Rice sheath blight, caused by Rhizoctonia solani, is a primary disease threatening global rice production, resulting in significant yield losses. This review explores the resistance mechanisms of the rice crop against sheath blight, focusing on recent advancements in genomics and plant immunology. This review covers key areas, including the identification of sheath blight resistance genes, mapping of Quantitative Trait Loci (QTL) in cultivated rice, and the utilization of wild rice germplasm for disease resistance. This paper examines how phytohormones, transcription factors, and receptor kinases regulate sheath blight resistance in rice. Understanding these mechanisms is essential for developing blight-resistant cultivars and improving management strategies. The findings provide valuable insights for breeding programs focused on enhancing sheath blight resistance in rice.

Sheath blight (ShB), caused by the necrotrophic fungus Rhizoctonia solani (R. solani), poses severe threats to global rice production. Developing a resistant variety with an ShB-resistance gene is one of most efficient and economical approaches to control the disease. Here, we identified a highly conserved chloroplast-localized stem-loop-binding protein encoding gene (OsCSP41b), which shows great potential in developing an ShB-resistant variety. OsCSP41b-knockout mutants exhibit chlorotic leaves and increased ShB susceptibility, whereas OsCSP41b-overexpressing lines (CSP41b-OE) display significantly enhanced resistance to R. solani, as well as to drought, and salinity stresses. Notably, CSP41b-OE lines present a completely comparable grain yield to the wild type (WT). Transcriptomic analyses reveal that chloroplast transcripts and photosynthesis-associated genes maintain observably elevated stability in CSP41b-OE plants versus WT plants following R. solani infection, which probably accounts for the enhanced ShB resistance of CSP41b-OE. Our findings nominate the OsCSP41b gene as a promising molecular target for developing a rice variety with stronger resistance to both R. solani and multi-abiotic stresses.

Sheath blight (ShB), caused by the necrotrophic fungus Rhizoctonia solani, is one of the most serious rice diseases worldwide. In this study, we successfully grafted salicylic acid (SA) onto mesoporous silica nanoparticles through an amide-bond coupling method, forming functionalized MSN-SA nanoparticles. Physicochemical characterization showed that the MSN-SA nanoparticles were spherical, with an average particle size of approximately 30 nm and an SA loading rate of around 7.21%. The assessment of ShB resistance revealed that both SA and MSN-OH treatments were capable of inducing resistance to a certain extent. When SA and MSN-OH were applied in combination, the resistance was further augmented, indicating an additive effect between them. Intriguingly, MSN-SA treatment (50% in Lemont) exhibited a higher and more durable control efficacy compared with SA + MSN-OH treatment (33%). Moreover, field experiments demonstrated that the MSN-SA was safe for rice, and under severe disease conditions, it could recover 16.7% of the yield loss, thus highlighting its substantial application value. Further transcriptome analysis and physicochemical assays suggested that MSN-SA released SA in a slow and continuous manner, thus persistently activating the immune response, and that MSN-SA integrated the effects of SA and MSN-OH, thereby enhancing the ShB resistance. Altogether, our results provide new perspectives and a novel nanomaterial-based immune elicitor for the green control of ShB.

Sheath blight (ShB), caused by necrotrophic fungus Rhizoctonia solani, is one of the most serious rice diseases worldwide. To the best of our knowledge, no genes with high potential for rice ShB resistance breeding have been previously characterized. Here we identify a ShB resistance receptor-like kinase 1 (SBRR1) gene via a genome-wide association study. The SBRR1-R elite allele, containing a 256-bp insertion in its promoter, is preferentially present in indica varieties in geographical regions with highly favorable conditions for ShB development. Introduction of SBRR1-R into a commercial japonica rice variety significantly reduces yield loss under severe ShB disease pressure. Transcription factor bHLH57 specifically binds to the 256-bp sequence and accounts for highly induced expression and stronger resistance of SBRR1-R. Localization of SBRR1 on plasma membrane, aided by SBRR1-interaction-protein 1, and phosphorylation of SBRR1 are required for SBRR1 to rapidly upregulate downstream chitinase genes for resistance. These findings offer mechanistical insights into ShB resistance hidden in natural rice varieties.

