Rice最新文献

Rice (Oryza sativa L.), one of the most vital staple crops globally, suffers severe yield losses due to metabolic dysregulation under salt stress. However, the systemic mechanisms by which non-coding RNAs (ncRNAs) coordinately regulate metabolic reprogramming remain elusive, and the genotype-specific regulatory networks in salt-tolerant cultivars are poorly characterized. To address this, we performed metabolomic analysis using ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) across different rice varieties under salt stress, identifying 327 metabolites, with the most notable fluctuations observed in lipids, polyamines, and phenolamides. The salt-tolerant variety Pokkali exhibited 51.96% and 31.37% fewer differentially accumulated metabolites (DAMs) in the shoots and roots respectively, compared to the salt-sensitive variety Nipponbare (NIP), which explains its superior salt-tolerant phenotype from a metabolic homeostasis perspective. Transcriptome profiling revealed 18,597 differentially expressed genes (DEGs), with 70.8% showing genotype-specific expression patterns. Pokkali-specific DEGs were markedly enriched in salt-responsive pathways, including reactive nitrogen species scavenging and ion compartmentalization. By integrating long non-coding RNA (lncRNA) and microRNA (miRNA) sequencing data, we constructed a four-tiered regulatory network comprising 6,201 DEGs, 458 miRNAs, 970 DElncRNAs, and 177 metabolites. In the regulatory network, Osa-miR408-3p was identified as a negative regulator of Os03 g0709300 expression. Network analysis revealed that 21 polyamine and phenolamides biosynthesis-related genes were co-regulated by eight miRNAs, each forming a feedback loop with 2-11 lncRNAs. This study constructed a four-way cascade of "lncRNA-miRNA-mRNA-metabolite", and proposed a new concept of ncRNA-mediated "network regulation instead of single-gene effect".

Azolla spp. are floating ferns used for centuries as biofertilizers to enrich the soil with inorganic nitrogen and improve rice yields. However, the molecular interactions between Azolla and co-cultivated rice plants only recently started to be thoroughly investigated. In this study, we exploited an experiment in which rice plants were grown together with Azolla by maintaining a low and constant concentration of inorganic nitrogen. We employed a combination of non-targeted metabolomics, chemometrics, and molecular networking to dissect the impact of Azolla co-cultivation on the metabolome of rice roots- and leaves, as well as to annotate the metabolites released by Azolla into the growing medium. Our analyses showed that Azolla can synthesize and release a broad range of metabolites in the culture medium, mainly comprising small peptides (i.e., di- and tri-peptides) and flavonoids, that may have stimulated the rice plant growth. We also observed a systemic response in the upregulation of rice metabolites, first in the roots and then in the leaves. Metabolomics analysis indicated that during the first stages of co-cultivation, the impact of Azolla on rice mainly resulted in the accumulation of small peptides, lipids and carbohydrates in roots, as well as flavonoid glycosides and carbohydrates in leaves. Consistent with these results, transcriptomics analysis of rice roots indicated significant changes in the expressions of genes coding for small peptide and lipid transporters and genes involved in the pathways of amino acid salvage and biosynthesis. Overall, our study provides new insights into Azolla's beneficial and growth-promoting effects on rice. Understanding the molecular mechanisms by which Azolla functions as a biostimulant in rice co-culture will facilitate the development of more sustainable and environmentally friendly techniques to increase yields.

Salt stress poses a severe threat to global rice productivity, and developing salt-tolerant cultivars represents a critical strategy to address this challenge. However, the molecular mechanisms underlying salt tolerance in rice remain elusive. This study focuses on NGY1, a crossbred offspring between YF47 and SN9903, which showed superior salt tolerance compared to its parent lines during the seedling stage. RNA sequencing (RNA-seq) of seedlings harvested at distinct temporal stages of salt stress identified over 10,000 differentially expressed genes (DEGs). Functional enrichment analyses (GO and KEGG) revealed that NGY1 uniquely mobilized a broader repertoire of stress-responsive genes within shorter timeframes than its parents lines, particularly those associated with redox homeostasis, phytohormone signaling, and MAPK cascades. Meanwhile, NGY1 can rapidly upregulate genes related to salt tolerance compared to its parent during the initial stress phase. Additionally, differences in salt tolerance between NGY1 and its parents were linked to variations in alternative splicing and the high expression of certain NBS-LRR protein genes early in salt stress exposure. These findings not only provide new insights into the molecular mechanisms of salt tolerance, but also provide a theoretical basis for genetic improvement of salt tolerance in rice.

