Bass / Birchler Plant Cytogenetics

Genome Structure and Chromosome Function
1. Auflage 2011
ISBN: 978-0-387-70869-0
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 4, 350 Seiten

Reihe: Plant Genetics and Genomics: Crops and Models

This reference book provides information on plant cytogenetics for students, instructors, and researchers. Topics covered by international experts include classical cytogenetics of plant genomes; plant chromosome structure; functional, molecular cytology; and genome dynamics. In addition, chapters are included on several methods in plant cytogenetics, informatics, and even laboratory exercises for aspiring or practiced instructors. The book provides a unique combination of historical and modern subject matter, revealing the central role of plant cytogenetics in plant genetics and genomics as currently practiced. This breadth of coverage, together with the inclusion of methods and instruction, is intended to convey a deep and useful appreciation for plant cytogenetics. We hope it will inform and inspire students, researchers, and teachers to continue to employ plant cytogenetics to address fundamental questions about the cytology of plant chromosomes and genomes for years to come.Hank W. Bass is a Professor in the Department of Biological Science at Florida State University.James A. Birchler is a Professor in the Division of Biological Sciences at the University of Missouri.

Autoren/Hrsg.

Bass, Hank

Birchler, James A.

Inhaltsverzeichnis

1;Plant Cytogenetics;3
1.1;Preface;5
1.2;Contents;7
1.3;Contributors;9
1.4;PartI: Structure, Variation, and Mapping in Plant Cytogenetics;11
1.4.1;Chapter 1: Plant Chromosomal Deletions, Insertions, and Rearrangements;12
1.4.1.1;1.1 Introduction;13
1.4.1.2;1.2 Deletions/Deficiencies;13
1.4.1.3;1.3 Insertions/Duplications;16
1.4.1.4;1.4 Chromosomal Rearrangements;21
1.4.1.4.1;1.4.1 Inversions;21
1.4.1.4.2;1.4.2 Reciprocal Translocations;27
1.4.1.4.3;1.4.3 Maize B-A Chromosomes and Their Uses;36
1.4.1.5;References;40
1.4.2;Chapter 2: Genome Structure and Chromosome Function;46
1.4.2.1;2.1 Plant Chromosome Addition;47
1.4.2.2;2.2 Native Addition Lines;47
1.4.2.3;2.3 Alien Addition Line;49
1.4.2.4;2.4 Substitution Line;53
1.4.2.5;2.5 Deletion Line;58
1.4.2.6;References;60
1.4.3;Chapter 3: Plant B Chromosomes: What Makes Them Different?;68
1.4.3.1;3.1 Introduction;69
1.4.3.2;3.2 Occurrence of B Chromosomes Among Angiosperms;69
1.4.3.3;3.3 What Does DNA Analysis Tell Us About the Origin of Bs?;70
1.4.3.4;3.4 Do the Chromatin Compositions of As and Bs Differ?;73
1.4.3.5;3.5 Segregation Behavior of B Chromosomes;75
1.4.3.6;3.6 Centromeres of B Chromosomes;78
1.4.3.7;3.7 Effects Associated with B Chromosomes and B Transcribed Sequences;79
1.4.3.8;3.8 Potential Uses of B Chromosomes;80
1.4.3.9;References;81
1.4.4;Chapter 4: Cytogenetic Mapping in Plants;87
1.4.4.1;4.1 Cytological Maps of Chromosome Features;89
1.4.4.1.1;4.1.1 Mapping of Visible Cytological Features;89
1.4.4.1.2;4.1.2 Use of Staining to Visualize Additional Cytological Features;92
