<i>Burkholderia glumae </i>is the Gram-negative bacterium causing bacterial panicle blight of rice. Major virulence factors of this pathogen, including toxoflavin (a phytotoxin), lipase and flagella, are known to be controlled by the quorum-sensing (QS) system composed of the LuxI and LuxR homologs, TofI and TofR. Our recent study with <i>B. glumae </i>336gr-1, a virulence strain isolated from a Louisiana rice field, revealed that toxoflavin production can be produced without <i>tofI </i>and/or <i>tofR </i>on a solid medium, implying the presence of unknown cell-to-cell signaling pathways independent of <i>tofI </i>and/or <i>tofR</i>. RNA sequencing and transcriptome analysis with <i>B. glumae </i>QS mutants revealed that genes predicted to function for the synthesis of BDSF (a fatty acid-type QS signaling molecule) and cyclic di-GMP (a key intracellular signaling molecule) as well as for bacterial programmed cell death were expressed in the dependence of the <i>tofI/tofR </i>QS system. In this study, it was also found that many genes involved in signal perception, transduction and transport were up-regulated specifically in the cells grown on a solid medium, suggesting that alternative cell-to-cell signaling pathways are activated in bacterial cells grown in a sessile form.