Rapid Determination of Rice Cultivar Responses to the Sheath Blight Pathogen Rhizoctonia solani Using a Micro-Chamber Screening Method

Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance

Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10-30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs) are recruited early on by the host plant to respond to pathogens. Wall-associated receptor kinases (WAKs), a subfamily of receptor-like kinases, have been shown to play a role in fungal defense. The rice gene WAK91 (OsWAK91), co-located in the major SB resistance QTL region on chromosome 9, was identified by us as a candidate in defense against rice sheath blight. An SNP mutation T/C in the WAK91 gene was identified in the susceptible rice variety Cocodrie (CCDR) and the resistant line MCR010277 (MCR). The consequence of the resistant allele C is a stop codon loss, resulting in an open reading frame with extra 62 amino acid carrying a longer protein kinase domain and additional phosphorylation sites. Our genotype and phenotype analysis of the parents CCDR and MCR and the top 20 individuals of the double haploid SB population strongly correlate with the SNP. The susceptible allele T is present in the japonica subspecies and most tropical and temperate japonica lines. Multiple US commercial rice varieties with a japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high-yielding commercial varieties to reduce yield losses incurred by the sheath blight disease.

Selection of reference genes for RT-qPCR analysis of rice with Rhizoctonia solani infection and biocontrol PGPR/KSi application

BACKGROUND

Rhizoctonia solani (AG1 IA) is an important pathogen of rice (Oryza sativa L.) that causes rice sheath blight (RSB). Since control of RSB by breeding and fungicides have had limited success, novel strategies like biocontrol with plant growth-promoting rhizobacteria (PGPR) can be an effective alternative.

METHOD AND RESULTS

Seven commonly used reference genes (RGs), 18SrRNA, ACT1, GAPDH2, UBC5, RPS27, eIF4a and CYP28, were evaluated for their stability in rice-R. solani-PGPR interaction for real-time quantitative PCR (RT-qPCR) analysis. Different algorithms were examined, Delta Ct, geNorm, NormFinder, BestKeeper, and comprehensive ranking by RefFinder, to evaluate RT-qPCR of rice in tissues infected with R. solani and treated with the PGPR strains, Pseudomonas saponiphilia and Pseudomonas protegens, with potassium silicate (KSi) alone or in combination with each PGPR strain. RG stability was affected for each treatment and treatment-specific RG selection was suggested. Validation analysis was done for nonexpressor of PR-1(NPR1) for each treatment.

CONCLUSION

Overall, ACT1 was the most stable RG with R. solani infection alone, GAPDH2 with R. solani infection plus KSi, UBC5 with R. solani infection plus P. saponiphilia, and eIF4a with R. solani infection plus P. protegens. Both ACT1 and RPS27 were the most stable with the combination of KSi and P. saponiphilia, while RPS27 was the most stable with the combination of KSi and P. protegens.

A natural allele of proteasome maturation factor improves rice resistance to multiple pathogens

Crops with broad-spectrum resistance loci are highly desirable in agricultural production because these loci often confer resistance to most races of a pathogen or multiple pathogen species. Here we discover a natural allele of proteasome maturation factor in rice, UMP1^R2115, that confers broad-spectrum resistance to Magnaporthe oryzae, Rhizoctonia solani, Ustilaginoidea virens and Xanthomonas oryzae pv. oryzae. Mechanistically, this allele increases proteasome abundance and activity to promote the degradation of reactive oxygen species-scavenging enzymes including peroxidase and catalase upon pathogen infection, leading to elevation of H₂O₂ accumulation for defence. In contrast, inhibition of proteasome function or overexpression of peroxidase/catalase-encoding genes compromises UMP1^R2115-mediated resistance. More importantly, introduction of UMP1^R2115 into a disease-susceptible rice variety does not penalize grain yield while promoting disease resistance. Our work thus uncovers a broad-spectrum resistance pathway integrating de-repression of plant immunity and provides a valuable genetic resource for breeding high-yield rice with multi-disease resistance.

Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice

Simple Summary

Rice, the staple food for more than half of humanity, is grown predominantly in Asia, the world’s most populous continent with the fastest-growing economy. The present-day rice industry must not only meet increasing demand but also changing consumer demands, with a strong emphasis placed on producing high-quality rice. While the rapid development of advanced genotyping methods can be useful for modern rice breeding programs, some methods (such as capillary electrophoresis or sequencing) can be costly to apply in laboratories with limited resources. To address this issue, we developed six novel multiplex polymerase chain reaction (PCR) assays that employ a standard agarose-based gel electrophoresis system to simultaneously detect at least two major grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) genes in rice. One of these assays, which can detect all three targeted biotic stresses, was found to be useful in screening Malaysian weedy rice that may contain novel sources of disease resistance. The universal protocol described in this study can be used in routine molecular laboratories to aid rice breeding initiatives in Malaysia and other resource-constrained countries.

Abstract

While previous research has demonstrated that multiplex polymerase chain reaction (PCR) can be a cost-effective approach to detect various genes in crops, the availability of multiplex assays to simultaneously screen both grain quality and biotic stress resistance traits in rice (Oryza sativa) is limited. In this work, we report six novel multiplex assays that use a universal protocol to detect major rice grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) traits with amplified products consisting of up to four primer pairs that can be analyzed using a standard agarose-based gel electrophoresis system. Recent studies have suggested that weedy rice has novel sources of disease resistance. However, an intensive screening of weedy biotypes has not been reported in Malaysia. Accordingly, we employed one of the developed multiplex assays to screen reported genes or quantitative trait loci (QTLs) associated with blast, sheath blight, and bacterial leaf blight diseases in 100 weedy rice biotypes collected from five local fields, with phenotyping performed to validate the genotyping results. In conclusion, our universal multiplex protocol is effective for the large-scale genotyping of rice genetic resources, and it can be employed in routine molecular laboratories with limited resources.

Comparative transcriptome analysis of rice cultivars resistant and susceptible to Rhizoctonia solani AG1-IA

Background

Rice sheath blight, which is caused by Rhizoctonia solani, is the most destructive disease affecting rice production, but the resistance mechanism to this pathogen has not been fully elucidated.

Results

In this study, we selected two rice cultivars based on their resistance to the pathogen and analyzed and compared the transcriptomic profiles of two cultivars, the moderately resistant variety Gangyuan8 and the highly susceptible variety Yanfeng47, at different time points after inoculation. The comparative transcriptome profiling showed that the expression of related genes gradually increased after pathogen inoculation. The number of differentially expressed genes (DEGs) in Yanfeng47 was higher than that in Gangyuan8, and this result revealed that Yanfeng47 was more susceptible to fungal attack. At the early stage (24 and 48 h), the accumulation of resistance genes and a resistance metabolism occurred earlier in Ganguan8 than in Yanfeng47, and the resistance enrichment entries were more abundant in Ganguan8 than in Yanfeng47.

