Viroid-infected Tomato and Capsicum Seed Shipments to Australia

Efficient border biosecurity inspection leverages superspreading to reduce biological invasion risk

Biological invasions are a growing threat to biodiversity, food security, and economies. Rising pressure from increased global trade requires improving border inspection efficiency. Here, we depart from the conventional consignment-by-consignment approach advocated in current inspection standards. Instead, we suggest a broader perspective: evaluating border inspection regimes based on their ability to reduce propagule pressure across entire pathways. Additionally, we demonstrate that most biosecurity pathways exhibit superspreading behavior, that is, consignments from the same pathway have varying infestation rates and contain rare right-tail events (also called overdispersion). We show that greater overdispersion leads to more pronounced diminishing returns, with consequences on the optimal allocation of sampling effort. We leverage these two insights to develop a simple and efficient border inspection regime that can significantly reduce propagule pressure compared to current standards. Our analysis revealed that consignment size is a key driver of biosecurity risk and that sampling proportional to the square root of consignment size is near optimal. In testing, our framework reduced propagule pressure by 31 to 38% compared to current standards. We also identified opportunities to further improve inspection efficiency by considering additional pathway characteristics (i.e., overdispersion parameters, zero inflation, relative risk, sampling cost, detectability) and developed solutions for these more complex scenarios. We anticipate our result will mitigate biological invasion risk with significant implications for biodiversity conservation, food security, and economies worldwide.

International Trade and Local Effects of Viral and Bacterial Diseases in Ornamental Plants

Since the 1950s, there have been major changes in the scope, value, and organization of the ornamental plant industry. With fewer individual producers and a strong trend toward consolidation and globalization, increasing quantities of diverse plant genera and species are being shipped internationally. Many more ornamentals are propagated vegetatively instead of by seed, further contributing to disease spread. These factors have led to global movement of pathogens to countries where they were not formerly known. The emergence of some previously undescribed pathogens has been facilitated by high-throughput sequencing, but biological studies are often lacking, so their roles in economic diseases are not yet known. Case studies of diseases in selected ornamentals discuss the factors involved in their spread, control measures to reduce their economic impact, and some potential effects on agronomic crops. Advances in diagnostic techniques are discussed, and parallels are drawn to the international movement of human diseases.

Prevalences of Tobamovirus Contamination in Seed Lots of Tomato and Capsicum

Seed lots of tomato and capsicum (Solanum lycopersicon and Capsicum annuum, respectively) are required to be free of quarantine pests before their entry to Australia is permitted. Testing of samples from 118 larger seed lots in the period 2019–2021 revealed that 31 (26.3%) carried one or more of four Tobamovirus species, including tomato mottle mosaic virus (ToMMV), which is a quarantine pest for Australia. Testing of samples from a further 659 smaller seed lots showed that 123 (18.7%) carried a total of five Tobamovirus species, including ToMMV and tomato brown rugose fruit virus (ToBRFV), which is also a quarantine pest for Australia. Estimated prevalence of contamination by tobamoviruses ranged from 0.388% to 0.004% in contaminated larger seed lots. Analyses of these data allow us to estimate probabilities of detection of contamination under different regulatory settings.

Major Soilborne Pathogens of Field Processing Tomatoes and Management Strategies

Globally, tomato is the second most cultivated vegetable crop next to potato, preferentially grown in temperate climates. Processing tomatoes are generally produced in field conditions, in which soilborne pathogens have serious impacts on tomato yield and quality by causing diseases of the tomato root system. Major processing tomato-producing countries have documented soilborne diseases caused by a variety of pathogens including bacteria, fungi, nematodes, and oomycetes, which are of economic importance and may threaten food security. Recent field surveys in the Australian processing tomato industry showed that plant growth and yield were significantly affected by soilborne pathogens, especially Fusarium oxysporum and Pythium species. Globally, different management methods have been used to control diseases such as the use of resistant tomato cultivars, the application of fungicides, and biological control. Among these methods, biocontrol has received increasing attention due to its high efficiency, target-specificity, sustainability and public acceptance. The application of biocontrol is a mix of different strategies, such as applying antagonistic microorganisms to the field, and using the beneficial metabolites synthesized by these microorganisms. This review provides a broad review of the major soilborne fungal/oomycete pathogens of the field processing tomato industry affecting major global producers, the traditional and biological management practices for the control of the pathogens, and the various strategies of the biological control for tomato soilborne diseases. The advantages and disadvantages of the management strategies are discussed, and highlighted is the importance of biological control in managing the diseases in field processing tomatoes under the pressure of global climate change.

