Cassava biology and physiology

On-Farm Multi-Environment Evaluation of Selected Cassava (Manihot esculenta Crantz) Cultivars in South Africa

Cassava is an important starchy root crop grown globally in tropical and subtropical regions. The ability of cassava to withstand difficult growing conditions and long-term storability underground makes it a resilient crop, contributing to food and nutrient security. This study was conducted to evaluate the performance and adaptability of exotic cassava cultivars across different environments in South Africa and to recommend genotypes for cultivation. A total of 11 cassava cultivars were evaluated at six on-farm sites, using a randomized complete block design with three replications. There were highly significant (p < 0.001) variations between genotypes, environments, and their interaction for all yield and yield-related traits studied. This indicates the need to test the genotypes in multiple environments before effective selection and commercialization can be undertaken. MSAF2 and UKF4 showed the overall best performances for most of the traits, whilst UKF9 (49.5%) and P1/19 (48.5%) had the highest dry matter yield. UKF4 (102.7 t ha−1) had the highest yield and greatest root yield stability across environments. MSAF2 did not perform consistently across environments because it was highly susceptible to cassava mosaic disease (CMD). MSAF2 could be used as a donor parent to generate novel clones with large numbers of marketable roots, and high fresh root yields, if the other parent can provide effective resistance to CMD. Based on genotype and environmental mean, Mabuyeni (KwaZulu-Natal), Mandlakazi (Limpopo), and Shatale (Mpumalanga) were found to be better environments for cassava cultivation and testing. This study is a pioneer in cassava research using multiple environments in South Africa. It provides baseline information on the performance of currently available cassava clones, their adaptation to multiple sites, the identification of suitable test sites, and information on current genetic resources for a future breeding program.

Characterization and Ofloxacin Adsorption Studies of Chemically Modified Activated Carbon from Cassava Stem

Cassava is a type of crop popular in Asian countries. It can be easily cultivated and grows to a mature plant in 9 months. Considering its availability, this work studied activated carbon based on cassava stem. Ofloxacin was chosen as the adsorbate, simulating the wastewater from the pharmaceutical industry. Cassava stem was ground into particles and heated to the activated state, 787 °C. The cassava-stem-activated carbon was further treated with the surface modifier, namely sodium hydroxide and zinc chloride, to study the improvement in ofloxacin adsorption. Prepared adsorbents were characterised using the SEM, FT-IR, XRD, DSC and TGA methods before being evaluated through batch adsorption, thermodynamic, and kinetic studies. The surface area analysis indicates that treatment of the activated carbon with NaOH and ZnCl₂ increases the surface area due to the removal of organic content by the chemicals. Better ofloxacin adsorption of all activated carbon samples can be obtained with solutions at pH 8. An endothermic reaction was predicted, shown by higher ofloxacin adsorption at a higher temperature, supported by a positive value of ΔH° in the thermodynamic studies. The negative values of ΔG° revealed that adsorptions were spontaneous. The higher R² values indicate that the adsorption process follows the pseudo-second-order equation of kinetic study. The maximum adsorption capacities are 42.37, 62.11, 62.89 and 58.82 mg/g for raw cassava stem (RC), cassava-stem-activated carbon (AC), NaOH-modified cassava-stem-activated carbon (NAC), and ZnCl₂ modified cassava-stem-activated carbon (ZAC). The adsorption capacity is good compared to previous works by other researchers, making it a possible alternative material for the pharmaceutical industry’s wastewater treatment.

A comparison of ImageJ and machine learning based image analysis methods to measure cassava bacterial blight disease severity

BACKGROUND

Methods to accurately quantify disease severity are fundamental to plant pathogen interaction studies. Commonly used methods include visual scoring of disease symptoms, tracking pathogen growth in planta over time, and various assays that detect plant defense responses. Several image-based methods for phenotyping of plant disease symptoms have also been developed. Each of these methods has different advantages and limitations which should be carefully considered when choosing an approach and interpreting the results.

RESULTS

In this paper, we developed two image analysis methods and tested their ability to quantify different aspects of disease lesions in the cassava-Xanthomonas pathosystem. The first method uses ImageJ, an open-source platform widely used in the biological sciences. The second method is a few-shot support vector machine learning tool that uses a classifier file trained with five representative infected leaf images for lesion recognition. Cassava leaves were syringe infiltrated with wildtype Xanthomonas, a Xanthomonas mutant with decreased virulence, and mock treatments. Digital images of infected leaves were captured overtime using a Raspberry Pi camera. The image analysis methods were analyzed and compared for the ability to segment the lesion from the background and accurately capture and measure differences between the treatment types.

CONCLUSIONS

Both image analysis methods presented in this paper allow for accurate segmentation of disease lesions from the non-infected plant. Specifically, at 4-, 6-, and 9-days post inoculation (DPI), both methods provided quantitative differences in disease symptoms between different treatment types. Thus, either method could be applied to extract information about disease severity. Strengths and weaknesses of each approach are discussed.

NMR-Based Metabolomic Approach for Evaluation of the Harvesting Time and Cooking Characteristics of Different Cassava Genotypes

Cassava is an important staple food for low-income countries. However, its cooking characteristics are especially affected by genotype. In this study, two groups of genotypes, namely hard to cook (HTC) and easy to cook (ETC), were harvested at different times (9 and 15 months), and evaluated by NMR coupled to chemometrics. Additionally, lignin of these materials was studied by ¹H-¹³C HSQC NMR. The carbohydrates were the most important class of compounds to differentiate the cassava genotypes. The correlation of NMR with cooking time and starch content showed that the higher content of primary metabolites, mostly glucose, can be associated with longer cooking times and reduction of starch, corroborating the metabolic pathways analysis. Furthermore, it was observed that the lignin from cell walls did not differentiate the cooking performance of the genotypes.

