Rice Bacterial Blight Research Articles

OsGRF6-OsYUCCA1/OsWRKY82 Signaling Cascade Upgrade Grain Yield and Bacterial Blight Resistance in Rice.

As a major crop in the world, the sustainable development of rice is often severely restricted by bacterial blight. Breeding crops with resistance is an efficient way to control bacterial blight. However, enhancing resistance often incurs a fitness penalty, making it challenging to simultaneously increase bacterial blight resistance and yield potential. In this study, it is found that OsGRF6, besides being a high-yield gene, can significantly improve rice bacterial blight resistance. Compared with wild-type, the lesion lengths of transgenic material overexpressing OsGRF6 are significantly reduced after inoculation with Xanthomonas oryzae pv. oryzae (Xoo). Furthermore, OsGRF6 can directly bind to the promoters of OsYUCCA1 and OsWRKY82, upregulating their transcription and thereby increasing rice bacterial blight resistance and yield. Haplotypic analysis based on the promoter and genome sequence combined with evolutionary analysis revealed that OsGRF6 is mainly comprised by the OsGRF6XI and OsGRF6GJ subtypes. The superior haplotype OsGRF6Hap4 increased its transcriptional activity and contributed to bacterial blight resistance and rice yield. Together, this study provides theoretical support for further revealing the synergistic regulatory mechanism and genetic improvement of rice high yield and bacterial blight resistance, offering a new strategy for developing disease-resistant cultivars.

Modeling climate-related global risk maps of rice bacterial blight caused by Xanthomonas oryzae (Ishiyama 1922) using geographical information system (GIS).

Rice is a critical staple crop that feeds more than half of the world's population. Still, its production confronts various biotic risks, notably the severe bacterial blight disease produced by Xanthomonas oryzae. Understanding the possible effects of climate change on the geographic distribution of this virus is critical to ensuring food security. This work used ecological niche modeling and the Maxent algorithm to create future risk maps for the range of X. oryzae under several climate change scenarios between 2050 and 2070. The model was trained using 93 occurrence records of X. oryzae and five critical bioclimatic variables. It has an excellent predictive performance, with an AUC of 0.889. The results show that X. oryzae's potential geographic range and habitat suitability are expected to increase significantly under low (RCP2.6) and high (RCP8.5) emission scenarios. Key climatic drivers allowing this development include increased yearly precipitation, precipitation during the wettest quarter, and the wettest quarter's mean temperature. These findings are consistent with broader research revealing that climate change is allowing many plant diseases and other dangerous microbes to spread across the globe. Integrating these spatial predictions with data on host susceptibility, agricultural practices, and socioeconomic vulnerabilities can help to improve targeted surveillance, preventative, and management methods for reducing the growing threat of bacterial blight to rice production. Proactive, multidisciplinary efforts to manage the changing disease dynamics caused by climate change will be critical to assuring global food security in the future decades.

Design, Synthesis, and Biological Evaluation of Novel Quinoline Derivatives against Phytopathogenic Bacteria Inspired from Natural Quinine Alkaloids.

A series of 2-(trifluoromethyl)-4-hydroxyquinoline derivatives were designed and synthesized with introduction of the antibacterial fragment amino alcohols, and their antibacterial activity against plant phytopathogenic bacteria was evaluated for the development of quinoline bactericides. It is worth noting that compound Qa5 exhibited excellent antibacterial activity in vitro with a minimum inhibitory concentration (MIC) value of 3.12 μg/mL against Xanthomonas oryzae (Xoo). Furthermore, in vivo assays demonstrated that the protective efficacy of Qa5 against rice bacterial blight at 200 μg/mL (33.0%) was superior to that of the commercial agent bismerthiazol (18.3%), while the curative efficacy (35.0%) was comparable to that of bismerthiazol (35.7%). The antibacterial mechanisms of Qa5 indicated that it affected the activity of bacteria by inducing intracellular oxidative damage in Xoo and disrupting the integrity of the bacterial cell membrane. The above results demonstrated that the novel quinoline derivative Qa5 possessed excellent in vitro and in vivo antibacterial activity, indicating its potential as a novel green agricultural antibacterial agent.

