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Tomato is one of the major vegetable crops consumed worldwide. Tomato yellow leaf curl virus (TYLCV) and fungal Oidium sp. are devastating pathogens causing yellow leaf curl disease and powdery mildew. Such viral and fungal pathogens reduce tomato crop yields and cause substantial economic losses every year. Several commercial tomato varieties include Ty-5 (SlPelo) and Mildew resistance locus o 1 (SlMlo1) locus that carries the susceptibility (S-gene) factors for TYLCV and powdery mildew, respectively. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is a valuable genome editing tool to develop disease-resistant crop varieties. In this regard, targeting susceptibility factors encoded by the host plant genome instead of the viral genome is a promising approach to achieve pathogen resistance without the need for stable inheritance of CRISPR components. In this study, the CRISPR/Cas9 system was employed to target the SlPelo and SlMlo1 for trait introgression in elite tomato cultivar BN-86 to confer host-mediated immunity against pathogens. SlPelo-knockout lines were successfully generated, carrying the biallelic indel mutations. The pathogen resistance assays in SlPelo mutant lines confirmed the suppressed accumulation of TYLCV and restricted the spread to non-inoculated plant parts. Generated knockout lines for the SlMlo1 showed complete resistance to powdery mildew fungus. Overall, our results demonstrate the efficiency of the CRISPR/Cas9 system to introduce targeted mutagenesis for the rapid development of pathogen-resistant varieties in tomato.

Tomato yellow leaf curl disease (TYLCD) and tomato leaf curl disease (TLCD) cause serious losses in tomato production, especially in tropical and sub-tropical regions. In 2014–2015, tomato samples with TYLCD/TLCD-like symptoms were collected from different provinces of Iraq and infection with tomato yellow leaf curl virus (TYLCV) identified. To study the diversity of TYLCV, DNA of eight positive samples from this survey was used for rolling-circle amplification, cloning and sequencing. Pairwise nucleotide sequence comparisons with complete genomes showed that the Iraqi TYLCV isolates belonged to the strains TYLCV-IL and TYLCV-Mld. In a phylogenetic analysis, the Iraqi TYLCV-IL isolates grouped into three distinct clades, consisting of TYLCV-IL (A) and the two new variants TYLCV-IL (D) and TYLCV-IL (E). The Iraqi isolate of TYLCV-Mld grouped into the newly proposed TYLCV-Mld (D) variant. For one sample, sequencing also revealed co-infection with tomato leaf curl Palampur virus (ToLCPalV). The phylogenetic tree of ToLCPalV DNA-A showed a close relationship between the isolates of different hosts from Iraq and Iran. No evidence of recombination was detected in ToLCPalV DNA-A, but recombination was observed for the TYLCV isolates. The results indicate that there is a high diversity of TYLCV in Iraq, including new variants, that is partly shared with Kuwait and countries in the Eastern Mediterranean Region. Occurrence of multiple TYLCV variants and ToLCPalV can act as a potential threat to tomato production in Iraq.

Whiteflies, Bemisia tabaci (Hemiptera), are pests causing economic damage to many crops, capable of transmitting hundreds of plant vector-borne viruses. They are believed to secrete salivary protein effectors that can improve vector colonization and reproductive fitness in host plants. However, little is known about effector biology and the precise mechanism of action of whitefly effectors. Here, we report a functional screening of B. tabaci salivary effector proteins (Bsp) capable of modulating plant innate immunity triggered by plant endogenous pattern peptide Pep1. Four immunity suppressors and two elicitors were identified. Bsp9, the most effective immunity suppressor, was further identified to directly interact with an immunity regulator WRKY33. We provide evidence that Bsp9 may suppress plant immune signalling by interfering with the interaction between WRKY33 and a central regulator in the MAPK cascade. The interference by Bsp9 therefore reduces plant resistance to whitefly by inhibiting activation of WRKY33-regulated immunity-related genes. Further detailed analysis based on transgenic plants found that whitefly effector Bsp9 could promote whitefly preference and performance, increasing virus transmission. This study enriches our knowledge on insect effector biology. This article is part of the theme issue ‘Biotic signalling sheds light on smart pest management’.