Tomato zonate spot virus induced hypersensitive resistance via an auxin-related pathway in pepper

Tomato zonate spotvirus (TZSV) often incurs significant losses in many food and ornamental crops in Yunnan province, China, and the surrounding areas. The pepper (Capsicum chinensePI152225)can develop hypersensitive resistance following infection with TZSV, through an as yet unknown mechanism. The transcriptome dataset showed a total of 45.81 GB of clean data were obtained from six libraries, and the average percentage of the reads mapped to the pepper genome was over 90.00 %. A total of 1403 differentially expressed genes (DEGs) were obtained after TZSV infection, including 825significantly up-regulated genes and 578 down-regulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that most up-regulated DEGs were involved in basal defenses. RT-qPCR, and virus induced gene silencing (VIGS) were used preliminarily to identifyBBC_22506 and BBC_18917, among total of 71 differentially expressed genes (DEGs), that play a key role in mediating the auxin-induced signaling pathway that might take part in hypersensitive response (HR) conferred resistance to viral infection in pepper (PI152225) byTZSV. This is the first study on the mechanism of auxin resistance, involved in defense responses of pepper against viral diseases, which lay the foundation for further study on the pathogenic mechanism of TZSV, as well as the mechanism of resistance to TZSV, in peppers.

Universal Primers for Rapid Detection of Six Pospiviroids in Solanaceae Plants Using One-Step Reverse-Transcription PCR and Reverse-Transcription Loop-Mediated Isothermal Amplification

A number of viruses and viroids infect solanaceous plants causing severe yield losses. Several seed-borne viroids are listed as quarantine pathogens in many countries. Among them, columnea latent viroid, pepper chat fruit viroid, potato spindle tuber viroid, tomato apical stunt viroid, tomato chlorotic dwarf viroid, and tomato planta macho viroid are of major concerns. The objective of this study was to design and test universal primers that could be used to detect six viroids in solanaceous plants using one-step reverse transcription PCR (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP). Results revealed that a pair of degenerate primers could be used in a one-step RT-PCR to amplify six pospiviroids from Solanaceae seeds and plants. Moreover, five primers were designed and used in RT-LAMP to amplify six pospiviroids. The minimal concentration of viroid RNA required for a successful detection varied, ranging from 1 fg to 10 ng, depending on the species of viroid and detection method. In general, RT-LAMP was more sensitive than RT-PCR, but both assays were rapid and highly sensitive tools to detect six pospiviroids. Detection methods in use for these viroids require at least two different sets of primers. The assays developed in this research could facilitate the ability to screen a large number of solanaceous plants and seeds intended for import and export.

Possible Overestimation of Seed Transmission in the Spread of Pospiviroids in Commercial Pepper and Tomato Crops Based on Large-Scale Grow-Out Trials and Systematic Literature Review

Several outbreaks of pospiviroids have been reported in pepper and tomato crops worldwide. Tracing back the origin of the infections has led to different sources. In some cases, the infections were considered to result from seed transmission. Other outbreaks were related to transmission from ornamental crops and weeds. Pospiviroids, in particular potato spindle tuber viroid, are regulated by many countries because they can be harmful to potatoes and tomatoes. Seed transmission has been considered an important pathway of introduction and spread. However, the importance of this pathway can be questioned. This paper presents data on seed transmission from large-scale grow-out trials of infested pepper and tomato seed lots produced under standard seed-industry conditions. In addition, it presents the results of a systematic review of published data on seed transmission and outbreaks in commercial pepper and tomato crops. Based on the results of the grow-out trials and review of the literature, it was concluded that the role of seed transmission in the spread of pospiviroids in practice is possibly overestimated.

Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification

Columnea latent viroid (CLVd) is a member of the Pospiviroid family and its naked circular RNA genome typically forms native “rod-like” secondary structures. In this work, the CLVd taxonomy was reevaluated based on sequence similarity and phylogenetic analysis, as well as the evaluation of the symptom development and disease severity of four selected CLVd isolates in a range of host species. The phylogenetic analysis showed that all CLVd isolates were clustered into five distinct clades: (I) severe isolates originally found in tomato crops in Thailand, (II) ornamental isolates, (III) mild isolates originally found in tomato crops in Thailand, and two clades (IV and V) containing mild isolates originating mainly from tomato crops in European countries, with different virulence levels on several hosts. Our analysis demonstrated that some CLVd isolates have a sequence similarity of less than 90% within the species taxon, as well as distinct biological characteristics (symptom development and virulence), both of which are important ICTV criteria for viroid classification. For these reasons, we propose that CLVd should be re-classified into at least three main taxonomic lineages: a “CLVd-tomato Asian lineage” (I), a “CLVd-tomato European lineage” (IV) and a “CLVd-ornamental European lineage” (II), plus two minor lineages (III and V), fitting the ICTV criteria.

Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.

An Inside Look into Biological Miniatures: Molecular Mechanisms of Viroids

Viroids are tiny single-stranded circular RNA pathogens that infect plants. Viroids do not encode any proteins, yet cause an assortment of symptoms. The following review describes viroid classification, molecular biology and spread. The review also discusses viroid pathogenesis, host interactions and detection. The review concludes with a description of future prospects in viroid research.

Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics

Tomato (Lycopersicum esculentum L.) and pepper (Capsicum annuum L.) plants belonging to the family Solanaceae are cultivated worldwide. The rapid development of next-generation sequencing (NGS) technology facilitates the identification of viruses and viroids infecting plants. In this study, we carried out metatranscriptomics using RNA sequencing followed by bioinformatics analyses to identify viruses and viroids infecting tomato and pepper plants in Vietnam. We prepared a total of 16 libraries, including eight tomato and eight pepper libraries derived from different geographical regions in Vietnam. We identified a total of 602 virus-associated contigs, which were assigned to 18 different virus species belonging to nine different viral genera. We identified 13 different viruses and two viroids infecting tomato plants and 12 viruses and two viroids infecting pepper plants with viruses as dominantly observed pathogens. Our results showed that multiple infection of different viral pathogens was common in both plants. Moreover, geographical region and host plant were two major factors to determine viral populations. Taken together, our results provide the comprehensive overview of viral pathogens infecting two important plants in the family Solanaceae grown in Vietnam.

Whole-Genome Deep Sequencing Reveals Host-Driven in-planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations

Columnea latent viroid (CLVd) is one of the most serious tomato diseases. In general, viroids have high mutation rates. This generates a population of variants (so-called quasi-species) that co-exist in their host and exhibit a huge level of genetic diversity. To study the population of CLVd in individual host plants, we used amplicon sequencing using specific CLVd primers linked with a sample-specific index sequence to amplify libraries. An infectious clone of a CLVd isolate Chaipayon-1 was inoculated on different solanaceous host plants. Six replicates of the amplicon sequencing results showed very high reproducibility. On average, we obtained 133,449 CLVd reads per PCR-replicate and 79 to 561 viroid sequence variants, depending on the plant species. We identified 19 major variants (>1.0% mean relative abundance) in which a total of 16 single-nucleotide polymorphisms (SNPs) and two single nucleotide insertions were observed. All major variants contained a combination of 4 to 6 SNPs. Secondary structure prediction clustered all major variants into a tomato/bolo maka group with four loops (I, II, IV and V), and a chili pepper group with four loops (I, III, IV and V) at the terminal right domain, compared to the CLVd Chaipayon-1 which consists of five loops (I, II, III, IV and V).

Effects of a Potato Spindle Tuber Viroid Tomato Strain on the Symptoms, Biomass, and Yields of Classical Indicator and Currently Grown Potato and Tomato Cultivars

