The handbook of plant mutation screening: mining of natural and induced alleles
Gespeichert in:
| Weitere Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Weinheim
Wiley-VCH
2010
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| Schriftenreihe: | Molecular plant biology handbook series
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| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | XXV, 435 S. Ill., graph. Darst. |
| ISBN: | 9783527326044 |
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Datensatz im Suchindex
| _version_ | 1805093864865792000 |
|---|---|
| adam_text |
EDITED BY KHALID MEKSEM AND GUNTER KAHL THE HANDBOOK OF PLANT MUTATION
SCREENING MINING OF NATURAL AND INDUCED ALLELES WILEY- VCH WILEY-VCH
VERLAG GMBH & CO. KGAA VII 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 ML
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 THE HANDBOOK OF PLANT
MUTATION SCREENING. EDITED BY GUNTER KAHL AND KHALID MEKSEM COPYRIGHT
2010 WILEY-VCH VERLAG GMBH & CO. KGAA, WEINHEIM ISBN: 978-3-527-32604-4
VIII CONTENTS 3 USE OF MUTANTS FROM T-DNA INSERTION POPULATIONS
GENERATED BY HIGH-THROUGHPUT SCREENING 31 RALF STRACKE, CUNNAR 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 TL SEED
HARVESTING 35 3.2.5 SULFADIAZINE SELECTION OF TRANSGENIC T 1 PLANTS 36
3.2.6 DNA PREPARATION FROM SULFADIAZINE-SELECTED TL 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. CESTL 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
CONTENTS IX 4.3.3 MUTARIONAL PROCESSING OF ALKYLATION DAMAGE BY DNA
POLYMERASES 75 4.3.4 DNA LESION DISCRIMINATION MECHANISMS 75 4.4
PERSPECTIVES 78 REFERENCES 79 5 TNTL INDUCED MUTATIONS IN MEDICAGO:
CHARACTERIZATION AND APPLICATIONS 83 PASCAL RATET, JIANGQI WEN, VIVIANE
COSSON, MILLION TADEGE, AND KIRANKUMAR S. MYSORE INTRODUCTION 83 METHODS
AND PROTOCOLS 84 IDENTIFICATION OF TNTL INSERTION SITES 84 REVERSE
GENETIC APPROACH 94 FST SEQUENCING 94 SCREENING DNA POOLS 94
APPLICATIONS 95 LINE WITH A MUTANT PHENOTYPE - NO FSTS IDENTIFIED 96
LINE WITH A MUTANT PHENOTYPE AND FSTS ALREADY IDENTIFIED 96 FST SEQUENCE
IN THE TNTL DATABASE MATCHES A GENE OF INTEREST - NO MUTANT PHENOTYPE IS
DESCRIBED IN THAT LINE 97 HAVE A GENE TO WORK WITH - NO FST OR MUTANT
PHENOTYPE 97 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, CEORGINA SALLMANN, AND RICHARD C.H.
COTTON 7.1 INTRODUCTION 121 7.2 METHODS AND PROTOCOLS 125 5.1 5.2 5.2
5.2 5.2 5.2 5.3 5.3 5.3 5.3 5.3 5.4 .1 .2 .2.1 .2.2 .1 .2 .3 .4 CONTENTS
7.3 7.4 8 8.1 8.2 8.3 8.4 APPLICATIONS 127 PERSPECTIVES 127 REFERENCES
128 MUTATION DETECTION IN PLANTS BY ENZYMATIC MISMATCH CLEAVAGE 131
BRADLEYJ. TILL INTRODUCTION 131 METHODS AND PROTOCOLS 136 APPLICATIONS
143 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, CUDRUN H. REED, MIKEAL WALL, ROBERT A. PALAIS,
ROBERT L JANET, 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 LUNAPROBE* (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 NEXTGENE* AND NEXT-GENERATION SEQUENCE
TECHNOLOGIES 175 10.4 MUTATION DETECTION WITH DNA FRAGMENTS USING
GENEMARKER 180 10.5 PERSPECTIVES 182 REFERENCES 182 CONTENTS XI 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
KEYPOINT* TECHNOLOGY 199 DIANA RIGOLA AND MICHIELJ.T. VAN EIJK
INTRODUCTION 199 METHODS AND PROTOCOLS 202 APPLICATIONS 206 EMS MUTATION
SCREENING AND VALIDATION 206 NATURAL POLYMORPHISM SCREENING AND
VALIDATION 208 PERSPECTIVES 211 REFERENCES 211 APPLICATIONS IN PLANT
BREEDING 215 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 BRIEF REVIEW OF BARLEY MUTANTS 217
APPLICATIONS IN BREEDING 221 SINGLE NUCLEOTIDE POLYMORPHISM GENOTYPING
TO IDENTIFY CANDIDATE GENES FOR MUTANTS 223 RESOURCES 223 CASE STUDY;
TWO/SIX-ROW LOCUS IN BARLEY 224 CASE STUDY: GRAPHICAL GENOTYPING OF A
