New dimensions for VIGS in plant functional genomics

Trends in Plant Science

Volumn 16, Issue 12, 2011, Pages 656-665

  Senthil Kumar, Muthappa ^a   Mysore, Kirankumar S ^a  

^a PLANT BIOLOGY DIVISION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE SILENCING; GENETICS; GENOMICS; PLANT; PLANT GENE; PLANT VIRUS; REVIEW;

GENE SILENCING; GENES, PLANT; GENOMICS; PLANT VIRUSES; PLANTS;

EID: 83055172783     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2011.08.006     Document Type: Review

References (107)

1. Becker A., Lange M. VIGS genomics goes functional. Trends Plant Sci. 2010, 15:1-4.
2. Burch-Smith T.M., et al. Applications and advantages of virus-induced gene silencing for gene function studies in plants. Plant J. 2004, 39:734-746.
3. Lu R., et al. Virus-induced gene silencing in plants. Methods 2003, 30:296-303.
4. Senthil-Kumar M., et al. Virus-induced gene silencing and its applications. CAB Rev. PAVSNNR 2008, 3:1-18.
5. Lindbo J.A., et al. Induction of a highly specific antiviral state in transgenic plants: implications for regulation of gene expression and virus resistance. Plant Cell 1993, 5:1749-1759.
6. Kumagai M.H., et al. Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc. Natl. Acad. Sci. U.S.A. 1995, 92:1679-1683.
7. Ruiz M.T., et al. Initiation and maintenance of virus-induced gene silencing. Plant Cell 1998, 10:937-946.
8. Liu Y., et al. Virus-induced gene silencing in tomato. Plant J. 2002, 31:777-786.
9. Dinesh-Kumar S.P., et al. Virus-induced gene silencing. Plant Functional Genomics 2003, 287-293. Humana Press. E. Grotewold (Ed.).
10. Llave C. Virus-derived small interfering RNAs at the core of plant-virus interactions. Trends Plant Sci. 2010, 15:701-707.
11. Molnar A., et al. Silencing signals in plants: a long journey for small RNAs. Genome Biol. 2011, 12:215.
12. Molnar A., et al. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 2010, 328:872-875.
13. Vainstein A., et al. Permanent genome modifications in plant cells by transient viral vectors. Trends Biotechnol. 2011, 29:363-369.
14. Carrillo-Tripp J., et al. Use of geminiviral vectors for functional genomics. Curr. Opin. Plant Biol. 2006, 9:209-215.
15. Robertson D. VIGS vectors for gene silencing: many targets, many tools. Annu. Rev. Plant Biol. 2004, 55:495-519.
16. Jones A.L., et al. De novo methylation and co-suppression induced by a cytoplasmically replicating plant RNA virus. EMBO J. 1998, 17:6385-6393.
17. Jones L., et al. RNA-DNA interactions and DNA methylation in post-transcriptional gene silencing. Plant Cell 1999, 11:2291-2302.
18. Alvarado V., Scholthof H.B. Plant responses against invasive nucleic acids: RNA silencing and its suppression by plant viral pathogens. Semin. Cell Dev. Biol. 2009, 20:1032-1040.
19. Ding S.-W., Voinnet O. Antiviral immunity directed by small RNAs. Cell 2007, 130:413-426.
20. Donaire L., et al. Structural and genetic requirements for the biogenesis of Tobacco rattle virus-derived small interfering RNAs. J. Virol. 2008, 82:5167-5177.
21. Qu F., et al. Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:14732-14737.
22. Brodersen P., et al. Widespread translational inhibition by plant miRNAs and siRNAs. Science 2008, 320:1185-1190.
23. Zheng X., et al. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J. 2007, 26:1691-1701.
24. Scofield S.R., Nelson R.S. Resources for virus-induced gene silencing in the grasses. Plant Physiol. 2009, 149:152-157.
25. Di Stilio V.S. Empowering plant evo-devo: virus induced gene silencing validates new and emerging model systems. BioEssays 2011, 33:711-718.
26. Burch-Smith T.M., et al. Efficient virus-induced gene silencing in Arabidopsis. Plant Physiol. 2006, 142:21-27.
27. Senthil-Kumar M., et al. Virus-induced gene silencing and its application in characterizing genes involved in water-deficit-stress tolerance. J. Plant Physiol. 2008, 165:1404-1421.
28. Zhang C., et al. The development of an efficient multipurpose Bean pod mottle virus viral vector set for foreign gene expression and RNA silencing. Plant Physiol. 2010, 153:52-65.
29. Yang Y., et al. Silencing Sl-EBF1 and Sl-EBF2 expression causes constitutive ethylene response phenotype, accelerated plant senescence, and fruit ripening in tomato. J. Exp. Bot. 2010, 61:697-708.
