Rajewsky / Jurga / Barciszewski Plant Epigenetics

1. Auflage 2017
ISBN: 978-3-319-55520-1
Verlag: Springer International Publishing
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 540 Seiten

Reihe: RNA Technologies

This book presents, in 26 chapters, the status quo in epigenomic profiling. It discusses how functional information can be indirectly inferred and describes the new approaches that promise functional answers, collectively referred to as epigenome editing. It highlights the latest important advances in our understanding of the functions of plant epigenomics and new technologies for the study of epigenomic marks and mechanisms in plants. Topics include the deposition or removal of chromatin modifications and histone variants, the role of epigenetics in development and response to environmental signals, natural variation and ecology, as well as applications for epigenetics in crop improvement. Discussing areas ranging from the complex regulation of stress and heterosis to the precise mechanisms of DNA and histone modifications, it presents breakthroughs in our understanding of complex phenotypic phenomena.


?Prof. Dr. Nikolaus Rajewsky,Berlin Inst. for Medical Systems Biology, MaxDelbrückCenter for Molecular Medicine,Berlin-Buch,[e-mail]
Prof. Dr. Stefan Jurga, Adam Mickiewicz University, Nanobiomedical Center,Poznan,[e-mail]
Prof. Dr. Jan Barciszewski, Polish Academy of Sciences,Institute of Bioorganic Chemistry,Poznan,[e-mail]

Autoren/Hrsg.

Rajewsky, Nikolaus

Jurga, Stefan

Barciszewski, Jan

Inhaltsverzeichnis

1;Preface;6
1.1;Plant Epigenetics: From Genotype to Phenotype;6
2;Contents;9
3;Conservation, Divergence, and Abundance of MiRNAs and Their Effect in Plants;12
3.1;1 Introduction;13
3.2;2 General Aspects of MiRNAs;13
3.3;3 Biogenesis and Action of MiRNAs;14
3.4;4 Classification, Conservation, Divergence, and Abundance of MiRNAs in Plants;16
3.5;5 MiRNA Functions in Plants;18
3.6;6 Pleiotropic Effects of MiRNAs;26
3.7;7 Conclusions and Future Prospects;27
3.8;References;27
4;The Role of MiRNAs in Auxin Signaling and Regulation During Plant Development;34
4.1;1 Introduction;35
4.1.1;1.1 Auxins;35
4.1.2;1.2 MiRNAs;37
4.2;2 Biogenesis and Function of MiRNAs in Plants;40
4.3;3 Evolution of Plant MicroRNA Genes;42
4.4;4 Gene Regulation by MicroRNAs in Plants;44
4.5;5 MiRNAs in Auxins Signaling and Homeostasis;45
4.5.1;5.1 Auxin Homeostasis and MiRNAs;47
4.5.2;5.2 Auxin Signaling and MiRNAs;48
4.6;6 Role of MiRNA in Plant Growth and Development Mediated by Auxins;49
4.7;7 Concluding Remarks;51
4.8;References;52
5;Growing Diversity of Plant MicroRNAs and MIR-Derived Small RNAs;60
5.1;1 Introduction;61
5.2;2 Micro RNAs in the Plant Small RNA World;61
5.3;3 MiRNA-Mediated DNA Methylation;63
5.3.1;3.1 First Evidences for an Indirect Link Between MiRNAs and DNA Methylation;64
5.3.2;3.2 MIR-Derived sRNAs: The Real Players in MiRNA-Mediated DNA Methylation;65
5.4;4 Epigenetic Control of MIR Genes;67
5.4.1;4.1 Impact of Histone Modifications of MIR Loci on MiRNA Expression;67
5.4.2;4.2 DNA Methylation of MIR Genes Affects MiRNA Expression;68
