Rice最新文献

Salinization threatens global crop productivity by compromising the growth, development, and ultimate yield of rice (Oryza sativa L.). In this study, we cloned and systematically investigated the function and physiological mechanism of OsABA45 (LOC_Os12g29400), a gene encoding a GRAM domain-containing protein, in mediating rice responses to salt stress. Subcellular localization confirmed OsABA45 as a cytoplasmic protein. Functional characterization of salinity tolerance at the seedling stage revealed that the survival rate of wild-type Nipponbare was 54.37%. By contrast, the OsABA45 knockout lines exhibited a significantly enhanced survival rate of 74.94%, indicating markedly improved salt tolerance. Conversely, the overexpression lines showed a reduced survival rate of 35.78%, reflecting compromised tolerance. Furthermore, the survival rate of wild-type Caidao was 42.90%, whereas the complementation lines reached 80.06%. These results collectively demonstrate that OsABA45 functions as a negative regulator of salt tolerance in rice. Interestingly, during seed germination and post-germination stages, OsABA45 knockout and complementation lines displayed increased sensitivity to abscisic acid (ABA), while overexpression lines exhibited decreased sensitivity. Meanwhile, exogenous ABA application restored salt stress tolerance in the overexpression lines. Further analysis demonstrated that OsABA45 knockout lines significantly upregulated the expression of key ABA biosynthesis genes, promoted endogenous ABA accumulation, and consequently enhanced salt tolerance, evidence OsABA45 mediates salt stress responses by regulating the ABA biosynthesis pathway. Notably, OsABA45 knockout and complemented lines also showed improved tolerance to ionic toxicity, osmotic stress, and oxidative stress, while overexpression lines exhibited reduced tolerance to these stresses. These results indicate that OsABA45 plays vital roles in ABA signal responses and salt tolerance in rice. This study provides novel molecular targets and breeding strategies for improving salt tolerance.

Phenol color reaction has been used to distinguish between two subspecies of Asian rice (Oryza sativa), indica and japonica. The trait is controlled by one single Phr1 gene, which encodes a PPO enzyme that catalyzes the oxidation of phenolic compounds into brown or black pigments upon contact to phenol solution. In O. sativa, ssp. indica responds to phenol chemical assay by altering the rice hull color to black, whereas ssp. japonica remains unaffected due to mutations that render the gene non-functional. Although the different characteristics between subspecies in Asian rice is well known, there is no information about the variation of this trait in African rice, Oryza glaberrima, which was originated and domesticated independently of Asian rice. In this study, we found both phenol negative and positive lines in O. glaberrima and its wild ancestor O. barthii and detected the responsible non-functional mutation (1-bp deletion) in the exon 1 of the Phr1 gene. Geographical distribution of its haplotype suggested that this mutation originated in O. barthii in Mali and was later inherited by O. glaberrima. The predominance of the non-functional Phr1 alleles in O. glaberrima lines and the occurrence of the identical haplotypes in negative group of both O. barthii and O. glaberrima suggest that the negative phenol reaction was favored during domestication and breeding selection. The presence of a selection event is also supported by low nucleotide diversity of Phr1 locus. However, genetic diversity of Phr1 persists in African rice germplasm, as the functional alleles are still present in O. glaberrima. We also compared the nucleotide diversity of Phr1 in African rice with that in Asian rice and found that their origins of the phenol responsive phenotype are independent. These findings expand the current understanding of African rice domestication and offer the valuable molecular marker for improved rice breeding.

Rice and Magnaporthe oryzae have co-evolved sophisticated molecular interaction mechanisms. While protein-coding genes (PCGs) involve in the response to M. oryzae have been intensively studied, yet the role of long noncoding RNAs (lncRNAs) remain poorly unclear. In this study, we performed whole transcriptome strand-specific RNA sequencing of rice seedlings from the susceptible recurrent parent cultivar LTH (compatible interaction) and the resistant rice monogenic line IRBLsh-S (incompatible interaction, harboring the resistance gene Pish) following the inoculation with the blast fungus strain Y92-66b. The results revealed that 16.8% of the identified lncRNAs were responsive to blast-infection in the Pish-line at 24-hour post inoculation (hpi). Notably, 45.1% of these blast responsive lncRNAs were novel. Functional analysis indicated that, 49 differentially expressed lncRNAs were co-expressed with genes enriched for the response to oxidative stress and diterpene phytoalexin biosynthetic process (particularly the synthesis of momilactone A). Furthermore, the expression pattern of four lncRNAs correlated with those of genes related to the cell wall macromolecule metabolic process. Here, two lncRNAs (XLOC_046130 and XLOC_040277) were predicted to act as endogenous target mimics (eTMs) for miRNAs and were co-expressed with transcription factors to induce the expression of genes involved in the synthesis of momilactone A. This demonstrates that lncRNAs regulate innate immunity through complex networks involving PCGs, transcription factors, and miRNAs. This study provides new insight into the regulatory mechanisms governed by R genes and highlight the potential role of lncRNAs in breeding and agricultural practices for improved disease management.