This study was conducted to determine the reaction of 14 tomato ( Solanum lycopersicom ) genotypes to Tomato yellow leaf curl virus (TYLCV), and the effect of the virus on the fruit content of the genotypes Narcan, 123, and Summer 21. The field experiment was carried out in the western orchards of Samawah, Al-Muthanna Governorate, Iraq. All experiments analyzing mineral elements in tomato fruits were done in laboratories of Ghayat Al-Marefa Company, Babylon. The results of inoculation of the tomato genotypes with TYLCV and testing them by polymerase chain reaction (PCR) showed that all these genotypes were susceptible to the virus with the difference of those genotypes in the time of appearance and severity of disease symptoms. The genotypes Nahrayn and Summer 21 were the most severely infected with TYLCV (96 and 87%, respectively) compared with the other genotypes. It was also found that the virus had a clear effect on the decrease in the fruit genotypes contents of the samples tested (123, Narcan, and Summer 21) of mineral elements of iron and zinc that reached 26.80 and 28.88 mg/L, respectively, and substantially different from their given values, which were 32.94 and 34.73 mg/L, respectively, in unaffected plants. Moreover, results proved that the content of TYLCV-infected fruits decreased significantly (1.26 mmol. L -1 ) with a significant difference from its normal level in non-infected plants which was 1.8 mmol. L -1 . Results also showed that TYLCV had a significant effect in reducing the concentrations of magnesium and phosphorous (0.244 and 0.248%), respectively, in the fruits of tomato genotypes compared with their concentrations in non-infected plants that were 0.348 and 0.383%, respectively.

Begomoviruses are vectored in a circulative persistent manner by the whitefly Bemisia tabaci. The insect ingests viral particles with its stylets. Virions pass along the food canal and reach the esophagus and the midgut. They cross the filter chamber and the midgut into the haemolymph, translocate into the primary salivary glands and are egested with the saliva into the plant phloem. Begomoviruses have to cross several barriers and checkpoints successfully, while interacting with would-be receptors and other whitefly proteins. The bulk of the virus remains associated with the midgut and the filter chamber. In these tissues, viral genomes, mainly from the tomato yellow leaf curl virus (TYLCV) family, may be transcribed and may replicate. However, at the same time, virus amounts peak, and the insect autophagic response is activated, which in turn inhibits replication and induces the destruction of the virus. Some begomoviruses invade tissues outside the circulative pathway, such as ovaries and fat cells. Autophagy limits the amounts of virus associated with these organs. In this review, we discuss the different sites begomoviruses need to cross to complete a successful circular infection, the role of the coat protein in this process and the sites that balance between virus accumulation and virus destruction.

The mechanism by which plant viruses manipulate the behavior of insect vectors has largely been described as indirect manipulation through modifications of the host plant. However, little is known about the direct interaction of the plant virus on the nervous system of its insect vector, and the substantial behavioral effect on virus transmission. Using a system consisting of a Tomato yellow leaf curl virus (TYLCV) and its insect vector whitefly, we found that TYLCV caused caspase-dependent apoptotic neurodegeneration with severe vacuolar neuropathological lesions in the brain of viruliferous whitefly by inducing a putative inflammatory signaling cascade of innate immunity. The sensory defects caused by neurodegeneration removed the steady preference of whitefly for virus-infected plants, thereby enhancing the probability of the virus to enter uninfected hosts, and eventually benefit TYLCV spread among the plant community. These findings provide a neuromechanism for virus transmission to modify its associated insect vector behavior. When a plant becomes infected by a virus, its defenses get weakened, which attracts insects that are looking for an easy meal. Insects detect which plants are infected based on the color of the sickened plant and the smell of chemicals it releases. Once an insect leaves the infected plant, it may carry the virus to new plants, allowing the virus to spread. Insects, however, prefer the easy pickings of plants that are already infected, making them less likely to spread the virus. Plant viruses have found ways to overcome this preference, but how they do this was not fully understood. Learning more about how plant viruses manipulate insects into helping them spread could allow scientists to develop new ways of protecting food crops from viral diseases. Viruses that infect insects can trigger excessive immune system responses that damage insects’ nerves and cause them to behave differently. For example, their senses may become impaired, they may move less, or be less able to remember things. This has led scientists to wonder whether plant viruses that use insects to spread might manipulate the insects’ behaviors using a similar mechanism. Now, Wang et al. have investigated whether the tomato yellow leaf curl virus –TYLCV for short – changes the behavior of whiteflies, which are known to spread the virus. The experiments showed that whiteflies typically prefer tomato plants infected with the virus, but after carrying TYLCV, they displayed equal preference for both infected and uninfected plants. Analyzing which genes were active in the whiteflies revealed that TYLCV triggers a harmful immune response which turns on genes that cause cells in the brain to die. This impairs the whiteflies' sight and sense of smell, making it harder for them to distinguish between infected and uninfected plants. These findings suggest that the immune response triggered by the virus may be essential for the spread of TYLCV. It also identified a protein that causes the death of brain cells, leading to behavioral changes in the whiteflies. This suggests that targeting this protein, or other steps in this process, could help stop the spread of TYLCV in tomato plants.

