Functional Insights into SlNPF, SlNRT2, and SlAMT Gene Families in Tomato: Leaf Metabolic Performance Controls Root-to-Shoot Nitrogen Partitioning

Nitrogen (N) is a critical macronutrient for crop production, however, it has been estimated that 50-70% of N applied is not used by the plant, negatively affecting crop development performance and environmental health. This low Nitrogen Use Efficiency (NUE) represents a major agricultural challenge. To identify the molecular mechanism responsible for NUE regulation, a comprehensive genomic annotation, transcriptomic, and functional analysis of the NPF, NRT2, and AMT transporter families in tomato (Solanum lycopersicum) were performed. The genomic analysis identified 29 SlNPF, 6 SlNRT2, and 4 SlAMT transporter genes. Also, the integrated analysis provided insights into a root-to-shoot signaling mechanism, in which the plant metabolic performance exerts a strong regulation on N transport capacity, under two commercial high-N supply conditions: N1 (11.4 mM NO3¯ and 2.3 mM NH4⁺) and N2 (10.5 mM NO3¯ and 0.5 mM NH4⁺). At the leaf level, the N1 condition induced a depressed N assimilation capacity, evidenced by NO3¯ accumulation (increased by 55.7%) and reduced Nitrate Reductase (NR) and Glutamine Synthetase (GS) activities (54.0% and 43.2% reduction, respectively). These responses were correlated with reduced chlorophyll synthesis capacity (reduced by 42.3%). This reduced metabolic demand consequently triggered the downregulation of the root-to-shoot NPF transporters, SlNPF2.13 and SlNPF7.3. This metabolic restriction limited the long-distance transport and promoted a significant N accumulation at the root level (NO3¯ increased by 41.8%). Overall, the present study reveals that leaf metabolic performance is the systemic metabolic regulator of N transport and provides evidence for the key role of SlNPF2.13 and SlNPF7.3 transporters as pivotal molecular checkpoints for improving NUE in tomato production.