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The browning reaction during the flue-curing process of tobacco ( L.) dramatically affects leaf quality and value, leading to significant economic losses. However, the molecular regulatory mode of the browning in flue-cured tobacco is still unclear. The two tobacco cultivars, Dabaijin and Yunyan87, with browning differences in upper, middle, and lower leaves during the flue-curing process, were characterized through transcriptomic and metabolomic analyses. The results showed that the significant browning in Dabaijin was mainly due to the preferential accumulation of products of amino acid metabolism (L-arginine, L-ornithine, L-leucine, and L-valine) and amino sugar and nucleotide sugar metabolism (L-fucose) which promoted the Maillard reaction. Meanwhile, riboflavin metabolism (downregulation of and expression) impaired the function of the antioxidant system, and imbalanced inositol phosphate metabolism affected membrane homeostasis through PIP2. However, the consumption rate of reduced hydrogen by oxidative phosphorylation, as well as enhanced sulfur metabolism, and taurine and hypotaurine metabolism for scavenging ROS was mainly increased in Yunyan87, ultimately reducing the accumulation of ROS and slowing membrane damage during the flue-curing process. This research revealed that the difference in browning between Yunyan87 and Dabaijin cultivars was mainly regulated by the accumulation of Maillard substrates and the efficiency of the antioxidant system, which provides a theoretical basis for improving tobacco cultivars resistant to browning and optimizing processing techniques.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s12870-025-07150-0.