African Cassava Research Articles

An Alarming Eastward Front of Cassava Mosaic Disease in Development in West Africa

Begomoviruses are a major threat to cassava production in Africa. Indeed, during the 1990s, the emergence of a recombinant begomovirus (East African cassava mosaic virus-Uganda, EACMV-Ug) resulted in crop devastation and severe famine in Uganda. In 2023, during a pre-survey of cassava farms at Forécariah, South-West Guinea, 22 samples showing peculiar cassava mosaic disease (CMD) symptoms were collected, and subsequent laboratory analysis confirmed the presence of EACMV-Ug in the samples. Deep analysis of DNA-A and DNA-B of the EACMV-Ug isolates from Guinea indicated that they are similar to those associated with the severe CMD epidemic in Uganda in the 1990s. Therefore, a country-wide survey was conducted throughout Guinea in April 2024 to evaluate the extent of the spread of EACMV-Ug in the country and to collect critical CMD epidemiological data. Findings showed a high whitefly population in Lower Guinea averaging 17 per plant; however, the data suggest a spread of EACMV-Ug via infected cuttings. High CMD incidence was found in Lower Guinea and Forest Guinea, whereas the highest CMD severity was observed in Forest Guinea (2.70 ± 0.06) and the lowest CMD severity was found in Middle Guinea (2.20 ± 0.05). Several cases of double and triple infections involving African cassava mosaic virus, East African cassava mosaic virus, East African cassava mosaic Cameroon virus, and EACMV-Ug were observed. EACMV-Ug was detected throughout Guinea, as well as from samples collected in 2022 in Kambia (Sierra Leone). The 63 accessions cultivated in Guinea that were assessed in this study were found susceptible to at least one of the viruses cited above. This study alerts us to an alarming situation in development in West Africa and provides scientific evidence to guide the rapid response needed to contain and stop the progression of EACMV-Ug in West Africa.

Analysis of inbreeding depression in five S1 Cassava families of elite varieties at the seedling nursery and clonal evaluation trial stages.

Background Cassava is an outcrossing, highly heterozygous plant that is reported to suffer from inbreeding depression. However, unraveling recessive traits and exploring additive genes would require a limited level of inbreeding for the genetic improvement of cassava. Method The impact of inbreeding depression (ID) on agronomic and biotic tolerance of cassava was evaluated using the S1 progenies of five African cassava varieties (TMS 30572, TME 419, TMS 98/0505, TMS 01/1371, and TMS 98/0002) at the seedling and clonal evaluation stages. Results At both trial stages, the effects of ID were severe on average performance of fresh root yield and fresh foliage yield; moderate on harvest index, dry matter content, vigor, and tolerance to cassava mosaic disease, cassava bacterial blight, and cassava anthracnose diseases; and less severe on plant height. Further examination of S1 families using molecular markers showed varying levels of heterozygosity at several loci across the genome. In addition, the degree of heterozygosity and ID varied by the S1 family. The TMS 01/1371 family showed the lowest degree of heterozygosity and ID on the average performance of different agronomic attributes, indicating that inbreeding may be strategically explored in this family to increase genetic gain and identify useful recessive traits. Lastly, the observed depression from inbreeding was higher in seedling evaluation than in clonal evaluation trials for fresh root yield, fresh foliage yield, harvest index, and dry matter content. Conclusion S1 individuals showing relatively low heterozygosity based on SNP data were selected as parents to advance genetic gain in cassava. Generally, reduced heterozygosity was prominent in traits with severe ID impacts on average phenotypic performance. Our results highlight the relative importance of exploring non-additive genetic effects and transgressive segregations for favorable allele combinations in cassava improvement.

Geminivirus C4/AC4 proteins hijack cellular COAT PROTEIN COMPLEX I for chloroplast targeting and viral infections.

