A team of academic, government and industry researchers has completed a first draft of the cassava (Manihot esculenta) genome using the 454 Sequencing System from 454 Life Sciences.
The project is an important first step in accelerating the pace of research on this subsistence crop and addressing some of the many limitations that face cassava farmers around the world.
Cassava is a root crop that serves as the primary food source for more than 750 million people each day.
Although it has many properties that make it an important food across much of Africa and Asia; it also has many limitations.
Cassava has poor nutritional content and is susceptible to many pathogens, particularly in Africa, where one-third of the continental harvest is lost each year to viral diseases.
One of these, Cassava Brown Streak Disease (CBSD), is currently the major threat to food security in some parts of eastern Africa.
In response to the urgency of this threat and building upon the newly available cassava genome sequence, the Bill and Melinda Gates Foundation has awarded a grant to University of Arizona (UA) researchers, who will lead an international consortium to develop a genome variation database that will provide breeding tools to aid farmers in improving cassava, with a special focus on increased resistance to the CBSD virus.
Steve Rounsley, associate professor in the School of Plant Sciences at the UA and a member of the BIO5 Institute, will coordinate the project that includes partners at the Institute for Genome Sciences, University of Maryland, Baltimore, the US Department of Energy Joint Genome Institute (DOE JGI) and 454 Life Sciences, a Roche company.
The impetus for the genome sequence began in 2003.
The full genome project gathered momentum in early 2009 when 454 Life Sciences and DOE JGI each pledged the resources to use 454 Life Sciences' Genome Sequencer FLX platform with long-read GS FLX titanium chemistry to rapidly generate the DNA sequence data needed for the project.
More than 61 million sequencing reads were generated and assembled into a draft genome that contains an estimated 95 per cent of cassava genes.
It is one of the first large genome projects to primarily use 454 Life Sciences' long-read sequencing platform, which enabled improved quality of the draft and rapid generation.
The availability of the genome sequence enables the project to study how cassava varieties differ from each other.
Researchers will use next-generation technologies to sample many varieties of cassava and develop a large database of markers that can be used to identify genes involved in many important traits.
The team will collaborate with researchers in Kenya, Uganda and Tanzania in applying these genetic markers toward identifying resistance to Cassava Brown Streak Disease.
All of the information and tools the project develops will be freely available worldwide.