The heading date is one of the important traits in rice, which greatly affects grain yield and regional adaptability. Although the flowering pathways in rice have been extensively investigated, the genes involved in flowering remain largely unknown. Here, we report a rice lhd mutant, which showed late flowering under both long-day (LD) and short-day (SD) conditions. Through MutMap+ and linkage analysis, a deletion mutation in OsMetAP10 was inferred as the most likely candidate for lhd late flowering. OsMetAP10 encodes a methionine aminopeptidase that belongs to the peptidase_M24 subfamily III. The OsMetAP10 gene is constitutively expressed in rice and is induced by light, with a rhythmic expression pattern. OsMetAP10 knockout lines displayed late heading as the lhd mutation, while no alternations in morphology and heading were observed on OsMetAP10 overexpression lines, further confirming the mutation of OsMetAP10 as responsible for the late heading of lhd. Through RT-qPCR and transcriptome analysis, we revealed that the upregulated expression of the FT-like gene OsFLT4, a negatively flowering regulator, and the downregulation of flower development-related genes, OsMADS14, OsMADS15, and OsMADS34, played critical roles in determining the late flowering of the OsMetAP10 mutation. This study reports a new gene affecting flowering and provides a new insight into the role of OsMetAP10 in regulating rice heading.

Rice (Oryza sativa) is a globally important crop that plays a central role in maintaining food security. This scientific review examines the critical role of genetic disease resistance in protecting rice yields, dissecting at the molecular level how rice plants detect and respond to pathogen attacks while evaluating modern approaches to developing improved resistant varieties. The analysis covers single-gene-mediated and multi-gene resistance systems, detailing how on one hand specific resistance proteins, defense signaling components, and clustered loci work together to provide comprehensive protection against a wide range of pathogens and yet their production is severely impacted by pathogens such as Xanthomonas oryzae (bacterial blight) and Magnaporthe oryzae (rice blast). The discussion extends to breakthrough breeding technologies currently revolutionizing rice improvement programs, including DNA marker-assisted selection for accelerating traditional breeding, gene conversion methods for introducing new resistance traits, and precision genome editing tools such as CRISPR/Cas9 for enabling targeted genetic modifications. By integrating advances in molecular biology and genomics, these approaches offer sustainable solutions to safeguard rice yields against evolving pathogens.

The emergence of multi-omics technologies has transformed our understanding of molecular mechanisms governing key traits across diverse plant species. Multi-omics approaches, including genomics, transcriptomics, metabolomics, and microbiome profiling, have provided unprecedented insights into the molecular basis of crop resilience and productivity. In rice, integrated genomics and metabolomics have identified key loci and metabolic pathways that control grain yield and nutritional quality. In maize, transcriptomic and genomic analyses have identified networks regulating flowering time and drought tolerance. In wheat, epigenomic and transcriptomic approaches have uncovered regulators of cold stress adaptation. These studies underscore the potential of multi-omics in linking molecular variation with complex agronomic traits, thereby providing a foundation for crop improvement. Emerging layers such as lipidomics, immunomics, glycomics, and RNomics further expand integrative potential, while advanced trait-analysis frameworks (GWAS, TWAS, WGCNA) offer practical pathways for breeding, resilience, and biofortification. We also discuss emerging trends and emphasize the role of advanced tools and interdisciplinary collaborations in addressing current scientific challenges. Together, these insights present a holistic perspective on advancing plant biology and agricultural innovation.

Ethylene response factors (ERFs) are plant transcription agents that play a pivotal role in disease resistance through the ethylene signaling pathway. However, whether and how ERFs regulate resistance to sheath blight (ShB), caused by Rhizoctonia solani in rice, remains largely unknown. Here, we demonstrated that OsERF7 negatively regulates rice resistance to ShB by inhibiting phytoalexin biosynthesis. Overexpression of OsERF7 (OsERF7OE) significantly decreased ShB resistance, whereas knockout of OsERF7 (oserf7) enhanced it. Mechanistically, antioxidant enzyme activities are significantly reduced in OsERF7OE plants, but increased in oserf7 plants. Furthermore, transcriptome analysis revealed that oserf7 plants exhibited significant upregulation of pathogenesis-related (PR) and phytoalexin biosynthesis genes upon R. solani infection. Consistently, transcript levels of phytoalexin biosynthesis genes, including OsKSL7, OsKSL8, OsKOL5, and OsCPS4, were significantly elevated in oserf7 plants, but reduced in OsERF7OE plants in response to R. solani infection. Electrophoretic mobility shift assays and dual-luciferase (LUC) reporter assays further confirmed that OsERF7 directly binds to the promoters of OsKSL8, OsKOL5, and OsCPS4, thereby repressing their expression. In summary, our study revealed that OsERF7 negatively regulated rice resistance to ShB primarily by inhibiting phytoalexin biosynthesis.

