Multi-omics dissection of CO2-induced metabolic reprogramming in broccoli: key regulators of growth and nutritional quality.

The rising global CO2 level influences plant growth, productivity, and nutritional quality, and elevated CO2 (ECO2) is commonly utilized in greenhouses to enhance vegetable crop yields. However, the molecular mechanism underlying plant responses to ECO2 remains unclear. This study examined the impacts of ECO2 on the nutritional quality and growth characteristics of two widely cultivated broccoli varieties, 'Yanxiu' and 'Qiuli'. A pot experiment was carried out in environmentally auto-controlled growth chambers over a period of 100 days, under both ambient CO2 (ACO2, 420/470 ppm, daytime/nighttime) and ECO2 (700/750 ppm) conditions. Our results demonstrated that ECO2 significantly enhanced photosynthetic efficiency, increased head biomass accumulation, and elevated carbohydrate content. However, it also reduced free amino acids, soluble proteins, nitrate content, and mineral nutrients including nitrogen, potassium, calcium, iron, zinc, and copper, while increasing sulphur content in both varieties. Notably, ECO2 substantially increased health-promoting phytochemicals such as ascorbate, carotenoids, and total flavonoids. Through integrated transcriptomic and metabolomic analyses revealed: (1) ECO2 enhanced carbon metabolism via upregulation of hexokinase (HK), pyruvate kinase (PK), and Rubisco in glycolysis/pentose phosphate pathway; (2) activated biosynthesis of glucosinolates (via upregulating UDP-glucosyl transferase 83A, UGT83A, and cytochrome P450 81 F, CYP81F), flavonoids (via chalcone synthas, CHS, and flavonol synthase, FLS), ascorbate (via phospholipase C, PLC, and myo-inositol oxygenase, MIOX), and carotenoids (via phytotene synthase, PSY, and lycopene ε-cyclase, LCYE); and (3) suppressed nitrogen assimilation (via downregulating nitrate transporter 2, NRT2, and nitrate reductase, NR, and upregulating glutamine synthetase and glutamate synthase, GS/GOGAT). These findings systematically reveal that ECO2 reprograms broccoli metabolism to favor carbon assimilation while compromising nutrient acquisition. Our study provides valuable molecular insights for optimizing CO2 supplementation strategies in protected cultivation systems, offering potential solutions to balance yield improvement with nutritional quality maintenance in future vegetable production.