Pest phenology models may be an effective way to reduce vector populations and pesticide applications when coupled with cultural, chemical, and biological practices. Tomatoes are produced in all South African provinces, but Limpopo province with its warm climate is best suited for production of tomatoes. Blast analysis of the RNA-2 segment ToCR2-186 (GenBank accession no. The grant holder is P.L. The phylogram was constructed using the Maximum likelihood method based on the Hasegawa-Kishino model and a bootstrap value of 1000 replicates in MEGA 6. For example, tomatoes infected with TICV or ToCV are indistinguishable based on visual inspection. PCR was performed in 20 μl volumes using a KAPA2G Fast HotStart ReadyMix PCR kit (KAPA Biosystems, USA) containing 0.75 ng/μl of each primer (Table 2), 30 ng of cDNA and 10 ul of KAPA master mix. 0000001310 00000 n Therefore, a national survey was initiated to investigate the occurrence and distribution of criniviruses infecting tomato crops in South Africa. Similarly, ToCR2-186 did not cluster with any of the isolates and formed a unique clade. The European and Mediterranean Plant Protection Organization (EPPO) listed ToCV as a quarantined pathogen in some parts of the world [8]. Apricots do well in temperate zones but thrive in areas with cold, dry winters and dry, hot summers. The total production of subtropical fruit increased by 1,5 %, … ToCV can be vectored by five types of whiteflies with varying levels of efficiency [2]. Data Availability: Data are available from the NCBI database: RNA-1 sequence ToCR1-186 (GenBank accession no. ORFs 1a and 1b translate proteins involved in virus replication. To remove the host sequence reads, the trimmed data were mapped against the reference genome: Solanum lycopersicum strain: Heinz 1706 (accession: GCF_000188115), where the whole genome sequence of Solanum lycopersicum strain: Heinz 1706 was downloaded from NCBI. A 59 kDa protein (P59), thought to associate with virion tails and movement is encoded by ORF-4 located at nucleotide position 2561–4114. Citation: Moodley V, Gubba A, Mafongoya PL (2019) Prevalence, epidemiology and molecular studies of Tomato chlorosis virus (ToCV) in South Africa. PCR products were resolved on a 1.5% agarose gel containing SYBR Safe DNA Gel Stain (Invitrogen, USA). B: Significant reduction in the yield and fruit size in symptomatic crops, however, fruit remain symptomless. ToCV is the most abundant and widespread whitefly-transmitted virus infecting tomato crops in South Africa and results in millions of dollars in crop losses throughout the world. 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. [27] relate to a study in which the CPm of Lettuce infectious yellows virus (LIYV) was linked to vector transmission [28]. Visualization, KT989862) on D. stramonium [14], was predominant among tomato crops and some arable weed species. The isolate of ToCV previously reported from South Africa (Nel-186Cr; Accession no. The putative 9 kDa (P9) protein encoded by ORF-5 (nucleotides 4096–4332) has no assigned function. were observed in most greenhouses and sampling sites located in the North-West province. Data curation, ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/) was used to identify ORFs and translate proteins. According to Farina et al. Criniviruses are exclusively transmitted by whiteflies belonging to the genera Bemisia and Trialeurodes in a semi-persistent manner [2]. Paramu L. Mafongoya, Roles 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. Only 2,101 contigs were not aligned to the Solanum genomes. Yes History Of Tomato Cultivation. Transmission electron microscopy (TEM) showed filamentous ‘hair-like’ virus particles approximately 800–900 nm in length and 10–12 nm wide (Fig 3), typically associated with members of the Closteroviridae family [1; 22]. Both whitefly genera are capable of transmitting criniviruses [20]. Yes See more about Tomato production data of South Sudan open_in_new. Validation, 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). Interestingly, the RNA-2 segment from South Africa (ToCR2-186; Accession no. A leaf dip was performed by gently squeezing the exudate onto a droplet of sterile water. https://doi.org/10.1371/journal.pone.0220298.t005. The fruit is rich in lycopene and Vitamin C. Tomatoes are used in various ways. 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. 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). The province account for more than 50% of the total area planted to tomatoes. Officials from a South African tomato production company, Odger & Belegging Corporation, are in Namibia to investigate possible investment in agricultural value-addition projects. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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). <<38EB37558A1C8543921FE05C0E99B621>]/Prev 145723>> Field observations showed that interveinal leaf chlorosis, chlorotic flecking, and leaf bronzing symptoms typically associated with crinivirus infection of tomatoes [10; 21] occurred more frequently amongst growers in South Africa [9] (Fig 2). The use of high-throughput sequencing was a rapid and effective method to generate the full genome sequence of ToCV from South Africa. The relative size and position of each ORF are represented accordingly. Therefore, the forecast is lowered by another 10,000 tonnes to 90,000 tonnes. Frost areas: sow under cover 6 weeks before last spring frost. Additionally, a comprehensive analysis of the ToCV genome is described. The raw data was trimmed using Trimmomatics version 0.36, (parameters: Leading:14, Trailing:14, sliding window:4:15 minlen:70), where the low-quality sequence regions and Illumina universal adapter sequences were trimmed and removed. Department of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa, Roles Supervision, Affiliation Each sample was lysed in a sterile 1.5 ml microcentrifuge tube containing plastic beads, and 500 μl of lysis buffer, using a BioSpec Mini-Beadbeater-16 high-energy cell disrupter (USA). https://doi.org/10.1371/journal.pone.0220298.g001, https://doi.org/10.1371/journal.pone.0220298.t001. 