Brown streak is the most destructive viral disease of cassava causing up to 100% yield loss whilst fungal diseases contribute up to 90% cassava yield loss in Sub Saharan Africa. Genetic diversity of novel virus and fungal species infecting cassava in Bagamoyo, Tanzania is not fully comprehended. For unclear reasons, it is difficulty to breed resistance for one causal pathogen of cassava brown streak disease (CBSD), Cassava Brown Streak Virus (CBSV) compared to another, Ugandan Cassava Brown Streak Virus (UCBSV) species. Furthermore, genetic basis for trait discrepancy between the two virus species is elusive. CBSD-resistance status of the improved KBH 2006/0026 genotype of cassava in Bagamoyo, Tanzania is controversial because sporadic outbreak of the disease has become common in the genotype since 2019, even though it was previously reported to exhibit maximum resistance to infection by both CBSV and UCBSV species within 2014 - 2017 period. Metatranscriptomic, time-series transcriptomic and in silico studies were conducted to understand diversity of virome and mycobiome of cassava in Bagamoyo Tanzania, resistance status of KBH 2006/0026 and basis for trait discrepancy between the CBSV and UCBSV species, correspondingly. This study reports for the first time, incidence of Manihot esculenta associated virus 1 (MEAV-1) belonging to Ampelovirus genus and Closteroviridae family in Kiroba genotype. Twenty-two fungal species were also identified from cassava leaves in Bagamoyo fields; some are pathogenic/mycotoxic whilst others have potential applications in medicine, food and pharmaceutical industries. This study has discovered that the CBSV and UCBSV species express Second 6-Kilodalton (6K2) protein with varied 3D structures and polarity, suspected reason for discrepancy in tissue titres and replication rate between them. By experimentation it was proved that, KBH 2006/0026 is no longer CBSD-resistant. This study suggests that: multiplex reverse transcription polymerase chain reaction (RT-PCR)-based assay needs to be developed and used for accurate diagnosis of multiple virus species causing the CBSD, 6K2 should be targeted for transgenesis of virus-specific, resistant cassava by RNA interference (RNAi) technology. Equally, fungal-resistant cassava needs to be produced and used.

Swedish International Development Cooperation Agency (SIDA) is highly appreciated for financing the current study. Special gratitude goes to my employer, University of Dar es Salaam, Mkwawa University College of Education (MUCE) for the given opportunity to pursue my PhD study. Eastern Hub of International Institute of Tropical Agriculture (IITA) is highly appreciated for research support especially, access to field trials for sample collection, use of screen house for experimentation, molecular ...

Plant Production and Health

Agronomy; Cassava; Food Security; Plant Breeding; Plant Diseases; Plant Health; Plant Production

Cassava; Plant Diseases; Genetic Diversity; Viruses; Plant Health; Tanzania

Africa; East Africa

Tanzania

Eastern Africa Hub