Farmers' Sources and Varieties of Cassava Planting Materials in Coastal Kenya

Cassava (Manihot esculenta Crantz) grows in diverse agro-ecological zones. In Kenya, it is widely cultivated in Western and Coastal regions. It is mainly grown for food and nutrition security and excess roots are sold to generate income for the farm households. Its productivity per unit of the land area is high compared to maize and wheat which are staple crops in the country. However, scarcity of cassava planting materials and pests and diseases limit production in these regions. This study aimed at revealing the sources and varieties of cassava planting materials used by farmers and other farmers' practices in coastal Kenya. Four focus group discussions (FGD) and a survey were conducted in 2018, using a semi-structured questionnaire targeting 250 farmers. The data collected on the sources of planting materials, preferred varieties and the practices employed by the farmers in cassava production, was analyzed using descriptive statistics. Majority of farmers (83%) interviewed indicated that they recycled planting materials from the previous crop while some 67% respondents obtained the planting material from their neighbors. Kenya Agricultural and Livestock Research Organization's (KALRO) and the local markets were reported as sources of planting materials by 11 and 5% farmer respondents, respectively. The only formal seed source reported was KALRO. The rest, own seed, neighbors, and the local markets, were informal seed sources. Piecemeal harvesting practiced by 98% of the farmers favored planting material recycling. Farmers dedicated a small proportion of their land (mean 0.2 ha) to cassava production as reported by 60 and 72.8% of farmers from Taita Taveta and Kilifi, respectively. Slightly above half (56%) of the farmers in Kilifi dedicated slightly more land to cassava, planting between 100 and 4,000 cuttings (2.5% of an acre up to a full acre) compared to 87% farmers from Taita Taveta who planted 100 cuttings or less (which is about 2.5% of an acre or less). A majority (81.1%) of farmers in Taita Taveta planted local cassava varieties compared to Kilifi's 57.8%. Slightly above half of the farmer respondents reported Kibandameno as the preferred variety followed by Tajirika as the second preferred variety as reported by 18% farmers. Kibandameno was preferred for its sweet taste by 75.6% farmers while Tajirika was preferred by 52.4% farmers because of the high yielding capacity. Nearly all farmer respondents, in Taita Taveta County obtained the planting material from informal seed sources, except a negligible number, who reported buying their planting material from KALRO, a formal seed source, far from their locality. Farmers sourcing cuttings from a formal seed source such as those from Kilifi County were more likely to use a tractor for land preparation compared to those who sourced planting materials informally who more likely had scarce knowledge on cassava production and the value of cassava. Therefore, interventions to establish a sustainable healthy cassava planting materials seed system are needed to address the systemic constraint and help develop a viable cassava value chain.

New cassava germplasm for food and nutritional security in Central Africa

Cassava is a key food security crop in Central Africa, but its production depends largely on the use of local farmers' varieties characterized by inherently low yield which is compounded by generally high susceptibility to various growth and yield-limiting pests and diseases. Improved cassava genotypes have demonstrated the potential to substantially improve cassava's contribution to food security and the development of the cassava industry and the improvement of nutrition status elsewhere in Western Africa. Eleven improved cassava genotypes were compared with a local landrace (LMR) used as a check under field conditions over two years in eight locations, grouped in four agro-ecologies in Cameroon. Pest and disease abundance/incidence and damage severity were evaluated. At harvest, root yield and carotenoid content were measured. Best linear unbiased predictors showed the lowest breeding value for LMR with the cassava mosaic virus disease (+ 66.40 ± 2.42) compared with 1.00 ± 0.02% for the most susceptible improved genotype. Two genotypes (I010040-27 and I011797) stood out for having higher predicted fresh root yield means which were at least 16 times greater compared with LMR. Predicted total carotenoid content was the highest (+ 5.04 ± 0.17) for improved genotype I070593 compared with LMR which showed the lowest (- 3.90 ± 0.06%) and could contribute to the alleviation of vitamin A deficiency from cassava-based food systems. Diffusion of high-yielding and nutritious genotypes could alleviate food and nutritional security in Central Africa.

Cassava production in Nigeria: trends, instability and decomposition analysis (1970-2018)

This study analyzed the compound growth rate (CGR) and the contributions of yield and area to cassava production output in Nigeria. During the period, TE1970 - TE2018, production followed an upward trajectory from 9.3 million tonnes (1970) to 59.5 million tonnes (2018) while yield oscillated between 7.9tonnes/ha (TE2014) and 11.9tonnes/ha (TE2010). At this period, the CGR per year for yield declined (-0.2%), harvested area increased (10.9%) and production increased (10.6%). The decomposition analysis for the period revealed that, increase in output was largely due to expansion of harvested area (152%) while the interaction between area and yield effect declined production output by 45.8%. Regrettably, during the period, cassava yield also declined production output by 5.8%. The study also found that harvested area has the highest instability index (11.8). In order to further increase and sustain cassava production in Nigeria, intense planting of high yield cassava stems instead of solely expanding cropped area is recommended.

Genotype by Environment Interaction on Resistance to Cassava Green Mite Associated Traits and Effects on Yield Performance of Cassava Genotypes in Nigeria

Cassava is the main source of carbohydrate for over 70% of the people in Nigeria, the world's largest producer and consumer of the crop. The yields of cassava are, however, relatively low in Nigeria largely due to pests and disease infections that significantly lead to inconsistencies in productivity of cassava genotypes in various environments. Fifty-eight F1 hybrid cassava genotypes plus their two parents which served as check varieties were evaluated in three locations for two years (that is six environments). The objectives of the study were to evaluate genotype by environment interactions (GEI) on resistance to cassava green mite [CGM, Mononychellus tanajoa (Bondar)] associated traits and effects on yield performance of cassava genotypes in Nigeria and to identify superior genotypes that exhibit high stability which combine CGM resistance and high fresh root yield with general and specific environmental adaptation using additive main effects and multiplicative interaction (AMMI) and genotype stability index (GSI). The combined analysis of variance based on AMMI revealed significant genotype, environment, and genotype by environment interactions (GEI) for all traits. The percentage variation due to environment was higher than the percentage variation due to genotype for cassava green mite severity (CGMS), leaf retention (LR), root dry matter content (RDMC), and fresh root yield (FRY) indicating that environment greatly influenced the expression of these traits. The percentage variation due to GEI accounted for higher percentage variation than that of genotype and environment separately for all traits, indicating the influence of genotype by environment interaction on expression of the traits. These findings reveal that screening/evaluating for these traits needs multi-environment trials. According to GSI ranking, genotypes G31 (IBA131794), G19 (IBA131762), the check variety G52 (TMEB778), and G11 (IBA131748) were identified as the most stable and most resistant to CGM which also combine high FRY and other useful agronomic traits, implying that these traits in cassava can even be incorporated as preferred by farmers. These genotypes can be tested in more environments to determine their adaptability and potential recommendation for release to farmers for growing.