30. Zhu X., et al. Virus-induced gene silencing offers a functional genomics platform for studying plant cell wall formation. Mol. Plant 2010, 3:818-833.
31. van der Linde K., et al. Systemic virus-induced gene silencing allows functional characterization of maize genes during biotrophic interaction with Ustilago maydis. New Phytol. 2011, 189:471-483.
32. Gronlund M., et al. Protocol: using virus-induced gene silencing to study the arbuscular mycorrhizal symbiosis in Pisum sativum. Plant Methods 2010, 6:28.
33. Mao Z.C., et al. The new CaSn gene belonging to the snakin family induces resistance against root-knot nematode infection in pepper. Phytoparasitica 2011, 39:151-164.
34. Mantelin S., et al. The receptor-like kinase SlSERK1 is required for Mi-1-mediated resistance to potato aphids in tomato. Plant J. 2011, 67:459-471.
35. Pacak A., et al. Investigations of Barley stripe mosaic virus as a gene silencing vector in barley roots and in Brachypodium distachyon and oat. Plant Methods 2010, 6:26.
36. Xia Z., et al. Molecular cloning and functional characterization of a putative sulfite oxidase (SO) ortholog from Nicotiana benthamiana. Mol. Biol. Rep. 2011, 10.1007/s11033-011-0993-x.
37. George G.M., et al. Virus-induced gene silencing of plastidial soluble inorganic pyrophosphatase impairs essential leaf anabolic pathways and reduces drought stress tolerance in Nicotiana benthamiana. Plant Physiol. 2010, 154:55-66.
38. Vaghchhipawala Z., et al. Agroinoculation and Agroinfiltration: simple tools for complex gene function analyses. Plant Reverse Genetics 2011, 65-76. Humana Press. A. Pereira (Ed.).
39. Bernacki S., et al. Virus-induced gene silencing as a reverse genetics tool to study gene function. Plant Developmental Biology 2010, 27-45. Humana Press. L. Hennig, C. Köhler (Eds.).
40. Todd A.T., et al. A functional genomics screen identifies diverse transcription factors that regulate alkaloid biosynthesis in Nicotiana benthamiana. Plant J. 2010, 62:589-600.
41. Anand A., et al. Identification and characterization of plant genes involved in Agrobacterium-mediated plant transformation by virus-induced gene silencing. Mol. Plant Microbe Interact. 2007, 20:41-52.
42. Pozo O.D., et al. MAPKKKalpha is a positive regulator of cell death associated with both plant immunity and disease. EMBO J. 2004, 23:3072-3082.
43. Wangdi T., et al. A virus-induced gene silencing screen identifies a role for thylakoid formation1 in Pseudomonas syringae pv. tomato symptom development in tomato and Arabidopsis. Plant Physiol. 2010, 152:281-292.
44. Velasquez A.C., et al. Virus-induced gene silencing (VIGS) in Nicotiana benthamiana and Tomato. J. Vis. Exp. 2009, 28:1292.
45. Senthil-Kumar M., et al. A systematic study to determine the extent of gene silencing in Nicotiana benthamiana and other Solanaceae species when heterologous gene sequences are used for virus-induced gene silencing. New Phytol. 2007, 176:782-791.
46. Hosseini Tafreshi S., et al. Heterologous virus-induced gene silencing as a promising approach in plant functional genomics. Mol. Biol. Rep. 2011, 10.1007/s11033-011-0965-1.
47. Zheng S.-J., et al. Silencing defense pathways in Arabidopsis by heterologous gene sequences from Brassica oleracea enhances the performance of a specialist and a generalist herbivorous insect. J. Chem. Ecol. 2011, 37:818-829.
48. Ding X.S., et al. Analysis of gene function in rice through virus-induced gene silencing. Plant-Pathogen Interactions 2007, 145-160. Humana Press. P.C. Ronald (Ed.).
49. Krenz B., et al. Cell-free construction of disarmed Abutilon mosaic virus-based gene silencing vectors. J. Virol. Methods 2010, 169:129-137.
50. Senthil-Kumar M., Mysore K.S. 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. 2011, 9:797-806.
51. Tuttle J.R., et al. Geminivirus-mediated gene silencing from Cotton leaf crumple virus is enhanced by low temperature in cotton. Plant Physiol. 2008, 148:41-50.
52. Chen J.-C., et al. Chalcone synthase as a reporter in virus-induced gene silencing studies of flower senescence. Plant Mol. Biol. 2004, 55:521-530.
53. Held M.A., et al. Small-interfering RNAs from natural antisense transcripts derived from a cellulose synthase gene modulate cell wall biosynthesis in barley. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:20534-20539.
