Integrative meta-analysis of RNA-Seq data reveals conserved orthologous gene modules and pathways in wheat and rice in response to plant growth-promoting bacteria.

Plant growth-promoting bacteria (PGPB) offer a promising avenue for sustainable cereal crop production, yet the conserved molecular mechanisms underlying their interactions with major crop plants remain poorly characterized. Transcriptomic studies on PGPB-treated wheat and rice differ substantially in experimental conditions, complicating the identification of reproducible host-response signatures. Here, we re-analyzed raw RNA-Seq data from eight independent PGPB-inoculation studies in root tissues of Oryza sativa and Triticum aestivum using a standardized bioinformatics pipeline. Cross-species ortholog mapping, applied post hoc to independently computed DEG lists, identified 69 differentially expressed (DE) orthologs with conserved expression patterns across diverse PGPB-cereal combinations. These genes encode transporters, metabolic enzymes, transcription factors, and defense-related signaling proteins, and are enriched in pathways including plant-pathogen interaction, MAPK signaling, and phenylpropanoid biosynthesis. Protein-protein interaction network analysis identified hub genes - including CHS1, AHT1, TBT1, PHT3, 4-coumarate-CoA ligase, B7F9W3, and A0A0P0W4Y6 - as potential molecular markers of PGPB responsiveness in cereals. This study provides both conserved candidate genes and a methodological framework for comparative transcriptomics of plant-microbe interactions across heterogeneous datasets.