Genetics, genomics, and breeding of tomato:
Gespeichert in:
| Weitere Verfasser: | |
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| Format: | Buch |
| Sprache: | English |
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Boca Raton
CRC Press
2013
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| Schriftenreihe: | Genetics, genomics and breeding of crop plants
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XL, 480 S. Ill., graph. Darst. 24 cm |
| ISBN: | 9781578088041 1578088046 |
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Datensatz im Suchindex
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| adam_text | GENETICS, GENOMICS
AND BREEDING OF
TOMATO
Editors
Barbara E Liedl
West Virginia State University
Gus R Douglass Institute
Agricultural and Environmental Research Station
Institute, WV
USA
Joanne A Labate
USDA-ARS Plant Genetic Resources Unit
Geneva, NY
USA
John R Stommel
USDA-ARS Vegetable Laboratory
BARC-West
Beltsville, MD
USA
Ann Slade
Arcadia Bioscience
Seattle, WV
USA
Chittaranjan Kole
Department of Genetics and Biochemistry
Clemson University
Clemson, SC
USA
CRC Press
Taylor amp; Francis Croup
Boca Raton London New York
CRC Press is an imprint of the
Taylor amp; Francis Croup, an informa business
A SCIENCE PUBLISHERS BOOK
Contents
dedication v
Preface to the Series vii
Preface to the Volume xiii
List of Contributors xxv
Abbreviations xxxi
1 Basic Information about Tomatoes and the Tomato Group 1
Ana Caicedo and Iris Peralta
1 1 Introduction 2
1 2 Economic and Nutritional Importance of Tomato 2
121 Economic Importance 2
122 Nutritional Composition 3
1 3 Academic Importance of Tomato and its Wild Relatives 5
131 Tomato as a Model Species 5
1311 The Genetic Basis of Quantitative Traits 6
1312 Fruit Development 6
132 The Tomato Clade as a Model System 7
1321 Plant Defense 7
1322 Mating System and Speciation 8
1323 Adaptation and Divergence 8
1 4 Taxonomy and Evolution 9
141 Taxonomic Position and Phylogenetic Relationships 9
1 5 Botanical Descriptions 13
151 Morphology 13
152 Ploidy Levels, Genome Size and Karyotype 16
1 6 Ecology and Biodiversity of the Tomato Clade 17
161 Distribution and Habitats 17
162 Mating System Evolution in the Tomato Clade 18
1621 Mating System Diversity 18
1622 The Genetic Basis of Mating System Diversity 19
163 Genetic Diversity in Wild Tomatoes 20
1631 Genetic Diversity and Mating System 20
1632 Genetic Diversity and Geography in SI Species 21
1633 Genetic Diversity and Geography in SC Species 22
xvi Genetics, Genomics and Breeding of Tomato
1 7 Tomato Domestication and Dissemination 23
1 8 Tomato Breeding and Research Resources 24
181 Genetic Resources 25
1811 Mutant Stocks 25
1812 Mapping Lines 25
1813 Wild and Cultivated Germplasm 26
182 Genomic Resources 26
183 Bioinformatic Resources 27
References 27
2 Classical Genetics and Traditional Breeding 37
John W Scott, James R Myers, Peter S Boches,
Courtland G Nichols and Frederic F Angell
2 1 Introduction 38
2 2 Classical Mapping Efforts with Morphological and 39
Isozyme Markers
2 3 Limitations of Classical Endeavors and Utility of 40
Molecular Mapping
2 4 Classical Tomato Breeding Achievements 45
241 Disease Resistance -s 45
242 Quantitatively Inherited Traits and 45
Cultivars—Processing Tomatoes
243 Quantitatively Inherited Traits and 46
Cultivars—Fresh Market Tomatoes
244 Qualitative Inheritance 51
245 Allozymes 51
