Rice Pathogen Research Articles

Antagonistic potential of soil fungi as biocontrol agent against rice pathogens

Antagonistic potential of six soil fungi viz., Aspergillus flavus Link., A. fumigatus Fresen., A. niger Tiegh., Penicillium sp., Trichoderma harzianum Refat. and T. viride Pers. against eight pathogenic fungi viz., Alternaria alternata (Fr.) Keissler, Curvularia lunata (Wakker) Boedijn, Drechslera oryzae Breda de Haan (Subramanian and Jain), Fusarium moniliforme Sheldon, F. solani (Mart.) Sacc. Microdochium oryzae (Hashloka and Yokogi) Sam. and Hal., Pestalotiopsis guepinii (Desm.) Stay. and Sarocladium oryzae (Sawada) W. Gams and D. Hawks of rice were evaluated. In colony interaction, the highest growth inhibition (88%) was observed owing to T. harzianum against Alternaria alternata.Volatile substances from soil fungi inhibited the radial growth of the test pathogens which varied from 8.33 to 57.36%.The highest inhibition (57.36%) was found owing to T. harzianum against P. guepinii. The inhibition of mycelial growth of the test pathogens ranged from 29.05 to 64.5% owing to non volatile substances of the soil fungi. The highest mycelial growth inhibition was observed owing to T. harzianum against C. lunata. Trichoderma harzianum may be exploited commercially to control rice pathogens. Bangladesh J. Bot. 53(1): 101-108, 2024 (March)

Green synthesis of chitosan nanoparticles using tea extract and its antimicrobial activity against economically important phytopathogens of rice

The aim of the present work is to biosynthesize Chitosan nanoparticles (CTNp) using tea (Camellia sinensis) extract, with potent antimicrobial properties towards phytopathogens of rice. Preliminary chemical analysis of the extract showed that they contain carbohydrate as major compound and uronic acid indicating the nature of acidic polysaccharide. The structure of the isolated polysaccharide was analyzed through FTIR and 1H NMR. The CTNp was prepared by the addition of isolated tea polysaccharides to chitosan solution. The structure and size of the CTNp was determined through FTIR and DLS analyses. The surface morphology and size of the CTNp was analysed by SEM and HRTEM. The crystalinity nature of the synthesized nanoparticle was identified by XRD analysis. The CTNp exhibited the antimicrobial properties against the most devastating pathogens of rice viz., Pyricularia grisea, Xanthomonas oryzae under in vitro condition. CTNp also suppressed the blast and blight disease of rice under the detached leaf assay. These results suggest that the biosynthesized CTNp can be used to control the most devastating pathogens of rice.

The rice endophytic bacterium Bacillus velezensis LS123N provides protection against multiple pathogens and enhances rice resistance to wind with increase in yield

Rice (Oryza sativa) is a globally important staple food, but its production was influenced by various biotic and abiotic stresses. This study involved screening endophytic bacterial strains for their antagonistic activities and control efficacy against multiple rice pathogens in planta assays. Subsequent greenhouse investigations identified Bacillus velezensis LS123N as the most promising strain for effectively controlling various rice diseases, including bacterial blight, rice blast, bakanae disease, Pythium disease, and brown spot disease. Field trials further demonstrated that LS123N significantly reduced naturally occurring brown spot disease caused by Bipolaris oryzae in both seedlings and mature rice plants, and increased rice yields. For disease control against bacterial blight, Pythium disease, and brown spot, only a single treatment during seed germination resulted in significant disease control efficacy. The application of LS123N during seed germination aligns with common rice cultivation practices. Additionally, LS123N exhibited the capacity to improve rice resistance to wind stress and enhance rice growth during the seedling stage. Endophytic colonization of LS123N was evidenced from seed to mature rice plants after seed treatment. Interestingly, the expression of many rice defense genes was suppressed within 48 h of the LS123N introduction. In vitro assays showed that LS123N inhibited spore germination and normal growth of germ tubes of B. oryzae, produced multiple hydrolases, siderophores, and IAA, and had the ability to solubilize phosphorus compounds. In summary, these results indicate that B. velezensis LS123N is a promising biocontrol agent and has the potential to be developed into a biofungicide, biofertilizer, and biostimulator.

