Tomato brown rugose fruit virus (ToBRFV) was identified in Israel during October 2014 in tomato plants (
). These plants, carrying the durable resistance gene against tomato mosaic virus,
, displayed ...severe disease symptoms and losses to fruit yield and quality. These plants were found infected with a tobamovirus similar to that discovered earlier in Jordan. This study was designed to screen and identify tomato genotypes resistant or tolerant to ToBRFV. The identified resistance and tolerance traits were further characterized virologically and genetically. Finally, DNA markers linked to genes controlling these traits were developed as tools to expedite resistance breeding. To achieve these objectives, 160 genotypes were screened, resulting in the identification of an unexpectedly high number of tolerant genotypes and a single genotype resistant to the virus. A selected tolerant genotype and the resistant genotype were further analyzed. Analysis of genetic inheritance revealed that a single recessive gene controls tolerance whereas at least two genes control resistance. Allelic test between the tolerant and the resistant genotype revealed that these two genotypes share a locus controlling tolerance, mapped to chromosome 11. This locus displayed a strong association with the tolerance trait, explaining nearly 91% of its variation in segregating populations. This same locus displayed a statistically significant association with symptom levels in segregating populations based on the resistant genotype. However, in these populations, the locus was able to explain only ~41% of the variation in symptom levels, confirming that additional loci are involved in the genetic control of the resistance trait in this genotype. A locus on chromosome 2, at the region of the
gene, was finally found to interact with the locus discovered on chromosome 11 to control resistance.
Tomato Brown Rugose Fruit Virus (ToBRFV) is a plant pathogen that infects important
crop species and can dramatically reduce tomato crop yields. The ToBRFV has rapidly spread around the globe due to ...its ability to escape detection by antiviral host genes which confer resistance to other tobamoviruses in tomato plants. The development of robust and reproducible methods for detecting viruses in the environment aids in the tracking and reduction of pathogen transmission. We detected ToBRFV in municipal wastewater influent (WWI) samples, likely due to its presence in human waste, demonstrating a widespread distribution of ToBRFV in WWI throughout Ontario, Canada. To aid in global ToBRFV surveillance efforts, we developed a tiled amplicon approach to sequence and track the evolution of ToBRFV genomes in municipal WWI. Our assay recovers 95.7% of the 6393 bp ToBRFV RefSeq genome, omitting the terminal 5' and 3' ends. We demonstrate that our sequencing assay is a robust, sensitive, and highly specific method for recovering ToBRFV genomes. Our ToBRFV assay was developed using existing ARTIC Network resources, including primer design, sequencing library prep, and read analysis. Additionally, we adapted our lineage abundance estimation tool, Alcov, to estimate the abundance of ToBRFV clades in samples.
The tobamovirus, tomato brown rugose fruit virus (ToBRFV), is a significant concern in global tomato production due to the ineffectiveness of the widely used
Tm-2
2
resistance gene. Our previous ...study showed that the tomato variety GCR237, a
Tm-1
homozygote, resisted an Israeli isolate of ToBRFV (DSMZ PV-1241) for up to 35 days post inoculation (dpi), suggesting
Tm-1
-homozygous cultivars could control ToBRFV. In the present study, we inoculated GCR237 plants with ToBRFV and cultivated them for a longer period of time. The plants resisted systemic infection up to 50 dpi, but mosaic symptoms appeared on the upper leaves by 100 dpi. We retrieved the virus from symptomatic leaves and established four single local lesion isolates. These isolates had several amino acid (AA) substitutions in the helicase domain of 126-kDa/183-kDa replication proteins, where the
Tm-1
protein likely binds to inhibit viral RNA replication. Back-inoculating these isolates onto GCR237 plants confirmed they had acquired the ability to overcome GCR237’s resistance and induced mosaic symptoms as early as 14 dpi. About 90% of 229 ToBRFV isolates in the NCBI database had identical AA sequences in the corresponding region to DSMZ PV-1241, while ~ 10% inherently had AA substitutions that would confer complete breaking ability to the
Tm-1
resistance. These results suggest that while
Tm-1
can inhibit ToBRFV RNA replication, ToBRFV can easily overcome
Tm-1
homozygotes.