5.4.3;4.3 Link Between MIR Gene DNA Methylation and Plant Stress Response;69
5.5;5 Computational Tools for Plant MiRNA Analysis from NGS Datasets;70
5.6;References;74
6;An Evolutionary View of the Biogenesis and Function of Rice Small RNAs;79
6.1;1 Introduction;80
6.2;2 Evolution of Core RNA Interference (RNAi) Pathway Genes in Rice;81
6.2.1;2.1 Dicer-Like;83
6.2.2;2.2 RNA-Dependent RNA Polymerases;84
6.2.3;2.3 Hua Enhancer 1;84
6.2.4;2.4 Argonaute;85
6.3;3 Evolution of Rice Small RNAs and Their Targets;86
6.3.1;3.1 Canonical miRNAs;86
6.3.1.1;3.1.1 Evolution of miRNAs in AA Genome Oryza Species;86
6.3.1.2;3.1.2 MiRNA Genes Under Positive Selection in Cultivated Rice;87
6.3.1.3;3.1.3 MiRNA Targets Under Positive Selection in Cultivated Rice;90
6.3.2;3.2 Long miRNAs;90
6.3.3;3.3 Phased siRNAs;91
6.3.4;3.4 Heterochromatic siRNAs;92
6.4;4 Conclusions and Future Prospects;93
6.5;References;93
7;Small RNAs: Master Regulators of Epigenetic Silencing in Plants;99
7.1;1 Introduction;100
7.2;2 Nuclear sRNA-Dependent Gene Silencing;102
7.3;3 Small RNA-Directed DNA Methylation in Plants;105
7.4;4 Mechanism of Transposon Repression by sRNAs and Silencing of Transposons;109
7.5;5 Conclusion and Future Perspectives;110
7.6;References;111
8;Small RNA Biogenesis and Degradation in Plants;117
8.1;1 Introduction;118
8.2;2 miRNA Biogenesis in Plants;118
8.3;3 The Biogenesis of ta-siRNAs and pha-siRNAs;121
8.4;4 The Biogenesis of Natural cis-antisense siRNAs (nat-siRNAs);123
8.5;5 The Production of sRNAs Involved in RNA-Direct DNA Methylation (RdDM);124
8.5.1;5.1 The Biogenesis of Canonical ra-siRNAs;124
8.5.2;5.2 The Biogenesis of Non-canonical sRNAs Involved in RdDM;125
8.6;6 Methylation Stabilizes miRNAs and siRNAs;126
8.7;7 Uridylation Triggers the Degradation of siRNAs and miRNAs;128
8.8;8 Exoribonucleases Degrading sRNAs in Plants;129
8.9;9 Perspective;130
8.10;References;131
9;Plant Epigenetics: Non-coding RNAs as Emerging Regulators;138
9.1;1 Introduction;139
9.2;2 MicroRNAs in Plants;140
9.3;3 Small Interfering RNAs (siRNAs);141
9.3.1;3.1 Secondary SiRNAs;141
9.3.2;3.2 Heterochromatic SiRNAs and RNA-Directed DNA Methylation;143
9.4;4 Long Non-Coding RNAs;145
9.4.1;4.1 Plant LncRNAs, Professional Hijackers;147
9.4.2;4.2 LncRNAs Mediate Chromatin Modifications and Remodeling;149
9.4.3;4.3 LncRNAs and Epigenomic Regulation of Flowering;150
9.4.4;4.4 LncRNAs Link Hormone Signaling with Chromatin Modifications and Genome 3D-Conformation;151
9.5;5 Concluding Remarks;151
9.6;References;152
10;Genome-Wide Function Analysis of lincRNAs as miRNA Targets or Decoys in Plant;157
10.1;1 Introduction;158
10.2;2 Materials;159
10.2.1;2.1 Hardware Requirements;159
10.2.2;2.2 Software Requirements;159
10.2.3;2.3 Data Resources;159
10.3;3 Methods;161
10.3.1;3.1 Identification of Unique Maize miRNAs;161
10.3.2;3.2 Set up the Relationship Between Unique miRNAs and lincRNAs;162
10.3.3;3.3 Set up the Relationship Between Unique miRNAs and mRNAs;162
10.3.4;3.4 Functional Prediction of lincRNAs Acting as miRNA Targets Based on the lincRNA-mRNA Co-expression Networks;163
