Source 1primary paper2004PLANT PHYSIOLOGY
Toolkit/virus-induced gene silencing
virus-induced gene silencing
Also known as: VIGS
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Virus-induced gene silencing (VIGS) was used in tomato (Solanum lycopersicum) to reduce CRY2 expression as part of a combined perturbation strategy alongside transgenic overexpression. In the cited study, CRY2 silencing in wild-type tomato produced a minor internode elongation phenotype.
Usefulness & Problems
Why this is useful
This method is useful for transiently perturbing endogenous gene expression in tomato without requiring stable loss-of-function lines. In the cited work, it enabled functional interrogation of CRY2 by providing a silencing-based contrast to transgenic overexpression.
Source:
Tomato CRY2 overexpressors show phenotypes similar to but distinct from their Arabidopsis counterparts (hypocotyl and internode shortening under both low- and high-fluence blue light)
Source:
CRY2 overexpression causes an unexpected delay in flowering, observed under both short- and long-day conditions, and an increased outgrowth of axillary branches.
Source:
but also several novel ones, including a high-pigment phenotype, resulting in overproduction of anthocyanins and chlorophyll in leaves and of flavonoids and lycopene in fruits
Source:
whereas in wild-type plants it causes a minor internode elongation
Problem solved
It addresses the problem of testing CRY2 gene function in tomato by reducing native CRY2 expression in planta. The available evidence specifically supports its use for assessing effects on vegetative development, with minor internode elongation reported after CRY2 silencing.
Published Workflows
Objective: Identify NAC transcription factors associated with leaf senescence in Clerodendrum japonicum and functionally test whether prioritized candidates positively regulate senescence and ABA/dark-induced responses.
Why it works: The workflow first narrows candidates by differential expression during senescence, then validates expression patterns, and finally tests causality using gain-of-function and silencing assays in complementary systems.
mediation of ABA signaling pathwaysmediation of dark signaling pathwaystranscriptome sequencingcandidate screeningqRT-PCR validationheterologous overexpressionVIGS
Stages
- 1.Transcriptome-based candidate discovery(broad_screen)
This stage identifies candidate genes associated with leaf senescence before targeted validation and functional testing.
Selection: Differential expression between mature and early-senescent leaves in C. japonicum.
- 2.Expression-pattern validation(secondary_characterization)
This stage confirms that transcriptome-nominated NAC candidates show expression patterns consistent with senescence association.
Selection: qRT-PCR validation of candidate NAC gene expression patterns.
- 3.Functional perturbation characterization(functional_characterization)
This stage tests whether prioritized NAC candidates causally promote or delay senescence when increased or reduced in expression.
Selection: Functional testing of CjNAC43 and CjNAC54 by heterologous overexpression in Arabidopsis thaliana and VIGS in C. japonicum.
- 4.ABA- and dark-induced senescence testing(confirmatory_validation)
This stage tests whether the senescence-promoting role of the candidate NAC genes extends to ABA- and darkness-associated stress contexts.
Selection: Assessment of candidate gene roles under ABA- and dark-induced senescence conditions.
Steps
- 1.Sequence transcriptomes from mature and early-senescent leavesdiscovery assay
Identify genes differentially expressed between mature and early-senescent C. japonicum leaves.
This is the initial broad discovery step used to generate candidate senescence-associated genes before targeted validation.
- 2.Screen candidate NAC genes from transcriptomic results
Prioritize NAC family members associated with senescence from the transcriptomic dataset.
Candidate screening follows transcriptome generation because the sequencing output provides the pool from which NAC candidates are selected.
- 3.Validate candidate expression patterns by qRT-PCRexpression validation assay
Confirm expression patterns of candidate NAC genes identified from transcriptomic screening.
Expression validation is performed after candidate screening to confirm that prioritized genes show the expected senescence-associated expression pattern before functional testing.
- 4.Characterize CjNAC43 and CjNAC54 by heterologous overexpression in Arabidopsis thalianagenes under functional test
Test whether increased expression of CjNAC43 or CjNAC54 promotes senescence phenotypes.
After expression-based prioritization, gain-of-function testing provides causal evidence that the selected NAC genes can accelerate senescence.
- 5.Silence CjNAC43 or CjNAC54 in C. japonicum using VIGSloss-of-function validation method and targets
Test whether reducing CjNAC43 or CjNAC54 expression delays senescence in the native species.
This complementary loss-of-function step follows gain-of-function testing to strengthen causal inference and assess native-species relevance.
