Advertisement

Strategies for Altering Plant Traits Using Virus-Induced Gene Silencing Technologies

  • Christophe Lacomme
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1287)

Abstract

The rapid progress in genome sequencing and transcriptome analysis in model and crop plants has made possible the identification of a vast number of genes potentially associated with economically important complex traits. The ultimate goal is to assign functions to these genes by using forward and reverse genetic screens. Plant viruses have been developed for virus-induced gene silencing (VIGS) to generate rapid gene knockdown phenotypes in numerous plant species. To fulfill its potential for high-throughput phenomics, it is of prime importance to ensure that parameters conditioning the VIGS response, i.e., plant–virus interactions and associated loss-of-function screens, are “fit for purpose” and optimized to unequivocally conclude the role of a gene of interest in relation to a given trait. This chapter will review and discuss the different strategies used for the development of VIGS-based phenomics in model and crop species.

Key words

Plant functional genomics Virus-induced gene silencing RNAi Forward and reverse screens Model plants Crops 

References

  1. 1.
    Bevan MW, Uauy C (2013) Genomics reveals new landscapes for crop improvement. Genome Biol 14(6):206CrossRefPubMedCentralPubMedGoogle Scholar
  2. 2.
    Alonso JM, Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet 7:524–536CrossRefPubMedGoogle Scholar
  3. 3.
    Lacomme C, Pogue GP, Wilson TMA et al (2001) Plant viruses. In: Ring CJA, Blair E (eds) Genetically engineered viruses: development and applications. BIOS Scientific Publishing Ltd, Oxford, UKGoogle Scholar
  4. 4.
    Baulcombe DC, Chapman S, Santa Cruz S (1995) Jellyfish green fluorescent protein as a reporter for virus infections. Plant J 6:1045–1053CrossRefGoogle Scholar
  5. 5.
    Rommens CM, Salmeron JM, Baulcombe DC et al (1995) Use of a gene expression system based on potato virus X to rapidly identify and characterize a tomato Pto homolog that controls fenthion sensitivity. Plant Cell 7:249–257CrossRefPubMedCentralPubMedGoogle Scholar
  6. 6.
    Karrer EE, Beachy RN, Holt CA (1998) Cloning of tobacco genes that elicit the hypersensitive response. Plant Mol Biol 5:681–690CrossRefGoogle Scholar
  7. 7.
    Lacomme C, Santa Cruz S (1999) Bax-induced cell death in tobacco is similar to the hypersensitive response. Proc Natl Acad Sci U S A 96:7956–7961CrossRefPubMedCentralPubMedGoogle Scholar
  8. 8.
    Takken FL, Luderer R, Gabriëls SH et al (2000) A functional cloning strategy, based on a binary PVX-expression vector, to isolate HR-inducing cDNAs of plant pathogens. Plant J 24:275–283CrossRefPubMedGoogle Scholar
  9. 9.
    Kumagai MH, Donson J, della-Cioppa G et al (1995) Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc Natl Acad Sci U S A 92:1679–1683CrossRefPubMedCentralPubMedGoogle Scholar
  10. 10.
    Ratcliff F, Martin-Hernandez AM, Baulcombe DC (2001) Tobacco rattle virus as a vector for analysis of gene function by silencing. Plant J 25:237–245CrossRefPubMedGoogle Scholar
  11. 11.
    Senthil-Kumar M, Anand A, Uppalapati SR et al (2008) Virus-induced gene silencing and its applications. CAB Rev 3:1–18CrossRefGoogle Scholar
  12. 12.
    Dunoyer P, Voinnet O (2005) The complex interplay between plant viruses and host RNA-silencing pathways. Curr Opin Plant Biol 8:415–423CrossRefPubMedGoogle Scholar