Inclination of leaf and plant height are important agronomic traits that are closely related to grain yields. Proteins involved in regulating free auxin (IAA) levels have a central role in modulating rice leaf angle and plant height. In this study, a rice mutant (named lc4) was found to have enlarged leaf angles and exhibit dwarfism compared to wild-type (WT) plants. Flanking analysis revealed that the mutation was caused by a T-DNA insertion at 270 bp upstream of the oxalate oxidase 2 (OsOxO2) ATG start codon. The insertion significantly increased the transcript levels of indole-3-acetic acid glucosyltransferase (OsIAAGLU), OsOxO1, OsOxO2 and OsOxO3 and OxO activity in lc4. Mutation of OsIAAGLU in lc4 led to partial restoration of the WT leaf angle and plant height phenotypes in iaaglu/lc4 which, however, still exhibited OxO activity comparable with that in lc4. On the other hand, mutation of OsOxO2 in lc4 also resulted in restoration of the WT leaf angle and plant height phenotypes, accompanied by reduced OxO activity and transcripts of OsIAAGLU, OsOxO1, OsOxO2 and OsOxO3. Nevertheless, overexpression of OsIAAGLU, but not OsOxO2 in the WT background, resulted in the transgenic plants showing leaf angle and plant height similar to lc4. Overexpression of OsOxO2 had no effect on the transcripts of OsIAAGLU, OsOxO1 and OsOxO3. These results suggest that activation of OsOxO2 and OsIAAGLU together resulted in altered plant architecture of lc4, while OsIAAGLU played a more direct role, OsOxO2 might be involved in regulating OsIAAGLU, OsOxO1 and OsOxO3 in a chromosome position-dependent manner.

Rice serves as the primary food source for over half the world's population, making its stable production is critical for global food security. The brown planthopper (BPH, Nilaparvata lugens Stål.) ranks among the most devastating rice pests in Asia. Developing BPH-resistant varieties through resistance gene discovery represents the most sustainable control strategy. Our study identified two novel resistance loci, Bph50 and Bph51, through analysis of the resistant wild rice germplasm GXU184 (Oryza rufipogon) using BSA-seq and QTL mapping. Interestingly, neither locus of Bph50 or Bph51 alone conferred resistance; rather, their combined presence in lines restored the high resistance observed in GXU184. Fine mapping localized Bph50 to a 177 kb region (6.732-6.909 Mb) on chromosome 4S and Bph51 to a 700 kb interval (15.035-15.735 Mb) on chromosome 4L. We developed a near-isogenic line (NIL) 9311^Bph50/Bph51 carrying both loci through marker-assisted selection (MAS), which exhibited strong BPH resistance without compromising agronomic performance. Integrated transcriptomic and histological analyses indicate that this resistance mechanism involves the coordinated upregulation of cellulose biosynthesis-related genes and the accumulation of polysaccharides such as cellulose in leaf sheaths. This enhancement of cell wall components likely increases tissue rigidity, forming a physical barrier that impedes stylet penetration during BPH feeding. Our findings unveil a novel resistance mechanism in which Bph50 and Bph51 genetically interact to confer BPH resistance, providing valuable insights for breeding durable pest-resistant rice varieties.

Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating diseases that affects rice production globally. Identifying new QTLs or R genes for blast resistance is crucial for developing rice varieties with enhanced resistance. In this study, a genome-wide association study (GWAS) to identify QTLs associated with blast resistance was conducted using phenotypic and genotypic data from 236 rice accessions. A total seven important QTLs linked to rice blast resistance were identified on chromosomes 1, 5, 6, 7, 10, and 12. Four main QTLs (qMZ6.1, qMZ7.1, qMZ10.1, and qMZ12.1) were key contributors to the blast resistance. Through combined analysis of differential expression and annotations of the predicted genes within qMZ12.1 based on haplotype and disease phenotype, we identified OsCBP606, which encodes a calmodulin protein, as the candidate gene for qMZ12.1. Compared with the wild-type plants, OsCBP606 knockout plants exhibited enhanced resistance to M. oryzae, while OsCBP606 overexpressing plants showed increased susceptibility. These findings highlight the critical role of OsCBP606 in modulating the rice immune response, making it a promising target for breeding programs aimed at improving rice blast resistance.

Rice serves as a fundamental staple crop, supporting the dietary needs of nearly one-third of the global population. This critical role necessitates immediate and strategic efforts to develop multi-attribute genotypes to ensure sustainable food and nutritional security for the burgeoning population. The augmentation of rice production is not only vital for addressing immediate food demands but also crucial for fostering long-term sustainability, thereby supporting livelihoods and driving economic development. Achieving this transformation necessitates a holistic and systems-level understanding of the molecular and regulatory networks that govern phenotypic plasticity and agronomic performance. While coding regions are pivotal for expression, non-coding elements play an even more prominent role in regulating transcriptional activity and orchestrating essential biological processes. Natural allelic variation within these non-coding elements serves as an evolutionary substrate for regulatory rewiring, contributing to adaptive plasticity, domestication traits, and intraspecific diversification. Therefore, the precise modulation of desirable agronomic traits could be facilitated by targeted engineering of such elements, which often allows for the fine-tuning of allelic effects in terms of the attenuation and partial restoration of alleles to impact desirable traits over coding components, which often results in complete exclusion or lethality. Therefore, we attempted to provide a comprehensive synthesis of functionally characterized non-coding elements exclusively for rice, highlight their functional roles, and emphasize how natural variation within these elements is critical for selecting traits associated with domestication and the breeding of elite genotypes. Notably, the potential of engineered non-coding RNA elements for the enhancement of agronomically advantageous traits is critically discussed. The future roadmap of non-coding element editing in rice is expected to be significantly shaped by continuous technological innovations in the editing toolbox, coupled with breakthrough discoveries for non-coding elements influencing agronomical traits. These advances have the potential to revolutionize the development of superior rice genotypes, ultimately contributing to the global effort to ensure food and nutritional security.