Plant-induced resistance plays a crucial role in the plant defense system by activating intrinsic immune mechanisms. In this study, a novel amidase- and redox-responsive codelivery nanosystem was developed by covalently linking salicylic acid (SA) to functionalized disulfide-doped mesoporous silica nanoparticles (MSNs-ss-NH2) for the efficient delivery of SA and bioavailable silicon concurrently. Physicochemical characterization confirmed the successful preparation of MSNs-ss-SA, demonstrating its structural integrity and glutathione and amidase responsive degradation mechanism. With a particle size of approximately 90 nm, MSNs-ss-SA could penetrate the stomata of rice leaves, facilitating the efficient intracellular transport of SA and bioavailable silicon. Biological activity assays revealed that MSNs-ss-SA exhibited superior efficacy in inducing resistance to rice sheath blight compared to conventional SA, which was primarily due to its ability to enhance physical barrier formation, strengthen antioxidant defense systems, upregulate the expression of key defense-related genes, and increase chitinase synthesis, collectively triggering both systemic acquired resistance and induced systemic resistance. Most importantly, biological safety assessments confirmed its excellent compatibility with rice plants, aquatic organisms, soil ecosystems, and human cell models. Therefore, the prodrug system of SA and bioavailable silicon shows a significant potential for sustainable agricultural plant disease management.

Rice blast disease, caused by the fungus Magnaporthe oryzae, poses a significant threat to global rice production, impacting food security for a substantial portion of the world’s population. This review explores the advancements in understanding the molecular mechanisms of rice blast resistance and the integrative strategies for breeding rice cultivars with enhanced resistance. Key focus areas include the genomic plasticity of M. oryzae, the role of repeat elements in its rapid evolution, and the identification of specific resistance genes (R genes) in rice. The review highlights the use of next-generation sequencing, gene editing technologies like Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9), and marker-assisted selection in developing resistant rice varieties. Additionally, the paper discusses the balance between rice yield and resistance, the role of transcription factors, ubiquitin ligases, and other regulatory proteins in mediating resistance, and the challenges and future directions in rice blast disease management. Integrating traditional breeding techniques with modern molecular tools is essential for sustainable and effective control of rice blast disease. This review will offer significant scientific and technological assistance in ensuring food security on a global scale.

