Identification of Cassava Varieties in Ex-Situ Collections and Global Farmer’s Fields: An Update from 1990 to 2020

The identification of cassava cultivars is important for understanding the crop’s production system, enabling crop improvement practitioners to design and deliver tailored solutions with which farmers can secure high yields and sustainable production. Across the lowland tropics today, a large number improved varieties and landraces of cassava are under cultivation, making it inefficient for breeders and geneticists to set improvement goals for the crop. The identification and characterization of cassava genotypes is currently based on either morphological characters or molecular features. The major aim of cultivar identification is to catalog the crop’s genetic diversity, but a consensus approach has still not been established. Of the two approaches to the identification of variety, morphological characters seem to account for most of the genetic variability reported in cassava. However, these characters must be treated with caution, as phenotypic changes can be due to environmental and climatic conditions as well as to the segregation of new highly heterozygous populations, thus, making the accurate identification of varieties difficult. The use of molecular markers has allowed researchers to establish accurate relationships between genotypes, and to measure and track their heterozygous status. Since the early 1990’s, molecular geneticists working with cassava have been developing and deploying DNA-based tools for the identification and characterization of landraces or improved varieties. Hence, in the last five years, economists and social scientists have adopted DNA-based variety identification to measure the adoption rates of varieties, and to support the legal protection of breeder’s rights. Despite the advances made in the deployment of molecular markers for cassava, multiple platform adoption, as well as their costs and variable throughput, has limited their use by practitioners of crop improvement of cassava. The post-genomic era has produced a large number of genome and transcriptome sequencing tools, and has increased our capacity to develop and deploy genome-based tools to account for the crop’s genetic variability by accurately measuring and tracking allele diversity. These technologies allow the creation of haplotype catalogs that can be widely shared across the cassava crop improvement community. Low-density genome-wide SNP markers might be the solution for the wide adoption of molecular tools for the identification of cultivars or varieties of cassava. In this review we survey the efforts made in the past 30 years to establish the tools for cultivar identification of cassava in farmer’s fields and gene banks. We also emphasize the need for a global picture of the genetic diversity of this crop, at its center of origin in South America

“Rambo root” to the rescue: How a simple, low‐cost solution can lead to multiple sustainable development gains

Rugged and resilient, cassava is a bulky root crop that can thrive on poor soils. Cultivating it offers the potential to restore degraded land, which in turn may reduce hunger, generate livelihoods, fight climate change and even promote peace. As such, farming cassava offers a nature‐based solution that can contribute to achieving numerous sustainable development targets. The authors acknowledge that scaling up production of any commodity may bring risks of deforestation and biodiversity loss through clearing forest areas. In the case of increasing cassava production, though, this may not be the case because cassava can be cultivated on land affected by degradation, and this resource is abundant; policies and initiatives exist to mitigate those risks; and the principal goal is to scale up a sustainable land use system

Cassava traits and end-user preference: relating traits to consumer liking, sensory perception, and genetics

Breeding efforts have focused on improving agronomic traits of the cassava plant however little research has been done to enhance the crop palatability. This review investigates the links between cassava traits and end-user preference in relation with sensory characteristics. The main trait is starch and its composition related to the textural properties of the food. Pectin degradation during cooking resulted in increased mealiness. Nutritional components such as carotenoids made the cassava yellow but also altered sweetness and softness; however yellow cassava was more appreciated by consumers than traditional (white) varieties. Components formed during processing such as organic acids gave fermented cassava products an acidic taste that was appreciated but the fermented smell was not always liked. Anti-nutritional compounds such as cyanogenic glucosides were mostly related to bitter taste. Post-harvest Physiological Deterioration (PPD) affected the overall sensory characteristics and acceptability. Genes responsible for some of these traits were also investigated. Diversity in cassava food products can provide a challenge to identifying acceptance criteria. Socio-economic factors such as gender may also be critical. This review leads to questions in relation to the adaptation of cassava breeding to meet consumer needs and preference in order to maximise income, health and food security

Farm management and varietal choice in cassava-based production systems in Colombia

Cassava is a commodity root crop grown globally for food and industrial purposes. In Colombia, it is the ninth most planted agricultural product involving more than 140 thousand farmers. Despite the key role it plays in the Colombian agricultural sector, information regarding the crop’s management or how cassava growers select on cultivars to grow for different purposes is limited or inexistent. This working paper exploits two separate primary data surveys at household-level in the Caribbean region and Cauca main cassava growing areas of Colombia. These data allowed to characterize these cassava production systems and discuss how to improve and strengthen this important agricultural sector. Detailed plot and household-level data was collected from 306 cassava growers in Cauca Department in 2014 and 395 cassava growers in Bolívar, Sucre, Córdoba, and Magdalena departments (known as the Caribbean region) in 2017. The analysis incorporates on-farm identification of cassava varieties using DNA fingerprinting analysis, providing insight into households’ decision about cassava variety management and the relative importance of these varieties in the country. The results indicate that most producers surveyed are smallholders, with agriculture as their principal occupation. These farmers have low or no access to extension services and low yields are observed when improved varieties have not been adopted vis-à-vis the national average, with large heterogeneity among departments. Regarding improved varieties, we identified low rates of adoption and considerably yields differences when compared with those farmers using non-improved germplasm. Thus, our results depict the importance of increasing the dissemination and adoption of improved varieties, which can help to close yield gaps and improve producers’ livelihoods. Furthermore, DNA analysis was a valuable tool to improve variety identification and helps to map the areas under improve against land races and accurate disaggregate the crop productivity. Finally, these households present high vulnerability according to poverty scorecards and ELCSA indicators, accompanied by low levels of education for all family members

Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid.