54. Orzaez D., et al. A visual reporter system for virus-induced gene silencing in tomato fruit based on anthocyanin accumulation. Plant Physiol. 2009, 150:1122-1134.
55. Quadrana L., et al. 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. 2011, 156:1278-1291.
56. Senthil-Kumar M., Mysore K.S. Caveat of RNAi in plants: the off-target effect. RNAi and Plant Gene Function Analysis 2011, 13-25. Humana Press. H. Kodama, A. Komamine (Eds.).
57. Xu P., et al. Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. Plant Physiol. 2006, 142:429-440.
58. Liu E., Page J. Optimized cDNA libraries for virus-induced gene silencing (VIGS) using Tobacco rattle virus. Plant Methods 2008, 4:5.
59. Rodrigo G., et al. Optimal viral strategies for bypassing RNA silencing. J. R. Soc. Interface 2011, 8:257-268.
60. Pflieger S., et al. Efficient virus-induced gene silencing in Arabidopsis using a 'one-step' TYMV-derived vector. Plant J. 2008, 56:678-690.
61. Lacomme C., Hrubikova K. Enhancement of virus-induced gene silencing through viral-based production of inverted-repeats. Plant J. 2003, 34:543-553.
62. Wu C., et al. The reliability of virus-induced gene silencing experiments using Tobacco rattle virus in tomato is influenced by the size of the vector control. Mol. Plant Pathol. 2011, 12:299-305.
63. Tufan H.A., et al. The Barley stripe mosaic virus system used for virus-induced gene silencing in cereals differentially affects susceptibility to fungal pathogens in wheat. J. Plant Physiol. 2011, 168:990-994.
64. Cakir C., Tör M. Factors influencing Barley stripe mosaic virus-mediated gene silencing in wheat. Physiol. Mol. Plant Pathol. 2010, 74:246-253.
65. Bruun-Rasmussen M., et al. Stability of Barley stripe mosaic virus-induced gene silencing in barley. Mol. Plant Microbe Interact. 2007, 20:1323-1331.
66. Faivre-Rampant O., et al. Potato virus X-induced gene silencing in leaves and tubers of potato. Plant Physiol. 2004, 134:1308-1316.
67. Renner T., et al. Virus-induced gene silencing in the culinary ginger (Zingiber officinale): an effective mechanism for down-regulating gene expression in tropical monocots. Mol. Plant 2009, 2:1084-1094.
68. Ahn C., Pai H.-S. Physiological function of a plastid MEP pathway gene for isoprenoid biosynthesis, in organelle biogenesis and cell morphogenesis in Nicotiana benthamiana. Plant Mol. Biol. 2008, 66:503-517.
69. Cakir C., et al. Rapid determination of gene function by virus-induced gene silencing in wheat and barley. Crop Sci. 2010, 50:S77-S84.
70. Yamagishi N., Yoshikawa N. Virus-induced gene silencing of endogenous genes and promotion of flowering in soybean by Apple latent spherical virus-based vectors. Soybean - Molecular Aspects of Breeding 2011, 43-56. InTech Publishers. A. Sudaric (Ed.).
71. Yamagishi N., Yoshikawa N. Virus-induced gene silencing in soybean seeds and the emergence stage of soybean plants with Apple latent spherical virus vectors. Plant Mol. Biol. 2009, 71:15-24.
72. Igarashi A., et al. 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 2009, 386:407-416.
73. Macfarlane S.A. Tobraviruses-plant pathogens and tools for biotechnology. Mol. Plant Pathol. 2010, 11:577-583.
74. Hull, R. (2002) Transmission 2: mechanical, seed, pollen and epidemiology. In: Matthews' Plant Virology (4th edn), pp. 533-581, Academic Press.
75. Johansen E., et al. Seed transmission of viruses: current perspectives. Annu. Rev. Phytopathol. 1994, 32:363-386.
76. Wang D., Maule A.J. Contrasting patterns in the spread of two seed-borne viruses in pea embryos. Plant J. 1997, 11:1333-1340.
77. McKinney H.H., Greeley L.W. Biological characteristics of Barley stripe-mosaic virus strains and their evolution. Tech. Bull. U. S. Dept. Agric. 1965, 1324:84.
78. McNeal F.H., et al. Barley stripe mosaic virus data from six infected spring wheat cultivars. Plant Dis. Rep. 1976, 60:730-733.
79. Kanazawa A., et al. Virus-mediated efficient induction of epigenetic modifications of endogenous genes with phenotypic changes in plants. Plant J. 2011, 65:156-168.
80. Sonoda S., Nishiguchi M. Delayed activation of post-transcriptional gene silencing and de novo transgene methylation in plants with the coat protein gene of sweet potato feathery mottle potyvirus. Plant Sci. 2000, 156:137-144.
81. Nagamatsu A., et al. Functional analysis of soybean genes involved in flavonoid biosynthesis by virus-induced gene silencing. Plant Biotechnol. J. 2007, 5:778-790.