- 6.Assess roles of CjNAC43 and CjNAC54 in ABA- and dark-induced senescencegenes under stress-context validation
Determine whether the candidate NAC genes enhance sensitivity to ABA and darkness during senescence.
This confirmatory step follows core functional characterization to test whether the senescence-promoting effect extends to specific signaling contexts highlighted by the study.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete method used to build, optimize, or evolve an engineered system.
Mechanisms
gene silencingTechniques
No technique tags yet.
Target processes
No target processes tagged yet.
Implementation Constraints
The evidence states only that tomato CRY2 expression was altered through virus-induced gene silencing in Solanum lycopersicum. The specific virus system, construct architecture, inoculation method, and experimental conditions are not described in the supplied material.
The supplied evidence is limited to one 2004 tomato study and one reported silencing phenotype, minor internode elongation. No details are provided here on silencing efficiency, viral vector design, tissue specificity, duration, off-target effects, or performance in other genes or species.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Overexpression of tomato CRY2 causes hypocotyl and internode shortening under both low- and high-fluence blue light.
Tomato CRY2 overexpressors show phenotypes similar to but distinct from their Arabidopsis counterparts (hypocotyl and internode shortening under both low- and high-fluence blue light)
Overexpression of tomato CRY2 causes hypocotyl and internode shortening under both low- and high-fluence blue light.
Tomato CRY2 overexpressors show phenotypes similar to but distinct from their Arabidopsis counterparts (hypocotyl and internode shortening under both low- and high-fluence blue light)
Overexpression of tomato CRY2 causes hypocotyl and internode shortening under both low- and high-fluence blue light.
Tomato CRY2 overexpressors show phenotypes similar to but distinct from their Arabidopsis counterparts (hypocotyl and internode shortening under both low- and high-fluence blue light)
Overexpression of tomato CRY2 causes hypocotyl and internode shortening under both low- and high-fluence blue light.
Tomato CRY2 overexpressors show phenotypes similar to but distinct from their Arabidopsis counterparts (hypocotyl and internode shortening under both low- and high-fluence blue light)
Overexpression of tomato CRY2 causes hypocotyl and internode shortening under both low- and high-fluence blue light.
Tomato CRY2 overexpressors show phenotypes similar to but distinct from their Arabidopsis counterparts (hypocotyl and internode shortening under both low- and high-fluence blue light)
Overexpression of tomato CRY2 causes hypocotyl and internode shortening under both low- and high-fluence blue light.
Tomato CRY2 overexpressors show phenotypes similar to but distinct from their Arabidopsis counterparts (hypocotyl and internode shortening under both low- and high-fluence blue light)
Overexpression of tomato CRY2 causes hypocotyl and internode shortening under both low- and high-fluence blue light.
Tomato CRY2 overexpressors show phenotypes similar to but distinct from their Arabidopsis counterparts (hypocotyl and internode shortening under both low- and high-fluence blue light)
Overexpression of tomato CRY2 delays flowering under both short-day and long-day conditions and increases axillary branch outgrowth.
CRY2 overexpression causes an unexpected delay in flowering, observed under both short- and long-day conditions, and an increased outgrowth of axillary branches.
Overexpression of tomato CRY2 delays flowering under both short-day and long-day conditions and increases axillary branch outgrowth.
CRY2 overexpression causes an unexpected delay in flowering, observed under both short- and long-day conditions, and an increased outgrowth of axillary branches.
Overexpression of tomato CRY2 delays flowering under both short-day and long-day conditions and increases axillary branch outgrowth.
CRY2 overexpression causes an unexpected delay in flowering, observed under both short- and long-day conditions, and an increased outgrowth of axillary branches.
Overexpression of tomato CRY2 delays flowering under both short-day and long-day conditions and increases axillary branch outgrowth.
CRY2 overexpression causes an unexpected delay in flowering, observed under both short- and long-day conditions, and an increased outgrowth of axillary branches.
Overexpression of tomato CRY2 delays flowering under both short-day and long-day conditions and increases axillary branch outgrowth.
CRY2 overexpression causes an unexpected delay in flowering, observed under both short- and long-day conditions, and an increased outgrowth of axillary branches.
Overexpression of tomato CRY2 delays flowering under both short-day and long-day conditions and increases axillary branch outgrowth.
CRY2 overexpression causes an unexpected delay in flowering, observed under both short- and long-day conditions, and an increased outgrowth of axillary branches.
Overexpression of tomato CRY2 delays flowering under both short-day and long-day conditions and increases axillary branch outgrowth.
