Transcriptomic responses of rice (Oryza sativa) during interaction with plant growth-promoting bacteria associated with systemic resistance to Burkholderia glumae

Abstract Herbaspirillum seropedicae strain HS09, previously isolated from commercial rice ( Oryza sativa ) and identified by molecular analysis, has shown biocontrol potential against Burkholderia glumae under greenhouse conditions. However, the molecular mechanisms by which HS09 induces systemic resistance against B. glumae in rice remain poorly understood. In this study, we investigated the molecular basis of plant growth-promoting bacteria-mediated systemic resistance against B. glumae in rice through transcriptomic analysis. Four treatments were evaluated: an untreated control, a treatment inoculated with the endophyte HS09, a treatment inoculated with the pathogen B. glumae , and an inducer treatment consisting of HS09 inoculation followed by B. glumae challenge. For the experiment, 90 seeds were used per treatment and randomly distributed under controlled greenhouse conditions. The results showed that HS09 activates key defense-related signaling pathways, particularly those mediated by jasmonic acid ( JAMyb and MYC2 ) and ethylene ( EIN3 , EILs , and ERF transcription factors). In addition, Rboh and CaMCML , genes associated with calcium-dependent signaling and the hypersensitive response (HR), were upregulated, indicating the involvement of Ca²⁺-mediated defense activation. Enrichment analyses also revealed induction of the phenylpropanoid biosynthesis pathway, promoting the production of antimicrobial secondary metabolites such as isoflavones. Notably, 404 differentially expressed genes were uniquely identified in the inducer treatment, supporting the role of HS09 in priming multiple molecular pathways involved in pathogen defense. These findings highlight the potential of H. seropedicae HS09 as a sustainable biocontrol agent against B. glumae and support its integration into crop protection programs and policies aimed at reducing dependence on chemical pesticides and promoting environmentally friendly disease management strategies in rice production systems.