Incorporation of the histone variant H2A.Z counteracts gene silencing mediated by H3K27 trimethylation in Fusarium fujikuroi

BackgroundFusarium fujikuroi is a pathogen of rice causing diverse disease symptoms such as ‘bakanae’ or stunting, most likely due to the production of various natural products (NPs) during infection. Fusaria have the genetic potential to synthesize a plethora of these compounds with often diverse bioactivity. The capability to synthesize NPs exceeds the number of those being produced by far, implying a gene regulatory network decisive to induce production. One such regulatory layer is the chromatin structure and chromatin-based modifications associated with it. One prominent example is the exchange of histones against histone variants such as the H2A variant H2A.Z. Though H2A.Z already is well studied in several model organisms, its regulatory functions are not well understood. Here, we used F. fujikuroi as a model to explore the role of the prominent histone variant FfH2A.Z in gene expression within euchromatin and facultative heterochromatin.ResultsThrough the combination of diverse ‘-omics‘ methods, we show the global distribution of FfH2A.Z and analyze putative crosstalks between the histone variant and two prominent histone marks, i.e., H3K4me3 and H3K27me3, important for active gene transcription and silencing, respectively. We demonstrate that, if FfH2A.Z is positioned at the + 1-nucleosome, it poises chromatin for gene transcription, also within facultative heterochromatin. Lastly, functional characterization of FfH2A.Z overexpression and depletion mutants revealed that FfH2A.Z is important for wild type-like fungal development and secondary metabolism.ConclusionIn this study, we show that the histone variant FfH2A.Z is a mark of positive gene transcription and acts independently of the chromatin state most likely through the stabilization of the + 1-nucleosome. Furthermore, we demonstrate that FfH2A.Z depletion does not influence the establishment of both H3K27me3 and H3K4me3, thus indicating no crosstalk between FfH2A.Z and both histone marks. These results highlight the manifold functions of the histone variant FfH2A.Z in the phytopathogen F. fujikuroi, which are distinct regarding gene transcription and crosstalk with the two prominent histone marks H3K27me3 and H3K4me3, as proposed for other model organisms.

Deciphering the biometeorological influences on mycoflora dynamics in rice seeds of Indo-gangetic ecosystem

Rice (Oryza sativa L.) is a vital global food source, particularly in Asia, where it constitutes 60 to 70 per cent of cereal production. However, rice cultivation faces many challenges including seed-borne fungal pathogens. This study aimed to comprehensively assess the incidence and severity of seed-borne fungal pathogens in various rice varieties and their relationship with environmental parameters during different growth stages. Seed samples were collected from different locations in Nadia district, West Bengal, and analyzed for seed health. The prevalence of Helminthosporium oryzae, Alternaria alternata, Fusarium sp., Curvularia lunata, Penicillium sp., Aspergillus flavus, Aspergillus niger and Trichoconis padwickii was recorded. Compared to the other diseases, Fusarium sp. shows a distribution with greater kurtosis deviation from normalcy, suggesting the occurrence of more extreme values. In contrast, the tailedness of Aspergillus niger's distribution is more akin to that of a normal distribution. Eight varieties of rice were examined for their susceptibility to various seed-borne fungal pathogens, revealing that variety Shatabdi exhibited a high vulnerability to these pathogens. The isolation of seed-borne pathogens was carried out at different growth stages of rice, and it was observed that the harvesting stage is particularly susceptible to seed-borne pathogens. Temperature and humidity influence pathogen intensity differently across years, indicating the complex interplay of environmental factors in disease dynamics. This research contributes to understanding the temporal and spatial dynamics of seed-borne fungal pathogens in rice, facilitating the development of targeted management strategies for improved crop health and yield. . KEYWORDS :Biometeorological parameters, growth stages, rice, seed borne, varieties

Exploring Microbial Solutions: A Comprehensive Study on Isolating, Characterizing, and Selecting Zinc-Solubilizing Fungi from Rhizospheric Soil

This study investigates the zinc solubilization potential of fungal isolates and their antagonistic activity against rice pathogens to address zinc deficiency and disease incidence in rice cultivation. Rhizospheric soil samples were collected, and zinc-solubilizing fungi were isolated and purified. Molecular characterization identified Talaromyces sp, Talaromyces versatilis, Talaromyces pinophilus, and Aspergillus terreus as zinc solubilizers. Qualitative and quantitative assays revealed varying solubilization efficiencies among isolates over time, with Talaromyces versatilis exhibiting the highest zinc solubilization. In inhibition assays conducted against rice pathogens, fungal isolates exhibited antagonistic potential, with Talaromyces versatilis demonstrating the highest percentage of inhibition. These findings underscore the potential of fungi as bio-based solutions for improving zinc nutrition and disease management in rice cultivation.

