Portable DNA sequencer helps farmers stymie devastating viruses

Abstract

Armed with a battery-operated minicomputer, a handheld DNA sequencer, and portable DNA-extraction machine, researchers gathered in a cassava field in Tanzania last August to chase down a major plant pest. Their plan was unprecedented: sequence the whole genome of the plant material to detect all potential viruses—and do so in a single day on a farm. “We called it tree lab, we were sitting under a tree,” says Laura Boykin, a computational biologist at the University of Western Australia. A group of farmers looks over a field of cassava in Mbinga, Tanzania, in 2016; unearthed cassava root is pictured ( Inset ). Researchers in the Cassava Virus Action Group have been able to increase yield by using portable DNA sequencers and extractors that facilitate the early detection of diseased plants. Image credit: Laura Boykin (photographer). Because plant samples are typically sent overseas to test for viruses, there’s a big distance between the farm and the laboratory—thousands of miles if you’re in eastern Africa. But within a few hours, a group of researchers, part of the Cassava Virus Action Project, determined what viruses infected the cassava crops on the farm and, more importantly, alerted farmers they would need to plant new crops that are resistant to the viruses they found. The researchers call themselves an “action group” because they’re “taking the level of knowledge we get as scientists, down to the farmer,” says Peter Sseruwagi, a research scientist at Mikocheni Agricultural Research Institute (MARI) in Tanzania. “We’re able to show the farmer in a single day, what their crops are infected with.” This is a big deal, especially in Africa, where cassava, a sweet potato–like starch, is intricately tied to lives and livelihoods for many of the people on the continent. The two main cassava diseases, cassava brown streak virus and cassava mosaic …