246 Stress Tolerance 51
247 Achievement Efforts 53
2 5 Breeding Objectives Positive and Negative 60
251 Historical Background 60
252 Jointless Pedicels 60
253 Parthenocarpy 61
254 High Pigment 61
255 Fruit Disorders 62
256 Flavor 62
257 Large Fruit Size 63
258 Multiple Disease Resistance 64
259 Genetic Backgrounds 65
2 5 10 Environmental Variation/Strong GxE Interactions 65
2 5 11 Combining Ability 66
2 6 Limitations of Traditional Breeding and Rationale for 67
Molecular Breeding
Acknowledgements 68
References 68
Contents xvii
3 Diversity within Cultivated Tomato 74
Esther van der Knaap, Claire Anderson and Gustavo Rodriguez
3 1 Introduction 74
3 2 Phenotypic Analysis of Tomato Fruit 77
3 3 The Effect of the Tomato Shape Genes on Fruit 80
Morphology
3 4 Genotype-Based Diversity Analysis 82
3 5 Genetic Diversity within Cultivated Tomato Germplasm 83
3 6 Future Prospects 87
Acknowledgements 88
References 88
4 Molecular Markers, Genetic Maps and Association 92
Studies in Tomato
Martin W Ganal
4 1 Introduction 92
4 2 Molecular Markers for Tomato Genome Mapping and 94
Marker/Trait Association Studies
421 RFLPs and RFLP-based PCR Markers 95
422 PCR-based Anonymous Markers 95
423 Microsatellite or SSR Markers 96
424 Single Nucleotide Polymorphism (SNP) Markers 97
4 3 Genetic Maps and Available Markers 97
4 4 Population Structure, Linkage Disequilibrium and 98
Association of Markers and Traits
441 Population Structure in Tomato 98
442 Linkage Disequilibrium 99
443 First Efforts towards Association Mapping in Tomato 100
444 Candidate Gene Analysis 100
4 5 Future Developments 101
451 Requirements on Markers for Marker/Trait 101
Associations
452 Large Scale SNP Identification for Marker/Trait 102
Associations
453 Genome-wide Association Studies 103
454 The Future—The Tomato Genome Sequence, Large 104
Scale Phenotyping and Association Studies
Acknowledgements 105
References 105
5 Mapping and Tagging of Simply Inherited Traits 109
Ilan Levin and Arthur A Schaffer
5 1 Introduction 110
xviii Genetics, Genomics and Breeding of Tomato
5 2 Importance of the Simply Inherited Traits 112
5 3 Genetic and Molecular Dissection of Simply Inherited 116
Traits
5 4 Identification of Markers Linked to Traits of Interest 119
541 Use of NILs to Identify Linkage with Molecular 120
Markers
542 Use of Bulked Segregant Analysis (BSA) to Identify 121
Linkage with Molecular Markers
543 Conversion of Dominant to Codominant Markers 123
5 5 Use of Genomics Tools for Mapping 126
5 6 Simply Inherited Traits Associated with Fruit Nutritional 126
Quality
5 7 Simply Inherited Traits Associated with Fruit Taste: 131
Brix, Sugars, Acids and Aroma Volatiles
5 8 Summary 140
Acknowledgements 141
References 142
6 Molecular Mapping of Complex Traits in Tomato 150
Silvana Grandillo, Pasquale Termolino and Esther van der Knaap ^
6 1 Introduction 151
6 2 Populations used for QTL Mapping 152
621 Primary Segregating Populations 153
622 Recombinant Inbred Populations 153
623 Advanced Backcross Populations 169
624 Backcross Inbred Lines 170
625 Introgression Lines 171
6 3 Framework Maps and Markers 171
6 4 QTL Mapping Approaches and Software 172
6 5 Introgression Line Mapping and Breeding Approach 174
651 Introgression Line Heterosis 177
6 6 Interactions between QTL and Genetic Background 178
6 7 MAS and QTL Pyramiding 179
6 8 Mendelizing QTLs 180
6 9 QTL Mapping on a Trait Basis 181
691 Disease Resistance 181