Identification and Characterization of Nigrospora Species and a Novel Species, Nigrospora anhuiensis, Causing Black Leaf Spot on Rice and Wild Rice in the Anhui Province of China.

Rice production in the Anhui province is threatened by fungal diseases. We obtained twenty-five fungal isolates from rice and wild rice leaves showing leaf spot disease collected along the Yangtze River. A phylogenetic analysis based on internal transcribed spacer (ITS), translation elongation factor 1 alpha (TEF1-α), and beta tubulin (TUB2) sequences revealed one isolate (SS-2-JB-1B) grouped with Nigrospora sphaerica, one (QY) with Nigrospora chinensis, twenty-two with Nigrospora oryzae, and one isolate (QY-2) grouped in its own clade, which are related to but clearly different from N. oryzae. Nineteen tested isolates, including sixteen strains from the N. oryzae clade and the three isolates of the other three clades, caused disease on detached rice leaves. The three isolates that did not belong to N. oryzae were also able to cause disease in rice seedlings, suggesting that they were rice pathogens. Isolate QY-2 differed from the other isolates in terms of colony morphology, cell size, and susceptibility to fungicides, indicating that this isolate represents a new species that we named Nigrospora anhuiensis. Our analysis showed that N. sphaerica, N. chinensis, and the new species, N. anhuiensis, can cause rice leaf spot disease in the field. This research provides new knowledge for understanding rice leaf spot disease.

OsWRKY65 enhances immunity against fungal and bacterial pathogens in rice

Diverse bacterial and fungal pathogens attack plants, causing biotic stress and severe yield losses globally. These losses are expected to become more serious as climate change improves conditions for many pathogens. Therefore, identifying genes conferring broad-spectrum disease resistance and elucidating their underlying mechanisms provides important resources for plant breeding. WRKY transcription factors affect plant growth and stress responses. However, the functions of many WRKY proteins remain to be elucidated. Here, we demonstrated the role of rice (Oryza sativa) WRKY group III transcription factor OsWRKY65 in immunity. OsWRKY65 localized to the nucleus and acted as transcriptional repressor. Genetic and molecular functional analyses showed that OsWRKY65 increases resistance to the fungal pathogen Fusarium fujikuroi through downregulation of GA signaling and upregulation of JA signaling. Moreover, OsWRKY65 modulated the expression of the key genes that confer susceptibility or resistance to Xanthomonas oryzae pv. oryzae to enhance immunity against the pathogen. In particular, OsWRKY65 directly bound to the promoter region of OsSWEET13 and repressed its expression. Taken together, our findings demonstrate that the OsWRKY65 enhances resistance to fungal and bacterial pathogens in rice.

Inhibitory role of copper and silver nanocomposite on important bacterial and fungal pathogens in rice (Oryza sativa)

Rice (Oryza sativa) being among the most important food crops in the world is also susceptible to various bacterial and fungal diseases that are the major stumbling blocks in the way of increased production and productivity. The bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae and the sheath blight disease caused by Rhizoctonia solani are among the most devastating diseases of the rice crop. In spite of the availability of array of chemical control, there are chances of development of resistance. Thus, there is a need for the nanotechnological intervention for management of disease in the form of copper and silver nano-composites. The copper (CuNPs) and silver nanoparticles (AgNPs) were synthesized using green route and characterized using different high throughput techniques, i.e., UV–Vis, FT-IR, DLS, XRD, FE-SEM, TEM. The particle size and zeta potential of synthesized CuNPs and AgNPs were found 273 nm and − 24.2 mV; 95.19 nm and − 25.5 mV respectively. The nanocomposite of CuNPs and AgNPs were prepared having particle size in the range of 375–306 nm with improved stability (zeta potential − 54.7 to − 39.4 mV). The copper and silver nanoparticle composites evaluated against Xanthomonas oryzae pv. oryzae and Rhizoctonia solani were found to have higher antibacterial (inhibition zone 13 mm) and antifungal activities (77%) compared to only the copper nanoparticle (8 mm; 62% respectively). Net house trials of nano-composite formulations against the bacterial blight of rice also corroborated the potential of nanocomposite formulation. In silico studies were carried out selecting two disease-causing proteins, peptide deformylase (Xanthomonas oryzae) and pectate lyase (Rhizoctonia solani) to perform the molecular docking. Interaction studies indicatedthat both of these proteins generated better complex with CuNPs than AgNPs. The study suggested that the copper and silver nano-composites could be used for developing formulations to control these devastating rice diseases.

