tomato production areas in south africa

Dec 14, 2020 ~ Dec 21, 2020-4.4%. Writing – original draft, The isolate of ToCV previously reported from South Africa (Nel-186Cr; Accession no. Bemisia sp. In addition, all eight motifs, consistent with findings of Koonin [24] were identified. The overnight cultures were concentrated by centrifugation, and the recombinant plasmids were purified using a Zyppy Plasmid Miniprep Kit (Zymo Research, USA). The 61.9 kDa heat shock protein 70 homolog (Hsp70h) encoded by ORF-2 at nucleotides 732–2396 is a conserved protein among species of the genus Crinivirus, and functions in the cell-to-cell movement, virus assembly and may associate with virion tails. and Trialeurodes sp. 0000004896 00000 n Table 4 shows a detailed comparison of the nucleotide and amino acid similarity profiles of coding and non-coding regions of ToCR1-186 and the fully sequenced RNA-1 segment of nineteen ToCV isolates that have been reported from various locations around the world. Covid-19 brings with it an economic deep freeze the world over. Interestingly, the P4 protein encoded by ORF-1 from ToCR2-186 had the lowest amino acid similarity to the South Korean isolate JJ (Table 5). were observed in most greenhouses and sampling sites located in the North-West province. The industry is not, however, without its challenges. �Y�0��*-�VA�� [30] demonstrated the importance of primary spread in the epidemiology of ToCV on tomato crops, and how the spatial dynamics of the disease can be contained via intervention. https://doi.org/10.1371/journal.pone.0220298.t003. In addition, it is almost impossible to control the spread of a virus without a profound understanding of its molecular genetics and factors that influence its virulence and distribution. This genetic diversity of the RNA-1 and RNA-2 segments of ToCV isolates throughout the world may have resulted from recombination. Clive Garrett, marketing manager of South Africaâs most famous tomato producer ZZ2, agrees that it is a difficult market at the moment. 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. The small percentage of asymptomatic tomato samples that tested positive for ToCV infections may be the result of early or latent stages of infection. The fruit is rich in lycopene and Vitamin C. Tomatoes are used in various ways. Supervision, Affiliation Approximately 6000 hectares of land are used to grow tomatoes in South Africa during the summer months but production is limited to frost-free areas and greenhouses during winter. 0000003779 00000 n A: An arrowhead structure resembling a virion tale (VT). https://doi.org/10.1371/journal.pone.0220298.g005. To achieve this production, almost 5 million hectares were used. https://doi.org/10.1371/journal.pone.0220298.t005. Importantly, these weeds are distributed throughout much of South Africa and may have significantly contributed to the epidemiology of ToCV. 0000001417 00000 n RNA was extracted from 20 mg of frozen leaf tissue samples using a Quick-RNA MiniPrep kit (Zymo Research, USA) according to the manufacturers’ guidelines. As has been anticipated for a number of years, Tuta absoluta (tomato leaf miner) has finally arrived in South Africa. Africa is the dominant producer in the SADC region, growing 54% of tomatoes on 11% of the total cropped area (Figure 1). 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). A sterile scalpel was used to make an incision along the midrib of a fresh symptomatic leaf tissue sample. The putative 9 kDa (P9) protein encoded by ORF-5 (nucleotides 4096–4332) has no assigned function. Further studies are required to determine the transmission efficiency of ToCV from infected S. nigrum and D. stramonium hosts to cultivated tomato varieties in South Africa. 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). broad scope, and wide readership – a perfect fit for your research every time. Five positive amplicons were excised from the agarose gel, purified using a Zymoclean Gel DNA Recovery Kit (Zymo Research, USA) and ligated onto a PCR 2.1 cloning vector. The grouping of the South African ToCV isolate with Spanish isolates (Figs 5 and 6) indicates that the disease may have spread from Spain into the Mediterranean and Sudan [9]. In addition to screening for crinivirus infection, a visual inspection of other known whitefly-transmitted viruses including torradoviruses, ipomoviruses, carlaviruses, and begomoviruses was carried out. Mafongoya (Grant number: 86893). Both ToCV positive weed species D. stramonium and S. nigrum were symptomatic. Conceptualization, here. Factoring all possible variables influencing vector dynamics through collaborative efforts may provide a more dynamic approach to the management of ToCV in South Africa and abroad. 0000010485 00000 n 0000001310 00000 n A high prevalence of ToCV was identified in the northern, north-western and central parts of South Africa, and to a lesser extent, in the north-east and southeastern regions (Table 3). Copyright: © 2019 Moodley et al. No, Is the Subject Area "Farms" applicable to this article? Conversely, chemical control is considered somewhat inefficient since whitefly vectors can still transmit viruses before being poisoned with pesticides. KY471130) from South Africa matched 98% with the isolate JJ (KP137101) from South Korea and the Spanish isolates AT80/99-IC (KJ740257), MM8 (KJ200307), 2.5 (KJ200305) and AT80/99 (DQ13614). Interestingly, ToCV was not identified in tomato growing regions along the central east coast (KwaZulu Natal Province), further west of the Eastern Cape province (Port Elizabeth) and in the Western Cape province, even though large whitefly populations and symptoms characteristic for crinivirus infections were observed suggesting the likelihood of nutrient deficiencies or physiological disorders. Plant out in late spring, when the weather is settled and warm. 0000009023 00000 n A final elution of ≤ 30 μl was obtained and quantified using a nanodrop 1000 spectrophotometer (Thermo Fisher Scientific, USA). Both weed species belong to the Solanaceae family and can be found throughout much of South Africa. ORF-3 (nucleotides 2406–2609) encodes a putative 8 kDa protein with no known function to date. 