CRY2 overexpression causes an unexpected delay in flowering, observed under both short- and long-day conditions, and an increased outgrowth of axillary branches.
Overexpression of tomato CRY2 produces a high-pigment phenotype with overproduction of anthocyanins and chlorophyll in leaves and flavonoids and lycopene in fruits.
but also several novel ones, including a high-pigment phenotype, resulting in overproduction of anthocyanins and chlorophyll in leaves and of flavonoids and lycopene in fruits
Overexpression of tomato CRY2 produces a high-pigment phenotype with overproduction of anthocyanins and chlorophyll in leaves and flavonoids and lycopene in fruits.
but also several novel ones, including a high-pigment phenotype, resulting in overproduction of anthocyanins and chlorophyll in leaves and of flavonoids and lycopene in fruits
Overexpression of tomato CRY2 produces a high-pigment phenotype with overproduction of anthocyanins and chlorophyll in leaves and flavonoids and lycopene in fruits.
but also several novel ones, including a high-pigment phenotype, resulting in overproduction of anthocyanins and chlorophyll in leaves and of flavonoids and lycopene in fruits
Overexpression of tomato CRY2 produces a high-pigment phenotype with overproduction of anthocyanins and chlorophyll in leaves and flavonoids and lycopene in fruits.
but also several novel ones, including a high-pigment phenotype, resulting in overproduction of anthocyanins and chlorophyll in leaves and of flavonoids and lycopene in fruits
Overexpression of tomato CRY2 produces a high-pigment phenotype with overproduction of anthocyanins and chlorophyll in leaves and flavonoids and lycopene in fruits.
but also several novel ones, including a high-pigment phenotype, resulting in overproduction of anthocyanins and chlorophyll in leaves and of flavonoids and lycopene in fruits
Overexpression of tomato CRY2 produces a high-pigment phenotype with overproduction of anthocyanins and chlorophyll in leaves and flavonoids and lycopene in fruits.
but also several novel ones, including a high-pigment phenotype, resulting in overproduction of anthocyanins and chlorophyll in leaves and of flavonoids and lycopene in fruits
Overexpression of tomato CRY2 produces a high-pigment phenotype with overproduction of anthocyanins and chlorophyll in leaves and flavonoids and lycopene in fruits.
but also several novel ones, including a high-pigment phenotype, resulting in overproduction of anthocyanins and chlorophyll in leaves and of flavonoids and lycopene in fruits
Virus-induced gene silencing of CRY2 in wild-type tomato plants causes a minor internode elongation.
whereas in wild-type plants it causes a minor internode elongation
Virus-induced gene silencing of CRY2 in wild-type tomato plants causes a minor internode elongation.
whereas in wild-type plants it causes a minor internode elongation
Virus-induced gene silencing of CRY2 in wild-type tomato plants causes a minor internode elongation.
whereas in wild-type plants it causes a minor internode elongation
Virus-induced gene silencing of CRY2 in wild-type tomato plants causes a minor internode elongation.
whereas in wild-type plants it causes a minor internode elongation
Virus-induced gene silencing of CRY2 in wild-type tomato plants causes a minor internode elongation.
whereas in wild-type plants it causes a minor internode elongation
Virus-induced gene silencing of CRY2 in wild-type tomato plants causes a minor internode elongation.
whereas in wild-type plants it causes a minor internode elongation
Virus-induced gene silencing of CRY2 in wild-type tomato plants causes a minor internode elongation.
whereas in wild-type plants it causes a minor internode elongation
In fruits of CRY2-overexpressing tomato plants, lycopene accumulation is accompanied by decreased expression of lycopene beta-cyclase genes.
The accumulation of lycopene in fruits is accompanied by the decreased expression of lycopene beta-cyclase genes.
In fruits of CRY2-overexpressing tomato plants, lycopene accumulation is accompanied by decreased expression of lycopene beta-cyclase genes.
The accumulation of lycopene in fruits is accompanied by the decreased expression of lycopene beta-cyclase genes.
In fruits of CRY2-overexpressing tomato plants, lycopene accumulation is accompanied by decreased expression of lycopene beta-cyclase genes.
The accumulation of lycopene in fruits is accompanied by the decreased expression of lycopene beta-cyclase genes.
In fruits of CRY2-overexpressing tomato plants, lycopene accumulation is accompanied by decreased expression of lycopene beta-cyclase genes.
The accumulation of lycopene in fruits is accompanied by the decreased expression of lycopene beta-cyclase genes.
