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Plant growth-promoting rhizobacteria (PGPR) are beneficial soil microorganisms that colonize plant roots for nutritional purposes and benefit plants by increasing plant growth or reducing plant disease. To clarify the complex mechanisms underlying plant-PGPR interactions, transcriptomic analyses of the response of rice ( Oryza sativa ) 9311 to Bacillus amyloliquefaciens FZB42 were carried out using RNA-Seq technology. This resulted in the identification of 379 differentially expressed genes in rice roots and 719 in rice leaves following FZB42 interaction that are likely to be related to plant-PGPR interactions, plant stress-resistance, pathogen-resistance, growth and development and basic and energy metabolism. We focused on plant disease-resistance mechanisms induced by FZB42. Variations in the expression of crucial genes COI1 , MEKK1 , WRKY, and PR that are involved in signal transduction following plant-pathogen interaction at different interaction time points were examined. Significantly up-regulated expression of PR , LOX, and ERF genes involved in the salicylic acid, jasmonic acid, and ethylene signal transduction pathways, respectively, were detected, suggest that defense reactions in rice were induced following interaction with FZB42. Phytoalexin changes in rice induced by FZB42 were examined and momilactone A, phytocassane A, phytocassane D, phytocassane E levels were low at 12 h, rose between 24 and 48 h, suggesting a PGPR-mediated mechanism of plant pathogen resistance. The study indicated that plant responses to PGPR in multi-metabolism pathways, which includes improving plant pathogen-resistance by mediating multi-signal transduction that regulates the expression of PRs and other defense genes, as well as influencing fundamental metabolic pathways to enhance the plant’s physical condition. [ABSTRACT FROM AUTHOR]