Smart β-cyclodextrin-dominated helical supramolecular dendritic assemblies improve the foliar affinity and biofilm disruption for treating alarming bacterial diseases

Recent outbreaks of alarming bacterial diseases have significantly impacted global agricultural productivity. Conventional bactericides exhibit certain limitations in efficiently impeding biofilm formation and annihilating biofilm-dispersed pathogens, and often expose to high off-target movement during foliar spraying. Here, we produce an innovative helical dendrimer-like supramolecular material (PhA28@β-CD) assembled by a bioactive small-molecule 2-chlorophenylisopropanolamine (PhA28) and β-cyclodextrin (β-CD) through host-guest recognition principle. In this system, the advisable optimization by a macrocyclic oligosaccharide—β-CD significantly enhances the water-solubility, biocompatibility, and bioavailability of PhA28. At a low-dose of 6.8 μg/mL, PhA28@β-CD discloses an outstanding biofilm disruption rate of 82.4 %, notably exceeding that of PhA28 (60.6 %), which thereby reduces the biofilm-associated virulence. Meanwhile, the self-assembled PhA28@β-CD possesses superior wetting and dispersing properties on hydrophobic leaves, leading to effective foliar deposition and prolong retention of active components. In vivo studies reveal that PhA28@β-CD exhibits superior curative (66.0 %) and protective (72.6 %) activities against citrus canker at 200 μg/mL, markedly surpassing those of the existing bactericide thiodiazole‑copper (46.8 % and 52.2 %) and single PhA28. This material also has broad-spectrum control efficiency (53.0 % ~ 59.5 %) against rice bacterial blight. This research lays the groundwork for developing carbohydrate-optimized multifunctional dendrimer-like assemblies aimed at disrupting biofilms and improving sustained bioavailability to combat bacterial diseases.

Noninvasive Raman spectroscopy for the detection of rice bacterial leaf blight and bacterial leaf streak

Plant diseases pose significant threats to agricultural yields and are responsible for nearly 20 % of losses in total food production. Therefore, the rapid detection of plant pathogens is critically important for preventing the rapid development of plant diseases and minimizing crop damage. Raman spectroscopy (RS) has been shown to be effective for detecting living biological samples. Compared with traditional detection methods, RS is fast, sensitive, and non-destructive; it also does not require sample labeling. In this study, we used Laser tweezers Raman spectroscopy combined with convolutional neural networks to detect two closely related strains of bacteria, Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), exuded from bacteria-infected rice leaves. The accuracy of this technique was 97.5 %. For the application of RS in the field, we used the portable Raman spectrometer to detect mock-inoculated as well as Xoo- and Xoc-infected rice leaves at different disease courses. The identification accuracy via this technique was 87.02 % in the early stage, in which no obvious symptoms were apparent. This method also revealed spectral differences in rice leaves caused by the two bacteria, which could be leveraged for subsequent analysis of the molecular mechanism of infection. Our results indicate that RS is a promising approach for the early detection of bacterial diseases in rice in the field, as well as for in-depth single-cell analysis in laboratory settings.

Strategies for sustainable rice bacterial leaf blight management: a holistic approach through phage biocontrol and nanoparticle encapsulation

Strategies for sustainable rice bacterial leaf blight management: a holistic approach through phage biocontrol and nanoparticle encapsulation

Horizontal transmission of a rice bacterial pathogen Pantoea ananatis among plants by rice planthoppers.

Pantoea ananatis is a bacterium commonly found in various agronomic crops and agricultural pests. In this study, we present findings on a genome-reduced strain of P. ananatis, known as Lstr, which was initially isolated from Laodelphax striatellus (small brown rice planthopper, SBPH). We identified Lstr as a plant pathogen causing disease in rice using Koch's postulates. The pathogenicity of Lstr on rice is comparable to that of Xanthomonas oryzae pv. oryzae, the main causative agent of rice bacterial blight. Through a series of experiments involving live insects, molecular investigations, and microscopy, we find that Lstr can accumulate within SBPH. Subsequently, Lstr can be transmitted from SBPH to rice plants, resulting in leaf blight, and can also be transmitted to other SBPH individuals. Collectively, our results suggest that SBPH serves as a vector for P. ananatis Lstr in rice plants. P. ananatis may encounter susceptible insect populations and become endemic through horizontal transmission from these insects. This could also be valuable for predicting future occurrences of bacterial leaf blight in rice and other crops caused by P. ananatis.

