Jain / Brar Molecular Techniques in Crop Improvement

2nd Edition
2. Auflage 2009
ISBN: 978-90-481-2967-6
Verlag: Springer Netherlands
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 772 Seiten

This book provides comprehensive information on the latest tools and techniques of molecular genetics and their applications in crop improvement. It thoroughly discusses advanced techniques used in molecular markers, QTL mapping, marker-assisted breeding, and molecular cytogenetics.

Autoren/Hrsg.

Jain, Shri Mohan

Brar, D. S.

Inhaltsverzeichnis

1;Preface;5
2;Contents;7
3;Part I Plant Breeding in the Genomics Era;10
3.1;Chapter 1 QTL Analysis in Plant Breeding;11
3.1.1;1.1 Introduction;11
3.1.2;1.2 The Scientific Value of QTL Analysis;13
3.1.3;1.3 QTL Analysis for MAS;16
3.1.4;1.4 QTL Analysis for Pre-Breeding;19
3.1.5;1.5 An Example of QTL Analyses for Utilization of Wild Species to Increase Salt Tolerance in Tomato;21
3.1.6;1.6 Concluding Remarks;23
3.1.7;References;25
3.2;Chapter 2 Comparative Genomics in Crop Plants;30
3.2.1;2.1 Introduction;30
3.2.2;2.2 Transition in Concept from Wet to Dry Lab;31
3.2.3;2.3 Dimensions of Comparative Genomics;35
3.2.3.1;2.3.1 Comparative Genome Organization;35
3.2.3.2;2.3.2 Gene Prediction;36
3.2.3.3;2.3.3 Synteny and Collinearity;36
3.2.3.4;2.3.4 Comparison of Sequenced Genomes;37
3.2.3.5;2.3.5 Conserved Gene Position Does Not Necessarily Mean Conserved Function;37
3.2.3.6;2.3.6 Comparative Analysis of Small RNA;38
3.2.3.7;2.3.7 QTL Comparisons Across Taxa;38
3.2.3.8;2.3.8 Defining Unification in Biological Terminology;40
3.2.4;2.4 Comparative Genomic Studies on Major Crops;40
3.2.4.1;2.4.1 Poaceae;40
3.2.4.2;2.4.2 Solanaceae (Tomato; Potato; Eggplant; Peppers);42
3.2.4.3;2.4.3 Fabaceae (Leguminosae);43
3.2.4.4;2.4.4 Brassicaceae;45
3.2.4.5;2.4.5 Malvaceae;46
3.2.5;2.5 Flow of Genetic Information from Well-Studied to Less Explored Genomes;47
3.2.6;2.6 Evolutionary Consequences;48
3.2.6.1;2.6.1 Phylogenomics: Contributions to Developing a Consensus Tree;48
3.2.6.2;2.6.2 Direct Implications in Gene Loss/Gain for Attaining New Functions;49
3.2.6.3;2.6.3 Domestications of New Forms;50
3.2.6.4;2.6.4 Polyploidy: Evolution of New Genomes;50
3.2.7;2.7 Concluding Remarks/Perspectives;53
3.2.8;References;54
3.3;Chapter 3 Functional Genomics For Crop Improvement;69
3.3.1;3.1 Introduction;69
3.3.2;3.2 Crop Improvement Strategies;71
3.3.3;3.3 Classical Breeding;72
3.3.4;3.4 Technology-Based Breeding;73
3.3.5;3.5 Expression Profiling;75
3.3.6;3.6 Advantages and Drawbacks of Gene Expression Profiling Techniques;77
3.3.7;3.7 Expression Profiling for Plant Improvement;79
3.3.8;3.8 eQTL, Gene Networks and Pathways;82
3.3.9;3.9 Transgene Technology and Gene Expression Analysis;83
3.3.10;3.10 Choice of Target Tissue for Gene Delivery;86
3.3.11;3.11 Gene Transfer Methods;88
3.3.12;3.12 Transgene Approach to Functional Genomics and Plant Breeding;90
3.3.13;3.13 Prospects and Challenges;91
