Disease Resistance In Rice Research Articles

MEMBRANE PROTEIN 1 encoding an amino acid transporter confers resistance to blast fungus and leaf-blight bacterium in rice.

Amino acid transporters (AATs) have been shown to be involved in immune responses during plant-pathogen interactions; however, the molecular mechanism by which they function in this process remains unclear. Here, we used a joint analysis of a genome-wide association study and quantitative trait locus (QTL) mapping to identify MEMBRANE PROTEIN 1, which acts as a QTL in rice against blast fungus. Heterogeneous expression of OsMP1 in yeast supported its function in transporting a wide range of amino acids, including Thr, Ser, Phe, His, and Glu. OsMP1 could also mediate 15N-Glu efflux and influx in Xenopus oocyte cells. The expression of OsMP1 was significantly induced by Magnaporthe oryzae in the resistant rice landrace Heikezijing, whereas no such induction was observed in the susceptible landrace Suyunuo. Overexpressing OsMP1 in Suyunuo enhanced disease resistance to blast fungus and leaf blight bacterium without resulting in a yield penalty. In addition, the overexpression of OsMP1 led to increased accumulation of Thr, Ser, Phe, and His in the leaves and this contributed to the reduced disease susceptibility, which was associated with up-regulation of the jasmonic acid pathway. Our results demonstrate the important role of OsMP1 in disease resistance in rice and provide a potential target for breeding more resistant cultivars without reducing yield.

OsFBN6 Enhances Brown Spot Disease Resistance in Rice

Brown spot (BS) is caused by necrotrophs fungi Cochliobolus miyabeanus (C. miyabeanus) which affects rainfed and upland production in rice, resulting in significant losses in yield and grain quality. Here, we explored the meJA treatment that leads to rice resistance to BS. Fibrillins (FBNs) family are constituents of plastoglobules in chloroplast response to biotic and abiotic stress, many research revealed that OsFBN1 and OsFBN5 are not only associated with the rice against disease but also with the JA pathway. The function of FBN6 was only researched in the Arabidopsis. We revealed gene expression levels of OsFBN1, OsFBN5, OsFBN6 and the JA pathway synthesis first specific enzyme OsAOS2 following infection with C. miyabeanus, OsAOS2 gene expression showed great regulation after C. miyabeanus and meJA treatment, indicating JA pathway response to BS resistance in rice. Three FBN gene expressions showed different significantly regulated modes in C. miyabeanus and meJA treatment. The haplotype analysis results showed OsFBN1 and OsFBN5 the diverse Haps significant with BS infection score, and the OsFBN6 showed stronger significance (**** p < 0.0001). Hence, we constructed OsFBN6 overexpression lines, which showed more resistance to BS compared to the wild type, revealing OsFBN6 positively regulated rice resistance to BS. We developed OsFBN6 genetic markers by haplotype analysis from 130 rice varieties according to whole-genome sequencing results, haplotype analysis, and marker development to facilitate the screening of BS-resistant varieties in rice breeding. The Caps marker developed by Chr4_30690229 can be directly applied to the breeding application of screening rice BS-resistant varieties.

Genetic Analysis of Key Traits for Sheath Blight Resistance and Yield Improvement in Rice (Oryza sativa)

Rice (Oryza sativa) is a staple crop for more than half of the global population, with significant production in India. However, rice production suffers yield losses of 25-30% due to diseases, particularly sheath blight (ShB), caused by Rhizoctonia solani. This study evaluated genetic variability, heritability, and genetic advance in ShB resistance and yield-related traits in 360 recombinant inbred lines (RILs) across two seasons (dry season of 2022-23 and wet season of 2023) at ICAR-IIRR, Hyderabad. Traits such as plant height, lesion height, relative lesion height, and panicle number showed high heritability (>80%) and genetic advance (>30%), indicating their strong genetic influence and responsiveness to selection. These traits, especially relative lesion height, were identified as key indicators for breeding ShB resistance. In contrast, grain yield under inoculated conditions showed lower heritability, reflecting environmental effects and suggesting that indirect selection through stable, heritable traits may be more effective. This research offers a foundation for breeding high-yielding, disease-resistant rice cultivars, advancing sustainability in ShB-prone regions by maintaining stable yields even under pathogen pressure.

