Plant Cytogenetics (eBook)

Plant Cytogenetics 3
Preface 5
Contents 7
Contributors 9
PartI: Structure, Variation, and Mapping in Plant Cytogenetics 11
Chapter 1: Plant Chromosomal Deletions, Insertions, and Rearrangements 12
1.1 Introduction 13
1.2 Deletions/Deficiencies 13
1.3 Insertions/Duplications 16
1.4 Chromosomal Rearrangements 21
1.4.1 Inversions 21
1.4.2 Reciprocal Translocations 27
1.4.3 Maize B-A Chromosomes and Their Uses 36
References 40
Chapter 2: Genome Structure and Chromosome Function 46
2.1 Plant Chromosome Addition 47
2.2 Native Addition Lines 47
2.3 Alien Addition Line 49
2.4 Substitution Line 53
2.5 Deletion Line 58
References 60
Chapter 3: Plant B Chromosomes: What Makes Them Different? 68
3.1 Introduction 69
3.2 Occurrence of B Chromosomes Among Angiosperms 69
3.3 What Does DNA Analysis Tell Us About the Origin of Bs? 70
3.4 Do the Chromatin Compositions of As and Bs Differ? 73
3.5 Segregation Behavior of B Chromosomes 75
3.6 Centromeres of B Chromosomes 78
3.7 Effects Associated with B Chromosomes and B Transcribed Sequences 79
3.8 Potential Uses of B Chromosomes 80
References 81
Chapter 4: Cytogenetic Mapping in Plants 87
4.1 Cytological Maps of Chromosome Features 89
4.1.1 Mapping of Visible Cytological Features 89
4.1.2 Use of Staining to Visualize Additional Cytological Features 92
4.2 Mapping of Chromosomal Rearrangements 95
4.2.1 Use of Irradiation to Produce Additional Chromosomal Rearrangements 95
4.2.2 Use of Gametocidal Genes to Produce Deletions for Mapping in Wheat 96
4.2.3 B-A Translocations in Maize Physical Mapping 98
4.3 Mapping by Electron Microscopy 98
4.3.1 Three-Dimensional Reconstructions of Chromosomes from Whole Nuclei 98
4.3.2 Mapping of Recombination Nodules on SC Spreads 99
4.4 In Situ Hybridization (ISH) 101
4.4.1 Radioactive In Situ Hybridization 101
4.4.2 Biotinylated Probes for In Situ Hybridization 101
4.4.3 Fluorescence In Situ Hybridization 102
4.5 Types of DNA Probes 103
4.5.1 Genetically Mapped Probes 103
4.5.2 Large DNA Fragment Probes 105
4.5.3 Repetitive Sequences Probes 110
4.6 Target Chromosomes for Plant Cytogenetic Mapping 111
4.6.1 Mitotic Metaphase and Prometaphase 113
4.6.2 Meiotic Prophase 113
4.7 High-Resolution Mapping 115
4.7.1 Extended or Superstretched Chromosomes 115
4.7.2 Interphase: Extended DNA Fibers 115
4.8 Utility of Cytogenetic Maps 116
References 116
Chapter 5: DNA and Chromatin Fiber-Based Plant Cytogenetics 128
5.1 Fiber-FISH Mapping of Repetitive DNA Sequences 129
5.2 Fiber-FISH Mapping of Large and Complex Genomic Loci 130
5.3 Fiber-FISH Mapping on Cloned and Organelle DNA Molecules 131
5.4 Optical Mapping of Extended DNA Molecules 132
5.5 Immunoassays on Extended Chromatin Fibers 133
References 134
Part II: Function, Organization, and Dynamics in Plant Cytogenetics 138
Chapter 6: Plant Centromeres 139
6.1 Introduction 140
6.2 Maize Centromeres 140
6.3 Arabidopsis 144
6.4 Rice 144
6.5 Concluding Remarks 145
References 145
Chapter 7: Plant Telomeres 149
7.1 Introduction 150
7.2 Plant Telomeric DNA 151
7.2.1 Telomere DNA Structure 151
7.2.1.1 The Telomere Contains an Array of Telomere Repeats and a Single-Strand Overhang 151
7.2.1.2 The T-Loop 152
7.2.1.3 Telomeric Chromatin 153
7.2.2 Plant Telomere Repeat Variants 154
7.2.2.1 Asparagales, a Monocot Order with Noncanonical Telomere Repeats 154
7.2.2.2 The Asparagales Telomerase Encodes the Vertebrate-Type Telomere Repeat 155
7.2.2.3 Some Asparagales Species Have Additional Microsatellites at Their Telomeres 156
7.2.2.4 Cloning and Characterization of Asparagales Telomerases 157
7.2.2.5 Allium Telomeres Consist of Unknown Sequences 157
7.2.2.6 A Dicot Lineage Without Arabidopsis -Type Telomere Repeats 158
7.2.3 Subtelomeric Regions 158
7.2.3.1 Subtelomeric Satellites 158
