Viruses of Economic Impact on Tomato Crops in Mexico: From Diagnosis to Management-A Review

Insights into the role of N6-methyladenosine (m6A) in plant-virus interactions

N6-methyladenosine (m6A) is a common and dynamic epitranscriptomic modification in eukaryotic RNAs, affecting stability, splicing, translation, and degradation. Recent technological advancements have revealed the complex nature of m6A modifications, highlighting their importance in plant and animal species. The m6A modification is a reversible process, with "writers" depositing methylation, "erasers" demethylating it, and "reader" proteins recognizing m6A and executing various biological functions. Studying the relationship between m6A methylation and viral infection is crucial. Animal viruses, including retroviruses, RNA viruses, and DNA viruses, often employ the host's m6A machinery to replicate or avoid immune responses. In plant viruses, host methyltransferases or demethylases can stabilize or degrade viral RNA, depending on the virus-host interaction. Additionally, viral infections can modify the host's m6A machinery, impacting the viral life cycle. This review examines the role of m6A modifications in plant viral pathogenesis, focussing on RNA viruses infecting crops like alfalfa, turnip, wheat, rice, and potato. Understanding the role of m6A in virus-host interactions can aid in studying plant viral disease development and discovering novel antiviral targets for crop protection. In this review, we summarize current information on m6A in RNA biology, focussing on its function in viral infections and plant-virus interactions.

Omics based approaches to decipher the leaf ionome and transcriptome changes in Solanum lycopersicum L. upon Tomato Brown Rugose Fruit Virus (ToBRFV) infection

The Tomato Brown Rugose Fruit Virus (ToBRFV) is a pathogen that mostly affects plants from the Solanaceae family. This virus severely affects the yield of tomato (Solanum lycopersicum L.) plants, thus creating an urgent need to research the basis of resistance to manage the disease. To understand the molecular basis of resistance, we employed omics-based approaches involving leaf ionomics and transcriptomics to help us decipher the interaction between elemental and nutritional composition and investigate its effect on the gene expression profile upon the ToBRFV infection in tomatoes. Ionomics was used to investigate the accumulation of trace elements in leaves, showcasing that the plants resistant to the virus had significantly higher concentrations of iron (p-value = 0.039) and nickel (p-value = 0.042) than the susceptible ones. By correlating these findings with transcriptomics, we identified some key genes involved in iron homeostasis and abscisic acid pathways, potentially responsible for conferring resistance against the pathogen. From the obtained list of differentially expressed genes, a panel of mutation profile was discovered with three important genes-Solyc02g068590.3.1 (K+ transporter), Solyc01g111890.3.1 (LRR), and Solyc02g061770.4.1 (Chitinase) showing persistent missense mutations. We ascertain the role of these genes and establish their association with plant resistance using genotyping assays in various tomato lines. The targeted selection of these genetic determinants can further enhance plant breeding and crop yield management strategies.

Tomato yellow leaf curl virus: Characteristics, influence, and regulation mechanism

Tomato yellow leaf curl virus (TYLCV), a DNA virus belonging to the genus Begomovirus, significantly impedes the growth and development of numerous host plants, including tomatoes and peppers. Due to its rapid mutation rate and frequent recombination events, achieving complete control of TYLCV proves exceptionally challenging. Consequently, identifying resistance mechanisms become crucial for safeguarding host plants from TYLCV-induced damage. This review article delves into the global distribution, dispersal patterns, and defining characteristics of TYLCV. Moreover, the intricate interplay between TYLCV and various influencing factors, such as insect vectors, susceptible host plants, and abiotic stresses, plays a pivotal role in plant-TYLCV interactions. The review offers an updated perspective on recent investigations focused on plant response mechanisms to TYLCV infection, including the intricate relationship between TYLCV, whiteflies, and regulatory factors. This comprehensive analysis aims to establish a foundation for future research endeavors exploring the molecular mechanisms underlying TYLCV infection and the development of plant resistance through breeding programs.

Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding

Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world's most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and confirmation with PCR and RT-PCR were used. Single and mixed infections with tomato mosaic virus (ToMV), tomato golden mosaic virus (ToGMoV), and pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3' UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3' UTR, as well as amino acid mutations in the ORFs encoding 126 KDa, 183 KDa, and MP of Mexican ToMV isolates, suggest that it is necessary to evaluate the capacity of these variants to overcome Tm-1, Tm-2, and Tm-22 resistance genes. This evaluation, along with the characterization of advanced lines using molecular markers linked to these resistant genes, will be addressed in future studies as part of the breeding strategy. This study emphasizes the importance of using HTS for accurate identification and characterization of plant viruses that naturally infect tomato germplasm based on the consensus genome sequences. This study provides crucial insights to select appropriate disease management strategies and resistance genes and guide breeding efforts toward the development of virus-resistant tomato varieties.