Identification and characterization of cysteine-rich polycomb-like protein (CPP) gene family in rice (Oryza sativa L.) in response to phytohormones and Xanthomonas oryzae pv. oryzae stress

Cysteine-rich polycomb-like proteins (CPPs) are found in both monocotyledonous and dicotyledonous plants. These CPPs are part of nine various families of proteolytic enzymes, and they play a crucial role in various physiological, especially defence mechanisms. Nevertheless, there is a lack of findings regarding the function of CPPs in disease resistance in rice (Oryza sativa). We recently discovered eleven CPPs in the rice genome. They can be divided into three clades: I, II, and III along with CPPs from other plants like Arabidopsis thaliana (eight members), Cucumis sativus (five members), and Glycine max (thirteen members) based on their phylogenetic relationships. It is interesting to observe how segmental duplication (SD) has assisted the emergence of the OsCPP genes in rice, whereas no evidence of tandem duplication (TD) has been detected. Synteny analyses revealed three pairs of orthologous CPP genes amongst O. sativa and A. thaliana, as well as three pairs between O. sativa and C. sativus. These OsCPPs possess ten conserved amino acid motifs and several exons and introns, as determined by their gene structures. Additionally, they possess distinctive domains such as TCR and TCR superfamily domains. Cis-regulatory elements identified in the OsCPP promoter sequences were shown to be sensitive to auxin, abscisic acid, gibberellins, salicylic acid, methyl jasmonate, and light. Furthermore, stress-responsive elements and tissue-specific expression elements were identified. A large number of OsCPP genes are expressed in different kinds of tissues and organs. Several of these genes are induced by abscisic acid and jasmonic acid. Moreover, specific OsCPP genes are stimulated by Xanthomonas oryzae pv. oryzae (Xoo), the pathogen responsible for bacterial leaf blight in rice. In particular, the pathogen causes a notable overexpression of OsCPP9, suggesting its potential involvement in the plant's defense system. These results highlight the possible contributions of OsCPP genes to rice resistance against Xoo disease.

Transcriptome Analysis of Rice Near-Isogenic Lines Inoculated with Two Strains of Xanthomonas oryzae pv. oryzae, AH28 and PXO99A.

Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a major threat to rice production and food security. Exploring new resistance genes and developing varieties with broad-spectrum and high resistance has been a key focus in rice disease resistance research. In a preliminary study, rice cultivar Fan3, exhibiting high resistance to PXO99A and susceptibility to AH28, was developed by enhancing the resistance of Yuehesimiao (YHSM) to BB. This study performed a transcriptome analysis on the leaves of Fan3 and YHSM following inoculation with Xoo strains AH28 and PXO99A. The analysis revealed significant differential expression of 14,084 genes. Among the transcription factor (TF) families identified, bHLH, WRKY, and ERF were prominent, with notable differences in the expression of OsWRKY62, OsWRKY76, and OsbHLH6 across samples. Over 100 genes were directly linked to disease resistance, including nearly 30 NBS-LRR family genes. Additionally, 11 SWEET family protein genes, over 750 protein kinase genes, 63 peroxidase genes, and eight phenylalanine aminolysase genes were detected. Gene ontology (GO) analysis showed significant enrichment in pathways related to defense response to bacteria and oxidative stress response. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis and diterpenoid biosynthesis pathways. Gene expression results from qRT-PCR were consistent with those from RNA-Seq, underscoring the reliability of the findings. Candidate genes identified in this study that may be resistant to BB, such as NBS-LRR family genes LOC_Os11g11960 and LOC_Os11g12350, SWEET family genes LOC_Os01g50460 and LOC_Os01g12130, and protein kinase-expressing genes LOC_Os01g66860 and LOC_Os02g57700, will provide a theoretical basis for further experiments. These results suggest that the immune response of rice to the two strains may be more concentrated in the early stage, and there are more up-regulated genes in the immune response of the high-resistant to PXO99A and medium-resistant to AH28, respectively, compared with the highly susceptible rice. This study offers a foundation for further research on resistance genes and the molecular mechanisms in Fan3 and YHSM.