Conclusions

Based on the GO and KEGG enrichment analyses at five infection stages, we concluded that phenylalanine metabolism and the jasmonic acid pathway play a crucial role in the resistance of rice to sheath blight. Through a comparative transcriptome analysis, we preliminarily analyzed the molecular mechanism responsible for resistance to sheath blight in rice, and the results lay the foundation for the development of gene mining and functional research on rice resistance to sheath blight.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08816-x.

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.

Comparative transcriptome profiling reveals the basis of differential sheath blight disease response in tolerant and susceptible rice genotypes

Rice sheath blight (ShB) disease, caused by the fungal pathogen Rhizoctonia solani AG1-IA, is one of the devastating diseases and causes severe yield losses all over the world. No completely resistant germplasm is known till now, and as a result, the progress in resistance breeding is unsatisfactory. Basic studies to identify candidate genes, QTLs, and to better understand the host-pathogen interaction are also scanty. In this study, we report the identification of a new ShB-tolerant rice germplasm, CR 1014. Further, we investigated the basis of tolerance by exploring the disease responsive differentially expressed transcriptome and comparing them with that of a susceptible variety, Swarna-Sub1. A total of 815 and 551 genes were found to be differentially regulated in CR 1014 and Swarna-Sub1, respectively, at two different time points. The result shows that the ability to upregulate genes for glycosyl hydrolase, secondary metabolite biosynthesis, cytoskeleton and membrane integrity, the glycolytic pathway, and maintaining photosynthesis make CR 1014 a superior performer in resisting the ShB pathogen. We discuss several putative candidate genes for ShB resistance. The present study, for the first time, revealed the basis of ShB tolerance in the germplasm CR1014 and should prove to be particularly valuable in understanding molecular response to ShB infection. The knowledge could be utilized to devise strategies to manage the disease better.

Accumulating candidate genes for broad-spectrum resistance to rice blast in a drought-tolerant rice cultivar

Biotic stresses, including diseases, severely affect rice production, compromising producers’ ability to meet increasing global consumption. Understanding quantitative responses for resistance to diverse pathogens can guide development of reliable molecular markers, which, combined with advanced backcross populations, can accelerate the production of more resistant varieties. A candidate gene (CG) approach was used to accumulate different disease QTL from Moroberekan, a blast-resistant rice variety, into Vandana, a drought-tolerant variety. The advanced backcross progeny were evaluated for resistance to blast and tolerance to drought at five sites in India and the Philippines. Gene-based markers were designed to determine introgression of Moroberekan alleles for 11 CGs into the progeny. Six CGs, coding for chitinase, HSP90, oxalate oxidase, germin-like proteins, peroxidase and thaumatin-like protein, and 21 SSR markers were significantly associated with resistance to blast across screening sites. Multiple lines with different combinations, classes and numbers of CGs were associated with significant levels of race non-specific resistance to rice blast and sheath blight. Overall, the level of resistance effective in multiple locations was proportional to the number of CG alleles accumulated in advanced breeding lines. These disease resistant lines maintained tolerance to drought stress at the reproductive stage under blast disease pressure.

Combined Use of PGPRs and Reduced Rates of Azoxystrobin to Improve Management of Sheath Blight of Rice

Farmers rely heavily on the use of strobilurin fungicides to manage sheath blight (ShB) caused by Rhizoctonia solani AG1-IA, the most important disease in rice in the southern United States. Greenhouse and field studies were conducted to evaluate the potential use of plant growth-promoting rhizobacteria (PGPRs) in combination with a reduced rate of azoxystrobin application as a strategy to improve the current fungicide-reliant management. Of the nine antagonistic PGPR strains screened in the greenhouse, Bacillus subtilis strain MBI600 provided the most significant and consistent suppression of ShB. Efficacy of strain MBI600 was further evaluated at the concentrations of 0, 10³, 10⁶, 10⁹, and 10¹¹ CFU/ml alone or in combinations with 0, 17, 33, 50, 67, 83, and 100% of the recommended application rate (0.16 kg a.i./ha) of azoxystrobin. Strain MBI600 applied at 10⁶,10⁹, and 10¹¹ CFU/ml alone was effective in reducing ShB severity. Combinations of this strain at these rates with ≥33% of the recommended application rate of azoxystrobin further reduced ShB severity. A dose-response model defining the relationships between strain MBI600, azoxystrobin, and ShB severity was established. Estimates of the effective concentrations (EC₅₀ and EC₉₀) of strain MBI600 when applied in combination with 50% of the recommended application rate of azoxystrobin were 10⁴ and 10⁹ CFU/ml, respectively. A field trial was conducted over 4 years to verify the efficacy of their combinations. Strain MBI600 alone, when applied at 10⁹ CFU/ml at the boot stage, reduced ShB severity but did not significantly increase grain yields each year. Combination of strain MBI600 with azoxystrobin at half of the recommended application rate improved efficacy of strain MBI600, reducing ShB severity to a level comparable to that of azoxystrobin applied at the full rate in all 4 years. The combined treatment also increased grain yield by 14 to 19%, comparable to the fungicide applied at the full rate in 3 of 4 years. Combined use of PGPR strain MBI600 with a reduced rate of azoxystrobin application can be a viable management option for control of ShB while allowing producers to use less fungicide on rice.

Field Sanitation and Foliar Application of Streptomyces padanus PMS-702 for the Control of Rice Sheath Blight

Rice sheath blight (ShB), caused by Rhizoctonia solani Kühn AG1-IA, is one of the destructive rice diseases worldwide. The aims of this study were to develop biocontrol strategies focusing on field sanitation and foliar application with a biocontrol agent for ShB management. Streptomyces padanus PMS-702 showed a great antagonistic activity against R. solani. Fungichromin produced by S. padanus PMS-702, at 3.07 mg/l inhibited 50% mycelial growth, caused leakage of cytoplasm, and inhibited the formation of infection structures of R. solani. Fungichromin could reach to 802 mg/l when S. padanus PMS-702 was cultured in MACC broth for 6 days. Addition of 0.5% S. padanus PMS-702 broth into soil decreased the survival rate of the pathogen compared to the control. Soil amended with 0.5% S. padanus broth and 0.5% tea seed pomace resulted in the death of R. solani mycelia in the infested rice straws, and the germination of sclerotia was inhibited 21 days after treatment. Greenhouse trials revealed that S. padanus cultured in soybean meal-glucose (SMGC-2) medium after mixing with different surfactants could enhance its efficacy for inhibiting the pathogen. Of six surfactants tested, the addition of 2% tea saponin was the most effective in suppressing the pathogen. S. padanus broth after being fermented in SMGC-2, mixed with 2% tea saponin, diluted 100 fold, and sprayed onto rice plants significantly reduced ShB disease severity. Thus, S. padanus PMS-702 is an effective biocontrol agent. The efficacy of S. padanus PMS-702 for disease control could be improved through formulation.