3.3.14;References;93
3.4;Chapter 4 Bioinformatics Tools for Crop Research and Breeding;102
3.4.1;4.1 Introduction;102
3.4.2;4.2 Bioinformatics Resources Available for Crop Research;103
3.4.2.1;4.2.1 Data Resources;103
3.4.2.2;4.2.2 Web and Web Services;105
3.4.2.3;4.2.3 Data Integration and the Semantic Web;106
3.4.2.4;4.2.4 Bioinformatics Tools for Comparative Genomics;108
3.4.2.5;4.2.5 Bioinformatics Tools for Functional Genomics;110
3.4.2.6;4.2.6 Availability of High Performance Clusters and Grid;112
3.4.2.7;4.2.7 Bioinformatics and Molecular Marker Technology;113
3.4.3;4.3 Closing the Gap to Meet Molecular Breeding Requirements;116
3.4.4;References;119
4;Part II Molecular Markers and Their Application;122
4.1;Chapter 5 Gene-Based Marker Systems in Plants: High Throughput Approaches for Marker Discovery and Genotyping;123
4.1.1;5.1 Introduction;123
4.1.2;5.2 Gene-Based Marker System: Moving from Genes to Genome;124
4.1.3;5.3 Marker Discovery;125
4.1.3.1;5.3.1 Sanger Sequencing-Based Marker Development;125
4.1.3.2;5.3.2 Expression Polymorphism-Based Markers;131
4.1.3.3;5.3.3 Next Generation Sequencing Technologies for Genome-Wide Marker Discovery;132
4.1.4;5.4 Genotyping Assays;135
4.1.4.1;5.4.1 Low-Throughput and Inexpensive Genotyping Assay;136
4.1.4.2;5.4.2 High-Throughput Genotyping Assays;137
4.1.5;5.5 Applications of Gene-Based Markers in Crop Improvement;139
4.1.5.1;5.5.1 Superiority of FMs over Traditional Markers in MAS;139
4.1.5.2;5.5.2 Utility of Gene-Based Markers for Allele Mining;140
4.1.6;5.6 Conclusions and Prospects;141
4.1.7;References;142
4.2;Chapter 6 Automation of DNA Marker Analysis for Molecular Breeding in Crops;147
4.2.1;6.1 Introduction;147
4.2.2;6.2 Plant Breeding and Molecular Markers;148
4.2.2.1;6.2.1 Molecular Approaches Used in Practical Plant Breeding;149
4.2.2.2;6.2.2 Need for Molecular Marker Automation;152
4.2.3;6.3 Experience of Automation at Svalöf Weibull Laboratory;152
4.2.3.1;6.3.1 Characterisation of Breeding Activities;155
4.2.3.2;6.3.2 Characterisation of Molecular Activities;156
4.2.3.3;6.3.3 Automation of Analytic-processes;157
4.2.3.4;6.3.4 Automation Performance;161
4.2.4;6.4 Conclusion;162
4.2.5;References;163
4.3;Chapter 7 Pyramiding Genes for Enhancing Tolerance to Abiotic and Biotic Stresses;166
4.3.1;7.1 Introduction;166
4.3.2;7.2 Gene Pyramiding for Biotic Stress Tolerance;167
4.3.2.1;7.2.1 Gene Pyramiding for Disease Resistance;168
4.3.2.2;7.2.2 Gene Pyramiding for Insect Resistance;171
4.3.3;7.3 Abiotic Stress Tolerance in Plants;173
4.3.3.1;7.3.1 Genetic Engineering Strategies to Improve Abiotic Stress Tolerance in Plants;174
4.3.4;7.4 Marker Assisted Gene Pyramiding;177
4.3.5;7.5 Conclusion;181
4.3.6;References;182
4.4;Chapter 8 Application of Molecular Markers for Breeding Disease Resistant Varieties in Crop Plants;188
4.4.1;8.1 Introduction;188
4.4.2;8.2 Molecular Marker Technologies;189
4.4.3;8.3 Molecular Markers in Breeding Applications;191