Using bioenergy crop cassava (Manihot esculenta) for reclamation of heavily metal-contaminated land

Heavy metal contamination of agricultural lands may give rise to health risks by cultivation and consumption of food crops from such lands, as well as result in economic loss. Phytoremediation is an eco-friendly and cost-effective approach to restore contaminated soil. However, the restoration process is slow and its sustainability is difficult to maintain. Bioenergy crops may provide alternative economic benefits to agriculture sector and reduce the risks associated with transfering heavy metals into food webs. In this study, a field experiment was carried out to determine the level of reclamation that would be attained in severely heavy metal-contaminated land by planting cassava (Manihot esculenta), a bioenergy crop. The results showed that cassava could grow well on the derelict land, with a fresh tuber yield of 23.13-26.22 t ha^-1 in one growing season, which could potentially produce 3680-4160 L ha^-1 bioethanol. The economic income of the cassava was estimated to be 11.6-13.1 × 10³ CNY ha^-1. Among the cassava tissues, metal concentrations were lowest in the tuber. The soil fertility and acidity were ameliorated after cassava plantation, and the mobile and bioavailable metal fractions in the soils were decreased. The cultivation of cassava as a renewable energy crop appears applicable for sustainable utilization and reclamation of heavy metal-contaminated land.

The search for yield predictors for mature field-grown plants from juvenile pot-grown cassava (Manihot esculenta Crantz)

Cassava is the 6th most important source of dietary energy in the world but its root system architecture (RSA) had seldom been quantified. Ability to select superior genotypes at juvenile stages can significantly reduce the cost and time for breeding to bridge the large yield gap. This study adopted a simple approach to phenotyping RSA traits of juvenile and mature cassava plants to identify genotypic differences and the relationships between juvenile traits and harvest index of mature plants. Root classes were categorised and root and shoot traits of eight (8) juvenile pot-grown cassava genotypes, were measured at 30 and 45 days after planting (DAP). The same or related traits were measured at 7 months after planting of the same genotypes grown in the field while yield and yield components were measured in 12-months old field-grown plants. The field experiment was done in 2017 and repeated in 2018. Differences between genotypes for the measured traits were explored using analysis of variance (ANOVA) while traits in juvenile plants were correlated or regressed onto traits measured in 7- and 12-months old plants. The results show significant genotypic variations for most of the traits measured in both juvenile and 7-months old plants. In the 12-months old plants, differences between genotypes were consistent for both 2017 and 2018. Broad-sense heritability was highest for the number of commercial roots (0.87) and shoot fresh weight (0.78) and intermediate for the total number of roots (0.60), harvest index (0.58), fresh weight of roots (0.45). For all the sampling time points or growth stages, there were greater correlations between traits measured at a particular growth stage than between the same traits at different growth stages. However, some juvenile-mature plant trait relationships were significant, positive and consistent for both 2017 and 2018. For example, total root length and the total number of roots in 30 DAP, and branching density of upper nodal roots in 45 DAP, positively correlated with harvest index of 12-months old plants in both 2017 and 2018. Similarly, the diameter of nodal roots, for example, had a negative, significant correlation with fresh shoot biomass of mature plants in both 2017 and 2018. Regression of traits measured in 30 DAP explained up to 22% and 36% of the variation in HI of mature plants in 2017 and 2018, respectively. It is concluded that the simple, rapid, inexpensive phenotyping approach adopted in this study is robust for identifying genotypic variations in juvenile cassava using root system traits. Also, the results provide seminal evidence for the existence of useful relationships between traits of juvenile and mature cassava plants that can be explored to predict yield and yield components.

Scopoletin increases glucose uptake through activation of PI3K and AMPK signaling pathway and improves insulin sensitivity in 3T3-L1 cells

Coumarins have been shown to reduce blood glucose levels and improve insulin sensitivity in other studies. The purpose of this study was to investigate the effects of scopoletin, which is a type of coumarin family, on glucose uptake in 3T3-L1 cells to test the hypothesis that scopoletin exerts an antidiabetic function on adipocytes. Scopoletin significantly increased glucose uptake, which was associated with increased expression of the plasma membrane glucose transporter type 4 (PM-GLUT4) in 3T3-L1 adipocytes. This increase in PM-GLUT4 expression was promoted by phosphorylation of protein kinase B, activation of phosphatidylinositol-3-kinase (PI3K), and enhanced intracellular glucose uptake. Scopoletin also promoted phosphorylation of adenosine monophosphate-activated protein kinase (AMPK) and enhanced PM-GLUT4 expression. Scopoletin-induced glucose uptake in 3T3-L1 adipocytes was inhibited by treatment with the PI3K inhibitor wortmannin and the AMPK inhibitor compound C. These results suggest that scopoletin has an antidiabetic effect by stimulating GLUT4 translocation to the PM through activation of the PI3K and AMPK pathways in 3T3-L1 adipocytes, thereby upregulating glucose uptake.

Protein Cross-Interactions for Efficient Photosynthesis in the Cassava Cultivar SC205 Relative to Its Wild Species

The underlying mechanisms of the higher photosynthetic efficiency of cultivated cassava relative to its wild species are poorly understood. In the present study, proteins in leaves and chloroplasts were analyzed to compare the differences among the cultivar SC205, its wild ancestor W14, and the related species Glaziovii. The functions of differential proteins are associated with 10 ontology groups including photosynthesis, carbohydrate and energy metabolism, as well as potential signal pathway. The protein-protein networks among 41 differential proteins showed that PGK1 is a hub protein and protein cross-interactions affected the differentiation of photosynthetic rate. Anatomy patterns and PEPC detection suggested that SC205 has more C₄ photosynthesis characteristics than Glaziovii and W14. Finally, a mechanism model of the efficient photosynthesis was proposed based on the remarkable variations in photosynthetic parameters and protein functions in the domestic cultivars.

Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach

Globally, cassava is an important source of starch, which is synthesized through carbon assimilation in cellular metabolism whereby harvested atmospheric carbon is assimilated into macromolecules. Although the carbon assimilation pathway is highly conserved across species, metabolic phenotypes could differ in composition, type, and quantity. To unravel the metabolic complexity and advantage of cassava over other starch crops, in terms of starch production, we investigated the carbon assimilation mechanisms in cassava through genome-based pathway reconstruction and comparative network analysis. First, MeRecon - the carbon assimilation pathway of cassava was reconstructed based upon six plant templates: Arabidopsis, rice, maize, castor bean, potato, and turnip. MeRecon, available at http://bml.sbi.kmutt.ac.th/MeRecon, comprises 259 reactions (199 EC numbers), 1,052 proteins (870 genes) and 259 metabolites in eight sub-metabolisms. Analysis of MeRecon and the carbon assimilation pathways of the plant templates revealed the overall topology is highly conserved, but variations at sub metabolism level were found in relation to complexity underlying each biochemical reaction, such as numbers of responsible enzymatic proteins and their evolved functions, which likely explain the distinct metabolic phenotype. Thus, this study provides insights into the network characteristics and mechanisms that regulate the synthesis of metabolic phenotypes of cassava.

The early transcriptome response of cassava (Manihot esculenta Crantz) to mealybug (Phenacoccus manihoti) feeding

The mealybug, Phenacoccus manihoti, is a leading pest of cassava (Manihot esculenta Crantz), damaging this crop globally. Although the biological control of this mealybug using natural predators has been established, resistance breeding remains an important means of control. Understanding plant responses to insect herbivory, by determining and identifying differentially expressed genes (DEGs), is a vital step towards the understanding of molecular mechanisms of defence responses in plants and the development of resistant cultivars by gene editing. Morphological and molecular analysis confirmed the mealybug identity as Phenacoccus manihoti (Matile-Ferrero). The transcriptome response of the green mite resistant cassava genotype AR23.1 was compared to P40/1 with no known resistance at 24 and 72 hours of mealybug infestation compared to non-infested mock. A total of 301 and 206 genes were differentially expressed at 24 and 72 of mealybug infestation for AR23.1 and P40/1 genotypes respectively, using a log2 fold change and P-value ≤ 0.05. Gene ontology functional classification revealed an enrichment of genes in the secondary metabolic process category in AR23.1 in comparison with P40/1, while genes in the regulation of molecular function, cellular component biogenesis and electron carrier categories were more significantly enriched in P40/1 than in AR23.1. Biological pathway analysis, based on KEGG, revealed a significant enrichment of plant-pathogen interaction and plant hormonal signal transduction pathways for a cohort of up-regulated and down-regulated DEGs in both genotypes. Defence-related genes such as 2-oxogluterate, gibberellin oxidase and terpene synthase proteins were only induced in genotype AR23.1 and not in P40/1, and subsequently validated by RT-qPCR. The study revealed a difference in response to mealybug infestation in the two genotypes studied, with AR23.1 showing a higher number of differentially expressed transcripts post mealybug infestation at 24 and 72 hours. Candidate defence-related genes that were overexpressed in the AR23.1 genotype post mealybug infestation will be useful in future functional studies towards the control of mealybugs.

Characterising shoot and root system trait variability and contribution to genotypic variability in juvenile cassava (Manihot esculenta Crantz) plants

The development of cassava genotypes with root system traits that increase soil resource acquisition could increase yields on infertile soils but there are relatively few work that has quantified cassava root system architecture (RSA). We used an easily adaptable and inexpensive protocol to: (i) measure genotypic variation for RSA and shoot traits of a range of cassava genotypes; and (ii) identify candidate variables that contribute the largest share of variance. Cassava genotypes were grown in soil-filled pots, maintained at 70% field capacity. Shoot and RSA traits were measured on plants grown up to 30, 45 and 60 days. Multivariate analysis was used to determine major traits contributing to variation. The study showed that cassava roots are adventitious in origin consisting of a main root axis and orders of lateral roots, and therefore the historically used term "fibrous roots" are redundant currently not contributing to clarity. There were significant differences (P < 0.05) for traits evaluated. The highest relative root growth rate occurred over the first 30 days and ranged from 0.39 to 0.48 cm day-1. Root fresh weight was significantly correlated with other traits, including root length (r = 0.79), leaf area (r = 0.72), number of lower nodal roots (r = 0.60), indicating that direct selection based on these traits might be sufficient to improve root biomass. Up to the first six principal components explained over 80% of the total variation among the genotypes for the traits measured at 30, 45 and 60 days. Leaf area, root diameter and branching density-related traits were the most important traits contributing to variation. Selection of cassava genotypes based on shoot and root biomass, root diameter and branching density at juvenile growth stage could be successful predictors of nutrient and water-use efficiency in the field. Further studies are required to relate studied juvenile cassava root traits with the performance of field-grown-mature plant with regard to drought, nutrient-use efficiency and yield.

Regional Heritability Mapping Provides Insights into Dry Matter Content in African White and Yellow Cassava Populations

The HarvestPlus program for cassava ( Crantz) fortifies cassava with β-carotene by breeding for carotene-rich tubers (yellow cassava). However, a negative correlation between yellowness and dry matter (DM) content has been identified. We investigated the genetic control of DM in white and yellow cassava. We used regional heritability mapping (RHM) to associate DM with genomic segments in both subpopulations. Significant segments were subjected to candidate gene analysis and candidates were validated with prediction accuracies. The RHM procedure was validated via a simulation approach and revealed significant hits for white cassava on chromosomes 1, 4, 5, 10, 17, and 18, whereas hits for the yellow were on chromosome 1. Candidate gene analysis revealed genes in the carbohydrate biosynthesis pathway including plant serine-threonine protein kinases (SnRKs), UDP (uridine diphosphate)-glycosyltransferases, UDP-sugar transporters, invertases, pectinases, and regulons. Validation using 1252 unique identifiers from the SnRK gene family genome-wide recovered 50% of the predictive accuracy of whole-genome single nucleotide polymorphisms for DM, whereas validation using 53 likely genes (extracted from the literature) from significant segments recovered 32%. Genes including an acid invertase, a neutral or alkaline invertase, and a glucose-6-phosphate isomerase were validated on the basis of an a priori list for the cassava starch pathway, and also a fructose-biphosphate aldolase from the Calvin cycle pathway. The power of the RHM procedure was estimated as 47% when the causal quantitative trait loci generated 10% of the phenotypic variance (sample size = 451). Cassava DM genetics are complex and RHM may be useful for complex traits.