Machine Learning-Based Presymptomatic Detection of Rice Sheath Blight Using Spectral Profiles

Early detection of plant diseases, prior to symptom development, can allow for targeted and more proactive disease management. The objective of this study was to evaluate the use of near-infrared (NIR) spectroscopy combined with machine learning for early detection of rice sheath blight (ShB), caused by the fungus Rhizoctonia solani. We collected NIR spectra from leaves of ShB-susceptible rice (Oryza sativa L.) cultivar, Lemont, growing in a growth chamber one day following inoculation with R. solani, and prior to the development of any disease symptoms. Support vector machine (SVM) and random forest, two machine learning algorithms, were used to build and evaluate the accuracy of supervised classification-based disease predictive models. Sparse partial least squares discriminant analysis was used to confirm the results. The most accurate model comparing mock-inoculated and inoculated plants was SVM-based and had an overall testing accuracy of 86.1% (N = 72), while when control, mock-inoculated, and inoculated plants were compared the most accurate SVM model had an overall testing accuracy of 73.3% (N = 105). These results suggest that machine learning models could be developed into tools to diagnose infected but asymptomatic plants based on spectral profiles at the early stages of disease development. While testing and validation in field trials are still needed, this technique holds promise for application in the field for disease diagnosis and management.

First Report of Collar and Stem Rot Caused by Rhizoctonia solani AG1-IA on Sesbania sesban in India

Sesbania sesban (L.) Merr., (family Fabaceae) commonly called as "dhaincha" in India, is a multi-purpose crop used as a cover crop, as green manure, in the paper industry as well as animal fodder. The leaves of Sesbania contain high amounts of pinitol, which acts as an anti-diabetic agent (Misra and Siddiqi 2004). During July/August from 2017 to 2019, Sesbania plants exhibiting typical Rhizoctonia-like symptoms, including collar rot, wilting, and necrotic lesions on stems were regularly observed at ICAR-Central Potato Research Institute Regional Station, Meerut, Uttar Pradesh. The disease incidence ranged between 5 and 10% in a Sesbania crop being grown on 25 ha in Sesbania-potato rotation. Ten diseased plants were collected from different fields and brought to the laboratory for diagnosis. Affected stem pieces approximately 5 mm in size were surface sterilized with 2% sodium hypochlorite, washed twice in sterilized water and air dried. Four diseased pieces per plate were inoculated on 2% water agar amended with 2% streptomycin sulfate and incubated at 28±1℃ in the dark. All four affected pieces began to produce Rhizoctonia-like colonies after 48 h of incubation and in total eight isolates were purified and stored at 4℃ for further use. The colonies of eight isolates were evaluated and all were whitish during early growth and became light brown after 72 h. Dark-brown sclerotia appeared in the random pattern on PDA after 120 h. Microscopic observations showed that all isolates had hyphal branching at right angles with slight constriction at the base of the branch, presence of dolipore septum near the branching and multinucleate individual hyphae compartments (Sneh 1991). Based on these morphological characteristics, the fungus was identified as Rhizoctonia solani. All isolates were further characterized to determine anastomosis group (AG) by pairing with a known AG tester of R. solani AG-1-IA (ITCC 7650), AG-1-IB (ITCC 5650), and AG-3 (RS-20) procured from Indian Type Culture Collection, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi and ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India, respectively. All eight isolates showed positive anastomosis with a known AG-1-IA tester isolate while no anastomosis was observed with other known tester isolates (Carling 1996). Furthermore, a single ~265 bp amplicon was amplified with AG-specific primer, which was specific to R. solani AG1-IA group; confirms the AG-specific identity of the isolates (Matsumoto 2002). Amplification was not observed with AG1-IB, AG3 and AG2 specific primers (Khodayari et al. 2009). The selected four isolates were molecularly characterized by amplifying the internal transcribed spacer (ITS) and ribosomal DNA (rDNA) 5.8s regions by polymerase chain reaction using ITS1 and ITS4 primer pairs (White et al. 1990). The nucleotide BLAST (BLASTn) analysis of the resulting four sequences i.e. GenBank acc. no. MT105386, MT105387, MT105388, and MT105389 supported the identification of the isolates as AG-1-IA sub-group and showed 95.12%, 98.93%, 96.79%, and 98.04%, respectively, sequence homology with known cultures of R. solani AG1-IA isolated from rice in China (KC285893), and India (MK481078). To confirm pathogenicity, Sesbania plants were grown in pots and maintained in the greenhouse at 25℃ with a 12-h-light/dark photoperiod. After 35 to 40 days of growth, the stems of ten Sesbania plant were artificially inoculated with PDA plugs containing R. solani mycelia (Jia et al. 2007) and covered with aluminium foil. Plants inoculated with noncolonized agar plugs served as control. After 96 h of incubation, all the plants inoculated presented the typical collar and stem rot symptoms. No symptoms were observed in the control plants. R. solani was re-isolated cent percent from these ten infected plants fulfilling Koch's postulates. R. solani AG1-IA has been reported to cause sheath blight and banded leaf and sheath blight diseases of rice and maize, respectively (Ogoshi 1987). To our knowledge, this is the first report of Sesbania sesban infected by R. solani AG1-IA, and serve as a host for the pathogen. The result from our findings will be helpful for planning of crop rotations in an agro-ecosystem.

Identification of new rice cultivars and resistance loci against rice black-streaked dwarf virus disease through genome-wide association study

BACKGROUND

The rice black-streaked dwarf virus (RBSDV) disease causes severe rice yield losses in Eastern China and other East Asian countries. Breeding resistant cultivars is the most economical and effective strategy to control the disease. However, few varieties and QTLs for RBSDV resistance have been identified to date.

