Integrated high-throughput phenomics and transcriptomics uncover the transcriptional mechanisms underlying rice...

Developing crop varieties with reduced cadmium (Cd) accumulation under elevated carbon dioxide (eCO₂) is a major global challenge. Identifying hub genes and elucidating the transcriptional mechanisms governing Cd stress and eCO₂ responses requires integrated, multi-tissue omics approaches. Here, we conducted high-throughput phenotyping of the rice cultivar Nipponbare across six key developmental stages under Cd stress and three eCO₂ concentrations. Image-based traits revealed shared and distinct phenotypic responses to these stresses. Multi-tissue transcriptome analyses showed that the differentially expressed genes (DEGs) and hormone-related genes exhibited a similar expression pattern under Cd and eCO₂. We further constructed an integrative co-expression network and identified five stress-responsive subnetworks. Among these, Multiple Stress Responsive Gene 3 (OsMSR3) emerged as a hub gene, with its haplotype 2 (Hap2) frequency decreasing from low- to high-latitude regions and from southern to northeastern China, mirroring the geographic distribution of Cd-contaminated soils. Collectively, our study reveals a transcriptional regulatory network underlying rice responses to Cd and eCO₂ stresses, providing mechanistic insights and valuable genetic resources for future molecular breeding of low-Cd accumulating rice varieties adapted to constant rising CO₂ levels.