Search Results (255)

Background: The coordinated improvement of yield, quality and resistance is a primary goal in rice breeding. Gene editing technology is a novel method for precise multiplex gene improvement. Methods: In this study, we constructed a multiplex CRISPR/Cas9 vector targeting yield-related genes (GS3, OsPIL15, Gn1a), fragrance gene (OsBADH2) and rice blast resistance gene (Pi21) to pyramid traits for enhanced yield, quality, and disease resistance in rice. A tRNA-assisted CRISPR/Cas9 multiplex gene editing vector, M601-OsPIL15/GS3/Gn1a/OsBADH2/Pi21-gRNA, was constructed. Genetic transformation was performed using the Agrobacterium-mediated method with the japonica rice variety Xin Dao 53 as the recipient. Mutation editing efficiency was detected in T₀ transgenic plants. Grain length, grain number per panicle, thousand-grain weight, 2-acetyl-1-pyrroline (2-AP) content, and rice blast resistance of homozygous lines were measured in the T₃ generations. Results: Effectively edited plants were obtained in the T₀ generation. The simultaneous editing efficiency for all five genes reached 9.38%. The individual gene editing efficiencies for Pi21, GS3, OsBADH2, Gn1a, and OsPIL15 were 78%, 63%, 56%, 54%, and 13%, respectively. Five five-gene homozygous edited lines with two genotypes were selected in the T₂ generation. In the T₃ generation, compared with the wild-type (WT), the edited homozygous lines showed increased grain number per panicle (14.60–25.61%), increased grain length (7.39–11.16%), increased grain length–width ratio (8.37–13.02%), increased thousand-grain weight (3.79–9.15%), a 42–64 folds increase in the fragrant substance 2-AP content, and significantly enhanced rice blast resistance. Meanwhile, there were no significant changes in other agronomic traits. Conclusions: CRISPR/Cas9-mediated multiplex gene editing technology enabled the simultaneous editing of genes related to rice yield, quality, and disease resistance. This provides an effective approach for obtaining new japonica rice germplasm with blast resistance, long grains, and fragrance. Full article

Straw returning, a core practice in conservation tillage, promotes sustainable intensification; however, it faces challenges such as inefficient decomposition, nutrient competition, and pathogen accumulation. To address these limitations, this study aimed to develop a multifunctional microbial consortium specifically designed for straw-incorporating cropping systems. The consortium comprises four Bacillus strains with complementary enzymatic systems, isolated from diverse ecological niches. It exhibited robust lignocellulolytic enzyme production, with manganese peroxidase (7709.33 U/L), laccase (450.65 U/L), endo-β-1,4-glucanase (154.67 U/mL), and filter paper activity (309.18 U/L). The consortium significantly enhanced rice straw degradation by 37.18% and increased nitrogen (N) release by 16.13% compared to the control. Moreover, the consortium exhibited a 67.56% inhibition rate against Magnaporthe oryzae and reduced both the incidence rate and disease index of leaf blast and panicle blast. Field trials revealed increases in the rice grain yield of 9.63% and 6.94% when applied alone and 6.75% and 5.18% when co-applied with straw residues. These findings highlight the multifunctional agricultural potential of the consortium and provide a sustainable strategy to overcome the limitations of straw-incorporating farming systems. Full article

Rice (Oryza sativa L.) is a major global staple crop, yet its productivity is severely constrained by rice blast disease caused by Magnaporthe oryzae. FK506-binding proteins (FKBPs) are peptidyl-prolyl cis-trans isomerases involved in protein folding, stress response, and signaling regulation, but their roles in rice blast resistance remain unclear. In this study, we performed a comprehensive identification and characterization of FKBP gene family members in two rice cultivars, Nipponbare (NIP) and Zhonghua 11 (ZH11), based on the latest T2T (telomere-to-telomere) genome assembly of ZH11 and the reference genome of NIP. A total of 24 and 29 FKBP genes were detected in NIP and ZH11, respectively, indicating a slight expansion in ZH11. Phylogenetic and collinearity analyses revealed strong conservation of FKBP family members between the two cultivars, while several ZH11-specific genes likely resulted from recent duplication events. Promoter analysis showed that FKBP genes are enriched in stress and hormone responsive cis-elements, particularly those related to ABA, MeJA, and SA signaling. Transcriptomic and RT-qPCR analyses demonstrated that multiple FKBP genes were significantly regulated during M. oryzae infection, suggesting their potential involvement in defense signaling pathways. This study provides a comprehensive overview of FKBP gene family evolution and expression in rice, identifies candidate genes potentially associated with blast resistance, and offers valuable insights for molecular breeding aimed at improving disease resistance in rice. Full article

