Nitrogen is an essential nutrient for crop growth and development. Although the functions of several genes associated with nitrogen deficiency tolerance have been studied, many genetic components remain unknown. In this study, 190 North Korean (NK) rice genotypes were used to identify genes linked to nitrogen deficiency resistance. The NK population was hydroponically cultivated for 31 days under normal nitrogen (NN) and low nitrogen (LN) conditions. After this period, phenotypic evaluations were conducted on six agronomic traits (SPAD, shoot length, root length, shoot fresh weight, root fresh weight, and tiller number). A genome-wide association study (GWAS) was performed using the phenotypic values and resequencing data from 190 NK rice genotypes. As a result, 107 significant lead SNPs were identified. Among the genes related to these lead SNPs, 12 previously identified NUE-related genes for nitrogen use efficiency (NUE) and 6 unknown candidate genes exhibited significant differences in haplotype analysis. Nine of the 12 known genes (OsNPF4.1, OsNPF5.16, OsNPF6.1, OsNPF7.2, OsNPF7.7, OsAMT1.2, OsNRT1.3, OsAAP4, and OsLBD37) are involved in nitrogen uptake, while two (OsAAT1 and OsGS1;2) play a role in nitrogen assimilation, and one (OsNLP3) activates nitrate-responsive genes. This work demonstrates that the 190 NK rice genotypes analyzed harbor multiple critical genes involved in nitrogen uptake and identifies additional candidate genes associated with nitrogen deficiency tolerance. The genetic resources containing these known and novel genes for NUE could contribute to breeding rice varieties with high nitrogen deficiency tolerance (NDT).

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