An Elite Haplotype of Nitrogen-Use-Efficiency Gene LHT5 Enhances Salt Tolerance in Rice

Amino acids serve as fundamental building blocks and signalling molecules in plants, orchestrating stress adaptation mechanisms against diverse biotic and abiotic environmental challenges. However, the mechanism by which plants alter their nutrient metabolism processes to coordinate nitrogen use efficiency (NUE) and salt tolerance remains elusive. Here, we identified a Lysine-Histidine-type transporter 5 (LHT5) gene through genome-wide association studies (GWAS) that enhances NUE via amino acid accumulation regulation. Further research showed that OsLHT5 also confers salt tolerance in rice by promoting proline biosynthesis through transcriptional upregulation of OsP5CS1 and OsP5CS2 genes, thereby increasing cellular proline levels for osmotic adjustment. Notably, we identified a functionally critical 30-bp deletion in the OsLHT5 coding region, designated as the elite haplotype LHT5^HapA, which substantially enhances amino acid transport capacity and consequently improves both NUE and salt tolerance. Functional validation demonstrated that overexpression of LHT5^HapA significantly increases amino acid content, nitrogen accumulation, grain yield and salt stress tolerance compared to the wildtype allele. This study establishes a novel molecular framework linking amino acid transport to the coordination of nutrient utilisation and stress tolerance, offering valuable genetic resources and breeding strategies for developing climate-resilient rice cultivars with enhanced productivity under both optimal and saline conditions.