RESULTS

In this study, we conducted a genome-wide association study (GWAS) on RBSDV resistance using the rice diversity panel 1 (RDP1) cultivars that were genotyped by a 44,000 high-density single nucleotide polymorphism (SNP) markers array. We found that less than 15% of these cultivars displayed resistance to RBSDV when tested under natural infection conditions at two locations with serious RBSDV occurrence. The aus, indica and tropical japonica sub-populations displayed higher RBSDV resistance than the aromatic and temperate japonica sub-populations. In particular, we identified four varieties that displayed stable levels of RBSDV resistance at all testing locations. GWAS identified 84 non-redundant SNP loci significantly associated with RBSDV resistance at two locations, leading to the identification of 13 QTLs for RBSDV resistance. Among them, qRBSDV-4.2 and qRBSDV-6.3 were detected at both locations, suggesting their resistance stability against environmental influence. Field disease evaluations showed that qRBSDV-6.3 significantly reduces RBSDV disease severity by 20%. Furthermore, introgression of qRBSDV-6.3 into two susceptible rice cultivars by marker-assisted selection demonstrated the effectiveness of qRBSDV-6.3 in enhancing RBSDV resistance.

CONCLUSIONS

The new resistant cultivars and QTLs against RBSDV disease identified in this study provide important information and genetic materials for the cloning of RBSDV resistance genes as well as developing RBSDV resistant varieties through marker-assisted selection.

Phenotypic and Molecular Analyses of Rhizoctonia spp. Associated with Rice and Other Hosts

Forty-two Rhizoctonia isolates were collected from rice, mung bean, and grasses from Laguna, Philippines. Sixteen isolates were binucleate Rhizoctonia (BNR), while 26 were multinucleate Rhizoctonia (MNR). BNR isolates produced white to brown, small sclerotia (<1.0 mm) except for mung bean isolates. Twenty MNR isolates produced big (>1.0 mm), light to dark brown sclerotia, three produced salmon-colored masses in the medium, and three did not produce sclerotia. Twenty-three MNR isolates were identified as R. solani AG1-IA using specific primers. Deduced Internal Transcribed Spacer (ITS) sequences of BNR isolates D1FL, NVL, and ScNL shared 100, 97, and 100% identity with R. oryzae-sativae, respectively, while MNR isolates BMgL, IbMgL, and MaSL that produced salmon-colored masses shared 100, 90, and 100% identity with R. oryzae, respectively. Preliminary analysis of the DNA fingerprint patterns generated by repetitive-element PCR (rep-PCR) clustered the 42 isolates into three: R. solani, R. oryzae-sativae, and R. oryzae, together with Ceratobasidium sp. R. solani isolates were pathogenic on rice (TN1), barnyard grass, mungbean (Pagasa 3), and tomato (Athena), while R. oryzae and R. oryzae-sativae isolates were only pathogenic on rice, Echinochloa crus-galli, and tomato. R. solani and R. oryzae were found to be more virulent than R. oryzae-sativae.

Complete Genome Sequence of Pseudomonas Parafulva PRS09-11288, a Biocontrol Strain Produces the Antibiotic Phenazine-1-carboxylic Acid

Rhizoctonia solani is a plant pathogenic fungus, which can infect a wide range of economic crops including rice. In this case, biological control of this pathogen is one of the fundmental way to effectively control this pathogen. The Pseudomonas parafulva strain PRS09-11288 was isolated from rice rhizosphere and shows biocontrol ability against R. solani. Here, we analyzed the P. parafulva genome, which is ~ 4.7 Mb, with 4310 coding sequences, 76 tRNAs, and 7 rRNAs. Genome analysis identified a phenazine biosynthetic pathway, which can produce antibiotic phenazine-1-carboxylic acid (PCA). This compound is responsible for biocontrol ability against R. solani Kühn, which is one of the most serious fungus disease on rice. Analysis of the phenazine biosynthesis gene mutant, ΔphzF, which is very important in this pathway, confirmed the relationship between the pathway and PCA production using LC-MS profiles. The annotated full genome sequence of this strain sheds light on the role of P. parafulva PRS09-11288 as a biocontrol bacterium.

Genotype by Environment Interaction: The Greatest Obstacle in Precise Determination of Rice Sheath Blight Resistance in the Field

Rice sheath blight (SB) is the most serious rice disease in China. Resistance of rice to SB is a quantitative trait that is easily influenced by the environment; however, the extent of environmental influence on SB field resistance is still poorly understood. To identify rice genotype by environment interactions for SB resistance, 211 rice genotypes originating from 15 countries were planted and evaluated for SB field resistance in six different environments between 2012 and 2016 after inoculation with the SB pathogen isolate ZJ03. In addition, 65 rice genotypes were evaluated for SB field resistance in another four environments between 2013 and 2016 using ZJ03. Variations in SB field resistance were observed in different genotypes in different environments using objective and subjective rating methods. Two-way analysis of variance indicated that the interaction between the genotype and environment had a highly significant effect on SB field resistance. This analysis indicated that the environment had more of an influence than the genotype itself on SB field resistance, and the genotype by environment interaction was the greatest obstacle in obtaining a precise determination of SB field resistance in rice. The most resistant genotype, GD66, is a good candidate for genetic studies and breeding.

Comparative Transcriptome Analyses of Gene Expression Changes Triggered by Rhizoctonia solani AG1 IA Infection in Resistant and Susceptible Rice Varieties

Rice sheath blight, caused by Rhizoctonia solani, is one of the most devastating diseases for stable rice production in most rice-growing regions of the world. Currently, studies of the molecular mechanism of rice sheath blight resistance are scarce. Here, we used an RNA-seq approach to analyze the gene expression changes induced by the AG1 IA strain of R. solani in rice at 12, 24, 36, 48, and 72 h. By comparing the transcriptomes of TeQing (a moderately resistant cultivar) and Lemont (a susceptible cultivar) leaves, variable transcriptional responses under control and infection conditions were revealed. From these data, 4,802 differentially expressed genes (DEGs) were identified. Gene ontology and pathway enrichment analyses suggested that most DEGs and related metabolic pathways in both rice genotypes were common and spanned most biological activities after AG1 IA inoculation. The main difference between the resistant and susceptible plants was a difference in the timing of the response to AG1 IA infection. Photosynthesis, photorespiration, and jasmonic acid and phenylpropanoid metabolism play important roles in disease resistance, and the relative response of disease resistance-related pathways in TeQing leaves was more rapid than that of Lemont leaves at 12 h. Here, the transcription data include the most comprehensive list of genes and pathway candidates induced by AG1 IA that is available for rice and will serve as a resource for future studies into the molecular mechanisms of the responses of rice to AG1 IA.