Geminiviruses infect numerous crops and cause extensive agricultural losses worldwide. During viral infection, geminiviral C4/AC4 proteins relocate from the plasma membrane to chloroplasts, where they inhibit the production of host defense signaling molecules. However, mechanisms whereby C4/AC4 proteins are transported to chloroplasts are unknown. We report here that tomato (Solanum lycopersicum) COAT PROTEIN COMPLEX I (COPI) components play a critical role in redistributing Tomato yellow leaf curl virus C4 protein to chloroplasts via an interaction between the C4 and β subunits of COPI. Coexpression of both proteins promotes the enrichment of C4 in chloroplasts that is blocked by a COPI inhibitor. Overexpressing or downregulating gene expression of COPI components promotes or inhibits the viral infection, respectively, suggesting a proviral role of COPI components. COPI components play similar roles in C4/AC4 transport and infections of two other geminiviruses: Beet curly top virus and East African cassava mosaic virus. Our results reveal an unconventional role of COPI components in protein trafficking to chloroplasts during geminivirus infection and suggest a broad-spectrum antiviral strategy in controlling geminivirus infections in plants.

Carbon usage in yellow-fleshed Manihot esculenta storage roots shifts from starch biosynthesis to cell wall and raffinose biosynthesis via the myo-inositol pathway.

Cassava is a crucial staple crop for smallholder farmers in tropical Asia and Sub-Saharan Africa. Although high yield remains the top priority for farmers, the significance of nutritional values has increased in cassava breeding programs. A notable negative correlation between provitamin A and starch accumulation poses a significant challenge for breeding efforts. The negative correlation between starch and carotenoid levels in conventional and genetically modified cassava plants implies the absence of a direct genomic connection between the two traits. The competition among various carbon pathways seems to account for this relationship. In this study, we conducted a thorough analysis of 49 African cassava genotypes with varying levels of starch and provitamin A. Our goal was to identify factors contributing to differential starch accumulation. Considering carotenoid levels as a confounding factor in starch production, we found that yellow- and white-fleshed storage roots did not differ significantly in most measured components of starch or de novo fatty acid biosynthesis. However, genes and metabolites associated with myo-inositol synthesis and cell wall polymer production were substantially enriched in high provitamin A genotypes. These results indicate that yellow-fleshed cultivars, in comparison to their white-fleshed counterparts, direct more carbon toward the synthesis of raffinose and cell wall components. This finding is underlined by a significant rise in cell wall components measured within the 20 most contrasting genotypes for carotenoid levels. Our findings enhance the comprehension of the biosynthesis of starch and carotenoids in the storage roots of cassava.

Ethnopharmaceutical Study of Plants as an Alternative Treatment Gastritis Baluwarti Society

The Baluwarti community is a community that lives around the Surakarta Hadiningrat Palace with consist of princes relatives, courtiers, and ordinary people. Baluwarti community to currently still carrying out traditional medicine traditions by utilizing medicinal plants as a treatment in Baluwarti village, gastritis is included in the category of 15 diseases frequent highs. This research is an ethnopharmaceutical research aimed at to find out the local name of the plant, the part used, the way of processing, the rules usage, and treatment methods used as an alternative treatment of gastritis carried out by the community around the Surakarta Hadiningrat Palace. This research is descriptive research that uses quantitative methods. The analysis parameters used are: Use Value (UV), Informant Consensus Factor (ICF), Fidelity Level (FL), and Plant Part Value (PPV). Sampling technique using snowball sampling through open ended interview with the community around the Surakarta Hadiningrat Palace. Based on results interviews with 17 informants found 13 types of medicinal plants used as alternatives treatment of gastritis includes African plants, neem plants, cassava genderuwo, white turmeric, temulawak, cassava, and ginger are processed by boiling. In addition, breadfruit pace and white duwet that can be eaten immediately. Turmeric by processing is ground and grated, as well as aloe vera that is taken mucus using a spoon. The result of the ICF value obtained disease gastritis with a value of 0.25. Plant species that have the highest UV value with a value 0.647 and the highest FL yield of 64.70% is turmeric (Curcuma longa L.) while the PPV value obtained the use of plant parts that are most often used as medicinal materials traditional is 30% rhizome, 18% leaf, 12% fruit, 12% tuber, and 6% mucus.

