Subtopic Deep Dive

Virus-Induced Gene Silencing in Functional Genomics
Research Guide

What is Virus-Induced Gene Silencing in Functional Genomics?

Virus-Induced Gene Silencing (VIGS) uses recombinant plant viruses like Tobacco rattle virus (TRV) to trigger RNA interference for rapid, transient knockdown of target genes in functional genomics studies.

VIGS enables high-throughput gene function analysis in non-model plants without stable transgenics (Liu et al., 2002; 1661 citations). TRV-based vectors silence genes in tomato and Nicotiana benthamiana, while Barley stripe mosaic virus (BSMV) works in monocots like barley (Holzberg et al., 2002; 644 citations). Over 5000 papers cite VIGS methods since 1999 (Baulcombe, 1999).

Curated Papers

Key Challenges

Why It Matters

VIGS accelerates functional genomics in crops like tomato and wheat by validating phenotypes for stress-response and developmental genes, bypassing lengthy transformation protocols (Liu et al., 2002; Holzberg et al., 2002). It supports breeding via Sol Genomics Network resources linking silenced phenotypes to genotypes (Fernández-Pozo et al., 2014; 686 citations). HIGS extends VIGS principles to silence fungal pathogen genes, enhancing disease resistance (Nowara et al., 2010; 718 citations).

Key Research Challenges

Vector Host Specificity

TRV vectors work in dicots like tomato but require BSMV adaptation for monocots (Liu et al., 2002; Holzberg et al., 2002). Silencing efficiency varies by plant species and gene locus. Off-target effects complicate phenotype interpretation (Lu, 2003).

Systemic Silencing Spread

Meristem invasion by viruses like Potato virus X depends on RNA-dependent RNA polymerases for signal propagation (Schwach et al., 2005; 487 citations). Incomplete silencing in shoot apices limits developmental gene studies. Signal mobility requires optimization for non-model plants.

Phenotype Validation Scale

High-throughput VIGS generates phenotypes needing genomic integration via resources like SGN (Fernández-Pozo et al., 2014). Distinguishing VIGS effects from viral symptoms challenges validation. CRISPR alternatives like Cas13a emerge but lack VIGS speed (Aman et al., 2018).

Essential Papers

Virus‐induced gene silencing in tomato

Yule Liu, Michael Schiff, Savithramma P. Dinesh‐Kumar · 2002 · The Plant Journal · 1.7K citations

Abstract We have previously demonstrated that a tobacco rattle virus (TRV)‐based vector can be used in virus‐induced gene silencing (VIGS) to study gene function in Nicotiana benthamiana . Here we ...

RNA virus interference via CRISPR/Cas13a system in plants

Rashid Aman, Zahir Ali, Haroon Butt et al. · 2018 · Genome biology · 1.5K citations

Two classes of short interfering RNA in RNA silencing

Andrew J. Hamilton · 2002 · The EMBO Journal · 997 citations

HIGS: Host-Induced Gene Silencing in the Obligate Biotrophic Fungal Pathogen <i>Blumeria graminis</i>

Daniela Nowara, Alexandra Gay, Christophe Lacomme et al. · 2010 · The Plant Cell · 718 citations

Abstract Powdery mildew fungi are obligate biotrophic pathogens that only grow on living hosts and cause damage in thousands of plant species. Despite their agronomical importance, little direct fu...

The Sol Genomics Network (SGN)—from genotype to phenotype to breeding

Noé Fernández‐Pozo, Naama Menda, Jeremy D. Edwards et al. · 2014 · Nucleic Acids Research · 686 citations

This FAIRsharing record describes: The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, pot...

<i>Barley stripe mosaic virus</i> ‐induced gene silencing in a monocot plant

Steve Holzberg, Paul Brosio, Cynthia Gross et al. · 2002 · The Plant Journal · 644 citations

Summary RNA silencing of endogenous plant genes can be achieved by virus‐mediated, transient expression of homologous gene fragments. This powerful, reverse genetic approach, known as virus‐induced...

Fast forward genetics based on virus-induced gene silencing

David C. Baulcombe · 1999 · Current Opinion in Plant Biology · 633 citations

Reading Guide

Foundational Papers

Read Liu et al. (2002; 1661 citations) first for TRV VIGS in tomato, then Holzberg et al. (2002; 644 citations) for monocot extension, and Hamilton (2002; 997 citations) for siRNA mechanisms.

