Multi-omics analyses reveal the virulence differentiation underlying natural variation in Burkholderia gladioli

Burkholderia gladioli is a critical pathogen causing bacterial panicle blight in rice, severely threatening global rice yield and grain quality. Here, B. gladioli strains were isolated and identified from two rice fields exhibiting markedly different severities of bacterial panicle blight. Although the two strains belong to the same species, they displayed significant differences in phenotype and pathogenicity. Comparative genomic and transcriptomic analyses revealed that natural variation between the strains not only arose from 79 single-nucleotide polymorphisms (SNPs), 12 insertions/deletions (INDELs), and 3 structural variations (SVs) across 27 mutated genes, which may affect protein function and stability, but also coincided with the significant downregulation of genes in multiple virulence-associated pathways, such as two-component systems, bacterial chemotaxis, quorum sensing, and flagellar assembly at the transcriptional level. The combined effects of genetic variation and transcriptional regulation ultimately contributed to the observed differences in pathogenicity. This study uncovers the potential mechanisms by which natural variation in B. gladioli influences pathogenicity, providing a theoretical basis and potential molecular targets for the precise control of rice bacterial panicle blight.

This study demonstrates that natural variation in Burkholderia gladioli, a major pathogen responsible for bacterial panicle blight in rice, has a significant impact on its pathogenicity and further explores the underlying mechanisms. These findings expand our understanding of how phytopathogens' virulence differentiates conditions of natural variation, and provide potential molecular targets for the development of novel bactericides. The identification of low-virulence strains and their associated gene variations in this study offers both theoretical and practical foundations for ecological disease management and biocontrol of rice bacterial diseases, highlighting their importance for promoting precision agriculture and sustainable development.