The Handbook of Plant Mutation Screening: Mining of Natural and Induced Alleles

chemistry

chemistry

مستشار كلية العلوم النهرالخالد
طاقم الإدارة
بسم الله الرحمن الرحيم

The Handbook of Plant Mutation Screening: Mining of Natural and Induced Alleles
(Molecular Plant Biology Handbook Series)

by
Khalid Meksem, Günter Kahl

**************
Publisher: Wiley-VCH
Number Of Pages: 460
Publication Date: 2010-03-29
ISBN-10 / ASIN: 3527326049
ISBN-13 / EAN: 9783527326044

Product Description
Induced mutagenesis is a common and promising method for screening for new crops with improved properties. This title introduces the different methods and then focuses on the screening, detection and analysis of the novel mutations. Written by a global team of authors the book is an indispensable tool for all scientists working on crop breeding in industry and academia.​

Contents
Preface XV
List of Contributors XVII
List of Abbreviations XXIII
Part I Induced Mutations 1
1 Physically Induced Mutation: Ion Beam Mutagenesis 3
Shimpei Magori, Atsushi Tanaka, and Masayoshi Kawaguchi
1.1 Introduction 3
1.1.1 LET 4
1.1.2 Mutational Effects of Ion Beams on Plants 5
1.2 Methods and Protocols 7
1.2.1 Ion Beam Irradiation 8
1.2.2 Dose Determination for Ion Beam Irradiation 9
1.2.3 Plant Radiation Sensitivity 10
1.2.4 Population Size of the M1 Generation 11
1.3 Applications 11
1.3.1 Ion Beams for Forward Genetics 12
1.3.2 Ion Beams for Plant Breeding 13
1.3.3 Limitations of Ion Beams 13
1.4 Perspectives 14
References 14
2 Ds Transposon Mutant Lines for Saturation Mutagenesis of the
Arabidopsis genome 17
Takashi Kuromori and Takashi Hirayama
2.1 Introduction 17
2.2 Methods and Protocols 18
2.3 Applications 26
2.4 Perspectives 28
References 28
VII
3 Use of Mutants from T-DNA Insertion Populations Generated by
High-Throughput Screening 31
Ralf Stracke, Gunnar Huep, and Bernd Weisshaar
3.1 Introduction 31
3.2 Methods and Protocols 34
3.2.1 Plant Material and Growth Conditions 34
3.2.2 Plasmid Design 34
3.2.3 Agrobacterium Culture 35
3.2.4 Plant Transformation and T1 Seed Harvesting 35
3.2.5 Sulfadiazine Selection of Transgenic T1 Plants 36
3.2.6 DNA Preparation from Sulfadiazine-Selected
T1 Plants 36
3.2.7 FST Production 37
3.2.8 Sequencing and Computational Sequence Analysis 40
3.2.9 Genetic Analysis of T-DNA Insertions 41
3.2.10 DNA-Preparation for Confirmation of FST Predicted
Insertion Sites 41
3.2.11 Confirmation PCR 42
3.2.12 Sequencing and Computational Sequence Analysis 44
3.2.13 Seed Donation 45
3.2.14 Identification of Homozygous Mutants 46
3.3 Applications and Considerations for Work with T-DNA
Insertion Mutants 47
3.3.1 Unconfirmed T-DNA Insertion Lines 48
3.3.2 Use of Selectable Marker 48
3.3.3 Aberrant T-DNA Insertions 48
3.3.4 Multiple T-DNA Insertions 49
3.3.5 T-DNA-Induced Dominant Effects 49
3.3.6 Allelic Series of Mutants 49
3.3.7 Lethal Knockout Mutants 50
3.3.8 Search for Knockout Phenotype 50
3.3.9 Handling of Non-Single-Copy Genes 50
3.4 Perspectives 51
References 52
4 Making Mutations is an Active Process: Methods to Examine
DNA Polymerase Errors 55
Kristin A. Eckert and Erin E. Gestl
4.1 Introduction 55
4.2 Methods and Protocols 56
4.2.1 Overview of the Genetic Assay 56
4.2.2 Overview of the Biochemical Assay for TLS 67
4.3 Applications 73
4.3.1 General Features of the In Vitro Genetic Assay 73
4.3.2 Polymerase Accuracy in the Absence of DNA Damage 74
VIII Contents
4.3.3 Mutational Processing of Alkylation Damage by DNA
Polymerases 75
4.3.4 DNA Lesion Discrimination Mechanisms 75
4.4 Perspectives 78
References 79