Cassava (Manihot esculenta Crantz) and Yam (Dioscorea spp.) Crops and Their Derived Foodstuffs: Safety, Security and Nutritional Value

Cassava (Manihot esculenta Crantz) and yam (Dioscorea spp.) are tropical crops consumed by ca. 2 billion people and represent the main source of carbohydrate and energy for the approximately 700 million people living in the tropical and sub-tropical areas. They are a guarantee of food security for developing countries. The production of these crops and the transformation into food-derived commodities is increasing, it represents a profitable business and farmers generate substantial income from their market. However, there are some important concerns related to the food safety and food security. The high post-harvest losses, mainly for yam, the contamination by endogenous toxic compounds, mainly for cassava, and the contamination by external agents (such as micotoxins, pesticides, and heavy metal) represent a depletion of economic value and income. The loss in the raw crops or the impossibility to market the derived foodstuffs, due to incompliance with food regulations, can seriously limit all yam tubers and the cassava roots processors, from farmers to household, from small-medium to large enterprises. One of the greatest challenges to overcome those concerns is the transformation of traditional or indigenous processing methods into modern industrial operations, from the crop storage to the adequate package of each derived foodstuff.

Increased activities of peroxidase and polyphenol oxidase enhance cassava resistance to Tetranychus urticae

In order to study the function of peroxidase (POD) and polyphenol oxidase (PPO) in cassava resistance to spider mites, we tested the changes of transcription levels and activities of these two protective enzymes in both cassava and Tetranychus urticae (=T. cinnabarinus) during the interaction. The results showed that after damage of the mite-susceptible cassava cultivar BRA900 by T. urticae for 1 and 8 days, the transcription levels of MePOD and MePPO and the activities of POD and PPO showed no significant difference compared with those in undamaged leaves. However, the corresponding transcription levels and activities in 1- and 8-day-damaged leaves of mite-resistant cassava cultivar C1115 increased to a significant level of approximately twofold. When T. urticae fed on BRA900 for 1 and 8 days, the transcription levels of TcPPO and TcPOD and the activities of PPO and POD showed no significant difference compared with those before feeding. However, the corresponding transcription levels and activities of these two protective enzymes in T. urticae feeding on C1115 significantly decreased by about half. This study preliminarily validates the function of POD and PPO in cassava resistance to T. urticae, and provides candidate gene resource for molecular breeding of spider mite-resistant cassava.

Overproduction of superoxide dismutase and catalase confers cassava resistance to Tetranychus cinnabarinus

To explore the role of protective enzymes in cassava (Manihot esculenta Crantz) resistance to mites, transgenic cassava lines overproducing copper/zinc superoxide dismutase (MeCu/ZnSOD) and catalase (MeCAT1) were used to evaluate and molecularly confirm cassava resistance to Tetranychus cinnabarinus. Laboratory evaluation demonstrated that, compared with the control cultivar TMS60444 (wild type, WT), the survival, reproduction, development and activities of SOD and CAT in T. cinnabarinus feeding on transgenic cassava lines SC2, SC4, and SC11 significantly inhibited. Furthermore, the activities of SOD and CAT in transgenic cassava lines SC2, SC4, and SC11 damaged by T. cinnabarinus significantly increased. These findings were similar to the results in the mite-resistant cassava cultivars. Besides, field evaluation indicated that the transgenic cassava lines SC2, SC4, and SC11 were slightly damaged as the highly mite-resistant control C1115, while the highly mite-susceptible WT was severely damaged by T. cinnabarinus. Laboratory and field evaluation demonstrated that transgenic cassava lines were resistant to T. cinnabarinus, which directly confirmed that the increase in SOD and CAT activities was positively related to cassava resistance to T. cinnabarinus. These results will help in understanding the antioxidant defense responses in the cassava-mite interaction and molecular breeding of mite-resistant cassava for effective pest control.

Cassava: Nutrient composition and nutritive value in poultry diets

Insufficient supply, high prices and competition with the human food and biofuel industries means there is a continuous demand for alternative energy sources for poultry. As a result, cassava is becoming an increasingly important ingredient in poultry diets, largely due to its high availability. Efficient use of cassava products has been shown to reduce feed costs of poultry production. The utilisation of cassava is, however, limited by a number of factors, including its high fibre and low energy content and the presence of anti-nutritional factors, primarily hydrocyanic acid (HCN). With correct processing the inclusion level of cassava in poultry diets could be increased. Extensive research has been conducted on cassava products for poultry, but there is still a lack of consistency amongst the measured nutritive values for cassava and its products, hence variation exists in results from poultry studies. This paper reviews the nutrient composition of cassava products and its value as an alternative energy source in poultry diets.

Physiological Investigation and Transcriptome Analysis of Polyethylene Glycol (PEG)-Induced Dehydration Stress in Cassava

Cassava is an important tropical and sub-tropical root crop that is adapted to drought environment. However, severe drought stress significantly influences biomass accumulation and starchy root production. The mechanism underlying drought-tolerance remains obscure in cassava. In this study, changes of physiological characters and gene transcriptome profiles were investigated under dehydration stress simulated by polyethylene glycol (PEG) treatments. Five traits, including peroxidase (POD) activity, proline content, malondialdehyde (MDA), soluble sugar and soluble protein, were all dramatically induced in response to PEG treatment. RNA-seq analysis revealed a gradient decrease of differentially expressed (DE) gene number in tissues from bottom to top of a plant, suggesting that cassava root has a quicker response and more induced/depressed DE genes than leaves in response to drought. Overall, dynamic changes of gene expression profiles in cassava root and leaves were uncovered: genes related to glycolysis, abscisic acid and ethylene biosynthesis, lipid metabolism, protein degradation, and second metabolism of flavonoids were significantly induced, while genes associated with cell cycle/organization, cell wall synthesis and degradation, DNA synthesis and chromatin structure, protein synthesis, light reaction of photosynthesis, gibberelin pathways and abiotic stress were greatly depressed. Finally, novel pathways in ABA-dependent and ABA-independent regulatory networks underlying PEG-induced dehydration response in cassava were detected, and the RNA-Seq results of a subset of fifteen genes were confirmed by real-time PCR. The findings will improve our understanding of the mechanism related to dehydration stress-tolerance in cassava and will provide useful candidate genes for breeding of cassava varieties better adapted to drought environment.