4.4.4;8.4 Efficient Applications of MAS in Breeding for Disease Resistance;192
4.4.4.1;8.4.1 Cereals;193
4.4.4.2;8.4.2 Legumes;197
4.4.4.3;8.4.3 Solanaceae;198
4.4.5;8.5 Future Challenges and Perspectives for MAS;199
4.4.6;References;202
4.5;Chapter 9 Molecular Markers Based Approaches for Drought Tolerance;209
4.5.1;9.1 Introduction;209
4.5.2;9.2 Traits Associated with Drought Tolerance;210
4.5.3;9.3 Marker-assisted Selection for Drought Tolerance;212
4.5.4;9.4 Candidate Genes for Drought Tolerance;217
4.5.5;9.5 Fine Mapping and Cloning of Drought Tolerance QTLs;222
4.5.6;9.6 Concluding Remarks;224
4.5.7;References;225
4.6;Chapter 10 Molecular Markers for Characterizing and Conserving Crop Plant Germplasm;233
4.6.1;10.1 Introduction;234
4.6.2;10.2 Genetic Characterization and Its Use in Decision-Making for the Conservation of Crop Germplasm: Basic Concepts;234
4.6.3;10.3 Use of Molecular Markers for the Characterization and Conservation of Plant Genetic Resources;236
4.6.4;10.4 Genetic Diversity and Similarity Statistics for Characterizing Plant Germplasm at the Population Level;240
4.6.5;10.5 Using Molecular Marker-assisted Characterization and Conservation of Crop Plant Germplasm: Case Studies;243
4.6.5.1;10.5.1 Genetic Anatomy of a Patented Yellow Bean (Phaseolus Vulgaris L.) Variety;244
4.6.5.2;10.5.2 Genetic Variation and Differentiation of Landraces of Lentil (Lens Culinaris Var. Microsperma L.) and Maize (Zea Mays Var. Indurata L.);245
4.6.5.3;10.5.3 Genetic Fingerprinting Durum Wheat (Triticum Durum l.) and Bread Wheat (Triticum Aestivum l.) Elite Germplasm Stocks for Multiple Breeding Purposes;248
4.6.5.4;10.5.4 Effects of Different Conservation Strategies on the Population Genetic Structure of Maize Landraces as Assessed with Molecular Markers;250
4.6.6;10.6 Using Molecular Characterization to Make Informed Decisions on the Conservation of Crop Genetic Resources;251
4.6.7;10.7 Conclusion;254
4.6.8;References;255
5;Part III Genomics;257
5.1;Chapter 11 Rice Genomics Gateway to Future Cereal Improvement;258
5.1.1;11.1 Introduction;258
5.1.2;11.2 Genome Sequence and Annotation;259
5.1.3;11.3 RNA Expression Studies;262
5.1.4;11.4 Small RNA Studies;265
5.1.5;11.5 Proteomics;267
5.1.6;11.6 Metabolomics;269
5.1.7;11.7 Natural and Induced Variants;270
5.1.8;11.8 Insertional Mutants;272
5.1.9;11.9 From Rice to Other Cereals – Comparative Genomics;274
5.1.10;11.10 Challenges and Prospects;275
5.1.11;References;276
5.2;Chapter 12 Genomics for Wheat Improvement;281
5.2.1;12.1 Introduction;282
5.2.2;12.2 Genetic Analysis;283
5.2.2.1;12.2.1 Genetic Maps of Wheat;283
5.2.2.2;12.2.2 Quantitative Trait Loci and Linkage Disequilibrium;285
5.2.3;12.3 Wheat Gene Discovery;286
5.2.3.1;12.3.1 Wheat BAC Libraries and Map-based Cloning;287
5.2.3.2;12.3.2 Comparative Genomics with Model Plant Species and Grasses;288
5.2.3.3;12.3.3 Wheat Genome Sequencing;289
5.2.4;12.4 Gene Function;290
5.2.4.1;12.4.1 Transgenics and Overexpression;291