H3K27me3 is vital for fungal development and secondary metabolite gene silencing, and substitutes for the loss of H3K9me3 in the plant pathogen Fusarium proliferatum.

Facultative heterochromatin marked by histone H3 lysine 27 trimethylation (H3K27me3) is an important regulatory layer involved in secondary metabolite (SM) gene silencing and crucial for fungal development in the genus Fusarium. While this histone mark is essential in some (e.g., the rice pathogen Fusarium fujikuroi), it appears dispensable in other fusaria. Here, we show that deletion of FpKMT6 is detrimental but not lethal in the plant pathogen Fusarium proliferatum, a member of the Fusarium fujikuroi species complex (FFSC). Loss of FpKmt6 results in aberrant growth, and expression of a large set of previously H3K27me3-silenced genes is accompanied by increased H3K27 acetylation (H3K27ac) and an altered H3K36me3 pattern. Next, H3K9me3 patterns are affected in Δfpkmt6, indicating crosstalk between both heterochromatic marks that became even more obvious in a strain deleted for FpKMT1 encoding the H3K9-specific histone methyltransferase. In Δfpkmt1, all H3K9me3 marks present in the wild-type strain are replaced by H3K27me3, a finding that may explain the subtle phenotype of the Δfpkmt1 strain which stands in marked contrast to other filamentous fungi. A large proportion of SM-encoding genes is allocated with H3K27me3 in the wild-type strain and loss of H3K27me3 results in elevated expression of 49% of them. Interestingly, genes involved in the biosynthesis of the phytohormones gibberellins (GA) are among the most upregulated genes in Δfpkmt6. Although several FFSC members harbor GA biosynthetic genes, its production is largely restricted to F. fujikuroi, possibly outlining the distinct lifestyles of these notorious plant pathogens. We show that H3K27me3 is involved in GA gene silencing in F. proliferatum and at least one additional FFSC member, and thus, may serve as a regulatory layer for gene silencing under non-favoring conditions.

Transcriptomic Approaches to Studying Rice Pathogen Interactions

Transcriptomic Approaches to Studying Rice Pathogen Interactions

Rice transcription factor OsNAC2 maintains the homeostasis of immune responses to bacterial blight.

Rice (Oryza sativa) bacterial blight, caused by Xanthomonas oryzae pv. Oryzae (Xoo), threatens plant growth and yield. However, the molecular mechanisms underlying rice immunity against Xoo remain elusive. Here, we identified a NAC (NAM-ATAF-CUC) transcription factor OsNAC2 as a negative regulator in the resistance to bacterial blight disease in rice. Constitutive overexpression of OsNAC2 inhibited the expression of salicylic acid (SA) biosynthesis-related genes (i.e. isochorismate synthase 1 (OsICS1), phenylalanine ammonia lyase 3 (OsPAL3), etc.) with adverse impacts on the pathogenesis-related proteins (PRs) responses and compromised blight resistance. Moreover, OsNAC2 interacted with APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factor OsEREBP1 and possibly threatened its protein stability, destroying the favorable interaction of OsEREBP1-Xa21-binding protein OsXb22a in the cytoplasm during Xoo-induced infection. On the contrary, downregulation of OsNAC2 resulted in enhanced resistance to bacterial blight in rice without any growth or yield penalties. Our results demonstrated that OsNAC2 inhibits SA signaling and stably interacted with OsEREBP1 to impair disease resistance. This OsNAC2-OsEREBP1-based homeostatic mechanism provided insights into the competition between rice and bacterial pathogens, and it will be useful to improve the disease resistance of important crops through breeding.