82. Kim S., Kim J.-S. Targeted genome engineering via zinc finger nucleases. Plant Biotechnol. Rep. 2011, 5:9-17.
83. Marton I., et al. Nontransgenic genome modification in plant cells. Plant Physiol. 2010, 154:1079-1087.
84. Kanazawa A., et al. RNA-mediated epigenetic modifications of an endogenous gene targeted by a viral vector: a potent gene silencing system to produce a plant that does not carry a transgene but has altered traits. Plant Signal. Behav. 2011, 6:1090-1093.
85. Baena-Gonzalez E., et al. A central integrator of transcription networks in plant stress and energy signalling. Nature 2007, 448:938-942.
86. Cheng S.-F., et al. Identification of differentially expressed genes induced by Bamboo mosaic virus infection in Nicotiana benthamiana by cDNA-amplified fragment length polymorphism. BMC Plant Biol. 2010, 10:286.
87. Cloutier S., et al. Leaf rust resistance gene Lr1, isolated from bread wheat (Triticum aestivum L.) is a member of the large psr567 gene family. Plant Mol. Biol. 2007, 65:93-106.
88. Brueggeman R., et al. The stem rust resistance gene Rpg5 encodes a protein with nucleotide-binding-site, leucine-rich, and protein kinase domains. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:14970-14975.
89. Romero I., et al. Virus-induced gene silencing in detached tomatoes and biochemical effects of phytoene desaturase gene silencing. J. Plant Physiol. 2011, 168:1129-1135.
90. Chai Y.-M., et al. FaPYR1 is involved in strawberry fruit ripening. J. Exp. Bot. 2011, 62:5079-5089.
91. Fu D.-Q., et al. Virus-induced gene silencing in tomato fruit. Plant J. 2005, 43:299-308.
92. Bouzayen M., et al. Mechanism of fruit ripening. Plant Developmental Biology - Biotechnological Perspectives 2010, 319-339. Springer. E.C. Pua, M.R. Davey (Eds.).
93. Giovannoni J.J. Genetic regulation of fruit development and ripening. Plant Cell 2004, 16:S170-S180.
94. Lu R., et al. High throughput virus-induced gene silencing implicates heat shock protein 90 in plant disease resistance. EMBO J. 2003, 22:5690-5699.
95. Todd A.T., et al. cDNA libraries for virus-induced gene silencing. Plant Epigenetics 2010, 221-236. Humana Press. I. Kovalchuk, F.J. Zemp (Eds.).
96. Goodin M.M., et al. Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions. Mol. Plant Microbe Interact. 2008, 21:1015-1026.
97. Yamagishi N., Yoshikawa N. Expression of FLOWERING LOCUS from Arabidopsis thaliana induces precocious flowering in soybean irrespective of maturity group and stem growth habit. Planta 2011, 233:561-568.
98. Yamagishi N., et al. Promotion of flowering and reduction of a generation time in apple seedlings by ectopical expression of the Arabidopsis thaliana gene using the Apple latent spherical virus vector. Plant Mol. Biol. 2011, 75:193-204.
99. Purwestri Y.A., et al. The 14-3-3 protein GF14c acts as a negative regulator of flowering in rice by interacting with the florigen Hd3a. Plant Cell Physiol. 2009, 50:429-438.
100. Wang Q., et al. Combined thermotherapy and cryotherapy for efficient virus eradication: relation of virus distribution, subcellular changes, cell survival and viral RNA degradation in shoot tips. Mol. Plant Pathol. 2008, 9:237-250.
101. Wang Q.C., Valkonen J.P.T. Elimination of two viruses which interact synergistically from sweetpotato by shoot tip culture and cryotherapy. J. Virol. Methods 2008, 154:135-145.
102. Wang Q., Valkonen J.P.T. Cryotherapy of shoot tips: novel pathogen eradication method. Trends Plant Sci. 2009, 14:119-122.
103. Podwyszyńska M., Sochacki D. Micropropagation of tulip: production of virus-free stock plants. Protocols for In Vitro Propagation of Ornamental Plants 2010, 243-256. Humana Press. S.M. Jain, S.J. Ochatt (Eds.).
104. Stamm P., et al. Feeding the extra billions: strategies to improve crops and enhance future food security. Plant Biotechnol. Rep. 2011, 5:107-120.
105. Anand A., et al. Salicylic acid and systemic acquired resistance play a role in attenuating crown gall disease caused by Agrobacterium tumefaciens. Plant Physiol. 2008, 146:703-715.
106. Gelvin S.B. Plant proteins involved in Agrobacterium-mediated genetic transformation. Annu. Rev. Phytopathol. 2010, 48:45-68.
107. Tang Y., et al. Virus-based microRNA expression for gene functional analysis in plants. Plant Physiol. 2010, 153:632-641.