6911 Viral Resistance 183
6912 Bacterial Resistance 183
6913 Fungal Resistance 185
692 Insect Resistance 186
693 Abiotic Stress Tolerance 187
6931 Cold Tolerance 188
6932 Drought Tolerance 188
Contents xix
6933 Salt Tolerance 189
694 Fruit Yield 191
695 Fruit Quality 192
6951 Fruit Weight 193
6952 Fruit Shape 194
6953 Fruit Color 196
6954 Fruit Firmness 197
6955 Primary Metabolic Traits 198
6956 Sugar and Acid Content 199
6957 Nutritional and Antioxidant Compounds 201
6958 Volatile Compounds 203
6959 Sensory Traits 205
696 Flowering and Ripening Time 206
697 Flower Morphology and Reproductive Barriers 207
698 Leaf, Sepal, and Petal Morphology 209
699 Seed Weight 210
6 10 Conclusions and Future Prospects 211
Acknowledgments 212
References 213
7 Molecular Breeding 228
Emidio Sabatini, Massimiliano Beretta, Tea Sala,
Nazareno Acciarri, Justyna Mile and Nicola Pecchioni
7 1 Introduction 229
7 2 Germplasm Characterization and Exploitation 230
721 Pre-breeding 231
722 Testing for Distinctness, Uniformity and 237
Stability (DUS)
723 Hybrid Purity Testing 238
7 3 Marker-Assisted Trait Introgression 239
731 Gene and QTL Introgression 239
732 Gene Pyramiding 261
733 Genetic Ideotype Breeding 265
7 4 Advantages, Limitations and Prospects of MAS 266
741 Advantages 267
742 Limitations and Solutions 268
7421 Unavailability of Closely-linked Markers 270
for Many Traits
743 Prospects for MAS 271
7431 From MAS to GAS 272
7 5 Transgenic Breeding 275
751 Traits and Objectives 279
7511 Sugars 279
7512 Carotenoids 280
xx Genetics, Genomics and Breeding of Tomato
7513 Virus Resistance 280
7514 Parthenocarpy 282
7515 Fruit Firmness 282
7516 Prolonged Vine Life 284
752 Perspectives 285
7 6 Concluding Remarks 286
Acknowledgement 287
References 287
8 Positional Cloning Strategies in Tomato 304
Cornelius S Barry
8 1 Introduction 305
8 2 Mutant Collections 306
8 3 Strategies for Generating Mapping Populations 308
8 4 Strategies for Extracting DNA for Genetic Mapping 309
8 5 Molecular Markers 311
8 6 Assigning Loci to Chromosomal Regions 312
8 7 Fine Genetic Mapping 313
8 8 Resources for Generating Physical Maps 314
8 9 Identification and Confirmation of Candidate Genes ni 316
8 10 The Impact of an Emerging Genome Sequence 319
8 11 Alternative Strategies for Identification of Mutant Loci 321
8 12 Future Perspectives 322
Acknowledgements 322
References 323
9 Structural Genomics: Studying Variation in Gene 327
Sequences
Allen E Van Deynze, Theresa Hill and Hamid Ashrafi
9 1 Introduction 327
9 2 Sources of Sequence 328
921 Expressed Sequence Tags 328
9211 Sources of ESTs 328
922 Gene Space 330
9 3 Targeted Marker Discovery 331
931 The Basis of DNA Markers 331
932 Annotated Sequence 332
933 Categorizing ESTs for Marker Discovery 333
934 Diversity of Tomato ESTs 334
9341 Diversity in the Gene Space of Tomato 334
9342 Mining for Variation 337
9343 ESTs as Templates 338
935 The Next Generation of Discovery 339
9 4 Conclusion 341
References 341
Contents xxi
10 The Tomato Genome Sequencing Project 345
Lukas A Mueller
10 1 Introduction 345
10 2 Sequencing Strategy 347
10 2 1 BAC by BAC Approach 348
10 2 2 Whole Genome Shotgun 351
10 3 Genome Annotation by ITAG 352
10 4 Conclusion 354
Acknowledgments 355
References 356
11 Comparative Genome Sequencing of Tomato and 361
Potato: Methods and Analysis
Sanwen Huang and Zhong-hua Zhang
11 1 Introduction 362
