Tobacco Ringspot Virus Research Articles

Pest categorisation of non-EU viruses and viroids of Prunus L.

Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Prunus L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of Ilarvirus S1 and Ilarvirus S2, for which very limited information exists, the pest categorisation was completed for 26 viruses and 1 viroid having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative plant propagation techniques, with plants for planting representing the major pathway for long‐distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Prunus seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Apple scar skin viroid, American plum line pattern virus, cherry mottle leaf virus, cherry rasp leaf virus, cherry rosette virus, cherry rusty mottle‐associated virus, cherry twisted leaf‐associated virus, peach enation virus, peach mosaic virus, peach rosette mosaic virus, tobacco ringspot virus and tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact in the EU territory, on which the Panel was unable to conclude, apricot vein clearing virus, Asian prunus virus 1, Asian prunus virus 2, Asian prunus virus 3, Caucasus prunus virus, cherry virus B, Mume virus A, nectarine stem pitting‐associated virus, nectarine virus M, peach chlorotic mottle virus, peach leaf pitting‐associated virus, peach virus D, prunus virus F and prunus virus T satisfy all the other criteria to be considered as potential Union QPs. Prunus geminivirus A does not meet the criterion of having negative impact in the EU. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically the non‐EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non‐quarantine pests.

Pest categorisation of non-EU viruses and viroids of Vitis L.

Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Vitis L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of grapevine virus 101‐14.N.23.9.1/South Africa/2009 for which very limited information exists, the pest categorisation was completed for 30 viruses or viroids having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative propagation techniques, with plants for planting representing the major pathway for long‐distance dispersal and thus considered as the major pathway for potential entry. Depending on the virus, additional pathway(s) can also be seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Grapevine yellow speckle viroid 2, blueberry leaf mottle virus, grapevine Ajinashika virus, grapevine Anatolian ringspot virus, grapevine berry inner necrosis virus, grapevine deformation virus, grapevine fabavirus, grapevine red blotch virus, grapevine stunt virus, grapevine Tunisian ringspot virus, grapevine vein‐clearing virus, temperate fruit decay‐associated virus, peach rosette mosaic virus, tobacco ringspot virus, tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact for the EU territory, on which the Panel was unable to conclude, blackberry virus S, grapevine geminivirus A, grapevine leafroll‐associated virus 7, grapevine leafroll‐associated virus 13, grapevine satellite virus, grapevine virus E, grapevine virus I, grapevine virus J, grapevine virus S, summer grape enamovirus, summer grape latent virus satisfy all the other criteria to be considered as potential Union QPs. Australian grapevine viroid, grapevine cryptic virus 1, grapevine endophyte endornavirus and wild vitis virus 1 do not meet all the criteria evaluated by EFSA to be regarded as potential Union QPs because they are not known to cause an impact on Vitis. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically non‐EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as a potential Union regulated non‐quarantine pests.

Pest categorisation of non-EU viruses and viroids of Cydonia Mill., Malus Mill. and Pyrus L.

Following a request from the EU Commission, the Panel on Plant Health performed a pest categorisation of 17 viruses and viroids, herein called viruses, of Cydonia Mill., Malus Mill. and Pyrus L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These viruses belong to different genera and are heterogeneous in their biology. They can be detected by available methods and are efficiently transmitted by vegetative propagation techniques, with plants for planting representing a major long‐distance spread mechanism and, potentially, a major entry pathway. Depending on the viruses, additional pathway(s) can also be seed, pollen and/or vector transmission. Most of the viruses categorised here are known to infect only one of few related plant genera, but some of them have a wider host range, thus extending the possible entry pathways. Three viruses (apple necrotic mosaic virus, cherry rasp leaf virus, temperate fruit decay‐associated virus) and one viroid (apple fruit crinkle viroid) satisfy all the criteria to be considered as Union quarantine pests. Five viruses (apple green crinkle‐associated virus, blackberry chlorotic ringspot virus, eggplant mottled crinkle virus, tobacco ringspot virus and tomato ringspot virus) and one viroid (apple scar skin viroid), satisfy the criteria to be considered as Union quarantine pests with the possible exception of being absent from the EU territory or having a restricted presence and being under official control. The remaining six viruses (apple geminivirus, apple latent spherical virus, apple‐associated luteovirus, Pyrus pyrifolia cryptic virus, Pyrus pyrifolia partitivirus 2 and Tulare apple mosaic virus) and one viroid (apple hammerhead viroid) were not found to satisfy one or more of these criteria. The Panel highlights that for several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly linked to the absence of data on biology and distribution. Since this opinion addresses specifically the non‐EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as a potential Union regulated non‐quarantine pests.