Phenotyping Brachiaria Genotypes to Assess Rhizoctonia Resistance by Comparing Three Inoculum Types

Rhizoctonia foliar blight, caused by Rhizoctonia solani, is an important disease of Brachiaria spp. in tropical America. Host-plant resistance is an attractive option for disease management. In this study, we evaluated three inoculum types (mycelium-infected agar disc, microdiscs suspensions, and microencapsulated-mycelium suspensions) in order to identify a rapid and accurate method for mass screening of Brachiaria genotypes for resistance to Rhizoctonia spp. in greenhouse trials. Visual damage score, area under the disease progress curve, and percent chlorophyll loss were estimated to determine the most accurate and precise method for evaluating Rhizoctonia resistance. The microencapsulated-mycelium solution (0.75 g/ml in potato dextrose broth sprayed on plants 30 days after planting) caused greater foliar damage than the other inoculum types and allowed effective discrimination between resistant and susceptible genotypes. The effectiveness of spray-applied, microencapsulated-mycelium was further corroborated by the evaluation of 350 genotypes not previously selected for resistance to Rhizoctonia spp., which varied significantly in their reaction to R. solani. The microencapsulated-mycelium methodology has several advantages over existing methods, including its high-throughput capacity, efficient use of time and space, ease of quantification of inoculum, and consistent results over replicate trials. This methodology could be applied to assess resistance to Rhizoctonia spp. in other crops.

Association between QTLs and morphological traits toward sheath blight resistance in rice (Oryza sativa L.)

Sheath blight is considered the most significant disease of rice and causes enormous yield losses over the world. Breeding for resistant varieties is the only viable option to combat the disease efficiently. Seventeen diverged rice genotypes along with 17 QTL-linked SSR markers were evaluated under greenhouse conditions. Pearson's correlation showed only the flag leaf angle had a significant correlation with sheath blight resistance under greenhouse screening. Multivariate analysis based on UPGMA clustering and principal component analysis (PCA) indicated that the flag leaf angle, flag leaf length, and plant compactness were significantly associated with the following SSR marker alleles: RM209 (116,130), RM202 (176), RM224 (126), RM257 (156), RM426 (175), and RM6971 (196), which are linked to the SB QTLs: QRlh11, qSBR11-3, qSBR11-1, qSBR9-1, qShB3-2, and qSB-9. A Mantel test suggested a weak relationship between the observed phenotypes and allelic variation patterns, implying the independent nature of morphological and molecular variations. Teqing and Tetep were found to be the most resistant cultivars. IR65482-4-136-2-2, MR219-4, and MR264 showed improved resistance potentials. These results suggest that the morphological traits and QTLs which have been found to associate with sheath blight resistance are a good choice to enhance resistance through pyramiding either 2 QTLs or QTLs and traits in susceptible rice cultivars.

The Urochloa Foliar Blight and Collar Rot Pathogen Rhizoctonia solani AG-1 IA Emerged in South America Via a Host Shift from Rice

The fungus Rhizoctonia solani anastomosis group (AG)-1 IA emerged in the early 1990s as an important pathogen causing foliar blight and collar rot on pastures of the genus Urochloa (signalgrass) in South America. We tested the hypothesis that this pathogen emerged following a host shift or jump as a result of geographical overlapping of host species. The genetic structure of host and regional populations of R. solani AG-1 IA infecting signalgrass, rice, and soybean in Colombia and Brazil was analyzed using nine microsatellite loci in 350 isolates to measure population differentiation and infer the pathogen reproductive system. Phylogeographical analyses based on the microsatellite loci and on three DNA sequence loci were used to infer historical migration patterns and test hypotheses about the origin of the current pathogen populations. Cross pathogenicity assays were conducted to measure the degree of host specialization in populations sampled from different hosts. The combined analyses indicate that the pathogen populations currently infecting Urochloa in Colombia and Brazil most likely originated from a population that originally infected rice. R. solani AG-1 IA populations infecting Urochloa exhibit a mixed reproductive system including both sexual reproduction and long-distance dispersal of adapted clones, most likely on infected seed. The pathogen population on Urochloa has a genetic structure consistent with a high evolutionary potential and showed evidence for host specialization.

Molecular characterization and screening for sheath blight resistance using Malaysian isolates of Rhizoctonia solani

Two field isolates of Rhizoctonia solani were isolated from infected paddy plants in Malaysia. These isolates were verified via ITS-rDNA analysis that yielded ~720 bp products of the ITS1-5.8S-ITS4 region, respectively. The sequenced products showed insertion and substitution incidences which may result in strain diversity and possible variation in disease severity. These strains showed some regional and host-specific relatedness via Maximum Likelihood and further phylogenetic analysis via Maximum Parsimony showed that these strains were closely related to R. solani AG1-1A (with 99-100% identity). Subsequent to strain verification and analysis, these isolates were used in the screening of twenty rice varieties for tolerance or resistance to sheath blight via mycelial plug method where both isolates (1801 and 1802) showed resistance or moderate resistance to Teqing, TETEP, and Jasmine 85. Isolate 1802 was more virulent based on the disease severity index values. This study also showed that the mycelial plug techniques were efficient in providing uniform inoculum and humidity for screening. In addition this study shows that the disease severity index is a better mode of scoring for resistance compared to lesion length. These findings will provide a solid basis for our future breeding and screening activities at the institution.

Identification of Two Major Rice Sheath Blight Resistance QTLs, qSB1-1HJX74 and qSB11HJX74, in Field Trials Using Chromosome Segment Substitution Lines

Sheath blight (SB) is among the most destructive rice (Oryza sativa) diseases worldwide. SB resistance (SBR) is controlled by quantitative trait loci (QTL). Only a few SB resistance QTLs were confirmed previously in field trials that were independent of morphological traits, a crucial factor in plant breeding. Here, we employed 63 chromosome segment substitution lines (CSSLs) to identify SBR QTLs derived from 'HJX74'. Importantly, these CSSLs all carried the same genetic background as 'HJX74', except in the substituted segment introgressed from susceptible 'Amol3(sona)'. In contrast to most reports that mapped SBR QTLs under complex genetic backgrounds, this approach allowed many CSSLs to consistently retain the agronomic traits of 'HJX74' with moderate resistance, giving the needed high reproducibility in SBR scoring. We have identified five SBR QTLs in field tests. Two of them, qSB11^HJX74 and qSB1-1^HJX74, conferred the greatest reduction in SB ratings by approximately 0.9 to 1.2 on a 0 to 9 scale. qSB11^HJX74 exhibited nearly perfect recessive heredity, whereas qSB1-1^HJX74 showed dominant heredity. Using a secondary F₂ population and overlapping substitution segment lines, we further mapped qSB11^HJX74 and qSB1-1^HJX74 to regions of approximately 430 and 930 kb, respectively. The results will accelerate the rice breeding process for resistance to SB disease.

