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.

Citations

Citations to this article as recorded by  

• Transcription factors in phosphorus utilization: enhancing crop productivity and stress resilience
  Manli Zhao, Yan Sun, Chenxi Fu, Siji Wang, Jianbo Shen, Sanyuan Tang, Lingyun Cheng
  Planta.2026;[Epub]     CrossRef
• Genome-wide association study identifies loci and candidate genes for root traits in rice grown in Brazil
  Gabriel Brandão das Chagas, Latóia Eduarda Maltzahn, Josiane Vargas de Oliveira Maximino, Viviane Kopp da Luz, Ariano Martins de Magalhães Junior, Antonio Costa de Oliveira, Luciano Carlos da Maia, Camila Pegoraro
  Crop Design.2025; 4(2): 100095.     CrossRef
• Genetic Exploration of β-glucan and Cellulose Synthesis in Barley
  Sehyun Choi, Young-Mi Yoon, Jin-CheonPark, On-SookHur, Changsoo Kim
  Korean Journal of Breeding Science.2025; 57(2): 159.     CrossRef
• RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice
  Quan Lu, Jiajun Xu, Renyi Zhang, Hangcheng Liu, Meng Wang, Xiaoshuang Liu, Zhenyu Yue, Yujia Gao
  Briefings in Bioinformatics.2024;[Epub]     CrossRef