Transcriptional analysis of South African cassava mosaic virus-infected susceptible and tolerant landraces of cassava highlights differences in resistance, basal defense and cell wall associated genes during infection

BACKGROUND

Cassava mosaic disease is caused by several distinct geminivirus species, including South African cassava mosaic virus-[South Africa:99] (SACMV). To date, there is limited gene regulation information on viral stress responses in cassava, and global transcriptome profiling in SACMV-infected cassava represents an important step towards understanding natural host responses to plant geminiviruses.

RESULTS

A RNA-seq time course (12, 32 and 67 dpi) study, monitoring gene expression in SACMV-challenged susceptible (T200) and tolerant (TME3) cassava landraces, was performed using the Applied Biosystems (ABI) SOLiD next-generation sequencing platform. The multiplexed paired end sequencing run produced a total of 523 MB and 693 MB of paired-end reads for SACMV-infected susceptible and tolerant cDNA libraries, respectively. Of these, approximately 50.7% of the T200 reads and 55.06% of TME3 reads mapped to the cassava reference genome available in phytozome. Using a log2 fold cut-off (p<0.05), comparative analysis between the six normalized cDNA libraries showed that 4181 and 1008 transcripts in total were differentially expressed in T200 and TME3, respectively, across 12, 32 and 67 days post infection, compared to mock-inoculated. The number of responsive transcripts increased dramatically from 12 to 32 dpi in both cultivars, but in contrast, in T200 the levels did not change significantly at 67 dpi, while in TME3 they declined. GOslim functional groups illustrated that differentially expressed genes in T200 and TME3 were overrepresented in the cellular component category for stress-related genes, plasma membrane and nucleus. Alterations in the expression of other interesting genes such as transcription factors, resistance (R) genes, and histone/DNA methylation-associated genes, were observed. KEGG pathway analysis uncovered important altered metabolic pathways, including phenylpropanoid biosynthesis, sucrose and starch metabolism, and plant hormone signalling.

CONCLUSIONS

Molecular mechanisms for TME3 tolerance are proposed, and differences in patterns and levels of transcriptome profiling between T200 and TME3 with susceptible and tolerant phenotypes, respectively, support the hypothesis that viruses rearrange their molecular interactions in adapting to hosts with different genetic backgrounds.

Present and future of folate biofortification of crop plants

Improving nutritional health is one of the major socio-economic challenges of the 21st century, especially with the continuously growing and ageing world population. Folate deficiency is an important and underestimated problem of micronutrient malnutrition affecting billions of people worldwide. More and more countries are adapting policies to fight folate deficiency, mostly by fortifying foods with folic acid. However, there is growing concern about this practice, calling for alternative or complementary strategies. In addition, fortification programmes are often inaccessible to remote and poor populations where folate deficiency is most prevalent. Enhancing folate content in staple crops by metabolic engineering is a promising, cost-effective strategy to eradicate folate malnutrition worldwide. Over the last decade, major progress has been made in this field. Nevertheless, engineering strategies have thus far been implemented on a handful of plant species only and need to be transferred to highly consumed staple crops to maximally reach target populations. Moreover, successful engineering strategies appear to be species-dependent, hence the need to adapt them in order to biofortify different staple crops with folate.

Drought adversely affects tuber development and nutritional quality of the staple crop cassava (Manihot esculenta Crantz)

Cassava (Manihot esculenta Crantz) is the staple food source for over 850million people worldwide. Cassava contains cyanogenic glucosides and can be toxic to humans, causing paralysing diseases such as konzo, and even death if not properly processed. Konzo epidemics are often associated with times of drought. This may be due to a greater reliance on cassava as it is drought tolerant, but it may also be due to an increase in cyanogenic glucosides. Episodic droughts are forecast to become more common in many cassava-growing regions. We therefore sought to quantify the effect of water-stress on both yield and cyanogenic glucoside concentration (CNc) in the developing tubers of cassava. Five-month-old plants were grown in a glasshouse and either well watered or droughted for 28 days. A subset of droughted plants was re-watered half way through the experiment. Droughted plants had 45% fewer leaves and lower tuber yield, by 83%, compared with well-watered plants. CNc was 2.9-fold higher in the young leaves of droughted plants, whereas CNc in tubers from droughted plants was 4-fold greater than in tubers from well-watered plants. Re-watered plants had a similar biomass to control plants, and lower CNc than droughted plants. These findings highlight the important link between food quality and episodic drought.

Variations in the chemical composition of cassava ( Manihot esculenta Crantz) leaves and roots as affected by genotypic and environmental variation

The purpose of this study was to assess the quality of cassava cultivars, in terms of cyanogenic potential and composition of macro- and micronutrients, sampled from different locations in rural Mozambique. Total cyanide concentrations in fresh cassava tissues were measured using portable cyanide testing kits, and elemental nutrients were later analyzed from dried plant tissue. Variation in cyanogenic potential and nutrient composition occurred both among cultivars and across locations. The majority of cultivars contained >100 ppm total cyanide, fresh weight, and are therefore considered to be dangerously poisonous unless adequately processed before consumption. Leaf cyanogenic and nutrient content varied with plant water status, estimated using carbon isotope discrimination (δ(13)C). The colonization of roots of all cultivars by arbuscular mycorrhizal fungi was also quantified and found to be high, indicating that mycorrhizas could play a key role in plant nutrient acquisition in these low-input farming systems.

Changes in scopoletin concentration in cassava chips from four varieties during storage

BACKGROUND

The use of the root crop cassava (Manihot esculenta Crantz) is constrained by its rapid deterioration after harvesting. Chemical and spectroscopic examination earlier revealed the accumulation of the four hydroxycoumarins esculetin, esculin, scopolin and scopoletin derived from the phenylpropanoid pathway, during the time course of postharvest deterioration. In this investigation the scopoletin level in parenchymal samples of four cassava cultivars used in Benin, i.e. Kpaki kpika, Kpaki soan, Logoguesse kotorou and BEN 86052, was investigated by high-performance liquid chromatography (HPLC).