5.2.4.2;12.4.2 Transgenics and RNA Interference;294
5.2.4.3;12.4.3 Virus Induced Gene Silencing (VIGS);294
5.2.4.4;12.4.4 Targeting Induced Local Lesions in Genomes;295
5.2.5;12.5 Application of Genomics to Wheat Breeding;296
5.2.6;References;297
5.3;Chapter 13 TILLING for Mutations in Model Plants and Crops;306
5.3.1;13.1 Introduction;307
5.3.2;13.2 TILLING Method;308
5.3.2.1;13.2.1 Selecting a Mutagen for TILLING;308
5.3.2.2;13.2.2 Selecting Tissue for Mutagenesis;312
5.3.2.3;13.2.3 DNA Extraction, Pooling and Mutation Discovery;315
5.3.3;13.3 Examples of TILLING Projects;319
5.3.3.1;13.3.1 High-Throughput Services;319
5.3.3.2;13.3.2 Other TILLING Projects;322
5.3.4;13.4 Challenges for Crops;322
5.3.5;13.5 The Role of TILLING in Orphan Crops;323
5.3.5.1;13.5.1 The Need to Improve Orphan Crops;324
5.3.5.2;13.5.2 TILLING Projects in Understudied Crops;324
5.3.6;13.6 Ecotilling;326
5.3.7;13.7 Conclusions;328
5.3.8;References;328
5.4;Chapter 14 Microarray Analysis for Studying the Abiotic Stress Responses in Plants;332
5.4.1;14.1 Introduction;332
5.4.2;14.2 Identification of the Genes Upregulated by the Stresses;333
5.4.3;14.3 Transcriptome Analysis for the Stress-Inducible Transcription Factor Genes;334
5.4.3.1;14.3.1 Stress-Inducible Transcription Factors;334
5.4.3.2;14.3.2 Identifying the Target Genes of Transcription Factors;335
5.4.4;14.4 Analysis of the Transcriptome Regulated by the Regulatory Proteins;344
5.4.5;14.5 Genetic Engineering of Abiotic Stress Tolerance Using the Stress-Inducible Genes;347
5.4.6;14.6 Conclusions and Future Perspectives;347
5.4.7;References;348
5.5;Chapter 15 Roles of MicroRNAs in Plant Abiotic Stress;355
5.5.1;15.1 Introduction;355
5.5.2;15.2 The Biogenesis of miRNAs and the Mechanism of miRNA-Directed Gene Regulation in Plants;356
5.5.3;15.3 Plant Abiotic Stress and miRNAs;356
5.5.3.1;15.3.1 ABA-Mediated Responses and the miRNAs;357
5.5.3.2;15.3.2 Oxidative Stress and the miRNAs;360
5.5.3.3;15.3.3 Water Stress and the miRNAs;361
5.5.3.4;15.3.4 Nutrient Scarcity and the miRNAs;362
5.5.3.5;15.3.5 Mechanical Stress Responses and the miRNAs;365
5.5.3.6;15.3.6 Dynamic Regulation of miRNAs in Response to Abiotic Stresses;365
5.5.4;15.4 Other Small RNAs and Abiotic Stress;366
5.5.5;15.5 MicroRNA, Abiotic Stress, and the Future of Plant Biology;367
5.5.6;References;368
5.6;Chapter 16 Molecular Tools for Enhancing Salinity Tolerance in Plants;371
5.6.1;16.1 Introduction;372
5.6.2;16.2 Salt Tolerance Mechanisms at Physiological and Molecular Levels;373
5.6.2.1;16.2.1 Plant Response to Osmotic Stress Induced by Salinity;374
5.6.2.2;16.2.2 Plant Response to Ionic Stress Induced by Salinity;375
5.6.2.3;16.2.3 Plant Response to Oxidative Stress Induced by Salinity;376
5.6.2.4;16.2.4 Homeostasis and Protection or Damage Repair Induced by Salinity;377
5.6.3;16.3 Breeding for Salinity Tolerance;380
5.6.3.1;16.3.1 Variability in Salinity Tolerance;380
5.6.3.2;16.3.2 Determinants Underlying Salinity Tolerance;381
