Indeterminate Domain Proteins Regulate Rice Defense to Sheath Blight Disease

BACKGROUND

Loose Plant Architecture 1 (LPA1), an indeterminate domain (IDD) protein, exhibits almost no expression in the leaves, but the overexpression of LPA1 significantly increases the resistance of rice to sheath blight disease (ShB) via the activation of PIN-FORMED 1a (PIN1a).

RESULTS

In this study, we determined that Rhizoctonia solani infection significantly induced LPA1 expression in the leaves, and lpa1 was more susceptible to R. solani compared with the wild-type and revertant plants. In addition, infection with R. solani altered the expression of IDD3, IDD5, IDD10, and IDD13, and yeast two-hybrid, split-GFP, and coimmunoprecipitation assays showed that LPA1 interacts with IDD3 and IDD13. IDD13 RNAi plants were more susceptible, while IDD13 overexpressors were less susceptible to ShB compared with the wild-type. In parallel, idd3 exhibited no significant differences, while IDD3 overexpressors were more susceptible compared to the wild-type response to ShB. Additional chromatin-immunoprecipitation and electrophoretic mobility shift assay experiments indicated that IDD13 and IDD3 bound to the PIN1a promoter, and the transient assay indicated that IDD13 and IDD3 positively and negatively regulate PIN1a expression, respectively. Moreover, IDD13, IDD3, and LPA1 form a transcription factor complex that regulates PIN1a. A genetic study showed that the LPA1 repressor lines were similar to lpa1/IDD13 RNAi and were more susceptible than the lpa1 and IDD13 RNAi plants in response to ShB. The overexpression of IDD13 increased resistance to ShB in the lpa1 background.

CONCLUSIONS

Taken together, our analyses established that IDD3, IDD13, and LPA1 form a transcription factor complex to regulate the defense of rice against ShB possibly via the regulation of PIN1a.

Functional characterization of tau class glutathione-S-transferase in rice to provide tolerance against sheath blight disease

Glutathione-S-transferase (GST) is an important defense gene that confers resistance against several abiotic and biotic stresses. The present study identifies a tau class GST in rice (Oryza sativa L.), OsGSTU5 (Os09g20220), which provided tolerance against sheath blight (SB) disease, caused by a necrotrophic fungus, Rhizoctonia solani (RS). Overexpression and knockdown rice transgenic lines of OsGSTU5 were generated and tested for the severity of infection during sheath blight disease. The results obtained after RS infection showed that the lesion cover area and hyphal penetration were more in knockdown line and lesser in the overexpression line. Analysis of reactive oxygen species (ROS) accumulation showed more spots of H2O2 and O2- in knockdown lines compared to overexpressed lines. Later, RS transcript level was analyzed in RS-infected transgenic lines, which manifested that the knockdown line had higher RS transcripts in comparison to the control line and least RS transcripts were observed in the overexpressed line. In conclusion, rice transgenic lines overexpressing OsGSTU5 were found to be more tolerant, while the knockdown lines were more prone to Rhizoctonia infection compared to control lines.

Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations

BACKGROUND

Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood.

RESULTS

We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato.

CONCLUSIONS

Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.

Assessment of Rice Sheath Blight Resistance Including Associations with Plant Architecture, as Revealed by Genome-Wide Association Studies

BACKGROUND

Sheath blight (ShB) disease caused by Rhizoctonia solani Kühn, is one of the most economically damaging rice (Oryza sativa L.) diseases worldwide. There are no known major resistance genes, leaving only partial resistance from small-effect QTL to deploy for cultivar improvement. Many ShB-QTL are associated with plant architectural traits detrimental to yield, including tall plants, late maturity, or open canopy from few or procumbent tillers, which confound detection of physiological resistance.

RESULTS

To identify QTL for ShB resistance, 417 accessions from the Rice Diversity Panel 1 (RDP1), developed for association mapping studies, were evaluated for ShB resistance, plant height and days to heading in inoculated field plots in Arkansas, USA (AR) and Nanning, China (NC). Inoculated greenhouse-grown plants were used to evaluate ShB using a seedling-stage method to eliminate effects from height or maturity, and tiller (TN) and panicle number (PN) per plant. Potted plants were used to evaluate the RDP1 for TN and PN. Genome-wide association (GWA) mapping with over 3.4 million SNPs identified 21 targeted SNP markers associated with ShB which tagged 18 ShB-QTL not associated with undesirable plant architecture traits. Ten SNPs were associated with ShB among accessions of the Indica subspecies, ten among Japonica subspecies accessions, and one among all RDP1 accessions. Across the 18 ShB QTL, only qShB4-1 was not previously reported in biparental mapping studies and qShB9 was not reported in the GWA ShB studies. All 14 PN QTL overlapped with TN QTL, with 15 total TN QTL identified. Allele effects at the five TN QTL co-located with ShB QTL indicated that increased TN does not inevitably increase disease development; in fact, for four ShB QTL that overlapped TN QTL, the alleles increasing resistance were associated with increased TN and PN, suggesting a desirable coupling of alleles at linked genes.

