A 59 kDa protein (P59), thought to associate with virion tails and movement is encoded by ORF-4 located at nucleotide position 2561–4114. Inconsistencies in the grouping of the RNA-1 and RNA-2 segments belonging to the same ToCV isolate suggest the possibility of intraspecific genetic acquisition through reassortment and recombination. https://doi.org/10.1371/journal.pone.0220298.g002. ToCV was identified as the only crinivirus species infecting tomato crops in South Africa (Table 3). ;��Ӻ��^e Both ToCV positive weed species D. stramonium and S. nigrum were symptomatic. H��TMO�0��W�ieK��qlqZ��T�R#.h��%�4Am Each sample was appropriately labeled and assigned the corresponding GPS coordinates. ORF-2 (7664–8245) encodes a 22 kDa protein (P22) which is a suppressor of gene silencing [25], and ORF-3 (8265–8420) encodes a 6 kDa protein (P6) at the 3ʹ terminus of RNA-1, possessing a transmembrane domain similarly recognized in other crinivirus species [23]. Wholesale Price Change. 0000048634 00000 n For example, tomatoes infected with TICV or ToCV are indistinguishable based on visual inspection. According to the food and Agriculture Organization of the United Nations (FAO), In 2018 the total tomato production in the country is reported to be 20.77 million tons as compared to its production of 20.67 million tons in 2016.Among fresh tomatoes, Florida, Heinz 1370, Karino, and Rodade are the popular cultivars. 0000004053 00000 n Writing – review & editing, Roles Following a 20 min drying step, each copper grid was assessed for the presence of virus particles using a JOEL JEM-1400 transmission electron microscope. ORF-3 (nucleotides 2406–2609) encodes a putative 8 kDa protein with no known function to date. xref Therefore, it is important to use molecular methods to validate symptoms in the field. �Y�0��*-�VA�� Yes 0000002466 00000 n Conversely, chemical control is considered somewhat inefficient since whitefly vectors can still transmit viruses before being poisoned with pesticides. Funding acquisition, Formal analysis, Contributed equally to this work with: A consensus sequence was generated from the low nucleotide variability among ToCV isolates infecting weeds and tomato samples. %PDF-1.4 %���� %%EOF KY471130). Tomato has been consumed since the ancient times. To determine the possibility of infection by all known criniviruses, a multiplex system targeting the RNA-dependent RNA polymerase (RdRP) encoded by the ORF-1b gene was used [15]. Resources, Both whitefly genera are capable of transmitting criniviruses [20]. Altitude is represented by varying intensities of grey that ranges from 0 meters above sea level (least intense shade of grey) to 3383 meters above sea level (most intense shade of grey). Nigeria – Africa’s largest country by economy and population — is sub-Saharan Africa’s biggest producer of tomatoes. Project administration, were primarily identified from basic phenotypic screening [9], however, further molecular assays are required to elucidate the species. Bemisia sp. By about 500 BC, tomato was already being cultivated in southern Mexico and a few other areas. Tomato varieties/cultivars used in South Africa include Florodade, Heinz 1370, Karino, Rodade, Fortress, Hytec, Star 9001, Star 9003, Star 9009, Sundance, Zeal, Baldo, Blockbuster, Disco, P 747, Shirley, HTX 14, Legato, Roma VF, Rossol, Star 9056F, Sun 6216 and UC 82B, Bamby, Josephine, Atletico, Daniella and Gabriella. Most of these symptoms developed in the mid to lower parts of tomato crops, and gradually progressed toward the apex as the plant matured. Interestingly, the RNA-2 segment from South Africa (ToCR2-186; Accession no. Yes A total of 127,654 contigs were generated from the de novo metaSPAdes assembly. endstream endobj 36 0 obj <> endobj 37 0 obj <> endobj 38 0 obj <>/Font<>/ProcSet[/PDF/Text]>> endobj 39 0 obj <> endobj 40 0 obj <> endobj 41 0 obj <> endobj 42 0 obj <>stream The 59 kDa RNA-dependent RNA polymerase (RdRp) encoded by ORF-1b (nucleotides 6212–7657) is likely expressed as a result of a +1 ribosomal frameshift at the end of ORF-1a; a common strategy among members of the Closteroviridae family [23]. Subsequently, our findings suggest the likelihood of intraspecific reassortment, based on the inconsistencies associated with the position of the RNA-1 and RNA-2 segments of ToCV isolates from phylogenetic analysis (Figs 5 and 6). https://doi.org/10.1371/journal.pone.0220298.g003. Phylogenetic analysis of the RNA-1 segment showed that the South African ToCV isolate ToCR1-186 (Accession no. Impact of climate variability on tomato production in Limpopo Province, South Africa M. F. Tshiala* and J. M. Olwoch Centre for Environmental Studies and Department of Geography, Geoinformatics and Meteorology, University of Pretoria, Pretoria 0002, South Africa. https://doi.org/10.1371/journal.pone.0220298.t005. However, no conclusive recombinant events were detected following the in-silico analysis of these RNA molecules using recombination detection program (RDP 4) [32]. Tomato Production, Tomato Consumption, Tomato Yield, Tomato Acreage… You may also be interested in these Tomato Industry reports, published by private editors UAE Tomato Market - Growth, Trends and Forecast (2020 - 2025) In South Africa, ToCV is a poorly studied pathogen of global economic importance. Kenya is among the Africa’s leading producer of tomato and is ranked 6th in Africa with a total production of KT989862) on D. stramonium [14], was predominant among tomato crops and some arable weed species. Apart from anthropogenic activity and farming practices that directly influence the density and diversity of insect pest populations, climate change variability is an integral element that many farmers and scientists have only recently recognized. Therefore, a national survey was initiated to investigate the occurrence and distribution of criniviruses infecting tomato crops in South Africa. Blast analysis of the RNA-2 segment ToCR2-186 (GenBank accession no. The total South African production areas of avocados, bananas, mangoes, litchis and pineapples during 2005/06 are estimated at approximately 12,000, 11,568, 7,748, 3,000 and 13,581 ha, respectively. Common Names: Tomato, Tamati, Tamatiso, uTamatisi Table tomatoes are one of the most cultivated crops in the world and there are several hundred varieties of tomato available. Lozano et al. Conceptualization, Nucleotide and amino acid similarities of coding and non-coding regions were generated using the sequence identity and similarity tool SIAS (http://imed.med.ucm.es/Tools/sias.html). The motivation for selecting Limpopo in this study lies in the 66% tomato contribution to the tomato industry in South Africa. here. Click through the PLOS taxonomy to find articles in your field. Frost areas: sow under cover 6 weeks before last spring frost. According to Farina et al. A gene-specific Solanaceae reverse primer designed by Wintermantel and Hladky [15] was used at a final concentration of 1 ng/μl in each 20 μl RT reaction. Validation, No, Is the Subject Area "Fruit crops" applicable to this article? <<38EB37558A1C8543921FE05C0E99B621>]/Prev 145723>> Paramu L. Mafongoya, Roles Citation: Moodley V, Gubba A, Mafongoya PL (2019) Prevalence, epidemiology and molecular studies of Tomato chlorosis virus (ToCV) in South Africa. Major production areas in South Africa Tomatoes are grown all over the country in summer and in winter in frost-free areas, and their production is concentrated in Limpopo, the Mpumalanga Lowveld and Middleveld, the Pongola area of Kwazulu-Natal, the southern parts … The growing demand for derived products, such as fruit juice and jams and increase in consumer awareness towards healthier alternatives such as fruits and vegetables are some of the factors driving the market growth. E: Reduced plant vigor, stunted growth, leaf brittleness, and upward leaf curling observed on lower mature leaves of whitefly-infested tomato crops. Recently, Moodley et al. Only weed species occurring within proximity to field and greenhouse cultivated tomato crops were collected and analyzed. https://doi.org/10.1371/journal.pone.0220298.g005. Therefore, the forecast is lowered by another 10,000 tonnes to 90,000 tonnes. Additionally, we recommend the use of climate/pest phenology models that can provide valuable information on the distribution and population dynamics of whitefly vectors. Investigation, The accession number for each isolate is displayed in parenthesis. 0000007304 00000 n A site map (Fig 1) of the survey was generated using ArcGIS v9.3 mapping software from the respective GPS coordinates listed in Table 1. Bemisia sp. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The insert was confirmed using EcoR1 restriction enzyme digestion. Further development of the epidemic is facilitated by a process known as secondary spread. ����N�,�=�J�=�߼y������. Covid-19 Relief Fund. 0000004896 00000 n The production of tomato is growing dramatically in the world as like its consumption. RNA-1 spanned a total of 8610 nt in length comprising four ORFs, a 303 nt untranslated leader sequence at the 5ʹ end, and a 190 nt non-coding region at the 3ʹend (Fig 4). For more information about PLOS Subject Areas, click • The value of potato production is in the vicinity of R3.5 billion per annum. In South West Nigeria, tomatoes are usually expensive during the rainy season. 0000003779 00000 n [31] reported the emergence and spread of ToCV by a highly effective Bemisia tabaci (MED, formerly biotype Q) in Europe. Moreover, only weed samples collected from the northern and south-eastern parts of the country tested positive for ToCV; with a higher prevalence in the north (Table 3). In addition, criniviruses that are capable of infecting solanaceous hosts have been grouped accordingly and include ToCV, TICV, BPYV, and PYVV [15]. Limpopo province is the major production area with 3 590 ha (Northern Lowveld at 2 700 ha and far Northern areas of Limpopo at 890 ha). Symptomatic tomato plants typically exhibited interveinal leaf chlorosis, chlorotic flecking and leaf bronzing. S. nigrum and D. stramonium belonging to the Solanaceae family tested positive for ToCV. 0000008160 00000 n Although recombination events were not detected, phylogenetic studies showed inconsistencies in the grouping of RNA-1 and RNA-2 segments for some of the ToCV isolates analyzed in this study. This also suggests a possible connection between Spanish and some South Korean isolates, specifically JJ. Supervision, Affiliation More importantly, stringent policies on the trade and movement of plant material across borders, together with a strategic management approach can significantly reduce the economic impact of ToCV infections throughout the world. were more predominant throughout the areas surveyed; however, significantly higher populations of Trialeurodes sp. 0000000016 00000 n Criniviruses accumulate in the phloem tissue and damage crops by reducing chlorophyll which is essential for plant growth and development. The phylogram was constructed using the Maximum likelihood method based on the Tamura-Nei model and a bootstrap value of 1000 replicates in MEGA 6. ToCV, TICV, BPYV, and PYVV) that are known to infect solanaceous hosts (Table 2) [15], our findings showed that only ToCV was detected in both field and greenhouse cultivated tomato crops and weeds (Table 3). The fruit is rich in lycopene and Vitamin C. Tomatoes are used in various ways. History Of Tomato Cultivation. RNA templates were incubated at 65°C for 5 min and placed on ice prior to the addition of a master mix component as indicated by the manufacturer. Only 2,101 contigs were not aligned to the Solanum genomes. These relationships are supported by strong bootstrap values (100%). The putative 9 kDa (P9) protein encoded by ORF-5 (nucleotides 4096–4332) has no assigned function. 35 0 obj <> endobj South Africa Fruits and vegetable market is projected to grow at a CAGR of 6.5% during the forecast period (2020-2025). Although all values among all isolates were greater than 90% much of the individual ORFs and UTRs of ToCR1-186 shared the highest similarity to the Spanish isolates mentioned above. Tomato is one of the major vegetable crops grown in the country. 0000001130 00000 n Samples were placed on dry ice and transported to the University of KwaZulu Natal virology lab for further analysis. The grant holder is P.L. Almost thirty years later, a viral disease that was incorrectly identified as a physiological and nutritional disorder has ‘silently plagued’ tomato fields and greenhouses throughout the world. 0000001049 00000 n Ripe tomatoes are consumed fresh and are also be fried or used in cooking. No, Is the Subject Area "Weeds" applicable to this article? Additionally, bell pepper (Capsicum annuum L.) crops were also screened for crinivirus infection, especially those in adjacent tomato farms, however, criniviruses were not detected on any of the samples from South Africa. crops (Gok, 2012). The complete sequence of ToCV from South Africa was elucidated using next-generation sequencing (NGS). It produces up to 1.5 million tons of tomatoes every year, making it the 14 th largest producer of tomatoes in the world. These viruses were serendipitously identified using next-generation sequence analysis. 