Strain of Xanthomonas oryzae pv. oryzae Loses Virulence through Dysregulation of Cardiolipin Synthase.

Small non-coding RNAs (sRNAs) are pivotal post-transcriptional regulatory factors influencing biological activity. Studies on the rice bacterial blight pathogen Xanthomonas oryzae pathovar oryzae strain PXO99A, previously identified a virulence-associated sRNA, trans3287. A mutant strain lacking this sRNA, named SK01, resulted in markedly diminished virulence towards rice. This study aims to further elucidate the underlying bacterial virulent function of trans3287. The expression of trans3287 was quantified in virulence-inducing and standard nutritional conditions to clarify its production mechanism. The detection of virulence-associated genes revealed that trans3287 regulated the synthesis processes of extracellular polysaccharides, lipopolysaccharides, and the type III secretion system. Moreover, bioinformatics prediction and quantitative PCR indicated a potential direct target of trans3287, PXO_03470, encoding cardiolipin synthase. A dual-plasmid system fusing with GFP tag and protein immunoblotting confirmed that sRNA trans3287 negatively regulated PXO_03470. Bacterial biofilms demonstrated trans3287 regulated the disruption of biofilm integrity through cardiolipin synthase. This study provides preliminary insights into the mechanistic underpinnings of the role of sRNA trans3287 in mediating bacterial virulence through cardiolipin synthase.

Resin Acid Copper Salt, an Interesting Chemical Pesticide, Controls Rice Bacterial Leaf Blight by Regulating Bacterial Biofilm, Motility, and Extracellular Enzymes.

Bacterial virulence plays an important role in infection. Antibacterial virulence factors are effective for preventing crop bacterial diseases. Resin acid copper salt as an effective inhibitor exhibited excellent anti-Xanthomonas oryzae pv. oryzae (Xoo) activity with an EC50 of 50.0 μg mL-1. Resin acid copper salt (RACS) can reduce extracellular polysaccharides' (EPS's) biosynthesis by down-regulating gumB relative expression. RACS can also effectively inhibit the bio-mass of Xoo biofilm. It can reduce the activity of Xoo extracellular amylase at a concentration of 100 μg mL-1. Meanwhile, the results of virtual computing suggested that RACS is an enzyme inhibitor. RACS displayed good curative activity with a control effect of 38.5%. Furthermore, the result of the phytotoxicity assessment revealed that RACS exhibited slight toxicity compared with the control at a concentration of 200 μg mL-1. The curative effect was increased to 45.0% using an additional antimicrobial agent like orange peel essential oil. RACS markedly inhibited bacterial pathogenicity at a concentration of 100 μg mL-1 in vivo.

Enhancing resistance to bacterial blight in rice using CRISPR-based base editing technology

Bacterial blight (BB), caused by Xanthomonas oryzae pathovar oryzae (Xoo), poses a significant threat to rice production, particularly in Asia and West Africa. Breeding resistance against BB in elite rice varieties is crucial to advancing rice breeding program and supporting smallholder farmers. Transcription Activator-Like effectors (TALes) are key virulence factors in Xoo, with some targeting the susceptibility (S) genes such as the sugar transporter SWEET genes in rice. Among these, SWEET14 is an important S gene, with its promoter bound by the TALe TalC which exists across all sequenced African Xoo isolates. In the present study, we utilized CRISPR/Cas9-based cytidine and adenine base editors to alter the effector binding element (EBE) of TalC in the promoter of SWEET14 in rice cultivars Kitaake, IR24, and Zhonghua 11. Mutations with C to T changes in EBE led to reduced SWEET14 induction by TalC-containing Xoo strains, resulting in resistance to African Xoo isolates reliant on TalC for virulence. Conversely, A to G changes retained SWEET14 inducibility and susceptibility to Xoo in edited lines. Importantly, no off-target mutations were detected at predicted sites, and the edited lines exhibited no obvious defects in major agronomic traits in Kitaake. These results underscore the effectiveness of base editing systems for both molecular biology research and crop improvement endeavors.

