Integrative genomics resolves rice loci associated with acidic soil-related aluminum, cadmium, and manganese stress responses.

Meta-QTL and transcriptomic integration prioritized transport, redox, and hormonal modules, while contrasting genotypes revealed coordinated differences in metal partitioning, cell-wall-associated spectral profiles and gene expression under combined stress. Rice in acidic and metal-affected soils may encounter aluminum (Al), cadmium (Cd), and manganese (Mn), whose distinct toxicities have partially overlapping effects on ion and redox homeostasis. We combined meta-quantitative trait locus (M-QTL) analysis with 14 public RNA-sequencing datasets and experimental evaluation of contrasting genotypes to identify recurrent regions without assuming a common tolerance mechanism. From 681 QTLs and marker-trait associations across 53 studies, 493 were projected onto a consensus map; 79 M-QTLs were retained, reducing the mean confidence interval from 6.90 to 1.85 cM. Ten intervals contained loci from all three combined metal datasets, indicating positional recurrence across heterogeneous traits. Integration of positional, transcriptomic, and functional evidence across 4702 interval genes prioritized 98 candidate genes spanning membrane transport, glutathione-dependent detoxification, redox regulation, and hormone signaling. M-QTL 10.9 contained a glutathione S-transferase-rich cluster, whereas M-QTL 9.5 included candidates associated with transport and transcriptional regulation. Shahsarang maintained greater root-system integrity than IR64 under several Al-containing treatments, whereas metal accumulation and translocation remained genotype-, metal-, and treatment-dependent. Qualitative FTIR profiles showed genotype- and treatment-associated spectral differences, while RT-qPCR revealed genotype-, tissue-, and treatment-dependent expression of selected candidates. Together, these findings identify recurrent intervals containing complementary, rather than identical, components of rice responses to Al, Cd, and Mn. The intervals and the candidate genes provide focused resources for functional validation and allele mining; breeding utility remains to be established experimentally.