Microbial Plant Pathogens-Detection and Disease Diagnosis: (eBook)

Viral and Viroid Pathogens, Vol.3

P. Narayanasamy (Autor)

eBook Download: PDF

2010 | 2011
XXI, 321 Seiten
Springer Netherland (Verlag)
978-90-481-9754-5 (ISBN)

Infos

The need for the development of techniques based on the characteristics of the viral proteins and genomic nucleic acids was realized in order to detect, identify, differentiate and quantify viruses in the infected plants/planting materials with or without symptoms of infection. Immunoassays have been successfully applied for the detection of viruses in crop and weed host plant species as well as in the vectors. Nucleic acid-based techniques have been demonstrated to be the most reliable and sensitive tests for detection, identification and differentiation of viruses and viroids present in plants and planting materials.. Inclusion of numerous protocols in appropriate chapters as appendix is a unique feature of this volume.

Inhalt

Preface 8
Acknowledgement 10
Contents 12
Table of Contents for Volumes 1 and 2 16
Volume 1 16
Volume 2 20
Chapter 1: Introduction 23
1.1 Microbial Plant Pathogens as a Major Limiting Factorof Crop Production 23
1.2 Discovery of Viruses and Viroids as Plant Pathogens 24
1.3 Detection of Viral and Viroid Plant Pathogens and Disease Diagnosis 25
References 26
Chapter 2: Detection of Virus and Viroid Pathogens in Plants 28
2.1 Detection of Plant Viruses in Plant Organs 29
2.1.1 Plant Virus Taxonomy 29
2.1.2 Biological Methods 30
2.1.2.1 Symptomatology 30
2.1.2.2 Mode of Transmission 35
Grafting and Budding 36
Mechanical Transmission 37
Transmission by Vectors 39
2.1.2.3 Cross-Protection 40
2.1.3 Morphological Characteristics 41
2.1.3.1 Negative Staining 41
2.1.3.2 Dip Method 44
2.1.4 Physical and Biochemical Techniques 46
2.1.5 Immunoassays 48
2.1.5.1 Enzyme-Linked Immunosorbent Assay 52
2.1.5.2 Dot Immunobinding Assay 64
2.1.5.3 Tissue Blot Immunoassay 66
2.1.5.4 Immunoblot Assay 71
2.1.5.5 Cytofluorimetric Technique 78
2.1.5.6 Immunochromatographic Assay 78
2.1.5.7 Microscopy-Based Immunoassays 79
Light Microscopy 79
Leaf-Dip Serology 79
Immunoelectron Microscopy 80
Immunosorbent Electron Microscopy and Gold Labeling Techniques 80
Decoration Technique 82
2.1.5.8 Artificial Neural Network Selection Technique 84
2.1.6 Nucleic Acid-based Techniques 85
2.1.6.1 Nucleic Acid Hybridization Techniques 85
2.1.6.2 Polymerase Chain Reaction-Based Methods 93
2.1.6.3 Real-Time PCR Assay 129
2.1.6.4 Molecular Beacon Technique 134
2.1.6.5 Single-Strand Conformation Polymorphism (SSCP) Analysis 136
2.1.6.6 Double-Stranded RNA Analysis 137
2.1.6.7 Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) Technique 139
2.1.6.8 Heteroduplex Mobility Analysis 141
2.1.6.9 DNA Array Technology 142
2.1.6.10 Next-Generation Sequencing and Metagenomic Analysis 143
2.2 Detection of Viroids in Plant Organs 144
2.2.1 Molecular Characteristics 144
2.2.2 Biological Methods 145
2.2.3 Physico-Chemical Methods 147
2.2.3.1 Phloroglucinol Test 147
2.2.3.2 Polyacrylamide Gel Electrophoresis Technique 148
2.2.4 Immunoassays 149
2.2.5 Nucleic Acid-based Techniques 150
2.2.5.1 Nucleic Acid Hybridization Techniques 150
2.2.5.2 RT-PCR Assay 154
2.3 Detection of Viral Pathogens in Seeds and Planting Materials 162
2.3.1 Detection of Viruses in Seeds 163
