This book describes both the theory of gene silencing and also the application. The first five chapters discuss different aspects of the gene silencing mechanism. Since the silencing pathways are particularly diverse in plants, a whole chapter is dedicated to describe these (chapter 1). It is a generally accepted view that gene silencing has evolved in plants as a defence mechanism against viruses, therefore chapter 2 discusses the 'arms race' between plants and viruses, how viruses trigger silencing and also evolved proteins that can suppress it. Another aspect of gene silencing is the epigenetic changes caused by silencing. This, and how epigenetic changes can be directed, is described in chapter 3. Finally, the theoretical part is closed by two chapters on how gene silencing works in algae (chapter 4) and fungi (chapter 5), two groups of organisms related to plants. The second part of the book is dedicated to application of gene silencing. Small non-coding RNAs are key molecules in the mechanism and chapter 6 discusses various strategies to produce small artificial RNAs. The following chapters describe the application of gene silencing to influence specific, agronomically important traits in plants, including traits for industrial use (chapter 7) and nutritional value (chapter 8). The last three chapters review the use of gene silencing to provide resistance against different types of pathogens including fungi (chapter 9), nematodes (chapter 10) and viruses (chapter 11).

• Plant Gene Silencing: Mechanisms and Applications
• Copyright
• Contents
• Contributors
• Preface
  • References
• 1: Diversity of RNA Silencing Pathways in Plants
  • 1.1 Introduction
  • 1.2 Transgene-based Genetic Screens to Unravel Silencing Pathways
  • 1.3 PTGS Pathways
    • 1.3.1 Antiviral PTGS
    • 1.3.2 RQC as a first layer of defence limiting PTGS
    • 1.3.3 Specialized PTGS pathways directed against certain endogenous mRNA
    • 1.3.4 PTGS pathways directed against transposons
  • 1.4 TGS Pathways
    • 1.4.1 PolIV-RdDM pathway
    • 1.4.2 DDM1/CMT2 pathway
  • 1.5 Conclusions
  • References
• 2: Induction and Suppression of Silencing by Plant Viruses
  • 2.1 Introduction
  • 2.2 Antiviral RNA Silencing Pathway in Plants
    • 2.2.1 vsiRNAs biogenesis
      • Initiation phase (DCLs, recognition and processing)
      • Amplification phase (RDRs + DCLs)
    • 2.2.2 Effector phase (AGOs + RNA-induced silencing complexes (RISC) complex)
  • 2.3 Induction of RNA Silencing to Indirectly Promote Defence Responses
  • 2.4 Viral Counter-defence Strategies against Antiviral RNA Silencing
  • 2.5 RNA Silencing Suppressors (RSSs) and Their Mechanism of Action
    • 2.5.1 Suppressors targeting the initiation phase of silencing (DCLs)
    • 2.5.2 Suppressors targeting the amplification phase of silencing (RDRs)
    • 2.5.3 Suppressors targeting the effector phase of silencing (AGOs + RISC)
  • 2.6 Effects of Antiviral RNA Silencing on Plant Gene Expression
  • 2.7 Concluding Remarks
  • References
• 3: Artificial Induction and Maintenance of Epigenetic Variations in Plants
  • 3.1 Introduction
  • 3.2 Cytosine Methylation, an Important Epigenetic Landscape among Plants
  • 3.3 Histone Modifications
  • 3.4 Two Additional DNA-dependent RNA Polymerases
  • 3.5 Artificial Induction of Epigenetic Variations
    • 3.5.1 Inverted repeat mediated RdDM induction
    • 3.5.2 Virus induced gene silencing (VIGS), an artificial tool to introduce epigenetic modification among plants
  • 3.6 VIGS-mediated TGS Mechanism: Gaps in Our Understanding
  • 3.7 Recipe for High Efficiency for Inheritance of Methylation
  • 3.8 Conclusions
  • Acknowledgements
  • References
• 4: Gene Silencing in Archaeplastida Algae
  • 4.1 Introduction
  • 4.2 DNA Cytosine Methyltransferases in Microalgae
    • 4.2.1 Phylogenetic analysis and domain organization of DNA cytosine methyltransferases
    • 4.2.2 Biological role(s) of DNA cytosine methylation in microalgae
  • 4.3 The RNA Interference Machinery in Microalgae
    • 4.3.1 Taxonomic distribution and phylogenetic analysis of core RNAi components
    • 4.3.2 Biological roles of the RNAi machinery in microalgae
  • 4.4 Perspective
  • Acknowledgements
  • References