The Chittering strain of potato spindle tuber viroid (PSTVd) infects solanaceous crops and wild plants in the subtropical Gascoyne Horticultural District of Western Australia. Classical PSTVd indicator hosts tomato cultivar Rutgers (R) and potato cultivar Russet Burbank (RB) and currently widely grown tomato cultivars Petula (P) and Swanson (S) and potato cultivars Nadine (N) and Atlantic (A) were inoculated with this strain to study its pathogenicity, quantify fruit or tuber yield losses, and establish whether tomato strains might threaten potato production. In potato foliage, infection caused spindly stems, an upright growth habit, leaves with ruffled margins and reduced size, and upward rolling and twisting of terminal leaflets (RB, A, and N); axillary shoot proliferation (A); severe plant stunting (N and RB); and necrotic spotting of petioles and stems (RB). Tubers from infected plants were tiny (N) or small and "spindle shaped" with (A) or without (RB) cracking. Potato foliage dry weight biomass was decreased by 30 to 44% in A and RB and 37% in N, whereas tuber yield was diminished by 50 to 89% in A, 69 to 71% in RB, and 90% in N. In tomato foliage, infection caused epinasty and rugosity in apical leaves, leaf chlorosis, and plant stunting (S, P, and N); cupped leaves (S and P); and reduced leaf size, flower abortion, and necrosis of midribs, petioles, and stems (R). Mean tomato fruit size was greatly decreased in all three cultivars. Tomato foliage dry weight biomass was diminished by 40 to 53% (P), 42% (S), and 37 to 51% (R). Tomato fruit yield was decreased by 60 to 76% (P), 52% (S), and 64 to 89% (R), respectively. Thus, the tomato strain studied was highly pathogenic to classical indicator and representative current tomato and potato cultivars, causing major losses in fruit and tuber yields. Tomato PSTVd strains, therefore, pose a threat to tomato and potato industries worldwide.

Prevalences of Pospiviroid Contamination in Large Seed Lots of Tomato and Capsicum, and Related Seed Testing Considerations

Analyses of pospiviroids in commercial seed lots of tomato and capsicum, determined by testing of 12,000 to 40,000 seeds per lot, have enabled the development of empirically-derived distribution curves for the observed prevalences of viroids in those commodities. Those distribution curves can be considered in conjunction with statistically-based estimates of detection that would be achieved using other sample sizes. Statistical calculations using binomial distributions show that sample sizes of 3000 and 9400 seeds allow detection of viroid prevalences as low as 0.1% and 0.032%, respectively, with 95% confidence. Applying those calculations to observed viroid prevalences in contaminated tomato seed lots, it is estimated that the use of sample sizes of 3000 and 9400 seeds would detect 15% and 42%, respectively, of the contaminated seed lots identified using the larger sample sizes of approximately 20,000 seeds reported in this study. It is concluded that the higher costs associated with testing of larger sample sizes represent a worthwhile investment in agricultural biosecurity.

Risk assessment of the entry of Pantoea stewartii subsp. stewartii on maize seed imported by the EU from the USA

Following a request from the European Commission, the EFSA Panel on Plant Health performed a risk assessment of the entry of Pantoea stewartii subsp. stewartii on maize seed imported by the EU from the USA. This pest is a Gram-negative bacterium which causes Stewart's vascular wilt and leaf blight of maize (including sweet corn), a disease responsible for serious crop losses throughout the world. The following scenarios were considered: scenario A0 (current practice), scenario A1 (US request for modification of EU conditions for derogation), and scenario A2 (EU conditions for derogation). Results from the quantitative seed pathway model presented here show that, despite the low rates of plant-to-seed and seed-to-seedling transmission that have been reported in the literature for Stewart's wilt, given the amount of traded seed, and in the case of voluntary (i.e. not mandatory) inspections of seed production fields at the origin (i.e. scenario A0), the frequency of introducing the disease is in the order of magnitude of some hundred introductions per year (median number). The EU conditions for derogation would lead to a decrease in the likelihood of entry compared to scenarios A0 (about 10,000 times fewer introductions) and A1 (about 2,000 times fewer introductions). This protective effect is mainly due to the requirement that only genotypes resistant to Stewart's wilt are traded, with the additional field inspection (two instead of one per season) providing additional reassurance. The Panel also concluded that seed lot inspections, as currently carried out (e.g. with a sample of 400 seeds) are not likely to lead to a relevant reduction in the level of infected imported maize seed, given the low prevalence of Stewart's wilt at the origin. If, however, there is aggregation in infection among consignments, inspection would work towards identifying the highly infected consignments. Recently, outbreaks of Stewart's wilt have occurred in Italy (Emilia Romagna, Friuli, Lombardy and Veneto). A review is provided of the available information to assess the possible role of seed imports in these outbreaks.