Occurrence of Tobacco streak virus on Peanut (Arachis hypogaea) in India

Revisiting a pollen-transmitted ilarvirus previously associated with angular mosaic of grapevine

We report the characterization of a novel tri-segmented RNA virus infecting Mercurialis annua, a common crop weed and model species in plant science. The virus, named "Mercurialis latent virus" (MeLaV) was first identified in a mixed infection with the recently described Mercurialis orthotospovirus 1 (MerV1) on symptomatic plants grown in glasshouses in Lausanne (Switzerland). Both viruses were found to be transmitted by Thrips tabaci, which presumably help the inoculation of infected pollen in the case of MeLaV. Complete genome sequencing of the latter revealed a typical ilarviral architecture and close phylogenetic relationship with members of the Ilarvirus subgroup 1. Surprisingly, a short portion of MeLaV replicase was found to be identical to the partial sequence of grapevine angular mosaic virus (GAMV) reported in Greece in the early 1990s. However, we have compiled data that challenge the involvement of GAMV in angular mosaic of grapevine, and we propose alternative causal agents for this disorder. In parallel, three highly-conserved MeLaV isolates were identified in symptomatic leaf samples in The Netherlands, including a herbarium sample collected in 1991. The virus was also traced in diverse RNA sequencing datasets from 2013 to 2020, corresponding to transcriptomic analyses of M. annua and other plant species from five European countries, as well as metaviromics analyses of bees in Belgium. Additional hosts are thus expected for MeLaV, yet we argue that infected pollen grains have likely contaminated several sequencing datasets and may have caused the initial characterization of MeLaV as GAMV.

Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies

Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.

Thrips diversity of cotton ecosystem and the role of parthenium pollen grains in the transmission of tobacco streak virus (TSV) infection in cotton

Survey in the cotton fields of Coimbatore and Erode districts confirmed the presence of three different thrips species including, Scirtothrips dorsalis, Scirtothrips oligochaetus, and Frankliniella occidentalis. Their identity was confirmed through morphometric analysis and molecular characterization. Tobacco streak virus (TSV) was detected in the leaves and pollen grains of both parthenium and cotton plants collected from infected cotton fields. The presence of TSV was confirmed through immuno-detection by direct antigen coating enzyme-linked immuno sorbent assay (DAC-ELISA). Further confirmation was accomplished by reverse transcriptase polymerase chain reaction (RT-PCR) using TSV coat protein-specific primers. Other than parthenium, weed plants in the cotton field such as Trianthema portulacastrum, Boerhavia diffusa, and Amaranthus sp. were also confirmed for TSV infection through RT-PCR. Parthenium hysterophorus plants acts as a silent carrier of TSV and they occasionally produced symptoms. Among all the randomly collected thrips samples, two pooled samples were detected positive for TSV through RT-PCR.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02967-6.

Molecular characterization and pathogenicity analysis of prunus necrotic ringspot virus isolates from China rose (Rosa chinensis Jacq.)

Prunus necrotic ringspot virus (PNRSV) is a viral pathogen with worldwide distribution, infecting many commercial fruit trees and ornamental plants. So far, the correlation between PNRSV infection and China rose mosaic disease has not been studied. Rose mosaic disease is characterized by severe symptoms, including mosaic, line pattern, and ringspot. Six viruses that were potentially associated with mosaic disease, including PNRSV, were tested in China roses. Only PNRSV was detected in China roses showing mosaic disease, and asymptomatic samples tested negative for this virus. This result was confirmed by small RNA sequencing, but rose leaf rosette-associated virus and rose spring dwarf-associated virus were also identified in both samples with mosaic disease and asymptomatic samples. This implied that PNRSV might be associated with China rose mosaic disease. Full genome sequences of two PNRSV isolates were determined, and the RNA1, 2 and 3 segments were found to be 3,332, 2,594 and 1,951 nucleotides (nt) in length, respectively. The three RNA segments shared 88.7-89.1% nt sequence identity in the 3'UTR, while RNA2 and RNA3 shared 98.2-99.4% identity. The higher variability in RNA1 suggests that it might have been under greater selection pressure. Phylogenetic analysis showed that the two PNRSV isolates clustered in group PV-32. Full-length infectious cDNA clones of PNRSV from China rose were constructed and used to agroinfiltrate cucumber seedlings. The inoculated cucumber leaves showed yellowing, chlorotic spots, necrosis, dwarfing, and decline at 23 to 39 days post-inoculation, demonstrating the virulence of the PNRSV isolate from China rose. These data lay a foundation for determining the molecular mechanism of rose mosaic disease caused by PNRSV.

