A simplified method for simultaneous detection of Rice stripe virus and Rice black-streaked dwarf virus in insect vector

Genome-Wide Association Study on Resistance to Rice Black-Streaked Dwarf Disease Caused by Rice black-streaked dwarf virus

Rice black-streaked dwarf disease caused by Rice black-streaked dwarf virus (RBSDV) is one of the most destructive viral diseases of rice. Thus, it is imperative that resistant rice germplasms are screened for novel RBSDV-resistant genes. RBSDV resistance of a diverse global collection comprising 1,953 rice accessions was evaluated under natural conditions across 3 years. The average disease incidences of the Xian/indica (XI) subgroup were significantly lower than those of the Geng/japonica (GJ) subgroup. Interestingly, most XI-1A accessions in the Xian subgroup were significantly more susceptible than XI-1B accessions, even though XI-1A and XI-1B have a close phylogenetic relationship. Four Xian accessions stably and highly resistant to RBSDV were consistently identified in 2 years. Ten genomic regions (GRs) with 147 single nucleotide polymorphisms associated with RBSDV resistance were detected by a single-locus genome-wide association study (GWAS), of which five were repeatedly identified in a multilocus GWAS. Two previously reported GRs, grRBSDV-6.1 and grRBSDV-6.3, which were repeatedly detected as stably and highly associated with RBSDV resistance, contained 17 and seven genes, respectively, with significant differences of resistance among haplotypes. Haplotype analyses of the candidate genes LOC_Os06g03150 in grRBSDV-6.1 and LOC_Os06g31190 in grRBSDV-6.3 suggested that the former gene is mainly associated with the differentiation of resistance within the Xian subgroup and the latter gene mainly explains the difference in the resistance between Xian and Geng. Another three novel resistance GRs (grRBSDV-1.1, grRBSDV-7.1, and grRBSDV-9.1) were identified. Our findings may enhance the application of disease-resistant rice germplasms for breeding RBSDV-resistant varieties.

Rice virus release from the planthopper salivary gland is independent of plant tissue recognition by the stylet

BACKGROUND

The transmission of plant viruses by arthropod vectors is closely related to feeding behavior. For persistently transmitted viruses, virus release means that virus moves through the salivary gland microvillus barriers of insects into plant via the stylet. However, whether virus release is dependent on plant tissue and component recognition by the stylet is unclear.

RESULTS

In this study, the small brown planthopper (SBPH) and two rice viruses transmitted by it were used as a model to explore this question. After the viruliferous insects penetrated a stretched membrane without plant tissue structure and ingested liquid food (rice sap, nutrient solution or water), both viruses were detected in the liquid food after only a 6 min inoculation access period, suggesting that the viruses were released from SBPH salivary gland independent of plant tissue and component recognition by the stylet. In subsequent electrical penetration graph (EPG) analysis, N4a-like and N4b-like waveforms, similar to N4a (phloem salivation before ingestion) and N4b (sieve element ingestion), were observed during SBPH penetrating the membrane, exhibiting normal feeding activity of planthopper on membrane, which further demonstrated that virus release from salivary gland was along with feeding activity, without the stylet sensing plant tissue. EPG analysis and identification of salivary proteins indicated more active feeding behavior and efficient salivation in viruliferous planthoppers.

CONCLUSION

These results suggest that the rice virus is released from insect salivary gland independent of plant tissue and component recognition by the stylet, and the simple virus release mode facilitates virus transmission by vectors. © 2020 Society of Chemical Industry.

Rice black-streaked dwarf virus: From multiparty interactions among plant-virus-vector to intermittent epidemics

Rice black-streaked dwarf virus (RBSDV) (species Rice black-streaked dwarf virus, genus Fijivirus, family Reoviridae) is the causal agent of rice black-streaked dwarf and maize rough dwarf diseases, which occur in intermittent epidemics in East Asian countries and are responsible for considerable yield losses. Intermittency of epidemics make accurate forecasting and designing of effective management strategies difficult. However, recent insights into host-virus-vector insect interactions are now informing forecasting and disease control measures. Resistance genes are also being identified and mapped.

SYMPTOMATOLOGY AND HOST RANGE

RBSDV induces extreme stunting, darkened, and stiff leaves of crops and weeds only in the family Poaceae, including Oryza sativa, Zea mays, and Triticum aestivum. Infected plants produce totally or partially deformed panicles and remain alive through harvest.

GENOME AND GENE FUNCTION

The nonenveloped virus particles comprise a double-layered capsid, 50-nm core with genomic double-stranded RNA (dsRNA), and six proteins. The genome of RBSDV contains 10 segments of dsRNA, named S1 to S10 in decreasing order of molecular weight. Segments 1, 2, 3, 4, 6, 8, and 10 encode the RNA-dependent RNA polymerase (RdRp), the major core structural protein, a protein with guanylyltransferase activity, an outer-shell B-spike protein, viral RNA-silencing suppressor, the major capsid protein, and the outer capsid protein, respectively. Each of the segments 5, 7, and 9 encodes two proteins: P5-1, a component of viroplasms; P5-2 of unknown function; nonstructural protein P7-1, involved in forming the structural matrix of tubular structures in infected tissues; P7-2 of unknown function; P9-1, the main component of viroplasms in infected cells and involved in viral replication; and P9-2 of unknown function.