Recent Advances

Study Aman et al. (2018; 1476 citations) for CRISPR/Cas13a augmentation of VIGS and Zhang et al. (2017; 498 citations) for wheat disease resistance links.

Core Methods

Core techniques: viral vector construction (TRV/BSMV), agroinfiltration, RT-PCR for silencing confirmation, and phenotype scoring (Liu et al., 2002; Lu, 2003).

How PapersFlow Helps You Research Virus-Induced Gene Silencing in Functional Genomics

Discover & Search

PapersFlow's Research Agent uses searchPapers('Virus-Induced Gene Silencing tomato TRV') to find Liu et al. (2002; 1661 citations), then citationGraph to map 5000+ citing works, and findSimilarPapers to identify monocot adaptations like Holzberg et al. (2002). exaSearch uncovers unpublished protocols in SGN-linked studies (Fernández-Pozo et al., 2014).

Analyze & Verify

Analysis Agent applies readPaperContent on Liu et al. (2002) to extract TRV vector designs, verifyResponse with CoVe against Baulcombe (1999) for silencing mechanisms, and runPythonAnalysis to quantify siRNA classes from Hamilton (2002) data using pandas for length distributions. GRADE grading scores VIGS efficiency claims at A-level for tomato phenotypes.

Synthesize & Write

Synthesis Agent detects gaps in monocot VIGS scalability beyond BSMV (Holzberg et al., 2002), flags contradictions in HIGS fungal targeting (Nowara et al., 2010), and uses exportMermaid for VIGS workflow diagrams. Writing Agent employs latexEditText for methods sections, latexSyncCitations to integrate 10 papers, and latexCompile for publication-ready reviews.

Use Cases

"Analyze siRNA profiles from VIGS in tomato using Python."

Research Agent → searchPapers('VIGS tomato TRV') → Analysis Agent → readPaperContent(Liu 2002) → runPythonAnalysis(pandas plot siRNA lengths from Hamilton 2002 data) → matplotlib histogram of 21nt vs 24nt classes.

"Draft LaTeX review of TRV VIGS protocols."

Research Agent → citationGraph(Liu 2002) → Synthesis Agent → gap detection → Writing Agent → latexEditText(vector optimization) → latexSyncCitations(5 papers) → latexCompile(PDF with phenotypes table).

"Find GitHub repos for BSMV VIGS vectors."

Research Agent → searchPapers('BSMV VIGS barley') → Code Discovery → paperExtractUrls(Holzberg 2002) → paperFindGithubRepo → githubRepoInspect(clone TRV-BSMV plasmids code).

Automated Workflows

Deep Research workflow scans 50+ VIGS papers via searchPapers → citationGraph → structured report ranking TRV vs BSMV by citations (Liu 2002 leads). DeepScan's 7-step chain verifies silencing signals in Schwach et al. (2005) with CoVe checkpoints and runPythonAnalysis on RdRP kinetics. Theorizer generates hypotheses linking VIGS to CRISPR/Cas13a hybrids from Aman et al. (2018).

Try Doxa for Virus-Induced Gene Silencing in Functional Genomics Research

Frequently Asked Questions

What defines Virus-Induced Gene Silencing?

VIGS delivers gene fragments via viral vectors like TRV to trigger RNA interference and silence homologous endogenous genes transiently (Liu et al., 2002).

What are core VIGS methods?

Recombinant TRV infects tomato for dicot silencing; BSMV targets monocots like barley (Liu et al., 2002; Holzberg et al., 2002). Methods include agroinfiltration and siRNA detection (Lu, 2003).

What are key VIGS papers?

Liu et al. (2002; 1661 citations) established TRV in tomato; Holzberg et al. (2002; 644 citations) extended to monocots; Baulcombe (1999; 633 citations) reviewed fast-forward genetics.

What open problems exist in VIGS?

Improving monocot vector efficiency, reducing off-targets, and scaling phenotype-genotype links via SGN remain challenges (Fernández-Pozo et al., 2014; Schwach et al., 2005).