Arbuscular mycorrhizal (AM) fungi establish symbiotic associations with a wide range of plant species. Root colonization by AM fungi improves the uptake of mineral nutrients in the host plant, mainly phosphorus, in exchange for photosynthetically fixed carbon. Rice is one of the most important cereal crops in the world that is cultivated in diverse ecosystems, mainly in flooded fields. Although rice is a host for AM fungi, flooding depresses colonization of rice roots by AM fungi. However, once fungal penetration into the rice root has occurred, the functional capacities of the AM fungus are not affected by flooding. In this study, we investigated mycorrhizal responsiveness in a panel of temperate japonica rice varieties in low fertility soil collected from rice fields. We show that inoculation with an AM fungus, either Rhizophagus irregularis or Funneliformis mosseae, stimulates seedling growth, improves Pi nutrition and enhances resistance to infection by the fungus Magnaporthe oryzae in aerobically grown rice plants in low fertility soil. The fungus M. oryzae is the causal agent of the rice blast disease, one of the most devastating diseases in cultivated rice worldwide. Field trials were conducted in flooded paddy fields of eastern Spain (mediterranean region) in 2023 and 2024. Three elite rice varieties were inoculated with R. irregularis and grown in nurseries under aerobic conditions during early vegetative stage. The AM-inoculated seedlings were then transplanted to flooded fields. We show that inoculation with R. irregularis increases grain yield and blast resistance, namely leaf blast, neck blast, node blast and panicle blast, in flooded field conditions. Although all the japonica rice varieties here examined benefited from the AM symbiosis, its effects varied depending on the rice variety and the geographical location. These findings demonstrated that the application of AM fungi in nurseries may be integrated with conventional rice cultivation systems in paddy fields for the development of sustainable rice production systems less dependent on chemical fertilizers and pesticides.

Tiller angle is a major component of rice plant architecture and affects planting density, photosynthetic efficiency, and ventilation. An extremely narrow or wide tiller angle adversely affects rice yield. Thus, a suitable tiller angle is considered a major factor to achieve ideal plant architecture in rice. In this study, we identified a major quantitative trait locus (QTL) that controls tiller angle and cloned the gene, TILLER ANGLE CONTROL 5 (TAC5), which encodes a NAC domain-containing transcription factor. Epigenetic variants at the CG site in the TAC5 promoter were stably inherited and associated with TAC5 mRNA expression. The TAC5 epiallele with a hypermethylated cytosine in the promoter exhibited an immediate response to gravistimulation with a simultaneous elevation of H₂O₂ levels at the early stage of gravistimulation. Furthermore, TAC5 affected the expression patterns of transcripts involved in reactive oxygen species (ROS) generation and the response to excessive ROS. Population genetics and evolutionary analyses revealed that TAC5 alleles for the narrow tiller angle originated from a wild progenitor and were selected independently in temperate japonica and indica subspecies during domestication. Our results provide insight into the genetic mechanism of tiller angle control in rice and suggest potential applications of TAC5 in developing rice varieties with an ideal plant architecture.