5.6.3.3;16.3.3 Transmission of Determinants Responsible of Salt Tolerance;384
5.6.4;16.4 Improving Salt Tolerance Trough Gene Transformation;386
5.6.5;16.5 Functional Analysis of Salt Tolerance-Related Genes;388
5.6.5.1;16.5.1 Complexity of the Trait and Sources of Genetic Variation;390
5.6.6;16.6 Genomic Approaches for Dissection of Salinity Tolerance;391
5.6.7;16.7 Conclusions;393
5.6.8;References;394
5.7;Chapter 17 DNA Microarray as Part of a Genomic-Assisted Breeding Approach;404
5.7.1;17.1 Introduction;405
5.7.1.1;17.1.1 Current Uses: Feed, Brewing and the Emerging Importance in Food;405
5.7.1.2;17.1.2 Breeding for Quality Traits;409
5.7.2;17.2 Genetic Analysis: Combining Methods;409
5.7.2.1;17.2.1 Genomic-Assisted Breeding;409
5.7.2.2;17.2.2 Molecular Genetic-Based Tools Underpinning GAB;410
5.7.3;17.3 Messenger RNA Expression Profiling Using DNA Microarray Technology;414
5.7.3.1;17.3.1 The Principle of mRNA Expression Profiling: What Can Be Expected?;414
5.7.3.2;17.3.2 The Development of Array Technology;415
5.7.3.3;17.3.3 Minimising Random Errors;418
5.7.3.4;17.3.4 Validation;421
5.7.3.5;17.3.5 Additional Regulatory Mechanisms in Gene Expression;422
5.7.3.6;17.3.6 Applications of DNA Microarrays;422
5.7.4;17.4 Specific Example: Studies of Profiling Global Gene Expression During Grain Filling in Monocot;423
5.7.4.1;17.4.1 Microarray in Plants: Specific Focus on Grain Fillings Studies in Monocots;423
5.7.4.2;17.4.2 Large Arrays vs Tissue/Pathway Specific Approaches;423
5.7.4.3;17.4.3 Can Focused Microarray Follow Predicted Changes During Grain Development?;426
5.7.4.4;17.4.4 Extension of the Study to Field Grown Material: Expression of Alleles Coding Storage Proteins During Grain Development;426
5.7.4.5;17.4.5 From Microarray to In Silico Plant Design;427
5.7.5;17.5 Conclusion;428
5.7.6;References;428
5.8;Chapter 18 Unravelling Gene Function Through Mutagenesis;434
5.8.1;18.1 Introduction;434
5.8.2;18.2 Forward Genetics;435
5.8.2.1;18.2.1 Gene Mapping and Cloning;438
5.8.3;18.3 Reverse Genetics;439
5.8.3.1;18.3.1 Arabidopsis Genome Sequence;439
5.8.3.2;18.3.2 T-DNA as a Mutagen;440
5.8.3.3;18.3.3 Collections of Insertional Mutants;441
5.8.3.4;18.3.4 Obtaining and Characterizing T-DNA Tagged Mutants from Publicly Available Collections;442
5.8.3.5;18.3.5 Activation Tagging Mutagenesis;445
5.8.3.6;18.3.6 Small RNAs as New Tools for Targeted Mutagenesis in Plants;445
5.8.3.7;18.3.7 Tilling;446
5.8.4;18.4 Recent Progress in Crop Mutations and Functional Genomics;447
5.8.4.1;18.4.1 Rice;448
5.8.4.2;18.4.2 Maize;449
5.8.4.3;18.4.3 Tomato;450
5.8.4.4;18.4.4 Other Important Crops and Species;451
5.8.4.5;18.4.5 Weeds;453
5.8.5;18.5 Conclusions and Perspectives;454
5.8.6;References;455
5.9;Chapter 19 Techniques in Plant Proteomics;465
5.9.1;19.1 Introduction;465
5.9.2;19.2 Protein Extractions;466
5.9.3;19.3 Protein Separation;468
5.9.3.1;19.3.1 Gel-based Proteomics;469
5.9.3.2;19.3.2 Gel-Free Proteomics;474
