Integrated transcriptomic, metabolomic and phenotypic analyses reveal the response of wheat to drought stress during the grain-filling stage

Wheat ( Triticum aestivum L.) is being increasingly threatened by recurrent drought stress. Therefore, determining the mechanisms underlying the drought response of this species and identifying core regulators is key to reducing yield losses and expediting the breeding of tolerant varieties. This study examined the phenotypic and physicochemical traits of the wheat cultivar Jinmai 47 at the jointing, heading and filling stages under irrigated and rainfed conditions, alongside transcriptomic and metabolomic profiling of flag leaves at the filling stage. Compared with the irrigated control condition, drought stress (rainfed) induced the most pronounced phenotypic and physicochemical changes at the filling stage. Moreover, drought stress led to the rapid accumulation of proline at all three growth stages. Transcriptome and metabolome analyses revealed that drought stress resulted in 11,381 upregulated and 12,662 downregulated genes, as well as 431 upregulated and 441 downregulated metabolites. Transcriptome analysis revealed that drought stress upregulated pathways related mainly to phagosomes, fatty acid degradation, peroxisomes, autophagy and amino acid degradation but downregulated pathways related to photosynthesis, ribosomes and chlorophyll metabolism. Metabolomic analysis revealed that the main upregulated pathways were tryptophan metabolism, glycolysis/gluconeogenesis, riboflavin metabolism, vitamin B6 metabolism and benzoxazinoid biosynthesis. In contrast, the downregulated pathways included glycine, serine and threonine metabolism; cysteine and methionine metabolism; lysine biosynthesis; flavone and flavanol biosynthesis; and zeatin biosynthesis. Integrative metabolomic and transcriptomic analyses further demonstrated that drought stress triggered transcriptional–metabolic reprogramming centred on carbon metabolism, glycolysis/gluconeogenesis and carbon fixation in photosynthetic organisms. L-tryptophan in the tryptophan–alkaloid pathway was significantly upregulated. In contrast, L-aspartic acid was downregulated and involved in five pathways: glycine, serine and threonine metabolism; carbon fixation in photosynthetic organisms; carbon metabolism; pantothenate and CoA biosynthesis; and beta-alanine metabolism. Transcriptomic and metabolomic integrative analyses revealed a drought response network in Jinmai 47 that is anchored in carbon–energy reprogramming and coordinated by tryptophan-driven secondary metabolism and amino acid-based osmotic/antioxidant regulation. These findings thus provide potential targets for the genetic improvement of drought tolerance in wheat.