A method for generating virus-free cassava plants to combat viral disease epidemics in Africa.

Here, we report a method to clean cassava plants from viral infections that cause cassava mosaic and brown streak diseases in Africa. Infected plants of resistant or tolerant varieties from Malawi, Mozambique, Kenya, Tanzania and Uganda were cleaned in the UK using a combination of tissue culture, chemotherapy and thermotherapy. In the first cycle of our virus-indexing procedure, we successfully cleaned 27 of the 31 varieties (87%), and after an additional three cleaning cycles, all plants were virus-free. Virus-free tissue-cultured plants were shipped back to Africa for distribution to farmers. This first cross-boundary effort provides important lessons for mitigating the two-major cassava viral diseases.

Assessing the Degeneration of Cassava Under High-Virus Inoculum Conditions in Coastal Tanzania.

Cassava brown streak disease (CBSD), caused by cassava brown streak ipomoviruses (CBSIs), has become the most debilitating biotic stress to cassava production in East and Central Africa. Lack of CBSD-resistant varieties has necessitated the search for alternative control measures. Most smallholder farmers reuse stems from previous crops for planting in the new season. Recycling planting material in this way can lead to "degeneration" owing to the compounding effects of disease. In this study, degeneration was defined as the increase in CBSD incidence and reduction in marketable root yield over time. An experiment was established to study the rates of degeneration in selected cassava varieties Chereko, KBH2002_135, Kipusa, Kizimbani, and Mkuranga1 and cultivars Kiroba and Kikombe under high-CBSD inoculum conditions in Bagamoyo, Tanzania from 2013 to 2017. The experiment was replicated across two seasons: the first planted during the long rains (Masika) between March and June and the second planted during the short rains (Vuli) between October and December. Mean abundance of the whitefly vector (Bemisia tabaci) was much greater during the Vuli season (>19 insects per plant) than the Masika season (<2 insects per plant). CBSD shoot symptoms occurred naturally and were observed only on Kikombe, Kiroba, and Kipusa. New materials had overall lower CBSD shoot incidences (1.5%) compared with recycled materials (6.9%) in Masika, although no significant differences were obvious in Vuli. However, Masika (8.7%) had an overall lower CBSD shoot incidence than Vuli (16.5%) in the varieties that had shoot symptoms. CBSD root incidences were higher in Vuli (10.3%) than Masika (4.4%), and root yields in Masika (29.4 t/ha) were significantly greater than those in Vuli (22.5 t/ha). The highest percentage of roots rendered unusable owing to CBSD was observed in Vuli. There was significantly higher unusable root incidence in recycled materials (3.7%) than in new materials (1.4%) in Masika but not in Vuli. Overall root yield was similar between recycled and new materials in either season. Significant reductions in root yield over the course of the experiment were observed both in Masika and Vuli, whereas changes in marketable yield were significant only in Masika. Differences in the response of varieties to degeneration led to the identification of four degeneration patterns, namely "strong," "moderate," "mild," and "delayed" degeneration. The strongest effects of degeneration were most obvious in the susceptible cultivar (Kikombe), which also had the lowest marketable yield in either season. Seasonal differences were a key driver of degeneration, because its effects were much greater in Vuli than Masika. To the best of our knowledge, this work reports the first study of degeneration caused by cassava viruses.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Use of low cost near-infrared spectroscopy, to predict pasting properties of high quality cassava flour.

Determination of pasting properties of high quality cassava flour using rapid visco analyzer is expensive and time consuming. The use of mobile near infrared spectroscopy (SCiO™) is an alternative high throughput phenotyping technology for predicting pasting properties of high quality cassava flour traits. However, model development and validation are necessary to verify that reasonable expectations are established for the accuracy of a prediction model. In the context of an ongoing breeding effort, we investigated the use of an inexpensive, portable spectrometer that only records a portion (740-1070 nm) of the whole NIR spectrum to predict cassava pasting properties. Three machine-learning models, namely glmnet, lm, and gbm, implemented in the Caret package in R statistical program, were solely evaluated. Based on calibration statistics (R2, RMSE and MAE), we found that model calibrations using glmnet provided the best model for breakdown viscosity, peak viscosity and pasting temperature. The glmnet model using the first derivative, peak viscosity had calibration and validation accuracy of R2 = 0.56 and R2 = 0.51 respectively while breakdown had calibration and validation accuracy of R2 = 0.66 and R2 = 0.66 respectively. We also found out that stacking of pre-treatments with Moving Average, Savitzky Golay, First Derivative, Second derivative and Standard Normal variate using glmnet model resulted in calibration and validation accuracy of R2 = 0.65 and R2 = 0.64 respectively for pasting temperature. The developed calibration model predicted the pasting properties of HQCF with sufficient accuracy for screening purposes. Therefore, SCiO™ can be reliably deployed in screening early-generation breeding materials for pasting properties.

Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources.

Cassava (Manihot esculenta Crantz) is a food and industrial storage root crop with substantial potential to contribute to managing risk associated with climate change due to its inherent resilience and in providing a biodegradable option in manufacturing. In Africa, cassava production is challenged by two viral diseases, cassava brown streak disease (CBSD) and cassava mosaic disease. Here we detect quantitative trait loci (QTL) associated with CBSD in a biparental mapping population of a Tanzanian landrace, Nachinyaya and AR37-80, phenotyped in two locations over three years. The purpose was to use the information to ultimately facilitate either marker-assisted selection or adjust weightings in genomic selection to increase the efficiency of breeding. Results from this study were considered in relation to those from four other biparental populations, of similar genetic backgrounds, that were phenotyped and genotyped simultaneously. Further, we investigated the co-localization of QTL for CBSD resistance across populations and the genetic relationships of parents based on whole genome sequence information. Two QTL on chromosome 4 for resistance to CBSD foliar symptoms and one on each of chromosomes 11 and 18 for root necrosis were of interest. Of significance within the candidate genes underlying the QTL on chromosome 4 are Phenylalanine ammonia-lyase (PAL) and Cinnamoyl-CoA reductase (CCR) genes and three PEPR1-related kinases associated with the lignin pathway. In addition, a CCR gene was also underlying the root necrosis-resistant QTL on chromosome 11. Upregulation of key genes in the cassava lignification pathway from an earlier transcriptome study, including PAL and CCR, in a CBSD-resistant landrace compared to a susceptible landrace suggests a higher level of basal lignin deposition in the CBSD-resistant landrace. Earlier RNAscope® in situ hybridisation imaging experiments demonstrate that cassava brown streak virus (CBSV) is restricted to phloem vessels in CBSV-resistant varieties, and phloem unloading for replication in mesophyll cells is prevented. The results provide evidence for the involvement of the lignin pathway. In addition, five eukaryotic initiation factor (eIF) genes associated with plant virus resistance were found within the priority QTL regions.

Managing cassava growth on nutrient poor soils under different water stress conditions.

Nitrogen (N), phosphorus (P) and potassium (K) fertiliser application, was able to counteract growth reductions, in cassava cultivated on nutrient poor soils, under one water stress condition. It however remains to be seen, whether N, P and K fertiliser application, would produce similar results, across different water stress conditions. A study was therefore conducted to determine how N, P and K fertiliser application, would influence cassava growth on nutrient poor soils, under various water stress conditions. Effects on new leaf formation and leaf size were also investigated. The study was a 2×3×4 factorial pot experiment, in a randomised complete block design. It included: two cassava varieties, three water stress levels and four fertiliser treatments. The water stress levels kept some plants watered at field capacities of 30% (severe water stress), 60% (mild water stress) and 100% (zero water stress). The fertiliser treatments consisted of a control (no fertiliser), a sole K fertiliser treatment (25 mg K/kg), a moderate N, P and K fertiliser treatment (25 mg N + 5 mg P + 25 mg K/kg) and a high N, P and K fertiliser treatment (50 mg N + 13 mg P + 50 mg K/kg). All data were analysed using the analysis of variance. Cassava growth was assessed by monitoring changes in the dry shoot mass of cassava plants. High and moderate N, P and K fertiliser application, produced cassava plants with higher and similar dry shoot masses, under mild water stress (10.5 g/plant, SE = 0.6 and 9.0 g/plant, SE = 0.6, respectively). High N, P and K fertiliser application, however gave cassava the highest dry shoot mass, under severe water stress (7.9 g/plant, SE = 0.4). Relatively high cassava growth was consistently achieved with high N, P and K fertiliser application, across all water stress conditions.

Plant tissue analysis as a tool for predicting fertiliser needs for low cyanogenic glucoside levels in cassava roots: An assessment of its possible use.

