Digital gene expression profiling of the pathogen-resistance mechanism of Oryza sativa 9311 in response to Bacillus amyloliquefaciens FZB42 induction

•Transcriptomic analyses in rice response to Bacillus were performed.•Five signal transduction pathways were affected by FZB42 in rice leaves.•Three signal transduction pathways were affected by FZB42 in rice roots.•Bacillus could induce phytoalexin production to improve disease resistance.