Caspofungin-guided identification of SsFKS1 as a host-induced gene-silencing target for Sclerotinia stem rot resistance in rapeseed

Sclerotinia stem rot (SSR) is a devastating disease caused by the necrotrophic fungus Sclerotinia sclerotiorum , it caused 20–80% yield loss in rapeseed every year. Host-Induced Gene Silencing (HIGS) represents a promising strategy to improve SSR resistance due to the scarcity of highly resistant rapeseed genotypes. However, the lack of robust targets remains a major bottleneck for the application of HIGS. This study presented a novel strategy to efficiently discover the HIGS targets using an antifungal drug caspofungin (CFN). It was found that CFN treatment not only modified rapeseed architecture but also suppressed S. sclerotiorum growth and pathogenicity. Transcriptomic analysis revealed that CFN significantly suppressed amino acid metabolism pathways in Sclerotinia sclerotiorum , while WGCNA identified SsFKS1 as a key gene associated with the CFN-induced inhibition of fungal growth and pathogenicity. The SsFKS1 knockout mutant failed to produce sclerotia and showed impaired mycelial growth, following analysis discovered that the pathogenicity of mycelium was completely abolished. It is confirmed that the dsRNA ( dsfks1 ) targeting to the domain of SsFKS1 inhibited the growth and pathogenicity of mycelia. Furthermore, HIGS-mediated silencing of SsFKS1 significantly enhanced resistance to SSR in transgenic rapeseed. Our findings demonstrated that clinical antifungals could be used as powerful and convenient tools for identifying potential HIGS targets, providing both a promising gene resource for SSR-resistant breeding and a broadly applicable strategy for protecting crops against fungal pathogens.