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The handbook of plant mutation screening : mining of natural and induced alleles / edited by Khalid Meksem, Günter Kahl. — Weinheim : Wiley-VCH, c2010. – (58.80581/H236) |
Contents
Contents
Preface
List of Contributors
List of Abbreviations
Part I Induced Mutations
1 Physically Induced Mutation: Ion Beam Mutagenesis 3
1.1 Introduction 3
1.2 Methods and Protocols 7
1.3 Applications 11
1.4 Perspectives 14
References 14
2 Ds Transposon Mutant Lines for Saturation Mutagenesis of the Arabidopsis genome
2.1 Introduction 17
2.2 Methods and Protocols 18
2.3 Applications 26
2.4 Perspectives 28
References 28
3 Use of Mutants from T-DNA Insertion Populations Generated by High-Throughput Screening 31
3.1 Introduction 31
3.2 Methods and Protocols 34
3.3 Applications and Considerations for Work with T-DNA Insertion Mutants 47
3.4 Perspectives 51
References 52
4 Making Mutations is an Active Process: Methods to Examine DNA Polymerase Errors
4.1 Introduction 55
4.2 Methods and Protocols 56
4.3 Applications 73
4.4 Perspectives 78
References 79
5 Tnt1 Induced Mutations in Medicago: Characterization and Applications 83
5.1 Introduction 83
5.2 Methods and Protocols 84
5.3 Applications 95
5.4 Perspectives 98
References 98
Part II Mutation Discovery 101
6 Mutation Discovery with the Illumina Genome Analyzer 103
6.1 Introduction 103
6.2 Methods and Protocols 107
6.3 Applications 116
6.4 Perspectives 118
References 118
7 Chemical Methods for Mutation Detection: The Chemical Cleavage of Mismatch Method
7.1 Introduction 121
7.2 Methods and Protocols 125
7.3 Applications 127
7.4 Perspectives 127
References 128
8 Mutation Detection in Plants by Enzymatic Mismatch Cleavage 131
8.1 Introduction 131
8.2 Methods and Protocols
8.3 Applications 143
8.4 Perspectives 144
References 145
9 Mutation Scanning and Genotyping in Plants by High-Resolution DNA Melting
9.1 Introduction 149
9.2 Methods and Protocols 150
9.3 Applications 159
9.4 Perspectives 162
References 163
10 In Silico Methods: Mutation Detection Software for Sanger Sequencing， Genome and Fragment Analysis 167
10.1 Introduction 167
10.2 Mutation Detection with Sanger Sequencing using Mutation Surveyor 168
10.3 Mutation Detection with NextGENe and Next-Generation Sequence Technologies
10.4 Mutation Detection with DNA Fragments Using GeneMarker 180
10.5 Perspectives 182
References 182
Part III High-Throughput Screening Methods 185
11 Use of TILLING for Reverse and Forward Genetics of Rice 187
11.1 Introduction 187
11.2 Methods and Protocols 188
11.3 Perspectives 196
References 197
12 Sequencing-Based Screening of Mutations and Natural Variation using the KeyPoint Technology
12.1 Introduction 199
12.2 Methods and Protocols 202
12.3 Applications 206
12.4 Perspectives 211
References 211
Part IV Applications in Plant Breeding 215
13 Natural and Induced Mutants of Barley: Single Nucleotide Polymorphisms in Genes Important for Breeding 217
13.1 Brief Review of Barley Mutants 217
13.2 Applications in Breeding 221
13.3 Single Nucleotide Polymorphism Genotyping to Identify Candidate Genes for Mutants 223
References 229
14 Association Mapping for the Exploration of Genetic Diversity and Identification of Useful Loci for Plant Breeding 231
14.1 Introduction 231
14.2 Methods and Protocols 233
14.3 Applications 238
14.4 Perspectives 242
References 243
15 Using Mutations in Corn Breeding Programs 247
15.1 Introduction 247
15.2 Methods and Protocols 249
15.3 Applications 258
15.4 Perspectives 259
References 261
16 Gene Targeting as a Precise Tool for Plant Mutagenesis 263
16.1 Introduction 263
16.2 Methods and Protocols 266
16.3 Applications 279
16.4 Perspectives 280
References 280
Part V Emerging Technologies 287
17 True Single Molecule Sequencing (tSMS) by Synthesis 289
17.1 Introduction 289
17.2 Methods， Protocols， and Technical Principles 291
17.3 Applications 301
17.4 Perspectives 304
References 306
18 High-Throughput Sequencing by Hybridization 307
18.1 Introduction 307
18.2 Methods and Protocol 308
18.3 Discussion 316
18.4 Applications 316
References 317
19 DNA Sequencing-by-Synthesis using Novel Nucleotide Analogs 319
19.1 Introduction 319
19.2 General Methodology for DNA SBS 321
19.3 Four-Color DNA SBS using CF-NRTs 323
19.4 Hybrid DNA SBS using NRTs and CF-ddNTPs 329
19.5 Perspectives 335
References 336
20 Emerging Technologies: Nanopore Sequencing for Mutation Detection 339
20.1 Introduction 339
20.2 Current Developments in Nanopore Sequencing 344
20.3 Work Done in Our Lab 350
20.4 Perspectives 351
References 352
Glossary 355
Index 427
