Plant viruses infect a wide range of commercially important crop plants and cause significant crop production losses worldwide. Numerous alterations in plant physiology related to the reprogramming ...of gene expression may result from viral infections. While conventional IPM-based strategies have been effective in reducing the impact of several viral diseases, continued emergence of new viruses and strains, expanding host ranges, and emergence of resistance breaking strains necessitate a sustained effort toward the development and application of new approaches for virus management that would complement existing tactics. RNA interference-based techniques, and more recently, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based genome editing technologies have paved the way for precise targeting of viral transcripts and manipulation of viral genomes and host factors. In-depth knowledge of the molecular mechanisms underlying the development of disease would further expand the applicability of these recent methods. Advances in next generation/high throughput sequencing have made possible more intensive studies into host-virus interactions. Utilizing the omics data and its application has the potential to expedite in fast tracking traditional plant breeding methods, as well as applying modern molecular tools for trait enhancement, including virus resistance. Here, we summarize the recent developments in CRISPR/Cas system, transcriptomics, endogenous RNA interference and exogenous application of dsRNA in virus disease management.
Tomato mosaic virus (ToMV), an economically important virus that affects a wide range of crops, is highly contagious, and its transmission is mediated by mechanical means, and through contaminated ...seeds or planting materials, making its management challenging. To contain its wide distribution, early and accurate detection of infection is required. A survey was conducted between January and May, 2023 in major tomato growing counties in Kenya, namely, Baringo, Kajiado, Kirinyaga and Laikipia, to establish ToMV disease incidence and to collect samples for optimization of the reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) assay. A RT-LAMP assay, utilizing primers targeting the coat protein, was developed and evaluated for its performance. The method was able to detect ToMV in tomato samples within 4:45 minutes, had a 1,000-fold higher sensitivity than conventional reverse transcription polymerase chain reaction (RT-PCR) method and was specific to ToMV. Furthermore, the practical applicability of the assay was assessed using tomato samples and other solanaecous plants. The assay was able to detect the virus in 14 tomato leaf samples collected from the field, compared to 11 samples detected by RT-PCR, further supporting the greater sensitivity of the assay. To make the assay more amenable for on-site ToMV detection, a quick-extraction method based on alkaline polyethylene glycol buffer was evaluated, which permitted the direct detection of the target virus from crude leaf extracts. Due to its high sensitivity, specificity and rapidity, the RT-LAMP method could be valuable for field surveys and quarantine inspections towards a robust management of ToMV infections.
The production of sweet potato has the potential to address food insecurity and malnutrition in the context of climate change. However, sustainable production of sweet potato is hampered by poor ...access to quality seed. We assess the level and determinants of farmers’ willingness to pay (WTP) for clean seed among smallholder sweet potato farmers and compare the estimated WTP with the cost of seed multiplication. Data for the paper were collected from 383 sweet potato farmers and 30 sweet potato seed multipliers in Kenya. WTP was estimated using the double bounded contingent valuation method while the determinants of WTP were analysed using an ordered probit regression model. Results show that the mean WTP for clean seed was KES 578.94 (about US$ 5.68) for a 90 kg bag with variations in WTP observed across geographical regions and prior use of clean seed. Results further show that WTP increases with prior use of clean seed and experience in sweet potato production. The net cost of clean seed multiplication was KES. 444.81 (US$ 4.36), which is lower than the estimated WTP. These results suggest that seed multiplication business may be economically viable but this will depend on other transaction costs and establishment of efficient distribution systems.