11 2 A Pipeline for the Comparative Sequencing of Tomato 362
and Potato Genomes
11 3 Advantages of Comparative Genome Sequencing 365
11 3 1 Improving the Physical Maps 365
11 3 2 Selecting Additional Seed BACs 368
11 3 3 Benefits to BAC Finishing 369
11 4 Comparative Analysis of Syntenic Clones Obtained 370
from Comparative Sequencing
11 4 1 Characterization of Syntenic Sequences 371
11 4 2 Ccilinearity between Tomato and Potato 373
11 4 3 Content and Distribution of Repetitive Elements 374
11 4 4 Inserted or Deleted (indel) Genes within Syntenic 374
Regions
11 4 5 Divergence of Synteny Length between Tomato 377
and Potato
11 5 Limitations and Opportunities 377
References 379
12 Developments in Tomato Transcriptomics 381
Antonio J Matas, Zhangjun Fei, James J Giovannoni and
Jocelyn K C Rose
12 1 Introduction 382
12 2 Transcriptomics Tools Developed 382
12 2 1 Microarrays 382
12 2 2 SAGE and Related Technologies 388
12 2 3 Massive Parallel Signature Sequencing 389
xxii Genetics, Genomics and Breeding of Tomato
12 3 Advances in Sequencing Technologies 389
12 3 1 454 Genome Sequencer FLX 390
12 3 2 Illumina 391
12 3 3 ABI Solid Sequencing 391
12 3 4 Third Generation and other Sequencing 392
Technologies
12 3 5 RNA-Seq 392
12 4 Bioinformatic Challenges and Data Analysis 393
12 5 Use of Related Species Resources 395
12 6 Application of Functional Genomics in 395
Genomics-Assisted Breeding
12 7 Summary 397
Acknowledgements 397
References 398
13 Proteomics and Metabolomics 403
Mireille Faurobert, Yoko Iijima and Koh Aoki
13 1 Introduction 404
13 2 Tomato Proteomics: Techniques, Applications, and QTL 406
Analyses
13 2 1 Proteomics Methods 406
13 211 Protein Extraction 406
13 212 Traditional 2DE-based Methods 406
13 213 Mass Spectrometry 407
13 214 Shotgun Proteomics 407
13 215 Analysis of Post-translational Modifications 408
13 216 Protein Complexes 409
13 2 2 Application of Proteomics to Functional Studies 409
13 221 Fruit Development and Ripening 409
13 222 Abiotic Stress 409
13 223 Biotic Stress 411
13 2 3 Proteomics and QTL Mapping 411
13 231 Pathogen Resistance 411
13 232 Fruit Quality Traits 412
13 3 Tomato Metabolomics: Techniques, Applications, and 412
QTL Analyses
13 3 1 Metabolomics Tools 412
13 311 Metabolite Extraction 412
13 312 GC-MS 413
13 313 LC-MS 413
13 314 CE-MS 414
13 315 NMR 414
13 316 Analytical Strategies 414
Contents xxiii
13 3 2 Application of Metabolomics to Functional Studies 416
13 321 Comprehensive Analysis of Tomato Fruit 416
Metabolites
13 322 Tissue-dependent Accumulation of 416
Metabolites
13 323 Metabolome Analysis in Transgenic 417
Tomato Plants
13 3 3 Metabolomics and QTL Mapping 418
13 331 Metabolic Profiling of Wild Species 418
13 332 Metabolic Profiling of ILs between 418
S pennellii and S lycopersicum
13 4 Application in Phenomics-Assisted Breeding 419
13 4 1 Integrated -omics 419
13 4 2 Databases 420
References 421
14 Role of Bioinformatics as a Tool in Tomato Research 428
Catherine M Ronning
14 1 Introduction 428
14 2 Gene and Genome Databases 429
14 2 1 International Tomato Genome Sequencing Project 430
14 2 2 Solanum lycopersicum Plant Genome Database 431
(S1GDB)
14 2 3 Solanaceae Genomics Resource 432
14 2 4 Tomato Genome Project at NCBI 433
14 25CM Rick Tomato Genetics Resource Center 433
(TGRC)
14 2 6 Genes That Make Tomatoes 434
14 2 7 Real-Time QTL (RTQ) 434
14 2 8 Other Plant Resources 434
14 3 Comparative Genome Databases 435