  13. 13.
    Zvereva AS, Pooggin MM (2012) Silencing and innate immunity in plant defense against viral and non-viral pathogens. Viruses 4:2578–2597CrossRefPubMedCentralPubMedGoogle Scholar
  14. 14.
    Himber C, Dunoyer P, Moissiard G et al (2003) Transitivity-dependent and -independent cell-to-cell movement of RNA silencing. EMBO J 22:4523–4533CrossRefPubMedCentralPubMedGoogle Scholar
  15. 15.
    Peele C, Jordan CV, Muangsan N et al (2001) Silencing of a meristematic gene using geminivirus-derived vectors. Plant J 27:357–366CrossRefPubMedGoogle Scholar
  16. 16.
    Hein I, Barciszewska-Pacak M, Hrubikova K et al (2005) Virus-induced gene silencing based functional characterization of genes associated with powdery mildew resistance in barley. Plant Physiol 138:2155–2164CrossRefPubMedCentralPubMedGoogle Scholar
  17. 17.
    Hiriart J, Aro E, Lehto K (2003) Dynamics of the VIGS-mediated chimeric silencing of the Nicotiana benthamiana ChlH gene and of the tobacco mosaic virus vector. Mol Plant Microbe Interact 16:99–106CrossRefPubMedGoogle Scholar
  18. 18.
    Bruun-Rasmussen M, Madsen CT et al (2007) Stability of barley stripe mosaic virus-induced gene silencing in barley. Mol Plant Microbe Interact 20:1323–1331CrossRefPubMedGoogle Scholar
  19. 19.
    Bennypaul HS, Mutti JS, Rustgi S (2012) Virus-induced gene silencing (VIGS) of genes expressed in root, leaf, and meiotic tissues of wheat. Funct Integr Genomics 12:143–156CrossRefPubMedGoogle Scholar
  20. 20.
    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 Biotechnol J 9:797–806CrossRefPubMedGoogle Scholar
  21. 21.
    Voinnet O, Pinto YM, Baulcombe DC (1999) Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci U S A 96:14147–14152CrossRefPubMedCentralPubMedGoogle Scholar
  22. 22.
    Ruiz MT, Voinnet O, Baulcombe DC (1998) Initiation and maintenance of virus-induced gene silencing. Plant Cell 10:937–946CrossRefPubMedCentralPubMedGoogle Scholar
  23. 23.
    Valentine T, Shaw J, Blok VC et al (2004) Efficient virus-induced gene silencing in roots using a modified tobacco rattle virus vector. Plant Physiol 136:3999–4009CrossRefPubMedCentralPubMedGoogle Scholar
  24. 24.
    Gossele V, Fache I, Meulewaeter F et al (2002) SVISS – a novel transient gene silencing system for gene function discovery and validation in tobacco plants. Plant J 32:859–866CrossRefPubMedGoogle Scholar
  25. 25.
    Zhou X, Huang C (2012) Virus-induced gene silencing using begomovirus satellite molecules. Methods Mol Biol 894:57–67CrossRefPubMedGoogle Scholar
  26. 26.
    Purkayastha A, Mathur S, Verma V et al (2010) Virus-induced gene silencing in rice using a vector derived from a DNA virus. Planta 232:1531–1540CrossRefPubMedGoogle Scholar
  27. 27.
    Thomas CL, Jones L, Baulcombe DC et al (2001) Size constraints for targeting post-transcriptional gene silencing and for RNA-directed methylation in Nicotiana benthamiana using a potato virus X vector. Plant J 25:417–425CrossRefPubMedGoogle Scholar
  28. 28.
    Smith NA, Singh SP, Wang MB et al (2000) Total silencing by intron-spliced hairpin RNAs. Nature 407:319–320CrossRefPubMedGoogle Scholar
  29. 29.
    Lacomme C, Hrubikova K, Hein I (2003) Enhancement of virus-induced gene silencing through viral-based production of inverted-repeats. Plant J 34:543–553CrossRefPubMedGoogle Scholar
  30. 30.
