Comparative analysis of cucumber germplasm identifies GABA as a modulator of low-nitrogen tolerance

Excessive nitrogen (N) fertilization in cucumber cultivation reduces nitrogen-use efficiency (NUE) and imposes severe environmental costs. Improving NUE requires coordinated regulation of systemic nitrogen signaling (SNS), which directs root foraging toward nitrate (NO3−)-rich zones, and nitrate uptake capacity, which defines the rate of N acquisition. Here, we established a hydroponic split-root assay and a 15N-nitrate tracing system to quantify SNS responsiveness and nitrate uptake capacity across 56 cucumber (Cucumis sativus L.) germplasms. Significant variation was identified across the germplasm, resulting in the selection of G47 (high SNS responsiveness and nitrate uptake capacity), and G23 (low SNS responsiveness and nitrate uptake capacity), as contrasting accessions for evaluation alongside the reference cultivar 9930. Comparative analysis of these three genotypes revealed that G47 exhibited superior low-nitrogen (LN) stress tolerance, showing the smallest declines in biomass and chlorophyll, incurring the lowest oxidative and membrane damage, and demonstrating greater osmolyte and antioxidant accumulation alongside sustained nitrate assimilation. Comparative transcriptomic analysis revealed strong induction of γ-aminobutyric acid (GABA)-associated metabolism in G47, with the GABA pathway gene CsGS1 markedly upregulated. Functionally, foliar GABA application enhanced, whereas the GABA-biosynthesis inhibitor 3-mercaptopropionic acid (3-MP) diminished, LN tolerance. These findings identify GABA as a metabolic modulator of LN adaptation in cucumber and establish an integrated framework based on SNS responsiveness and nitrate uptake capacity for discovering high-NUE germplasm and molecular targets for nutrient-efficient breeding.