The use of plant tissue analysis as a tool for attaining low cyanogenic glucoside levels in cassava roots, has hardly been investigated. Just as the quality of crops is improved through the use of plant tissue analysis, the same can probably be done to consistently attain the lowest possible cyanogenic glucoside levels in cassava roots. High levels of cyanogenic glucosides in consumed fresh cassava roots or in their products have the potential of causing cyanide intoxication, hence the need to lower them. An experiment was thus conducted to assess the occurrence of meaningful relationships between plant nutritional status and cyanogenic glucoside production in cassava roots. Total hydrogen cyanide (HCN) levels in cassava roots were used to assess cyanogenic glucoside production. Using NPK fertiliser application to induce changes in plant nutritional status, the main objective of the study was investigated using the following sub-objectives; (1) to determine the effects of increased NPK fertiliser application on cassava root HCN levels; (2) and to show the occurrence of relationships between changes in nutrient levels in plant 'indicator tissue' and HCN levels in cassava roots. The study was a field experiment laid out as a split-plot in a randomized complete block design with three replicates. It was repeated in two consecutive years, with soil nutrient deficiencies only being corrected in the second year. The varieties Salanga, Kalinda, Supa and Kiroba were used in the experiment, while the NPK fertiliser treatments included; a control with no fertiliser applied; a moderate NPK treatment (50 kg N + 10 kg P + 50 kg K /ha); and a high NPK treatment (100 kg N + 25 kg P + 100 kg K /ha). A potassium only treatment (50 kg K/ha) was also included, but mainly for comparison. The root HCN levels of Salanga, Kalinda and Kiroba were significantly influenced by NPK fertiliser application in at least one of the two field experiments, while those of Supa remained uninfluenced. Changes in plant nutritional status in response to fertiliser application were thus shown to influence cyanogenic glucoside production. The results of the multiple linear regression analysis for the first field experiment, generally showed that the root HCN levels of some cassava varieties could have been 'reduced' by decreasing concentrations of nitrogen, potassium and magnesium in plants, or by improving plant calcium concentrations along with NPK fertiliser application. However, in the second field experiment (with corrected soil nutrient deficiencies) the regression analysis generally showed that the root HCN levels of some cassava varieties could have been 'reduced' by improving either one or a combination of the nutrients phosphorous, zinc and potassium in plants along with NPK fertiliser application. Although the results obtained in the two experiments had been contradicting due to slight differences in how they were conducted, the study had nonetheless demonstrated the occurrence of meaningful relationships between plant nutritional status and cyanogenic glucoside production; confirming the possible use of plant tissue analysis in predicting fertiliser needs for the consistent attainment of low cyanogenic glucosides in cassava roots.

Genetic analysis and QTL mapping for multiple biotic stress resistance in cassava.

In Sub-Saharan Africa cassava (Manihot esculenta Crantz) is one of the most important food crops where more than 40% of the population relies on it as their staple carbohydrate source. Biotic constraints such as viral diseases, mainly Cassava Mosaic Disease (CMD) and Cassava Brown Streak Disease (CBSD), and arthropod pests, particularly Cassava Green Mite (CGM), are major constraints to the realization of cassava's full production potential in Africa. To address these problems, we aimed to map the quantitative trait loci (QTL) associated with resistance to CBSD foliar and root necrosis symptoms, foliar CMD and CGM symptoms in a full-sib mapping population derived from the genotypes AR40-6 and Albert. A high-density linkage map was constructed with 2,125 SNP markers using a genotyping-by-sequencing approach. For phenotyping, clonal evaluation trials were conducted with 120 F1 individuals for two consecutive field seasons using an alpha-lattice design at Chambezi and Naliendele, Tanzania. Previously identified QTL for resistance to CBSD foliar symptoms were corroborated, and a new putative QTL for CBSD root necrosis identified (qCBSDRNc14AR) from AR40-6. Two QTL were identified within the region of the previously recognized CMD2 locus from this population in which both parents are thought to possess the CMD2 locus. Interestingly, a minor but consistent QTL, qCGM18AR, for CGM resistance at 3 months after planting stage was also detected and co-localized with a previously identified SSR marker, NS346, linked with CGM resistance. Markers underlying these QTL may be used to increase efficiencies in cassava breeding programs.

Genotype by environment cultivar evaluation for cassava brown streak disease resistance in Tanzania.