DISEASE RESISTANCE LOCUS 227 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 ANDRE BELO AND STANLEY D. LUCK 14.1
INTRODUCTION 231 14.2 METHODS AND PROTOCOLS 233 14.2.1 POPULATION FOR
ASSOCIATION MAPPING 233 12.1 12.2 12.3 12.3 12.3 12.4 PART 13 13.1 13.2
13.3 13.3 13.3 13.3 13.3 .1 .2 IV .1 .2 .3 .4 XII CONTENTS 14.2.2 14.2.3
14.2.4 14.3 14.3.1 14.3.2 14.4 GENOTYPING PHENOTYPING 234 234
STATISTICAL PROCEDURES 235 APPLICATIONS QTL MAPPIN LIMITATIONS
PERSPECTIVES REFERENCES 238 I VERSUS ASSOCIATION MAPPING 240 241 242 243
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)* BY SYNTHESIS
289 SCOTT JENKINS AND AVAK KAHVEJIAN 17.1 INTRODUCTION 289 17.2 METHODS,
PROTOCOLS, AND TECHNICAL PRINCIPLES 291 CONTENTS XIII 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 CUO, NINGXU, ZENGMIN LI, ANDJINGYUEJU 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 ANDJIALI 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
XIV CONTENTS 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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| id | DE-604.BV025554521 |
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| indexdate | 2024-07-20T10:34:16Z |
| institution | BVB |
| isbn | 9783527326044 |
| language | English |
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| physical | XXV, 435 S. Ill., graph. Darst. |
| publishDate | 2010 |
| publishDateSearch | 2010 |
| publishDateSort | 2010 |
| publisher | Wiley-VCH |
| record_format | marc |
| series2 | Molecular plant biology handbook series |
| spelling | The handbook of plant mutation screening mining of natural and induced alleles ed. by Khalid Meksem ... Weinheim Wiley-VCH 2010 XXV, 435 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Molecular plant biology handbook series Pflanzen (DE-588)4045539-7 gnd rswk-swf Screening (DE-588)4054045-5 gnd rswk-swf Mutation (DE-588)4170883-0 gnd rswk-swf Pflanzen (DE-588)4045539-7 s Mutation (DE-588)4170883-0 s Screening (DE-588)4054045-5 s DE-604 Meksem, Khalid 1967- (DE-588)11446748X edt text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3294532&prov=M&dok_var=1&dok_ext=htm Inhaltstext HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020154496&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | The handbook of plant mutation screening mining of natural and induced alleles Pflanzen (DE-588)4045539-7 gnd Screening (DE-588)4054045-5 gnd Mutation (DE-588)4170883-0 gnd |
| subject_GND | (DE-588)4045539-7 (DE-588)4054045-5 (DE-588)4170883-0 |
| title | The handbook of plant mutation screening mining of natural and induced alleles |
| title_auth | The handbook of plant mutation screening mining of natural and induced alleles |
| title_exact_search | The handbook of plant mutation screening mining of natural and induced alleles |
| title_full | The handbook of plant mutation screening mining of natural and induced alleles ed. by Khalid Meksem ... |
| title_fullStr | The handbook of plant mutation screening mining of natural and induced alleles ed. by Khalid Meksem ... |
| title_full_unstemmed | The handbook of plant mutation screening mining of natural and induced alleles ed. by Khalid Meksem ... |
| title_short | The handbook of plant mutation screening |
| title_sort | the handbook of plant mutation screening mining of natural and induced alleles |
| title_sub | mining of natural and induced alleles |
| topic | Pflanzen (DE-588)4045539-7 gnd Screening (DE-588)4054045-5 gnd Mutation (DE-588)4170883-0 gnd |
| topic_facet | Pflanzen Screening Mutation |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=3294532&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020154496&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT meksemkhalid thehandbookofplantmutationscreeningminingofnaturalandinducedalleles |