Identifying Cassava Genotypes Resistant to the African Cassava Whitefly, Bemisia tabaci (Gennadius)

Identifying Cassava Genotypes Resistant to the African Cassava Whitefly, Bemisia tabaci (Gennadius)

Using PCR and RCA Techniques to Investigate the Variants of Cassava Mosaic Virus and Their Distribution in Ghana

Cassava mosaic disease (CMD) caused by cassava begomoviruses is the major constraint to cassava production in Ghana. The disease is known to cause reduction in root yield. To ascertain the distribution of viruses causing CMD, 95 diseased cassava samples were collected in two agroecological zones of Ghana-Deciduous Forest zone and the Transitional zone. On a scale of 1-5, CMD severity was scored. Mean CMD severity score was 2.9, however there was no significant difference (p > 0.05) between the zones. Averagely, CMD score of > 2.8 in 71% of farms visited was recorded. Polymerase chain reaction (PCR) and rolling circle amplification (RCA) were employed for virus identification. PCR revealed that African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV) and mixed infections were prevalent in both zones. EACMV-Cameroon strain was also identified to be common within these zones. The transitional zone had the highest percentage of CMD infection. Unamplified samples from PCR were amplified using rolling circle amplification (RCA) technique. Amplification and characterisation of complete genome sequences of two isolates were carried out. The complete genome of 2780 nucleotides from samples showed a high similarity to African cassava mosaic virus-Ghana (ACMV-GH). Sequences clustered with ACMV-Ivory Coast, ACMV Nigeria-Ogo, ACMV-BF, ACMV-UG having > 96% identity. This shows the close relation that exists amongst the ACMV strains in Africa. These findings highlight the need for a continuous survey of CMD to help manage the disease in the country.

A Coiled-Coil Nucleotide-Binding Domain Leucine-Rich Repeat Receptor Gene MeRPPL1 Plays a Role in the Replication of a Geminivirus in Cassava.

Disease resistance gene (R gene)-encoded nucleotide-binding leucine-rich repeat proteins (NLRs) are critical players in plant host defence mechanisms because of their role as receptors that recognise pathogen effectors and trigger plant effector-triggered immunity (ETI). This study aimed to determine the putative role of a cassava coiled-coil (CC)-NLR (CNL) gene MeRPPL1 (Manes.12G091600) (single allele) located on chromosome 12 in the tolerance or susceptibility to South African cassava mosaic virus (SACMV), one of the causal agents of cassava mosaic disease (CMD). A transient protoplast system was used to knock down the expression of MeRPPL1 by clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9). The MeRPPL1-targeting CRISPR vectors and/or SACMV DNA A and DNA B infectious clones were used to transfect protoplasts isolated from leaf mesophyll cells from the SACMV-tolerant cassava (Manihot esculenta) cultivar TME3. The CRISPR/Cas9 silencing vector significantly reduced MeRPPL1 expression in protoplasts whether with or without SACMV co-infection. Notably, SACMV DNA A replication was higher in protoplasts with lower MeRPPL1 expression levels than in non-silenced protoplasts. Mutagenesis studies revealed that protoplast co-transfection with CRISPR-MeRPPL1 silencing vector + SACMV and transfection with only SACMV induced nucleotide substitution mutations that led to altered amino acids in the highly conserved MHD motif of the MeRPPL1-translated polypeptide. This may abolish or alter the regulatory role of the MHD motif in controlling R protein activity and could contribute to the increase in SACMV-DNA A accumulation observed in MeRPPL1-silenced protoplasts. The results herein demonstrate for the first time a role for a CNL gene in tolerance to a geminivirus in TME3.