Cassava brown steak disease (CBSD), caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), is the most important biotic constraint to cassava production in East and Central Africa. Concerted efforts are required to prevent further spread into West Africa as well as to reduce losses in areas already affected. The study reported here was part of a five-country (Kenya, Malawi, Mozambique, Tanzania and Uganda) programme that aimed to identify superior cassava cultivars resistant to CBSD and to disseminate them widely in the region. Seventeen tissue-cultured and virus-tested cultivars were evaluated in Tanzania across nine sites with diverse CBSD inoculum conditions. Experiments were planted using an alpha-lattice design and assessments were made of surrounding inoculum pressure, CBSD foliar and root incidence and root yield at harvest. There were large differences in CBSD infection between sites, with greatest spread recorded from the north-western Lake (Victoria) zone. Differences were driven by Bemisia tabaci whitefly vector abundance and CBSD inoculum pressure. Both CBSV and UCBSV were almost equally represented in cassava fields surrounding experimental plots, although CBSV predominated in the north-west whilst UCBSV was more frequent in coastal and southern sites. However, the incidence of CBSV was much greater than that of UCBSV in initially virus-free experimental plots, suggesting that CBSV is more virulent. Cultivars could be categorised into three groups based on the degree of CBSD symptom expression in shoots and roots. The seven cultivars (F10_30R2, Eyope, Mkumba, Mkuranga1, Narocass1, Nase3 and Orera) in the most resistant category each had shoot and root incidences of less than 20%. Fresh root yield differed between sites and cultivars, but there was no genotype by environment interaction for this trait, probably attributable to the large fertility and soil moisture differences between sites. Susceptible cultivars and the local check performed well in the absence of CBSD pressure, highlighting the importance of exploiting quality and yield traits of local landraces in breeding programmes. Overall, our results emphasized the importance of applying a balanced strategy for CBSD management. This should use both improved and local germplasm resources to generate high yielding cultivars for specific end-user traits, and combine the deployment of improved cultivars with phytosanitary control measures including the use of healthy planting material and planting during periods of reduced CBSD infection.

Farmers' perceptions on the causes of cassava root bitterness: A case of konzo-affected Mtwara region, Tanzania.

In areas where konzo (a cassava cyanide related paralytic disorder) persists, the agronomic factors causing increased cyanogenic glucoside levels in cassava, during periods without water stress, are hardly known. However, through their assessment of cassava root toxicity, using its bitter taste, farmers may have noticed factors unrelated to water stress that additionally influence the cyanogenic glucoside content of cassava cultivated in these areas. Increased cassava root bitterness is often associated with an increase in cyanogenic glucoside levels, making it a good indicator of changes in root cyanogenic glucoside content. Bitter cassava varieties that are preferentially planted by people living in most konzo-affected areas, are an additional known contributor to high cyanogenic glucosides. It is water stress that further increases the inherent toxicity of the planted bitter cassava varieties. Using konzo-affected Mtwara region in Tanzania as a case study, a household survey was carried out to identify the overlooked agronomic factors that additionally influence cyanogenic glucoside levels in cassava cultivated in konzo-affected areas. A total of 120 farmers were interviewed and they mentioned a number of factors unrelated to water stress, as agronomic factors that influenced cassava root bitterness and hence cyanogenic glucoside production in cassava. The mentioned factors included; certain soil characteristics (14.2%), plant age at harvest (7.5%), poor weeding (0.8%), piecemeal harvesting (0.8%), and branch pruning (0.8%). The revealed factors constitute permanent environmental characteristics and crop management practices commonly used by farmers living in konzo-affected Mtwara region in Tanzania. The revealed factors could be contributing to increased cyanogenic glucoside levels in cassava, during periods without water stress in areas where konzo persists.

Soil nutrient adequacy for optimal cassava growth, implications on cyanogenic glucoside production: A case of konzo-affected Mtwara region, Tanzania.

Soils in areas affected by konzo (a cassava cyanide intoxication paralytic disorder) are predominantly infertile and probably unable to supply cultivated cassava with the nutrients it needs to achieve optimal growth. Soil nutrient supply in these areas could also be influencing cyanogenic glucoside production in cassava, however there is hardly any knowledge on this. An assessment of soil nutrient levels on crop fields in konzo-affected areas was therefore carried out to determine their adequacy for optimal cassava growth. Konzo-affected Mtwara region of Tanzania, was used as a case study. Whether soil nutrient supply influences cyanogenic glucoside production in cassava cultivated in konzo-affected areas and how it could be doing this, was additionally investigated. To investigate this, correlations between total hydrogen cyanide (HCN) levels (a measure of cyanogenic glucoside content) in cassava roots and various soil nutrient levels on crops fields were carried out. This was followed by an investigation of relationships between cases of cassava cyanide intoxication and soil nutrient levels on crop fields from which the consumed toxic cassava roots had been harvested. Cases of cassava cyanide intoxication were used as a proxy for high cyanogenic glucoside levels in cassava roots. Logistic regression analysis was used in the latter investigation. Other important non-nutrient soil chemical characteristics, like pH and soil organic carbon, were also included in all analysis performed. The results revealed that most soil nutrients known to have reducing effects on cassava cyanogenic glucosides, like potassium (mean = 0.09 cmol/kg, SD = 0.05 cmol/kg), magnesium (mean = 0.26 cmol/kg, SD = 0.14 cmol/kg) and zinc (mean = 1.34 mg/kg, SD = 0.26 mg/kg) were deficient on several crop fields. The results also showed that cyanogenic glucosides in cassava roots could be increased with the increased supply of sulphur in soils in bitter cassava varieties (rs = 0.593, p = 0.032), and with the increased supply of P in soils in all cassava varieties (rs = 0.486, p = 0.026). The risk of cassava cyanide intoxication occurring (and thus high cyanogenic glucoside levels in cassava) was found to be likely increased by cultivating cassava on soils with high pH (X2 = 8.124, p = 0.004) and high iron (X2 = 5.740, p = 0.017). The study managed to establish that cassava grows under conditions of severe nutrient stress and that soil nutrient supply influences cyanogenic glucoside production in cassava cultivated in konzo-affected areas of Mtwara region. Despite the multiple soil nutrient deficiencies on crop fields, low soil fertility was however not the only probable cause of increased cyanogenic glucosides in cassava, as high soil nutrient levels were also found to be potential contributors.

