New portable DNA sequencing technology has for the first time been deployed in East Africa to help collaborating scientists and farmers fight the devastating impact of crop disease.

For the first time, farmers struggling with diseased cassava crops can take immediate, positive action to save their livelihoods based on information about the health of their plants, generated using a portable, real-time DNA analysis device.  The team now plans to expand the project; 800 million people worldwide depend on the threatened cassava crop. The project aims to reduce the risk of community crop failure and help preserve livelihoods.

Cassava, a carbohydrate crop from which tapioca originates, plays a critical role in agriculture in developing countries. 800 million people depend on it worldwide as their primary food staple. It is currently being devastated by several viruses causing two diseases; ‘Cassava mosaic disease’ (CMD), which led to major famines in the 1920s and 1990s, and ‘Cassava brown streak disease’ (CBSD), an epidemic of which is rapidly expanding in eastern Africa.

Both diseases, carried by the whitefly, prevent normal growth of cassava plants. This leads to significantly reduced harvests or even complete losses by farmers.  Both viruses, carried by the whitefly, make the plant inedible and unsellable, and their presence means the crop must be destroyed to stop its spread.

Oxford Nanopore’s portable MinION DNA sequencer was used to identify which strain of virus was destroying the cassava crops of farmers in Tanzania and Uganda as part of a collaboration of scientists and farmers, known as the Cassava Virus Action Project (CVAP). As MinION delivers the information in real time (compared to the usual three months), farmers were able to take action much faster. One was advised to destroy the crop and plant a different variety that is more resistant to the virus for example.

“We have shown that pocket DNA sequencers can benefit rural farming communities who would not normally have access to such technologies as they are usually more expensive and slower,” said Joseph Ndunguru, co-PI, and Director of the Mikocheni Agricultural Research Institute in Tanzania.

Even within this pilot project, through rapid and accurate identification of viruses, farmers can now understand which crops to plant, which are resistant to a particular virus species/strain. This is key to attaining durable disease resistance and improved crop productivity. This technology also is easy to use, making it possible to do without major infrastructure and staffing.

Titus Alicai, co-PI, Research Programme Leader with the National Agricultural Research Organisation, Uganda, said “We were successful in field application of the powerful mobile MinION sequencing tool for rapid, precise, unbiased detection and identification of viruses in farmers’ cassava fields. This eases monitoring of field virus strain populations which is essential for timely control actions such as production of clean planting material and development of resistant varieties.”


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