2.3.1.1 Biological Methods 163
2.3.1.2 Immunoassays 164
Enyzme-Linked Immunosorbent Assay 164
Dot Immunobinding Assay 167
Fluorescent Antibody Technique 168
Electron Microscopy-Based Immunoassays 169
2.3.1.3 Nucleic Acid-Based Techniques 169
Nucleic Acid Hybridization Technique 169
Reverse Transcription-Polymerase Chain Reaction Assay 171
2.3.2 Detection of Viruses in Asexually Propagated Planting Materials 173
2.3.2.1 Bioindexing Methods 174
2.3.2.2 Immunoassays 174
2.3.2.3 Nucleic Acid-Based Techniques 178
Nucleic Acid Hybridization Techniques 178
Reverse Transcription (RT)-PCR Assay 179
2.4 Detection of Viroids in Seeds and Planting Materials 185
2.4.1 Detection of Viroids in Seeds 185
2.4.1.1 Biological Methods 185
2.4.1.2 Nucleic Acid-Based Techniques 186
2.4.2 Detection of Viroids in Propagative Planting Materials 187
Appendix 1: Detection of Plant Viruses by Different Formats of Enzyme-Linked Immunosorbent Assay (ELISA) (Clark and Adams 1977) 189
Double-Antibody Sandwich (DAS)-ELISA 189
Direct Antigen Coating (DAC)-ELISA 189
Protein A-Coating ELISA 190
Indirect ELISA 190
Appendix 2: Detection of Grapevine leaf roll-associated virus-3 Using a Single-Chain Fragment Variable Antibody in ELISA (Cogotzi et al. 2009) 190
Appendix 3: Detection of Iris yellow spot virus (IYSV) by ELISA Incorporating a Blocking Agent (Smith et al. 2006) 191
Appendix 4: Detection of Cucumber mosaic virus (CMV) by Dot Immunobinding Assay (DIBA) (Zein and Miyatake 2009) 191
Appendix 5: Detection of Tomato spotted wilt virus (TSWV) in Different Tissues of Infected Plants by Tissue Blot Immunoassay (TBIA) (Whitefield et al. 2003) 192
Appendix 6: Detection of Citrus psorosis virus (CPsV) by Direct Tissue Blot Immunoassay (DTBIA) (Martin et al. 2002) 193
Appendix 7: Detection of Citrus psorosis virus (CPsV) by Western Blotting Technique (Loconsole et al. 2006) 193
Appendix 8: Detection of an Ampelovirus by Western Blot Analysis (Valverde et al. 1990 Maliogka et al. 2009)194
Extraction of ds-RNA from Virus-Infected Plants 194
Production of Virus-Specific Antiserum with Recombinant Coat Protein (CP) 194
Appendix 9: Detection of Phalaenopsis Orchid Viruses by Immunoblot Technique (Jan and Yeh 1995 Zheng et al. 2008a,b)195
Appendix 10: Detection of Passion fruit woodines virus (PWV) by Light Microscopic Staining Technique (Jan and Yeh 1995) 196
Appendix 11: Detection of Potato virus Y (PVY) by Immunohistochemistry Method (Ryang et al. 2004) 196
Appendix 12: Detection of Grapevine leaf roll-associated virus 3 (GLRaV-3) by Electron Microscopic Decoration Technique (Cogotzi et al. 2009) 196
Appendix 13: Detection of Grapevine fan leaf virus (GFLV) by RT-PCR Assay (Bashir and Hajizadeh 2007) 197
Extraction of Total RNA 197
Synthesis of First Strand cDNA 197
Polymerase Chain Reaction (PCR) 198
Appendix 14: Detection of Strawberry Viruses by Multiplex RT-PCR Assay (Chang et al. 2007) 198
Total Nucleic Acid Extraction 198
Extraction of Total RNA 198
Reverse Transcription (RT) Reaction 199
Polymerase Chain Reaction (PCR) 199
Duplelx PCR Assay 199
Multiplex PCR Assay 199
Appendix 15: Detection of Pepino mosaic virus (PepMV) by Multiplex One-Step RT-PCR Assay (Alfaro-Fernández et al. 2009) 200
Extraction of Total Nucleic Acids 200
Primers Employed 200
RT-PCR Assay 201