A Novel Single Base Mutation in OsSPL42 Leads to the Formation of Leaf Lesions in Rice.

Rice spotted-leaf mutants serve as valuable resources for studying plant programmed cell death (PCD) and disease resistance mechanisms, making them crucial for research on disease resistance in rice. Map-based cloning was used to identify and clone the spotted-leaf gene OsSPL42. Then, functional complementation and CRISPR/Cas9 techniques were also employed to further validate the function of this gene. By applying leaf clippings for bacterial blight (BB) inoculation, the BB resistance of different rice lines was assessed. The results in this study were as follows: The OsSPL42 behaved as a recessive nuclear gene and was narrowed down to a 111 kb region on chromosome 8. All T0 transgenic rice plants in the complementation experiments exhibited a wild-type phenotype, without any lesion spots on the rice leaves. This suggests that the LOC_Os08g06100 encoding O-methyltransferase is the candidate gene for the mutant spl42. The OsSpl42 is widely expressed and the OsSPL42-GFP protein is mainly localized in the cytoplasm. OsSPL42 overexpression lines are more susceptible to BBs, which indicates that OsSPL42 may act as a negative regulator of rice resistance to BB. In summary, we speculate that OsSPL42 plays an important role in the regulation of pathogen response, providing new insights into plant defense mechanisms.

CRISPR–Cas9-mediated promoter editing of FERONIA-Like receptor 13 increases plant growth and disease resistance in rice

Receptor kinases play a pivotal role in detecting environmental signals, and consequently, gene pleiotropy is frequently observed within this family. However, the trade-off in trait expression resulting from gene pleiotropy poses a constraint on the utilization of such genes in agricultural breeding. In this study, we identified the receptor kinase gene FERONIA-Like Receptor 13 (FLR13) as a pleiotropic gene influencing plant height, tillering, grain yield, and disease resistance. Using promoter editing, we generated novel alleles (FLR13T5T6-1, FLR13T5T6-2) that confer resistance to rice blast and increase per-plant yield. The knockout of the T5T6 segment alleviates the inhibitory effects of two transcription factors, OsGBP1 and OsWRKY53, on FLR13 expression. In summary, our study presents a promising avenue for enhancing the pivotal attributes of receptor-like kinases through a promoter-editing strategy.

Using Marker-Assisted Selection to Develop a Drought-Tolerant Rice Line with Enhanced Resistance to Blast and Brown Planthopper

Rice is a major global staple crop, but rising temperatures and freshwater shortages have made drought one of the most severe abiotic stresses affecting agriculture. Additionally, rice blast disease and brown planthopper infestations significantly impact yields. Therefore, developing water-saving, drought-resistant, high-yielding, and disease-resistant rice varieties is critical for sustainable rice production. The new water-saving and drought-resistant (WDR) rice ‘Huhan 1516’, bred using marker-assisted selection (MAS) and marker-assisted backcrossing (MABC) techniques, addresses these challenges. This variety is highly adaptable to drought-prone and water-scarce regions such as the Yangtze and Huai River basins. With its high yield, drought tolerance, and broad-spectrum resistance to rice blast (conferred by the Pi2 gene) and brown planthopper (BPH), ‘Huhan 1516’ is suitable for various farming systems and environments. Field trials show that this variety outperforms control varieties by 2.2% in yield and exhibits moderate resistance to both rice blast and brown planthopper. ‘Huhan 1516’ has been recognized as a new water-saving and drought-resistant rice variety by the state, and as a released cultivar, it has great potential for market promotion and application.

