Silencing to illuminate: virus-induced gene silencing for accelerated dissection of gene function

The post-genomic era has significantly advanced the identification of target genes through high-throughput methodologies, such as routine transcriptomics, single-cell sequencing, genome-wide association studies, spatial transcriptomics, and machine learning-based gene-prediction pipelines. However, the swift identification of candidate genes has surpassed their functional validation, creating a critical bottleneck. The functional genomics methods, including stable genetic transformation, transgenic knockouts, and chemical mutagenesis, are excessively slow, labor-intensive, and costly, particularly for nonmodel crops and polyploid species. Virus-induced gene silencing (VIGS) provides a rapid, transient, and cost-effective complementary approach to stable transformation and genome editing for functional validation, particularly in species where transformation is difficult. This review comprehensively outlines the biology of VIGS, tracing the evolution of viral vector design and technical optimizations for enhanced silencing efficiency. We examine the applications of VIGS across essential agronomic areas, including resilience to abiotic stresses such as drought, heat, and cold; defense against biotic factors like pathogens and insects; developmental biology; and plant-microbe interactions, highlighting VIGS’s versatility across both model and crop species. Potential challenges influencing the VIGS efficiency are also discussed. VIGS represents a scalable, nontransgenic solution for accelerating functional validation pipelines, supporting climate-resilient crop breeding to address global food security in the post-genomic era.