Background Long Noncoding-RNAs (LncRNAs) are known to be involved in some biological processes, but their roles in plant-virus interactions remain largely unexplored. While circular RNAs (circRNAs) have been studied in animals, there has yet to be extensive research on them in a plant system, especially in tomato-tomato yellow leaf curl virus (TYLCV) interaction. Results In this study, RNA transcripts from the susceptible tomato line JS-CT-9210 either infected with TYLCV or untreated, were sequenced in a pair-end strand-specific manner using ribo-zero rRNA removal library method. A total of 2056 lncRNAs including 1767 long intergenic non-coding RNA (lincRNAs) and 289 long non-coding natural antisense transcripts (lncNATs) were obtained. The expression patterns in lncRNAs were similar in susceptible tomato plants between control check (CK) and TYLCV infected samples. Our analysis suggested that lncRNAs likely played a role in a variety of functions, including plant hormone signaling, protein processing in the endoplasmic reticulum, RNA transport, ribosome function, photosynthesis, glulathione metabolism, and plant-pathogen interactions. Using virus-induced gene silencing (VIGS) analysis, we found that reduced expression of the lncRNA S-slylnc0957 resulted in enhanced resistance to TYLCV in susceptible tomato plants. Moreover, we identified 184 circRNAs candidates using the CircRNA Identifier (CIRI) software, of which 32 circRNAs were specifically expressed in untreated samples and 83 circRNAs in TYLCV samples. Approximately 62% of these circRNAs were derived from exons. We validated the circRNAs by both PCR and Sanger sequencing using divergent primers, and found that most of circRNAs were derived from the exons of protein coding genes. The silencing of these circRNAs parent genes resulted in decreased TYLCV virus accumulation. Conclusion In this study, we identified novel lncRNAs and circRNAs using bioinformatic approaches and showed that these RNAs function as negative regulators of TYLCV infection. Moreover, the expression patterns of lncRNAs in susceptible tomato plants were different from that of resistant tomato plants, while exonic circRNAs expression positively associated with their respective protein coding genes. This work provides a foundation for elaborating the novel roles of lncRNAs and circRNAs in susceptible tomatoes following TYLCV infection.

Tomato yellow leaf curl virus (TYLCV) is a virus species causing epidemics in tomato ( ) worldwide. Many efforts have been focused on identification of resistance sources by screening wild tomato species. In many cases, the accession numbers were either not provided in publications or not provided in a consistent manner, which led to redundant screenings. In the current study, we summarized efforts on the screenings of wild tomato species for TYLCV resistance from various publications. In addition, we screened 708 accessions from 13 wild tomato species using different inoculation assays (i.e., whitefly natural infection and Agrobacterium-mediated inoculation) from which 138 accessions exhibited no tomato yellow leaf curl disease (TYLCD) symptoms. These symptomless accessions include 14 accessions from , 43 from , 1 from , 28 from , 5 from , 4 from , 2 from , 1 from , 39 from , and 1 from . Most of the screened accessions remained symptomless. Many symptomless accessions were also identified in , , and . A large number of accessions were screened. However, almost all of the tested accessions showed TYLCD symptoms. Further, we studied allelic variation of the / gene in few accessions by applying virus-induced gene silencing and allele mining, leading to identification of a number of allele-specific polymorphisms. Taken together, we present a comprehensive overview on TYLCV resistance and susceptibility in wild tomato germplasm, and demonstrate how to study allelic variants of the cloned -genes in TYLCV-resistant accessions.

Background The basic helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that can bind to specific DNA target sites. They have been well characterized in model plants such as Arabidopsis and rice and have been shown to be important regulatory components in many different biological processes. However, no systemic analysis of the bHLH transcription factor family has yet been reported in tomatoes. Tomato yellow leaf curl virus (TYLCV) threatens tomato production worldwide by causing leaf yellowing, leaf curling, plant stunting and flower abscission. Results A total of 152 bHLH transcription factors were identified from the entire tomato genome. Phylogenetic analysis of bHLH domain sequences from Arabidopsis and tomato facilitated classification of these genes into 26 subfamilies. The evolutionary and possible functional relationships revealed during this analysis are supported by other criteria, including the chromosomal distribution of these genes, the conservation of motifs and exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Distribution mapping results showed bHLH genes were localized on the 12 tomato chromosomes. Among the 152 bHLH genes from the tomato genome, 96 bHLH genes were detected in the TYLCV-susceptible and resistant tomato breeding line before (0 dpi) and after TYLCV (357 dpi) infection. As anticipated, gene ontology (GO) analysis indicated that most bHLH genes are related to the regulation of macromolecule metabolic processes and gene expression. Only four bHLH genes were differentially expressed between 0 and 357 dpi. Virus-induced gene silencing (VIGS) of one bHLH genes SlybHLH131 in resistant lines can lead to the cell death. Conclusion In the present study, 152 bHLH transcription factor genes were identified. One of which bHLH genes, SlybHLH131 , was found to be involved in the TYLCV infection through qRT-PCR expression analysis and VIGS validation. The isolation and identification of these bHLH transcription factors facilitated clarification of the molecular genetic basis for the genetic improvement of tomatoes and the development of functional gene resources for transgenic research. In addition, these findings may aid in uncovering an unexplored mechanism during the TYLCV infection in tomatoes.