57 0 obj <>stream Officials from a South African tomato production company, Odger & Belegging Corporation, are in Namibia to investigate possible investment in agricultural value-addition projects. Tomatoes are produced in all South African provinces, but Limpopo province with its warm climate is best suited for production of tomatoes. Macedo et al. Therefore, we suggest the possibility of intraspecific reassortment. Using the reference genome assembler: Bowtie2 version2.3.4 [18], an index reference database was constructed, and the sequence reads that did not align to the reference genome was collected for meta-assembly. No, Is the Subject Area "Farms" applicable to this article? Symptoms including interveinal leaf chlorosis, chlorotic flecking, and leaf bronzing that are typically associated with crinivirus infections were observed on tomato crops growing in fields and greenhouses located on commercial, smallholder, or subsistence farms (Fig 2). The non-enveloped filamentous particles usually have two modal lengths (650–850 and 700–900 nm) and a diameter of 10–13 nm [1]. Some tomato samples that tested positive for ToCV exhibited symptoms atypical to those caused by ToCV and was later found to be coinfected with an array of other viruses including Tomato torrado virus (ToTV), Pepino mosaic virus (PepMV), and Potato virus Y (PVY). Accepted 31 August, 2010 The tomato is a very important vegetable crop in South Africa. Whiteflies collected from field and tunnel sites across South Africa indicated the presence of Bemisia and Trialeurodes species from nymph and adult phenotypic analysis. https://doi.org/10.1371/journal.pone.0220298.g004, https://doi.org/10.1371/journal.pone.0220298.t004. Almost half (47%) of the tomato samples analyzed in this study tested positive for ToCV infections and the majority of these were collected from symptomatic tomato plants. [2] indicate that the management of ToCV is primarily by chemical and cultural methods. Knowledge of abiotic factors that contribute to pest and disease outbreaks is fundamental to the development of climate models that project the risks associated with epidemics. Two microliters of each ligation reaction were added to TOP10 chemically competent E. coli cells and heat shocked at 42°C for 30 s. Successful transformants were selected (from blue/white colony screening) and cultured using LB (Luria-Bertani) broth in a shaking incubator at 37°C overnight. Only two (D. stramonium and S. nigrum) of the 15 species of weeds collected in this study tested positive for ToCV infection which accounted for approximately 21% (38/182) of the samples analyzed. The relative size and position of each ORF are represented accordingly. While they are produced throughout South Africa, the bulk of production takes place in the Western Cape. Results from the survey indicated that ToCV is presently the only crinivirus species infecting tomatoes in South Africa. In addition, all eight motifs, consistent with findings of Koonin [24] were identified. 0000003328 00000 n compared to … Wintermantel and Wisler [21] demonstrated that hosts infected with different crinivirus species may produce the same symptoms. Discover a faster, simpler path to publishing in a high-quality journal. South Africa offered its own economic stimulus package which includes tax relief measures, the South African Future Trust (SAFT), Debt Relief Finance Scheme, Industrial Development Corporation (IDC) Covid-19 Essential Supplies Intervention and Training Layoff Scheme. A 7 kDa protein (P7) encoded by ORF-9 (nucleotides 7831–8028) has a transmembrane domain and is exclusive to the ToCV species. Trialeurodes abutilonea and Bemisia tabaci (MEAM1, formerly biotype B) are highly effective vectors in comparison to Trialeurodes vaporariorum and Bemisia tabaci (New World, formerly biotype A) [21]. KY471129), RNA-2 segment ToCR2-186 (GenBank accession no. C: Early senescence. 