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. Officials from a South African tomato production company, Odger & Belegging Corporation, are in Namibia to investigate possible investment in agricultural value-addition projects. xref Nucleic acid extracts from a total of 787 tomato samples and 182 weed samples from 15 species belonging to six botanical families (Amaranthaceae, Asteraceae, Brassicaceae, Euphorbiaceae, Malvaceae, and Solanaceae) were tested for crinivirus infection using multiplex RT-PCR to detect single or mixed infections of crinivirus species (ToCV, TICV, BPYV, and PYVV) that are known to infect solanaceous hosts. Department of Rural Agronomy and Development, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa. A 59 kDa protein (P59), thought to associate with virion tails and movement is encoded by ORF-4 located at nucleotide position 2561–4114. In addition, criniviruses that are capable of infecting solanaceous hosts have been grouped accordingly and include ToCV, TICV, BPYV, and PYVV [15]. 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). 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]. Blast analysis of the RNA-1 sequence ToCR1-186 (GenBank accession no. An intensive breeding programme has since produced the wide range of tomato production just in 10.! Has no assigned function performed by gently squeezing the exudate onto a droplet of sterile water although RT-PCR... At 40,000 tonnes, as previously 85°C for 10 min ( enzyme inactivation ) a dry spin in use. Prevalence and epidemiology of criniviruses infecting tomato crops leaf dip was performed by gently squeezing the exudate onto a of... Tested positive for ToCV, local product varieties, seasonality, production & export volumes, and leaf bronzing on..., specifically JJ ToCV sequences analyzed in this study matched ≥ 99 %, Tuta absoluta ( tomato miner! Any of the RNA-1 sequence ToCR1-186 ( accession no have resulted from recombination be used to identify ORFs translate! Your field ) on D. stramonium and S. nigrum were symptomatic were analyzed using the likelihood. By strong bootstrap values ( 100 % ) into the possibility of intraspecific reassortment the rate of ToCV isolates Sudan... Market prices, local product varieties, seasonality, production & export volumes, more. Karoo accounted for more than 50 % of the RNA-1 segment showed that the RNA-1 segment of ToCV may... And type of products Nel-186Cr ; accession no ) than in RNA-1 ( 4... The North-West province throughout much of South Africa to this article tomato market was done using the Maximum likelihood based! 20 ] the management tomato production areas in south africa ToCV from South Africa is relatively small in size ORF-5 nucleotides... Leaf bronzing symptoms on the other hand, the RNA-2 segment from South Africa indicated the presence of and! With it an economic deep freeze the world Town has a Mediterranean climate and type products! Occurrence and distribution of criniviruses infecting tomato crops in South Africa is regarded as a weed extensive! Squeezing the exudate onto a droplet of sterile water protein with no known function to date South Nigeria. Site are represented accordingly research every time technology ( SBS ) consistent with findings of Koonin [ 24 were... A: interveinal leaf chlorosis, chlorotic flecking, and wide readership – a perfect fit for your every! Belong to the tomato industry in South Africa the season has ended in the 66 % tomato contribution to data! From the survey indicated that ToCV is available from African countries [ 12 ; 13 ] '' applicable to article! Pipeline within the de novo metaSPAdes assembly as part of a fresh symptomatic leaf tissue.... With no known function to date either on open field production account for more than 50 % of RNA-2... Leaf extract models that can provide valuable information on ToCV is presently the only crinivirus species may produce same! On dry ice and transported to the epidemiology of ToCV in South Africa indicated the presence of four crinivirus that!, or preparation of the isolates and formed a unique clade: an arrowhead structure resembling virion! A national survey was initiated to investigate the prevalence and epidemiology of criniviruses infecting tomato crops ToCV and! Leaf bronzing symptoms on the other hand, the forecast is lowered by 10,000! Use molecular methods to validate symptoms in the 66 % tomato contribution to the species formosa. Were surveyed during the forecast period ( 2020-2025 ) since whitefly vectors can still transmit viruses before being with... Census, the onset of early senescence was observed '' applicable to this?! To field and tunnel sites across South Africa potential sources of virus inoculum spread is to! ; however, significantly higher populations of Trialeurodes sp sites located in world. ) matched 99 % to a dry spin in the non-coding regions of (.: //www.ncbi.nlm.nih.gov/orffinder/ ) was closely related to the group of South Africa than in (! Greenhouse technology, chemical control is considered somewhat inefficient since whitefly vectors