Prevalence of African Mosaic and Morphological Characterization of Cassava (Manihot esculenta Cranz) Varieties in Two Agroecological Zones of Cameroon

The objective of this work is to conduct an epidemiological study of African cassava mosaic and to characterize the diversity of local cultivars in circulation in the monomodal and bimodal rainforest zones of Cameroon. Disease-related parameters (incidence and severity index) were studied as well as morphological parameters (plant height, leaflet color, petiole color, lobe length, number of lobes, number of branches, petiole length). The results show that 96 cassava varieties were identified with 89 local varieties and 07 improved varieties. Diseased plants showed a symptom severity index of 1 to 5, which could reduce production by half in the areas considered. The leaf color was dark green, the number of branches was 3, the lobe and petiole lengths were 16.46 and 22 cm respectively, while the number of lobes was 5 the disease incidence for the two agro-ecological zones as a whole is 57.58% for a symptom severity index of 3. The epidemiological study reveals that the desease incidence of both agro-ecological zones was 57.58 % for a symptom severity index of 2 corresponding to 40 %. In the humid forest zone with monomodal spray the average incidence was 49.74% and a leaf attack rate was 29.03 % in the locality of Njombé (Cameroon's littoral region). At Ekona in southwestern Cameroon, the average incidence was 63% and leaf attack index was 1 corresponding to 20 %. In the bimodal rainforest zone (central Cameroon region), the average incidence was 60 % for a leaf attack rate was 37.11%. The expected results highlight a relatively worrying situation. Principal Component Analysis (PCA) confirms the convergence of tolerance towards the mosaic and grouped the different varieties into more or less homogeneous groups according to the morphological and epidemiological cassava descriptors. The results of the present work show that the introduction of cassava local varieties tolerant to mosaic disease in middling could be an alternative for the control of the cassava mosaic disease.

In silico prediction of candidate gene targets for the management of African cassava whitefly (Bemisia tabaci, SSA1-SG1), a key vector of viruses causing cassava brown streak disease.

Whiteflies (Bemisia tabaci sensu lato) have a wide host range and are globally important agricultural pests. In Sub-Saharan Africa, they vector viruses that cause two ongoing disease epidemics: cassava brown streak disease and cassava mosaic virus disease. These two diseases threaten food security for more than 800 million people in Sub-Saharan Africa. Efforts are ongoing to identify target genes for the development of novel management options against the whitefly populations that vector these devastating viral diseases affecting cassava production in Sub-Saharan Africa. This study aimed to identify genes that mediate osmoregulation and symbiosis functions within cassava whitefly gut and bacteriocytes and evaluate their potential as key gene targets for novel whitefly control strategies. The gene expression profiles of dissected guts, bacteriocytes and whole bodies were compared by RNAseq analysis to identify genes with significantly enriched expression in the gut and bacteriocytes. Phylogenetic analyses identified three candidate osmoregulation gene targets: two α-glucosidases, SUC 1 and SUC 2 with predicted function in sugar transformations that reduce osmotic pressure in the gut; and a water-specific aquaporin (AQP1) mediating water cycling from the distal to the proximal end of the gut. Expression of the genes in the gut was enriched 23.67-, 26.54- and 22.30-fold, respectively. Genome-wide metabolic reconstruction coupled with constraint-based modeling revealed four genes (argH, lysA, BCAT & dapB) within the bacteriocytes as potential targets for the management of cassava whiteflies. These genes were selected based on their role and essentiality within the different essential amino acid biosynthesis pathways. A demonstration of candidate osmoregulation and symbiosis gene targets in other species of the Bemisia tabaci species complex that are orthologs of the empirically validated osmoregulation genes highlights the latter as promising gene targets for the control of cassava whitefly pests by in planta RNA interference.