Appendix 16: Detection of Orchid Viruses by Multiplex RT-PCR Assay (Lee and Chang 2006) 201
Simplex RT-PCR Assay 201
Multiplex RT-PCR Assay 202
Agarose Gel Electrophoresis 202
Appendix 17: Detection of Orchid Viruses by Multiplex RT-PCR Assay Using Simple-Direct-Tube (SDT) Method for RNA Extraction (Suehiro et al. 2005 Yamane et al.2008)202
Extraction of Total RNA by SDT Method 202
Multiplex RT-PCR Assay 203
Appendix 18: Detection of Pepper Tobamoviruses by Immunocapture (IC)-RT-PCR Assay (Kim et al. 2006) 203
Double Antibody Sandwich (DAS)-ELISA 203
Immunocapture RT-PCR Assay 204
Appendix 19: Detection of Florida hibiscus virus by Immunocapture (IC)-RT-PCR Assay (Kamenova and Adkins 2004) 204
Appendix 20: Detection of Potato virus Y (PVY) by PCR-ELISA Test (Hataya et al. 1994 Varveri 2000)205
Appendix 21: Detection of Plum pox virus (PPV) by Spot Real-Time PCR Assay (Capote et al. 2009) 205
Preparation of Crude Extracts 205
Spot Real-Time PCR Assay 205
Appendix 22: Detection of Strawberry vein banding virus (SVBV) by Real-Time NASBA Technique (Vašková et al. 2004) 206
Extraction of Nucleic Acids 206
Real-Time Nucleic Acid Sequence-Based Amplification (NASBA) 206
Appendix 23: Detection and Differentiation of Citrus tristeza virus (CTV) Isolates by Single-Strand Conformation Polymorphism (SSCP) Analysis 207
cDNA Synthesis 207
Single-Strand Conformation Polymorphism (SSCP) Analysis 207
Appendix 24: Isolation of ds RNA of Plant Viruses (Zhang et al. 1998) 207
Appendix 25: Detection of Plant RNA Viruses by Macroarray Technique (Agindotan and Perry 2007) 208
Extraction of Total RNA from Plants 208
Probes for Target cDNAs 208
Printing of Oligonucleotide Probes on Membranes 208
Labeling and Hybridization 209
Appendix 26: Detection of Peach latent mosaic viroid (PLMVd) by Hybridization Techniques (Hadidi et al. 1997) 209
Extraction of Total Nucleic Acids 209
Dot Blot Hybridization 210
Northern (RNA) Blot Hybridization 210
Appendix 27: Detection of Coconut cadang-cadang viroid (CCCVd) by Dot Blot Hybridization Technique (Vadamalai et al. 2009) 210
Extraction of Nucleic Acids Enriched with the Viroid 210
Dot Blot Hybridization Assay 211
Appendix 28: Detection of Coconut cadang-cadang viroid (CCCVd) by Ribonuclease Protection Assay (Vadamalai et al. 2009) 212
Appendix 29: Extraction of Citrus Viroids for Multiplex RT-PCR Assay (Wang et al. 2009) 212
Extraction of Total Nucleic Acids 212
References 213
Chapter 3: Detection of Viral and Viroid Plant Pathogens in the Environment 242
3.1 Detection of Plant Viruses in the Environment 243
3.1.1 Detection of Plant Viruses in Soil 243
3.1.1.1 Detection of Viruses with Abiotic Transmission 243
Biological Methods 243
Immunoassays 244
3.1.1.2 Detection of Viruses with Biotic Soil Transmission 245
Immunoassays 245
Nucleic Acid-Based Techniques 246
3.1.2 Detection of Plant Viruses in Water 250
3.1.2.1 Biological Methods 250
3.1.2.2 Nucleic Acid-Based Techniques 250
3.1.3 Detection of Plant Viruses in Air 251
3.1.3.1 Detection of Viruses with Abiotic Transmission 251
3.1.3.2 Detection of Viruses with Biotic Transmission 252
Immuoassays 252
Nucleic Acid-Based Techniques 255
3.1.4 Detection of Plant Viruses in Alternative HostPlant Species 258
3.1.4.1 Immunoassays 258
3.1.4.2 Nucleic Acid-Based Techniques 261
3.2 Detection of Viroids in the Environment 262