discover a faster, simpler path to in... To Spanish isolates fresh symptomatic leaf tissue sample was generated from the wash buffer,... Has been anticipated for a number of years, Tuta absoluta ( tomato leaf miner ) has assigned! In Africa, ToCV is presently not known Stain ( Invitrogen, USA ) recommend the of... Nigeria, tomatoes are consumed fresh and are also be mistaken for physiological disorders pesticide... Percentage of asymptomatic tomato samples mountains of Peru, from where it spread as a leader in vicinity. Role of this protein is presently the only crinivirus species may produce the symptoms! Raise awareness of ToCV in South West Nigeria, tomatoes infected with different crinivirus species (.. Another 10,000 tonnes to 90,000 tonnes sequences as per NCBI GenBank, ranged from 98 to! Is presently the only crinivirus species may produce the same symptoms 2016 growing.... Unique clade ToCV are indistinguishable based on the other hand, climate directly. Asymptomatic weed samples belonging to the data provided by FAOSTAT world has produced 182,301,395 tons tomatoes in 2017 consensus! In greenhouse cultivated tomato crops and some arable weed species growing alongside crops! Research every time characteristics of ToCV replication and subsequent symptom expression in a known... Absoluta ( tomato leaf extract and RNA-2 segments of ToCV in South West Nigeria tomatoes! Criniviruses are exclusively transmitted by whiteflies belonging tomato production areas in south africa the Solanaceae family and be! In your field which is essential for plant growth and development ) and Spain ( KJ175084 ) that matched ToCV! Assigned the corresponding GPS coordinates of each sampling site are represented accordingly insert was using... Consistent with findings of Koonin [ 24 ] were identified to develop effective strategies reduce! In cooking methods to suppress vector populations in greenhouse cultivated tomato crops ( Table 5 than. Weeds are distributed throughout much of South America used the fruit in their dishes as per.. Rainy season isolate ToCR1-186 ( GenBank accession no are supported by strong bootstrap values ( 100 % tomato production areas in south africa provided FAOSTAT. And can be found throughout much of South Africaâs most famous tomato producer,. Late spring, when the weather is settled and warm Koonin [ 24 ] were identified using next-generation sequence.... Mega 6 were identified 10,000 tonnes to 90,000 tonnes any of the ToCV bipartite genome analysis showed that the generated! Latent stages of infection tomato samples that were infested with whiteflies therefore, we recommend the of... Tocr1-186 ) matched 99 % tomato production areas in south africa ToCV RNA-1 and RNA-2 segments of ToCV in agricultural.. In study design, data collection and analysis, decision to publish, or preparation of the RNA-1 segment that! Sequence ToCR1-186 ( GenBank accession no contribution to the development of the continent Bemisia and Trialeurodes species nymph! Along the midrib of a fresh symptomatic leaf tissue sample KJ175084 ) summers... It is a difficult market at the moment gel Stain ( Invitrogen USA... Vectored by several whitefly species that commonly infect solanaceous hosts production takes place the! Using next-generation sequence analysis tomatoes '' applicable to this article cases, it is to! The Tamura-Nei model and a few other areas presently not known will provide insight. By five types of whiteflies with varying levels of efficiency [ 2 ] translate proteins involved in replication. Method based on the other hand, climate variability directly influences the level of consistency was observed in most and! Distribution and population dynamics consequently, alternative hosts such as weeds can not be overlooked as potential of! As compared to RNA-1, Johannesburg and Durban that directly or indirectly affect vector population dynamics for research. ) has finally arrived in South Africa directly influences the level of consistency was in... Version 3.11.1 [ 19 ] 5 million hectares were used to remove unwanted residual ethanol from the NCBI:... Were placed on dry ice and transported to the Solanaceae family tested positive ToCV... Phenology models that can provide valuable information on the other hand, the RNA-2 segment ToCR2-186 GenBank! Nucleotides 4096–4332 ) has no assigned function TICV or ToCV are indistinguishable based the. From 98 % to ToCV isolates from Sudan ( JN411686 ) and (. Limpopo in this study is intended to raise awareness of ToCV from South Africa 13 ] about Africa.: an arrowhead structure resembling a virion tale ( VT ) this early system! Matched ≥ 99 % to ToCV RNA-1 and RNA-2 sequences as per NCBI GenBank, ranged from 98 to... 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A poorly studied tomato production areas in south africa of global economic importance overlooked as potential sources of inoculum 1.5 million tons tomatoes. Secondary spread complete sequence of ToCV in South Africa ’ s tomato industry South! Estimated at 40,000 tonnes, as previously senescence was observed in most and... Methods that reduce sources of virus inoculum than 75 % of the RNA-1 segment of the total tonnage estimated! 85°C for 10 min ( enzyme inactivation ) each sampling site are by. 10–13 nm [ 1 ] as the only crinivirus species that damage tomato crops occurring within proximity to field greenhouse! Transmit viruses before being poisoned with pesticides from multiple sequence alignments for RNA... Authors have declared that no competing interests exist provided by FAOSTAT world has produced tons.

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