Auxins play an essential role in regulating plant growth and adaptation to abiotic stresses, such as nutrient stress. Our current understanding of auxins is based almost entirely on the results of research on the eudicot Arabidopsis thaliana, however, the role of the rice PIN-FORMED (PIN) auxin efflux carriers in the regulation of the ammonium-dependent response remains elusive. Here, we analyzed the expression patterns in various organs/tissues and the ammonium-dependent response of rice PIN-family genes (OsPIN genes) via qRT–PCR, and attempted to elucidate the relationship between nitrogen (N) utilization and auxin transporters. To investigate auxin distribution under ammonium-dependent response after N deficiency in rice roots, we used DR5::VENUS reporter lines that retained a highly active synthetic auxin response. Subsequently, we confirmed that ammonium supplementation reduced the DR5::VENUS signal compared with that observed in the N-deficient condition. These results are consistent with the decreased expression patterns of almost all OsPIN genes in the presence of the ammonium-dependent response to N deficiency. Furthermore, the ospin1b mutant showed an insensitive phenotype in the ammonium-dependent response to N deficiency and disturbances in the regulation of several N-assimilation genes. These molecular and physiological findings suggest that auxin is involved in the ammonium assimilation process of rice, which is a model crop plant.

The rice (Oryza sativa) PSEUDO-ETIOLATION IN LIGHT (OsPEL) microProtein family members function as dominant-negative regulators of chloroplast development and are conserved among land plants. Knockout of all 3 OsPEL genes enhanced plant greening traits and was accompanied by leaf anatomical modifications associated with chloroplast-enriched bundle sheath cells in rice. These phenotypic changes correlated with increased CO2 assimilation efficiency and yield. OsPEL1 specifically interacts with key positive regulators of photosynthesis, the rice GOLDEN2-LIKE (OsGLK) transcription factors and the PHOTOSYSTEM I ASSEMBLY 2 (OsPSA2) chaperone. OsPEL1 inhibits these regulators by sequestering OsGLK1 and OsPSA2 in the cytoplasm, which prevents their proper localization to the nucleus and chloroplast, respectively. Supported by RNA-seq evidence of transcriptional homeostasis in greening-related genes, we reveal a multilayered regulatory mechanism and identify the OsPEL family as a promising target for crop improvement.

Rice is an important cereal crop worldwide, the growth of which is affected by rice blast disease, caused by the fungal pathogen Magnaporthe oryzae. As climate change increases the diversity of pathogens, the disease resistance genes (R genes) in plants must be identified. The major blast-resistance genes have been identified in indica rice varieties; therefore, japonica rice varieties with R genes now need to be identified. Because leucine-rich repeat (LRR) domain proteins possess R-gene properties, we used bioinformatics analysis to identify the rice candidate LRR domain receptor-like proteins (OsLRR-RLPs). OsLRR-RLP2, which contains six LRR domains, showed differences in the DNA sequence, containing 43 single-nucleotide polymorphisms (SNPs) in indica and japonica subpopulations. The results of the M. oryzae inoculation analysis indicated that indica varieties with partial deletion of OsLRR-RLP2 showed susceptibility, whereas japonica varieties with intact OsLRR-RLP2 showed resistance. The oslrr-rlp2 mutant, generated using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), showed increased pathogen susceptibility, whereas plants overexpressing this gene showed pathogen resistance. These results indicate that OsLRR-RLP2 confers resistance to rice, and OsLRR-RLP2 may be useful for breeding resistant cultivars.

Promoters are key components for the application of biotechnological techniques in crop plants. Reporter genes such as GUS or GFP have been used to test the activity of promoters for diverse applications. A huge number of T-DNAs carrying promoterless GUS near their right borders have been inserted into the rice genome, and 105,739 flanking sequence tags from rice lines with this T-DNA insertion have been identified, establishing potential promoter trap lines for 20,899 out of 55,986 genes in the rice genome. Anatomical meta-expression data and information on abiotic stress related to these promoter trap lines enable us to quickly identify new promoters associated with various expression patterns. In the present report, we introduce a strategy to identify new promoters in a very short period of time using a combination of meta-expression analysis and promoter trap lines.

Rice is an important cereal crop worldwide, the growth of which is affected by rice blast disease, caused by the fungal pathogen Magnaporthe oryzae. As climate change increases the diversity of pathogens, the disease-resistance genes (R genes) in plants must be identified. The major blast-resistance genes have been identified in indica rice varieties; therefore, japonica rice varieties with R genes now need to be identified. Because leucine-rich repeat (LRR) domain proteins possess R-gene properties, we used bioinformatics analysis to identify the rice candidate LRR domain receptor-like proteins (OsLRR-RLPs). OsLRR-RLP2, which contains six LRR domains, showed differences in the DNA sequence, containing 43 single-nucleotide polymorphisms (SNPs) in indica and japonica subpopulations. The results of M. oryzae inoculation analysis indicated that indica varieties with partial deletion of OsLRR-RLP2 showed susceptibility, whereas japonica varieties with intact OsLRR-RLP2 showed resistance. oslrr-rlp2 mutant generated using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) showed increased pathogen susceptibility, whereas plants overexpressing this gene showed pathogen resistance. These results indicate that OsLRR-RLP2 confers resistance to rice, and OsLRR-RLP2 may be useful for breeding resistant cultivars.

Phosphorus (P) management has long been a challenge in agriculture, particularly improving P use efficiency (PUE) in crop plants, including rice. Although several studies have documented enhanced PUE in rice varieties, the underlying molecular mechanisms remain poorly understood, hindering crop engineering efforts. In this study, we expressed the rice ribonuclease 1 (OsRNS1) gene, which encodes a Class I monocot-specific ribonuclease, throughout the root under P deficiency, which was confirmed via green fluorescent protein and histochemical β-glucuronidase assays. Notably, the OsRNS1 protein localized in the cell wall and endoplasmic reticulum. Overexpression of OsRNS1 promoted ribosomal RNA (rRNA) degradation and PUE, while knockout of OsRNS1 reduced rRNA degradation. Moreover, OsRNS1 overexpression, driven by a root-preferred promoter, enhanced tolerance to P-deficiency stress compared with the wild type. OsRNS1 was regulated by the rice PHOSPHATE STARVATION RESPONSE 2 protein, and changes in OsRNS1 transcript levels influenced the expression of other acid phosphatase and phosphate transporter genes. Collectively, these findings indicate that OsRNS1, a P deficiency-induced ribonuclease, regulates P homeostasis via rRNA degradation during P-deficiency stress. This molecular mechanism of P-deficiency tolerance holds promise for biotechnological applications aimed at developing rice varieties with improved PUE.