Review Virus-induced gene silencing and its applications Muthappa Senthil-Kumar, Ajith Anand, Srinivasa Rao Uppalapati and Kirankumar S. Mysore* Address: Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pky, Ardmore, OK 73402, USA. *Correspondence: Kirankumar S. Mysore. Fax. 580-224-6692. Email: ksmysore@noble.org Received: 8 November 2007 Accepted: 14 January 2008 doi: 10.1079/PAVSNNR20083011 The electronic version of this article is the definitive one. It is located here: http://www.cababstractsplus.org/cabreviews g CAB International 2008 (Online ISSN 1749-8848) Abstract Virus-induced gene silencing (VIGS) is an efficient tool for plant functional genomics. Our current understanding about the phenomenon of post-transcriptional gene silencing (PTGS) in plant defence against viruses has enabled us to modify virus genomes for VIGS in different plant species. In this review, we provide a comprehensive update on the application of VIGS. We have attempted to cover the following topics in this review: different VIGS vectors available to date; VIGS as a tool to identify novel genes involved in various aspects of plant biology; VIGS in different plant species; utility of VIGS in different plant organs; VIGS for deciphering cellular functions of known genes; and future application of VIGS in modern plant biology. Keywords: VIGS, Plant functional genomics, Viral vectors, PTGS, Fast-forward genetics, Reverse genetics Review Methodology: The relevant literature was collected through a detailed search of the PubMed, SCIRUS and Google Scholar Web-based search engines. Some of our unpublished research is also included in this review. Introduction The genomics era has generated large-scale information in the form of DNA sequences, and the function of the majority of these is still unknown. Translation of the DNA sequences in databases for functional utility is well illus- trated by the fact that only less than 10% of the predicted genes in the Arabidopsis genome have been experimentally characterized [1]. Functional characterization of the genes from whole-genome sequencing or of the predicted genes based on expression analyses has been confined to plant species that have good genetic maps and large-scale mutant collections with an efficient plant transformation technology. These traditional approaches for gene char- acterization require generation of transgenic plants and are not very conducive for high-throughput analyses. Hence, a powerful tool for functional genomics and an alternative to the massive generation of transgenic plants are essential [2]. The onset of the ‘omics’ era has seen the development of many modern tools for gene discovery and validation. Some of the omics tools currently available for large-scale systems biology include transcriptomics, proteomics and metabolomics. Even though these tools have been applied for relating a gene to a function in many plant species, there is an immense need for platforms for gene knockout or knockdown to study gene function. The four general methods that are commonly used to knockout or knock- down gene expression in plants are: post-transcriptional gene silencing (PTGS), chemical mutagenesis, radiation mutagenesis and insertional mutagenesis. Chemical and radiation mutagenesis approaches are very powerful and convenient to generate mutants. However, it is more difficult and time-consuming to clone the mutated genes as this involves map-based cloning or transcript profiling. Even the Targeting Induced Local Lesion IN Genomes (TILLING) technique that can be used to screen these mutant lines [3] is only a reverse genetics tool and is limited to plant species for which complete sequence information is available. When employing insertional mutagenesis, on the other hand, it is time-consuming to generate the mutant population but relatively easy and fast to clone the mutated genes using the mutagens as tags. PTGS is a better alternative in some instances and has gained more popularity during recent years. PTGS can be induced by antisense and sense transgenic techno- logies, or by expressing double-stranded RNA (dsRNA) through stable or transient transformation with RNA http://www.cababstractsplus.org/cabreviews CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 2008 3, No. 011