5.9.3.3;19.3.3 Alternative Separation Technologies;478
5.9.4;19.4 Protein Identification;479
5.9.4.1;19.4.1 Protein Digestion;479
5.9.4.2;19.4.2 Mass Spectrometry;480
5.9.4.3;19.4.3 MS Data for Protein Identification;482
5.9.5;19.5 Conclusions;483
5.9.6;References;484
5.10;Chapter 20 Metabolomics: Novel Tool for Studying Complex Biological Systems;488
5.10.1;20.1 Introduction;488
5.10.2;20.2 Characteristics of Metabolomics;489
5.10.3;20.3 Plant Metabolomics;491
5.10.4;20.4 Analytical Tools;492
5.10.4.1;20.4.1 Methodologies Employed;492
5.10.4.2;20.4.2 Data Processing and Mining;496
5.10.5;20.5 Applications of Plant Metabolomics;498
5.10.6;20.6 Conclusions;501
5.10.7;References;501
5.11;Chapter 21 Transcriptomic Analysis of Multiple Enviornmental Stresses in Plants;506
5.11.1;21.1 Introduction;506
5.11.2;21.2 Physiological Studies of Combined Stresses;507
5.11.3;21.3 Molecular Genetics and Genomics;508
5.11.4;21.4 Analysis of Combined Stresses;510
5.11.4.1;21.4.1 Heat and High Light;510
5.11.4.2;21.4.2 Drought and Heat;511
5.11.4.3;21.4.3 Drought and Ozone;512
5.11.4.4;21.4.4 Carbon Dioxide and Ozone;512
5.11.4.5;21.4.5 Ozone and Biotic Stress Interactions;513
5.11.5;21.5 Future Directions;514
5.11.6;References;515
6;Part IV Transgenic Technologies;520
6.1;Chapter 22 Marker-Free Targeted Transformation;521
6.1.1;22.1 Introduction;521
6.1.2;22.2 Targeted Transformation Using a Site-Specific Recombination System;522
6.1.3;22.3 Development of Targeted Transformation Methods;524
6.1.3.1;22.3.1 Modification of Recognition Sequences;524
6.1.3.2;22.3.2 Control of Recombinase Gene Expression;527
6.1.3.3;22.3.3 DNA Delivery Methods;529
6.1.3.4;22.3.4 Selection of Targeted Transgenic Plants;530
6.1.4;22.4 Marker-Free Targeted Transgenic Plants;530
6.1.5;22.5 Reproducibility of Transgene Expression;534
6.1.6;22.6 Conclusion;534
6.1.7;References;535
6.2;Chapter 23 Promoter Trapping in Plants Using T-DNA Mutagenesis;538
6.2.1;23.1 Introduction;538
6.2.2;23.2 T-DNA-Based Promoter Trapping: Advantages and Limitations;542
6.2.3;23.3 T-DNA Promoter Trapping;543
6.2.3.1;23.3.1 Arabidopsis Thaliana;544
6.2.3.2;23.3.2 Tobacco;545
6.2.3.3;23.3.3 Other Plants;547
6.2.4;23.4 T-DNA Based Enhancer Trapping in Plants;547
6.2.5;23.5 Promoter Cloning Strategies in Plants;548
6.2.6;23.6 Characterization of Plant Promoters;550
6.2.6.1;23.6.1 In Silico Analysis;550
6.2.6.2;23.6.2 Determination of TSS in Plant Promoters;552
6.2.6.3;23.6.3 Transgenic-Based Promoter Analysis;552
6.2.7;23.7 Conclusions;562
6.2.8;References;563
6.3;Chapter 24 Plant Genome Engineering Using Zinc Finger Nucleases;571
6.3.1;24.1 Introduction;571
6.3.2;24.2 Homologous Recombination and Gene Targeting in Plants;572
6.3.3;24.3 Double-Strand Breaks at the Target Site Stimulate Homologous Recombination;574
6.3.4;24.4 Zinc Finger Nucleases;576
6.3.5;24.5 Zfn in Plant Systems;577
6.3.6;24.6 Conclusion and Future Prospects;579
6.3.7;References;579