• 5: Gene Silencing in Fungi: A Diversity of Pathways and Functions
  • 5.1 Introduction
  • 5.2 RNAi as a Genome Defence Mechanism in Fungi
    • 5.2.1 Quelling and transposon control in Neurospora crassa
    • 5.2.2 Gene silencing triggered by non-integrative transgenes in Mucor circinelloides
    • 5.2.3 An antiviral defence mechanism
    • 5.2.4 Meiotic silencing by unpaired DNA
  • 5.3 Regulatory Endogenous Small RNAs in Fungi
    • 5.3.1 RNAi and heterochromatin formation in yeasts
    • 5.3.2 qiRNAs: small RNAs induced by DNA damage in Neurospora
    • 5.3.3 microRNA-like RNAs in Neurospora and other filamentous fungi
    • 5.3.4 dicer-dependent and dicer-independent exon-derived esRNAs in Mucor
    • 5.3.5 Other fungal regulatory esRNAs
  • 5.4 Regulation of Physiology and Development by esRNAs in Fungi
    • 5.4.1 esRNAs in the response to environmental signals
    • 5.4.2 esRNAs in fungal pathogenesis
  • Acknowledgements
  • References
• 6: Artificial Small RNA-based Strategies for Effective and Specific Gene Silencing in Plants
  • 6.1 Introduction
  • 6.2 Plant Artificial Small RNAs
    • 6.2.1 Artificial microRNAs
    • 6.2.2 Synthetic trans-acting siRNAs
  • 6.3 Design of Plant Artificial Small RNAs
  • 6.4 Engineering Artificial Small RNA Constructs
    • 6.4.1 AmiRNA cloning
    • 6.4.2 Syn-tasiRNA cloning
  • 6.5 Validation of Artificial Small RNA Constructs
  • 6.6 Conclusions and Future Challenges
  • References
• 7: Application of RNA Silencing in Improving Plant Traits for Industrial Use
  • 7.1 Introduction
  • 7.2 Biomass Recalcitrance in Industrial Processing
  • 7.3 Oil Yield and Quality
  • 7.4 Therapeutic Proteins
  • 7.5 Phytochemicals of Pharmaceutical and Industrial Importance
  • 7.6 Starch for Industrial Use
  • 7.7 Post-harvest Stability
  • 7.8 Inducing Male Sterility
  • 7.9 Other Industrial Traits
  • 7.10 Conclusion
  • References
• 8: Increasing Nutritional Value by RNA Silencing
  • 8.1 Introduction
  • 8.2 Modifying Macro-nutrient Content
    • 8.2.1 Essential amino acids
    • 8.2.2 Carbohydrates: starch
    • 8.2.3 Oils and fatty acids
  • 8.3 Enrichment with Phytonutrients/Functional Metabolites
  • 8.4 Reduction in Antinutrients, Toxins and Allergens
  • Acknowledgements
  • References
• 9: RNA-based Control of Plant Diseases: A Case Study with Fusarium graminearum
  • 9.1 Introduction
  • 9.2 Fusarium is a Cereal Killer Which Requires More Efficient Strategies for Disease Control
  • 9.3 Application Opportunities for RNAi in Agriculture
    • 9.3.1 Host-induced gene silencing against Fusarium graminearum
    • 9.3.2 Spray-induced gene silencing against Fusarium graminearum
    • 9.3.3 Mechanistic considerations
  • 9.4 Questions to Be Resolved in the Future
  • Acknowledgements
  • References
• 10: Targeting Nematode Genes by RNA Silencing
  • 10.1 Introduction
  • 10.2 Nematodes: Caenorhabditis Species
  • 10.3 Plant-parasitic Nematodes of Economic Importance
  • 10.4 RNA Silencing in Nematodes
  • 10.5 C. elegans as an Invaluable Model for RNA Silencing
  • 10.6 RNA Silencing and Functional Analysis of PPN Genes
  • 10.7 Plant-derived RNA Silencing of Nematode Genes: Applications
  • 10.8 Factors that Affect the Application and Efficacy of HIGS of Nematode Genes
  • References
• 11: Gene Silencing Provides Efficient Protection against Plant Viruses
  • 11.1 Introduction
  • 11.2 Pathogen-derived RNA Silencing-mediated Resistance: A Brief History
  • 11.3 Commercialized Crops Resistant to Viruses by Transgenic RNA Silencing Activation
  • 11.4 Virus-derived Hairpin-RNA-mediated Resistance: A Robust Tool for Introducing New Virus Resistance Traits in Crops
    • 11.4.1 Sugarcane
    • 11.4.2 Maize
    • 11.4.3 Rice
    • 11.4.4 Wheat
    • 11.4.5 Potato
    • 11.4.6 Soybean
    • 11.4.7 Cassava
    • 11.4.8 Sugarbeet
    • 11.4.9 Tomato
    • 11.4.10 Barley
    • 11.4.11 hpRNA reviewed
  • 11.5 Artificial miRNAs and ta-siRNAs: New Tools for Conferring Virus Resistance
    • 11.5.1 Artificial miRNAs
    • 11.5.2 Artificial ta-siRNAs
  • 11.6 RNA Silencing of Plant Susceptibility Genes: An Additional Route for Virus Resistance
  • 11.7 Aspects to Be Considered when Designing an RNA Silencing-mediated Resistance Strategy
  • 11.8 Concluding Remarks
  • References
• Index