CONCLUSIONS

Nineteen accessions identified as containing the most SNP alleles associated with ShB resistance for each subpopulation were resistant in both AR and NC field trials. Rice breeders can utilize these accessions and SNPs to develop cultivars with enhanced ShB resistance along with increased TN and PN for improved yield potential.

Heterologous overexpression of PDH45 gene of pea provides tolerance against sheath blight disease and drought stress in rice

Biotic and abiotic stress tolerant crops are required for sustainable agriculture as well as ensuring global food security. In a previous study, we have reported that heterologous overexpression of pea DNA helicase (PDH45), a DEAD-box family member protein, provides salinity stress tolerance in rice. The improved management of photosynthetic machinery and scavenging of reactive oxygen species (ROS) are associated with PDH45 mediated salinity stress tolerance. However, the role of PDH45 in biotic and other abiotic stress (drought) tolerance remains unexplored. In the present study, we have generated marker-free transgenic IR64 rice lines that overexpress PDH45 under the CaMV35S promoter. The transgenic rice lines exhibited a significant level of tolerance against sheath blight disease, caused by Rhizoctonia solani, a polyphagous necrotrophic fungal pathogen. The defense as well as antioxidant responsive marker genes were significantly upregulated in the PDH45 overexpressing (OE) rice lines, upon pathogen infection. Moreover, the OE lines exhibited tolerance to drought stress and various antioxidant as well as drought responsive marker genes were significantly upregulated in them, upon drought stress. Overall, the current study emphasizes that heterologous overexpression of PDH45 provides abiotic as well as biotic stress tolerance in rice. Tolerance against drought as well as sheath blight disease by overexpression of a single gene (PDH45) signifies the practical implication of the present study. Moreover, considering the conserved nature of the gene in different plant species, we anticipate that PDH45 can be gainfully deployed to impart tolerance against multiple stresses in agriculturally important crops.

Identification of Novel QTL Conferring Sheath Blight Resistance in Two Weedy Rice Mapping Populations

BACKGROUND

Rice sheath blight (ShB) disease, caused by the pathogenic fungus Rhizoctonia solani, causes significant yield losses globally. US weedy rice populations, which are de-domesticated forms of indica and aus cultivated rice, appear to be more resistant to ShB than local japonica cultivated rice. We mapped quantitative trait loci (QTL) associated with ShB resistance using two F₈ recombinant inbred line populations generated from crosses of an indica crop variety, Dee-Geo-Woo-Gen (DGWG), with individuals representing the two major US weed biotypes, straw hull (SH) and black hull awned (BHA).

RESULTS

We identified nine ShB resistance QTL across both mapping populations. Five were attributable to alleles that affect plant height (PH) and heading date (HD), two growth traits that are known to be highly correlated with ShB resistance. By utilizing an approach that treated growth traits as covariates in the mapping model, we were able to infer that the remaining four QTL are involved in ShB resistance. Two of these, qShB1-2 and qShB4, are different from previously identified ShB QTL and represent new candidates for further study.

CONCLUSION

Our findings suggest that ShB resistance can be improved through favorable plant growth traits and the combined effects of small to moderate-effect resistance QTL. Additionally, we show that including PH and HD as covariates in QTL mapping models is a powerful way to identify new ShB resistance QTL.

Bacteria-fungal Confrontation and Fungal Growth Prevention Assay

There are some bacteria which can grow and multiply at the cost of living fungal biomass. They can potentially utilize fungi as a source of nutrients to forage over them. Such phenomenon is known as bacterial mycophagy, however, its mechanistic insights need to be explored to identify the molecules involved in mycophagy for potential utilization in controlling various fungal diseases. Recently we have demonstrated that a rice-associated bacteria Burkholderia gladioli strain NGJ1 exhibits mycophagous ability on several fungi, including Rhizoctonia solani, the necrotrophic fungal pathogen causing sheath blight disease in rice. We hereby describe our validated and efficient methods used to study B. gladioli strain NGJ1-R. solani interactions. These methodologies would be useful for designing assays to study the confrontation between bacteria and fungi which in turn enable discovery of novel antifungal molecules from such bacteria.

Loose Plant Architecture 1-Interacting Kinesin-like Protein KLP Promotes Rice Resistance to Sheath Blight Disease

BACKGROUND

Sheath blight disease (ShB) is a destructive disease affecting rice production. Previously, we have reported that Loose Plant Architecture 1 (LPA1) promotes resistance to ShB. However, the mechanisms by which LPA1 confers resistance against this disease have not been extensively investigated. Notably, interactors that regulate LPA-1 activity remain elusive.