In fruits of CRY2-overexpressing tomato plants, lycopene accumulation is accompanied by decreased expression of lycopene beta-cyclase genes.
The accumulation of lycopene in fruits is accompanied by the decreased expression of lycopene beta-cyclase genes.
In fruits of CRY2-overexpressing tomato plants, lycopene accumulation is accompanied by decreased expression of lycopene beta-cyclase genes.
The accumulation of lycopene in fruits is accompanied by the decreased expression of lycopene beta-cyclase genes.
In fruits of CRY2-overexpressing tomato plants, lycopene accumulation is accompanied by decreased expression of lycopene beta-cyclase genes.
The accumulation of lycopene in fruits is accompanied by the decreased expression of lycopene beta-cyclase genes.
Virus-induced gene silencing of CRY2 reverses leaf anthocyanin accumulation, internode shortening, and late flowering in CRY2-overexpressing tomato plants.
Virus-induced gene silencing of CRY2 results in a reversion of leaf anthocyanin accumulation, of internode shortening, and of late flowering in CRY2-overexpressing plants
Virus-induced gene silencing of CRY2 reverses leaf anthocyanin accumulation, internode shortening, and late flowering in CRY2-overexpressing tomato plants.
Virus-induced gene silencing of CRY2 results in a reversion of leaf anthocyanin accumulation, of internode shortening, and of late flowering in CRY2-overexpressing plants
Virus-induced gene silencing of CRY2 reverses leaf anthocyanin accumulation, internode shortening, and late flowering in CRY2-overexpressing tomato plants.
Virus-induced gene silencing of CRY2 results in a reversion of leaf anthocyanin accumulation, of internode shortening, and of late flowering in CRY2-overexpressing plants
Virus-induced gene silencing of CRY2 reverses leaf anthocyanin accumulation, internode shortening, and late flowering in CRY2-overexpressing tomato plants.
Virus-induced gene silencing of CRY2 results in a reversion of leaf anthocyanin accumulation, of internode shortening, and of late flowering in CRY2-overexpressing plants
Virus-induced gene silencing of CRY2 reverses leaf anthocyanin accumulation, internode shortening, and late flowering in CRY2-overexpressing tomato plants.
Virus-induced gene silencing of CRY2 results in a reversion of leaf anthocyanin accumulation, of internode shortening, and of late flowering in CRY2-overexpressing plants
Virus-induced gene silencing of CRY2 reverses leaf anthocyanin accumulation, internode shortening, and late flowering in CRY2-overexpressing tomato plants.
Virus-induced gene silencing of CRY2 results in a reversion of leaf anthocyanin accumulation, of internode shortening, and of late flowering in CRY2-overexpressing plants
Virus-induced gene silencing of CRY2 reverses leaf anthocyanin accumulation, internode shortening, and late flowering in CRY2-overexpressing tomato plants.
Virus-induced gene silencing of CRY2 results in a reversion of leaf anthocyanin accumulation, of internode shortening, and of late flowering in CRY2-overexpressing plants
Approval Evidence
2 sources3 linked approval claimsfirst-pass slug virus-induced-gene-silencing
The functions of CjNAC43 and CjNAC54 were characterized through heterologous overexpression in Arabidopsis thaliana and Virus-Induced Gene Silencing (VIGS) in C. japonicum.
Source:
Expression of the tomato (Solanum lycopersicum) CRY2 gene was altered through a combination of transgenic overexpression and virus-induced gene silencing.
Source:
loss of function effectsupports
Silencing CjNAC43 or CjNAC54 in Clerodendrum japonicum delays leaf senescence.
Conversely, silencing CjNAC43 or CjNAC54 in C. japonicum delayed senescence.
Source:
functional effectsupports
Virus-induced gene silencing of CRY2 in wild-type tomato plants causes a minor internode elongation.
whereas in wild-type plants it causes a minor internode elongation
Source:
genetic reversionsupports
Virus-induced gene silencing of CRY2 reverses leaf anthocyanin accumulation, internode shortening, and late flowering in CRY2-overexpressing tomato plants.
Virus-induced gene silencing of CRY2 results in a reversion of leaf anthocyanin accumulation, of internode shortening, and of late flowering in CRY2-overexpressing plants
Source:
Comparisons
Source-backed strengths
The study demonstrates that VIGS could alter tomato CRY2 expression in vivo and generate a detectable developmental phenotype. It was also compatible with a broader perturbation framework in which silencing data were interpreted alongside overexpression phenotypes.
Ranked Citations
- 1.