The traditional method of screening plants for disease resistance phenotype is both time-consuming and costly. Genomic selection offers a potential solution to improve efficiency, but accurately predicting plant disease resistance remains a challenge. In this study, we evaluated eight different machine learning (ML) methods, including random forest classification (RFC), support vector classifier (SVC), light gradient boosting machine (lightGBM), random forest classification plus kinship (RFC_K), support vector classification plus kinship (SVC_K), light gradient boosting machine plus kinship (lightGBM_K), deep neural network genomic prediction (DNNGP), and densely connected convolutional networks (DenseNet), for predicting plant disease resistance. Our results demonstrate that the three plus kinship (K) methods developed in this study achieved high prediction accuracy. Specifically, these methods achieved accuracies of up to 95% for rice blast (RB), 85% for rice black-streaked dwarf virus (RBSDV), and 85% for rice sheath blight (RSB) when trained and applied to the rice diversity panel I (RDPI). Furthermore, the plus K models performed well in predicting wheat blast (WB) and wheat stripe rust (WSR) diseases, with mean accuracies of up to 90% and 93%, respectively. To assess the generalizability of our models, we applied the trained plus K methods to predict RB disease resistance in an independent population, rice diversity panel II (RDPII). Concurrently, we evaluated the RB resistance of RDPII cultivars using spray inoculation. Comparing the predictions with the spray inoculation results, we found that the accuracy of the plus K methods reached 91%. These findings highlight the effectiveness of the plus K methods (RFC_K, SVC_K, and lightGBM_K) in accurately predicting plant disease resistance for RB, RBSDV, RSB, WB, and WSR. The methods developed in this study not only provide valuable strategies for predicting disease resistance, but also pave the way for using machine learning to streamline genome-based crop breeding. (c) 2024 THE AUTHORS. Published by Elsevier LTD on behalf of Chinese Academy of Engineering and Higher Education Press Limited Company. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Rice blast, caused by Magnaporthe Oryzae ( M. oryzae ), is one of the most serious diseases all over the world. Development of blast-resistant rice varieties can effectively control the damage of rice blast and reduce the application of chemical pesticides. In this study, 477 sequenced rice germplasms from 48 countries were inoculated and identified at booting stage. We found that 23 germplasms displayed high panicle blast resistance against M. oryzae. 43 quantitative trait loci (QTLs) significantly ( P < 10 − 4 ) associated with rice panicle blast resistance were identified by genome-wide association analysis (GWAS). These QTL intervals contain four genes ( OsAKT1 , OsRACK1A , Bsr-k1 and Pi25 / Pid3 ) have been reported to be involved in rice blast resistance. We select QTLs with -Log10(Pvalue) higher than 6.0 or those detected in two-year replicates, totaling 12 QTLs, for candidate gene analysis. We identified three blast resistance candidate genes ( Os06g0316800 , Os06g0320000 , Pi25 / Pid3 ) based on the significant SNP distribution of annotated gene sequences in these 12 QTL and the difference of expression levels among blast resistant varieties after 72h inoculation. Os06g0316800 encodes a protein similar to Glycine-rich protein, an important component of plant cell walls involved in cellular stress responses and signaling, named as OsGrp6 . Os06g0320000 encodes a protein of unknown function DUF953, belonging to the thioredoxin-like family, crucial for maintaining reactive oxygen species (ROS) homeostasis in vivo, named as OsTrxl1 . Lastly, Pi25 / Pid3 encodes a disease resistance protein, emphasizing its potential significance in plant biology. By analyzing the haplotypes of these 3 genes, we identified the favorable haplotypes with blast resistance, which will provide genetic resources for future rice blast resistance breeding.

Sheath blight (ShB) disease, caused by Rhizoctonia solani Kühn, is one of the most serious rice diseases. Rice breeding against ShB has been severely hindered because no major resistance genes or germplasms are available in rice. Here, we report that introduction of Gastrodia antifungal protein (GAFP) genes from Gastrodia elata B1 into rice significantly enhances resistance to rice ShB. Four GAFP genes were cloned from G. elata B1, and all displayed a strong ability to inhibit R. solani growth in plate assays. Two versions, with or without a signal peptide, for each of the four GAFP genes were introduced into XD3 and R6547 rice cultivars, and all transgenic lines displayed stronger ShB resistance than the corresponding wild-type control in both greenhouse and field conditions. Importantly, GAFP2 showed the highest ShB resistance; GAFPs with and without its signal peptide showed no significant differences in enhancing ShB resistance. We also evaluated the agronomic traits of these transgenic rice and found that ectopic expression of GAFPs in rice at appropriate levels did not affect agronomic traits other than enhancing ShB resistance. Together, these results indicate that GAFP genes, especially GAFP2, have great potential in rice breeding against ShB disease.

Rice blast is a major problem in agriculture, affecting rice production and threatening food security worldwide. This disease, caused by the fungus Magnaporthe oryzae, has led to a lot of research since the discovery of the first resistance gene, pib, in 1999. Researchers have now identified more than 50 resistance genes on eight of the twelve chromosomes in rice, each targeting different strains of the pathogen.These genes are spread out across seventeen different loci. These genes, which primarily code for nucleotide-binding and leucine-rich repeat proteins, play an important part in the defense of rice against the pathogen, either alone or in combination with other genes. An important characteristic of these genes is the allelic or paralogous interactions that exist within these loci. These relationships contribute to the gene’s increased capacity for evolutionary adaptation. The ability of resistance proteins to recognize and react to novel effectors is improved by the frequent occurrence of variations within the domains that are responsible for recognizing pathogen effectors. The purpose of this review is to summarize the progress that has been made in identifying these essential genes and to investigate the possibility of utilizing the allelic variants obtained from these genes in future rice breeding efforts to increase resistance to rice blast.