Biological and molecular characterization of citrus bent leaf viroid

Background and aim

Citrus bent leaf viroid (CBLVd) is one of the emerging and widely distributed viroids in citrus-growing areas of the world, including Pakistan. Previously, CBLVd has been reported in Pakistan for the first time in 2009. Therefore, characterization of CBLVd is required to monitor the viroid status in the citrus orchards concerning citrus decline.

Methods

Biological and molecular characterization of CBLVd was studied through biological indexing and confirmation through RT-PCR, followed by phylogenetic analysis of selected CBLVd isolates. Among four citrus cultivars viz., Kinnow (Citrus nobilis × Citrus deliciosa), Mosambi (C. sinensis), Futrell's Early (C. reticulata) and Lemon (C. medica) used as indicator plants for two transmission trials viz., graft inoculation and mechanical inoculation. Graft inoculation was more efficient than mechanical inoculation.

Results

Symptoms such as mild mosaic, slight backward leaf bending, and leaf curling were observed after eight months' post-inoculation. Citrus nobilis × Citrus deliciosa, C. reticulata and C. sinensis were more sensitive to CBLVd as compared to C. medica. Inoculated plants were reconfirmed through RT-PCR amplicons of 233 bp. The phylogenetic tree of submitted sequences showed more than 90% relevance of CBLVd in Pakistan compared to the rest of the world.

Conclusions

There was slight genetic variability, but more than 90% relevance was found among the submitted and already reported CBLVd isolate from Pakistan. Scanty literature is available regarding the biological and molecular studies of CBLVd in Pakistan. Therefore, the transmission and molecular characterization of CBLVd in Pakistan were studied for the first time.

Advances and Prospects of Virus-Resistant Breeding in Tomatoes

Plant viruses are the main pathogens which cause significant quality and yield losses in tomato crops. The important viruses that infect tomatoes worldwide belong to five genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus. Tomato resistance genes against viruses, including Ty gene resistance against begomoviruses, Sw gene resistance against orthotospoviruses, Tm gene resistance against tobamoviruses, and Pot 1 gene resistance against potyviruses, have been identified from wild germplasm and introduced into cultivated cultivars via hybrid breeding. However, these resistance genes mainly exhibit qualitative resistance mediated by single genes, which cannot protect against virus mutations, recombination, mixed-infection, or emerging viruses, thus posing a great challenge to tomato antiviral breeding. Based on the epidemic characteristics of tomato viruses, we propose that future studies on tomato virus resistance breeding should focus on rapidly, safely, and efficiently creating broad-spectrum germplasm materials resistant to multiple viruses. Accordingly, we summarized and analyzed the advantages and characteristics of the three tomato antiviral breeding strategies, including marker-assisted selection (MAS)-based hybrid breeding, RNA interference (RNAi)-based transgenic breeding, and CRISPR/Cas-based gene editing. Finally, we highlighted the challenges and provided suggestions for improving tomato antiviral breeding in the future using the three breeding strategies.

Highly sensitive fluorescence detection of tobacco mosaic virus RNA based on polysaccharide and ARGET ATRP double signal amplification

Plant diseases caused by tobacco mosaic viruses (TMV) reduce the yield and quality of crops and cause significant losses. Early detection and prevention of TMV has important value of research and reality. Herein, a fluorescent biosensor was constructed for highly sensitive detection of TMV RNA (tRNA) based on the principle of base complementary pairing, polysaccharides and atom transfer radical polymerization by electron transfer activated regeneration catalysts (ARGET ATRP) as double signal amplification strategy. The 5'-end sulfhydrylated hairpin capture probe (hDNA) was first immobilized on amino magnetic beads (MBs) by a cross-linking agent, which specifically recognizes tRNA. Then, chitosan binds to BIBB, providing numerous active sites for fluorescent monomer polymerization, which successfully significantly amplifying the fluorescent signal. Under optimal experimental conditions, the proposed fluorescent biosensor for the detection of tRNA has a wide detection range from 0.1 pM to 10 nM (R² = 0.998) with a limit of detection (LOD) as low as 1.14 fM. In addition, the fluorescent biosensor showed satisfactory applicability for the qualitative and quantitative analysis of tRNA in real samples, thereby demonstrating the potential in the field of viral RNA detection.