Genetic diversity and pathogenicity of fungi associated with rice sheath rot in the Fogera plain, Northwest Ethiopia

AbstractSheath rot is a widespread rice disease that affects rice crops worldwide. It is particularly prevalent in Ethiopia, with the Fogera plains exhibiting the highest incidence and severity. However, the lack of reliable molecular‐level identification of rice fungal pathogens in Ethiopia has hindered the development of effective management practices. This study aimed to assess the diversity of fungal agents causing sheath rot disease in rice crops around the Fogera plains, Ethiopia, using both morphology and nucleotide sequences of the ITS1 rDNA region. Additionally, the pathogenicity of the isolates was evaluated using attached tiller assay methods. A total of 16 fungal isolates were recovered from diseased plant samples. Among these, five species; Phoma spp., Phoma herbarium, Epicoccum sorghinum, Epicoccum lantuscollum and Microdochium seminicola were identified and reported as new records of sheath rot disease in rice. The predominant genus was Phoma (75%) followed by Epicoccum (18.75%). The pathogenicity caused by E. sorghinum was particularly severe and significantly different from the symptoms caused by other isolates, resulting in a mean lesion length of 167.7 mm and a disease severity of 55.7%. These findings suggest that E. sorghinum is the most important rice pathogen in the region. Our results have identified the most predominant and pathogenic fungal species associated with sheath rot disease in the region. Importantly, this study marks the first report of sheath rot‐causing fungi identified in rice using the ITS rDNA‐sequencing technique in Ethiopia. Therefore, this research may contribute to the development of fungal disease management strategies in rice and provide evidence to initiate a rice breeding program focused on developing sheath‐rot‐resistant rice varieties.

Genetic analysis, purification and docking studies of trihydroxynaphthalene reductase involved in pathogenesis of rice pathogen, Curvularia lunata

Curvularia lunata causes black kernel disease in rice (Oryza sativa) kernel and enzyme, trihydroxynaphthalene reductase (3HNR) catalyzes a crucial reaction in melanin biosynthesis which aids in appressorium formation. However, the molecular mechanism of pathogenesis and characterization of 3HNR are poorly understood due to the limited research conducted on this pathosystem. Therefore, the C. lunata (GVBR1) was isolated from the diseased rice kernel and identified using microscopic, SEM and molecular methods. To elucidate the molecular mechanism of 3HNR, the C. lunata was treated with different concentrations of systemic fungicide tricyclazole and the gene expression of C. lunata trihydroxynaphthalene reductase (Cl3HNR) analyzed with different concentrations of tricyclazole treated, downregulated the Cl3HNR gene expression as compared to the control. Further, Cl3HNR was cloned into pGEX expression vector, heterologously expressed in Escherichia coli BL21 cells and the expressed protein corresponds to 28 kDa. The molecular docking and dynamic simulation revealed the interaction points within the active site of Cl3HNR. This study highlights the importance of the melanin biosynthetic gene involved in the pathogenesis of the rice fungal pathogen, C. lunata, which paves the way in developing the HNR enzyme inhibitor to control the rice disease.

A Relationship Prediction Method for Magnaporthe oryzae-Rice Multi-Omics Data Based on WGCNA and Graph Autoencoder.

Magnaporthe oryzae Oryzae (MoO) pathotype is a devastating fungal pathogen of rice; however, its pathogenic mechanism remains poorly understood. The current research is primarily focused on single-omics data, which is insufficient to capture the complex cross-kingdom regulatory interactions between MoO and rice. To address this limitation, we proposed a novel method called Weighted Gene Autoencoder Multi-Omics Relationship Prediction (WGAEMRP), which combines weighted gene co-expression network analysis (WGCNA) and graph autoencoder to predict the relationship between MoO-rice multi-omics data. We applied WGAEMRP to construct a MoO-rice multi-omics heterogeneous interaction network, which identified 18 MoO small RNAs (sRNAs), 17 rice genes, 26 rice mRNAs, and 28 rice proteins among the key biomolecules. Most of the mined functional modules and enriched pathways were related to gene expression, protein composition, transportation, and metabolic processes, reflecting the infection mechanism of MoO. Compared to previous studies, WGAEMRP significantly improves the efficiency and accuracy of multi-omics data integration and analysis. This approach lays out a solid data foundation for studying the biological process of MoO infecting rice, refining the regulatory network of pathogenic markers, and providing new insights for developing disease-resistant rice varieties.