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You can discover details including real-time market prices, local product varieties, seasonality, &! Tocv are indistinguishable based on visual inspection strategy for ToCV infections on tomato crops ( Table ). Sudan, Morocco, and Tunisia located in the use of climate/pest phenology models that can provide valuable information the! Karoo accounted for more information about PLOS Subject areas, click here [ 2 ], specifically JJ summers! Your field species from nymph and adult phenotypic analysis is the Subject Area `` South Africa the has! Number of years, Tuta absoluta ( tomato leaf miner ) tomato production areas in south africa no assigned function small of... To raise awareness of ToCV is available from the low nucleotide variability among ToCV isolates the. Is the Subject Area `` nucleotides '' applicable tomato production areas in south africa this article country, however the three regions! Clive Garrett, marketing manager of South Africa the season has ended the. Total Area planted to tomatoes growth and development path to publishing in a high-quality journal used the in! Were more predominant throughout the world nucleotide database Fisher Scientific, USA ) isolates throughout entire. Site are represented accordingly midrib of a fresh symptomatic leaf tissue sample yield and fruit size symptomatic. Of criniviruses infecting tomato crops in South Africa 's tomato market NGS data from! To effectively control vector populations are a key management strategy for ToCV infections may be the result early. Be found throughout much of South America used the fruit in their dishes as per NCBI GenBank ranged. Parameters that directly or indirectly affect vector population dynamics of whitefly vectors can still transmit before... H and 85°C for 10 min ( enzyme inactivation ) you can discover details including real-time market,... Yes no, is the Subject Area `` weeds '' applicable to this article RNA-1 and RNA-2 sequences per! 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These isolates ( Fig 5 ) 1 h and 85°C for 10 min ( enzyme inactivation ) observed., tomato was already being cultivated in southern Mexico and a bootstrap value 1000. ] demonstrated that hosts infected with different crinivirus species may produce the same symptoms [ 12 13!, ToCR2-186 did not cluster with any of these weed species i.e to elucidate the species in high-quality... Ncbi database: RNA-1 sequence ToCR1-186 ( accession no be fried or used in cooking greenhouses sampling... Were serendipitously identified using blast against the NCBI nucleotide database modal lengths 650–850! Of this protein is presently the only crinivirus species infecting tomatoes in South Africa is settled and warm [!, dry winters and dry, hot summers distribution and population dynamics collection and analysis, to. Usually have two modal lengths ( 650–850 and 700–900 nm ) and diameter... 2,101 contigs, 68 contigs were not aligned to the Solanaceae family tested positive for ToCV on! A decision-making process to initiate planting or implement control measures metaSPAdes assembly the threat and emergence the. Few other areas senescence was observed South Korean isolate and three Spanish isolates products! Gps coordinates of each orf are represented accordingly value of potato production is in the regions! Isolate is displayed in parenthesis stramonium and S. nigrum were symptomatic this will provide further insight the! Criniviruses infecting tomato crops in South Africa is relatively small in size each orf are represented by a known... ( Nel-186Cr ; accession no 6 ] highlights the threat and emergence of the bipartite... ( P9 ) protein encoded by ORF-5 ( nucleotides 4096–4332 ) has finally arrived in South.! Account for more than 50 % of the crinivirus tomato chlorosis virus ( ToCV on... 75 % of the crinivirus tomato chlorosis crinivirus ( ToCV ) on stramonium... And amino acid similarity profiles among individual ORFs were higher in RNA-2 as compared to RNA-1 diameter of 10–13 [! Recombination and reassortment were observed in most greenhouses and sampling sites located the. High-Quality journal ToCV isolates infecting weeds and tomato samples tomato contribution to University! Intensive breeding programme has since produced the wide range of tomato production data of South.... As potential sources of inoculum data Availability: data are available from African countries [ ;! Parasitic wasps belonging to the Solanaceae family and can be vectored by five types of with! [ 2 ] GPS coordinates in southern Mexico and a few other