Role of Thrips palmi and Parthenium hysterophorus pollen in active spread of tobacco streak virus in the cotton ecosystem

Tobacco streak virus incidence in the cotton field, cv.CO14 at Department of Cotton, Tamil Nadu Agricultural University (TNAU), Coimbatore, India was nearly 36.50 %. Cotton plants infected with TSV exhibits different types of symptoms, including necrotic spots, lesions, mosaic, purplish necrotic rings, square drying, veinal necrosis and drying of terminal shoots. The highly prevalent thrips species in this cotton ecosystem was established as Thrips palmi (60.00 %) by morphological (ESEM) and molecular methods (RT-PCR using mtCOI primers). The density of the alternate weed host, Parthenium hysterophorus, was 15.05 plants per m² in these fields. Association of Thrips palmi with Parthenium was confirmed, when observed under environmental scanning electron microscope (ESEM), Parthenium pollen grains (i.e., average size @ 15000X =12.94 μm) were found adhering to its body. Molecular studies through RT-PCR confirmed the presence of TSV in the leaves and pollen grains of symptomatic and symptom-free Parthenium plants collected from the cotton field (cv. CO14). Therefore, the combined role of Thrips palmi and the Parthenium pollen grains in the transmission of TSV was examined; acquiring of TSV and its presence in the body of Thrips palmi instars and adults after 72 h of AAP was convincingly demonstrated using RT-PCR, NASH and qPCR. However virus acquired thrips could not transmit the virus. Pollen from TSV infected Parthenium plants when dusted on cotton (ANKUR 2110) seedlings along with virus acquired or non-acquired thrips led to symptom development 22 days after sowing. From the study it is evident that thrips only facilitate the movement of TSV borne pollen grains, and thereby contributing to active spread of the virus.

Rapid detection of Tobacco streak virus (TSV) in cotton (Gossypium hirsutum) based on Reverse Transcription Loop Mediated Isothermal Amplification (RT-LAMP)

Tobacco Streak Virus (TSV) belongs to the genus Ilarvirus of the family Bromoviridae an emerging pathogen posing threat to the crop species worldwide. Identification of symptoms due to TSV infection by visual observation of plants often results in misdiagnosis as symptoms produced by this virus can match with those reflecting physiological and nutritional disorders affecting cotton. Development of diagnostic tools with rapidity will have immense role to play in detection and management of the emerging virus. The protocol for rapid diagnosis of TSV infected samples by using Reverse Transcription-Loop Mediated Isothermal Amplification (RT-LAMP) was optimised and this is the first report of its use for diagnosis of TSV on cotton and Soybean. The colorimetric detection for diagnostic simplicity of amplified RT-LAMP product by using different dyes lead to enhanced applicability of this technique. The RT-LAMP diagnostic tool can be utilized not only for laboratory research but also for quarantine and field diagnosis of this important emerging pathogen affecting cotton.

Complete genome sequence and phylogenetic relationships of tobacco streak virus causing groundnut stem necrosis disease in India

Tobacco streak virus (TSV, genus Ilarvirus family Bromoviridae) is known to cause stem necrosis disease (SND) in groundnut (Arachis hypogaea) since 2000 in Southern India. The TSV isolate infecting groundnut so far has not been characterized based on the complete genome sequence. In this study, TSV was isolated from a naturally infecting groundnut plant in Kadiri, the hot-spot of the SND in southern India. During the Kharif season of 2014, groundnut plants in an experimental field were affected with chlorosis and necrosis in leaf, stem and buds. The cent percent of the 48 samples with these symptoms collected from the field tested positive for TSV in ELISA samples in this context. One isolate, GN-Kad was established from a single lesion on cowpea cv. C-152 through successive sap inoculation. Cloning and sequencing of coat protein gene (717 nucleotides) of the isolate showed high sequence identity (98-99%) with the TSV isolates reported from different crops in India. The isolate produced local necrotic rings or veinal necrosis following sap inoculation to cowpea (cultivars C-152, Pusa Komal, Pusa Sukomal and Krishi Kanchan), French bean and sunflower; whereas, it produced systemic chlorotic mottling symptoms in Nicotiana benthamiana. The three segments of the virus genome (RNA 1, RNA 2 and RNA 3) contained 3523, 2903 and 2232 nucleotides, respectively. The overall genome sequence (8639 nt) of the present isolate shared 77-99% of nucleotide sequence identity with that of the other seven isolates reported from Australia, India and USA. The GN-Kad shared very close phylogenetic relationship with the okra and pumpkin isolates reported from India. The present report is the first comprehensive study of the molecular characterization of TSV associated with the stem necrosis disease of groundnut.