FINDINGS

In this study, we identified the interaction of kinesin-like protein (KLP) with LPA1 in the nucleus of rice cells by yeast two-hybrid, bimolecular fluorescent complimentary (BiFC), and co-immunoprecipitation (co-IP) assays. To investigate the role of KLP in promoting resistance to ShB, wild-type, klp mutant, and KLP overexpressor (KLP OX) rice plants were inoculated with Rhizoctonia solani AG1-IA. The results indicated that, compared with the wild-type control, klp mutants were more susceptible while KLP OX plants were less susceptible to ShB. Since LPA1 transcriptionally activates PIN-FORMED 1a (PIN1a), we examined the expression of 8 related PIN genes. The results showed that only the expression of PIN1a and PIN3b coincided with KLP expression levels. In addition, a chromatin immunoprecipitation (ChIP) assay showed that KLP bound directly to the promoter region of PIN1a but not of PIN3b. Transient expression assays confirmed that LPA1 and KLP transcriptionally activate PIN1a, and that coexpression of KLP and LPA1 had an additive effect on the activation of PIN1a, suggesting that KLP enhances LPA1 transcriptional activation activity.

CONCLUSIONS

Taken together, our results show that KLP is a novel LPA1 interactor that promotes resistance of rice to ShB.

Mangrove endophytic fungi: Biocontrol potential against Rhizoctonia solani and biofertilizers for fragrant rice cultivation

The mangrove ecosystem has emerged as a fascinating source for exploring novel bioresources which have multiple applications in modern agriculture. This study evaluates the potential applications of mangrove endophytic fungi (MEF), such as biocontrol agents against Rhizoctonia solani and as biofertilizers for improving the yield of fragrant rice variety Malaysian Rice Quality 76 (MRQ76). Through the antagonism assays, it is observed that among the 14 MEF studied, 4 fungal isolates (Colletotrichum sp. MEFN02, Aspergillus sp. MEFN06, Annulohypoxylon sp. MEFX02 and Aspergillus sp. MEFX10) exhibited promising antagonistic effect against the pathogen R. solani compared to the chemical fungicide (Benomyl). These isolates also revealed significant production of enzymes, phytochemicals, indoleacetic acid (40.96 mg/mL) and ammonia (32.54 mg/mL) and displayed tolerance to salt and temperature stress up to 2000 mM and >40 °C respectively. Furthermore, employing the germination and pathogenicity test, inoculation of these endophytes showed lower percentage of disease severity index (DSI%) against R. solani, ranging from (24 %-46 %) in MRQ76 rice seedlings. The in-vivo experiments of soil and seed inoculation methods conducted under greenhouse conditions revealed that these endophytes enhanced plant growth (8-15 % increase) and increased crop yield (≥50 %) in comparison to control treatments. The current findings provide valuable insights into eco-friendly, cost-effective and sustainable alternatives for addressing R. solani infection and improving the agronomic performance of the fragrant rice cultivar MRQ76, contributing to food security.

Synergistic Antifungal Activity of Green Synthesized Zinc Oxide Nanoparticles and Fungicide Against Rhizoctonia solani Causing Rice Sheath Blight Disease

The biosynthesis of metal oxide nanoparticles using leaf extract of medicinal plants is a promising substitute for the traditional chemical method. This work aimed to synthesize zinc oxide nanoparticles using a green approach from local "Dholkolmi" (Ipomoea carnea) leaf extract which is a medicinal plant growing outside the roads of different regions of Bangladesh. The biosynthesized zinc oxide nanoparticles (ZnONPs) were characterized using ultraviolet-visible spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, particle size analyzer, zeta-potential, scanning electron microscopy-energy dispersive spectroscopy, field emission scanning electron microscopy, and transmission electron microscopy. The results of UV-visible spectrophotometers observed an absorption peak at 373 nm wavelength, which confirmed the synthesis of ZnONPs in the solution. ZnONP sizes determined by XRD, DLS, and TEM are approximately ~37 nm, 105.61 nm, and 19.66 nm, respectively. ZnONPs were present because of the strong oxygen and zinc signals in the EDX profile. Additionally, this research assessed the antifungal activity of the biosynthesized ZnONPs and as well as folicur-incorporated ZnONPs against Rhizoctonia solani by the poison bait technique. According to the result of this study, ZnONPs synthesized from Ipomoea carnea leaf extract showed no promising result against Rhizoctonia solani mycelial growth reduction. But folicur-incorporated ZnONPs revealed a significant finding with a maximum 100% inhibition of mycelial growth at 1:1 and 3:1 ratio of ZnONPs with folicur fungicide under in vitro conditions. In the net house experiment, folicur-incorporated ZnONPs at a 1:1 ratio of ZnONPs with folicur showed considerable disease inhibition (26.96% RLH) as compared to disease control (52.83% RLH). In the case of rainfed transplanted Aus (March-June), the highest percentage of RLH was recorded in disease control (64.61%), and the lowest RLH was found in folicur (24.79%) followed by a 1:1 ratio of ZnONPs with folicur (32.10%) in field condition. On the other hand, the highest percentage of RLH was recorded in disease control (65.31%) and the lowest RLH was found in folicur (18.14%) followed by a 1:1 ratio of ZnONPs with folicur (21.39%) in rainfed transplanted Aman (July-November) season. The findings of the in vitro and in vivo studies provided evidence that ZnONPs and folicur had a strong synergistic antifungal impact and may be employed as a possible rice sheath blight disease management agent.