Identification of Genetic Loci for Grain Traits and Disease Resistance Reveals a Potential Trade-Off in Rice

Understanding how plants utilize limited resources for reproductivity and disease resistance can improve the efficiency of plant breeding. In the present study, we mapped genes for grain traits, including grain length and width and thousand grain weight (TGW). A previously constructed linkage map of a recombinant inbred line population (MHM) was used, which was derived from a cross between an indica restorer rice variety (Minghui 63) and a temperate japonica rice variety (M-202). The MHM population was grown in replicated field plots, and grain trait data were collected. Upon a 3-year field evaluation, a total of 16 loci were mapped on 9 of 12 chromosomes, including 7 for grain length, 4 for grain weight, and 5 for TGW. A TGW locus ( qTGW2) and a grain width locus ( qWIG2.2) were mapped at the known blast resistance locus qBLAST2 on chromosome 2 that harbors a major blast resistance allele Pi-b. Another TGW locus ( qTGW3.3) and a grain length locus ( qLNG3.3) were mapped at qBLAST3 on chromosome 3. These results reveal potential trade-offs between disease resistance and productivity, which are important for breeders to develop high-yielding and disease-resistant rice varieties. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

Exploring the molecular mechanisms of rice blast resistance and advances in breeding for disease tolerance.

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.

Preparation of pH-Responsive Kas@ZnO Quantum Dots for Synergistic Control of Rice Blast and Enhanced Disease Resistance in Rice.

The construction of controlled-release formulations improves the sustained-release performance and utilization efficiency of pesticides, which are important aspects in plant protection and environmental chemistry. The current study employs kasugamycin (Kas), which is widely used to control Magnaporthe oryzae, conjugated with carboxyl-functionalized ZnO quantum dots via amide linkages to yield a pH-responsive pesticide delivery system (Kas@ZnO). Physicochemical characterizations indicated the successful preparation of the Kas@ZnO nanoparticles. In vitro drug release assessments indicated that Kas@ZnO exhibited a loading capacity of 21.05% and could effect the controlled release of Kas in an acidic environment, which is beneficial given the unique acidic microenvironment of M. oryzae. Bioactivity assays demonstrated that Kas@ZnO could simultaneously inhibit mycelial growth and spore germination. Additionally, bioactivity tests showed that the control efficacy of Kas@ZnO against rice blast reached 67.43% after 14 days of in vivo spray inoculation, which was higher than that obtained with Kas (55.50%), suggesting improved beneficial effects of Kas@ZnO application over a prolonged duration. Moreover, Kas@ZnO enhanced the activity of defense-related enzymes in rice and upregulated the expression of defense-related genes, such as OsPR2, OsPR3, OsPR5, OsWRKY45, OsLYP6, and OsNAC4. Ultimately, the biosafety assessments revealed that Kas@ZnO did not exert any harmful effects on rice and demonstrated slight toxicity toward zebrafish. These findings indicate that Kas@ZnO can function as a pH-sensitive pesticide delivery system, allowing for targeted release of the pesticide within plant tissues. This technology demonstrates significant potential for eco-friendly plant disease management.

Cellulose synthase-like OsCSLD4: a key regulator of agronomic traits, disease resistance, and metabolic indices in rice.

