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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• Machine Learning Method to Select Single Nucleotide Polymorphism Markers for Protein Content, Grain Filling Rate, Height, and Panicle Length in Korean Rice
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  Korean Journal of Breeding Science.2025; 57(4): 403.     CrossRef

Rice yield is severely affected by phosphorus (P) deficiency, and plants have evolved various strategies to cope with this limitation. While some rice genotypes are adapted to low phosphate (Pi) availability, others remain sensitive to Pi deficiency. In this study, we conducted a genome-wide association study (GWAS) using a hydroponically cultivated population of 190 North Korean (NK) rice plants to identify genes associated with phosphorus use efficiency (PUE) and Pi deficiency tolerance. The rice plants were grown in Yoshida nutrient media with either full (10 mg/L) or low-P (1 mg/L) concentrations for 40 days. The phenotypic response to Pi deficiency was assessed at the seedling stage, followed by an evaluation of eight agricultural traits: chlorophyll content (SPAD), shoot length (SL), shoot fresh weight (SFW), shoot dry weight (SDW), root fresh weight (RFW), root dry weight (RDW), and tiller number (TN). The GWAS analysis revealed a total of 166 significant lead SNPs, with six located near known genes for Pi deficiency tolerance: OsTre6P and OsPT3 for RL, OsGH3.12 for SPAD, OsCPK30 for SL, OsWRKY74 for RSL, and OsPT10 for RSL and RRFW. An additional six lead SNPs were identified as novel genes. The haplotypes of 12 candidate genes showed significant differences in the phenotypic values of the corresponding traits. In conclusion, both known and novel genes identified in this GWAS have significant impacts on Pi deficiency tolerance in the NK rice population.

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