulic Architecture to Drought;240
7.7.4;4 Abscission as a Drought Stress Avoidance Strategy;242
7.7.4.1;4.1 Stress Induced Abscission;244
7.7.4.2;4.2 Abscission Induced by Seasonal Drought Stress;245
7.7.5;5 Conclusions;250
7.8;References;250
7.9;Defense and Nutrient Mutualisms in Populus ;257
7.9.1;1 Introduction;257
7.9.2;2 Ecological Relevance;258
7.9.3;3 Defense Mutualisms;260
7.9.4;4 Mycorrhizal Fungi;265
7.9.5;5 Plant Symbiont Communities Diversity;273
7.9.6;6 Endophytes Associated with Populus ;274
7.9.7;7 Plant Symbiont Communities Assembly Rules;275
7.9.8;8 Applications of Fungal Symbionts of Populus ;275
7.9.9;9 Evolutionary History and Fossil Record;277
7.10;References;279
7.11;The Impact of Genomics on Advances in Herbivore Defenseand Secondary Metabolism in Populus;288
7.11.1;1 Introduction;288
7.11.2;2 Overview of Populus Defense and Secondary Metabolism;289
7.11.2.1;2.1 Populus as the ''Ecogenomics'' Model Plant;289
7.11.2.2;2.2 Populus Secondary Metabolites and Their Effects on Herbivores;290
7.11.2.3;2.3 Herbivory and Induction of Defenses in Populus ;292
7.11.3;3 Impact of Populus Genomics on Knowledge of Inducible Defense Proteins ;294
7.11.3.1;3.1 Discovery of Defense-Related Genes via ESTs and Gene Arrays;294
7.11.3.2;3.2 Global Gene Expression Patterns and Insights into the Populus Defense Response;296
7.11.3.3;3.3 Whole Genome Perspectives on Populus Defense;297
7.11.4;4 The Impact of Genomic Analysis on Advances in Phenylpropanoid and Other Secondary Metabolite Pathways;298
7.11.4.1;4.1 Genomic Analysis of Known Secondary Pathways -- Insights into Flavonoid Biosynthesis and Regulation;298
7.11.4.2;4.2 Genomic Analysis and Discovery of Novel Pathways and Metabolites;302
7.11.5;5 Functional Analysis of Genes Important for Populus Defense and Secondary Metabolism;304
7.11.6;6 The Importance of Variation in Plant Defense and Secondary Metabolite Profiles in Populus ;305
7.11.7;7 Key Issues and Future Directions;307
7.12;References;309
8;Part IV Populus for the Future;315
8.1;Populus Breeding: From the Classical to the Genomic Approach;316
8.1.1;1 Introduction;316
8.1.2;2 Genecology;317
8.1.3;3 Controlled Breeding;322
8.1.3.1;3.1 Examples of Long-Term Breeding Programs;328
8.1.4;4 Testing and Selection;331
8.1.5;5 Translational Genomics;339
8.1.5.1;5.1 Discovery of Marker-Trait Associations;340
8.1.5.2;5.2 Marker-Assisted Selection;344
8.1.6;6 Conclusion;345
8.2;References;346
8.3;Conservation Genomics;356
8.3.1;1 Introduction;356
8.3.2;2 Conservation of Genetic Diversity in Populus Traditional Approaches ;359
8.3.3;3 Hybridization and Genetic Conservation;360
8.3.4;4 Population Genomics Provides New Tools for Populus Conservation ;362
8.3.5;5 Conservation Genetics and Genomics in Forest Management and Restoration Ecology;366
8.3.6;Glossary;368
8.4;References;369
9;Index;376