    Pflieger S, Blanchet S, Camborde L et al (2008) Efficient virus-induced gene silencing in Arabidopsis using a ‘one-step’ TYMV-derived vector. Plant J 56:678–690CrossRefPubMedGoogle Scholar
  31. 31.
    Senthil-Kumar M, Mysore KS (2011) Caveat of RNAi in plants: the off-target effect. Methods Mol Biol 744:13–25CrossRefPubMedGoogle Scholar
  32. 32.
    Tang Y, Wang F, Zhao J et al (2010) Virus-based microRNA expression for gene functional analysis in plants. Plant Physiol 153:632–641CrossRefPubMedCentralPubMedGoogle Scholar
  33. 33.
    Schwab R, Ossowski S, Riester M et al (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18:1121–1133CrossRefPubMedCentralPubMedGoogle Scholar
  34. 34.
    Meng Y, Moscou MJ, Wise RP (2009) Blufensin1 negatively impacts basal defense in response to barley powdery mildew. Plant Physiol 149:271–285CrossRefPubMedCentralPubMedGoogle Scholar
  35. 35.
    Ryu CM, Anand A, Kang L et al (2004) Agrodrench: a novel and effective agroinoculation method for virus-induced gene silencing in roots and diverse solanaceous species. Plant J 40:322–331CrossRefPubMedGoogle Scholar
  36. 36.
    Dong Y, Burch-Smith TM, Liu YL et al (2007) A ligation-independent cloning TRV vector for high-throughput virus-induced gene silencing identifies roles for NbMADS4-1 and -2 in floral development. Plant Physiol 145:1161–1170CrossRefPubMedCentralPubMedGoogle Scholar
  37. 37.
    Burch-Smith TM, Schiff M, Liu Y et al (2006) Efficient virus-induced gene silencing in Arabidopsis. Plant Physiol 142:21–27CrossRefPubMedCentralPubMedGoogle Scholar
  38. 38.
    Goodin MM, Zaitlin D, Naidu RA et al (2008) Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions. Mol Plant Microbe Interact 21:1015–1026CrossRefPubMedGoogle Scholar
  39. 39.
    Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641CrossRefGoogle Scholar
  40. 40.
    Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195CrossRefGoogle Scholar
  41. 41.
    Bombarely A, Rosli HG, Vrebalov J et al (2012) A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Mol Plant Microbe Interact 25:1523–1530CrossRefPubMedGoogle Scholar
  42. 42.
    Lacomme C (2011) Milestones in the development and applications of plant virus vector as gene silencing platforms. Curr Top Microbiol Immunol 375:89–105Google Scholar
  43. 43.
    Muruganantham M, Moskovitz Y, Haviv S et al (2009) Grapevine virus A-mediated gene silencing in Nicotiana benthamiana and Vitis vinifera. J Virol Methods 155:167–174CrossRefPubMedGoogle Scholar
  44. 44.
    Scofield SR, Huang L, Brandt AS et al (2005) Development of a virus-induced gene silencing system for hexaploid wheat and its use in functional analysis of the Lr21-mediated leaf rust resistance pathway. Plant Physiol 138:2165–2173CrossRefPubMedCentralPubMedGoogle Scholar
  45. 45.
    Chai YM, Jia HF, Li CL et al (2011) FaPYR1 is involved in strawberry fruit ripening. J Exp Bot 62:5079–5089CrossRefPubMedGoogle Scholar
  46. 46.
    Lu R, Malcuit I, Moffett P et al (2003) High-throughput virus-induced gene silencing implicates heat shock protein 90 in plant disease resistance. EMBO J 22:5690–5699CrossRefPubMedCentralPubMedGoogle Scholar
  47. 47.
    Liu YL, Schiff M, Czymmek K et al (2005) Autophagy regulates programmed cell death during the plant innate immune response. Cell 121:567–577CrossRefPubMedGoogle Scholar
  48. 48.
    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 39:734–746CrossRefPubMedGoogle Scholar
  49. 49.