Gradual Emergence of East African cassava mosaic Cameroon virus in Cassava Farms in Côte d’Ivoire

Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are endemic threats to cassava production, causing significant yield losses. They are caused respectively by begomoviruses and ipomoviruses that are transmitted by whiteflies and infected cuttings. This study aimed to monitor and characterize viruses responsible for these diseases in order to fill existing gaps in understanding their epidemiology in Côte d’Ivoire. Field surveys were conducted in 2016, 2017, and 2020, and no CBSD symptoms were observed. However, an increase in CMD incidence was noted from 45.95% in 2016 to 51.37% in 2020, while CMD severity remained moderate over the years with a mean value of 2.29. The number of whiteflies was relatively low and decreased over the years. Molecular diagnostics carried out on cassava leaf samples allowed the detection of East African cassava mosaic Cameroon virus (EACMCMV) that occurs in single as well as in mixed infection with African cassava mosaic virus (ACMV). Single EACMCMV infection, which was detected only in three agroecological zones of eastern Côte d’Ivoire in 2016, spread throughout the country in 2017 and became more widespread in 2020 with a preponderance in central and southern zones, whereas ACMV and EACMCMV coinfection has spread to the entire zones. Phylogenetic analysis of the viral isolates showed that they are closely related to those from Burkina Faso, Ghana, and Nigeria. This changing population of cassava virus species constitutes a serious threat to cassava cultivation. Understanding the evolutionary dynamics of these viruses could help in adopting better disease management strategies to control the disease.

Application of Integrated Computational Approaches in Prediction of Plant Virus Encoded miRNAs and Their Targeted Plant Genes.

This chapter presents a comprehensive approach to predict novel miRNAs encoded by plant viruses and identify their target plant genes, through integration of various ab initio computational approaches. The predictive process begins with the analysis of plant viral sequences using the VMir Analyzer software. VMir Viewer software is then used to extract primary hairpins from these sequences. To distinguish real miRNA precursors from pseudo miRNA precursors, MiPred web-based software is employed. Verified real pre-miRNA sequences with a minimum free energy of< -20 Kcal/mol, arefurther analyzedusingthe RNAshapes software. Validation of predictions involves comparing them with available Expressed Sequence Tags (ESTs) from the relevant plant using BlastN. Short sequences with lengths ranging from 19 to 25 nucleotides and exhibiting <5 mismatches are prioritized for miRNA prediction. The precise locations of these short sequences within pre-miRNA structures generated using RNAshapes are meticulously identified, with a focus on those situated on the 5' and 3' arms of the structures, indicating potential miRNAs. Sequences within the arms of pre-miRNA structures are used to predict target sites within the ESTs of the specific plant, facilitated by psRNA Target software, revealing genes with potential regulatory roles in the plant. To confirm the outcome of target prediction, results are individually submitted to the RNAhybrid web-based software. For practical demonstration, this approach is applied to analyze African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) viruses, as well as the ESTs of Jatropha and cassava.

East African Cassava Mosaic Virus and East African Cassava Mosaic Cameroon Virus: Two Species Emerging in Togo

East African Cassava Mosaic Virus and East African Cassava Mosaic Cameroon Virus: Two Species Emerging in Togo

First report of the severe Uganda variant of East African cassava mosaic virus in Zambia

First report of the severe Uganda variant of <i>East African cassava mosaic virus</i> in Zambia

Integrative transcriptomics reveals association of abscisic acid and lignin pathways with cassava whitefly resistance