Rice blast, caused by Magnaporthe oryzae, is a devastating disease that jeopardizes global rice production and food security. Precision agriculture demands timely and accurate monitoring tools to enable targeted intervention. This study introduces a novel deep learning framework that fuses time-series hyperspectral imaging with an advanced Autoformer model (AutoMSD) to dynamically track rice blast progression. The proposed AutoMSD model integrates multi-scale convolution and adaptive sequence decomposition, effectively decoding complex spatio-temporal patterns associated with disease development. When deployed on a 7-day hyperspectral dataset, AutoMSD achieved 86.67% prediction accuracy using only 3 days of historical data, surpassing conventional approaches. This accuracy at an early infection stage underscores the model’s strong potential for practical field deployment. Our work provides a scalable and robust decision-support tool that paves the way for site-specific disease management, reduced pesticide usage, and enhanced sustainability in rice cultivation systems. Full article

Rice blast, caused by Magnaporthe oryzae, is a devastating global disease. Its control through the deployment of host resistance genes relies on a detailed knowledge of the pathogen’s race structure and the corresponding avirulence (Avr) genes. To guide effective rice breeding for blast resistance, this study investigated the population dynamics of M. oryzae in Jilin Province from 2022 to 2024. The distribution frequencies of seven Avr genes were detected using PCR and Avr gene-specific primers, and the physiological race structure of 193 isolates was characterized using a set of Chinese differential cultivars, which contains seven cultivars. The results revealed a high prevalence and stability of specific Avr genes, with Avr-Pi9, Avr-Pias, Avr-Piz-t, and Avr-Pib all exhibiting detection frequencies exceeding 80%. In particular, Avr-Pib showed a high frequency (80.83%) and a very low disease incidence (0.64%) on the differential variety Sifeng 43 (which carries Pib), confirming its low mutation rate and the ongoing effectiveness of the corresponding resistance gene. Conversely, the significant decline in Avr-co39 suggests that its corresponding resistance gene should be avoided. Race diversity increased over the three-year period, characterized by a shift toward a more complex structure dominated by ZG1, ZA17, ZA43, and ZB31. Based on the gene-for-gene interactions and pathogen population structure, we recommend a breeding strategy that prioritizes the incorporation of the highly effective Pib, Pi54, and Pik genes, utilizing resistant donors like Sifeng 43. These results can help inform the design of sustainable management strategies adapted to the changing pathogen population. Full article

This study explores the use of remote sensing and machine learning (ML) for early detection of Pyricularia oryzae (rice blast) in ‘Bomba’ rice. Conducted in Spain’s Albufera Natural Park over four seasons (2021–2024), 94 fields were monitored using Sentinel-2 imagery and Topcon Yield Trakk data. Principal Component Analysis (PCA) identified key spectral bands (B03, B04, B05, B07, B08, B11) at early stages (35 and 55 DAS). Three ML classifiers—K-Nearest Neighbors (KNN), Random Forest (RF) and Support Vector Machines (SVMs)—were tested to categorize fields by yield-based infection levels. RF achieved the best performance (up to 94% Accuracy), showing high robustness across band combinations and dates. KNN was more input-sensitive, and SVM performed weakest. Integrating multispectral and multitemporal data enhanced accuracy. Overall, RF and remote sensing proved reliable tools for early disease detection, supporting Precision Agriculture and real-time pest management. Full article

Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases threatening global rice production. Although host resistance represents a sustainable control strategy, the underlying mechanisms mediated by the rhizosphere microbiome remain poorly understood. In this study, we selected four rice varieties with varying resistance to blast and demonstrated, through an integrated approach of 16S rRNA/ITS amplicon sequencing, untargeted metabolomics, and soil physicochemical analysis, that the rice genotype reprograms the genotype-root exudate-rhizosphere microbiome system. Results showed that the resistant variety P104 significantly decreased the soil pH while increasing the contents of total nitrogen, ammonium nitrogen, and nitrate nitrogen. On the other hand, the susceptible variety P302 exhibited higher pH and available phosphorus content. Furthermore, the rhizosphere of P104 was enriched with specific beneficial microbes such as Desulfobacterota, Ascomycota, and Pseudeurotium, and activated defense-related metabolic pathways including cysteine and methionine metabolism and phenylpropanoid biosynthesis. In contrast, susceptible varieties showed reduced bacterial diversity and fostered a microecological environment more conducive to pathogen proliferation. Our findings indicate that blast-resistant rice genotypes are associated with a protective rhizosphere microbiome, potentially mediated by alterations in root metabolism, thereby suppressing pathogen establishment. These insights elucidate the underground mechanisms of blast resistance and highlight the potential of microbiome-assisted breeding for sustainable crop protection. Full article

The crude ethyl acetate extract of the culture of a marine sponge-associated fungus, Aspergillus unguis KUFA 0098, was tested for its capacity to inhibit the growth of ten phytopathogenic fungi, viz. Alternaria brassicicola, Bipolaris oryzae, Colletotrichum capsici, Curvularia oryzae, Fusarium semitectum, Lasiodiplodia theobromae, Phytophthora palmivora, Pyricularia oryzae, Rhizoctonia oryzae, and Sclerotium roflsii. At a concentration of 1 g/L, the crude extract was most active against P. palmivora, causing the highest growth inhibition (55.32%) of this fungus but inactive against R. oryzae and S. roflsii. At a concentration of 10 g/L, the crude extract completely inhibited the growth of most of the fungi, except for L. theobromae, R. oryzae, and S. roflsii, with 94.50%, 74.12%, and 67.80% of inhibition, respectively. The crude extract of A. unguis KUFA 0098 exhibited growth-inhibitory effects against B. oryzae and P. oryzae, causative agents of brown leaf spot disease and leaf blast disease, respectively, on rice plant var. KDML105, under greenhouse conditions. Chromatographic fractionation and purification of the extract led to the isolation of four previously described depsidones, viz. unguinol (1), 2-chlorounguinol (2), 2,4-dichlorounguinol (3), and folipastatin (4), as well as one polyphenol, aspergillusphenol A (5). The major compounds, i.e., 1, 2, and 4, were tested against the ten phytopathogenic fungi. Compounds 1 and 4 were able to inhibit growth of most of the fungi, except L. theobromae, R. oryzae, and S. roflsii. Compound 1 showed the same minimum inhibitory concentration (MIC) values as that of carbendazim against A. brassicicola, C. capsici, C. oryzae, and P. oryzae, while compound 4 showed the same MIC values as that of carbendazim against only C. capsici and P. oryzae. Compound 2 was not active against all of the ten phytopathogenic fungi tested. Full article

The TATA box and 5′untranslated region (5′UTR) are critical regulatory elements that influence gene expression in plant defense responses. In rice (Oryza sativa), these elements modulate transcriptional and translational regulation during infection by the blast pathogen Magnaporthe oryzae. This study investigates the functional significance of the TATA box and 5′UTR in rice defense signaling by analyzing promoter and 5′UTR variations in key defense-related genes. Through comparative genomics, expression profiling, and mutagenesis assays, we show that 60% of defense genes with specific TATA box motifs exhibit enhanced transcription, while 5′UTR variants increase translational efficiency by up to 2-fold, contributing to blast resistance. These regulatory mechanisms provide a framework for targeted breeding and biotechnological interventions to enhance disease resistance in rice. Our findings highlight the importance of these elements in fine-tuning rice immune responses and suggest potential targets for improving disease resistance in rice cultivars. Full article