<i>In vitro</i> assessment of bacterial endophytes for antagonistic activity against <i>Magnaporthe oryzae</i> and <i>Cochliobolus miyabeanus</i> in rice

Rice is the global staple food, contributing over half of the world’s agricultural production. Excessive fungicide use in rice farming poses environmental, fungicide resistance, and beneficial microbial disruption concerns, making biocontrol, particularly bacteria, a promising biocontrol agent due to their rapid growth, ease of handling, and robust colonization attributes. Endophytes are endosymbionts residing within host plants, playing a pivotal role in plant health without inciting any pathogenic effects. In this study, we investigated the antagonistic potential of four characterized bacterial endophytic strains, viz., Bacillus velezensis strains A6 and P42, B. pseudomycoides HP3d and Paenibacillus polymyxa PGSS-1 against major foliar rice pathogens viz., Magnaporthe oryzae and Cochliobolus miyabeanus. Against M. oryzae, all the endophytic strains exhibited significant per cent inhibition (50.00-66.67%) and the highest inhibition of 66.67% was achieved by B. pseudomycoides strain HP3d, while the lowest inhibition of 50 and 51.11% was by B. velezensis strain A6, P42, and P. polymyxa PGSS1, respectively. These endophytes outperformed the positive control, P. fluorescens which showed 44.44% inhibition. Similarly, against C. miyabeanus, 31.25-43.75% inhibition was recorded, of which B. velezensis strain A6 exhibited the highest inhibition (43.75%), while B. velezensis strain P42 showed the lowest (31.25%). Furthermore, a double Petri dish assay was conducted to evaluate the volatile compounds produced by these endophytes against the two rice pathogens. It was observed that the volatile compounds produced by B. pseudomycoides strain HP3d and P. polymyxa strain PGSS1 significantly and effectively inhibited the growth of M. oryzae by 88.89% when compared to P. fluorescens (50.00%), whereas B. velezensis strain A6 showed the lowest inhibition (33.33%). Against the brown spot pathogen, C. miyabeanus, the endophytes demonstrated inhibition ranging from 56.25-87.50%, with B. pseudomycoides strain HP3d and P. fluorescens achieving the highest inhibition (87.50%) and B. velezensis strain P42 showing the lowest (56.25%). These results highlight the significant and varied inhibitory effects of volatile compounds released by these endophytes against fungal pathogens of rice. Overall, our findings highlight the promising biocontrol potential of these endophytic strains under in vitro conditions with B. pseudomycoides strain HP3d and P. polymyxa PGSS1 showing exceptional efficacy and they can be deployed in the field for the management of foliar fungal pathogens in rice.

Biogenic Silver and Copper Nanoparticles: Potential Antifungal Agents in Rice and Wheat Crops

Metal nanoparticles are widely studied due to their various applications, such as their potential use in the control of phytopathogens and the promotion of plant growth, with a significant impact on agriculture. Various microbial metabolites are used to reduce and stabilize metals and metal oxides to the nanoscale. In the present work, the biological synthesis of silver and copper oxide nanoparticles using Trichoderma harzianum TA2 is reported. The nanoparticles were purified and characterized with complementary methodologies to obtain information on the size, distribution, morphology, surface charge, and functional groups of the nanoparticles. The in vitro antifungal activity of the nanoparticles against pathogens of rice and wheat, as well as their effect on seed germination, were evaluated. In general, the nanoparticles showed a spherical shape, an average size of 17–26 nm, and low polydispersity. Furthermore, they showed antifungal activity at low concentrations against Sclerotium oryzae (0.140 ηM), Rhizoctonia oryzae-sativae (0.140 ηM), Fusarium graminearum (0.034 ηM), and Pyricularia oryzae (0.034 ηM). The germination of seeds treated with nanoparticles was not negatively affected. This is the first report of biogenic silver and copper oxide nanoparticles from a single strain of T.harzianum with antifungal activity against four phytopathogens of interest in Uruguay. Furthermore, the synthesis of the biogenic nanoparticles was faster and more efficient than previous reports using other fungi. In conclusion, this work reveals that biogenic metallic nanoparticles from T. harzianum TA2 can be considered as candidates for the control of phytopathogens affecting important crops.