14 4 Gene Expression Databases 436
14 4 1 Tomato Gene Index (at DFCI) 437
14 4 2 Tomato Functional Genomics Database (TFGD) 439
14 4 3 Kazusa Micro-Tom Database (MiBase) 439
14 4 4 Kazusa Full-Length Tomato cDNA Database 440
(KafTomj
14 4 5 Affymetrix GeneChip® Tomato Genome Array 440
14 4 6 RNA-Seq 440
14 4 7 Applications 440
14 5 Molecular Marker and Genetic Map Databases 442
14 5 1 Maps 443
14 511 Genetic Maps 443
14 512 Physical Map 444
xxiv Genetics, Genomics and Breeding of Tomato
14 513 Cytological Map 444
14 514 Sequence Progress Map 444
14 515 Other Maps 445
14 5 2 Transposon Tagging 445
14 5 3 Targeting Induced Local Lesions IN Genomes 445
(TILLING)
14 6 Protein and Metabolome Databases 446
14 6 1 Tomato Metabolite Data at TFGD 446
14 6 2 Secretom 446
14 6 3 Other Plant Resources 447
14 6 4 Applications 448
14 7 Integration of Different Data Types 449
14 7 1 The SOL Genomics Network (SGN) 449
14 7 2 Solanaceous MapMan 450
14 7 3 Fruit Biology Laboratory at INRA Bordeaux 450
14 7 4 MIPSPlantsDB 451
14 7 5 Other Resources 451
14 7 6 Applications 452
14 8 Conclusions 453
Acknowledgements 453
References 454
Index 459
Color Plate Section 469
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| id | DE-604.BV040347598 |
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| indexdate | 2024-07-10T00:22:10Z |
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| series2 | Genetics, genomics and breeding of crop plants |
| spelling | Genetics, genomics, and breeding of tomato eds. by Barbara E. Liedl ... Boca Raton CRC Press 2013 XL, 480 S. Ill., graph. Darst. 24 cm txt rdacontent n rdamedia nc rdacarrier Genetics, genomics and breeding of crop plants Tomate (DE-588)4060370-2 gnd rswk-swf Genetik (DE-588)4071711-2 gnd rswk-swf Tomatenzüchtung (DE-588)4291782-7 gnd rswk-swf Genanalyse (DE-588)4200230-8 gnd rswk-swf Tomatoes / Genetics Tomatoes / Genome mapping Tomatoes / Breeding Tomatenzüchtung (DE-588)4291782-7 s DE-604 Tomate (DE-588)4060370-2 s Genetik (DE-588)4071711-2 s Genanalyse (DE-588)4200230-8 s Liedl, Barbara E. edt HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025201721&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Genetics, genomics, and breeding of tomato Tomate (DE-588)4060370-2 gnd Genetik (DE-588)4071711-2 gnd Tomatenzüchtung (DE-588)4291782-7 gnd Genanalyse (DE-588)4200230-8 gnd |
| subject_GND | (DE-588)4060370-2 (DE-588)4071711-2 (DE-588)4291782-7 (DE-588)4200230-8 |
| title | Genetics, genomics, and breeding of tomato |
| title_auth | Genetics, genomics, and breeding of tomato |
| title_exact_search | Genetics, genomics, and breeding of tomato |
| title_full | Genetics, genomics, and breeding of tomato eds. by Barbara E. Liedl ... |
| title_fullStr | Genetics, genomics, and breeding of tomato eds. by Barbara E. Liedl ... |
| title_full_unstemmed | Genetics, genomics, and breeding of tomato eds. by Barbara E. Liedl ... |
| title_short | Genetics, genomics, and breeding of tomato |
| title_sort | genetics genomics and breeding of tomato |
| topic | Tomate (DE-588)4060370-2 gnd Genetik (DE-588)4071711-2 gnd Tomatenzüchtung (DE-588)4291782-7 gnd Genanalyse (DE-588)4200230-8 gnd |
| topic_facet | Tomate Genetik Tomatenzüchtung Genanalyse |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025201721&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT liedlbarbarae geneticsgenomicsandbreedingoftomato |