Exchanging and managing in-vitro elite germplasm to combat Cassava Brown Streak Disease (CBSD) and Cassava Mosaic Disease (CMD) in Eastern and Southern Africa.

Cassava varieties resistant to cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are needed for the food and income security of the rural poor in eastern and southern Africa (ESA). The International Institute of Tropical Agriculture led five national cassava breeding programs (Malawi, Mozambique, Kenya, Tanzania and Uganda) in virus-cleaning and exchanging elite cassava germplasm resistant to both diseases. This paper documents the experiences and lessons learned from the process. Thirty-one clones (25 elite, two standard and four national) were submitted by the five breeding programs to the Natural Resources Institute and Kenya Plant Health Inspectorate Services for virus cleaning and indexing. Subsequently, ca 75 invitro virus-indexed plantlets per clone were sent to Genetic Technologies International Limited (GTIL), a private tissue culture (TC) lab in Kenya, and micro-propagated to produce ≥1500 plantlets. After fulfilling all the formal procedures of germplasm exchange between countries ≥300 plantlets per clone were sent to each partner country. National check clones susceptible to CMD/CBSD were sent only to their countries of origin. In each country, the in-vitro plantlets were acclimatized under screen house conditions and transferred to clean isolated sites for field multiplication. All the clones were cleaned of the viruses, except Tomo. The cleaning process was slow for F19-NL, NASE1, and Kibandameno and TC micro-propagation at GTIL was less efficient for Pwani, Tajirika, NASE1, and Okhumelela than for the other clones. Difficulties in cleaning recalcitrant clones affected the timeline for establishing the multi-site evaluation trials in target countries. The initiative is the one of the kind to successfully clean and exchange elite germplasm as a joint action to combat CBSD in ESA. Adequate preparation in terms of infrastructure and personnel are critical to successfully receiving and adapting the indexed in-vitro plants as new germplasm.

QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii.

Genetic mapping of quantitative trait loci (QTL) for resistance to cassava brown streak disease (CBSD), cassava mosaic disease (CMD), and cassava green mite (CGM) was performed using an F1 cross developed between the Tanzanian landrace, Kiroba, and a breeding line, AR37-80. The population was evaluated for two consecutive years in two sites in Tanzania. A genetic linkage map was derived from 106 F1 progeny and 1,974 SNP markers and spanned 18 chromosomes covering a distance of 1,698 cM. Fifteen significant QTL were identified; two are associated with CBSD root necrosis only, and were detected on chromosomes V and XII, while seven were associated with CBSD foliar symptoms only and were detected on chromosomes IV, VI, XVII, and XVIII. QTL on chromosomes 11 and 15 were associated with both CBSD foliar and root necrosis symptoms. Two QTL were found to be associated with CMD and were detected on chromosomes XII and XIV, while two were associated with CGM and were identified on chromosomes V and X. There are large Manihot glaziovii introgression regions in Kiroba on chromosomes I, XVII, and XVIII. The introgression segments on chromosomes XVII and XVIII overlap with QTL associated with CBSD foliar symptoms. The introgression region on chromosome I is of a different haplotype to the characteristic "Amani haplotype" found in the landrace Namikonga and others, and unlike some other genotypes, Kiroba does not have a large introgression block on chromosome IV. Kiroba is closely related to a sampled Tanzanian "tree cassava." This supports the observation that some of the QTL associated with CBSD resistance in Kiroba are different to those observed in another variety, Namikonga.

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity.

Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.