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Nitrogen-based nutrients are the main factors affecting rice growth and development. As the nitrogen (N) application rate increased, the nitrogen use efficiency (NUE) of rice decreased. Therefore, it is important to understand the molecular mechanism of rice plant morphological, physiological, and yield formation under low N conditions to improve NUE. In this study, changes in the rice morphological, physiological, and yield-related traits under low N (13.33 ppm) and control N (40.00 ppm) conditions were performed. These results show that, compared with control N conditions, photosynthesis and growth were inhibited and the carbon (C)/N and photosynthetic nitrogen use efficiency (PNUE) were enhanced under low N conditions. To understand the post-translational modification mechanism underlying the rice response to low N conditions, comparative phosphoproteomic analysis was performed, and differentially modified proteins (DMPs) were further characterized. Compared with control N conditions, a total of 258 DMPs were identified under low N conditions. The modification of proteins involved in chloroplast development, chlorophyll synthesis, photosynthesis, carbon metabolism, phytohormones, and morphology-related proteins were differentially altered, which was an important reason for changes in rice morphological, physiological, and yield-related traits. Additionally, inconsistent changes in level of transcription and protein modification, indicates that the study of phosphoproteomics under low N conditions is also important for us to better understand the adaptation mechanism of rice to low N stress. These results provide insights into global changes in the response of rice to low N stress and may facilitate the development of rice cultivars with high NUE by regulating the phosphorylation level of carbon metabolism and rice morphology-related proteins. [ABSTRACT FROM AUTHOR]

Rice salt tolerance at the germination stage directly affects the germination rate and seedling establishment of rice directly seeded in saline soils, which in turn affects yield. In this study, we determined the relative germination potential (RGP) and relative germination index (RGI) under 200 mM salt stress and control conditions using 295 japonica rice accessions. Statistical analysis showed extensive phenotypic variations under salt stress conditions. Twenty-one varieties with an RGP ≥ 80% and an RGI ≥ 80% were screened. Based on genotypic data including, 788,396 single-nucleotide polymorphisms (SNPs), 40 quantitative trait loci (QTL) were localized on rice chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12, which were shown to be significantly associated with rice salt tolerance at the germination stage, including 20 for RGP and 20 for RGI, using genome-wide association analysis. Six QTL with ≥ 3 consecutive significant SNP loci and localized in the same LD interval were selected for further analysis. Four rice genes (LOC_Os01g04920, LOC_Os10g38350, LOC_Os10g38470, and LOC_Os10g38489) were selected as important candidates for salt tolerance based on haplotype analysis and functional annotation. The findings could facilitate the development of valuable rice varieties for direct seeding in salinized soil and improve japonica rice salt tolerance at the germination stage through molecular breeding. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]