Virus-Induced Gene Silencing as a Tool to Study Tomato Fruit Biochemistry

  • Elio FantiniEmail author
  • Giovanni GiulianoEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1363)


Virus-Induced Gene Silencing (VIGS) is an excellent reverse genetic tool for the study of gene function in plants, based on virus infection. In this chapter, we describe a high-throughput approach based on VIGS for the study of tomato fruit biochemistry. It comprises the selection of the sequence for silencing using bioinformatics tools, the cloning of the fragment in the Tobacco Rattle Virus (TRV), and the agroinfiltration of tomato fruits mediated by Agrobacterium tumefaciens.

Key words

VIGS Silencing Reverse genetics TRV Tomato 



This work was supported by the Italian Ministry of Research (Project “Integrated Knowledge for the Sustainability and Innovation of Italian Agri-Food”), by the Italian Ministry of Agriculture (Projects “Nutrisol” and “Biomassval”), and by the European Commission (FP7 Project “From discovery to products: A next generation pipeline for the sustainable generation of high-value plant products,” contract no. 613513; Horizon 2020 project “Traditional tomato varieties and cultural practices: a case for agricultural diversification with impact on food security and health of European population,” contract no. 634561) and benefited from the networking activities of COST Action FA1106 “QualityFruit.” We thank Alessandro Nicolia for critical reading of the manuscript.


  1. 1.
    Baulcombe DC (1999) Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol 2(2):109–113CrossRefPubMedGoogle Scholar
  2. 2.
    Robertson D (2004) VIGS vectors for gene silencing: many targets, many tools. Annu Rev Plant Biol 55:495–519CrossRefPubMedGoogle Scholar
  3. 3.
    Burch‐Smith TM, Anderson JC, Martin GB et al (2004) Applications and advantages of virus‐induced gene silencing for gene function studies in plants. Plant J 39(5):734–746CrossRefPubMedGoogle Scholar
  4. 4.
    Senthil-Kumar M, Mysore KS (2011) New dimensions for VIGS in plant functional genomics. Trends Plant Sci 16(12):656–665CrossRefPubMedGoogle Scholar
  5. 5.
    Sahu PP, Puranik S, Khan M et al (2012) Recent advances in tomato functional genomics: utilization of VIGS. Protoplasma 249(4):1017–1027CrossRefPubMedGoogle Scholar
  6. 6.
    Lacomme C (2014) Milestones in the development and applications of plant virus vector as gene silencing platforms. In: Palmer K, Gleba Y (eds) Plant viral vectors. Springer, Berlin, pp 89–105Google Scholar
  7. 7.
    Scofield SR, Nelson RS (2009) Resources for virus-induced gene silencing in the grasses. Plant Physiol 149(1):152–157CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Jiang Y, Ye S, Wang L et al (2014) Heterologous gene silencing induced by tobacco rattle virus (TRV) is efficient for pursuing functional genomics studies in woody plants. Plant Cell Tissue Organ Cult 116(2):163–174CrossRefGoogle Scholar
  9. 9.
    Orzaez D, Medina A, Torre S et al (2009) A visual reporter system for virus-induced gene silencing in tomato fruit based on anthocyanin accumulation. Plant Physiol 150(3):1122–1134CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Quadrana L, Rodriguez MC, López M et al (2011) Coupling virus-induced gene silencing to exogenous green fluorescence protein expression provides a highly efficient system for functional genomics in Arabidopsis and across all stages of tomato fruit development. Plant Physiol 156(3):1278–1291CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Ratcliff F, Martin‐Hernandez AM, Baulcombe DC (2001) Technical advance: tobacco rattle virus as a vector for analysis of gene function by silencing. Plant J 25(2):237–245CrossRefPubMedGoogle Scholar
  12. 12.
    Senthil‐Kumar M, Mysore KS (2011) Virus‐induced gene silencing can persist for more than 2 years and also be transmitted to progeny seedlings in Nicotiana benthamiana and tomato. Plant Biotech J 9(7):797–806CrossRefGoogle Scholar
  13. 13.
    Liu Y, Schiff M, Marathe R et al (2002) Tobacco Rar1, EDS1 and NPR1/NIM1 like genes are required for N‐mediated resistance to tobacco mosaic virus. Plant J 30(4):415–429CrossRefPubMedGoogle Scholar
  14. 14.
    Liu Y, Schiff M, Dinesh‐Kumar SP (2002) Virus‐induced gene silencing in tomato. Plant J 31(6):777–786CrossRefPubMedGoogle Scholar
  15. 15.
    Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635–641CrossRefGoogle Scholar
  16. 16.
    Fantini E, Falcone G, Frusciante S et al (2013) Dissection of tomato lycopene biosynthesis through Virus-Induced Gene Silencing. Plant Physiol 163(2):986–998CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Fu DQ, Zhu BZ, Zhu HL et al (2005) Virus-induced gene silencing in tomato fruit. Plant J 43(2):299–308CrossRefPubMedGoogle Scholar
  18. 18.
    Liu E, Page JE (2008) Optimized cDNA libraries for virus-induced gene silencing (VIGS) using tobacco rattle virus. Plant Methods 4(5):1–13Google Scholar
  19. 19.
    Xu P, Zhang Y, Kang L et al (2006) Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. Plant Physiol 142(2):429–440CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Trisaia Research CenterENEA (Italian National Agency for New Technologies, Energy, and Sustainable Development)RotondellaItaly
  2. 2.Casaccia Research CenterENEA (Italian National Agency for New Technologies, Energy, and Sustainable Development)RomeItaly

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