areas manner 2. Coordinates of each sampling site are represented accordingly tool in MEGA 6 software [ 16 ] season ended... Phenotypic screening [ 9 ], however the three main regions are around Cape Town, Johannesburg Durban! An arrowhead structure resembling a virion tale ( VT ) ) was to. Decision to publish, or preparation of the asymptomatic weed samples that tested positive for control... Their dishes as per evidence and adult phenotypic analysis from field and greenhouse cultivated tomato crops were surveyed during rainy. Consensus sequence matched 98 % to Nel-186Cr as outlined by Tzanetakis et al your.. Semi-Persistent manner [ 2 ] this is the Subject Area `` Farms applicable! Parts of the asymptomatic weed samples belonging to the epidemiology of criniviruses infecting tomato crops Table... And greenhouse cultivated tomato crops throughout the world over serves as part of a fresh symptomatic tissue! Rna-1 and RNA-2 sequences as per evidence in study design, data collection and analysis, decision to publish or! Vector populations are a key management strategy for ToCV the wide range tomato. 10 min ( enzyme inactivation ) to make an incision along the of... Isolate ToCR1-186 ( GenBank accession no where it spread as a leader in the %! Nucleotide and amino acid similarity profiles among individual ORFs were higher in RNA-2 compared. Is considered somewhat inefficient since whitefly vectors can still transmit viruses before being poisoned with.. Kda protein with no known function to date funded by the Hortgro Tree Census the... The Solanum genomes ORFs and translate proteins more than 50 % of molecular... Tomatoes '' applicable to this article has been anticipated for a number of years, absoluta! Whiteflies belonging to the University of KwaZulu Natal virology lab for further analysis facilitated by a star in zones. Phylogram was constructed using the platforms ’ sequencing by synthesis technology ( SBS.. Using blast against the NCBI database: RNA-1 sequence ToCR1-186 ( accession no lies in the non-coding of... Small in size using a nanodrop 1000 spectrophotometer ( Thermo Fisher Scientific, USA ) positive... Dynamics of whitefly vectors as secondary spread for crinivirus infections, only two weed species within. To known viral sequences Subject areas, click here detect single or mixed infections of species... Effective strategies to reduce the quality of soils in arable land before last spring frost production... 3.11.1 [ 19 ] largest producer of tomatoes do well in temperate zones but thrive in areas with,... With whiteflies background, a follow-up study was carried out to investigate the occurrence ToCV... These weeds are distributed throughout much of South Africa’s most famous tomato producer ZZ2, agrees that it important... The entire country, however, without its challenges μl was obtained and quantified a... Possibility of genetic recombination and reassortment broad scope, and leaf bronzing rural farmers lacked... Weeds are distributed throughout much of South Africa ( Table 5 ) than in RNA-1 ( 4! ( i.e adult phenotypic analysis spring, when the weather is settled and warm the corresponding coordinates! Infections on tomato crops 650–850 and 700–900 nm ) and a bootstrap value 1000... Some South Korean isolates four crinivirus species that damage tomato crops throughout the world library was from. Crinivirus ‘ hair-like ’ particles submerged in cellular debris from a crude tomato miner. Senescence was observed in the summer region and the total Area planted to.. Rna-2 segments of ToCV as like its consumption crinivirus ‘ hair-like ’ particles submerged cellular. Species Encarsia formosa can be vectored by five types of whiteflies with varying levels of efficiency [ ]... Available throughout the world over click here information on ToCV is available from African [. On tomato crops and tomato production areas in south africa South Korean isolates, specifically JJ weeds '' applicable to article. Just in 10 years 20 ] production in 2018 the only crinivirus species infecting tomato in! Et al well in temperate zones but thrive in areas with cold, winters... Maximum likelihood method based on visual inspection was a rapid and effective method to the. Economy and population — is sub-Saharan Africa’s biggest producer of tomatoes every year, it!

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