Their role as reservoirs of viral pathogens has had a significant impact on viral epidemiology in many parts of the world. The role of weeds as reservoirs of viral pathogens has significantly influenced viral epidemiology in many parts of the world, including South Africa.
WEED ECOLOGY
Classification of weeds
- Morphology
- Lifecycle
- Habitat
- Origin
- Nature of stem
- Soil pH
- Special Classification
In addition, weeds are known to harbor viral vectors and thus contribute to the persistence of viral diseases in agroecosystems worldwide (Asala et al., 2014).
Weeds in agriculture
Parthenium has an allelopathic effect on surrounding plants, inhibiting plant germination and growth (Kaur et al., 2014). Amaranthus cultivation and consumption is encouraged in Africa to alleviate malnutrition and micronutrient deficiencies (Achigan-Dako et al., 2014).
Effect of climate change on weeds
One such weed is the edible pigweed (Amaranthus spp.) which is said to be one of Africa's most nutritious and widespread leafy vegetables (Achigan-Dako et al., 2014).
IMPORTANT VECTOR-BORNE VIRUSES INFECTING TOMATO CROPS…
- Potato virus Y (PVY)
- Tomato spotted wilt virus (TSWV)
- Tomato yellow leaf curl virus (TYLCV)
- Tomato chlorosis virus (ToCV)
- Tomato torrado virus (ToTV)
PVY isolates have different biological, serological and molecular characteristics, leading to a complex classification of the virus (Janzac et al., 2015). It is the cause of yellow leaf disorders in tomato plants (Orílio et al., 2014).
IMPORTANT INSECT VECTORS OF PLANT VIRUSES INFECTING
Whiteflies
Aphids
It has a large host range, affecting more than 400 species within 40 different plant families (Bass et al., 2014). Successful transmission of some aphid-borne viruses depends on more than just transmission of virions (Whitfield et al., 2015).
Thrips
The green peach aphid (Myzus persicae) is the most important aphid species due to its polyphagy and ubiquitous nature (Figure 1.7b; Przewodowska et al., 2015). Aphid infestations can occur rapidly due to the asexual stage in the aphid life cycle, resulting in increased population growth (Jaouannet et al., 2014).
ROLE OF WEEDS IN VIRUS EPIDEMIOLOGY
Virus infection induces volatile organic compounds (VOCs) in plants that modulate insect vector attraction (Vafaei and Mahmoodi, 2015). Viruses that were not persistently transmitted induced anti-feeding compounds, which caused rapid movement of vectors to the next crop after virus acquisition (Carmo-Sousa et al., 2014).
DETECTION OF VIRUSES
The innovative next-generation sequencing (NGS) platforms offer relatively high throughput potential compared to previous single-analyte microarrays (Lefterova et al., 2015). The short reads are aligned and reassembled according to a reference genome, resulting in the complete sequence of the original nucleic acid (Fig. 1.8D and 1.8E; Roy et al., 2016).
CONTROL OF WEEDS IN AGRICULTURE
Commercially, there are several NGS platforms available, including Roche's 454, Illumina's Genome Analyzer, ABI's SOLiD and Heliscope from Helicos (Magi et al., 2010). Some cover crops have an allelopathic effect on certain weed species, thereby reducing the occurrence of weeds in crop fields (Mhlanga et al., 2016).
CONCLUSION
Possible strategies proposed to improve the problem of weed management are biological means and the use of cover crops among other cultural practices. It provides adequate weed management, especially when used in rotation with the main crop, however, careful monitoring is required throughout the proposed period that the cover crops will be used.
One-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) for detection of Tomato torrado virus. Weed species in tomato production and their role as alternative hosts of the Tomato Spotted Wilt virus and its vector Frankliniella occidentalis. Transmission of Tomato Yellow Leaf Curl Virus by Bemisia tabaci influenced by sex and biotype of whitefly.
Sequence characterization, molecular phylogeny reconstruction, and recombination analysis of large RNA tomato spotted wilt virus (Tospovirus: Bunyaviridae) from the United States.
INTRODUCTION
The density and distribution of weeds in South Africa highlights their role in viral epidemiology. It is well known that weeds serve as alternative hosts of viral diseases, but research on the impact this has on viral ecology and epidemiology is often neglected (Mubin et al., 2009). Weeds play an integral role in virus epidemiology as reservoirs of viral pathogens and by acting as initial sources of viral inoculum (Thresh, 2003).
Consequently, this provides initial sources of viral infections which can be transmitted by insect vectors to neighboring field crops.
MATERIALS AND METHODS
- Field survey
- Identification of weed species sampled
- Nucleic acid extraction
- RT-PCR, PCR of total nucleic acid and Crinivirus multiplex
- ELISA
- TSWV
- PVY
- Phylogenetic analysis
Total RNA and DNA were extracted from symptomatic weed leaf material using the Quick-RNATM MiniPrep Kit (Zymo Research, USA) and Quick-DNATM Universal Kit (Zymo Research, USA), respectively, according to the manufacturer's instructions. RT was performed using the RevertAid First Strand cDNA Synthesis Kit (Thermo Scientific, USA) according to the manufacturer's instructions. Positive PCR amplicons were purified using the QIAquick® Gel Extraction Kit (Qiagen, Germany) according to.
The amplified nucleotide sequences were analyzed and aligned using the Molecular Evolutionary Genetics Analysis (MEGA 6; Tamura et al., 2013) software and Clustal W.