10.3.4.1;3.4.1 Identification of lincRNAs Acting as miRNA Targets;163
10.3.4.2;3.4.2 Construction of lincRNA-mRNA Co-expression Networks;164
10.3.4.3;3.4.3 Functional Prediction of lincRNAs as miRNA Targets;165
10.3.5;3.5 Functional Prediction of lincRNAs Acting as miRNA Decoys Based on CeRNA Hypothesis;166
10.3.5.1;3.5.1 Identification of mRNAs Acting as miRNA Targets;166
10.3.5.2;3.5.2 Identification of lincRNAs as miRNA Decoys;166
10.3.5.3;3.5.3 Functional Prediction of lincRNAs as miRNA Decoys Based on CeRNA Hypothesis;168
10.4;4 Notes;168
10.5;References;169
11;Plant Non-coding RNAs and the New Paradigms;171
11.1;1 Introduction;172
11.2;2 LncRNAs;173
11.2.1;2.1 LncRNA Transcriptional Activity;173
11.2.2;2.2 LncRNA Posttranscriptional Activity;175
11.2.3;2.3 LncRNAs: Non-coding Transcripts or Dual RNAs?;177
11.3;3 MiRNAs;178
11.3.1;3.1 MiRNAs: Specialized Products of LncRNAs;178
11.3.2;3.2 MiRNA Activity;181
11.3.3;3.3 Function of MiRNA-Guided Translation Inhibition;183
11.4;4 Conclusion;185
11.5;References;185
12;Epigenetic Regulation by Noncoding RNAs in Plant Development;191
12.1;1 Introduction;192
12.2;2 Diverse Noncoding RNAs;192
12.3;3 miRNAs and Epigenetics in Plant;193
12.3.1;3.1 MiRNAs and Vegetable Organ Development;193
12.3.2;3.2 miRNAs and Floral Transition;195
12.3.3;3.3 miRNAs and Male Reproductive Development;195
12.3.4;3.4 miRNAs and Female Reproductive Development;197
12.4;4 lncRNAs and Epigenetics in Plant;198
12.4.1;4.1 lncRNAs Discoveries in Different Plant Model Species;198
12.4.2;4.2 The Regulation Pathways of lncRNAs Related to Plant Development;199
12.4.3;4.3 lncRNAs in Reproductive Development;200
12.4.4;4.4 Stress-Responsive lncRNAs in Plants;201
12.5;5 Conclusion and Prospects;202
12.6;References;203
13;RNAi Suppressors: Biology and Mechanisms;207
13.1;1 Introduction;209
13.2;2 RNAi and the Suppressors;209
13.3;3 Antiviral RNAi;210
13.3.1;3.1 Viral SiRNA Generation;210
13.3.2;3.2 Transcriptional Control of Viral Genes;212
13.3.3;3.3 Post-transcriptional Control of Viral Proteins;213
13.3.3.1;3.3.1 Post-transcriptional Gene Silencing;213
13.3.3.2;3.3.2 Host MiRNA Control of Viral Genes;214
13.4;4 Viral Counterstrategy;217
13.4.1;4.1 Earlier Experiments to Confirm RNA Silencing Suppression;217
13.4.2;4.2 Assays to Detect RNA Silencing Suppressors;218
13.4.2.1;4.2.1 Agrobacterium-Mediated Transient Assay;218
13.4.2.2;4.2.2 Reversal of Transgene Induced Silencing;219
13.4.2.3;4.2.3 Crossing Assay;219
13.4.2.4;4.2.4 Grafting Assay;219
13.4.2.5;4.2.5 Specific Biochemical Assays;220
13.5;5 Functional Mechanism of Viral Suppressors of RNAi;220
13.5.1;5.1 Interaction Between DsRNA-VSRs;220
13.5.2;5.2 Viral Suppressors Target RNAi Effectors;221
13.5.3;5.3 Suppression of Systemic RNAi by VSRs;221
13.5.4;5.4 Epigenetic Modifications;221
13.6;6 Few Representative VSRs;222
13.6.1;6.1 HC-Pro of Potyviruses;222
13.6.2;6.2 Cucumoviruses 2b (CMV-2b);223
13.6.3;6.3 Tombusviruses P19;224
13.6.4;6.4 Geminivirus AC2;225
13.6.5;6.5 Polerovirus P0;227
13.7;7 Disease or Pathogenicity: Host MicroRNA Dysregulation and Affected Functions;227