5 Tnt1 Induced Mutations in Medicago: Characterization
and Applications 83
Pascal Ratet, Jiangqi Wen, Viviane Cosson, Million Tadege,
and Kirankumar S. Mysore
5.1 Introduction 83
5.2 Methods and Protocols 84
5.2.1 Identification of Tnt1 Insertion Sites 84
5.2.2 Reverse Genetic Approach 94
5.2.2.1 FST Sequencing 94
5.2.2.2 Screening DNA Pools 94
5.3 Applications 95
5.3.1 Line with a Mutant Phenotype – No FSTs Identified 96
5.3.2 Line with a Mutant Phenotype and FSTs Already Identified 96
5.3.3 FST Sequence in the Tnt1 Database Matches a Gene of
Interest – No Mutant Phenotype is Described in that Line 97
5.3.4 Have a Gene to Work With – No FST or Mutant Phenotype 97
5.4 Perspectives 98
References 98
Part II Mutation Discovery 101
6 Mutation Discovery with the Illumina Genome Analyzer 103
Abizar Lakdawalla and Gary P. Schroth
6.1 Introduction 103
6.1.1 Overview of the Illumina Genome Analyzer Sequencing Process 103
6.1.2 Resequencing Strategies 104
6.1.2.1 Resequencing Whole Genomes 105
6.1.2.2 Targeted Genome Selection 105
6.1.2.3 Sequencing Transcriptomes 107
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 121
Tania Tabone, Georgina Sallmann, and Richard G.H. Cotton
7.1 Introduction 121
7.2 Methods and Protocols 125
Contents IX
7.3 Applications 127
7.4 Perspectives 127
References 128
8 Mutation Detection in Plants by Enzymatic
Mismatch Cleavage 131
Bradley J. Till
8.1 Introduction 131
8.2 Methods and Protocols 136
8.3 Applications 143
8.4 Perspectives 144
References 145
9 Mutation Scanning and Genotyping in Plants by High-Resolution
DNA Melting 149
Jason T. McKinney, Lyle M. Nay, David De Koeyer, Gudrun H. Reed,
Mikeal Wall, Robert A. Palais, Robert L. Jarret, and Carl T. Wittwer
9.1 Introduction 149
9.2 Methods and Protocols 150
9.2.1 LightScanner Instrument 151
9.2.2 LightScanner for Variant Scanning 151
9.2.3 LightScanner for LunaprobeTM (Unlabeled Probe)
Genotyping 156
9.3 Applications 159
9.3.1 Sensitivity and Specificity for SNP Heterozygote
Detection 159
9.3.2 Variant Scanning by High-Resolution Melting 160
9.3.3 Bell Pepper Multiplex Genotyping with Two Unlabeled
Probes 161
9.3.4 Potato Tetraploid Genotyping including Allele Dosage using an
Unlabeled Probe 161
9.4 Perspectives 162
References 163
10 In Silico Methods: Mutation Detection Software for Sanger
Sequencing, Genome and Fragment Analysis 167
Kevin LeVan, Teresa Snyder-Leiby, C.S. Jonathan Liu, and Ni Shouyong
10.1 Introduction 167
10.2 Mutation Detection with Sanger Sequencing using
Mutation Surveyor 168
10.3 Mutation Detection with NextGENeTM and Next-Generation
Sequence Technologies 175
10.4 Mutation Detection with DNA Fragments Using GeneMarker1 180
10.5 Perspectives 182
References 182
X Contents
Part III High-Throughput Screening Methods 185
11 Use of TILLING for Reverse and Forward Genetics of Rice 187
Sujay Rakshit, Hiroyuki Kanzaki, Hideo Matsumura, Arunita Rakshit,
Takahiro Fujibe, Yudai Okuyama, Kentaro Yoshida, Muluneh Oli,
Matt Shenton, Hiroe Utsushi, Chikako Mitsuoka, Akira Abe,
Yutaka Kiuchi, and Ryohei Terauchi
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 KeyPointTM Technology 199
Diana Rigola and Michiel J.T. van Eijk
12.1 Introduction 199
12.2 Methods and Protocols 202
12.3 Applications 206
12.3.1 EMS Mutation Screening and Validation 206
12.3.2 Natural Polymorphism Screening and Validation 208
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
William T.B. Thomas, Brian P. Forster, and Robbie Waugh
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
13.3.1 Resources 223
13.3.2 Case Study: Two/Six-Row Locus in Barley 224
