Integrated high‐throughput phenomics and transcriptomics uncover the transcriptional mechanisms underlying rice responses to elevated CO 2 concentration and cadmium stress

Developing crop varieties with reduced cadmium (Cd) accumulation under elevated carbon dioxide (eCO 2 ) is a major global challenge. Identifying hub genes and elucidating the transcriptional mechanisms governing Cd stress and eCO 2 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 eCO 2 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 eCO 2 . 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 eCO 2 stresses, providing mechanistic insights and valuable genetic resources for future molecular breeding of low‐Cd accumulating rice varieties adapted to constant rising CO 2 levels.