First evidence of viruses infecting berries in Mexico

The first search for viruses in berries (blackberry, raspberry and blueberry) was conducted in Mexico. In September 2017, 24 berry plants displaying virus-like symptoms were sampled in the main berry-producing areas of Mexico and later analyzed for the presence of 29 different viruses via enzyme linked immunosorbent assay (ELISA) and reverse transcription PCR (RT-PCR). Additionally, virus screening was verified using high throughput sequencing (HTS). As a result of this study, two blackberry plants collected in Los Reyes de Salgado, Michoacan were determined positive for tobacco ringspot virus (TRSV; genus Nepovirus), such plants exhibited yellowing and ringspot on leaves. In contrast, the rest of berry samples tested negative for any other virus. This is the first detection of TRSV or any other virus infecting blackberries in Mexico. Lastly, the sequence diversity of characterized TRSV isolates was investigated using an identity matrix and phylogenetics.

Selection, optimization and characterization of molecular tests for the detection of Tobacco ringspot virus (TRSV)

The aim of the study was to select, optimize and characterize RT‐PCR tests for the detection of Tobacco ringspot virus (TRSV) in post‐entry quarantine. Among five different tests, the Poojari et al. (Journal of Virological Methods 235, 112–118) and Jossey & Babadoost (Plant Disease 90, 1361) conventionnal RT‐PCR tests were chosen and optimized for this purpose. Ten TRSV isolates, 17 healthy plants from the genera Vitis, Prunus and Malus, four other Nepoviruses or Secoviridae isolates and serial dilutions of three TRSV isolates were used for the complete characterization of the optimized tests. In the tested conditions, the Poojari and Jossey & Babadoost tests respectively showed 100% and 95% inclusivity, 100% and 100% exclusivity, 100% and 96.4% analytical specificity, 100% and 100% diagnostic specificity, [10−7; 10−1] and [10−8; 10−2] limit of detection dilution factors (analytical sensitivity), 91.1% and 90.0% repeatability, 90.3% and 91.1% reproducibility and 100% and 100% selectivity. Due to its higher inclusivity, the optimized Poojari test is recommended for the detection of TRSV isolates for post‐entry quarantine purposes, but can also be used for global surveys. The optimized Jossey & Babadoost test showed the best analytical sensitivity, suggesting that combining both tests can further enhance detection.

Survey of grapevine pathogens in Pakistan

Grapevines from 13 vineyards in Pakistan were surveyed for the prevalence of several pathogens. Using RT-qPCR, 257 samples were tested for 19 viruses, phytoplasmas and Xylella fastidiosa. Prevalent viruses were: grapevine virus A (GVA, 47.8%), grapevine leafroll-associated virus 2 (GLRaV-2, 37.3%), grapevine rupestris stem pitting-associated virus (GRSPaV, 36.1%), and grapevine fleck virus (GFkV, 35%). Other viruses detected were: grapevine leafroll-associated virus 1 (GLRaV-1, 2.3%), grapevine leafroll-associated virus 2RG (GLRaV-2RG, 5%), grapevine leafroll-associated virus 3 (GLRaV-3, 7%), grapevine leafroll-associated virus 4 (GLRaV-4) and its strains (5, 6, and Pr, 16.6%), grapevine leafroll-associated virus 7 (GLRaV-7, 4.2%), grapevine fanleaf virus (GFLV, 11.6%), grapevine virus B (GVB, 4.2%), grapevine virus D (GVD, 0.7%), grapevine virus E (GVE, 1.1%), and grapevine Pinot gris virus (GPGV, 1.9%). Mixed infections were detected in 75.9% of samples. Pathogens tested for, but not detected include GLRaV-4 strains 9 and Car, grapevine red blotch virus (GRBV), tomato ringspot virus (ToRSV), tobacco ringspot virus (TRSV), Arabis mosaic virus (ArMV), grapevine virus F (GVF), phytoplasmas and X. fastidiosa. Additionally, 16 samples were analyzed by high-throughput sequencing (HTS) to confirm RT-qPCR results. In this paper we present an extensive survey for grapevine pathogens and thus the first report of GVA, GVB, GVD, GVE, GRSPaV, GFkV, GLRaV-1, GLRaV-2, GLRaV-2RG, GLRaV-3, GLRaV-4, GLRaV-4 strains 5, 6, and Pr, and GLRaV-7 in Pakistan.