Examples of Subtelomeric Satellites from Plants 160
Triticeae 160
Oryza 160
Organization of Chromosome Ends with Satellite Repeats 161
DNA Sequence Organization 161
Cytological Observations of Telomere-Subtelomere Macrostructure 161
Subtelomeric Sequence Variation in Arabidopsis and Other Plants Without Large Satellite Arrays 162
7.3 The Shelterin Complex 163
7.3.1 Shelterin at Human Telomeres 163
7.3.2 Shelterin Components in Plants 164
7.3.3 Shelterin Components as Transcription Factors 168
7.3.3.1 Single-Strand Binding Proteins 169
Oligonucleotide/Oligosaccharide-Fold-Containing Proteins 169
Other Single-Strand Telomere Binding Proteins 170
7.4 Telomerase RNP in Plants 171
7.4.1 TERT 171
7.4.1.1 Telomerase RNA Template 172
7.4.1.2 Dyskerin 173
7.4.1.3 POT1a 173
7.5 Telomere Dynamics 174
7.5.1 Introduction 174
7.5.1.1 Telomere Length Is Highly Variable 174
7.5.1.2 Telomere Length Is Under Genetic Control 174
7.5.2 Model of Telomere Length Homeostasis 176
7.5.2.1 End-Replication Problem and End Processing 177
7.5.2.2 Addition of Telomere Repeats by Telomerase 177
7.5.2.3 Recombination Pathways for Telomere Length Maintenance 178
Telomere Rapid Deletion 178
Alternative Lengthening of Telomeres 179
7.6 Consequences of Telomere Dysfunction 180
7.7 Role of Telomeres in Chromosome Movement and Positioning 183
7.7.1 The Rabl Structure 183
7.7.2 Bouquet Formation During Meiosis 185
7.8 De Novo Telomere Formation 187
7.8.1 Telomere Formation from a Nontelomeric Substrate 187
7.8.2 Telomere Formation at Telomere Repeat Arrays 188
7.8.3 Application of DNTF for Chromosome Engineering 189
References 190
Chapter 8: Genetics and Cytology of Meiotic Chromosome Behavior in Plants 198
8.1 Introduction 200
8.2 The Plant Life Cycle 201
8.3 Cytological Approaches Used to Study the Behavior of Plant Meiotic Chromosomes 202
8.3.1 Light Microscopy 202
8.3.2 Electron Microscopy 204
8.4 The Commitment to and Initiation of Meiosis 205
8.5 Meiotic Prophase I 207
8.5.1 Sister Chromatid Cohesion and Condensin 208
8.5.2 Cytology and Behavior of Leptotene Chromosomes 210
8.5.3 Meiotic Chromosome Loop Domains 211
8.5.4 Initiation of Meiotic Chromosome Pairing 211
8.5.5 The Leptotene-to-Zygotene Transition 212
8.5.6 The Telomere Bouquet Arrangement of Meiotic Chromosomes 212
8.5.7 The Mechanism of Bouquet Formation in Plants 213
8.5.8 Telomere Bouquet Proteins 214
8.5.9 Chromosome Synapsis and the Synaptonemal Complex in Plants 215
8.5.10 Early Recombination Pathway in Plants 216
8.5.11 Cytology of Early Recombination Nodules 218
8.5.12 Late Recombination Nodules and Crossover Interference in Plants 218
8.5.13 Recombination and Chiasma Distribution in Plants 219
8.5.14 Cytology and Behavior of Chromosomes in Middle and Late Meiotic Prophase 219
8.6 Bivalent-Spindle Interactions in Meiosis I 220
8.7 Meiosis II 221
8.8 Meiotic Centromeres 222
8.9 Meiotic Chromatin 222
8.10 Ploidy Level and Meiotic Challenges 223
8.11 Future Directions for Cytogenetics of Plant Meiosis 223
References 224
Chapter 9: Chromosomal Distribution and Functional Interpretation of Epigenetic Histone Marks in Plants 235
9.1 Introduction 236
9.2 Histone Acetylation 236
9.3 Histone Phosphorylation 238
9.4 Histone Methylation 242
9.5 Interplay Between Histone Methylation and DNA Methylation in Arabidopsis 247
9.6 Summary and Outlook 249
References 250
Part III: Methods, Informatics, and Instruction in Plant Cytogenetics 258
Chapter 10: Chromosome Microdissection and Utilization of Microisolated DNA 259
10.1 Chromosome Recognition and Microdissection Equipment 260
10.2 Handling and Amplification of Microdissected Chromosomal DNA 261
10.3 Use of Microdissected Chromosomes 263
10.4 Materials and Methods 265
10.4.1 Materials 265
10.4.2 Equipment 265
10.4.3 Solutions 265
10.4.4 Procedures 266