Tomato (Solanum spp.) is the second most-consumed vegetable after potato and grown all over the world. Tomato brown rugose fruit virus (ToBRFV) was first identified in 2014 on tomato plants, since ...then it has been reported in many countries. It is a significant threat to tomato production. This work aimed to identify the disease resistance source(s). To achieve this aim, a total of 44 tomato materials including 28 accessions of eight wild species, two accessions of Solanum arcanum Peralta, S. pennellii Correll, and S. sitiens I.M. Johnst, seven accessions of S. chilense (Dunal) Reiche, fve accessions of S. pimpinellifolium L., four accessions of S. habrochaites S. Knapp & D.M. Spooner, three accessions of S. peruvianum L., one accession of S. chmielewskii (CM. Rick et al.) D.M. Spooner et al. and S. huaylasense Peralta, 5 cultivated tomatoes (S. lycopersicum L.) and 11 interspecific F1 hybrids derived from S. habrochaites and S. pennellii were tested with ToBRFV isolates by using the biological testing method. Mechanical inoculation method was used for biological testing. ToBRFV was inoculated to 10 plants with 2-3 true leaves two replicates for each genotype. As a result, S. pimpinellifolium (LA1651), S. penellii (LA0716), and S. chilense (LA4117A, LA2747) were found tolerant to ToBRFV with the lowest disease severity index (DSI) with 19.6%, 28.3% and 35.0%, respectively. Also, molecular genetic analysis of the plant material by using molecular markers revealed that there was no interaction between other virus resistance genes (Tm-22 and Tm-1) and ToBRFV resistance. These wild tomato species identified in the present study are valuable genetic resources to develop new resistance cultivars for ToBRFV resistance in tomato breeding programs. Key words: Resistance, ToBRFV, tomato, wild species.
In this study, bioinformatic analyses were carried out according to the fully coded CP and MP gene regions of the agent, using six novel tomato brown rugose fruit virus (ToBRFV) variants obtained ...from the production greenhouses in Antalya, where the infection was first detected in Turkey and global variants. Molecular evolutionary analyses using both CP and MP gene regions showed that all variants were distributed in three major clades. Population dynamics studies for both gene regions have shown that there was very low nucleotide diversity and haplotype diversity. The low haplotype diversity for the CP and MP genes indicated almost no recombination status. A strong negative selection was determined for CP and MP gene regions, dN/dS= 0.0877 and dN/dS=0.2104, respectively. Neutrality test results revealed that ToBRFV populations are in an expansion phase. Pairwise comparisons were performed between populations separated in the geographic hierarchy as American, European, and Asian variants, and the findings showed intense gene flow and high genetic similarity (FST<0,33 and migration rate >1). The results of this study reveal the recent population structure of the virus and suggest that necessary precautions should be taken in the international seed trade against contaminated seeds.
Plant viruses can evolve towards new pathogenic entities that may eventually cause outbreaks and become epidemics or even pandemics. Seven years ago, tomato brown rugose fruit virus (ToBRFV) emerged, ...overcoming the genetic resistance that had been employed for more than sixty years against tobamoviruses in tomato. Since then, ToBRFV has spread worldwide, producing significant losses in tomato crops. While new resistances are deployed, the only means of control is the implementation of effective prevention and eradication strategies. For this purpose, in this work, we have designed, assessed, and compared an array of tests for the specific and sensitive detection of the ToBRFV in leaf samples. First, two monoclonal antibodies were generated against a singular peptide of the ToBRFV coat protein; antibodies were utilized to devise a double-antibody-sandwich enzyme-linked immunosorbent assay (DAS-ELISA) test that sensitively detects this virus and has no cross-reactivity with other related tobamoviruses. Second, a real-time quantitative PCR (RT-qPCR) test targeting the RNA-dependent replicase open reading frame (ORF) was designed, and its performance and specificity validated in comparison with the CaTa28 and CSP1325 tests recommended by plant protection authorities in Europe. Third, in line with the tendency to use field-deployable diagnostic techniques, we developed and tested two sets of loop-mediated isothermal amplification (LAMP) primers to double-check the detection of the movement protein ORF of ToBRFV, and one set that works as an internal control. Finally, we compared all of these methods by employing a collection of samples with different ToBRFV loads to evaluate the overall performance of each test.
