Appropriate nitrogen application reactivates root-leaf nitrogen metabolic coordination and sustains cottonseed kernel yield under moderate short-term drought

Cottonseed is a major source of edible oil and plant protein, yet its development is highly sensitive to drought. Short-term droughts frequently occur during cotton reproductive growth, but how nitrogen supply regulates root-leaf nitrogen metabolic coordination and post-drought kernel recovery remains poorly understood. Using a controlled pot experiment, we examined the effects of short-term drought and nitrogen application on nitrogen metabolism in cotton root and the leaf subtending the cotton boll (LSCB), as well as on cottonseed kernel nutrient accumulation after re-watering. Short-term drought suppressed nitrate assimilation and nitrogen transport in both root and LSCB by inhibiting key nitrogen-assimilating enzymes, resulting in reduced 15 N allocation to the developing kernel. Nitrogen application alleviated these constraints by enhancing nitrate reduction, restoring enzymatic activity, and promoting nitrogen translocation. Under moderate drought, optimal nitrogen supply (150 kg N ha −1 ) enabled rapid nitrogen metabolic recovery after re-watering and fully restored cottonseed kernel yield and nutrient production, whereas severe drought caused sustained inhibition. Integrative analyses indicated that LSCB nitrogen metabolism acts as an important metabolic hub linking root nitrogen processes with kernel nutrient accumulation, with nitrate reductase and glutamate synthase emerging as key regulatory components. Overall, these results demonstrate that an appropriate nitrogen fertilization of 150 kg N ha −1 can reestablish root–LSCB nitrogen metabolic coordination under moderate short-term drought, thereby sustaining cottonseed kernel development. This study provides physiological guidance for optimizing water–nitrogen management in cotton production under transient drought conditions.