Formononetin derivatives containing benzyl piperidine: A brand new, highly efficient inhibitor targeting Xanthomonas spp

IntroductionPlant bacterial diseases take an incalculable toll on global food security. The indiscriminate use of chemical synthetic pesticide not only facilitates pathogen resistance of pathogenic bacteria, but also poses a major threat to human health and environmental protection. Therefore, it is of great economic value and scientific significance to develop a new antibacterial drug with environmental friendliness and unique mechanism of action. ObjectivesTo design and synthesize formononetin derivatives based on natural products, evaluate their in vitro and in vivo antibacterial activities and elucidate the mechanisms involved. MethodsThe synthesis was carried out by classical active group splicing method. The antibacterial activities were evaluated using turbidimetry and pot experiments. The antibacterial mechanism was further investigated using scanning electron microscopy (SEM), virulence factors, defense enzymes activities, proteomics and metabolomics. Results40 formononetin derivatives containing benzyl piperidine were designed and synthesized. The antibacterial results demonstrated that H32 exhibited the most potent inhibitory effect against Xanthomonas oryzae pv. Oryzae (Xoo) with the EC50 of 0.07 μg/mL, while H6 displayed the highest inhibitory activity against Xanthomonas axonopodis pv. Citri (Xac) with the EC50 of 0.24 μg/mL. Furthermore, the control efficacy of H32 against rice bacterial leaf blight (BLB) and H6 against citrus canker (CC) was validated through pot experiments. SEM, virulence factors and host enzyme activities assay indicated that H32 could not only reduce the virulence of Xoo, but also activate the activities of defense enzymes and improve the disease resistance of host plants. The proteomics and metabolomics analysis demonstrated that H32 could inhibit the synthesis of branched-chain amino acids, make Xoo cells in a starvation state, inhibit its proliferation, weaken its virulence and reduce its colonization and infection of host cells. ConclusionFormononetin derivatives containing benzyl piperidine could be used as potentially effective inhibitors against Xanthomonas spp.

Closing the information gap between the field and scientific literature for improved disease management- with a focus on rice and bacterial blight.

A path to sustainably reduce world hunger, food insecurity, and malnutrition is to close the crop yield gap, particularly, losses due to pathogens. Breeding resistant crops is key to achieving this goal, an effort requiring collaboration among stakeholders, scientists, breeders, farmers and policymakers. During a disease outbreak, epidemiologists survey the occurrence of a disease after which pathologists investigate mechanisms to stop an infection. Policymakers then implement strategies with farmers and breeders to overcome the outbreak. Information flow from the field to the lab and back to the field involves several processing hubs that require different information inputs. Failure to communicate the necessary information results in the transfer of meaningless data. Here, we discuss gaps in information acquisition and transfer between the field and laboratory. Using rice bacterial blight disease as an example, we discuss pathogen biology and disease resistance to point out the importance of reporting pathogen strains that caused an outbreak to optimize the deployment of resistant crop varieties. We examine differences between infection in the field and assays performed in the laboratory to draw awareness of possible misinformation concerning plant resistance or susceptibility. We discuss key data considered useful for reporting disease outbreaks, sampling bias, and suggestions for improving data quality. We also touch on the knowledge gap in the state-of-the-art literature regarding disease dispersal and transmission. We use a recent case study to exemplify the gaps mentioned. We conclude by highlighting potential actions that may contribute to food security and to closing of the yield gap.