13.3.3 Case Study: Graphical Genotyping of a Disease Resistance Locus 227
13.3.4 General Protocol for using High-Throughput Genotyping to
Localize Mutants 227
References 229
14 Association Mapping for the Exploration of Genetic Diversity
and Identification of Useful Loci for Plant Breeding 231
André Beló and Stanley D. Luck
14.1 Introduction 231
14.2 Methods and Protocols 233
14.2.1 Population for Association Mapping 233
Contents XI
14.2.2 Genotyping 234
14.2.3 Phenotyping 234
14.2.4 Statistical Procedures 235
14.3 Applications 238
14.3.1 QTL Mapping versus Association Mapping 240
14.3.2 Limitations 241
14.4 Perspectives 242
References 243
15 Using Mutations in Corn Breeding Programs 247
Anastasia L. Bodnar and M. Paul Scott
15.1 Introduction 247
15.1.1 Factors to Consider Before Starting a Breeding Program 248
15.1.2 Alternatives to Breeding 249
15.2 Methods and Protocols 249
15.2.1 Backcross Breeding 249
15.2.2 Forward Breeding 252
15.2.3 Supplementary Protocols 253
15.2.3.1 Determining How Many Seeds to Plant 253
15.2.3.2 Working with Recessive Mutations 255
15.2.3.3 Intermating 256
15.2.4 Complication: Pleiotropic Effects 257
15.3 Applications 258
15.3.1 Breeding with a Natural Mutation: QPM 258
15.3.2 Breeding with a Transgene: GFP 259
15.4 Perspectives 259
15.4.1 Marker-Assisted Selection 259
15.4.1.1 Marker-Assisted Selection in Backcross Breeding 259
15.4.1.2 Marker-Assisted Selection in Forward Breeding 260
15.4.2 Doubled Haploids 260
References 261
16 Gene Targeting as a Precise Tool for Plant Mutagenesis 263
Oliver Zobell and Bernd Reiss
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)TM by Synthesis 289
Scott Jenkins and Avak Kahvejian
17.1 Introduction 289
17.2 Methods, Protocols, and Technical Principles 291
XII Contents
17.2.1 Single Molecule Sequencing Technical Challenges and Solutions 291
17.2.2 Flow Cell Surface Architecture 294
17.2.3 Cyclic SBS 295
17.2.4 Optical Imaging of Growing Strands 297
17.2.5 Mechanical Operation 300
17.2.6 System Components 300
17.2.7 Data Analysis 301
17.3 Applications 301
17.3.1 Single Molecule DGE and RNA-Seq 301
17.3.1.1 DNA Sequencing Applications 303
17.3.2 Single Molecule Sequencing Techniques under Development 303
17.4 Perspectives 304
References 306
18 High-Throughput Sequencing by Hybridization 307
Sten Linnarsson 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
Lin Yu, Jia Guo, Ning Xu, Zengmin Li, and Jingyue Ju
19.1 Introduction 319
19.2 General Methodology for DNA SBS 321
19.3 Four-Color DNA SBS using CF-NRTs 323
19.3.1 Overview 323
19.3.2 Design, Synthesis, and Characterization of CF-NRTs 324
19.3.3 DNA Chip Construction 326
19.3.4 Four-Color SBS using CF-NRTs 326
19.4 Hybrid DNA SBS using NRTs and CF-ddNTPs 329
19.4.1 Overview 329
19.4.2 Design and Synthesis of NRTs and CF-ddNTPs 331
19.4.3 Four-Color Hybrid DNA SBS 333
19.5 Perspectives 335
References 336
20 Emerging Technologies: Nanopore Sequencing for
Mutation Detection 339
Ryan Rollings and Jiali Li
20.1 Introduction 339
20.1.1 Nanopore Detection Principle 340
20.1.2 Important Parameters and Nanopore Sensing Resolution 341
20.1.3 Biological Nanopore History 341
20.1.4 Solid-State Nanopore History 343
Contents XIII
20.1.5 Nanopore Promise 343
20.2 Current Developments in Nanopore Sequencing 344
20.2.1 Improving Biological Nanopores 344
20.2.2 Improving Solid-State Nanopores 345
20.2.3 Slowing Translocation and Trapping 347
20.2.4 Modification of the DNA 347
20.2.5 Resequencing Applications 349
20.3 Work Done in Our Lab 350
20.4 Perspectives 351
References 352
Glossary 355
Index 427
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