Assessing the Resistance of Brachiaria Hybrids to Pathogenic Rhizoctonia

Rhizoctonia foliar blight, caused by Rhizoctonia solani anastomosis group 1, is an economically important fungal disease found throughout the world. The fungus attacks numerous crops, including cereals, roots and tubers, legumes, and cruciferous, horticultural, and ornamental plants. In tropical America, this invasive and destructive disease also attacks most Brachiaria spp. used as forages in the ranching industry, especially in the production of cattle. Research to solve this constraint has been ongoing at the International Center for Tropical Agriculture and has generated new Brachiaria hybrids with excellent agronomic performance, tolerance to poor soils, and, particularly, high resistance to biotic factors such as Rhizoctonia foliar blight. These hybrids belong to lines obtained from Brachiaria humidicola, B. brizantha, and B. decumbens. To identify resistance among Brachiaria hybrid genotypes, the hybrid clones were evaluated for their variability in resistance, and their disease reaction was also determined and characterized. Results led to the identification of hybrids that not only were highly resistant to the blight but also had excellent agronomic characteristics.

Diversity of Rhizoctonia spp. Causing Foliar Blight on Brachiaria in Colombia and Evaluation of Brachiaria Genotypes for Foliar Blight Resistance

Up to 50% of Brachiaria production in the tropics is affected by foliar blight caused by Rhizoctonia spp. Monothallic isolates of Rhizoctonia (n = 147) were cultured from different Brachiaria genotypes in Colombia and morphologically characterized and evaluated in pathogenicity trials in the greenhouse. Based on restriction fragment length polymorphism of the internal transcribed spacer region, 101 of the isolates were identified as Rhizoctonia solani anastomosis group (AG)-1 IA and were multinucleated, with high growth rate, brown mycelium, and high virulence; and 46 isolates were identified as Rhizoctonia sp. AG-D and were binucleated, with low growth rate, white mycelium, and lower virulence on the Brachiaria genotypes tested. The Rhizoctonia isolates also showed variation according to geographic origin, with R. solani AG-1 IA prevalent in warm lowland areas and Rhizoctonia sp. AG-D occurring in cooler areas. Ten Brachiaria genotypes were challenged with different Rhizoctonia isolates and resistant reactions were seen in three of these genotypes, including Brachiaria hybrid (International Center for Tropical Agriculture [CIAT] 36062), Brachiaria brizantha 'Marandú' (CIAT 6294), and Brachiaria hybrid 'Mulato II' (CIAT 36087). These results will contribute to a greater understanding of the interaction of diverse Rhizoctonia isolates on different Brachiaria genotypes, supporting improvement of Brachiaria spp. for disease resistance.

Fine mapping of qSB-11(LE), the QTL that confers partial resistance to rice sheath blight

Sheath blight (SB), caused by Rhizoctonia solani kühn, is one of the most serious global rice diseases. No major resistance genes to SB have been identified so far. All discovered loci are quantitative resistance to rice SB. The qSB-11(LE) resistance quantitative trait locus (QTL) has been previously reported on chromosome 11 of Lemont (LE). In this study, we report the precise location of qSB-11 (LE) . We developed a near isogenic line, NIL-qSB11(TQ), by marker-assisted selection that contains susceptible allele(s) from Teqing (TQ) at the qSB-11 locus in the LE genetic background. NIL-qSB11(TQ) shows higher susceptibility to SB than LE in both field and greenhouse tests, suggesting that this region of LE contains a QTL contributing to SB resistance. In order to eliminate the genetic background effects and increase the accuracy of phenotypic evaluation, a total of 112 chromosome segment substitution lines (CSSLs) with the substituted segment specific to the qSB-11 (LE) region were produced as the fine mapping population. The genetic backgrounds and morphological characteristics of these CSSLs are similar to those of the recurrent parent LE. The donor TQ chromosomal segments in these CSSL lines contiguously overlap to bridge the qSB-11 (LE) region. Through artificial inoculation, all CSSLs were evaluated for resistance to SB in the field in 2005. For the recombinant lines, their phenotypes were evaluated in the field for another 3 years and during the final year were also evaluated in a controlled greenhouse environment, showing a consistent phenotype in SB resistance across years and conditions. After comparing the genotypic profile of each CSSL with its phenotype, we are able to localize qSB-11 (LE) to the region defined by two cleaved-amplified polymorphic sequence markers, Z22-27C and Z23-33C covering 78.871 kb, based on the rice reference genome. Eleven putative genes were annotated within this region and three of them were considered the most likely candidates. The results of this study will greatly facilitate the cloning of the genes responsible for qSB-11 (LE) and marker-assisted breeding to incorporate qSB-11 (LE) into other rice cultivars.

Confirming QTLs and Finding Additional Loci Responsible for Resistance to Rice Sheath Blight Disease

Rice sheath blight disease, caused by Rhizoctonia solani AG1-1A, is one of the most destructive rice diseases worldwide. Utilization of host resistance is the most economical and environmentally sound strategy in managing sheath blight (ShB). Ten ShB quantitative trait loci (QTLs) were previously mapped in a Lemont × Jasmine 85 recombinant inbred line (LJRIL) population using greenhouse inoculation methods at an early vegetative stage. However, confirmation of ShB-resistant QTLs under field conditions is critical for their utilization in marker-assisted selection (MAS) for improving ShB resistance in new cultivars. In the present study, we evaluated ShB resistance using 216 LJRILs under field conditions in Arkansas, Texas, and Louisiana during 2008 and 2009. We confirmed the presence of the major ShB-QTL qShB9-2 based on the field data and also identified one new ShB-QTL between markers RM221 and RM112 on chromosome 2 across all three locations. Based on the field verification of ShB evaluations, the microchamber and mist-chamber assays were simple, effective, and reliable methods to identify major ShB-QTLs like qShB9-2 in the greenhouse at early vegetative stages. The markers RM215 and RM245 were found to be closely linked to qShB9-2 in greenhouse and field assays, indicating that they will be useful for improving ShB resistance in rice breeding programs using MAS.

Inoculation and scoring methods for rice sheath blight disease

Sheath blight disease of rice caused by the soilborne fungal pathogen Rhizoctonia solani has been a major disease of rice with a serious threat to stable rice production worldwide. Although various cultural practices have been used to manage the disease, it is advantageous and important to screen rice germplasm and identify resistant rice cultivars for more effective disease control. Recent advances in methods for the fungal inoculation and disease evaluation have enabled a better measurement of host resistance by minimizing confounding factors from plant architectures and environmental conditions. This chapter introduces five such methods: (1) detached leaf method; (2) micro-chamber method; (3) mist-chamber method; (4) parafilm sachet method; and (5) aluminum foil method. These methods are useful for screening and evaluating disease reactions of rice germplasm and facilitating the genetic mapping of disease resistance genes.