XrvB regulates the type III secretion system by directly repressing hrpG transcription in Xanthomonas oryzae pv. oryzicola

Xrv proteins are a group of regulators in Xanthomonas spp., belonging to the histone-like nucleoid-structuring (H-NS) proteins of Gram-negative bacteria. The rice bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc) harbors three Xrv proteins, the XrvA, XrvB, and XrvC. Here, we report that in Xoc, the XrvB but not XrvA and XrvC is involved in negative regulation of the type III secretion system (T3SS) encoded by hrp genes. As with other Xanthomonas spp., the T3SS is an essential virulence determinant of Xoc and the expression of the hrp genes in Xoc is controlled by the HrpG/HrpX regulatory cascade. HrpG positively regulates the expression of HrpX, which in turn activates the transcription of the hrp genes. We provide evidences to demonstrate that the XrvB binds to the promoter region of hrpG and represses its transcription. Furthermore, we found that XrvB production was induced in the Xoc cells cultured in a nutrient-rich medium compared to a hrp-inducing minimal medium. We also found that in Xoc, the hrpG expression level is inversely correlated with the content of XrvB, and XrvB occupancy at hrpG promoter region is positively correlated with XrvB levels. Our data suggest that XrvB is a determinative factor controlling the expression levels of HrpG. In addition, mutation analysis revealed that the Xoc XrvB also plays positive roles in regulating bacterial growth, cell motility, and stress tolerance. Our findings provide important insights into the molecular mechanism of T3SS expression regulation in Xoc.

Available cloned genes and markers for genetic improvement of biotic stress resistance in rice.

Biotic stress is one of the major threats to stable rice production. Climate change affects the shifting of pest outbreaks in time and space. Genetic improvement of biotic stress resistance in rice is a cost-effective and environment-friendly way to control diseases and pests compared to other methods such as chemical spraying. Fast deployment of the available and suitable genes/alleles in local elite varieties through marker-assisted selection (MAS) is crucial for stable high-yield rice production. In this review, we focused on consolidating all the available cloned genes/alleles conferring resistance against rice pathogens (virus, bacteria, and fungus) and insect pests, the corresponding donor materials, and the DNA markers linked to the identified genes. To date, 48 genes (independent loci) have been cloned for only major biotic stresses: seven genes for brown planthopper (BPH), 23 for blast, 13 for bacterial blight, and five for viruses. Physical locations of the 48 genes were graphically mapped on the 12 rice chromosomes so that breeders can easily find the locations of the target genes and distances among all the biotic stress resistance genes and any other target trait genes. For efficient use of the cloned genes, we collected all the publically available DNA markers (~500 markers) linked to the identified genes. In case of no available cloned genes yet for the other biotic stresses, we provided brief information such as donor germplasm, quantitative trait loci (QTLs), and the related papers. All the information described in this review can contribute to the fast genetic improvement of biotic stress resistance in rice for stable high-yield rice production.

Molecular analysis of broad-spectrum induced resistance in rice by the green leaf volatile Z-3-hexenyl acetate.

Green leaf volatiles (GLVs), volatile organic compounds released by plants upon tissue damage, are key signaling molecules in plant immunity. The ability of exogenous GLV application to trigger an induced resistance (IR) phenotype against arthropod pests has been widely reported, but its effectiveness against plant pathogens is less well understood. In this study, we combined mRNA sequencing-based transcriptomics and phytohormone measurements with multispectral imaging-based precision phenotyping to gain insights into the molecular basis of Z-3-hexenyl acetate-induced resistance (Z-3-HAC-IR) in rice. Furthermore, we evaluated the efficacy of Z-3-HAC-IR against a panel of economically significant rice pathogens: Pyricularia oryzae, Rhizoctonia solani, Xanthomonas oryzae pv. oryzae, Cochliobolus miyabeanus, and Meloidogyne graminicola. Our data revealed rapid induction of jasmonate metabolism and systemic induction of plant immune responses upon Z-3-HAC exposure, as well as a transient allocation cost due to accelerated chlorophyll degradation and nutrient remobilization. Z-3-HAC-IR proved effective against all tested pathogens except for C. miyabeanus, including against the (hemi)biotrophs M. graminicola, X. oryzae pv. oryzae, and P. oryzae. The Z-3-HAC-IR phenotype was lost in the jasmonate (JA)-deficient hebiba mutant, which confirms the causal role of JA in Z-3-HAC-IR. Together, our results show that GLV exposure in rice induces broad-spectrum, JA-mediated disease resistance with limited allocation costs, and may thus be a promising alternative crop protection approach.