Transcriptome network analysis prioritizes Lsi1 as a candidate gene associated with rice responses to Bacillus amyloliquefaciens under salinity

Soil salinity is a major constraint on rice production worldwide, while plant growth-promoting bacteria (PGPB), such as Bacillus amyloliquefaciens , can improve plant performance under saline conditions. However, the molecular basis underlying rice responses to beneficial bacteria under salinity remains poorly understood. This study aimed to identify candidate genes associated with rice responses to B. amyloliquefaciens by integrating transcriptome network analysis with independent physiological assessment. Publicly available rice root RNA-seq datasets were exploratorily reanalyzed using transcriptome network analysis to generate hypotheses and prioritize candidate genes associated with the combined treatment of salinity and bacterial inoculation. Guided by these predictions, we evaluated two rice genotypes that differ in salinity tolerance under saline conditions, with or without B. amyloliquefaciens inoculation. We then assessed plant growth, physiological and biochemical traits, gene expression, silicon (Si) accumulation, and multivariate analyses. Transcriptome network analysis consistently prioritized the silicon transporter gene Low silicon rice 1 ( Lsi1 ) among the candidate genes. Compared with uninoculated plants, bacterial inoculation alleviated salinity-induced growth inhibition, improved antioxidant capacity, osmotic adjustment, and biomass production, altered Lsi1 expression, and was accompanied by corresponding changes in Si accumulation. Hierarchical clustering and PLS-DA further supported treatment separation and identified Lsi1 expression, oxidative stress markers, and antioxidant enzymes as major contributors to the observed physiological responses. The convergence of transcriptomic, molecular, physiological, and multivariate evidence supports Lsi1 as a candidate gene associated with rice responses to B. amyloliquefaciens under salinity. Our findings further suggest that modulating Si uptake is an important component of host responses to beneficial bacterial inoculation and provide a rational basis for future functional studies investigating the role of Lsi1 in PGPB-mediated salinity tolerance.