13.8;8 VSR-Targeted Antiviral Strategy;228
13.8.1;8.1 Artificial MiRNA Strategy;228
13.8.2;8.2 Artificial TasiRNA Strategy;229
13.9;9 Future Perspectives;229
13.10;References;231
14;Analysis of Nucleic Acids Methylation in Plants;239
14.1;1 General Functions of DNA and RNA Methylation in Plants;240
14.1.1;1.1 DNA Cytosine Methylation in Plants;240
14.1.2;1.2 RNA Cytosine Methylation in Plants;240
14.1.3;1.3 RNA Adenine Methylation in Plants;241
14.2;2 Global Detection of DNA and RNA Methylation in Plants;241
14.2.1;2.1 Liquid Chromatography;241
14.2.2;2.2 Liquid Chromatography-Mass Spectrometry;243
14.2.3;2.3 Capillary Electrophoresis;244
14.2.4;2.4 Thin Layer Chromatography;244
14.2.5;2.5 Immuno-Based Detection;245
14.3;3 Location Analysis of DNA and RNA Methylation in Plants;245
14.3.1;3.1 Affinity Enrichment-Sequencing Analysis;246
14.3.2;3.2 Bisulfite Conversion-Sequencing Analysis;247
14.3.3;3.3 Single-Molecule Detection;249
14.4;4 Conclusions and Perspectives;249
14.5;References;250
15;DNA Methylation in Plants by microRNAs;254
15.1;1 Introduction;255
15.2;2 DNA Methylation by 20-22 nt Canonical miRNAs;257
15.2.1;2.1 In Arabidopsis;257
15.2.2;2.2 In Moss;257
15.3;3 DNA Methylation by siRNAs Produced from miRNA Loci;258
15.4;4 DNA Methylation by lmiRNAs;260
15.5;5 DNA Methylation by siRNAs or lmiRNAs Originating from miRNA Genes Located in the Introns;261
15.6;6 DNA Methylation by miRNA-Triggered TAS/PHAS Loci-Derived siRNAs;261
15.7;7 miRNA-Triggered easiRNA Biogenesis to Prevent RDR2-Dependent RdDM;263
15.8;8 miRNAs Directly Regulating Players of Methylation;264
15.9;9 Conclusions and Perspectives;264
15.10;References;267
16;DNA Methylation in Plants and Its Implications in Development, Hybrid Vigour, and Evolution;270
16.1;1 Introduction;271
16.1.1;1.1 The Machinery of DNA Methylation and Demethylation;271
16.1.2;1.2 Features and Distribution of DNA Methylation in Plants;272
16.1.3;1.3 General Aspects of the Possible Roles of DNA Methylation in Plants;274
16.2;2 Patterns of DNA Methylation Are Proposed to Change in Response to Environmental Stresses;275
16.2.1;2.1 Some Examples of Responses to Biotic and Abiotic Stresses;276
16.3;3 DNA Methylation During Plant Development;277
16.3.1;3.1 Does DNA Methylation Change During Development and Among Plant Tissues?;278
16.4;4 DNA Methylation and Its Suggested Role for Evolution in Plants;279
16.5;5 Proposed Function and Evidences for the Influence of the Epigenetic State in Heterosis;280
16.6;6 Conclusions and Perspectives;281
16.7;References;282
17;Dynamic DNA Methylation Patterns in Stress Response;288
17.1;1 Introduction;289
17.2;2 DNA Methylation in Plants;290
17.3;3 Genome-Wide DNA Methylation Under Stress;291
17.3.1;3.1 Correlation of DNA Methylation Patterns with Stress Tolerance of Different Genotypes;293
17.3.2;3.2 Inheritable Changes in DNA Methylation Patterns in Plants Subjected to Stress;294
17.4;4 Involvement of DNA Methylation Changes in the Control of Stress-Responsive Genes;296
17.4.1;4.1 Changes in DNA Methylation of Specific Stress-Responsive Genes;296