35 0 obj <> endobj Methodology, A total of 787 tomato samples, and 182 weed samples exhibiting virus-like symptoms in the presence of whitefly populations, as well as asymptomatic leaf tissue, were collected and stored in zip-lock plastic bags. A 29 kDa coat protein (CP) encoded by ORF-6 (nucleotides 4332–5105) encapsidates the major part of ToCV virions whilst the 76 kDa minor coat protein (CPm) encoded by ORF-7 (nucleotides 5111–7120) encapsidates the 5ʹ end and is associated with virion tails and possibly cell-to-cell movement [26]. Resources, In addition, the onset of early senescence was observed. ORF-1 (nucleotides 238–339) encodes a 4 kDa protein that may function as a transmembrane protein because of the large hydrophobic domain [26]. ZZ2 tomatoes are produced in different areas of the Limpopo Province, including Mooketsi, Polokwane, Waterpoort, Pontdrift, as well as near Tshipise along the Limpopo River. 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). The non-enveloped filamentous particles usually have two modal lengths (650–850 and 700–900 nm) and a diameter of 10–13 nm [1]. Although weed samples belonging to six botanical families were assayed for crinivirus infections, only two weed species i.e. Tomato production in this country accounts to 38 percent of all vegetable production in turkey and has about 25,000 acres in greenhouses.70% of turkey tomatoes are consumed locally while 30% is processed. By about 500 BC, tomato was already being cultivated in southern Mexico and a few other areas. All samples were sequenced in the forward and reverse direction at Inqaba Biotec (Pretoria, South Africa) using a 3500xL Genetic Analyzer (Applied Biosystems, USA). Explore detailed information about the global Tomato markets. 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. 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. KY471129) was closely related to the group of Spanish isolates but did not cluster with any of these isolates (Fig 5). 0000002198 00000 n Is the Subject Area "Tomatoes" applicable to this article? Much of their efforts were further hampered by the absence of skilled government extension workers able to bridge the gap between the technical jargon associated with research and farmers. Importantly, these weeds are distributed throughout much of South Africa and may have significantly contributed to the epidemiology of ToCV. In addition, Solanum nigrum (a short-lived perennial shrub occurring throughout South Africa) and Datura stramonium featured in Fig 2D (a category 1b invasive annual shrub species occurring throughout South Africa) tested positive for ToCV infection [14]. The tomato is a very important vegetable crop in South Africa. Methods to suppress vector populations are a key management strategy for ToCV control as outlined by Tzanetakis et al. 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. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Lozano et al. 0000004896 00000 n Covid-19 Relief Fund. Project administration, ORF-1a (5838 nt/1945 aa) located at position 304 to 6141 encodes a 221 kDa multifunctional protein comprising a protease, methyltransferase and helicase domain. Clive Garrett, marketing manager of South Africa’s most famous tomato producer ZZ2, agrees that it is a difficult market at the moment. ���sC�w���~O+�ɖ�_�+�YE�|�k:��N5q�g}�qɌ�&��ey �#�T �[��uny�f��wq:���\���S�l\=��d��m����UXŘ�4&�9�_L��,�����4eAs����O�p*Q��R1˥�(:`� All subsequent aligned ToCV sequences analyzed in this study matched ≥ 99% to Nel-186Cr. Insecticide treatment to control vector populations must be used sparingly and rotated with different active ingredients (AI’s) to minimize treadmill effects. A higher level of consistency was observed in the non-coding regions of RNA-2 (Table 5) than in RNA-1 (Table 4). For more information about PLOS Subject Areas, click On the other hand, climate variability directly influences the level of biotic and abiotic stress in agricultural systems. 0000007304 00000 n Sequences were analyzed using the BLAST tool in MEGA 6 software [16]. 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). 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. Wintermantel and Wisler [21] demonstrated that hosts infected with different crinivirus species may produce the same symptoms. These symptoms may also be mistaken for physiological disorders and pesticide toxicity. In addition, criniviruses that are capable of infecting solanaceous hosts have been grouped accordingly and include ToCV, TICV, BPYV, and PYVV [15]. Cape Town has a Mediterranean climate and South Africa The season has ended in the summer region and the total tonnage is estimated at 40,000 tonnes, as previously. 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