Comparative Transcriptomics Reveals Distinct Molecular Responses to Acid Stress between Conventional and Hybrid Rice

• Core 381 genes mediate conserved acid adaptation via transport and iron metabolism. • Tolerance prioritizes homeostasis over stress response, a paradigm shift. • Conventional rice uses active transcriptional defense, hybrids show passive suppression. • Hybrid vulnerability under severe stress links to network-wide downregulation. Soil acidification poses a significant threat to rice production, yet the molecular mechanisms underlying acid tolerance remain poorly understood. Employing a combination of comprehensive phenotypic screening with multi-omics analysis, this study investigates acid stress responses in rice. Screening of 81 cultivars identified contrasting acid-tolerant and acid-sensitive genotypes from both conventional and hybrid backgrounds. Acid stress induced pronounced alterations in root architecture and triggered extensive transcriptional reprogramming. Root transcriptomes were profiled under a gradient of acidic pH (3.5 to 6.0, with pH 6.0 as control). Physiological analyses confirmed that tolerant genotypes maintained superior membrane stability and antioxidant enzyme activities under stress. Transcriptome analysis revealed 7,451 acid-responsive differentially expressed genes (FDR < 0.05, |log₂FC| > 1), with 381 core genes commonly responsive across all genotypes. These core genes were enriched in transmembrane transport, iron homeostasis, and reactive nitrogen species metabolism. Variety-specific analysis indicated that acid-tolerant cultivars were enriched for protein repair and transport functions, while sensitive genotypes predominantly activated glutathione and phenylpropanoid pathways. Co-expression network analysis (Pearson’s |r| > 0.6) identified key modules involved in signal transduction, oxidative homeostasis, and ion balance. Transcription factor analysis revealed that conventional rice exhibited stronger activation of ERF, WRKY, and MYB families, while hybrids displayed a pattern of ion transporter and ROS-related genes, validated by qRT-PCR, aligned with physiological measurements: conventional rice maintained better ion homeostasis and antioxidant capacity, whereas the hybrid genotypes examined in this study exhibited contrasting responses, the tolerant hybrid DXY901 maintained robust defense activation, while the sensitive hybrid RFY838 showed a concurrent downregulation of proton pumps and peroxidase systems under severe stress. Collectively, our findings elucidate the transcriptional framework and physiological basis of acid stress adaptation in rice, providing potential targets for breeding acid-tolerant rice varieties.