17.4.2;4.2 Hierarchic Control of DNA Methylation in the Induction of Stress-Related Genes;299
17.5;5 Regulation of Dynamics of DNA Methylation Under Stress;301
17.6;6 Conclusions;303
17.7;References;304
18;Locus-Specific DNA Methylation Analysis and Applications to Plants;310
18.1;1 Introduction;311
18.2;2 DNA Methylation in Plants;312
18.2.1;2.1 Generalities;312
18.2.2;2.2 Distribution of DNA Methylation in Plants;313
18.2.3;2.3 Differences Between Plant Genomes;314
18.3;3 Locus-Specific DNA Methylation Analysis Methods;315
18.3.1;3.1 Methods Not Involving Sodium Bisulfite Conversion;315
18.3.1.1;3.1.1 Methods Involving Methylation-Sensitive Restriction Enzyme and PCR;315
18.3.1.2;3.1.2 Methods Involving Anti-meCytosine Antibody and PCR;318
18.3.2;3.2 Methods Involving Sodium Bisulfite Conversion;319
18.3.2.1;3.2.1 Bisulfite Conversion;320
18.3.2.2;3.2.2 Primer Design;321
18.3.2.3;3.2.3 Methods Without Sequencing;322
18.3.2.3.1;High Resolution Melting Analysis;323
18.3.2.3.2;Other Methods;323
18.3.2.4;3.2.4 Methods Including Sequencing Experiments;324
18.3.2.4.1;Cloning Combined to Sanger Sequencing;324
18.3.2.4.2;Pyrosequencing;326
18.4;4 Conclusion: Perspectives;328
18.5;References;329
19;Epigenetics in Plant Reproductive Development: An Overview from Flowers to Seeds;335
19.1;1 Introduction;336
19.2;2 Flowering and Pollen Development;338
19.3;3 Flower and Fruit Development;339
19.3.1;3.1 Histone Acetylation Mediated Regulation;339
19.3.2;3.2 DNA Methylation-Mediated Regulation;341
19.3.3;3.3 MiRNA Mediated Regulation;342
19.4;4 Fruit Ripening;344
19.4.1;4.1 DNA Methylation-Mediated Regulation;346
19.4.2;4.2 MiRNA Mediated Regulation;347
19.4.3;4.3 LncRNA Mediated Regulation;348
19.5;5 Seed Development;349
19.5.1;5.1 Seed Dormancy;350
19.5.2;5.2 Embryo-Endosperm Interaction;353
19.5.3;5.3 Genomic Imprinting;355
19.6;6 Conclusions and Future Prospects;356
19.7;References;357
20;Epigenetic Regulation of Phase Transitions in Arabidopsis thaliana;364
20.1;1 Introduction;365
20.2;2 Epigenetic Regulation of the Embryo-to-Seedling Transition;368
20.3;3 Epigenetic Regulation of the Juvenile-to-Adult and Vegetative-to-Reproductive Transitions;372
20.4;4 Epigenetic Reprogramming;377
20.5;5 Conclusions and Future Prospects;379
20.6;References;382
21;Epigenetics in Plant-Pathogen Interactions;389
21.1;1 Introduction;390
21.2;2 Epigenetic Modification Marks in Plants;391
21.2.1;2.1 DNA Methylation;391
21.2.2;2.2 Histone Modifications;393
21.3;3 Overview of Gene/Genomic Regulation in Plants Based on Epigenetics;394
21.3.1;3.1 Control of Developmental Switches: Vegetative to Reproductive Transition;394
21.3.2;3.2 Silencing of Transposable Elements;395
21.3.3;3.3 The RNA Silencing Pathways Involved in TE Silencing: 24nt-Long and 22nt-Long siRNAs in RNA-Directed DNA Methylation;395
21.3.4;3.4 Parental Imprinting;396
21.3.5;3.5 Paramutation;397
21.3.6;3.6 Virus-Induced Gene Silencing;397
21.3.6.1;3.6.1 RdRM-Induced by Viral and Subviral Infectious Entities;399
21.3.6.2;3.6.2 Influence of Viral Silencing Suppressor on Virus-Induced RdRM;400
21.4;4 Epigenetic Modifications and Systemic Acquired Resistance;401