Tomato brown rugose fruit virus (ToBRFV; genus, Tobamovirus, family, Virgaviridae) was first reported in 2015 infecting tomatoes grown under protected cropping in the Jordan Valley. Since then, ...ToBRFV has been detected in tomatoes grown in both protected and open fields across Jordan. The increased incidence of ToBRFV prompted this investigation of the potential role of natural weed hosts in the dissemination of ToBRFV. A survey was conducted in the Jordan Valley and highlands to determine possible reservoir hosts of ToBRFV in fields and greenhouse complexes in which tomatoes were grown. Detection of ToBRFV infection was made by double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) and further confirmation by reverse-transcription polymerase chain reaction (RT-PCR), followed by DNA cloning and sequencing, and bioassays. Thirty weed species belonging to twenty-six genera from sixteen families were tested. Twelve species belonging to eight families were infected of which ten species are newly reported hosts for ToBRFV. Seed transmission of ToBRFV in Solanum nigrum was confirmed in a grow-out experiment. To our knowledge, this is the first report of the natural occurrence of ToBRFV on weed hosts. Identification of natural reservoirs of ToBRFV can help to develop management practices focused on weed plant species to prevent ToBRFV transmission. The extent to which ToBRFV survives in diverse alternate weed host species outside tomato growing seasons in different world regions requires further research in order to establish the risk associated with the possible contribution of weeds as a reservoir for primary infections in tomato crops.
Tomato is the most consumed vegetable in the world. The tomato brown rugose fruit virus (ToBRFV) is an important destructive virus that damages tomatoes and peppers with significant economic impact. ...The detection and characterization of this important viral pathogen were evaluated at the molecular and morphological level. The viral isolate was purified and inoculated on tomato and pepper plants. Small RNAs were sequenced in both plants and the profiles were compared. The complete genome of the isolate was obtained, and microRNA (miRNA) profiles were unveiled by small RNA sequencing. Symptoms caused by the isolate were also described and the morphology of the isolate was observed by transmission electron microscopy. Our results contribute to further understanding of the role of miRNAs in ToBRFV pathogenesis, which may be crucial for understanding disease symptom development in tomatoes and peppers.
Physostegia chlorotic mottle virus (PhCMoV; genus:
, family:
) and tomato brown rugose fruit virus (ToBRFV; genus:
, family:
) are newly emerging plant viruses that have a dramatic effect on tomato ...production. Among various known virus-control strategies, RNAi-mediated defence has shown the potential to protect plants against various pathogens including viral infections. Micro(mi)RNAs play a major role in RNAi-mediated defence.
Using in silico analyses, we investigated the possibility of tomato-encoded miRNAs (TomiRNA) to target PhCMoV and ToBRFV genomes using five different algorithms, i.e., miRanda, RNAhybrid, RNA22, Tapirhybrid and psRNATarget.
The results revealed that 14 loci on PhCMoV and 10 loci on ToBRFV can be targeted by the TomiRNAs based on the prediction of at least three algorithms. Interestingly, one TomiRNA, miR6026, can target open reading frames from both viruses, i.e., the phosphoprotein encoding gene of PhCMoV, and the two replicase components of ToBRFV. There are currently no commercially available PhCMoV- or ToBRFV-resistant tomato varieties, therefore the predicted data provide useful information for the development of PhCMoV- and ToBFRV-resistant tomato plants.
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