Cellulose synthase-like OsCSLD4 plays a pivotal role in regulating diverse agronomic traits, enhancing resistance against bacterial leaf blight, and modulating metabolite indices based on the multi-omics analysis in rice. To delve deeper into this complex network between agronomic traits and metabolites in rice, we have compiled a dataset encompassing genome, phenome, and metabolome, including 524 diverse accessions, 11 agronomic traits, and 841 metabolites, enabling us to pinpoint eight hotspots through GWAS. We later discovered four distinct metabolite categories, encompassing 15 metabolites that are concurrently present on the QTL qC12.1, associated with leaf angle of flag and spikelet length, and finally focused the cellulose synthase-like OsCSLD4, which was pinpointed through a rigorous process encompassing sequence variation, haplotype, ATAC, and differential expression across diverse tissues. Compared to the wild type, csld4 exhibited significant reductions in the plant height, flag leaf length, leaf width, spikelet length, 1000-grain weight, grain width, grain thickness, fertility, yield per plant, and bacterial blight resistance. However, there were significant increase in tiller numbers, degree of leaf rolling, flowering period, growth period, grain length, and empty kernel rate. Furthermore, the content of four polyphenol metabolites, excluding metabolite N-feruloyltyramine (mr1268), notably rose, whereas the levels of the other three polyphenol metabolites, smiglaside C (mr1498), 4-coumaric acid (mr1622), and smiglaside A (mr1925) decreased significantly in mutant csld4. The content of amino acid L-tyramine (mr1446) exhibited a notable increase, whereas the alkaloid trigonelline (mr1188) displayed a substantial decrease among the mutants. This study offered a comprehensive multi-omics perspective to analyze the genetic mechanism of OsCSLD4, and breeders can potentially enhance rice's yield, bacterial leaf blight resistance, and metabolite content, leading to more sustainable and profitable rice production.

OsHRZ1 negatively regulates rice resistant to Magnaporthe oryzae infection by targeting OsVOZ2.

Rice blast disease caused by Magnaporthe oryzae significantly reduces yield production. Blast resistance is closely associated with iron (Fe) status, but the mechanistic basis linking iron status to immune function in rice remains largely unknown. Here, iron-binding haemerythrin RING ubiquitin ligases OsHRZ1 was confirmed to play key roles in iron-mediated rice blast resistance. The expression of OsHRZ1 was suppressed by M. oryzae inoculation and high iron treatment. Both mutants of OsHRZ1 enhanced rice resistance to M. oryzae. OsPR1a was up-regulated in OsHRZ1 mutants. Yeast two-hybrid, bimolecular fluorescence complementation, and Co-IP assay results indicated that OsHRZ1 interacts with Vascular Plant One Zinc Finger 2 (OsVOZ2) in the nucleus. Additionally, the vitro ubiquitination assay indicated that OsHRZ1 can ubiquitinate OsVOZ2 and mediate the degradation of OsVOZ2. The mutants of OsVOZ2 showed reduced resistance to M. oryzae and down-regulated the expression of OsPR1a. Yeast one-hybrid, EMSA, and dual-luciferase reporter assay results indicated that OsVOZ2 directly binds to the promoter of OsPR1a, activating its expression. In summary, OsHRZ1 plays an important role in rice disease resistance by mediated degradation of OsVOZ2 thus shaping PR gene expression dynamics in rice cells. This highlights an important link between iron signaling and rice pathogen defenses.

Improvement of Quality and Disease Resistance for a Heavy-Panicle Hybrid Restorer Line, R600, in Rice (Oryza sativa L.) by Gene Pyramiding Breeding.

The utilization of heavy-panicle hybrid rice exemplifies the successful integration of architectural enhancement and heterosis, which has been widely adopted in the southwest rice-producing area of China. Iterative improvement in disease resistance and grain quality of heavy-panicle hybrid rice varieties is crucial to promote their sustainable utilization. Here, we performed a molecular design breeding strategy to introgress beneficial alleles of broad-spectrum disease resistance and grain quality into a heavy-panicle hybrid backbone restorer line Shuhui 600 (R600). We successfully developed introgression lines through marker-assisted selection to pyramid major genes (Wxb + ALKA-GC + Pigm + Xa23) derived from three parents (Huanghuazhan, I135, I488), which significantly enhance grain quality and confer resistance to rice blast and bacterial blight (BB). The improved parental R600 line (iR600) exhibited superior grain quality and elevated disease resistance while maintaining the heavy-panicle architecture and high-yield capacity of R600. Moreover, the iR600 was crossed with male sterility line 608A to obtain a new heavy-panicle hybrid rice variety with excellent eating and cooking quality (ECQ) and high yield potential. This study presents an effective breeding strategy for rice breeders to expedite the improvement of grain quality and disease resistance in heavy-panicle hybrid rice.