TRANSMISSION AND EPIDEMIOLOGY

RBSDV is transmitted by Laodelphax striatellus in a persistent propagative manner. The vector insect is the only means of virus spread in nature, so its migration and transmission efficiency are obligatory for disease epidemics to develop. Susceptible varieties are widely planted, but efficient transmission by vectors is the primary reason for the epidemics. Cultivation system, pesticide overuse, and climatic conditions also contribute to epidemics by affecting the development of the vector insects and their population dynamics.

DISEASE MANAGEMENT

In the absence of resistant varieties, integrated disease management aims at disrupting the cycle of virus transmission by the insect vector. Inheritance studies have indicated that resistance is mostly governed by quantitative trait loci or multiple genes. Genetic engineering through RNA-interference and gene-editing strategies are potential approaches for disease control.

Development of a colloidal gold-based immunochromatographic strip for rapid detection of Rice stripe virus

Rice stripe virus (RSV) causes dramatic losses in rice production worldwide. In this study, two monoclonal antibodies (MAbs) 16E6 and 11C1 against RSV and a colloidal gold-based immunochromatographic strip were developed for specific, sensitive, and rapid detection of RSV in rice plant and planthopper samples. The MAb 16E6 was conjugated with colloidal gold and the MAb 11C1 was coated on the test line of the nitrocellulose membrane of the test strip. The specificity of the test strip was confirmed by a positive reaction to RSV-infected rice plants and small brown planthopper (SBPH), and negative reactions to five other rice viruses, healthy rice plants, four other vectors of five rice viruses, and non-viruliferous SBPH. Sensitivity analyses showed that the test strip could detect the virus in RSV-infected rice plant tissue crude extracts diluted to 1:20 480 (w/v, g/mL), and in individual viruliferous SBPH homogenate diluted to 1:2560 (individual SPBH/μL). The validity of the developed strip was further confirmed by tests using field-collected rice and SBPH samples. This newly developed test strip is a low-cost, fast, and easy-to-use tool for on-site detection of RSV infection during field epidemiological studies and paddy field surveys, and thus can benefit decision-making for RSV management in the field.

Rice black-streaked dwarf virus P10 acts as either a synergistic or antagonistic determinant during superinfection with related or unrelated virus

Rice black-streaked dwarf virus (RBSDV), a member of the genus Fijivirus, is a devastating pathogen of crop plants. RBSDV S10 encodes a capsid protein (P10) that is an important component of the double-layered particle. However, little information is available on the roles of RBSDV P10 in viral infection or in interactions with other viruses. Here, we demonstrate that the expression of P10 in plants alleviates the symptoms of both RBSDV and the closely related Southern rice black-streaked dwarf virus (SRBSDV), and reduces the disease incidence, but renders the plants more susceptible to the unrelated Rice stripe virus (RSV). Further experiments suggest that P10-mediated resistance to RBSDV and SRBSDV operates at the protein level, rather than the RNA level, and is not a result of post-transcriptional gene silencing. Transcriptomic data reveal that the expression of P10 in plants significantly suppresses the expression of rice defence-related genes, which may play important roles in resistance to RSV infection. After infection with RBSDV, plants are more resistant to subsequent challenge by SRBSDV, but more susceptible to RSV. Overall, these results indicate that P10 acts as an important effector in virus interactions.

A simple method for obtaining rice black-streaked dwarf virus-infected small brown planthopper nymphs

Rice black-streaked dwarf virus (RBSDV), an important rice virus, is transmitted by vector small brown planthopper (SBPH) in a persistent manner, but not transovarial transmission. In order to obtain viruliferous SBPH nymphs for relevant research, a simple and reliable method was developed, through allowing SBPH adults laying eggs on RBSDV-infected rice plants. The results showed the hatching nymphs on diseased plants could early acquire virus, and the virus was detected in 2nd-instar nymphs from the spawning method, which was earlier than insect feed on diseased plant. The average viruliferous rate of SBPH from the spawning method was 32.9%, which was not lower than the feeding diseased plant method. The novel method was very easy to operate and time-saving, facilitating the study on the interaction between RBSDV and SBPH nymphs (especially young 2nd-4th instar nymphs), such as, the effect of RBSDV on nymph development, host plant orientation preference of viruliferous nymph, identification of viral interacting protein in nymph, etc.