Surveys reveal a complex association of phytoplasmas and viruses with the blueberry stunt disease on Canadian blueberry farms

Surveys for phytoplasmas and viruses were conducted during September 2014 and 2015 on highbush blueberry farms in the Région Montérégie, Quebec. Total DNA and RNA were extracted from blueberry bushes showing blueberry stunt (BBS) symptoms and from symptomless blueberry bushes, and utilised as templates for PCR and RT‐PCR assays, respectively. Phytoplasma DNA was amplified with universal phytoplasma primers that target the 16S rRNA, secA and secY genes from 12 out of 40 (30%) plants tested. Based on 16S rRNA, secA and secY gene sequence identity, phylogenetic clustering, actual and in silico RFLP analyses, phytoplasma strains associated with BBS disease in Quebec were identified as ‘Candidatus Phytoplasma asteris’‐related strains, closely related to the BBS Michigan phytoplasma strain (16SrI‐E). The secY gene sequence‐based single nucleotide polymorphism analysis revealed that one of the BBS phytoplasma strains associated with a leaf marginal yellowing is a secY‐I RFLP variant of the subgroup 16SrI‐E. Two viruses were detected in blueberry bushes. The Blueberry Red Ringspot Virus (BRRV) was found in a single infection in the cultivar Bluecrop with no apparent typical BRRV symptoms. The Tobacco Ringspot Virus (TRSV) was found singly infecting blueberry plants and co‐infecting a BBS phytoplasma‐infected blueberry cv. Bluecrop plant. This is the first report of TRSV in the cv. Bluecrop in Quebec. The Quebec BBS phytoplasma strain was identified in the leafhopper Graphocephala fennahi, which suggests that G. fennahi may be a potential vector for the BBS phytoplasma. The BBS disease shows a complex aetiology and epidemiology; therefore, prompt actions must be developed to support focused BBS integrated management strategies.

First Report of Soybean Vein Necrosis Virus Infecting Kudzu (Pueraria montana) in the United States of America

