In East African cassava fields, a new genomics tool is saving crops and lives / by Karen Frances Eng

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.

 Dr  Emmanuel Ogwok , John Francis Osingada, Geoffrey Okao-Okuja, and Phillip Abidrabo collect samples on Naomi Kutesakwe’s farm in Wakiso, Uganda. Photo: Laura Boykin

Dr Emmanuel Ogwok, John Francis Osingada, Geoffrey Okao-Okuja, and Phillip Abidrabo collect samples on Naomi Kutesakwe’s farm in Wakiso, Uganda. Photo: Laura Boykin

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.

 Charles Kayuki shows Asha Mohammad Nanopore sequencing technology. Photo: Laura Boykin

Charles Kayuki shows Asha Mohammad Nanopore sequencing technology. Photo: Laura Boykin

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.

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Source: https://fellowsblog.ted.com/a-new-genomics...