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Determining the Pan-African sweet potato virome: understanding virus diversity, distribution and evolution and their impacts on sweet potato production in Africa

Project Complete

Key Project Information

Sweet potato is among the most important food crops in the world and an extremely important food crop for subsistence farmers in sub-Saharan Africa (SSA). It is grown throughout the African continent and currently around 34.5% of global sweet potato area is in Africa. One major limitation in sweet potato production is cultivar decline, mostly due to the cumulative effect of virus infection on this vegetatively propagated crop. Thus, viral diseases are considered a major limiting factor in sweet potato production worldwide, and particularly in SSA. The objective of this project is to evaluate a novel approach, deep sequencing of small RNAs from field-grown sweet potato samples collected throughout Africa, to systematically and efficiently identify known and novel virus genome sequences. A total of around 1750 geo-referenced field-grown samples of sweet potato will be collected from more than ten countries in Africa. Small RNA populations of these samples will be prepared and sequenced using high throughput next-generation sequencing technology, and then assembled to identify known and novel sweet potato viruses.   Broader Impacts: Food security remains a huge challenge for millions of Africans, particularly for those in sub-Saharan regions, who depend on agriculture for their subsistence. Emerging and reemerging pathogens, including many viruses, continue to cause devastating losses of food production in Africa. Current knowledge of crop viruses in Africa is limited and sporadic at best. Novel virus genome identification technology through deep sequencing of small RNA population is potentially applicable to continental surveys as its efficiency in virus identification has been proven with both greenhouse and field grown samples. This technology can then be applied to systematically determine the total virus genome sequences (virome) on a number of other major crop plants in Africa such as maize, rice, tomato, bean, and cassava. Public availability of such information will provide the scientific community and government unprecedented possibilities to understand crop virus distribution in Africa, guide phytosanitary requirements, predict risks of future epidemics, and suggest regional disease management strategies. Data generated under this project will be disseminated through the project website ( and raw and processed small RNA sequences will also be available through EBI Sequence Read Archive and NCBI Gene Expression Omnibus, respectively. Novel virus genome sequences will be deposited into GenBank.  

Co-PI: Jan Kreuze [International Potato Center (CIP), Peru]

Key Collaborators: Martin Chiona (National Agricultural Research Organization, Zambia); Paul Demo (CIP-Malawi); Britta Kowalski (CIP-Angola); Douglas Miano (Kenya Agricultural Research Institute, Kenya);  Settumba Mukasa (Makerere University, Uganda); Joseph Ndunguru (Mikocheni Agricultural Research Institute, Tanzania); Ian Robertson and Elizabeth Ngadze (University of Zimbabwe);  Steffen Schulz (CIP-Ethiopia); Martine Tachin (Université d’Abomey-Calavi, Rép. Bénin)

Start date July 01, 2011
End date June 30, 2015
Lead organization Boyce Thompson Institute for Plant Research
Collaborating organizations International Potato Center (CIP)
Region Sub-Saharan Africa
Countries The project is a collaboration with scientists from USA, Zambia, Malawi, Angola, Kenya, Uganda, Tanzania, Zimbabwe, Ethiopia and Benin.
Type of project Development / Dissemination and Research
Financing Sources National Science Foundation
Members Jan Kreuze, Martin Chiona, Steffen Schulz


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