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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.

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.

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Highlights Sugarcane mosaic virus (SCMV) and Maize chlorotic mottle virus (MCMV) were the only MLN causing viruses detected. MCMV and SCMV are widely distributed in all maize growing regions in Kenya. SCMV was more diverse and MCMV was largely conserved with little genetic diversity. MCMV alone can lead to severe MLN development. Genetic viral recombination signals detected only in SCMV viral genome samples.

Maize lethal necrosis (MLN) disease is a major constraint on maize production in Eastern Africa since its first report in 2012 in Kenya. The main causative agent is maize chlorotic mottle virus (MCMV) which co-infects maize with other viruses from the family Potyviridae. In Africa, Sugarcane mosaic virus (SCMV) is the most common potyvirus that co-infects maize synergistically with MCMV. MCMV can be transmitted by insect vectors, mechanically and via contaminated seeds. Monitoring of MCMV is important in farmers' fields, seed fields, seed-lots and in grain. Robust diagnostic tools are essential in epidemiological studies, germplasm screening and exchange of disease-free materials across the regions and globally. Therefore, a sensitive, reliable and affordable diagnostic tool for MCMV is necessary in the laboratory and also in the field. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with two-end point analysis was developed to detect MCMV in active vegetative stages and in seed. Six sets of specific primers were designed and evaluated. Amplification was detected in 60 min using the SYBR green colour change and in 10 to 20 min for real-time amplification in the Genie II platform. The assay discriminated the common viruses infecting maize in Eastern Africa. The assay showed excellent specificity to MCMV. The simplicity, rapidity, and inexpensiveness of this technique make it a suitable choice for large-scale sample processing, especially by laboratories with limited resources and for field analysis performed by regulatory agencies in the region.

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