RESULTS
- Field assessment
- RT-PCR, PCR and multiplex RT-PCR
- DAS-ELISA and TAS-ELISA of TSWV and PVY
- Phylogenetic analysis
The results corresponded to the visual assessment of yellow color development in the positive samples (data not shown). The sequence of the PVY isolate did not show any genetic diversity and clustered within an African subgroup of PVY lineage (Fig. 2.3). In contrast, the sequences of ToTV and both TSWV isolates did not cluster with either of the parental ToTV and TSWV isolates.
Phylogenetic analysis of the TSWV isolates (TOSP-186 and LAV10) together with the high bootstrap value indicates that these isolates are the same (Figure 2.6).
DISCUSSION
The high bootstrap value between these isolates suggests that they may be the same isolate or very closely related genetically (Fig. 2.3). Therefore, the increased vector population observed on weed and tomato crops can be attributed to the elevated temperatures recently observed in South Africa. Interestingly, even though whiteflies are known to infest more than 600 different plant species, they have shown a clear affinity with the families Asteraceae, Compositae, Cruciferae, Cucurbitaceae, Euphorbiaceae, Fabaceae, Labiatae, Leguminosae, Malvaceae and Solanaceae (Shah et al. , 2015). ).
Due to the paucity of available information on non-potato PVY strains, a more extensive characterization of the isolate identified in this study was performed.
CONCLUSION
Furthermore, it has been found that warmer climates can also contribute to increased vector populations (Broadbent, 2013). Alternatively, it is possible that a recombinant PVYC strain with cleaved PVYO-type RNA fragments in the coat protein region could be present in the P.
Overcoming host- and pathogen-mediated resistance in tomato and tobacco cards against the M RNA of Tomato Spotted Wilt virus. The NSs protein of Tomato Spotted Wilt virus is required for persistent infection and transmission by Frankliniella occidentalis. Evidence of a resistance-breaking strain of Tomato Spotted Wilt virus arose from a natural reassortment between two evolutionarily distinct isolates.
The movement protein NSm of Tomato Spotted Wilt Tospovirus (TSWV): RNA binding, interaction with the TSWV N protein and identification of interacting plant proteins.
INTRODUCTION
The S(+) strand encodes a nonstructural protein (NSs) associated with the repression of gene silencing, and the S(−) encodes the nucleocapsid (N) protein (Plyusnin et al., 2012). However, resistance-breaking strains have emerged in many parts of the world (Margaria et al., 2015). Molecular studies of the TSWV genome are a crucial step in understanding the molecular mechanism of TSWV resistance (Moyle et al., 2016).
Since then, TSWV has been detected on tomato and Amaranthus thunbergii has been found to be a new host of TSWV in South Africa (Chapter 2; section 2.4.2).
MATERIALS AND METHODS
- Bioassay
- Virus isolate
- Sample preparation
- Next-generation sequencing and data analysis
- Sequence analysis and phylogeny of TSWV
- Recombination analysis
The complete genome sequences of the South African isolate of TSWV have been deposited in the GenBank nucleotide database. Nucleotide and amino acid sequences of the NSm ORF were aligned using Clustal W on MEGA 6 to determine possible point mutations characteristic of TSWV resistance-breaking isolates. Recombination events of the whole LK-1 genome sequence were identified using the Recombination Detection Program 4 (RDP4) software with default settings (Martin et al., 2015).
The L, M, and S segment sequences of LK-1 were used in combination with the isolates in Table 3.1.
RESULTS
- Bioassay
- RNA quality assessment and Next-generation sequencing
- TSWV genome organisation
- Sequence and phylogenetic analysis
- Recombination analysis
The nucleotide and amino acid composition of LK-1 was consistent with other TSWV isolates (Table 3.4; 3.5). The phylogenetic relationships of the LK-1 TSWV isolate compared to other global TSWV isolates differed for each ORF. The ORF RdRp (L segment) of isolate LK-1 did not cluster with any of the parental TSWV isolates (Figure 3.1).
No recombination events were observed on the L and M segments when tested with parental and recombinant TSWV isolates (data not shown).
DISCUSSION
The TSWV isolates detected in this study were identified in the eastern part of the country (Chapter 2; Section 2.4.2). Phylogenetic analysis of LK-1 using complete sequences of the RdRp ORF showed genetic diversity, as RdRp did not form a cluster with any of the parental TSWV isolates (Fig. 3.1). It was noted that the majority of recombination events for all the tested isolates occurred at the same time (Fig. 3.7).
Most recombination events on the S segment occurred between 1383–1711 nt, which is part of NS's ORF and 5'.
CONCLUSION
The amino acid substitution associated with overcoming the Tsw resistance is unknown at this stage (Debreczeni et al., 2015). However, a recombination event was observed on the S segments when assessed for recombination using other recombinant TSWV isolates (Fig. 3.7). These results suggest that the C-G1 isolate may have been introduced to South Africa through imports from China.
Therefore, the use of molecular analysis will improve the understanding of how TSWV evolves and the rate at which it evolves.
First report of tomato spotted wilt virus infecting butternut squash (Cucurbita moschata Duch.) in Zimbabwe. Population genetic analysis of tomato spotted wilt virus on peanut in North Carolina and Virginia. Analysis of the first complete genome sequence of an Australian tomato spotted wilt virus isolate.
Isolation and molecular characterization of isolates of the Tomato Spotted Wilt Virus (TSWV) occurring in South Africa.
WAY FORWARD
However, examination of amino acid substitutions involved in the breakdown of resistance to Sw-5 showed that the point mutation was not present in the LK-1 isolate. Recombination analysis detected one recombination event on the S segment, which showed a clear regional preference to NS and the 5' untranslated region of the S segment.