Effect of mutation of phaC on carbon supply, extracellular polysaccharide production, and pathogenicity of Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight in rice. Polyhydroxyalkanoates (PHAs) consitute a diverse group of biopolyesters synthesized by bacteria under nutrient-limited conditions. The phaC gene is important for PHA polymerization. We investigated the effects of phaC gene mutagensis in Xoo strain PXO99A. The phaC gene knock-out mutant exhibited reduced swarming ability relative to that of the wild-type. Under conditions where glucose was the sole sugar source, extracellular polysaccharide (EPS) production by ΔphaC declined by 44.8%. ΔphaC showed weak hypersensitive response (HR) induction in the leaves of non-host Nicotiana tabacum, concomitant with downregulation of hpa1 gene expression. When inoculated in rice leaves by the leaf-clipping method, ΔphaC displayed reduced virulence in terms of lesion length compared with the wild-type strain. The complemented strain showed no significant difference from the wild-type strain, suggesting that the deletion of phaC in Xoo induces significant alterations in various physiological and biological processes. These include bacterial swarming ability, EPS production, transcription of hrp genes, and glucose metabolism. These changes are intricately linked to the energy utilization and virulence of Xoo during plant infection. These findings revealed involvement of phaC in Xoo is in the maintaining carbon metabolism by functioning in the PHA metabolic pathway.

Design, synthesis and antimicrobial activity of novel berberine derivatives.

The threats to the safety of humans and the environment and the resistance of agricultural chemicals to plant pathogenic fungi and bacteria highlight an urgent need to find safe and efficient alternatives to chemical fungicides and bactericides. In this study, a series of Berberine (BBR) derivatives were designed, synthesized and evaluated for in vitro and in vivo antimicrobial activity against plant pathogenic fungi and bacteria. Bioassay results indicated that compounds A11, A14, A20, A21, A22, A25, A26, E1, E2, E3, Z1 and Z2 showed high inhibitory activity against Sclerotinia sclerotiorum and Botrytis cinerea. Especially, A25 showed a broad spectrum and the highest antifungal activity among these compounds. Its EC50 value against Botrytis cinerea was 1.34 μg mL-1. Compound E6 possessed high inhibitory activity against Xanthomonas oryzae and Xanthomonas Campestris, with MIC90 values of 3.12 μg mL-1 and 1.56 μg mL-1. A Topomer CoMFA model was generated for 3D-QSAR studies based on anti-B. cinerea effects, with high predictive accuracy, showed that the addition of an appropriate substituent group at the para-position of benzyl of BBR derivatives could effectively improve the anti-B. cinerea activity. In addition, compound A25 could significantly inhibit the spore germination of Botrytis cinerea at low concentration, and compound F4 exhibited remarkable curative and protective efficiencies on rice bacterial leaf blight. This study indicates that the BBR derivatives are hopeful for further exploration as the lead compound with novel antimicrobial agents. © 2024 Society of Chemical Industry.

Novel trans-Resveratrol Derivatives: Design, Synthesis, Antibacterial Activity, and Mechanisms.

Rice bacterial leaf blight and rice bacterial leaf streak have induced tremendous damage to production of rice worldwide. To discover an effective novel antibacterial agent, a series of novel trans-resveratrol (RSV) derivatives containing 1,3,4-oxadiazole and amide moieties were designed and synthesized for the first time. Most of them showed excellent antibacterial activities against Xanthomonas oryzae pv oryzicola and Xanthomonas oryzae pv oryzae. Especially, compound J12 had the best inhibitory with the half-maximal effective concentration values of 4.2 and 5.0 mg/L, respectively, which were better than that of RSV (63.7 and 75.4 mg/L), bismerthiazol (79.5 and 89.6 mg/L), and thiodiazole copper (105.4 and 112.8 mg/L). Furthermore, compound J12 had an excellent control effect against rice bacterial leaf streak and rice bacterial leaf blight, with protective activities of 46.2 and 42.1% and curative activities of 44.5 and 41.7%, respectively. Preliminary mechanisms indicated that compound J12 could not only remarkably decrease biofilm formation, extracellular polysaccharide production, and the synthesis of extracellular enzymes but also destroy bacterial cell surface morphology, thereby reducing the pathogenicity of bacteria. In addition, compound J12 could increase the activity of defense-related enzymes and affect the expression of multiple pathogenic-related genes including plant-pathogen interaction, the MAPK signaling pathway, and phenylpropanoid biosynthesis, and this could improve the defense of rice against rice bacterial leaf streak infection. The present work indicates that the RSV derivatives can be used as promising candidates for the development of antibacterial agents.