Appendix 1: Detection of Tobacco ringspot virus (TRSV)in the Nematode Vector by Immunofluorescence Technique (Wang and Gergerich 1998) 263
Appendix 2: Detection of Plant Viruses in Vector Nematodes by Nested PCR Assay (Martin et al. 2009) 263
Extraction of Viral RNA from Nematodes 263
Nested PCR Assay 264
Appendix 3: Detection of Raspberry bushy dwarf virus (RBDV) in the Nematode Vector Longidorus juvenilis by Nested PCR Assay (Pleško et al. 2009) 264
Appendix 4: Detection of Polymyxa DNA in the Soil by Real-Time PCR Assay (Ward et al. 2004) 265
Extraction of DNA from Soils 265
TaqMan Real-Time PCR 265
Appendix 5: Detection of Impatiens necrotic spot virus (INSV) by DAS-ELISA in Thrips Vectors (Sakurai et al. 2004) 266
Appendix 6: Detection of Citrus tristeza virus RNA Targets by Tissue Squash Real-Time RT-PCR Assay in Aphids (Bertolini et al. 2008) 266
Preparation of Single Aphid Squash Samples 266
Real-Time RT-PCR Assay 267
References 267
Chapter 4: Assessment of Variability in Plant Viral and Viroid Pathogens 271
4.1 Assessment of Variability in Plant Viral Pathogens 272
4.1.1 Assessment of Variations in Biological Characteristics 272
4.1.2 Assessment of Variations in Physico-chemical Characteristics 275
4.1.3 Assessment of Variations in Immunological Characteristics 276
4.1.3.1 Immunoblot Analysis 277
4.1.3.2 Enzyme-Linked Immunosorbent Assay 278
4.1.4 Assessment of Variations in Genomic Characteristics 282
4.1.4.1 Double-Stranded RNA Analysis 282
4.1.4.2 Hybridization Assays 283
4.1.4.3 Polymerase Chain Reaction-Based Techniques 284
4.1.4.4 Heteroduplex Mobility Analysis 300
4.1.4.5 Single-Strand Conformation Polymorphism Analysis 301
4.2 Assessment of Variability in Viroid Pathogens 302
4.2.1 Assessment of Variations in Nucleic Acid Characteristics 302
4.2.1.1 Hybridization-Based Techniques 302
4.2.1.2 PCR-Based Techniques 303
4.2.1.3 Heteroduplex Mobility Analysis 305
4.2.1.4 Single-Strand Conformation Polymorphism Analysis 306
Appendix: Differentiation of Peach latent mosaic viroid (PLMVd) Isolates by SSCP Analysis (Xu et al. 2008) 307
References 307
Chapter 5: Diagnosis of Viral and Viroid Diseases of Plants 315
5.1 Choice of Diagnostic Tests for Viral Diseases 317
5.1.1 Biological Tests 317
5.1.1.1 Symptomatology 317
5.1.1.2 Transmission Tests 318
5.1.2 Physico-chemical Tests 318
5.1.3 Immunoassays 319
5.1.4 Nucleic Acid-based Techniques 320
5.2 Choice of Diagnostic Tests for Viroid Diseases 323
5.2.1 Biological Tests 323
5.2.2 Nucleic Acid-based Techniques 324
5.2.2.1 Hybridization-Based Techniques 324
5.2.2.2 Polymerase Chain Reaction-Based Methods 324
5.3 Agencies Involved in Disease Diagnosis 325
5.3.1 Disease Diagnostic Centers 326
5.3.2 Plant Quarantines 328
References 329
Index 333

Produkt-Details

• Erscheint lt. Verlag: 26.10.2010
• Zusatzinfo: XXI, 321 p.
• Verlagsort: Dordrecht
• Sprache: englisch
• Themenwelt: Studium ► 1. Studienabschnitt (Vorklinik) ► Biochemie / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Botanik
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Themenwelt: Technik
• Schlagworte: Disease diagnosis • Disease Management • Entomology • Pathogen environment • Pathogen variability • Viral and viroid pathogen detection
• ISBN-10: 90-481-9754-6 / 9048197546
• ISBN-13: 978-90-481-9754-5 / 9789048197545