BackgroundWhiteflies are a global threat to crop yields, including the African subsistence crop cassava (Manihot esculenta). Outbreaks of superabundant whitefly populations throughout Eastern and Central Africa in recent years have dramatically increased the pressures of whitefly feeding and virus transmission on cassava. Whitefly-transmitted viral diseases threaten the food security of hundreds of millions of African farmers, highlighting the need for developing and deploying whitefly-resistant cassava. However, plant resistance to whiteflies remains largely poorly characterized at the genetic and molecular levels. Knowledge of cassava-defense programs also remains incomplete, limiting characterization of whitefly-resistance mechanisms. To better understand the genetic basis of whitefly resistance in cassava, we define the defense hormone- and Aleurotrachelus socialis (whitefly)-responsive transcriptome of whitefly-susceptible (COL2246) and whitefly-resistant (ECU72) cassava using RNA-seq. For broader comparison, hormone-responsive transcriptomes of Arabidopsis thaliana were also generated.ResultsWhitefly infestation, salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) transcriptome responses of ECU72 and COL2246 were defined and analyzed. Strikingly, SA responses were largely reciprocal between the two cassava genotypes and we suggest candidate regulators. While susceptibility was associated with SA in COL2246, resistance to whitefly in ECU72 was associated with ABA, with SA-ABA antagonism observed. This was evidenced by expression of genes within the SA and ABA pathways and hormone levels during A. socialis infestation. Gene-enrichment analyses of whitefly- and hormone-responsive genes suggest the importance of fast-acting cell wall defenses (e.g., elicitor recognition, lignin biosynthesis) during early infestation stages in whitefly-resistant ECU72. A surge of ineffective immune and SA responses characterized the whitefly-susceptible COL2246’s response to late-stage nymphs. Lastly, in comparison with the model plant Arabidopsis, cassava’s hormone-responsive genes showed striking divergence in expression.ConclusionsThis study provides the first characterization of cassava’s global transcriptome responses to whitefly infestation and defense hormone treatment. Our analyses of ECU72 and COL2246 uncovered possible whitefly resistance/susceptibility mechanisms in cassava. Comparative analysis of cassava and Arabidopsis demonstrated that defense programs in Arabidopsis may not always mirror those in crop species. More broadly, our hormone-responsive transcriptomes will also provide a baseline for the cassava community to better understand global responses to other yield-limiting pests/pathogens.

Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)

Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions.

SNP-based marker-assisted selection for high provitamin A content in African cassava genetic background

Vitamin A deficiency (VAD) contributes to significant levels of mortality and morbidity, particularly among children and women in Africa. Cassava is a major staple crop whose biofortification with betacarotene can contribute to reducing the VAD prevalence in a cost-effective and sustainable approach. Developing high provitamin A content (pVAC) cassava varieties through the conventional approach is a laborious and slow process, partly due to the breeding bottlenecks caused by the biology of the crop. To complement the phenotypic screening for pVAC and increase selection efficiency as well as accuracy, we employed four Kompetitive Allele-Specific PCR (KASP) assays to predict the level of carotenoids in a cassava population developed from open-pollinated crosses. There was significant correlation (r= 0.88) between total carotenoid content (TCC) and root tissue colour score in the study population. Marker S1_24155522 at the phytoene synthase gene explained most of the phenotypic variation in TCC and root colour (R2= 0.37 and 0.55, respectively) among the genotypes evaluated in this study. The other markers did not individually account for much phenotypic variation in the trait in our study population. Three genotypes – namely UIC-17-679, UIC-17-1713, and UIC-17-2823 – had higher TCCs, ranging from 10.07 μg/g to 10.88 μg/g, than the national yellow check variety IITA-IBA-TMS070593 (9.20 μg/g). Marker PSY572/S124155522 is therefore recommended for routine use in marker-assisted selection for pVAC enhancement in African cassava germplasm. Significance: We evaluated the performance of the SNP markers associated with provitamin A content in a cassava population and draw relevant conclusions that will foster the applications of these markers in different cassava improvement programmes with similar interests. Marker-assisted selection was sufficiently accurate for an early screening of individuals for carotenoid content, especially when thousands of genotypes are usually handled. This screening will reduce efficiently the challenges and burden attached to the use of sophisticated instruments for carotenoid quantification (e.g. HPLC and I-check) for the benefit of breeders and researchers in the field.