Allelic analysis of sheath blight resistance with association mapping in rice

Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r = -0.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice.

Quantification of the Components of Resistance to Rice Sheath Blight Using a Detached Tiller Test Under Controlled Conditions

Resistance of rice (Oryza sativa) to sheath blight, caused by Rhizoctonia solani, is quantitative and involves two mechanisms: physiological resistance and disease escape. The epidemiological concept of components of resistance was applied using a detached tiller method under controlled conditions, to specifically address physiological resistance to sheath blight in rice. A sclerotium was inserted below the leaf collar of individual rice tillers maintained in tubes filled with water. Different variables were measured after incubation: number of lesions, lesion length, vertical sheath colonization, presence or absence of dark margin at the edge of lesions, and survival duration of the leaf blade. Several rice varieties reported to have different levels of susceptibility to sheath blight were assessed, together with varieties that are cultivated over large areas. Although numerical differences between rice varieties were observed for all disease variables, only the number of lesions significantly differed among varieties tested in this study. The varieties Pecos and IR64 had the consistently lowest and highest disease intensities, respectively. This methodology may allow the detection of sources of resistance that specifically involve defense mechanisms. When combined with field assessment, this methodology should also enable to quantitatively assess the relative role of both mechanisms of resistance to sheath blight.

Divergence between sympatric rice- and maize-infecting populations of Rhizoctonia solani AG-1 IA from Latin America

ABSTRACT The basidiomycetous fungus Rhizoctonia solani anastomosis group (AG)-1 IA is a major pathogen in Latin America causing sheath blight (SB) of rice. Particularly in Venezuela, the fungus also causes banded leaf and sheath blight (BLSB) on maize, which is considered an emerging disease problem where maize replaced traditional rice-cropping areas or is now planted in adjacent fields. Our goals in this study were to elucidate (i) the effects of host specialization on gene flow between sympatric and allopatric rice and maize-infecting fungal populations and (ii) the reproductive mode of the fungus, looking for evidence of recombination. In total, 375 isolates of R. solani AG1 IA sampled from three sympatric rice and maize fields in Venezuela (Portuguesa State) and two allopatric rice fields from Colombia (Meta State) and Panama (Chiriquí State) were genotyped using 10 microsatellite loci. Allopatric populations from Venezuela, Colombia, and Panama were significantly differentiated (Phi(ST) of 0.16 to 0.34). Partitioning of the genetic diversity indicated differentiation between sympatric populations from different host species, with 17% of the total genetic variation distributed between hosts while only 3 to 6% was distributed geographically among the sympatric Venezuelan fields. We detected symmetrical historical migration between the rice- and the maize-infecting populations from Venezuela. Rice- and maize-derived isolates were able to infect both rice and maize but were more aggressive on their original hosts, consistent with host specialization. Because the maize- and rice-infecting populations are still cross-pathogenic, we postulate that the genetic differentiation was relatively recent and mediated via a host shift. An isolation with migration analysis indicated that the maize-infecting population diverged from the rice-infecting population between 40 and 240 years ago. Our findings also suggest that maize-infecting populations have a mainly recombining reproductive system whereas the rice-infecting populations have a mixed reproductive system in Latin America.

Mapping quantitative trait Loci responsible for resistance to sheath blight in rice

Rice sheath blight (ShB), caused by the soilborne pathogen Rhizoctonia solani, annually causes severe losses in yield and quality in many rice production areas worldwide. Jasmine 85 is an indica cultivar that has proven to have a high level of resistance to this pathogen. The objective of this study was to determine the ability of controlled environment inoculation assays to detect ShB resistance quantitative trait loci (QTLs) in a cross derived from the susceptible cv. Lemont and the resistant cv. Jasmine 85. The disease reactions of 250 F(5) recombinant inbred lines (RILs) were measured on the seedlings inoculated using microchamber and mist-chamber assays under greenhouse conditions. In total, 10 ShB-QTLs were identified on chromosomes 1, 2, 3, 5, 6, and 9 using these two methods. The microchamber method identified four of five new ShB-QTLs, one on each of chromosomes 1, 3, 5, and 6. Both microchamber and mist-chamber methods identified two ShB-QTLs, qShB1 and qShB9-2. Four of the ShB-QTLs or ShB-QTL regions identified on chromosomes 2, 3, and 9 were previously reported in the literature. The major ShB-QTL qShB9-2, which cosegregated with simple sequence repeat (SSR) marker RM245 on chromosome 9, contributed to 24.3 and 27.2% of total phenotypic variation in ShB using microchamber and mistchamber assays, respectively. qShB9-2, a plant-stage-independent QTL, was also verified in nine haplotypes of 10 resistant Lemont/Jasmine 85 RILs using haplotype analysis. These results suggest that multiple ShB-QTLs are involved in ShB resistance and that microchamber and mist-chamber methods are effective for detecting plant-stage-independent QTLs. Furthermore, two SSR markers, RM215 and RM245, are robust markers and can be used in marker-assisted breeding programs to improve ShB resistance.

Prospect of the QTL-qSB-9Tq utilized in molecular breeding program of japonica rice against sheath blight

The major QTL-qSB-9(Tq) conferring partial resistance to rice (Oryza sativa L.) sheath blight (Rhizoctonia solani Kühn) has been verified on chromosome 9 of the indica rice cultivar, Teqing. In this study, the prospect of this QTL utilized in molecular breeding program of japonica rice for sheath blight resistance was investigated. Most of the japonica rice cultivars showed lower level of sheath blight resistance than the indica rice cultivars. At the corresponding site of qSB-9(Tq), nine typical japonica rice cultivars from different ecological regions or countries proved to possess the susceptible allele(s). Introgression of qSB-9(Tq) into these cultivars enhanced their resistance level by decreasing sheath blight score of 1.0 (0.5-1.3), which indicated that qSB-9(Tq) had a large potential in strengthening the resistance of japonica rice to sheath blight. The use of the three molecular markers, which were polymorphic between Teqing and many japonica rice cultivars, promotes the application of qSB-9(Tq) in a concrete molecular breeding program.

