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Over-application of nitrogen (N) fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high N use efficiency (NUE) reduce fertilizer requirements, enabling sustainable agriculture. Genome-wide association study (GWAS) analysis of N absorption and utilization traits under low and high N conditions was performed to obtain 12 quantitative trait loci (QTLs) based on genotypic data including 151,202 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 267 japonica rice varieties. Eighteen candidate genes were obtained by integrating GWAS and transcriptome analyses; among them, the functions of  OsNRT2.4 ,  OsAMT1.2 , and  OsAlaAT  genes in N transport and assimilation have been identified, and OsJAZ12 and OsJAZ13 also play important roles in rice adaptation to abiotic stresses. A NUE-related candidate gene,  OsNAC68 , was identified by quantitative real-time PCR (qRT-PCR) analyses.  OsNAC68  encodes a NAC transcription factor and has been shown to be a positive regulator of the drought stress response in rice. Overexpression of  OsNAC68  significantly increased rice NUE and grain yield under deficient N conditions, but the difference was not significant under sufficient N conditions. NUE and grain yield significantly decreased under both N supply conditions in the  osbnac68  mutant. This study provides crucial insights into the genetic basis of N absorption and utilization in rice, and a NUE-related gene,  OsNAC68 , was cloned to provide important resources for rice breeding with high NUE and grain yield.

Candidate Gene Analysis for Nitrogen Absorption and Utilization in Japonica Rice at the Seedling Stage Based on a Genome-Wide Association Study