Fungal effectors play an important role in plant immunity. The Magnaporthe oryzae effector PWL2 plays a significant role in rice blast disease caused by this fungus. However, the function of PWL2 in rice immunity is not fully understood. In this study, transgenic rice lines overexpressing PWL2 showed resistance to rice blast. Subcellular localization showed that PWL2-GFP fusion protein is localized on the plasma membrane and cytoplasm. Salicylic acid (SA) induces rice resistance to M. oryzae. Notably, the expression of the NPR1 gene exhibited a rhythmic pattern during the early stages of M. oryzae infection in the transgenic rice lines. However, during later stages of infection, transgenic plants showed reduced levels of the NPR1, WRKY45, PR1a and PR10a genes, along with decreased H₂O₂ accumulation, while SA levels remained unchanged. Transcriptome analysis revealed that SA treatment induced the expression of the ARGONAUTE11 (AGO11) gene in rice. Furthermore, during the later infection stage in the transgenic rice lines, the expression levels of both AGO11 and PWL2 genes increased. Intriguingly, PWL2-derived small interfering RNAs (siRNA) were detected in these transgenic rice lines. It suggests that both the SA signaling pathway and PWL2-derived siRNAs function in rice resistance to blast disease caused by M. oryzae. Full article

This study investigated the effects of different water management practices on the growth, yield, and grain quality of rice grown under environmentally friendly farming methods in Apgok-Ri, Gungnyu-Myeon, Uiryeong-Gun, from 2022 to 2024. Treatments included mid-season drainage for 2, 3, or 4 weeks (2MD, 3MD, 4MD), followed by either low-level water management (MD-1) or alternate wetting and drying (MD-2), with continuous flooding (CF) as the control. The rice variety was machine-transplanted on 9–10 June, and organic fertilizer (90 kg N/ha) was applied as a basal dressing. Water treatments were initiated in mid-July each year. The highest yield was consistently recorded in the 2MD-2 treatment, with 5.85, 5.74, and 5.38 tons/ha from 2022 to 2024, representing 15.0%, 14.5%, and 7.8% increases over CF, respectively. On average, alternate irrigation (MD-2) resulted in higher yields than low-level water management (MD-1) by 1.19–5.90%. Grain quality was also highest in 2MD-2, showing the greatest percentage of ripened grains each year, whereas CF had the highest proportion of immature and unripe grains. Crude protein content in brown rice was lowest in 3MD-2 (6.12%), followed by 2MD-2 (7.51%). Incidences of major diseases such as sheath blight, rice blast, panicle blight, and bacterial grain blight were highest in the CF treatment. Rice leaf blight was not significantly different in 2022, but was most prevalent in CF in 2023 and 2024. There were no major differences in brown planthopper and false smut incidence, although false smut peaked in CF in 2024. These findings suggest that 2-week mid-season drainage followed by alternate irrigation (2MD-2) is an effective strategy to improve yield, grain quality, and disease resistance in sustainable rice farming systems. Full article

Rice blast, caused by Magnaporthe oryzae (M. oryzae), severely threatens global rice production with substantial yield losses, endangering food security and driving demand for resistant varieties. Fuhui2165 (FH2165), an elite restorer line with stable blast resistance, superior agronomic traits, and high grain quality, is valuable for hybrid breeding, but its resistance mechanisms remain unclear. In this study, we investigated the rice blast resistance and underlying mechanisms in FH2165 and its parental lines (Huahangsimiao/HHSM, Minghui86/MH86, and Shuhui527/SH527) using transcriptome sequencing analysis. Phenotypic analysis revealed that FH2165 and HHSM exhibited stronger resistance compared to MH86 and SH527. Differential expression analysis identified 3886, 2513, 3390, and 4678 differentially expressed genes (DEGs) in FH2165, HHSM, MH86, and SH527, respectively. Gene Ontology (GO) enrichment analysis highlighted DEGs associated with chloroplasts, plastids, thylakoids, and related cellular components. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified significant enrichment in pathways such as carbon metabolism, amino acid biosynthesis, and photosynthesis. This suggested that defense strategies could involve energy reprogramming and the synthesis of secondary metabolites. Additionally, the DEGs co-expressed specifically in FH2165 and HHSM were enriched in functions related to RNA processing, GTP binding, and L-ascorbic acid binding, with purine metabolism playing a role in the regulation of energy and signaling. These findings elucidated the critical metabolic and signaling networks that underlie the blast resistance of FH2165 and offered potential targets for breeding high-yield, disease-resistant hybrid rice varieties. Full article