Soybean vein necrosis virus (SVNV) is a virus originally discovered in Arkansas and Tennessee and is currently present in all major soybean-producing states in the United States and Canada (Zhou and Tzanetakis 2013). Studies were carried out to investigate the role of kudzu (Pueraria montana) in SVNV epidemiology. Kudzu is present in millions of acres in the southeastern United States and is known to host at least another soybean-infecting virus, tobacco ringspot virus (TRSV) (Aboughanem-Sabanadzovic et al. 2014; Khankum et al. 2013). Eighty-five samples collected from 15 Mississippi counties during September 2015 were tested for SVNV infections using DAS-ELISA (Agdia Inc, U.S.A.) and three were infected by the virus. Two of the samples displayed mild deformation of young leaves, whereas the third was symptomless. In order to verify the results, virus-specific RT-PCR tests were performed on nucleic acid extracts from all ELISA-positive samples along with three SVNV-free kudzu plants and controls, represented by SVNV-infected and healthy soybeans. A DNA band of 236 bp corresponding to the NSs gene (Zhou and Tzanetakis 2013) was amplified only from the three ELISA-positive kudzu samples and positive controls. The products were directly sequenced in both directions and confirmed to be SVNV-specific as they shared 96 to 99% nt identity with corresponding region of the SVNV reference isolate (GenBank accession no. GU722319). In a greenhouse-based study, first instar larvae of soybean thrips (Neohydatothrips variabilis Beach) were fed on symptomatic soybean for virus acquisition and transferred to eight SVNV-free kudzu seedlings as described (Zhou and Tzanetakis 2013). Leaf and root tissues were randomly collected from virus-inoculated and mock-inoculated kudzu, respectively, at 6 weeks post inoculation. Total nucleic acids were isolated and RT-PCR was performed using primer set SdetF/SdetR (Zhou et al. 2011). Amplification products corresponding to the complete NP gene (834 bp) were obtained in both leaf and root tissues from five inoculated plants and shared 97 to 99% identity with the reference isolate (GenBank accession no. GU722319), whereas there was no amplification from mock-inoculated controls. Those results were further confirmed by dot blot immunoassay with infected plants remaining asymptomatic for at least a month post inoculation. Our findings represent the first report of SVNV infections of kudzu in the U.S.A. and the world. Kudzu is likely to play a role in the epidemiology of virus and disease. Furthermore, our results expand the range of pathogens (Asian soybean rust, TRSV) and insects (kudzu bug) that kudzu can sustain, indicating its ecological impact as an invasive species.

Viral Diseases of Crops in Nepal

Viral diseases are the important diseases next to the fungal and bacterial in Nepal. The increase in incidence and severity of viral diseases and emergence of new viral diseases causes the significant yield losses of different crops in Nepal. But the research and studies on plant viral diseases are limited. Most of the studies were focused in viral diseases of rice (Rice tungro virus and Rice dwarf virus), tomato (Yellow leaf curl virus) and potato (PVX and PVY). Maize leaf fleck virus and mosaic caused by Maize mosaic virus were recorded as minor disease of maize. Citrus Tristeza Virus is an important virus of citrus fruit in Nepal while Papaya ringspot potyvirus, Ageratum yellow vein virus (AYVV), Tomato leaf curlJava betasatellite and Sida yellow vein Chinaalphasatellite were recorded from the papaya fruit. The Cucumber mosaic virus (CMV) and Zucchini yellow mosaic potyvirus (ZYMV) are the viral diseases of cucurbitaceous crop reported in Nepal. Mungbean yellow mosaic India virus (MYMIV) found to infect the many crops Limabean, Kidney bean, blackgram and Mungbean. Bean common mosaic necrosis virus in sweet bean, Pea leaf distortion virus (PLDV), Cowpea aphid‐borne mosaic potyvirus (CABMV), Peanut bud necrosis virus (PBNV) in groundnut, Cucumber mosaic virus (CMV). Chili veinal mottle potyvirus (CVMV) and Tomatoyellow leaf curl gemini virus (TYLCV) were only reported and no any further works have been carried out. The 3 virus diseases Soyabean mosaic (SMV), Soybean yellow mosaic virus and Bud blight tobacco ring spot virus (TRSV) were found in soybean.Int. J. Appl. Sci. Biotechnol. Vol 6(2): 75-80

Pest categorisation of Xiphinema californicum.

The Panel on Plant Health performed a pest categorisation of Xiphinema californicum (Nematoda: Longidoridae) for the EU. The nematode is a well‐defined taxon belonging to a group of morphologically similar species called Xiphinema americanum sensu lato. The nematode was described from the USA and is present in some North and South American countries. The nematode is not present in the EU and is regulated by Council Directive 2000/29/EC, listed in Annex I A I as X. californicum Lamberti and Bleve‐Zacheo. It is a polyphagous pest found in soil associated with a number of plant species. As a migratory ectoparasitic species, it punctures the cells of plant roots. X. californicum is in principle able to cause direct damage to plants, but its main damage is caused by vectoring the American nepoviruses: Tobacco ringspot virus (TRSV), Tomato ringspot virus (ToRSV) and Cherry rasp leaf virus (CRLV). Soil is a potential pathway for this nematode for entry into the EU. Moist soil, such as soil attached to plants for planting, increases survival of the nematode. The viruses may persist over prolonged periods inside the nematode and viruliferous nematodes may introduce American nepoviruses. Climatic conditions in the EU are similar to those found in the areas where the pest is currently present. Hosts of the nematode (and of associated viruses) are, e.g. grapes, apples and plums, which are also widely cultivated in the EU. The nematode only moves short distances (around 1 m) but may be spread with soil moving activities. Measures are available to inhibit entry via soil as such. Entry of the nematode with soil attached to plants for planting that are not regulated is possible. X. californicum does satisfy all the criteria that are within the remit of EFSA to assess to be regarded as a Union quarantine pest.