1.4.4.2;4.2 Mapping of Chromosomal Rearrangements;95
1.4.4.2.1;4.2.1 Use of Irradiation to Produce Additional Chromosomal Rearrangements;95
1.4.4.2.2;4.2.2 Use of Gametocidal Genes to Produce Deletions for Mapping in Wheat;96
1.4.4.2.3;4.2.3 B-A Translocations in Maize Physical Mapping;98
1.4.4.3;4.3 Mapping by Electron Microscopy;98
1.4.4.3.1;4.3.1 Three-Dimensional Reconstructions of Chromosomes from Whole Nuclei;98
1.4.4.3.2;4.3.2 Mapping of Recombination Nodules on SC Spreads;99
1.4.4.4;4.4 In Situ Hybridization (ISH);101
1.4.4.4.1;4.4.1 Radioactive In Situ Hybridization;101
1.4.4.4.2;4.4.2 Biotinylated Probes for In Situ Hybridization;101
1.4.4.4.3;4.4.3 Fluorescence In Situ Hybridization;102
1.4.4.5;4.5 Types of DNA Probes;103
1.4.4.5.1;4.5.1 Genetically Mapped Probes;103
1.4.4.5.2;4.5.2 Large DNA Fragment Probes;105
1.4.4.5.3;4.5.3 Repetitive Sequences Probes;110
1.4.4.6;4.6 Target Chromosomes for Plant Cytogenetic Mapping;111
1.4.4.6.1;4.6.1 Mitotic Metaphase and Prometaphase;113
1.4.4.6.2;4.6.2 Meiotic Prophase;113
1.4.4.7;4.7 High-Resolution Mapping;115
1.4.4.7.1;4.7.1 Extended or Superstretched Chromosomes;115
1.4.4.7.2;4.7.2 Interphase: Extended DNA Fibers;115
1.4.4.8;4.8 Utility of Cytogenetic Maps;116
1.4.4.9;References;116
1.4.5;Chapter 5: DNA and Chromatin Fiber-Based Plant Cytogenetics;128
1.4.5.1;5.1 Fiber-FISH Mapping of Repetitive DNA Sequences;129
1.4.5.2;5.2 Fiber-FISH Mapping of Large and Complex Genomic Loci;130
1.4.5.3;5.3 Fiber-FISH Mapping on Cloned and Organelle DNA Molecules;131
1.4.5.4;5.4 Optical Mapping of Extended DNA Molecules;132
1.4.5.5;5.5 Immunoassays on Extended Chromatin Fibers;133
1.4.5.6;References;134
1.5;Part II: Function, Organization, and Dynamics in Plant Cytogenetics;138
1.5.1;Chapter 6: Plant Centromeres;139
1.5.1.1;6.1 Introduction;140
1.5.1.2;6.2 Maize Centromeres;140
1.5.1.3;6.3 Arabidopsis;144
1.5.1.4;6.4 Rice;144
1.5.1.5;6.5 Concluding Remarks;145
1.5.1.6;References;145
1.5.2;Chapter 7: Plant Telomeres;149
1.5.2.1;7.1 Introduction;150
1.5.2.2;7.2 Plant Telomeric DNA;151
1.5.2.2.1;7.2.1 Telomere DNA Structure;151
1.5.2.2.1.1;7.2.1.1 The Telomere Contains an Array of Telomere Repeats and a Single-Strand Overhang;151
1.5.2.2.1.2;7.2.1.2 The T-Loop;152
1.5.2.2.1.3;7.2.1.3 Telomeric Chromatin;153
1.5.2.2.2;7.2.2 Plant Telomere Repeat Variants;154
1.5.2.2.2.1;7.2.2.1 Asparagales, a Monocot Order with Noncanonical Telomere Repeats;154
1.5.2.2.2.2;7.2.2.2 The Asparagales Telomerase Encodes the Vertebrate-Type Telomere Repeat;155
1.5.2.2.2.3;7.2.2.3 Some Asparagales Species Have Additional Microsatellites at Their Telomeres;156
1.5.2.2.2.4;7.2.2.4 Cloning and Characterization of Asparagales Telomerases;157
1.5.2.2.2.5;7.2.2.5 Allium Telomeres Consist of Unknown Sequences;157
1.5.2.2.2.6;7.2.2.6 A Dicot Lineage Without Arabidopsis -Type Telomere Repeats;158
1.5.2.2.3;7.2.3 Subtelomeric Regions;158
1.5.2.2.3.1;7.2.3.1 Subtelomeric Satellites;158
1.5.2.2.3.1.1; Examples of Subtelomeric Satellites from Plants;160
1.5.2.2.3.1.1.1; Triticeae;160