    Fu DQ, Zhu BZ, Zhu HL et al (2006) Enhancement of virus-induced gene silencing in tomato by low temperature and low humidity. Mol Cells 21:153–160CrossRefPubMedGoogle Scholar
  50. 50.
    Voinnet O (2005) Non-cell autonomous RNA silencing. FEBS Lett 579:5858–5871CrossRefPubMedGoogle Scholar
  51. 51.
    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 150:1122–1134CrossRefPubMedCentralPubMedGoogle Scholar
  52. 52.
    Nelson RS, Citovsky V (2005) Plant viruses. Invaders of cells and pirates of cellular pathways. Plant Physiol 138:1809–1814CrossRefPubMedCentralPubMedGoogle Scholar
  53. 53.
    Yang SJ, Carter SA, Cole AB, Cheng NH, Nelson RS (2004) A natural variant of a host RNA-dependent RNA polymerase is associated with increased susceptibility to viruses by Nicotiana benthamiana. Proc Natl Acad Sci U S A 101(16):6297–6302CrossRefPubMedCentralPubMedGoogle Scholar
  54. 54.
    Dubreuil G, Magliano M, Dubrana MP (2009) Tobacco rattle virus mediates gene silencing in a plant parasitic root-knot nematode. J Exp Bot 60:4041–4050CrossRefPubMedGoogle Scholar
  55. 55.
    Nowara D, Gay A, Lacomme C et al (2010) HIGS: host-induced gene silencing in the obligate biotrophic fungal pathogen Blumeria graminis. Plant Cell 22:3130–3141CrossRefPubMedCentralPubMedGoogle Scholar
  56. 56.
    Panwar V, McCallum B, Bakkeren G (2013) Host-induced gene silencing of wheat leaf rust fungus Puccinia triticina pathogenicity genes mediated by the Barley stripe mosaic virus. Plant Mol Biol 81:595–608CrossRefPubMedGoogle Scholar
  57. 57.
    Liu YL, Schiff M, Dinesh-Kumar SP (2002) Virus-induced gene silencing in tomato. Plant J 31:777–786CrossRefPubMedGoogle Scholar
  58. 58.
    Brigneti G, Martín-Hernández AM, Jin H (2004) Virus-induced gene silencing in Solanum species. Plant J 39:264–272CrossRefPubMedGoogle Scholar
  59. 59.
    Liu YL, 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 30:415–429CrossRefPubMedGoogle Scholar
  60. 60.
    Hileman LC, Drea S, de Martino G et al (2005) Virus induced gene silencing is an effective tool for assaying gene function in the basal eudicot species Papaver somniferum (opium poppy). Plant J 44:334–341CrossRefPubMedGoogle Scholar
  61. 61.
    Spitzer B, Zvi MM, Ovadis M et al (2007) Reverse genetics of floral scent: application of tobacco rattle virus-based gene silencing in Petunia. Plant Physiol 145:1241–1250CrossRefPubMedCentralPubMedGoogle Scholar
  62. 62.
    Galis I, Schuman MC, Gase K et al (2013) The use of VIGS technology to study plant-herbivore interactions. Methods Mol Biol 975:109–137CrossRefPubMedGoogle Scholar
  63. 63.
    Senthil-Kumar M, Lee HK, Mysore KS (2013) VIGS-mediated forward genetics screening for identification of genes involved in non-host resistance. J Vis Exp (78): e51033, doi:  10.3791/51033
  64. 64.
    Anand A, Vaghchhipawala Z, Ryu CM et al (2007) Identification and characterization of plant genes involved in Agrobacterium-mediated plant transformation by virus-induced gene silencing. Mol Plant Microbe Interact 20:41–52CrossRefPubMedGoogle Scholar
  65. 65.
    Constantin GD, Krath BN, MacFarlane SA et al (2004) Virus-induced gene silencing as a tool for functional genomics in a legume species. Plant J 40:622–631CrossRefPubMedGoogle Scholar
  66. 66.
    Faivre-Rampant O, Gilroy E, Hrubikova K et al (2004) Potato virus X-induced gene silencing in leaves and tubers of potato. Plant Physiol 134:1308–1316CrossRefPubMedCentralPubMedGoogle Scholar
