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Identifying hub genes and elucidating the transcriptional mechanisms governing Cd stress and eCO\n                    <jats:sub>2<\/jats:sub>\n                    responses requires integrated, multi\u2010tissue omics approaches. Here, we conducted high\u2010throughput phenotyping of the rice cultivar Nipponbare across six key developmental stages under Cd stress and three eCO\n                    <jats:sub>2<\/jats:sub>\n                    concentrations. Image\u2010based traits revealed shared and distinct phenotypic responses to these stresses. Multi\u2010tissue transcriptome analyses showed that the differentially expressed genes (DEGs) and hormone\u2010related genes exhibited a similar expression pattern under Cd and eCO\n                    <jats:sub>2<\/jats:sub>\n                    . We further constructed an integrative co\u2010expression network and identified five stress\u2010responsive subnetworks. Among these,\n                    <jats:italic>Multiple Stress Responsive Gene 3<\/jats:italic>\n                    (\n                    <jats:italic>OsMSR3<\/jats:italic>\n                    ) emerged as a hub gene, with its haplotype 2 (Hap2) frequency decreasing from low\u2010 to high\u2010latitude regions and from southern to northeastern China, mirroring the geographic distribution of Cd\u2010contaminated soils. Collectively, our study reveals a transcriptional regulatory network underlying rice responses to Cd and eCO\n                    <jats:sub>2<\/jats:sub>\n                    stresses, providing mechanistic insights and valuable genetic resources for future molecular breeding of low\u2010Cd accumulating rice varieties adapted to constant rising CO\n                    <jats:sub>2<\/jats:sub>\n                    levels.\n                  <\/jats:p>","DOI":"10.1002\/imo2.70100","type":"journal-article","created":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T07:44:09Z","timestamp":1779263049000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated high\u2010throughput phenomics and transcriptomics uncover the transcriptional mechanisms underlying rice responses to elevated CO\n                    <sub>2<\/sub>\n                    concentration and cadmium 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