BACKGROUND:Whiteflies are a threat to cassava (Manihot esculenta), an important staple food in many tropical/subtropical regions. Understanding the molecular mechanisms regulating cassava's responses against this pest is crucial for developing control strategies. Pathogenesis-related (PR) protein families are an integral part of plant immunity. With the availability of whole genome sequences, the annotation and expression programs of the full complement of PR genes in an organism can now be achieved. An understanding of the responses of the entire complement of PR genes during biotic stress and to the defense hormones, salicylic acid (SA) and jasmonic acid (JA), is lacking. Here, we analyze the responses of cassava PR genes to whiteflies, SA, JA, and other biotic aggressors. RESULTS:The cassava genome possesses 14 of the 17 plant PR families, with a total of 447 PR genes. A cassava PR gene nomenclature is proposed. Phylogenetic relatedness of cassava PR proteins to each other and to homologs in poplar, rice and Arabidopsis identified cassava-specific PR gene family expansions. The temporal programs of PR gene expression in response to the whitefly (Aleurotrachelus socialis) in four whitefly-susceptible cassava genotypes showed that 167 of the 447 PR genes were regulated after whitefly infestation. While the timing of PR gene expression varied, over 37% of whitefly-regulated PR genes were downregulated in all four genotypes. Notably, whitefly-responsive PR genes were largely coordinately regulated by SA and JA. The analysis of cassava PR gene expression in response to five other biotic stresses revealed a strong positive correlation between whitefly and Xanthomonas axonopodis and Cassava Brown Streak Virus responses and negative correlations between whitefly and Cassava Mosaic Virus responses. Finally, certain associations between PR genes in cassava expansions and response to biotic stresses were observed among PR families. CONCLUSIONS:This study represents the first genome-wide characterization of PR genes in cassava. PR gene responses to six biotic stresses and to SA and JA are demonstrably different to other angiosperms. We propose that our approach could be applied in other species to fully understand PR gene regulation by pathogens, pests and the canonical defense hormones SA and JA

The metabotyping of an East African cassava diversity panel: A core collection for developing biotic stress tolerance in cassava

Cassava will have a vital role to play, if food security is to be achieved in Sub-Saharan Africa, especially Central and East Africa. The whitefly Bemisia tabaci poses a major threat to cassava production by small holder farmers in part due to their role as a vector of cassava mosaic begomoviruses (CMBs) and cassava brown streak ipomoviruses (CBSIs). In the present study untargeted metabolomics has been used as a tool to assess natural variation, similarities and attempts to identify trait differentiators among an East African cassava diversity panel that displayed tolerance/resistance to the effects of Bemisia tabaci infestation. The metabolome captured, was represented by 1529 unique chemical features per accession. Principal component analysis (PCA) identified a 23% variation across the panel, with geographical origin/adaption the most influential classification factors. Separation based on resistance and susceptible traits to Bemisia tabaci could also be observed within the data and was corroborated by genotyping data. Thus the metabolomics pipeline represented an effective metabotyping approach. Agglomerative Hierarchical Clustering Analysis (HCA) of both the metabolomics and genotyping data was performed and revealed a high level of similarity between accessions. Specific differentiating features/metabolites were identified, including those potentially conferring vigour to whitefly tolerance on a constitutive manner. The implications of using these cassava varieties as parental breeding material and the future potential of incorporating more exotic donor material is discussed

A metabolomics characterisation of natural variation in the resistance of cassava to whitefly

Background: Cassava whitefly outbreaks were initially reported in East and Central Africa cassava (Manihot esculenta Crantz) growing regions in the 1990's and have now spread to other geographical locations, becoming a global pest severely affecting farmers and smallholder income. Whiteflies impact plant yield via feeding and vectoring cassava mosaic and brown streak viruses, making roots unsuitable for food or trading. Deployment of virus resistant varieties has had little impact on whitefly populations and therefore development of whitefly resistant varieties is also necessary as part of integrated pest management strategies. Suitable sources of whitefly resistance exist in germplasm collections that require further characterization to facilitate and assist breeding programs. Results: In the present work, a hierarchical metabolomics approach has been employed to investigate the underlying biochemical mechanisms associated with whitefly resistance by comparing two naturally occurring accessions of cassava, one susceptible and one resistant to whitefly. Quantitative differences between genotypes detected at pre-infestation stages were consistently observed at each time point throughout the course of the whitefly infestation. This prevalent differential feature suggests that inherent genotypic differences override the response induced by the presence of whitefly and that they are directly linked with the phenotype observed. The most significant quantitative changes relating to whitefly susceptibility were linked to the phenylpropanoid super-pathway and its linked sub-pathways: monolignol, flavonoid and lignan biosynthesis. These findings suggest that the lignification process in the susceptible variety is less active, as the susceptible accession deposits less lignin and accumulates monolignol intermediates and derivatives thereof, differences that are maintained during the time-course of the infestation. Conclusions: Resistance mechanism associated to the cassava whitefly-resistant accession ECU72 is an antixenosis strategy based on reinforcement of cell walls. Both resistant and susceptible accessions respond differently to whitefly attack at biochemical level, but the inherent metabolic differences are directly linked to the resistance phenotype rather than an induced response in the plant