Discovery of a novel series of phenylthiazole thioether (sulfone) compounds based on natural thiasporine A as potential candidates for controlling rice fungal and bacterial diseases

AbstractHalf of the world's population depends on rice for their calories. Protecting rice in the growth period from damage caused by phytopathogens is faced with a great challenge under the frequent extreme climate. To find novel fungicides to control rice diseases, 35 novel phenylthiazole‐1,3,4‐oxadiazole‐thioether (sulfone) derivatives were synthesized and evaluated for their efficacy against destructive fungal and bacterial diseases of rice. Bioassay results demonstrated that most of G‐series compounds possessed excellent antifungal and antibacterial activities. In particular, compounds G1 (EC50 = 2.22 μg/mL, R.s) and G7 (EC50 = 2.76 μg/mL, R.s) showed the most promising antifungal activities in vitro and exhibited superior protective and curative activities against rice sheath blight in vivo compared with commercial carbendazim. Surprisingly, compound G2 exhibited the remarkable antibacterial activity against Xanthomonas oryzae pv. oryzae (Xoo) with an EC50 value of 1.98 μg/mL, and demonstrated superior protective activity (88.08%) than thiodiazole copper (79.39%) against rice bacterial leaf blight at 200 μg/mL. The abovementioned results fully manifested that the phenylthiazole‐1,3,4‐oxadiazole‐sulfone structure, especially compounds G1 and G2, had the potential to develop as commercial agents for controlling rice fungal and bacterial diseases.

Efficient Damage Assessment of Rice Bacterial Leaf Blight Disease in Agricultural Insurance Using UAV Data

In Indonesia, where the agricultural insurance system has been in full operation since 2016, a new damage assessment estimation formula for rice diseases was created through integrating the current damage assessment method and unmanned aerial vehicle (UAV) multispectral remote sensing data to improve the efficiency and precision of damage assessment work performed for the payments of insurance claims. The new method can quickly and efficiently output objective assessment results. In this study, UAV images and bacterial leaf blight (BLB) rice damage assessment data were acquired during the rainy and dry seasons of 2021 and 2022 in West Java, Indonesia, where serious BLB damage occurs every year. The six-level BLB score (0, 1, 3, 5, 7, and 9) and damage intensity calculated from the score were used as the BLB damage assessment data. The relationship between normalized UAV data, normalized difference vegetation index (NDVI), and BLB score showed significant correlations at the 1% level. The analysis of damage intensities and UAV data for paddy plots in all cropping seasons showed high correlation coefficients with the normalized red band, normalized near-infrared band, and NDVI, similar to the results of the BLB score analysis. However, for paddy plots with damage intensities of 70% or higher, the biased numbering of the BLB score data may have affected the evaluation results. Therefore, we conducted an analysis using an average of 1090 survey points for each BLB score and confirmed a strong relationship, with correlation coefficients exceeding 0.9 for the normalized red band, normalized near-infrared band, and NDVI. Through comparing the time required by the current assessment method with that required by the assessment method integrating UAV data, it was demonstrated that the evaluation time was reduced by more than 60% on average. We are able to propose a new assessment method for the Indonesian government to achieve complete objective enumeration.

Design, synthesis, and evaluation of novel 3-(piperazin-1-yl)propan-2-ol-modified carbazole derivatives targeting the bacterial membrane

Grain of high yield and quality is needed worldwide due to the needs of a rapidly increasing human population. However, diseases caused by some stubborn types of phytopathogenic bacteria can limit the health and yields of crops. Even worse, conventional commercial bactericides have limited efficacy against such diseases. Therefore, exploring some efficacious bactericidal alternatives is urgently needed. In this work, a new type of 3-(piperazin-1-yl)propan-2-ol modified carbazole derivatives was synthesized and assessed for their bactericidal activity. Among them, compound B16 was the optimal active molecule, giving the EC50 values of 3.11 (Xanthomonas oryzae pv. oryzae), 3.20 (Xanthomonas axonopodis pv. citri) and 3.54 μg/mL (Pseudomonas syringae pv. actinidiae). Pot experiments revealed compound B16 to be able to control rice bacterial leaf blight. Some biochemical assays illustrated that our designed compounds could destroy the integrality of bacterial cell membranes and thereby leading to leaking the intracellular protein. These findings may be regard as a reference for the design of novel membrane-targeting antimicrobial agents for managing stubborn plant bacterial diseases.