6.4;Chapter 25 Cisgenesis Next Step in Classical Plant Breeding;583
6.4.1;25.1 Introduction;584
6.4.1.1;25.1.1 Domestication of Crops and Traits;584
6.4.2;25.2 Intragenics, RNAI and Induced Mutation Breeding;587
6.4.3;25.3 Regulation of Cisgenesis and Intragenics;587
6.4.4;25.4 Autogamous Crops;588
6.4.4.1;25.4.1 Introgression and Pre-Breeding;589
6.4.4.2;25.4.2 Induced Translocation Breeding;590
6.4.4.3;25.4.3 Cisgenesis and Its Potential Use in Further Breeding;591
6.4.5;25.5 Hybrid Varieties in Allogamous Crops;592
6.4.5.1;25.5.1 Male Sterility in Traditional Breeding;592
6.4.5.2;25.5.2 Transgenesis for Introduction of Male Sterility;593
6.4.5.3;25.5.3 Cisgenesis and Introduction of Male Sterility;594
6.4.5.4;25.5.4 Self-Incompatibility and a Possible Role of Cisgenesis;594
6.4.6;25.6 Vegetatively Propagated Crops;595
6.4.6.1;25.6.1 Traditional Breeding;595
6.4.6.2;25.6.2 Extension of Genetic Variation;596
6.4.6.3;25.6.3 Potato–Phytophthora Interaction;596
6.4.6.4;25.6.4 Cisgenic Approach in Vegetatively Crops;601
6.4.7;25.7 Concluding Remarks;601
6.4.8;References;601
6.5;Chapter 26 Gene Stacking;604
6.5.1;26.1 Introduction;604
6.5.2;26.2 Combining Individual Transgenes;606
6.5.2.1;26.2.1 Cross-Breeding and Re-Transformation;606
6.5.2.2;26.2.2 Co-Transformation;607
6.5.3;26.3 Polycistronic Transgenes;609
6.5.3.1;26.3.1 Internal Ribosome Entry Sites (IRES);609
6.5.3.2;26.3.2 Chloroplast Transformation;611
6.5.4;26.4 Expression of Multiple Genes from Polyproteins;612
6.5.4.1;26.4.1 The NIa Protease;612
6.5.4.2;26.4.2 Linker Sequences;613
6.5.4.3;26.4.3 FMDV 2A;614
6.5.4.4;26.4.4 Ubiquitin Vectors;615
6.5.4.5;26.4.5 Suppression of Multiple Genes via Chimeric Transgenes;616
6.5.5;26.5 Gene Stacking Using Mini-Chromosomes;617
6.5.6;26.6 Conclusions;618
6.5.7;References;618
6.6;Chapter 27 Gene Silencing;621
6.6.1;27.1 Introduction;622
6.6.2;27.2 Co-suppression and Gene Silencing;622
6.6.3;27.3 Transgene Silencing;623
6.6.4;27.4 Gene Silencing in Rice;623
6.6.5;27.5 Post-transcriptional Gene Silencing and Virus Resistance;625
6.6.6;27.6 RNA Mediated Gene Silencing;626
6.6.7;27.7 Plant Viruses and RNA Silencing;628
6.6.8;27.8 Virus Induced Gene Silencing (VIGS);628
6.6.9;27.9 SiRNA and DNA Methylation;629
6.6.10;27.10 microRNA (MiRNA);630
6.6.11;27.11 RNA Silencing for Crop Improvement;633
6.6.12;27.12 Artificial miRNA (AmiRNA) – an Emerging Approach of Great Promise;633
6.6.13;References;634
6.7;Chapter 28 Plant RNAi and Crop Improvement;643
6.7.1;28.1 Introduction;643
6.7.2;28.2 Outline of the RNAi Pathway;644
6.7.3;28.3 Plant RNAi Vectors;646
6.7.4;28.4 RNAi-Mediated Metabolic Engineering;648
6.7.4.1;28.4.1 Starch Metabolism;648
6.7.4.2;28.4.2 Improvement of Seed Oils;651
6.7.4.3;28.4.3 Manipulation of Storage Proteins;652
6.7.4.4;28.4.4 RNAi-Mediated Reduction of Plant Allergens;653
6.7.4.5;28.4.5 Engineering of Secondary Metabolism by RNAi;654
6.7.5;28.5 Viral Resistance by RNAi;655
6.7.6;28.6 Control of Plant-Feeding Pests by Host RNAi;656
