Antiviral Resistance in Plants Methods and Protocols

Studies related to pathogen-mediated virus resistance in plants were instrumental in providing some of the historical observations which ultimately led to the vital discovery of double-stranded RNA (dsRNA)-induced gene silencing or RNA interference (RNAi), which has since revolutionized research on plant-virus interactions. In Antiviral Resistance in Plants: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study the phenomenon of RNA silencing in relation to viral infections of plants.  These include methods and techniques for the isolation and quantitative/qualitative analyses of plant small 21-24 nucleotide RNAs such as small interfering RNAs (siRNAs) and microRNAs (miRNAs) as well as the analysis and manipulation of virus-induced gene silencing (VIGS) in both monocotyledonous and dicotyledenous plants and the use of hairpin RNA (hpRNA) transgenes.  Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

1. An  Historical Overview of RNAi in Plants

            John A. Lindbo

2. RNA Silencing and Antiviral Defense in Plants

            Claire Agius, Andrew Eamens, Tony Millar, John M. Watson, and Ming-Bo Wang

3. Biological Chemistry of Virus-encoded Suppressors of RNA Silencing:  An Overview

            Rustem T. Omarov and Herman B. Scholtof

4. Virus-Induced Gene Silencing Using Begomovirus Satellite Molecules

            Xueping Zhou and Changjun Huang

5. Strategies for Viral Cross Protection in Plants

            Changyong Zhou and Yan Zhou

6. Tobacco Rattle Virus (TRV)-Based Virus-Induced Gene Silencing

            Shawn Bachan and S.P. Dinesh-Kumar

7. Virus-Induced Gene Silencing in Hexaploid Wheat Using Barley Stripe Mosaic Virus Vectors

            Steven R. Scofield and Amanda S. Brandt

8. Characterization of Plant Virus-Encoded Gene Silencing Suppressors

            Hajime Yaegashi, Masamichi Isogai, and Nobuyuki Yoshikawa

9. Generation of Plant Small RNA cDNA Libraries for High-Throughput Sequencing

            Qian-Hao Zhu and Chris Helliwell

10. Modelling Antiviral Resistance in Plants

            Robert S. Anderssen and Peter M. Waterhouse

11. Isolation and Detection of Small RNAs from Plant Tissues

            Neil A. Smith and Andrew L. Eamens

12. Isolation and Analysis of Small RNAs from Virus-Infected Plants

            Shaun J. Curtin, Agustin Zsögön, John M. Watson, and Peter M. Waterhouse

13. Use of Hairpin RNA Constructs for Engineering Plant Virus Resistance

            Neena Mitter and Ralf G. Dietzgen

14. Artificial MicroRNAs for Plant Virus Resistance

            Jing Qu, Jian Ye, and Rongxiang Fang

15. Isolation and Biochemical Analysis of Plant Small RNAs

            H. Alexander Ebhardt, Mariana Oviedo Ovando, and Peter J. Unrau

16. Isolation and Analysis of Plant RNA-Dependent RNA Polymerases

            Julien Curaba

17. Plant Viroids: Isolation, Characterization/Detection, and Analysis

            Robert A. Owens, Teruo Sano,  and Nuria Duran-Vila

18. Structural and Functional Analysis of CMV Satellite RNAs in RNA Silencing

            Hanako Shimura and Chikara Masuta

19. Virus-Induced Gene Silencing in Soybean

            Aardra Kachroo and Said Ghabrial

20. Chimeric, Infectious, and Stable Virus Transcripts to Study RNA Silencing in ‘Dark Green’ Islands

            Robin M. MacDiarmid

21. Rolling Circle Amplification-Mediated Hairpin RNA (RMHR) Library Construction in Plants

            Lei Wang and Yun-Liu Fan

22. The Interaction Between Plant Viroid-Induced Symptoms and RNA Silencing

            Vicente Pallas, German Martinez, and Gustavo Gomez

23. Identification of Small Molecule Inhibitors of Tomato Bushy Stunt Virus (TBSV) Replication