  67. 67.
    Zhang C, Ghabrial SA (2006) Development of bean pod mottle virus-based vectors for stable protein expression and sequence-specific virus-induced gene silencing in soybean. Virology 344:401–411CrossRefPubMedGoogle Scholar
  68. 68.
    Zhang C, Yang C, Whitham SA et al (2009) Development and use of an efficient DNA-based viral gene silencing vector for soybean. Mol Plant Microbe Interact 22:123–131CrossRefPubMedGoogle Scholar
  69. 69.
    Holzberg S, Brosio P, Gross C et al (2002) Barley stripe mosaic virus-induced gene silencing in a monocot plant. Plant J 30:315–327CrossRefPubMedGoogle Scholar
  70. 70.
    Pacak A, Geisler K, Jørgensen B et al (2010) Investigations of barley stripe mosaic virus as a gene silencing vector in barley roots and in Brachypodium distachyon and oat. Plant Methods 6:26CrossRefPubMedCentralPubMedGoogle Scholar
  71. 71.
    Eichmann R, Bischof M, Weis C et al (2010) BAX INHIBITOR-1 is required for full susceptibility of barley to powdery mildew. Mol Plant Microbe Interact 23:1217–1227CrossRefPubMedGoogle Scholar
  72. 72.
    Yuan C, Li C, Yan L et al (2011) A high throughput barley stripe mosaic virus vector for virus induced gene silencing in monocots and dicots. PLoS One 6:e26468CrossRefPubMedCentralPubMedGoogle Scholar
  73. 73.
    Van der Linde K, Kastner C, Kumlehn J et al (2011) Systemic virus-induced gene silencing allows functional characterization of maize genes during biotrophic interaction with Ustilago maydis. New Phytol 189:471–483CrossRefPubMedGoogle Scholar
  74. 74.
    Ding XS, Schneider WL, Chaluvadi SR et al (2006) Characterization of a brome mosaic virus strain and its use as a vector for gene silencing in monocotyledonous hosts. Mol Plant Microbe Interact 19:1229–1239CrossRefPubMedGoogle Scholar
  75. 75.
    Ramanna H, Ding XS, Nelson RS (2013) Rationale for developing new virus vectors to analyze gene function in grasses through virus-induced gene silencing. Methods Mol Biol 975:15–32CrossRefPubMedGoogle Scholar
  76. 76.
    Igarashi A, Yamagata K, Sugai T et al (2009) Apple latent spherical virus vectors for reliable and effective virus-induced gene silencing among a broad range of plants including tobacco, tomato, Arabidopsis thaliana, cucurbits, and legumes. Virology 386:407–416CrossRefPubMedGoogle Scholar
  77. 77.
    Sasaki S, Yamagishi N, Yoshikawa N et al (2011) Efficient virus-induced gene silencing in apple, pear and Japanese pear using Apple latent spherical virus vectors. Plant Methods 10:15CrossRefGoogle Scholar
  78. 78.
    Kjemtrup S, Sampson KS, Peele CG et al (1998) Gene silencing from plant DNA carried by a Geminivirus. Plant J 14:91–100CrossRefPubMedGoogle Scholar
  79. 79.
    Turnage MA, Muangsan N, Peele CG et al (2002) Geminivirus-based vectors for gene silencing in Arabidopsis. Plant J 30:107–114CrossRefPubMedGoogle Scholar
  80. 80.
    Cai X, Wang C, Xu Y et al (2007) Efficient gene silencing induction in tomato by a viral satellite DNA vector. Virus Res 125:169–175CrossRefPubMedGoogle Scholar
  81. 81.
    Golenberg EM, Sather DN, Hancock LC et al (2009) Development of a gene silencing DNA vector derived from a broad host range geminivirus. Plant Methods 5:9. doi: 10.1186/1746-4811-5-9 CrossRefPubMedCentralPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Virology and Zoology SectionScience and Advice for Scottish Agriculture (SASA)EdinburghUK

Personalised recommendations