Bacterial co-fermentation mediated synthesis of chitosan from Procambarus clarkii enhances disease resistance in rice

The increasing dietary demand for red swamp crayfish (Procambarus clarkii) in China has resulted in a significant rise in the quantity of its by-products, which are currently underutilized or discarded. Chitosan, a widely used plant immune inducer, is one of the major components found in red swamp crayfish shells (RSCS). However, the utilization of chitosan derived from RSCS in agriculture is hindered by the lack of an efficient microbial fermentation-based production system. To address this issue, this study aims to establish a chitosan fermentation procedure by using RSCS as substrate. The efficiency by using Bacillus followed with Acetobacter for a continuous co-fermentation tested. Bacillus NJ-B2 or NJ-B3 with Acetobacter NJ-A1 demonstrated the highest co-fermentation efficacy, achieving 95 % deproteinization and 90 % demineralization of RSCS, respectively. The extracted chitosan was characterized by fourier transform infrared and scanning electron microscopy. Notably, the application of this RSCS-derived chitosan significantly improves rice resistance against Xanthomonas oryzae pv. oryzae, Magnaporthe oryzae, and Ustilaginoidea virens. These findings collectively indicate that this established method can effectively produce chitosan from RSCS via microbial fermentation, providing an environmentally friendly way for plant protection.

Rice Varieties Intercropping Induced Soil Metabolic and Microbial Recruiting to Enhance the Rice Blast (Magnaporthe Oryzae) Resistance.

[Background] Intercropping is considered an effective approach to defending rice disease. [Objectives/Methods] This study aimed to explore the resistance mechanism of rice intraspecific intercropping by investigating soil metabolites and their regulation on the rhizosphere soil microbial community using metabolomic and microbiome analyses. [Results] The results showed that the panicle blast disease occurrence of the resistant variety Shanyou63 (SY63) and the susceptible variety Huangkenuo (HKN) were both decreased in the intercropping compared to monoculture. Notably, HKN in the intercropping system exhibited significantly decreased disease incidence and increased disease resistance-related enzyme protease activity. KEGG annotation from soil metabolomics analysis revealed that phenylalanine metabolic pathway, phenylalanine, tyrosine, and tryptophan biosynthesis pathway, and fructose and mannose metabolic pathway were the key pathways related to rice disease resistance. Soil microbiome analysis indicated that the bacterial genera Nocardioides, Marmoricola, Luedemannella, and Desulfomonile were significantly enriched in HKN after intercropping, while SY63 experienced a substantial accumulation of Ruminiclostridium and Cellulomonas. Omics-based correlation analysis highlighted that the community assembly of Cellulomonas and Desulfomonile significantly affected the content of the metabolites D-sorbitol, D-mannitol, quinic acid, which further proved that quinic acid had a significantly inhibitory effect on the mycelium growth of Magnaporthe oryzae, and these three metabolites had a significant blast control effect. The optimal rice blast-control efficiency on HKN was 51.72%, and Lijiangxintuanheigu (LTH) was 64.57%. [Conclusions] These findings provide a theoretical basis for rice varieties intercropping and sustainable rice production, emphasizing the novelty of the study in elucidating the underlying mechanisms of intercropping-mediated disease resistance.

The atypical Dof transcriptional factor OsDes1 contributes to stay-green, grain yield, and disease resistance in rice.