Gaps and opportunities in research on food systems; a micro-institutional analysis of the University of Nairobi

Research conducted on food systems by higher institutions can contribute to sustainable food security and nutrition at a local level and reduce the impact of societal challenges such as malnutrition. Unfortunately, malnutrition itself manifests as hidden hunger causing unintended consequences such as illness negatively affecting economic progress. Traditionally, research in agriculture has not taken a food systems approach which is looking at challenges of food systems from farm to fork (all stages from production to consumption). Therefore, as we embrace the compelling call to transition from agriculture to food systems research approaches, mapping studies at a local level are needed. However, studies on food systems have been carried out at a macro (global or regional level), a micro-perspective investigation is needed to inform future research. A systematic review on existing literature (journals and thesis) was conducted to identify gaps and opportunities in research on food systems undertaken by researchers at the University of Nairobi. Information collected included; 1. institutions (faculties and department at the university, national policy, and international institutions collaborating with university of Nairobi), 2. crop types (cereals, legumes, vegetables, roots and tubers, and nuts), 3. food systems activities (production, postharvest, processing, and preservation, value addition and branding, consuming foods, input and output markets, obtaining nutrients as well as logistics and distribution) driving research on food systems. The contribution of each of the components (institutions, food systems activity and crop type) was also investigated through citation scores. The findings show that low research outputs on food systems were generated by the university of Nairobi compared to selected universities in Africa and across the globe. Research was focused on carbohydrate rich crops (maize, sorghum, cassava, irish potato, sweet potato, and rice) as compared to protective bioactive vitamin crops (vegetables, mango, and beans). This demonstrated low crop diversity and dietary quality. Research priority was given mainly to maize compared to traditional crops such as sorghum, African Leafy Vegetables, cassava and millets. Faculties such as health, science and technology, engineering, and humanities were involved in research in food systems in addition to agriculture, a potential indication of transdisciplinary research. Additionally, there was more collaborative research between university of Nairobi with institutions at a global level than with local institutions. The involvement of policy institutions in research was low, mainly restricted to the discipline of agriculture, production food system activity and in a few crops such as maize, cassava, and medicinal plants. Disparities in research existed along the food systems activities as more attention was focused on production activities. Other food system activities such as harvesting, processing and preservation, consumption, value addition and branding, input and output markets, as well as logistics and distribution activities, received low research priority. Each component (food system activity, crop type and institution) demonstrated contribution to sustainable food security as shown by citation scores. The findings demonstrate skewed focus in food systems research at the university of Nairobi. Agricultural research investment within institutions of higher learning will need to consider all food systems activities, under-researched crops and collaborations that advance transdisciplinary studies to promote inclusive contribution of food systems to food security at a local level. Further studies can focus on developing frameworks to advance transdisciplinary research.

SEGS-1 a cassava genomic sequence increases the severity of African cassava mosaic virus infection in Arabidopsis thaliana.

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.

Virulence and Molecular Detection of Cassava Mosaic and Brown Streak Virus Genes on Elite Mutant Cassava Lines

Unavailability of germplasm with Cassava Brown Streak Disease (CBSD) and Cassava Mosaic Disease (CMD) tolerance genes remains the main bottleneck towards management of the two diseases in tropic and sub-tropic regions in Africa. We assessed the pathogenicity of two viruses and established the presence of genes linked to CBSD and CMD among some elite cassava lines using field techniques and PCR methods. The screen-house experiment was arranged in split plot in completely randomized block design replicated thrice. Severity data was done on a scale of 1 - 5 at an interval of 14 days post inoculation. Symptomatic fresh leaves were used in the extraction of genomic deoxyribonucleic acid and amplification done using markers linked to African cassava mosaic virus (ACMV), separated bands scored as present (+) or absent (-) and visualized under UV trans-illuminator. Virulence and pathogenicity results showed higher tolerance to CBSD and CMD under single inoculation. In contrast, dual inoculation synergistically increased severity expression leading defoliation at early stages of growth. DNA amplification found no CBSD and CMD alleles in CAS1. However, some traces of the alleles were amplified on CAS2, CAS3, KME3 and KME4. Mutant cassava lines exhibited low severity compared to parental lines which were genetically different in terms of viral genes detected by the ACMV linked markers.