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.