DEVELOPMENT OF A FAST AMPLIFYRP ACCELER8 DIAGNOSTIC ASSAY FOR GRAPEVINE RED BLOTCH VIRUS

Polymerase chain reaction (PCR) is routinely used for the detection of grapevine red blotch virus (GRBV), a virus with a circular single-stranded DNA genome, in grapevine tissue. Since the preparation of purified grapevine DNA is time consuming, a user-friendly AmplifyRP Acceler8 assay was developed to quickly, specifically, and sensitively identify GRBV-infected grapevine samples. The sensitivity of AmplifyRP Acceler8 for GRBV detection is approximately 100 times higher than that of PCR. GRBV is consistently detected by AmplifyRP Acceler8 up to a 10-8 dilution of infected grapevine leaf crude extracts diluted in healthy grapevine leaf crude extracts and nearly 10 copies of plasmid DNA containing a GRBV genomic fragment in a matrix of healthy grapevine leaf crude extracts. The test has no cross reactivity to grapevine tissue, nor to several grapevine-infecting pathogens, including arabis mosaic virus, grapevine fanleaf virus, grapevine fleck virus, grapevine leafroll-associated virus 1, grapevine leafroll-associated virus 2, grapevine leafroll-associated virus 3, grapevine leafroll-associated virus 4 strain 5, tomato 2 ringspot virus, tobacco ringspot virus, Xylella fastidiosa, and Botrytis cinerea. Dried GRBV reaction pellets provided in the AmplifyRP Acceler8 kit contain all the necessary reaction components and are stable for at least 5 weeks at -20°C, 4°C, 22°C, and 37°C, providing convenience for transportation and field application. The AmplifyRP Acceler8 assay generated results consistent with PCR and real-time PCR outputs.

Rapid detection of fifteen known soybean viruses by dot-immunobinding assay

A dot-immunobinding assay (DIBA) was optimized and used successfully for the rapid detection of 15 known viruses [Alfalfa mosaic virus (AMV), Bean pod mottle virus (BPMV), Bean yellow mosaic virus (BYMV), Cowpea mild mottle virus (CPMMV), Cowpea severe mosaic virus (CPSMV), Cucumber mosaic virus (CMV), Peanut mottle virus (PeMoV), Peanut stunt virus (PSV), Southern bean mosaic virus (SBMV), Soybean dwarf virus (SbDV), Soybean mosaic virus (SMV), Soybean vein necrosis virus (SVNV), Tobacco ringspot virus (TRSV), Tomato ringspot virus (ToRSV), and Tobacco streak virus (TSV)] infecting soybean plants in Oklahoma. More than 1000 leaf samples were collected in approximately 100 commercial soybean fields in 24 counties of Oklahoma, during the 2012–2013 growing seasons. All samples were tested by DIBA using polyclonal antibodies of the above 15 plant viruses. Thirteen viruses were detected, and 8 of them were reported for the first time in soybean crops of Oklahoma. The highest average incidence was recorded for PeMoV (13.5%) followed by SVNV (6.9%), TSV (6.4%), BYMV, (4.5%), and TRSV (3.9%), while the remaining seven viruses were detected in less than 2% of the samples tested. The DIBA was quick, and economical to screen more than 1000 samples against 15 known plant viruses in a very short time.