Tolprocarb (TPC), a fungicide primarily used for controlling rice blast, was recently shown to stimulate disease resistance in rice. To elucidate the molecular basis of this immunostimulatory effect, we conducted transcriptomic, metabolic, and field-based analyses focusing on diterpenoid phytoalexins, key antimicrobial and allelopathic compounds in rice. Microarray analysis revealed that TPC treatment induced a broad transcriptional activation of genes involved in phytoalexin biosynthesis, including DPF, a master regulator of diterpenoid metabolism. Consistent with this, LC-MS/MS analyses confirmed the accumulation of momilactones A and B, as well as phytocassanes B, C, and E, in rice leaves after TPC application, a response not observed with conventional resistance inducers such as probenazole or carpropamid. In root tissues under controlled conditions, phytoalexin accumulation was limited, and exudation into the rhizosphere was minimal. However, field experiments showed that TPC treatment led to a transient increase in leaf momilactones around 14 days post-transplanting, followed by increased exudation into the rhizosphere at 21 days. Notably, this increase in root exudation coincided with a reduction in total weed biomass, although weed species composition remained unchanged. These findings suggest that TPC not only enhances rice immunity through phytoalexin induction but may also contribute to weed suppression via allelopathic root exudates in field settings. Our study highlights a dual role for TPC in rice cultivation, boosting disease resistance and suppressing weed growth, and underscores the potential of phytoalexin-focused strategies for integrated crop protection. Full article

Most terrestrial plants establish symbiotic relationships with microorganisms to acquire nutrients and simultaneously restrict pathogen infection. In rice, the receptor-like kinase OsARK1 is essential for the colonization and development of arbuscular mycorrhizal (AM) fungi. However, whether OsARK1 participates in plant–pathogen interactions remain unknown. Here, we demonstrate that OsARK1 is involved in the transcriptional reprogramming of immune defense-related genes prior to and following AM colonization. Mutation of OsARK1 resulted in increased susceptibility to Magnaporthe oryzae (blast fungus) and Xanthomonas oryzae (bacterial blight). Transcriptomic profiling during blast infection demonstrated OsARK1 coordinates early immune responses; particularly, the upregulation of genes encoding lectin receptor-like kinases (LecRLKs), nucleotide-binding leucine-rich repeat (NLR) immune receptors and secondary metabolism-related genes was significantly impaired in Osark1 mutant. Collectively, OsARK1 acts as a positive regulator of rice immunity against pathogens while fine-tuning defense suppression during beneficial AM symbiosis. Full article

Long non-coding RNAs (lncRNAs) have emerged as pivotal regulators in plant immune responses, yet their roles in rice resistance against Magnaporthe oryzae (M. oryzae) remain inadequately explored. In this study, we integrated translatome data with conventional genome annotations to construct an optimized protein-coding dataset. Subsequently, we developed a robust pipeline (“RiceLncRNA”) for the accurate identification of rice lncRNAs. Using strand-specific RNA-sequencing (ssRNA-seq) data from the resistant (IR25), susceptible (LTH), and Nipponbare (NPB) varieties under M. oryzae infection, we identified 9003 high-confidence lncRNAs, significantly improving identification accuracy over traditional methods. Among the differentially expressed lncRNAs (DELs), those unique to IR25 were enriched in the biosynthetic pathways of phenylalanine, tyrosine, and tryptophan, which suggests that they are associated with the production of salicylic acid (SA) and auxin (IAA) precursors, which may be involved in defense responses. Conversely, DELs specific to LTH primarily clustered within carbon metabolism pathways, indicating a metabolic reprogramming mechanism. Notably, 21 DELs responded concurrently in both IR25 and LTH at 12 h and 24 h post-inoculation, indicating a synergistic regulation of jasmonic acid (JA) and ethylene (ET) signaling while partially suppressing IAA pathways. Weighted gene co-expression network analysis (WGCNA) and competing endogenous RNA (ceRNA) network analysis revealed that key lncRNAs (e.g., LncRNA.9497.1) may function as miRNA “sponges”, potentially influencing the expression of receptor-like kinases (RLKs), resistance (R) proteins, and hormone signaling pathways. The reliability of these findings was confirmed through qRT-PCR and cloning experiments. In summary, our study provides an optimized rice lncRNA annotation framework and reveals the mechanism by which lncRNAs enhance rice blast resistance through the regulation of hormone signaling pathways. These findings offer an important molecular basis for rice disease-resistant breeding. Full article