Tropical food legumes: virus diseases of economic importance and their control

Diverse array of food legume crops (Fabaceae: Papilionoideae) have been adopted worldwide for their protein-rich seed. Choice of legumes and their importance vary in different parts of the world. The economically important legumes are severely affected by a range of virus diseases causing significant economic losses due to reduction in grain production, poor quality seed, and costs incurred in phytosanitation and disease control. The majority of the viruses infecting legumes are vectored by insects, and several of them are also seed transmitted, thus assuming importance in the quarantine and in the epidemiology. This review is focused on the economically important viruses of soybean, groundnut, common bean, cowpea, pigeonpea, mungbean, urdbean, chickpea, pea, faba bean, and lentil and begomovirus diseases of three minor tropical food legumes (hyacinth bean, horse gram, and lima bean). Aspects included are geographic distribution, impact on crop growth and yields, virus characteristics, diagnosis of causal viruses, disease epidemiology, and options for control. Effectiveness of selection and planting with virus-free seed, phytosanitation, manipulation of crop cultural and agronomic practices, control of virus vectors and host plant resistance, and potential of transgenic resistance for legume virus disease control are discussed.

The N-terminal region containing the zinc finger domain of tobacco streak virus coat protein is essential for the formation of virus-like particles

Tobacco streak virus (TSV), a member of the genus Ilarvirus (family Bromoviridae), has a tripartite genome and forms quasi-isometric virions. All three viral capsids, encapsidating RNA 1, RNA 2 or RNA 3 and subgenomic RNA 4, are constituted of a single species of coat protein (CP). Formation of virus-like particles (VLPs) could be observed when the TSV CP gene was cloned and the recombinant CP (rCP) was expressed in E. coli. TSV VLPs were found to be stabilized by Zn(2+) ions and could be disassembled in the presence of 500 mM CaCl2. Mutational analysis corroborated previous studies that showed that an N-terminal arginine-rich motif was crucial for RNA binding; however, the results presented here demonstrate that the presence of RNA is not a prerequisite for assembly of TSV VLPs. Instead, the N-terminal region containing the zinc finger domain preceding the arginine-rich motif is essential for assembly of these VLPs.

Comparative reaction of popular high yielding spanish and virginia bunch groundnut varieties to Tobacco streak virus

Reaction of five spanish (JL 24, TMV 2, Kadiri 6, Kadiri 9 and Anantha) and a virginia (Kadiri 7 Bold) groundnut cultivars was studied against Tobacco streak virus (TSV) by sap inoculation using different age group of plants [7-84 days after sowing (DAS)]. Among different cultivars, incubation period varied from 4 to 28 days and high incubation period recorded in Kadiri 7 Bold. The percent infection decreased with increase in the age of the plants in all the cultivars as it ranged up to 100 % in both pre-flowering (7-21 DAS) and flowering stage (28-63 DAS) plants followed by 50-100 % in maturity stage plants (70-84 DAS) except Kadiri 7 Bold. Similarly, 100 % wilting was observed in pre flowering stage plants against no wilting in maturity stage plants. However, cultivars differed in per cent wilting of flowering stage plants by recording maximum wilting (100 %) in JL24, Kadiri 6 and minimum (25.0 %) in Kadiri 7 Bold. Both localized (necrotic spots, veinal necrosis) and systemic (petiole necrosis, necrotic spots on young leaves, top growing bud and stem necrosis, axillary shoot proliferation, stunting, peg necrosis, pod necrosis, wilting of plant) symptoms induced by TSV were similar among all cultivars without any new symptoms. Prolonged stage of axillary shoot proliferation was observed for the first time in all the cultivars. In maturity stage plants of Kadiri 7 Bold, Kadiri 9 and Anantha, systemic symptoms restricted to leaf and petiole necrosis only. Virus titer varied significantly with the age of plants and inoculum harvest at days post inoculation and least virus titer recorded by Kadiri 7 Bold at all stages of infection. Among different cultivars, Kadiri 7 Bold was least susceptible/tolerant to TSV by registering higher incubation period with less per cent infection, wilt and titer.