6.7.6.1;28.6.1 Nematode-Resistant Crops;656
6.7.6.2;28.6.2 Insect-Resistant Crops;657
6.7.7;28.7 Caveats and Future Perspectives of RNAi Technology;658
6.7.8;References;659
6.8;Chapter 29 Metabolomics in Fruit Development;664
6.8.1;29.1 Introduction;665
6.8.2;29.2 Metabolomics in Plant Science;665
6.8.2.1;29.2.1 What Is Metabolomics?;665
6.8.2.2;29.2.2 Analytical Platforms used In Metabolomics Assays;666
6.8.2.3;29.2.3 Metabolomics Data Processing and Its Mining in a Biological Context;668
6.8.3;29.3 Metabolomics Applications in Fruit Development;669
6.8.3.1;29.3.1 The Process of Fruit Development;669
6.8.3.2;29.3.2 Metabolomics in Tomato Fruit Development;671
6.8.3.3;29.3.3 Metabolomics in Strawberry Fruit Development;674
6.8.3.4;29.3.4 Comparison of Tomato and Strawberry Metabolite Profiles During Development;676
6.8.4;29.4 Conclusions;680
6.8.5;References;680
6.9;Chapter 30 Genetic Engineering in Floriculture;683
6.9.1;30.1 Introduction;683
6.9.2;30.2 Principles of Molecular Breeding;684
6.9.3;30.3 Modification of Flower Color;685
6.9.3.1;30.3.1 Biosynthetic Pathways;685
6.9.3.2;30.3.2 Engineering Toward Pelargonidin;685
6.9.3.3;30.3.3 Engineering Toward Delphinidin;688
6.9.3.4;30.3.4 Engineering Toward Yellow;690
6.9.3.5;30.3.5 Modification of the Amount of Anthocyanins;691
6.9.4;30.4 Modification of Scent;691
6.9.4.1;30.4.1 Scent Compounds and Their Biosynthesis;691
6.9.4.2;30.4.2 Engineering a Terpenoid Biosynthetic Pathway;692
6.9.4.3;30.4.3 Benzenoids/Phenylpropanoids;693
6.9.5;30.5 Improvement of Postharvest Quality;694
6.9.5.1;30.5.1 Values of Long Life;694
6.9.5.2;30.5.2 Preventing Flower Senescence;694
6.9.5.3;30.5.3 Preventing Leaf Senescence;695
6.9.6;30.6 Modification of Plant Shapes;696
6.9.6.1;30.6.1 Plant Morphogenesis;696
6.9.6.2;30.6.2 Modification of Flower Shape;697
6.9.6.3;30.6.3 Modification of Plant Form;698
6.9.7;30.7 Control of Flowering – Florigen;699
6.9.8;30.8 Present and Future of Transgenic Flowers;700
6.9.9;References;700
6.10;Chapter 31 Transgenesis and Genomics in Forage Crops;706
6.10.1;31.1 Introduction;706
6.10.2;31.2 Transgenesis;707
6.10.2.1;31.2.1 Biolistic Transformation;708
6.10.2.2;31.2.2 Agrobacterium-Mediated Transformation;708
6.10.2.3;31.2.3 Selection Schemes;709
6.10.2.4;31.2.4 Manipulation of Lignin Biosynthesis;709
6.10.2.5;31.2.5 Manipulation of Fructan Biosynthesis;710
6.10.2.6;31.2.6 Gene Flow and Biosafety;710
6.10.3;31.3 Genomics;711
6.10.3.1;31.3.1 Genome Resources;711
6.10.3.2;31.3.2 Transcriptomics;712
6.10.3.3;31.3.3 DNA Markers;712
6.10.3.4;31.3.4 Genetic Map;714
6.10.3.5;31.3.5 Trait Dissection;715
6.10.3.6;31.3.6 Marker-Assist Selection;717
6.10.3.7;31.3.7 Association Analysis;718
6.10.4;31.4 Candidate Gene Approach – Cold Responsible Genes;719
6.10.4.1;31.4.1 CBF Genes;719
6.10.4.2;31.4.2 Fructosyltransferase Genes and Fructan QTL;720
6.10.4.3;31.4.3 Other Genes;721
6.10.5;31.5 Conclusion;721
6.10.6;References;722
7;Author Index;732