10.4.4.1 Preparation of Microdissection Needles 266
10.4.4.2 Preventive Measures Against DNA Contamination of PCR 266
10.4.4.3 Preparation of Chromosomes for Microdissection 266
Preparation of Mitotic Chromosomes 266
Preparation of Meiotic Chromosomes 267
10.4.4.4 Chromosome Microdissection Procedure 267
10.4.4.5 PCR Amplification of Microdissected Chromosomal DNA by DOP-PCR 268
Proteinase K Treatment 268
DOP-PCR 268
References 270
Chapter 11: Maize Antibody Procedures: Immunolocalization and Chromatin Immunoprecipitation 273
11.1 Immunofluorescence with Maize Male Meiotic Cells 274
11.2 Chromatin Immunoprecipitation Procedures 277
11.2.1 Native Chromatin Immunoprecipitation 277
11.2.1.1 Preparation of Chromatin 277
11.2.1.2 Immunocomplex Formation and Capture 279
11.2.1.3 Washing the Captured Immunocomplexes 279
11.2.1.4 Nucleic Acid Purification 279
11.2.2 Crosslinked Chromatin Immunoprecipitation 281
11.2.2.1 Crosslinking of Protein and DNA Interactions 281
11.2.2.2 Isolation and Fragmentation of Chromatin 281
11.2.2.3 Immunocomplex Formation and Capture 283
11.2.2.4 Nucleic Acid Purification 284
11.3 Notes 284
References 288
Chapter 12: Methods of Fluorescence In Situ Hybridization on Extended DNA Fibers (Fiber-FISH) 289
12.1 Isolation of Plant Nuclei 290
12.2 Preparation of Extended DNA Fibers on Glass Slides 291
12.3 FISH and Signal Detection 292
12.4 Detection Procedure Using Three Layers of Antibodies 292
12.5 Notes 293
12.6 Most Frequently Asked Questions 294
Chapter 13: Fluorescence In Situ Hybridization and In Situ PCR 296
13.1 Introduction 297
13.2 Chromosome Preparations 297
13.3 Probe Preparation 298
13.4 Chromosome Painting for Karyotype Analysis 299
13.5 Retroelement Genome Painting 299
13.6 Retroelement Distribution 300
13.7 Single-Gene, Transgene, and Transposon Detection 300
13.8 Bacterial Artificial Chromosomes as FISH Probes 301
13.9 Banding Paints 302
13.10 B Chromosomes 304
13.11 Endoreduplicated Endosperm Chromosomes 304
13.12 Pollen FISH 305
13.13 Minichromosomes 305
13.14 Meiosis 305
13.15 Primed In Situ Labeling of Plant Chromosomes 306
References 307
Chapter 14: Plant Cytogenetics in Genome Databases 311
14.1 What Sorts of Chromosomal Maps Exist? 312
14.2 What Is a Cytogenetic Map? 312
14.3 In What Ways Are Cytogenetic Maps Useful? 313
14.4 Online Cytogenetic Resources 316
14.4.1 Individual Cytogenetic Projects 316
14.4.2 Maize: Integration of the Genetic Map and the Genetic Positions of Cytological Breakpoints in the Maize Genetics and Genomics Database in the “Genetic Map” 316
14.4.3 Maize and Tomato: Recombination Nodule Maps Are Used to Infer Genetic Position from a Cytological Position and Vice Versa 317
14.4.3.1 What Is a Recombination Nodule? 317
14.4.3.2 What Is an RN map? 318
14.4.3.3 Database Resources for the Maize and Tomato RN Maps 318
14.4.3.4 The Morgan2McClintock Translator 319
14.4.4 Maize: Fluorescence in Situ Hybridization Cytogenetic Maps at MaizeGDB 319
14.4.5 Maize and Other Grasses: Comparing Cytogenetic and Genetic Maps at Gramene 320
14.4.5.1 Tomato 320
14.4.5.2 Wheat 321
References 321
Chapter 15: Practical Laboratory Exercises for Plant Molecular Cytogenetics 323
15.1 Introduction 324
15.2 Laboratory Exercises 325
15.2.1 Unknowns 326
15.2.1.1 Mutants 326
15.2.1.2 Aneuploids 326
15.2.1.3 Various Ploidy Levels 327
15.2.2 Mitosis Labs 327
15.2.2.1 Onion 327
15.2.2.2 Wheat and Other Cereals 328
15.2.3 Meiosis 329
15.2.3.1 Tradescantia 329
15.2.3.2 Pollen Fertility as a Measure of Cytological Abnormality 329
15.2.3.3 Maize or Tomato 329
15.2.3.4 Barley, Wheat, and Triticale 330
15.2.4 Chromosome Aberrations 330
15.2.5 Genomic In Situ Hybridization 331
15.2.6 Fluorescence In Situ Hybridization 331
15.2.7 Polytene Chromosomes 331
15.2.8 Fiber-FISH 332
15.2.9 Human Chromosomes 332
References 333
Index 334