1.5.2.2.3.1.1.2;Oryza;160
1.5.2.2.3.1.2; Organization of Chromosome Ends with Satellite Repeats;161
1.5.2.2.3.1.2.1; DNA Sequence Organization;161
1.5.2.2.3.1.2.2; Cytological Observations of Telomere-Subtelomere Macrostructure;161
1.5.2.2.3.1.2.3; Subtelomeric Sequence Variation in Arabidopsis and Other Plants Without Large Satellite Arrays;162
1.5.2.3;7.3 The Shelterin Complex;163
1.5.2.3.1;7.3.1 Shelterin at Human Telomeres;163
1.5.2.3.2;7.3.2 Shelterin Components in Plants;164
1.5.2.3.3;7.3.3 Shelterin Components as Transcription Factors;168
1.5.2.3.3.1;7.3.3.1 Single-Strand Binding Proteins;169
1.5.2.3.3.1.1;Oligonucleotide/Oligosaccharide-Fold-Containing Proteins ;169
1.5.2.3.3.1.2;Other Single-Strand Telomere Binding Proteins;170
1.5.2.4;7.4 Telomerase RNP in Plants;171
1.5.2.4.1;7.4.1 TERT;171
1.5.2.4.1.1;7.4.1.1 Telomerase RNA Template;172
1.5.2.4.1.2;7.4.1.2 Dyskerin;173
1.5.2.4.1.3;7.4.1.3 POT1a;173
1.5.2.5;7.5 Telomere Dynamics;174
1.5.2.5.1;7.5.1 Introduction;174
1.5.2.5.1.1;7.5.1.1 Telomere Length Is Highly Variable;174
1.5.2.5.1.2;7.5.1.2 Telomere Length Is Under Genetic Control;174
1.5.2.5.2;7.5.2 Model of Telomere Length Homeostasis;176
1.5.2.5.2.1;7.5.2.1 End-Replication Problem and End Processing;177
1.5.2.5.2.2;7.5.2.2 Addition of Telomere Repeats by Telomerase;177
1.5.2.5.2.3;7.5.2.3 Recombination Pathways for Telomere Length Maintenance;178
1.5.2.5.2.3.1; Telomere Rapid Deletion;178
1.5.2.5.2.3.2; Alternative Lengthening of Telomeres;179
1.5.2.6;7.6 Consequences of Telomere Dysfunction;180
1.5.2.7;7.7 Role of Telomeres in Chromosome Movement and Positioning;183
1.5.2.7.1;7.7.1 The Rabl Structure;183
1.5.2.7.2;7.7.2 Bouquet Formation During Meiosis;185
1.5.2.8;7.8 De Novo Telomere Formation;187
1.5.2.8.1;7.8.1 Telomere Formation from a Nontelomeric Substrate;187
1.5.2.8.2;7.8.2 Telomere Formation at Telomere Repeat Arrays;188
1.5.2.8.3;7.8.3 Application of DNTF for Chromosome Engineering;189
1.5.2.9;References;190
1.5.3;Chapter 8: Genetics and Cytology of Meiotic Chromosome Behavior in Plants;198
1.5.3.1;8.1 Introduction;200
1.5.3.2;8.2 The Plant Life Cycle;201
1.5.3.3;8.3 Cytological Approaches Used to Study the Behavior of Plant Meiotic Chromosomes;202
1.5.3.3.1;8.3.1 Light Microscopy;202
1.5.3.3.2;8.3.2 Electron Microscopy;204
1.5.3.4;8.4 The Commitment to and Initiation of Meiosis;205
1.5.3.5;8.5 Meiotic Prophase I;207
1.5.3.5.1;8.5.1 Sister Chromatid Cohesion and Condensin;208
1.5.3.5.2;8.5.2 Cytology and Behavior of Leptotene Chromosomes;210
1.5.3.5.3;8.5.3 Meiotic Chromosome Loop Domains;211
1.5.3.5.4;8.5.4 Initiation of Meiotic Chromosome Pairing;211
1.5.3.5.5;8.5.5 The Leptotene-to-Zygotene Transition;212
1.5.3.5.6;8.5.6 The Telomere Bouquet Arrangement of Meiotic Chromosomes;212
1.5.3.5.7;8.5.7 The Mechanism of Bouquet Formation in Plants;213
1.5.3.5.8;8.5.8 Telomere Bouquet Proteins;214
1.5.3.5.9;8.5.9 Chromosome Synapsis and the Synaptonemal Complex in Plants;215
1.5.3.5.10;8.5.10 Early Recombination Pathway in Plants;216
1.5.3.5.11;8.5.11 Cytology of Early Recombination Nodules;218