Cassava is a major crop in Sub-Saharan Africa, where it is grown primarily by smallholder farmers. Cassava production is constrained by Cassava mosaic disease (CMD), which is caused by a complex of ...cassava mosaic begomoviruses (CMBs). A previous study showed that SEGS-1 (sequences enhancing geminivirus symptoms), which occurs in the cassava genome and as episomes during viral infection, enhances CMD symptoms and breaks resistance in cassava. We report here that SEGS-1 also increases viral disease severity in
Arabidopsis thaliana
plants that are co-inoculated with African cassava mosaic virus (ACMV) and SEGS-1 sequences. Viral disease was also enhanced in Arabidopsis plants carrying a SEGS-1 transgene when inoculated with ACMV alone. Unlike cassava, no SEGS-1 episomal DNA was detected in the transgenic Arabidopsis plants during ACMV infection. Studies using
Nicotiana tabacum
suspension cells showed that co-transfection of SEGS-1 sequences with an ACMV replicon increases viral DNA accumulation in the absence of viral movement. Together, these results demonstrated that SEGS-1 can function in a heterologous host to increase disease severity. Moreover, SEGS-1 is active in a host genomic context, indicating that SEGS-1 episomes are not required for disease enhancement.
Cassava mosaic disease is caused by cassava mosaic begomoviruses (CMBs) and can result in crop losses up to 100% in cassava (Manihot esculenta) in Tanzania. We investigated the efficacy of ...chemotherapy and thermotherapy for elimination of East African cassava mosaic virus (EACMV) of Tanzanian cassava. In vitro plantlets from EACMV‐infected plants obtained from coastal Tanzania were established in the greenhouse. Leaves were sampled from the plants and tested to confirm the presence of EACMV. Plantlets of plants positive for EACMV were initiated in Murashige and Skoog (MS) medium. On the second subculture, they were subjected into chemical treatment in the medium containing salicylic acid (0, 10, 20, 30 and 40 mg/L) and ribavirin (0, 5, 10, 15 and 20 mg/L). In the second experiment, EACMV‐infected plantlets were subjected to temperatures between 35 and 40°C with 28°C as the control. After 42 days of growth, DNA was extracted from plant leaves and PCR amplification was performed using EACMV specific primers. It was found that plant survival decreased with increasing levels of both salicylic acid and ribavirin concentrations. In general, plants treated with salicylic acid exhibited a lower plant survival % than those treated with ribavirin. However, the percentage of virus‐free plants increased with an increase in the concentration of both ribavirin and salicylic acid. The most effective concentrations were 20 mg/L of ribavirin and 30 mg/L of salicylic acid; these resulted in 85.0% and 88.9% virus‐free plantlets, respectively. With regard to thermotherapy, 35°C resulted in 79.5% virus‐free plantlets compared to 69.5% at 40°C. Based on virus elimination, ribavirin at 20 mg/L, salicylic acid 30 mg/L and thermotherapy at 35°C are recommended for production of EACMV free cassava plantlets from infected cassava landraces.
LAMP on-site sweetpotato virus detection workflow.
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•LAMP assays were developed to detect the three main sweetpotato viruses.•Unpurified extracts could be used, and results were ...obtained from 5 to 45 minutes.•The sensitivity was higher than RT-PCR and PCR assays.•The assays showed 100 % concordance with standard virus indexing in laboratory.•On-site, in-field testing at different location in Kenya demonstrated high accuracy.
Globally, Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV) occur frequently and in combination cause sweetpotato virus disease (SPVD). Many viral diseases are economically important and negatively impact the production and movement of germplasm across regions. Rapid detection of viruses is critical for effective control. Detection and quantification of viruses directly from sweetpotato remains a challenge. Current diagnostic tests are not sensitive enough to reliably detect viruses directly from the plant or require expensive laboratory equipment and expertise to perform. We developed a simple and rapid loop‐mediated isothermal amplification (LAMP) assay for the detection of SPFMV, SPCSV and begomoviruses related to sweet potato leaf curl virus (SPLCV). Laboratory validation recorded 100 % diagnostic sensitivity for all the three viruses. The LAMP assays were customized for field testing using a lyophilized thermostable isothermal master mix in a ready-to-use form that required no cold chain. The average time to positivity (TTP) was: SPFMV 5−30 min, SPCSV 15–43 min s and begomoviruses 28−45 mins. LAMP on-site testing results were comparable to PCR and RT-PCR confirmatory laboratory tests. The LAMP assay is a powerful tool for rapid sweetpotato virus detection at a reasonable cost and thus could serve as quality control systems for planting materials.