The regulation of leaf senescence and disease resistance plays a crucial role in determining rice grain yield and quality, which are important to meet the ever-increasing food demands of the world. Here, we identified an atypical Dof transcriptional factor OsDes1 that contributes to the stay-green phenotype, grain yield, and disease resistance in rice. The expression level of OsDes1 is positively associated with stay-green in natural variations of japonica rice, suggesting that OsDes1 would be alternatively used in breeding programs. Mechanistically, OsDes1 targets the promoter of the Rieske FeS protein gene OsPetC to activate its expression and interacts with OsPetC to protect against its degradation, thus promoting stay-green and ultimately improving the grain yield. OsDes1 also binds to the promoter region of defense-related genes, such as OsPR1b, and activates their expression, leading to enhanced disease resistance. These findings offer a potential strategy for breeding rice to enhance grain yield and disease resistance.

Identification of novel QTL for bakanae disease resistance in non-basmati indica rice

Identification of novel QTL for bakanae disease resistance in non-basmati indica rice

Extensive immune receptor repertoire diversity in disease-resistant rice landraces

Plants have powerful defense mechanisms and extensive immune receptor repertoires, yet crop monocultures are prone to epidemic diseases. Rice (Oryza sativa) is susceptible to many diseases, such as rice blast caused by Magnaporthe oryzae. Varietal resistance of rice to blast relies on intracellular nucleotide binding, leucine-rich repeat (NLR) receptors that recognize specific pathogen molecules and trigger immune responses. In the Yuanyang terraces in southwest China, rice landraces rarely show severe losses to disease whereas commercial inbred lines show pronounced field susceptibility. Here, we investigate within-landrace NLR sequence diversity of nine rice landraces and eleven modern varieties using complexity reduction techniques. We find that NLRs display high sequence diversity in landraces, consistent with balancing selection, and that balancing selection at NLRs is more pervasive in landraces than modern varieties. Notably, modern varieties lack many ancient NLR haplotypes that are retained in some landraces. Our study emphasizes the value of standing genetic variation that is maintained in farmer landraces as a resource to make modern crops and agroecosystems less prone to disease. The conservation of landraces is, therefore, crucial for ensuring food security in the face of dynamic biotic and abiotic threats.

A Novel Method for Mining Regulatory sRNAs Related to Rice Resistance Against Blast Fungus from Multi-Omics Data

Background: Due to infection by the rice blast fungus, rice, a major global staple, faces yield challenges. While chemical control methods are common, their environmental and economic costs are growing concerns. Traditional biological experiments are also inefficient for exploring resistance genes. Therefore, understanding the interaction between rice and the rice blast fungus is urgent and important. Objective: This study aims to use multi-omics data to uncover key elements in rice's defense against rice blast fungus Magnaporthe oryzae. We built a detailed, multi-layered heterogeneous interaction network, employing an innovative graph embedding feature with a cross-layer random walk algorithm to identify crucial crucial resistance factors.This could inform strategies for enhancing disease resistance in rice. objective: This study aims to use multi-omics data to uncover key elements in rice's defense against rice blast fungus Magnaporthe oryzae. We built a detailed, multi-layered heterogeneous interaction network, employing an innovative graph embedding feature with a cross-layer random walk algorithm, to identify crucial crucial resistance factors. This could inform strategies for enhancing disease resistance in rice. Methods: We integrated genomics, transcriptomics, and proteomics data on Magnaporthe oryzae infecting rice. This multi-omics data was used to construct a multi-layer heterogeneous network.An advanced graph embedding algorithm (BINE) provided rich vector representations of network nodes. A multi-layer network walking algorithm was then used to analyze the network and identify key regulatory small RNA (sRNAs) in rice. Results: Node similarity rankings allowed us to identify significant regulatory sRNAs in rice that are integral to disease resistance. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses further revealed their roles in biological processes and key metabolic pathways.Our integrative method precisely and efficiently identified these crucial elements, offering a valuable systems biology tool. Conclusion: By integrating multi-omics data with computational analysis, this study reveals key regulatory sRNAs in rice's disease resistance mechanism. These findings enhance our understanding of rice disease resistance and provide genetic resources for breeding disease-resistant rice. Despite limitations in sRNA functional interpretation, this research demonstrates the power of applying multi- omics data to address complex biological problems.