1.5.3.5.12;8.5.12 Late Recombination Nodules and Crossover Interference in Plants;218
1.5.3.5.13;8.5.13 Recombination and Chiasma Distribution in Plants;219
1.5.3.5.14;8.5.14 Cytology and Behavior of Chromosomes in Middle and Late Meiotic Prophase;219
1.5.3.6;8.6 Bivalent-Spindle Interactions in Meiosis I;220
1.5.3.7;8.7 Meiosis II;221
1.5.3.8;8.8 Meiotic Centromeres;222
1.5.3.9;8.9 Meiotic Chromatin;222
1.5.3.10;8.10 Ploidy Level and Meiotic Challenges;223
1.5.3.11;8.11 Future Directions for Cytogenetics of Plant Meiosis;223
1.5.3.12;References;224
1.5.4;Chapter 9: Chromosomal Distribution and Functional Interpretation of Epigenetic Histone Marks in Plants;235
1.5.4.1;9.1 Introduction;236
1.5.4.2;9.2 Histone Acetylation;236
1.5.4.3;9.3 Histone Phosphorylation;238
1.5.4.4;9.4 Histone Methylation;242
1.5.4.5;9.5 Interplay Between Histone Methylation and DNA Methylation in Arabidopsis;247
1.5.4.6;9.6 Summary and Outlook;249
1.5.4.7;References;250
1.6;Part III: Methods, Informatics, and Instruction in Plant Cytogenetics;258
1.6.1;Chapter 10: Chromosome Microdissection and Utilization of Microisolated DNA;259
1.6.1.1;10.1 Chromosome Recognition and Microdissection Equipment;260
1.6.1.2;10.2 Handling and Amplification of Microdissected Chromosomal DNA;261
1.6.1.3;10.3 Use of Microdissected Chromosomes;263
1.6.1.4;10.4 Materials and Methods;265
1.6.1.4.1;10.4.1 Materials;265
1.6.1.4.2;10.4.2 Equipment;265
1.6.1.4.3;10.4.3 Solutions;265
1.6.1.4.4;10.4.4 Procedures;266
1.6.1.4.4.1;10.4.4.1 Preparation of Microdissection Needles;266
1.6.1.4.4.2;10.4.4.2 Preventive Measures Against DNA Contamination of PCR;266
1.6.1.4.4.3;10.4.4.3 Preparation of Chromosomes for Microdissection;266
1.6.1.4.4.3.1; Preparation of Mitotic Chromosomes;266
1.6.1.4.4.3.2; Preparation of Meiotic Chromosomes;267
1.6.1.4.4.4;10.4.4.4 Chromosome Microdissection Procedure;267
1.6.1.4.4.5;10.4.4.5 PCR Amplification of Microdissected Chromosomal DNA by DOP-PCR;268
1.6.1.4.4.5.1; Proteinase K Treatment;268
1.6.1.4.4.5.2; DOP-PCR;268
1.6.1.5;References;270
1.6.2;Chapter 11: Maize Antibody Procedures: Immunolocalization and Chromatin Immunoprecipitation;273
1.6.2.1;11.1 Immunofluorescence with Maize Male Meiotic Cells;274
1.6.2.2;11.2 Chromatin Immunoprecipitation Procedures;277
1.6.2.2.1;11.2.1 Native Chromatin Immunoprecipitation;277
1.6.2.2.1.1;11.2.1.1 Preparation of Chromatin;277
1.6.2.2.1.2;11.2.1.2 Immunocomplex Formation and Capture;279
1.6.2.2.1.3;11.2.1.3 Washing the Captured Immunocomplexes;279
1.6.2.2.1.4;11.2.1.4 Nucleic Acid Purification;279
1.6.2.2.2;11.2.2 Crosslinked Chromatin Immunoprecipitation;281
1.6.2.2.2.1;11.2.2.1 Crosslinking of Protein and DNA Interactions;281
1.6.2.2.2.2;11.2.2.2 Isolation and Fragmentation of Chromatin;281
1.6.2.2.2.3;11.2.2.3 Immunocomplex Formation and Capture;283
1.6.2.2.2.4;11.2.2.4 Nucleic Acid Purification;284
1.6.2.3;11.3 Notes;284
1.6.2.4;References;288
1.6.3;Chapter 12: Methods of Fluorescence In Situ Hybridization on Extended DNA Fibers (Fiber-FISH);289