21.5;5 Conclusions and Perspectives;404
21.6;References;405
22;Epigenetic Reprogramming During Plant Reproduction;409
22.1;1 Introduction;410
22.2;2 Epigenetic Mechanisms Mediated by DNA Methylation;411
22.2.1;2.1 DNA Methylation by DNA Methyltransferases;411
22.2.2;2.2 DNA Demethylation by DEMETER Family Glycosylases;412
22.3;3 Epigenetic Mechanisms Mediated by Histone Modifications;412
22.3.1;3.1 Histone Modification by the PRC2;412
22.3.1.1;3.1.1 Endosperm Development;413
22.3.1.2;3.1.2 Seed to Seedling Phase Transition;413
22.3.1.3;3.1.3 Vegetative to Reproductive Phase Transition;414
22.3.1.4;3.1.4 Vernalization;414
22.4;4 Epigenetic Reprogramming During Arabidopsis Male Gametogenesis (Fig. 1);414
22.4.1;4.1 Microgametogenesis in Arabidopsis;414
22.4.2;4.2 Chromatin Reorganization During Pollen Mother Cell Differentiation;416
22.4.3;4.3 Chromatin Remodeling During Male Gametogenesis;416
22.4.4;4.4 Dynamic Changes of DNA Methylation During Male Gametogenesis;417
22.5;5 Epigenetic Reprogramming During Arabidopsis Female Gametogenesis (Fig. 2);419
22.5.1;5.1 Megagametogenesis in Arabidopsis;419
22.5.2;5.2 Mobile siRNAs During Megaspore Mother Cell Differentiation and Meiosis;420
22.5.3;5.3 Chromatin Reorganization During Megasporogenesis and Megagametogenesis;421
22.5.4;5.4 Active DNA Demethylation by the DEMETER Glycosylase in the Gametophytes;421
22.6;6 Conclusions and Future Perspectives;423
22.7;References;424
23;Rice Epigenomics: How Does Epigenetic Manipulation of Crops Contribute to Agriculture?;430
23.1;1 Introduction;431
23.2;2 Epigenome Regulation in Arabidopsis and Rice;432
23.3;3 Epigenome Regulation in Response to Abiotic Stresses;436
23.4;4 Stable Maintenance of Altered Epigenomic State for Agricultural Applications;438
23.5;5 Perspectives;439
23.6;References;440
24;Epigenetic Characterization of Satellite DNA in Sugar Beet (Beta vulgaris);447
24.1;1 Introduction: Sugar Beet (Beta vulgaris) and Its Wild Relatives;448
24.2;2 Genomes, Chromosomes and Satellite DNAs;449
24.3;3 Satellite DNAs Are a Major Repeat Class in Sugar Beet Heterochromatin and Centromeric Chromatin;450
24.4;4 Epigenetic Characterization of Satellite DNA Suggests Their Potential Function in the Establishment and Maintenance of Heter...;454
24.5;5 Satellite DNA-Directed Heterochromatization;459
24.6;6 Conclusion;461
24.7;References;462
25;Universal and Lineage-Specific Properties of Linker Histones and SWI/SNF-Chromatin Remodeling Complexes in Plants;465
25.1;1 Introduction: Chromatin in Plants and Animals: Commonalities and Differences After Over One Billion Years of Separate Evolut...;466
25.2;2 Linker Histones and SWI/SNF Remodeling Complexes in Chromatin Organization and Regulatory Mechanisms: Conclusions from Studi...;467
25.2.1;2.1 Linker Histones;467
25.2.2;2.2 SWI/SNF Chromatin Remodeling Complexes;470
25.2.2.1;2.2.1 Mechanisms of Chromatin Remodeling;471
25.2.2.2;2.2.2 Biological Roles of SWI/SNF Remodelers;473
25.2.2.3;2.2.3 Targeting of SWI/SNF Complexes to Specific Sites in the Genome;474
25.3;3 Linker Histones in Plants;475