Insights into the virulence profiles and molecular diversity of Xanthomonas oryzae pv. oryzae isolates associated with bacterial blight of rice in major districts of Karnataka, India

Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating disease affecting rice worldwide. In this study, to characterize Xoo isolates and evaluate the effectiveness of various BLB-resistant genes in rice, a set of 29 rice differentials each carrying, single or combinations of BLB resistant genes were used for characterizing Xoo isolates under glasshouse condition. None of the tested isolates were able to show complete virulence across all Near Isogenic Lines (NILs). All isolates varied with degrees of resistance and susceptibility. Notably, isolate KXo-3 exhibited high virulence. Among single BLB resistant genes, IRBB-8 (xa8) and IRBB-13 (xa13) were found highly promising while among two gene combinations, IRBB-51 (Xa4+xa13), IRBB-52 (Xa4+Xa21) and IRBB-53 (xa5+xa13). Among three and four gene combination of BB resistant genes, IRBB-56 (Xa4+xa5+xa13), IRBB-57 (Xa4+xa5+Xa21), IRBB-58 (Xa4+xa13+Xa21), IRBB-59 (Xa5+xa13+Xa21), IRBB-60 (Xa4+xa5+xa13+Xa21), IRBB-63 (xa5+Xa7+xa13) and IRBB-65 (Xa4+Xa7+xa13+Xa21) were resistant against almost all the Xoo isolates. Based on disease reactions, Xoo isolates were grouped into 6 pathotypes, as IXoPt # 1, 2, 4, 5, 17 and 22. IXoPt-22 was highly virulent and IXoPt-1 was least virulent. IXoPt-2 was widely distributed with the maximum distribution frequency of 23.8. Molecular diversity using IS1112 repetitive elements showed that the Xoo isolates were genetically very diverse with three major clusters, I, II and III. The haplotype diversity resulted in 27 haplotypes generation. The isolates of Belagavi, Haveri and Davanagere were very diverse with distinct haplotypes. These findings enhance our understanding of BLB resistance mechanisms and Xoo population diversity, aiding in the development of effective disease management strategies in rice cultivation.

Integrative genomic and transcriptomic analysis of Xanthomonas oryzae pv. oryzae pathotype IV, V, and IX in China reveals rice defense-responsive genes

Bacterial blight of rice is a devastating disease caused by the gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo). Chinese Xoo strain pathotypes IV, V, and IX are the major virulent Xoo strain types in South China sequentially from the 1990s to the present. Here, we report the isolation of GD0201 and GD0202, which belong to pathotypes IV and IX, respectively, and the complete genome sequence and transcriptomic analysis of GD0201 (IV), GD1358 (V), and GD0202 (IX). We found that resistance genes xa5, Xa23, and Xa27 confer strong resistance to all three Xoo strains, indicating that they are currently good choices for resistance rice breeding. The genome analysis reveals fewer TAL and non-TAL effector coding genes in GD0202 than in the other two strains, potentially contributing to its strong virulence. Transcriptomic analysis of ZH11 inoculated with the three Xoo strains strongly suggests that three Xoo strains for better infection repress the ethylene response factor (ERF) gene family members. Furthermore, weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) analysis revealed 14 hub genes potentially associated with rice response to the three Xoo strains. The expression of several hub genes was validated to be induced by all three Xoo strains, suggesting its role in bacterial blight disease response to Xoo strains. Genomic analysis of the Xoo strains belonging to pathotypes IV, V, and IX, identification of effectors and genes related to Xoo virulence in rice plants will provide insights into understanding the molecular mechanism underlying rice-Xoo interaction and the gene expression pattern in response to Xoo infection.