Direct-seeded rice offers multiple advantages, including lower labour costs and a reduced CO₂ footprint. However, the risk of flooding during germination and at the early seedling and vegetative stages is high. Therefore, the capacity for anaerobic germination in waterlogged soils, as well as tolerance to partial and complete submergence, are both essential. It remains unclear whether anaerobic germination and flood tolerance are linked or if they act independently in the environment. Therefore, it is timely to investigate the relationship between these two traits in the context of progressing climate change. We investigated the submergence tolerance of 4-week-old plants of three African landraces, which had previously been shown to possess anaerobic germination capacity. Additionally, we included one submergence-sensitive check and two tolerant checks. These six genotypes were evaluated at three time points: initially (prior to submergence), after three days of submergence, and at the time of desubmergence following 29 days of submergence. We measured survival, key photosynthetic traits (leaf gas films, underwater net photosynthesis, chlorophyll concentration), and carbohydrate reserves. We found that the African landraces tolerant to anaerobic germination all outlived the submergence-sensitive check, 'IR42,' during 29 days of complete submergence. Moreover, all tested genotypes exhibited significant declines over the 29 days of submergence in gas film thickness, underwater net photosynthesis, leaf chlorophyll concentration, and leaf water-soluble carbohydrates and starch. However, no significant differences were observed among the genotypes. The underlying mechanisms of anaerobic germination tolerance in the three African landraces remain unknown, as they do not possess the gene Anaerobic Germination 1 (AG1). Furthermore, it is unclear whether the three genotypes contain the gene Submergence 1 (SUB1); however, SUB1 confers submergence tolerance only and does not provide tolerance to anaerobic germination. Based on the present study, we cannot rule out the possibility that the novel anaerobic germination tolerance observed in the three African landraces is somehow linked to submergence tolerance as well. A thorough bioinformatic analysis is therefore needed to further characterize these landraces.

Efficient callus induction is essential for the genetic transformation of rice (Oryza sativa), yet its regulatory mechanisms remain elusive. Previously, through a genome-wide association study (GWAS), we identified a significant associated locus on chromosome 8. In this study, we characterized this locus and demonstrated that OsSDG715, encoding a histone H3K9 methyltransferase, is the causal gene that positively regulates callus formation in rice. Results revealed that OsSDG715 is highly expressed during callus induction and exhibits natural variations associated with callus induction rate (CIR). Knockout of OsSDG715 via CRISPR/Cas9 led to a significant decrease in CIR and impaired callus morphology, indicating its positive regulation of callus formation. RNA-seq analyses revealed that 326 and 705 differentially expressed genes (DEGs) were upregulated and downregulated in sdg715 mutants, including auxin-responsive genes (OsIAA14, OsYUCCA6), cytokinin-related genes (OsCKX4, ARR10), and stress-responsive factors. Further analysis showed reduced endogenous indole-3-acetic acid (IAA) levels and increased zeatin levels in sdg715 mutants. These findings advance our understanding of the molecular mechanisms underlying rice callus formation, and offering valuable insights for optimizing tissue culture in molecular breeding.

Background: Hybrid sterility is a common phenomenon in hybrids between the Asian cultivated rice (Oryza sativa L.) and its relatives with AA genome, which limits the utilization of interspecific heterosis and favorable gene introgression. Numerous loci for hybrid sterility have been identified between O. sativa and its relatives. However, it remains elusive whether hybrid sterility between different species is controlled by a set of conserved loci, and whether there are variations in the genetic mode of these loci.

Results: In this study, six novel hybrid sterility loci for pollen sterility were identified from different cross combinations between O. sativa and its three wild relatives. S59 caused hybrid pollen sterility in hybrids between O. sativa and O. rufipogon. S60 and S61 controlled the hybrid pollen sterility between O. sativa and O. glumaepatula. S62, S63 and S64 governed the hybrid pollen sterility between O. sativa and O. barthii. Genetic and linkage analysis showed that S59, S60, and S62 were located in near the same region on the short arm of chromosome 5. S61 and S63 were mapped near RM27460 on the short arm of chromosome 12. S64 was restricted into the 60.27 kb region between RM4853 and RM3372 on the short arm of chromosome 3. The genetic behavior of six novel hybrid sterility loci follows one-locus allelic interaction model, the male gametes carrying the alleles of O. sativa in the heterozygotes were selectively aborted except for S62.

Conclusions: The findings from this research would provide a better understanding for the genetic nature of interspecific hybrid sterility in rice.