A germin-like protein gene family functions as a complex quantitative trait locus conferring broad-spectrum disease resistance in rice

Plant disease resistance governed by quantitative trait loci (QTL) is predicted to be effective against a broad spectrum of pathogens and long lasting. Use of these QTL to improve crop species, however, is hindered because the genes contributing to the trait are not known. Five disease resistance QTL that colocalized with defense response genes were accumulated by marker-aided selection to develop blast-resistant varieties. One advanced backcross line carrying the major-effect QTL on chromosome (chr) 8, which included a cluster of 12 germin-like protein (OsGLP) gene members, exhibited resistance to rice (Oryza sativa) blast disease over 14 cropping seasons. To determine if OsGLP members contribute to resistance and if the resistance was broad spectrum, a highly conserved portion of the OsGLP coding region was used as an RNA interference trigger to silence a few to all expressed chr 8 OsGLP family members. Challenge with two different fungal pathogens (causal agents of rice blast and sheath blight diseases) revealed that as more chr 8 OsGLP genes were suppressed, disease susceptibility of the plants increased. Of the 12 chr 8 OsGLPs, one clustered subfamily (OsGER4) contributed most to resistance. The similarities of sequence, gene organization, and roles in disease resistance of GLP family members in rice and other cereals, including barley (Hordeum vulgare) and wheat (Triticum aestivum), suggest that resistance contributed by the chr 8 OsGLP is a broad-spectrum, basal mechanism conserved among the Gramineae. Natural selection may have preserved a whole gene family to provide a stepwise, flexible defense response to pathogen invasion.

Tobacco OPBP1 enhances salt tolerance and disease resistance of transgenic rice

Osmotin promoter binding protein 1 (OPBP1), an AP2/ERF transcription factor of tobacco, has been demonstrated to function in disease resistance and salt tolerance in tobacco. To increase stress tolerant capability of rice, we generated rice plants with an OPBP1 overexpressing construct. Salinity shock treatment with 250 mM NaCl indicated that most of the OPBP1 transgenic plants can survive, whereas the control seedlings cannot. Similar recovery was found by using the seedlings grown in 200 mM NaCl for two weeks. The OPBP1 transgenic and control plants were also studied for oxidative stress tolerance by treatment with paraquat, showing the transgenic lines were damaged less in comparison with the control plants. Further, the OPBP1 overexpression lines exhibited enhanced resistance to infections of Magnaporthe oryzae and Rhizoctonia solani pathogens. Gene expressing analysis showed increase in mRNA accumulation of several stress related genes. These results suggest that expression of OPBP1 gene increase the detoxification capability of rice.

Rice Sheath Blight Disease Resistance Identified in Oryza spp. Accessions

Oryza spp., wild relatives of cultivated rice (Oryza sativa), may contain novel resistance genes for sheath blight, caused by Rhizoctonia solani, that could be used to enhance resistance to this important disease in commercial rice. To identify resistant sources for sheath blight disease, 73 Oryza genotypes were evaluated with three different methods conducted in the greenhouse, growth chamber, or laboratory because there are significant limitations to screening wild Oryza spp. under field conditions. For the microchamber method, 4-week-old seedlings were inoculated with a potato dextrose agar plug containing mycelia, covered with a 2-liter soft drink bottle, and rated 1 week after inoculation. A detached-leaf method involved placing a potato dextrose agar plug containing mycelia on the abaxial surface of a leaf section that was cut from a 5-week-old plant and placed on moist filter paper in a petri dish under constant light, then evaluated after 72 h. For the toothpick inoculation method, toothpicks colonized with mycelia were placed in the leaf collar region of plants at the panicle initiation stage, plants were placed in a growth chamber, and disease symptoms were evaluated after 7 days. The microchamber method gave a more uniform, reproducible response, and was easier to use under greenhouse conditions. Seven Oryza spp. accessions were identified as moderately resistant with three accessions classified as O. nivara (IRGC104705, IRGC100898, and IRGC104443) and one each as O. barthii (IRGC100223), O. meridionalis (IRGC105306), O. nivara/O. sativa (IRGC100943), and O. officinalis (IRGC105979).

A Method for Inoculation and Evaluation of Rice Sheath Blight Disease

Sheath blight of rice, caused by Rhizoctonia solani, is one of the most important rice diseases worldwide; however, no rice cultivar has been found to be completely resistant to this fungus. To facilitate detailed analysis of sheath blight resistance at genetic, molecular, biochemical, and functional genomic levels, new methods were developed for effective and uniform infection and accurate evaluation of the disease. The efficiency of R. solani infection was tested on two resistant (Tetep and Jasmine 85) and two susceptible (Chucheongbyeo, Junambyeo) cultivars using three different inoculum types (agar block, liquid cultured mycelia ball, and mycelia suspension). By covering the inoculated sheaths with aluminum foil to maintain humidity, 100% infection rate was achieved in this study. Liquid cultured mycelia balls caused significantly longer lesions (5.4 cm) than other types of inoculum, including agar block (2.4 cm) and mycelia suspension (1.6 cm). An improved method for evaluating sheath blight disease was selected by comparing two methods for evaluating disease severity among three partially resistant cultivars and five susceptible cultivars inoculated with liquid cultured mycelia balls. In addition, a new formula was developed to calculate the disease susceptibility index. Lesion length and the susceptibility index generally were correlated in each leaf, but there were discrepancies between the two evaluation methods due to differences in plant architecture among the cultivars. The susceptibility index calculated using the new formula was the most accurate method for evaluating sheath blight disease across all cultivars. The effect of heading date and panicle number also was evaluated in relation to sheath blight resistance. Cultivars with late heading dates generally were more resistant to sheath blight than those with early heading dates.

Sensitivity to a Phytotoxin from Rhizoctonia solani Correlates with Sheath Blight Susceptibility in Rice

ABSTRACT Sheath blight is one of the most important and intractable diseases of rice (Oryza sativa) where limited control has been achieved using traditional approaches. Quantitative inheritance, extraneous traits, and environmental factors confound genetic analysis of host resistance. A method was developed to isolate and utilize a phytotoxin from Rhizoctonia solani to investigate the genetics of sheath blight susceptibility. Infiltration of the toxin preparation into plant leaves induced necrosis in rice, maize, and tomato. Using 17 rice cultivars known to vary in sheath blight resistance, genotypes were identified that were sensitive (tox-S) and insensitive (tox-I) to the toxin, and a correlation (r = 0.66) between toxin sensitivity and disease susceptibility was observed. Given the broad host range of R. solani, genotypes of host species may be both tox-S and tox-I. A total of 154 F(2) progeny from a cross between Cypress (tox-S) and Jasmine 85 (tox-I) segregated in a 9:7 ratio for tox-S/tox-I, indicating an epistatic interaction between two genes controls sensitivity to the toxin in rice. This work provides the means to genetically map toxin sensitivity genes and eliminate susceptible genotypes when developing sheath blight-resistant rice cultivars.