Rice blast, caused by the fungus Magnaporthe oryzae (syn. Pyricularia oryzae), is a major problem in rice cultivation and ranks among the most severe fungal diseases. Cloning and identifying resistance genes in rice, coupled with a comprehensive examination of the interaction between M. oryzae and rice, may provide insights into the mechanisms of rice disease resistance and facilitate the creation of new rice varieties with improved germplasm. These efforts are essential for protecting food security. This review examines the discovery of genes that confer resistance or susceptiblity to M. oryzae in rice over the last decade. It also discusses how knowledge of molecular mechanisms has been used in rice breeding and outlines key strategies for creating rice varieties resistant to this disease. The strategies discussed include gene pyramiding, molecular design breeding, editing susceptibility genes, and increasing expression of resistance genes through pathogen challenge. We address the prospects and challenges in breeding for rice blast resistance, emphasizing the need to fully exploit germplasm resources, employ cutting-edge methods to identify new resistance genes, and develop innovative breeding cultivars. Additionally, we underscore the importance of understanding the molecular basis of rice blast resistance and developing novel cultivars with broad-spectrum disease resistance.

BACKGROUND: Rice is one of the most consumed cereals in the world. Productivity losses are caused by different biotic stresses. One of the most common is the phytophagous mite Schizotetranychus oryzae Rossi de Simons (Acari: Tetranychidae), which inhibits plant development and seed production. The identification of plant defense proteins is important for a better understanding of the mite-plant interaction. We previously detected a high expression of Osmotin1 protein in mite-resistant rice cultivars, under infested conditions, suggesting it could be involved in plant defense against mite attack. We therefore aimed to evaluate the responses of three rice lines overexpressing Osmotin1 (OSM1-OE) and three lines lacking the Osmotin1 gene (osm1-ko) to mite attack.RESULTS: The numbers of individuals (adults, immature stages, and eggs) were significantly lower in OSM1-OE lines than those in wild-type (WT) plants. On the other hand, the osm1-ko lines showed larger numbers of mites per leaf than WT plants. When plants reached the full maturity stage, two out of the three infested OSM1-OE lines presented lower plant height than WT, while the three osm1-ko lines (infested or not) presented higher plant height than WT. The reduction in seed number caused by mite infestation was lower in OSM1-OE lines (12-19%) than in WT plants (34%), while osm1-ko lines presented higher reduction (24-54%) in seed number than WT plants (13%).CONCLUSION: These data suggest that Osmotin1 is involved in rice resistance to S. oryzae infestation. This is the first work showing increased plant resistance to herbivory overexpressing an Osmotin gene. (c) 2023 Society of Chemical Industry.

Sheath blight (ShB), caused by Rhizoctonia solani, is a highly destructive disease in many crops worldwide and no major resistance genes are available. Here, we identified a sbr1 (sheath blight resistance 1) rice mutant, which shows enhanced ShB resistance and maintains wildtype agronomic traits including yield, but carries an undesired stay-green phenotype. Through map-based cloning and transgenic validation, we found that an insertion disrupting the Stay-Green (OsSGR) gene is responsible for sbr1 phenotypes. Mechanistically, the sbr1/Ossgr mutants reduce the expression of most OsCKX genes, which function in cytokinin (CK) degradation, to accumulate CK leading to ShB resistance. Importantly, knockout of OsCKX7, predominantly expressed in the leaf sheath and highly induced by R. solani, significantly enhances ShB resistance without stay-green phenotype nor yield penalty, showing high application potential. Thus, our study reveals novel insights that OsSGR and cytokinin play key roles in rice-R. solani interaction and generates a valuable ShB-resistant germplasm.

Rice is one of the staple foods for the majority of the global population that depends directly or indirectly on it. The yield of this important crop is constantly challenged by various biotic stresses. Rice blast, caused by Magnaporthe oryzae (M. oryzae), is a devastating rice disease causing severe yield losses annually and threatening rice production globally. The development of a resistant variety is one of the most effective and economical approaches to control rice blast. Researchers in the past few decades have witnessed the characterization of several qualitative resistance (R) and quantitative resistance (qR) genes to blast disease as well as several avirulence (Avr) genes from the pathogen. These provide great help for either breeders to develop a resistant variety or pathologists to monitor the dynamics of pathogenic isolates, and ultimately to control the disease. Here, we summarize the current status of the isolation of R, qR and Avr genes in the rice–M. oryzae interaction system, and review the progresses and problems of these genes utilized in practice for reducing rice blast disease. Research perspectives towards better managing blast disease by developing a broad-spectrum and durable blast resistance variety and new fungicides are also discussed.