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

Abstract

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.

Integrated genetic and metabolic characterisation of diverse Latin American cassava (Manihot esculentaCrantz) germplasm; implications for future breeding strategies

“…Thus, in comparison to other analytical apparatus it provides the closest reflection of the metabolome that can be achieved using one analytical platform. The overriding feature of the genotyping data across the CIAT diversity panel was the clustering on agro-ecological location, previously reported in smaller scale studies (19-22). In the case of the leaf metabolome there was a clear correlation with the genotypic data.…”

Integrated genetic and metabolic characterization of Latin American cassava (Manihot esculenta) germplasm

“…These criteria have typically resulted in local advanced collections being the focus of analysis. ( Ferguson et al 2019 ; Drapal et al 2020 ; Perez-Fons et al 2020 ; Ogbonna et al 2021a , Ogbonna et al 2021b ; Alves-Pereira et al 2022 ; Ocampo et al 2022 ) ( Supplemental Fig. S1 ).…”

“…S1 ). In addition to genomic approaches, independent metabolomic studies in cassava collections have been focused on selected discovery panels ( Drapal et al 2019 ; Perez-Fons et al 2019 ; Drapal et al 2020 ; Perez-Fons et al 2020 ). The present study represents one of the largest genomic and metabolomic study performed on cassava to date by exploiting genetic resources present in the CIAT genebank collection, which is the largest and most diverse for this crop worldwide (Reinhardt Howeler et al 2013 ; Supplemental Fig.…”

A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculentaCrantz)

“…While transcriptomics has relied on contrasting individuals, our study provides a population-based resource, unique to previously described available transcriptomics cassava resources. Resources including genomics, transcriptomics, metabolomics, epigenomics and proteomics to support cassava improvement and intensification have been previously described 15,32,[61][62][63][64][65][66][67][68][69][70][71] . In this study, we characterized the transcriptomics of 150 accessions across five different tissue types.…”