Various modes of edible coating application vary in their coat dispersion and film formation, hence the need to determine the most effective mode of application for cassava. Edible surface coatings ...have been found to be effective in preserving the quality of various food products. However, there are variations in effectiveness among the different coating solutions, hence the need for optimization of the concentrations of the gums used. This study aimed at determining the most efficient coating application method on the cassava postharvest quality. Physiologically mature cassava (variety KME 1) was harvested and divided into seven portions. The various portions were coated using 1.5% xanthan gum, 1.5% xanthan/guar gum, and 2% xanthan/guar gum by both dipping and spraying method. There was no significant difference on the colour, total cyanide, ethylene production, and total phenolic content between the two application methods. The 2% xanthan/guar gum coating showed a significant difference on the dry matter content while the 1.5% xanthan gum coating had a significant difference on the respiration rate and weight loss. The 1.5 xanthan treated roots had a final dry matter content of 72.5% for the sprayed samples and 75.98% for the dipped sample while the 2% xanthan/guar gum treated roots had a final dry matter content of 64.6% and 74.1% for the dipped and sprayed root samples, respectively. The 1.5% xanthan and 2% xanthan/guar gum treated roots showed no significant difference in their action on dry matter content. The 1.5% xanthan/guar dipped and sprayed samples differed significantly on their effect on flesh firmness with final values of 35.4N and 46.1N, respectively, at 20 days after harvest. This study suggested that based on the coating solution and the parameters being observed, there generally was no varying effect of dipping and spraying methods of coating application. The choice of the efficient mode of application to use will depend on other factors such as the easiness of application.
Cassava brown streak disease (CBSD) has a viral aetiology and is caused by viruses belonging to the genus Ipomovirus (family Potyviridae), Cassava brown streak virus (CBSV) and Ugandan cassava brown ...streak virus (UCBSV). Molecular and serological methods are available for detection, discrimination and quantification of cassava brown streak viruses (CBSVs) in infected plants. However, precise determination of the viral RNA localization in infected host tissues is still not possible pending appropriate methods.
We have developed an in situ hybridization (ISH) assay based on RNAscope® technology that allows the sensitive detection and localization of CBSV RNA in plant tissues. The method was initially developed in the experimental host Nicotiana rustica and was then further adapted to cassava. Highly sensitive and specific detection of CBSV RNA was achieved without background and hybridization signals in sections prepared from non-infected tissues. The tissue tropism of CBSV RNAs appeared different between N. rustica and cassava.
This study provides a robust method for CBSV detection in the experimental host and in cassava. The protocol will be used to study CBSV tropism in various cassava genotypes, as well as CBSVs/cassava interactions in single and mixed infections.
In the context of climate change and its effects, production and consumption of orphaned crops such as sweet potato has been promoted as alternative food diets in sub-Saharan Africa (SSA). However, ...sustainable production of these crops is hampered by poor access to seed. This paper assesses seed security among smallholder sweet potato producers in Kenya and its implications on household food security. Data for the paper were collected through a survey of 383 sweet potato producing households in Kirinyaga and Homabay Counties of Kenya. Seed security was measured through an adaptation and modification of the FAO's seed security framework based on four parameters – availability, accessibility, varietal suitability and seed quality. We measured food security using the Food Insecurity Experience Scale (FIES). Data were analysed using descriptive statistics and poisson regression models. Results show that our respondents experienced mild seed insecurity with a score of 4.8 out of a possible maximum score of 12. Results further show that seed security positively and significantly influenced food security and seed access is the most critical element influencing food security. The regression results also show that wealth index, distance to the market, income and education level positively and significantly influence household food security. Our findings underscore the importance of promoting seed security for orphaned crops, especially among the low-income households as a mechanism for improving household and by implication national food and nutrition security.
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•Orphan crops as a strategy for enhancing food security.•Poor quality planting material dominating among sweet potato farmers.•Seed security assessment metrix for vegetative propagated crops.•Seed security is positively associated with food security.
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