12. タバコ輪点ウイルスにおけるL-乾燥と凍結乾燥保存の比較(昭和61年度第32回凍結及び乾燥研究会研究報告)

12. タバコ輪点ウイルスにおけるL-乾燥と凍結乾燥保存の比較(昭和61年度第32回凍結及び乾燥研究会研究報告)

First Report of Tobacco ringspot virus Infecting an American Hybrid Grape Cultivar in Texas

First Report of <i>Tobacco ringspot virus</i> Infecting an American Hybrid Grape Cultivar in Texas

NATURAL INFECTION OF GLYCINE MAX BY SEVEN VIRUSES BELONGING TO DIFFERENT GENERA IN INDIA

Seventy seven soya bean accessions were screened at the Indian Agricultural Research Institute (IARI) experimental field during kharif season in the months of July to October to determine the prevalence and number of viruses affecting soya bean. Prominent symptoms included yellow mosaic, green mosaic/mottling and necrosis. ELISA, PCR and RT-PCR analysis showed mixed infection of seven viruses (Bean yellow mosaic virus, Blackgram mottle virus, Cowpea mild mottle virus, Cucumber mosaic virus, Groundnut bud necrosis virus, Mungbean yellow mosaic India virus and Tobacco streak virus) in different soya bean accessions. The predominant virus was Mungbean yellow mosaic India virus in 71 accessions followed by Tobacco streak virus infecting 60 accessions. None of the accessions was found to be infected with Tobacco ringspot virus or Soybean mosaic virus. Mixed infection with as many as five viruses (BMoV, CMV, GBNV, MYMIV, TSV) was observed in twelve accessions. Other accessions were infected with one to four viruses in different combination. Our study described the first report of Cucumber mosaic virus and Blackgram mottle virus infecting soya bean under natural conditions in India. Multiple viral infections potentially lead to increased symptom severity, therefore our findings have implications in the management of these viruses affecting soya bean.

Inhibition of Tobacco Ringspot Virus by the Culture Fluid of L-Lysine-α-Oxidase Producing Strain.

A producing strain of an anti-tumor and antiviral enzyme L-lysine-α-oxidase from Trichoderma was cultured using a technological device of G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences (Pushchino). L-lysine-α-oxidase activity in the obtained metabolite concentrate was 5.4 U/ml. We studied the effects of the concentrate of active L-lysine-α-oxidase producer on the highly infectious Tobacco ringspot virus and revealed anti-viral activity of it when enzyme concentration was at least 1.0 U/ml.

Development of tobacco ringspot virus-based vectors for foreign gene expression and virus-induced gene silencing in a variety of plants

We report here the development of tobacco ringspot virus (TRSV)-based vectors for the transient expression of foreign genes and for the analysis of endogenous gene function in plants using virus-induced gene silencing. The jellyfish green fluorescent protein (GFP) gene was inserted between the TRSV movement protein (MP) and coat protein (CP) regions, resulting in high in-frame expression of the RNA2-encoded viral polyprotein. GFP was released from the polyprotein via an N-terminal homologous MP-CP cleavage site and a C-terminal foot-and-mouth disease virus (FMDV) 2 A catalytic peptide in Nicotiana benthamiana. The VIGS target gene was introduced in the sense and antisense orientations into a SnaBI site, which was created by mutating the sequence following the CP stop codon. VIGS of phytoene desaturase (PDS) in N. benthamiana, Arabidopsis ecotype Col-0, cucurbits and legumes led to obvious photo-bleaching phenotypes. A significant reduction in PDS mRNA levels in silenced plants was confirmed by semi-quantitative RT-PCR.

Genome-wide association and genomic prediction identifies associated loci and predicts the sensitivity of Tobacco ringspot virus in soybean plant introductions.