RESULTS

Presence was shown in all four varieties with a mean in fresh roots between 4.1 and 11.1 mg kg(-1) dry weight. A strong increase in the content of scopoletin was noticed after a peeling and drying process (6 days) for chip production, the mean content reaching 242.5 mg kg(-1) dry weight in the cultivar BEN 86052. After 3 months of storage this had decreased to 0.7 mg kg(-1) dry weight.

CONCLUSION

Strong accumulation of scopoletin in cassava roots used for chip production in Benin is followed by a decrease in its concentration.

RNAi-mediated resistance to Cassava brown streak Uganda virus in transgenic cassava

Cassava brown streak disease (CBSD), caused by Cassava brown streak Uganda virus (CBSUV) and Cassava brown streak virus (CBSV), is of new epidemic importance to cassava (Manihot esculenta Crantz) production in East Africa, and an emerging threat to the crop in Central and West Africa. This study demonstrates that at least one of these two ipomoviruses, CBSUV, can be efficiently controlled using RNA interference (RNAi) technology in cassava. An RNAi construct targeting the near full-length coat protein (FL-CP) of CBSUV was expressed constitutively as a hairpin construct in cassava. Transgenic cassava lines expressing small interfering RNAs (siRNAs) against this sequence showed 100% resistance to CBSUV across replicated graft inoculation experiments. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis showed the presence of CBSUV in leaves and some tuberous roots from challenged controls, but not in the same tissues from transgenic plants. This is the first demonstration of RNAi-mediated resistance to the ipomovirus CBSUV in cassava.

RNAi-mediated resistance to diverse isolates belonging to two virus species involved in Cassava brown streak disease

Cassava brown streak disease (CBSD) is emerging as one of the most important viral diseases of cassava (Manihot esculenta) and is considered today as the biggest threat to cassava cultivation in East Africa. The disease is caused by isolates of at least two phylogenetically distinct species of single-stranded RNA viruses belonging to the family Potyviridae, genus Ipomovirus. The two species are present predominantly in the coastal lowland [Cassava brown streak virus (CBSV); Tanzania and Mozambique] and highland [Cassava brown streak Uganda virus (CBSUV); Lake Victoria Basin, Uganda, Kenya and Malawi] in East Africa. In this study, we demonstrate that CBSD can be efficiently controlled using RNA interference (RNAi). Three RNAi constructs targeting the highland species were generated, consisting of the full-length (FL; 894 nucleotides), 397-nucleotide N-terminal and 491-nucleotide C-terminal portions of the coat protein (CP) gene of a Ugandan isolate of CBSUV (CBSUV-[UG:Nam:04]), and expressed constitutively in Nicotiana benthamiana. After challenge with CBSUV-[UG:Nam:04], plants homozygous for FL-CP showed the highest resistance, followed by the N-terminal and C-terminal lines with similar resistance. In the case of FL, approximately 85% of the transgenic plant lines produced were completely resistant. Some transgenic lines were also challenged with six distinct isolates representing both species: CBSV and CBSUV. In addition to nearly complete resistance to the homologous virus, two FL plant lines showed 100% resistance and two C-terminal lines expressed 50-100% resistance, whereas the N-terminal lines succumbed to the nonhomologous CBSV isolates. Northern blotting revealed a positive correlation between the level of transgene-specific small interfering RNAs detected in transgenic plants and the level of virus resistance. This is the first demonstration of RNAi-mediated resistance to CBSD and protection across very distant isolates (more than 25% in nucleotide sequence) belonging to two different species: Cassava brown streak virus and Cassava brown streak Uganda virus.

Cassava: an appraisal of its phytochemistry and its biotechnological prospects

The present state of knowledge of the phytochemistry of small molecules isolated from the roots and leaves of cassava, Manihot esculenta Crantz (Euphorbiaceae), is reviewed. Cassava roots are an important source of dietary and industrial carbohydrates, mainly eaten as a source of starch, forming the staple food to over 500 million; additionally, the roots have value as a raw material for industrial starch production and for animal feed giving the crop high economic value, but it suffers markedly from post-harvest physiological deterioration (PPD). The hydroxycoumarins scopoletin and its glucoside scopolin as well as trace quantities of esculetin and its glucoside esculin are identified from cassava roots during PPD. The biotechnological prospects for cassava are also reviewed including a critical appraisal of transgenic approaches for crop improvement, together with its use for bioethanol production, due to cassava's efficient ability to fix carbon dioxide into carbohydrate.

AFLP-based transcript profiling for cassava genome-wide expression analysis in the onset of storage root formation

Cassava (Manihot esculenta Crantz) is a root crop that accumulates large quantities of starch, and it is an important source of carbohydrate. Study on gene expressions during storage root development provides important information on storage root formation and starch accumulation as well as unlock new traits for improving of starch yield. cDNA-Amplified Fragment Length Polymorphism (AFLP) was used to compare gene expression profiles in fibrous and storage roots of cassava cultivar Kasetsart 50. Total of 155 differentially expressed transcript-derived fragments with undetectable or low expression in leaves were characterized and classified into 11 groups regarding to their functions. The four major groups were no similarity (20%), hypothetical or unknown proteins (17%), cellular metabolism and biosynthesis (17%) and cellular communication and signaling (14%). Interestingly, sulfite reductase (MeKD82), calcium-dependent protein kinase (CDPK) (MeKD83), ent-kaurene synthase (KS) (MeKD106) and hexose transporter (HT) (MeKD154) showed root-specific expression patterns. This finding is consistent with previously reported genes involved in the initiation of potato tuber. Semi-quantitative reverse transcription polymerase chain reaction of early-developed root samples confirmed that those four genes exhibited significant expression with similar pattern in the storage root initiation and early developmental stages. We proposed that KS and HT may involve in transient induction of CDPK expression, which may play an important role in the signaling pathway of storage root initiation. Sulfite reductase, on the other hand, may involve in storage root development by facilitating sulfur-containing protein biosynthesis or detoxifying the cyanogenic glucoside content through aspartate biosynthesis.