1.6.3.1;12.1 Isolation of Plant Nuclei;290
1.6.3.2;12.2 Preparation of Extended DNA Fibers on Glass Slides;291
1.6.3.3;12.3 FISH and Signal Detection;292
1.6.3.4;12.4 Detection Procedure Using Three Layers of Antibodies;292
1.6.3.5;12.5 Notes;293
1.6.3.6;12.6 Most Frequently Asked Questions;294
1.6.4;Chapter 13: Fluorescence In Situ Hybridization and In Situ PCR;296
1.6.4.1;13.1 Introduction;297
1.6.4.2;13.2 Chromosome Preparations;297
1.6.4.3;13.3 Probe Preparation;298
1.6.4.4;13.4 Chromosome Painting for Karyotype Analysis;299
1.6.4.5;13.5 Retroelement Genome Painting;299
1.6.4.6;13.6 Retroelement Distribution;300
1.6.4.7;13.7 Single-Gene, Transgene, and Transposon Detection;300
1.6.4.8;13.8 Bacterial Artificial Chromosomes as FISH Probes;301
1.6.4.9;13.9 Banding Paints;302
1.6.4.10;13.10 B Chromosomes;304
1.6.4.11;13.11 Endoreduplicated Endosperm Chromosomes;304
1.6.4.12;13.12 Pollen FISH;305
1.6.4.13;13.13 Minichromosomes;305
1.6.4.14;13.14 Meiosis;305
1.6.4.15;13.15 Primed In Situ Labeling of Plant Chromosomes;306
1.6.4.16;References;307
1.6.5;Chapter 14: Plant Cytogenetics in Genome Databases;311
1.6.5.1;14.1 What Sorts of Chromosomal Maps Exist?;312
1.6.5.2;14.2 What Is a Cytogenetic Map?;312
1.6.5.3;14.3 In What Ways Are Cytogenetic Maps Useful?;313
1.6.5.4;14.4 Online Cytogenetic Resources;316
1.6.5.4.1;14.4.1 Individual Cytogenetic Projects;316
1.6.5.4.2;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
1.6.5.4.3;14.4.3 Maize and Tomato: Recombination Nodule Maps Are Used to Infer Genetic Position from a Cytological Position and Vice Versa;317
1.6.5.4.3.1;14.4.3.1 What Is a Recombination Nodule?;317
1.6.5.4.3.2;14.4.3.2 What Is an RN map?;318
1.6.5.4.3.3;14.4.3.3 Database Resources for the Maize and Tomato RN Maps;318
1.6.5.4.3.4;14.4.3.4 The Morgan2McClintock Translator;319
1.6.5.4.4;14.4.4 Maize: Fluorescence in Situ Hybridization Cytogenetic Maps at MaizeGDB;319
1.6.5.4.5;14.4.5 Maize and Other Grasses: Comparing Cytogenetic and Genetic Maps at Gramene;320
1.6.5.4.5.1;14.4.5.1 Tomato;320
1.6.5.4.5.2;14.4.5.2 Wheat;321
1.6.5.5;References;321
1.6.6;Chapter 15: Practical Laboratory Exercises for Plant Molecular Cytogenetics;323
1.6.6.1;15.1 Introduction;324
1.6.6.2;15.2 Laboratory Exercises;325
1.6.6.2.1;15.2.1 Unknowns;326
1.6.6.2.1.1;15.2.1.1 Mutants;326
1.6.6.2.1.2;15.2.1.2 Aneuploids;326
1.6.6.2.1.3;15.2.1.3 Various Ploidy Levels;327
1.6.6.2.2;15.2.2 Mitosis Labs;327
1.6.6.2.2.1;15.2.2.1 Onion;327
1.6.6.2.2.2;15.2.2.2 Wheat and Other Cereals;328
1.6.6.2.3;15.2.3 Meiosis;329
1.6.6.2.3.1;15.2.3.1 Tradescantia;329
1.6.6.2.3.2;15.2.3.2 Pollen Fertility as a Measure of Cytological Abnormality;329
1.6.6.2.3.3;15.2.3.3 Maize or Tomato;329
1.6.6.2.3.4;15.2.3.4 Barley, Wheat, and Triticale;330
1.6.6.2.4;15.2.4 Chromosome Aberrations;330
1.6.6.2.5;15.2.5 Genomic In Situ Hybridization;331
1.6.6.2.6;15.2.6 Fluorescence In Situ Hybridization;331
1.6.6.2.7;15.2.7 Polytene Chromosomes;331
1.6.6.2.8;15.2.8 Fiber-FISH;332
1.6.6.2.9;15.2.9 Human Chromosomes;332
1.6.6.3;References;333
1.7;Index;334