Joint multi-omics analysis reveals the response mechanism in rapeseed (Brassica Rapa L.) under low nitrogen stress

Nitrogen is fundamental macronutrient that regulates plant growth by modulating a wide array of physiological and metabolic processes. However, the excessive application of nitrogen fertilizers has led to substantial environmental concerns, emphasizing the need for sustainable nitrogen management in agriculture. In this study, an integrative analysis encompassing morphological, physiological, transcriptomic, and metabolomic approaches was employed to investigate the adaptive responses of Brassica rapa (rapeseed) under contrasting nitrogen regimes. Morphological assessments demonstrated significant enhancements in root length and surface area under low nitrogen conditions, while photosynthesis traits particularly chlorophyll content were markedly reduced, underscoring nitrogen`s essential role in photosynthetic efficiency. Enzymatic activity assays revealed tissue-specific responses: roots exhibited elevated enzymatic activities under nitrogen deficiency, indicative of compensatory nitrogen uptake strategies, whereas leaves showed a decline in enzymatic functions, reflecting Limited nitrogen availability. Transcriptomic profiling identified 1,481 and 1,917 differentially expressed genes (DEGs) in roots and leaves, respectively, which were primarily associated with photosynthesis, amino acid metabolism, and oxidative stress responses. These transcriptomic shifts were corroborated by metabolic profiling, which reveled significant alterations in metabolites involved in amino acid metabolism, phenylpropanoid biosynthesis, and energy production pathways. Integration of transcriptomic and metabolomic datasets through Weighted Gene Co-expression Network Analysis (WGCNA) identified key gene metabolite modules implicated in nitrogen stress adaptation. Quantitative RT-PCR validation of selected DEGs confirmed the RNA-Seq expression patterns, further substantiating the reliability of the transcriptomic data. Collectively, this comprehensive multi-omics investigation elucidates the molecular basis of B. rapa`s adaptation to nitrogen deficient conditions, providing valuable insights for enhancing nitrogen use efficiency and guiding sustainable crop management strategies. © 2025 Elsevier B.V., All rights reserved.