Bacterial microbiota in small brown planthopper populations with different rice viruses

The small brown planthopper (SBPH) is an important virus vector, transmitting Rice stripe virus (RSV), and Rice black-streaked dwarf virus (RBSDV). Insect symbionts play an essential role in the insect fitness, however, it is still unclear about their contributions to viral transmission by SBPH. Here, we investigated endosymbiont communities in non-viruliferous, RSV-infected, and RBSDV-infected SBPH populations using Illumina 16S rRNA gene MiSeq sequencing. In total, 281,803 effective sequences of the 16S rRNA gene were generated from different samples. Sequence analysis revealed the percentages of these bacterial groups in different SBPH populations on several taxonomic levels ranging from phyla to genera. The extremely consistent bacterial diversity and abundance indicated that RSV or RBSDV infection did not affect the composition and abundance of symbionts in SBPH. It was notable that Wolbachia was dominant in all populations. The symbiosis between Wolbachia and SBPH might be potentially studied and utilized to control pest SBPH in the future.

Development of a simplified RT-PCR without RNA isolation for rapid detection of RNA viruses in a single small brown planthopper (Laodelphax striatellus Fallén)

BACKGROUND

The small brown planthopper (SBPH) is an important pest of cereal crops and acts as a transmission vector for multiple RNA viruses. Rapid diagnosis of virus in the vector is crucial for efficient forecast and control of viral disease. Reverse transcription polymerase chain reaction (RT-PCR) is a rapid, sensitive and reliable method for virus detection. The traditional RT-PCR contains a RNA isolation step and is widely used for virus detection in insect. However, using the traditional RT-PCR for detecting RNA virus in individual SBPHs becomes challenging because of the expensive reagents and laborious procedure associated with RNA isolation when processing a large number of samples.

RESULTS

We established a simplified RT-PCR method without RNA isolation for RNA virus detection in a single SBPH. This method is achieved by grinding a single SBPH in sterile water and using the crude extract directly as the template for RT-PCR. The crude extract containing the virus RNA can be prepared in approximately two minutes. Rice stripe virus (RSV), rice black streaked dwarf virus (RBSDV) and Himetobi P virus (HiPV) were successfully detected using this simplified method. The detection results were validated by sequencing and dot immunobinding assay, indicating that this simplified method is reliable for detecting different viruses in insects. The evaluation of the sensitivity of this method showed that both RSV and HiPV can be detected when the cDNA from the crude extract was diluted up to 103 fold. Compared to the traditional RT-PCR with RNA isolation, the simplified RT-PCR method greatly reduces the sample processing time, decreases the detection cost, and improves the efficiency by avoiding RNA isolation.

CONCLUSIONS

A simplified RT-PCR method is developed for rapid detection of RNA virus in a single SBPH without the laborious RNA isolation step. It offers a convenient alternative to the traditional RT-PCR method.

Viruliferous rate of small brown planthopper is a good indicator of rice stripe disease epidemics

Rice stripe virus (RSV), its vector insect (small brown planthopper, SBPH) and climatic conditions in Jiangsu, China were monitored between 2002 and 2012 to determine key biotic and abiotic factors driving epidemics of the disease. Average disease severity, disease incidence and viruliferous rate of SBPH peaked in 2004 and then gradually decreased. Disease severity of RSV was positively correlated with viruliferous rate of the vector but not with the population density of the insect, suggesting that the proportion of vectors infected by the virus rather than the absolute number of vectors plays an important role in RSV epidemics and could be used for disease forecasting. The finding of a positive correlation of disease severity and viruliferous rate among years suggests that local infection is likely the main source of primary inoculum of RSV. Of the two main climatic factors, temperature plays a more important role than rainfall in RSV epidemics.

Assessment of reference gene stability in Rice stripe virus and Rice black streaked dwarf virus infection rice by quantitative Real-time PCR

BACKGROUND

Stably expressed reference gene(s) normalization is important for the understanding of gene expression patterns by quantitative Real-time PCR (RT-qPCR), particularly for Rice stripe virus (RSV) and Rice black streaked dwarf virus (RBSDV) that caused seriously damage on rice plants in China and Southeast Asia.

METHODS

The expression of fourteen common used reference genes of Oryza sativa L. were evaluated by RT-qPCR in RSV and RBSDV infected rice plants. Suitable normalization reference gene(s) were identified by geNorm and NormFinder algorithms.

RESULTS

UBQ 10 + GAPDH and UBC + Actin1 were identified as suitable reference genes for RT-qPCR normalization under RSV and RBSDV infection, respectively. When using multiple reference genes, the expression patterns of OsPRIb and OsWRKY, two virus resistance genes, were approximately similar with that reported previously. Comparatively, by using single reference gene (TIP41-Like), a weaker inducible response was observed.

CONCLUSIONS

We proposed that the combination of two reference genes could obtain more accurate and reliable normalization of RT-qPCR results in RSV- and RBSDV-infected plants. This work therefore sheds light on establishing a standardized RT-qPCR procedure in RSV- and RBSDV-infected rice plants, and might serve as an important point for discovering complex regulatory networks and identifying genes relevant to biological processes or implicated in virus.