BackgroundGenome-wide association study (GWAS) is a useful tool for detecting and characterizing traits of interest including those associated with disease resistance in soybean. The availability of 50,000 single nucleotide polymorphism (SNP) markers (SoySNP50K iSelect BeadChip; www.soybase.org) on 19,652 soybean and wild soybean plant introductions (PIs) in the USDA Soybean Germplasm Collection allows for fast and robust identification of loci associated with a desired phenotype. By using a genome-wide marker set to predict phenotypic values, genomic prediction for phenotype-unknown but genotype-determined PIs has become possible. The goal of this study was to describe the genetic architecture associated with sensitivity to Tobacco ringspot virus (TRSV) infection in the USDA Soybean Germplasm Collection.ResultsTRSV-induced disease sensitivities of the 697 soybean PIs were rated on a one to five scale with plants rated as one exhibiting mild symptoms and plants rated as five displaying terminal bud necrosis (i.e., bud blight). The GWAS identified a single locus on soybean chromosome 2 strongly associated with TRSV sensitivity. Cross-validation showed a correlation of 0.55 (P < 0.01) to TRSV sensitivity without including the most significant SNP marker from the GWAS as a covariate, which was a better estimation compared to the mean separation by using significant SNPs. The genomic estimated breeding values for the remaining 18,955 unscreened soybean PIs in the USDA Soybean Germplasm Collection were obtained using the GAPIT R package. To evaluate the prediction accuracy, an additional 55 soybean accessions were evaluated for sensitivity to TRSV, which resulted in a correlation of 0.67 (P < 0.01) between actual and predicted severities.ConclusionA single locus responsible for TRSV sensitivity in soybean was identified on chromosome 2. Two leucine-rich repeat receptor-like kinase genes were located near the locus and may control sensitivity of soybean to TRSV infection. Furthermore, a comprehensive genomic prediction for TRSV sensitivity for all accessions in the USDA Soybean Germplasm Collection was completed.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2487-7) contains supplementary material, which is available to authorized users.

Incidence of viruses in highbush blueberry (Vaccinium corymbosum L.) in Serbia

A large-scale survey for highbush blueberry (Vaccinium corymbosum L.) viruses in Serbia was performed from 2011 to 2015. A total of 81 leaf samples from 15 locations were collected and analyzed for the presence of 8 viruses. Serological ELISA assay was performed to determine the presence of: Blueberry scorch virus (BlScV), Blueberry shock virus (BlShV), Blueberry shoestring virus (BSSV), Blueberry leaf mottle virus (BLMoV), Tobacco ringspot virus (TRSV) and Tomato ringspot virus (ToRSV). All samples were tested for the presence of Blueberry red ringspot virus (BRRV) by PCR and for Blueberry mosaic-associated virus (BlMaV) by RT-PCR test. The analyses confirmed the presence of BlMaV in 8 (9.9%) samples and BRRV in 1 (1.2%) sample. No BlScV, BlShV, BLMoV, BSSV, TRSV or ToRSV viruses were detected in any of the analyzed samples.

Assessment of Common Soybean-Infecting Viruses in Ohio, USA, Through Multi-site Sampling and High-Throughput Sequencing

Multi-site sampling was conducted during 2011 and 2012 to assess the scope of virus disease problems of soybean in Ohio, USA. A total of 259 samples were collected from 80 soybean fields distributed in 42 Ohio counties, accounting for more than 90% of major soybean-growing counties in Ohio. A high-throughput RNA-Seq approach was adopted to identify all viruses in the samples that share sufficient sequence similarities with known plant viruses. To minimize sequencing costs, total RNA extracted from up to 20 samples were first pooled to make up regional pools, resulting in eight regional pools per year in both 2011 and 2012. These regional pools were further pooled into two yearly master pools of RNA, and sequenced using the Illumina's HiSeq2000 platform. Bioinformatic analyses of sequence reads led to the identification of signature sequences of nine different viruses. The originating locations of these viruses were then mapped with PCR or RT-PCR. This study confirmed the widespread distribution of Bean pod mottle virus, Soybean vein necrosis virus, Tobacco ringspot virus, and Tobacco streak virus in Ohio. It additionally revealed occasional association of Alfalfa mosaic virus, Bean yellow mosaic virus, Clover yellow vein virus, Soybean mosaic virus, and Soybean Putnam virus with Ohio soybean. This is the first statewide survey of soybean viruses in Ohio, and provides the much-needed baseline information for management of virus diseases of soybean. Accepted for publication 20 May 2016. Published 10 June 2016.