Co-elevated atmospheric CO2 and temperature increase rice yield but degrade nutrient quality in a cold temperature region.

The responses of three Japonica rice cultivars were investigated throughout a full growing season in computer-controlled open-top chambers under four treatments: control (CK), elevated CO2 (700 ppm, eC), elevated temperature (+2 °C, eT), and their combination (eCeT). To assess the impact of climate change factors, the present study performed comprehensive physiological measurements and flag leaf transcriptomic analysis to evaluate rice yield and quality. Both eC and eCeT synergistically upregulated genes related to photosystem II (PsbA) and photosystem I (PsaA/B/C), thereby enhancing photochemical efficiency (ΦPSII by +18% and 12%) through improved electron transport and ATP/NADPH synthesis. This molecular reprogramming, coupled with RBCL-mediated carbon assimilation and NEMDH-facilitated photorespiratory bypass, contributed to a 37% increase in net photosynthetic rate (Pn) under eC. eT alone activated phosphoenolpyruvate carboxylase (PEPC) while maintaining ΦPSII stability, supporting continued starch accumulation (+22% NPQ) without diminishing the CO2 fertilization effect. Although eCeT induced more synergistic gene regulation (32 differentially expressed genes vs. 22 under eC + eT), no significant interaction effect on Pn was observed (p > 0.05), suggesting maintenance of post-transcriptional homeostasis. Ultimately, eC significantly enhanced Pn and ΦPSII, resulting in a 24% yield increase that was not offset by warming. However, CO2-induced carbohydrate accumulation led to reductions in grain protein (-7.2%) and mineral contents (P, K, Mg, Mn), with elevated temperature only partially mitigating mineral losses. The identification of RBCL and NEMDH as key climate-resilience biomarkers, along with PEPC-mediated thermal adaptation, provides promising molecular targets for breeding nutrient-enriched rice cultivars suited to warming, high-latitude environments. These findings indicate that while warming helps sustain the yield benefits of elevated CO2 in cold regions, it exacerbates nutrient dilution, highlighting the need for strategies that jointly optimize both yield and nutritional quality under future climate scenarios.