Zebrafish: Genetics and Genomics (eBook)

Front Cover 1
Methods in Cell Biology, Volume 60 4
Copyright Page 5
Contents 8
Contributors 14
Preface 18
Chapter 1. A Gynogenesis-Based Screen for Maternal-Effect Genes in the Zebrafish, Danio rerio 20
I. Introduction 20
II. Optimization of the Gynogenetic Method 23
III. A Pilot Screen for Maternal-Effect Mutations 29
IV. Recovery of Mutations 30
V. Solutions, Materials, and Protocols for Gynogenetic Methods 31
VI. Conclusions 35
References 36
Chapter 2. Developmental Mutant Screens in the Zebrafish 40
I. Introduction 41
II. Mutagenesis 41
III. Breeding Scheme 45
IV. Screening Procedure 46
V. Allele Screens 50
VI. Dominant Screens 53
VII. Managing the Outcome of Screens 54
VIII. Potential of Future Screens 56
Appendix—Recipes and Media 57
References 57
Chapter 3. Haploid Screens and Gamma-Ray Mutagenesis 62
I. Introduction 63
II. Production of Haploid Embryos 63
III. Development of Haploid Embryos 67
IV. Genetic Background 70
V. The Haploid Screen 72
VI. Limitations of Haploids 76
VII. Mosaicism in F1 Screens 78
VIII. Haploid Screens and Gamma-Ray Mutagenesis 79
IX. Nature of Gamma-Ray-Induced Mutations 83
X. Conclusion 86
References 87
Chapter 4. Early Pressure Screens 90
I. Introduction 90
II. Rationale for Use of Early Pressure to Produce Diploid Embryos for Genetic Screens 91
III. Rationale for Use of Screens Focused on Specific Phenotypes 95
IV. Design of Our Screen and Mutant Phenotypes Isolated 95
V. Closing Remarks 101
References 102
Chapter 5. Retrovirus-Mediated Insertional Mutagenesis in Zebrafish 106
I. Introduction 106
II. Insertional Mutagenesis: A Pilot Screen 108
III. Considerations for a Large-Scale Screen 114
References 116
Chapter 6. Genetic Applications of Transposons and Other Repetitive Elements in Zebrafish 118
I. Introduction 118
II. Classification of Repetitive Elements 120
III. Genetic Applications of Repetitive Elements 132
IV. Summary and Perspectives 143
References 145
Chapter 7. Transgenesis 152
I. Introduction 152
II. Materials 153
III. Methods 155
IV. Discussion 165
References 166
Chapter 8. The Zebrafish Genome 168
I. Introduction 168
II. Mapping the Zebrafish Genome 169
III. The Zebrafish Gene Map 171
IV. Two Genes in Zebrafish for One in Mammals 176
V. Gene Nomenclature in Zebrafish 178
VI. Conclusions 179
References 180
Chapter 9. Using Random Amplified Polymorphic DNAs in Zebrafish Genomic Analysis 184
I. Introduction 184
II. What Are RAPDs? 185
III. Advantages and Disadvantages of RAPDs as Polymorphic Markers 189
IV. Methods for Developing RAPD Markers 190
V. Using RAPDs to Identify Markers Closely Linked to a Mutation 191
VI. Conversion of RAPD Markers to Sequence Tagged Sites 195
VII. Conclusions 196
References 196
Chapter 10. Simple Sequence-Length Polymorphism Analysis 200
I. Analysis in DNA Sequencing Gels 201
II. Alternative Analysis of SSLP-Containing PCR Product in High-Resolution Agarose Gels 201
III. Troubleshooting and Other Considerations 202
References 202
Chapter 11. Gene Mapping in Zebrafish Using Single-Strand Conformation Polymorphism Analysis 204
I. Introduction 204
II. SSCP Methodology 206
III. Gene Mapping 208
IV. Methods 209
References 211
Chapter 12. Mapping Zebrafish Mutations by AFLP 214
I. Introduction 214
II. Extraction of Zebrafish Genomic DNA 217
III. AFLP Methods 218
IV. General Considerations 228
References 229
Chapter 13. Zebrafish Expressed Sequence Tags and Their Applications 232
I. Introduction 232
II. Procedure of cDNA Clone Tagging 233
III. Management of Tagged cDNA Clones 239
IV. Applications of Tagged cDNA Clones 242
References 251
Chapter 14. Zebrafish YAC, BAC, and PAC Genomic Libraries 254
I. Introduction 255
II. Cloning Systems 255
III. Available Zebrafish Genomic Libraries and the Need for Multiple Libraries 258
IV. Screening Methods 260
V. Positional Cloning Using YAC, BAC, and PAC Libraries 262
VI. Further Applications of YAC, BAC, and PAC Resources to Zebrafish Genetics 269
VII. Summary 270
Internet Web Sites Relevant to YAC, BAC, and PAC Cloning 271
References 271
Chapter 15. Positional Cloning of Mutated Zebrafish Genes 278
I. Introduction 279
II. Initiating a Positional Cloning Project 281
III. Isolating Genomic Clones and Defining the Critical Region 291
IV. Gene Discovery 298
References 303
Chapter 16. Construction and Characterization of Zebrafish Whole Genome Radiation Hybrids 306
I. Introduction 307
II. Basic Protocol: Construction of Radiation Hybrids 307
III. Characterization of Radiation Hybrids by PCR 311
IV. Characterization of Radiation Hybrids Using FISH Analysis 313
V. Commentary 317
VI. Critical Parameters and Troubleshooting 318
References 321
Chapter 17. Zebrafish/Mouse Somatic Cell Hybrids for the Characterization of the Zebrafish Genome 322
I. Introduction 323
II. Production of Zebrafish/Mouse Somatic Cell Hybrids 323
III. Analysis of Zebrafish Chromosomes in Hybrid Cells by Fluorescence in Situ Hybridization 327
IV. Identification of Chromosomes in Hybrids Using PCR 332
V. Inter-DANA/Mermaid PCR on Hybrids 336
VI. Stability of Zebrafish/Mouse Hybrids 337
VII. Perspectives 338
References 339
Chapter 18. Banded Chromosomes and the Zebrafish Karyotype 342
I. Introduction 342
II. Methods 343
III. Results and Discussion 351
References 355
Chapter 19. Zebrafish Informatics and the ZFIN Database 358
I. Introduction 358
II. Database Design Process 359
III. The Data Model and the Contents of the Database 361
IV. Using the ZFIN Database 370
References 373
Appendix 1. Genetic Backgrounds and Some Standard Stocks and Strains Used in Zebrafish Developmental Biology and Genetics 376
Summary of Genetic Backgrounds 376
References 378
Appendix 2. Centromeric Markers in the Zebrafish 380
References 382
Appendix 3. Collection, Storage, and Use of Zebrafish Sperm 384
I. Introduction 384
II. Materials 385
III. Collection of Zebrafish Sperm 387
IV. Cryopreservation of Zebrafish Sperm 388
V. In Vitro Fertilization 389
VI. General Considerations 390
References 391
Appendix 4. Zebrafish Web Site Listings 392
Zebrafish Web Servers 392
Lab URLs 393
Index 406
Color Plate Sections 416