            Zsuzsanna Sasvari and Peter D. Nagy

24. Expression of Dominant-Negative Mutants to Study Host Factors Affecting Plant Virus Infections

            Daniel Barajas and Peter D. Nagy

            Hajime Yaegashi, Masamichi Isogai, and Nobuyuki Yoshikawa

9. Generation of Plant Small RNA cDNA Libraries for High-Throughput Sequencing

            Qian-Hao Zhu and Chris Helliwell

10. Modelling Antiviral Resistance in Plants

            Robert S. Anderssen and Peter M. Waterhouse

11. Isolation and Detection of Small RNAs from Plant Tissues

            Neil A. Smith and Andrew L. Eamens

12. Isolation and Analysis of Small RNAs from Virus-Infected Plants

            Shaun J. Curtin, Agustin Zsögön, John M. Watson, and Peter M. Waterhouse

13. Use of Hairpin RNA Constructs for Engineering Plant Virus Resistance

            Neena Mitter and Ralf G. Dietzgen

14. Artificial MicroRNAs for Plant Virus Resistance

            Jing Qu, Jian Ye, and Rongxiang Fang

15. Isolation and Biochemical Analysis of Plant Small RNAs

            H. Alexander Ebhardt, Mariana Oviedo Ovando, and Peter J. Unrau

16. Isolation and Analysis of Plant RNA-Dependent RNA Polymerases

            Julien Curaba

17. Plant Viroids: Isolation, Characterization/Detection, and Analysis

            Robert A. Owens, Teruo Sano,  and Nuria Duran-Vila

18. Structural and Functional Analysis of CMV Satellite RNAs in RNA Silencing

            Hanako Shimura and Chikara Masuta

19. Virus-Induced Gene Silencing in Soybean

            Aardra Kachroo and Said Ghabrial

20. Chimeric, Infectious, and Stable Virus Transcripts to Study RNA Silencing in ‘Dark Green’ Islands

            Robin M. MacDiarmid

21. Rolling Circle Amplification-Mediated Hairpin RNA (RMHR) Library Construction in Plants

            Lei Wang and Yun-Liu Fan

22. The Interaction Between Plant Viroid-Induced Symptoms and RNA Silencing

            Vicente Pallas, German Martinez, and Gustavo Gomez

23. Identification of Small Molecule Inhibitors of Tomato Bushy Stunt Virus (TBSV) Replication

            Zsuzsanna Sasvari and Peter D. Nagy

24. Expression of Dominant-Negative Mutants to Study Host Factors Affecting Plant Virus Infections

            Daniel Barajas and Peter D. Nagy

            Neil A. Smith and Andrew L. Eamens

12. Isolation and Analysis of Small RNAs from Virus-Infected Plants

            Shaun J. Curtin, Agustin Zsögön, John M. Watson, and Peter M. Waterhouse

13. Use of Hairpin RNA Constructs for Engineering Plant Virus Resistance

            Neena Mitter and Ralf G. Dietzgen

14. Artificial MicroRNAs for Plant Virus Resistance

            Jing Qu, Jian Ye, and Rongxiang Fang

15. Isolation and Biochemical Analysis of Plant Small RNAs

            H. Alexander Ebhardt, Mariana Oviedo Ovando, and Peter J. Unrau

16. Isolation and Analysis of Plant RNA-Dependent RNA Polymerases

            Julien Curaba

17. Plant Viroids: Isolation, Characterization/Detection, and Analysis

            Robert A. Owens, Teruo Sano,  and Nuria Duran-Vila

18. Structural and Functional Analysis of CMV Satellite RNAs in RNA Silencing

            Hanako Shimura and Chikara Masuta

19. Virus-Induced Gene Silencing in Soybean

            Aardra Kachroo and Said Ghabrial

20. Chimeric, Infectious, and Stable Virus Transcripts to Study RNA Silencing in ‘Dark Green’ Islands

            Robin M. MacDiarmid

21. Rolling Circle Amplification-Mediated Hairpin RNA (RMHR) Library Construction in Plants

            Lei Wang and Yun-Liu Fan

22. The Interaction Between Plant Viroid-Induced Symptoms and RNA Silencing

            Vicente Pallas, German Martinez, and Gustavo Gomez

23. Ide