In East African cassava fields, a new genomics tool is saving crops and lives
The latest in the fight against whitefly-borne virus that threatens a world staple food: new portable DNA sequencing technology that lets farmers in East Africa identify the disease, and helps scientists develop a solution.
TED Senior Fellow and computational biologist Laura Boykin has made her life’s work to rid cassava — a staple root crop on which 800 million people around the world rely for their daily calories — of whitefly-borne virus. Now, with a team of international scientists, including co-Principal Investigators Dr Joseph Ndunguru and Dr Titus Alicai and farmers collaborating as the Cassava Virus Action Project (CVAP), she’s taken her quest to the field with a newly developed portable DNA sequencer that allows scientists to work with farmers to identify which strain of virus is attacking their cassava crop.
Cassava, also known as manioc and tapioca, is currently being devastated by several viruses that cause 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, make the plant inedible, and can severely damage or wipe out whole harvests. The only way to stop its spread is to destroy the crop.
Enter the portable, affordable Oxford Nanopore MinION DNA sequencer, which sequences the virus and transmits the information in real time so that it can be analyzed by a nearby lab. Within 48 hours, local scientists can offer instructions to farmers about how best to respond to whitefly infestation. In the past, the process involved sending samples overseas for DNA sequencing, which required three months, over which time samples degrade, says Boykin. Meanwhile, the cost of the Nanopore MinION is $1,000, compared to upwards of US$1 million for standard sequencing equipment.
An example of the MinION at work: Tanzanian farmer Asha Mohammad has had low cassava yields, but by using the MinION’s capacity for rapid, local DNA analysis to identify the viruses affecting her plants, she’s now armed with information needed to plant healthier crops by choosing cassava varieties known to be resistant to the viruses in her field. “Asha’s next steps will be to remove her infected crops immediately, and she’ll be receiving virus-free planting material to increase her cassava yields,” Boykin says. The farmer who receives this information can then also share this knowledge with other women farmers in her community, and beyond.
The portable sequencer weighs 100 grams and can be used anywhere, plugged into a laptop or PC — and has been used to monitor changes in Zika and Ebola. Its versatility means it can sequence cassava plants as well as whiteflies — a level of precision that helps farmers better understand which varieties of cassava to plant, and learn which are resistant to particular virus strains. “This is key to attaining durable disease resistance and improved crop productivity,” says Boykin’s colleague Joseph Ndunguru, director of the Mikocheni Agricultural Research Institute in Tanzania. The project will also contribute to the ongoing research of cassava disease. “All of the data that’s been gathered will be written up for a scientific publication and made publicly available in GenBank,” says Boykin.
Boykin says that currently, ten scientists working with ten farmers are using the Oxford Nanopore MinION in Tanzania and Uganda — two countries that are severely affected by cassava brown streak disease. “We hope to scale up very quickly to help fight food insecurity, especially in the most vulnerable communities of smallholder farmers around the world,” she says. “We’re also looking forward to using these technologies for other pests and diseases.”
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