Integrated high-throughput phenomics and transcriptomics uncover the transcriptional mechanisms underlying rice responses to elevated CO2 concentration and cadmium stress.

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.