25.3.1;3.1 Structural Features and Phylogenetic Relationships Distinguishing Plant H1s;475
25.3.2;3.2 Universally Conserved and Lineage-Specific Functions of Plant H1s;478
25.4;4 SWI/SNF Complexes in Plants;480
25.4.1;4.1 Composition of Plant SWI/SNF Complexes;480
25.4.2;4.2 Biological Roles of Plant SWI/SNF Complexes;482
25.4.3;4.3 Mechanisms Underlying the Functions and Targeting of Plant SWI/SNF Complexes;483
25.5;5 Are Linker Histones and Chromatin Remodeling Structurally and Functionally Coupled?;486
25.6;6 Concluding Remarks;488
25.7;References;488
26;Abiotic Stress Induced Epigenetic Modifications in Plants: How Much Do We Know?;495
26.1;1 Introduction;497
26.2;2 The Pillars of Epigenetics;498
26.2.1;2.1 DNA Methylation;498
26.2.2;2.2 Histone Modifications;500
26.2.3;2.3 Small RNAs;500
26.3;3 RNA-Directed DNA Methylation Pathway;501
26.4;4 Chromatin Modifications;502
26.5;5 Abiotic Stress Directed Epigenetic Changes;502
26.5.1;5.1 Stress Memory;503
26.6;6 Abiotic Stressors;504
26.6.1;6.1 Salt Stress;504
26.6.2;6.2 Drought Stress;505
26.6.3;6.3 Heat Stress;506
26.6.4;6.4 Submergence Stress;507
26.6.5;6.5 Cold Stress;508
26.6.6;6.6 Heavy Metal Stress;509
26.7;7 Conclusion and Future Prospectus;509
26.8;References;510
27;Apple Latent Spherical Virus (ALSV) Vector as a Tool for Reverse Genetic Studies and Non-transgenic Breeding of a Variety of C...;515
27.1;1 Introduction: Significance of ALSV Vector in Plant Reverse Genetics and Epigenetic Breeding Technology;516
27.2;2 Characteristics of the ALSV Vector;517
27.3;3 Practical Protocol for Preparation and Infection of ALSV Vector;523
27.3.1;3.1 Vector Preparation;523
27.3.2;3.2 Agroinoculation of N. benthamiana;523
27.3.2.1;3.2.1 Preparation of Agrobacterium Cultures;523
27.3.2.2;3.2.2 Pre-treatment of Agrobacterium;524
27.3.2.3;3.2.3 Agroinoculation;524
27.3.3;3.3 RT-PCR Analysis for Detection of ALSV Infection;524
27.3.3.1;3.3.1 Sampling of Leaves;524
27.3.3.2;3.3.2 RNA Extraction;526
27.3.3.3;3.3.3 RT-PCR Analysis;526
27.3.4;3.4 Rub-inoculation of Leaf Sap onto C. quinoa;527
27.3.4.1;3.4.1 Sampling of N. benthamiana Leaves;527
27.3.4.2;3.4.2 Rub-inoculation;528
27.3.5;3.5 Bentonite Solution;528
27.3.5.1;3.5.1 Preparation of Phosphate Buffers;528
27.3.5.2;3.5.2 Preparation of Bentonite Solution;528
27.3.6;3.6 Virus Extraction;529
27.3.6.1;3.6.1 Crushing Infected Leaves in Blender;529
27.3.6.2;3.6.2 Rough Purification by Using Bentonite Solution;529
27.3.6.3;3.6.3 Preparation of Virus Particle;530
27.3.6.4;3.6.4 Extraction of Viral RNA;530
27.3.7;3.7 Preparation of Gold Particle;530
27.3.7.1;3.7.1 Mixing Viral RNA with Gold Particle;531
27.3.7.2;3.7.2 Preparation of RNA-coated Gold Particle;531
27.3.8;3.8 Particle Bombardment with NepaGene System;531
27.3.8.1;3.8.1 Setting up the Gene Gun;531
27.3.8.2;3.8.2 Shooting Gold Particle;532
27.3.8.3;3.8.3 RT-PCR Analysis;533
27.4;4 Application of ALSV Vector for Gene Expression and Gene Silencing;533
27.5;5 Application of ALSV Vector for Transcriptional Gene Silencing;534
27.6;References;537
28;Erratum to: Growing Diversity of Plant MicroRNAs and MIR-Derived Small RNAs;539