Nutritional Value of Cassava for Use as a Staple Food and Recent Advances for Improvement

  Cassava is a drought-tolerant, staple food crop grown in tropical and subtropical areas where many people are afflicted with undernutrition, making it a potentially valuable food source for developing countries. Cassava roots are a good source of energy while the leaves provide protein, vitamins, and minerals. However, cassava roots and leaves are deficient in sulfur-containing amino acids (methionine and cysteine) and some nutrients are not optimally distributed within the plant. Cassava also contains antinutrients that can have either positive or adverse effects on health depending upon the amount ingested. Although some of these compounds act as antioxidants and anticarcinogens, they can interfere with nutrient absorption and utilization and may have toxic side effects. Efforts to add nutritional value to cassava (biofortification) by increasing the contents of protein, minerals, starch, and β-carotene are underway. The transfer of a 284 bp synthetic gene coding for a storage protein rich in essential amino acids and the crossbreeding of wild-type cassava varieties with Manihot dichotoma or Manihot oligantha have shown promising results regarding cassava protein content. Enhancing ADP glucose pyrophosphorylase activity in cassava roots or adding amylase to cassava gruels increases cassava energy density. Moreover, carotenoid-rich yellow and orange cassava may be a foodstuff for delivering provitamin A to vitamin A-depleted populations. Researchers are currently investigating the effects of cassava processing techniques on carotenoid stability and isomerization, as well as the vitamin A value of different varieties of cassava. Biofortified cassava could alleviate some aspects of food insecurity in developing countries if widely adopted.

The chloroplast protein translocation complexes of Chlamydomonas reinhardtii: a bioinformatic comparison of Toc and Tic components in plants, green algae and red algae

The recently completed genome of Chlamydomonas reinhardtii was surveyed for components of the chloroplast protein translocation complexes. Putative components were identified using reciprocal BlastP searches with the protein sequences of Arabidopsis thaliana as queries. As a comparison, we also surveyed the new genomes of the bryophyte Physcomitrella patens, two prasinophyte green algae (Ostreococcus lucimarinus and Ostreococcus tauri), the red alga Cyanidioschizon merolae, and several cyanobacteria. Overall, we found that the components of the import pathway are remarkably well conserved, particularly among the Viridiplantae lineages. Specifically, C. reinhardtii contained almost all the components found in A. thaliana, with two exceptions. Missing from C. reinhardtii are the C-terminal ferredoxin-NADPH-reductase (FNR) binding domain of Tic62 and a full-length, TPR-bearing Toc64. Further, the N-terminal domain of C. reinhardtii Toc34 is highly acidic, whereas the analogous region in C. reinhardtii Toc159 is not. This reversal of the vascular plant model may explain the similarity of C. reinhardtii chloroplast transit peptides to mitochondrial-targeting peptides. Other findings from our genome survey include the absence of Tic22 in both Ostreococcus genomes; the presence of only one Toc75 homolog in C. merolae; and, finally, a distinctive propensity for gene duplication in P. patens.

Sugar-mediated semidian oscillation of gene expression in the cassava storage root regulates starch synthesis

Starch branching enzyme (SBE) activity in the cassava storage root exhibited a diurnal fluctuation, dictated by a transcriptional oscillation of the corresponding SBE genes. The peak of SBE activity coincided with the onset of sucrose accumulation in the storage, and we conclude that the oscillatory mechanism keeps the starch synthetic apparatus in the storage root sink in tune with the flux of sucrose from the photosynthetic source. When storage roots were uncoupled from the source, SBE expression could be effectively induced by exogenous sucrose. Turanose, a sucrose isomer that cannot be metabolized by plants, mimicked the effect of sucrose, demonstrating that downstream metabolism of sucrose was not necessary for signal transmission. Also glucose and glucose-1-P induced SBE expression. Interestingly, induction by sucrose, turanose and glucose but not glucose-1-P sustained an overt semidian (12-h) oscillation in SBE expression and was sensitive to the hexokinase (HXK) inhibitor glucosamine. These results suggest a pivotal regulatory role for HXK during starch synthesis. Abscisic acid (ABA) was another potent inducer of SBE expression. Induction by ABA was similar to that of glucose-1-P in that it bypassed the semidian oscillator. Both the sugar and ABA signaling cascades were disrupted by okadaic acid, a protein phosphatase inhibitor. Based on these findings, we propose a model for sugar signaling in regulation of starch synthesis in the cassava storage root.

In vitro cultured primary roots derived from stem segments of cassava (Manihot esculenta) can behave like storage organs

BACKGROUND AND AIMS

Cassava (Manihot esculenta) has three adventitious root types: primary and secondary fibrous roots, and storage roots. Different adventitious root types can also regenerate from in vitro cultured segments. The aim of this study was to investigate aspects of in vitro production of storage roots.

METHODS

Morphological and anatomical analyses were performed to identify and differentiate each root type. Twenty-nine clones were assayed to determine the effect of genotype on the capacity to form storage roots in vitro. The effects of cytokinins and auxins on the formation of storage roots in vitro were also examined.

KEY RESULTS

Primary roots formed in vitro and in vivo had similar tissue kinds; however, storage roots formed in vitro exhibited physiological specialization for storing starch. The only consistent diagnostic feature between secondary fibrous and storage roots was their functional differentiation. Anatomical analysis of the storage roots formed in vitro showed that radial expansion as a consequence of massive proliferation and enlargement of parenchymatous cells occurred in the middle cortex, but not from cambial activity as in roots formed in vivo. Cortical expansion could be related to dilatation growth favoured by hormone treatments. Starch deposition of storage roots formed in vitro was confined to cortical tissue and occurred earlier than in storage roots formed in vivo. Auxin and cytokinin supplementation were absolutely required for in vitro storage root regeneration; these roots were not able to develop secondary growth, but formed a tissue competent for starch storing. MS medium with 5 % sucrose plus 0.54 microM 1-naphthaleneacetic acid and 0.44 microM 6-benzylaminopurine was one of the most effective in stimulating the storage root formation. Genotypes differed significantly in their capacity to produce storage roots in vitro. Storage root formation was considerably affected by the segment's primary position and strongly influenced by hormone treatments.

CONCLUSIONS

The storage root formation system reported here is a first approach to develop a tuberization model, and additional efforts are required to improve it. Although it was not possible to achieve root secondary growth, after this work it will be feasible to advance in some aspects of in vitro cassava tuberization.