Coat protein-mediated transgenic resistance of peanut (Arachis hypogaea L.) to peanut stem necrosis disease through Agrobacterium-mediated genetic transformation

The absence of resistance genes against biotic stresses like Tobacco streak virus (TSV) within compatible peanut germplasm necessitates the deployment of genetic engineering strategy to develop transgenic resistance. Transgenic resistance in peanut (Arachis hypogaea L.) to peanut stem necrosis disease caused by TSV was obtained by transferring coat protein (CP) gene of TSV through Agrobacterium-mediated transformation of de-embryonated cotyledons and immature leaves of peanut cultivars Kadiri 6 (K6) and Kadiri 134 (K134). Integration of the transgene in T1, T2 and T3 generations were confirmed by PCR with gene-specific primers. On the basis of segregation analysis of the PCR amplicons, homozygosity was confirmed in progeny from five transgenic lines. Six transgenic plants from three different single copy transgenic lines homozygous for the transgene were selected for challenge inoculation in T3 generations. The transgenic lines remained symptomless throughout and showed traces or no systemic accumulation of virus indicating the tolerance/resistance to the TSV infection. CP gene expression was observed in transgenic lines by RT-PCR, real-time PCR and ELISA. The findings provide an effective strategy for developing peanut with resistance to peanut stem necrosis disease.

New Experimental Hosts of Tobacco streak virus and Absence of True Seed Transmission in Leguminous Hosts

Of 70 plant species tested, 50 species were susceptible to Tobacco streak virus (TSV) on sap inoculation. Both localized (necrotic and chlorotic spots) and systemic (necrotic spots, axillary shoot proliferation, stunting, total necrosis and wilt) symptoms are observed by majority of plant species. Eleven new experimental hosts were identified viz., Amaranthus blitum var. oleracea (Chaulai sag), Celosia cristata (Cocks comb), Beta vulgaris var. bengalensis (Palak/Indian spinach), Calendula officinalis (Pot marigold), Chrysanthemum indicum, Cosmos sulphurens (Yellow cosmos), Citrullus lunatus (Watermelon), Lagenaria siceraria (Bottle gourd), Coriandrum sativum (Coriander), Hibiscus subderiffa var. subderiffa (Roselle) and Portulaca oleraceae (Little hogweed). Detected groundnut seed infection with TSV for the first time by Direct antigen coated immunosorbent assay (DAC-ELISA) using whole seed. The seed infection ranged from 18.9 to 28.9% among the seeds collected from naturally infected and sap inoculated groundnut varieties (JL 24, TMV 2, Prasuna, Kadiri 6, Kadiri 9, Anantha and Kadiri 7 Bold) belonging to spanish and virginia types. Further, TSV was detected both in pod shell and seed testa and none of the samples showed the presence of TSV either in cotyledon or embryo. Grow-out and bio-assay tests proved the absence of seed transmission in groundnut and other legume crops. Hence, TSV isolate was not a true seed transmission case under Indian conditions in legumes.

Sources of Resistance to Tobacco streak virus in Wild Arachis (Fabaceae: Papilionoidae) Germplasm

Stem necrosis disease caused by Tobacco streak virus (TSV), first recognized in 2000, has emerged as a potential threat to peanut (Arachis hypogaea) in southern states of India. The virus induces severe necrosis of shoots leading to death of the plant, and plants that survive are malformed, with severe reduction in pod yield. All the currently grown peanut cultivars in India are highly susceptible to the virus. Therefore, wild relatives of peanut were evaluated to identify potential sources of resistance to TSV infection. In all, 56 germplasm accessions from 20 wild Arachis spp. in four sections (Arachis, Erectoides, Procumbente, and Rhizomatosae), along with susceptible peanut cultivars (JL 24 and K 1375), were evaluated for resistance to TSV under greenhouse conditions using mechanical sap inoculations. Systemic virus infection, determined by enzyme-linked immunosorbent assay (ELISA), in the test accessions ranged between 0 and 100%. Twenty-four accessions in section Arachis that had 0 to 35% systemically infected plants were retested, and systemic infection was not detected in eight of these accessions in repeated trials in the greenhouse. These are International Crops Research Institute for the Semi-Arid Tropics groundnut (ICG) accession nos. 8139, 8195, 8200, 8203, 8205, and 11550 belonging to A. duranensis; ICG 8144 belonging to A. villosa; and ICG 13210 belonging to A. stenosperma. Even though the resistant accessions had 0 to 100% TSV infection in inoculated leaves, TSV was not detected in the subsequently emerged leaves. This is the first report of TSV resistance in Arachis spp. The eight TSV resistant accessions are cross compatible with A. hypogaea for utilization in breeding for stem necrosis disease resistance.