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Change Generation

An Ambitious Genome Sequencing Project Is Tackling Africa's Nutrition Crisis

Scientists and companies like Google and Mars are using figuring out how to breed Africa's traditional crops to be more nutritious and easier to grow.

Photo: Jasni via [url=http://www.shutterstock.com/pic-378725935/stock-photo-close-up-shot-on-okra-image-has-grain-or-noise-and-soft-focus-when-view-at-full-resolution-shallow.html]Shutterstock

Across Africa, some of the most nutritious crops are the indigenous, traditional foods that grow in the wild or in backyard gardens. People have eaten foods like amaranth, okra, and breadfruit for centuries, but most of them have never been grown in formal agriculture systems and their seeds never bred for qualities like yield or higher nutrient content. The continent's major cash food crops are far less healthy grains, mainly corn and rice.

When Howard-Yana Shapiro, a world-renowned plant scientist and chief agricultural officer at the food giant Mars, attended a lecture about childhood stunting in Africa, he thought he could help by improving the quality of crops that millions in rural parts of the continent were already eating.

A Problem Of Diet

Childhood stunting—when children, because of poor health or nutrition, fail to grow to their age-appropriate height— has declined in much of the world since 1990. But it has remained at a stubbornly high 40% of children in Africa, according to World Health Organization estimates. Nutrient deficiencies, such as iron, vitamin A, zinc and iodine, are also common and can lead to health problems such as anemia, child blindness and mental impairment, and in extreme cases, death.

Much of the problem comes down to diet. Many poorer African families eat diets mostly consisting of staple crops like rice or corn, rather than far more nutritious fruits, vegetables, legumes, and other kinds of grains. Unlike rice or corn—which have been finely tuned for cheap, mass production—these crops have lower yields. A subsistence farmer might not be able to grow or buy enough to feed the family.

Shapiro realized that traditional foods can be a key to reducing the continent’s high rates of stunted growth and other malnutrition-related illnesses. The important part would be to breed them to boost yield or allow farmers to choose specific varieties with high nutrient content (any one crop has multiple, sometimes dozens, of varieties—all of which have their own nutritional profiles, some better than others).

He began seeking partners, thinking they'd work on about a dozen crops. He wanted to breed better varieties and also sequence their genomes.

"You want to change the whole basic rural food system"

Shapiro had already led the global effort to sequence the cacao genome, so taking on 12 plants sounded like an ambitious goal for a man who might otherwise have retired. (Globally, only 57 plants have been sequenced to date, according to Shapiro.) But when he met with the head of BGI, formerly the Beijing Genomics Institute, a potential partner in the sequencing part of the effort, he was told 12 wouldn't be enough.

"He said let's really think about this. You want to change the whole basic rural food system," Shapiro recalls from that meeting. The problem of childhood stunting in Africa is so widespread that if he really wanted to make a dent in the malnutrition rates across an area as large as Africa, he was going to have to work on more than 12 crops. So he doubled the number—and did so again and again, until they finally agreed to a goal of 100 crops. Several African leaders then demanded the iconic baobab tree be added to the list, bringing the final total to 101. The list includes vegetables like green bean and vine spinach, grains such as finger millet and amaranth, as well as fruits, including mangosteen and custard apple.

The effort is now known as the African Orphan Crops Consortium (AOCC); the crops are considered "orphan" because while they have been a crucial part of local diets, they have been largely neglected by breeders and ignored by agricultural business interests. "What we want to do is not only promote them for good nutrition, but we also want to promote them for future income," said Ramni Jamnadass, research project leader at the World Agroforestry Center, or ICRAF, a lead partner in the AOCC. "Instead of focusing on five to 10 crops, there's a whole potential to improve our nutrition and livelihood opportunities generally."

Proponents of the project think that by focusing on such a wide variety of crops and by training plant breeders from around Africa, they have the potential to reach rural populations across the continent. Breeders can take the data produced by the project to breed crops appropriate for their own local markets. That may mean boosting the yield of finger millet in one area, while in another it might mean making a breadfruit tree more drought-tolerant. The ultimate goal, for all of the crops, is to increase access to nutritious foods throughout Africa.

Making the Roadmap

The AOCC was launched formally at the 2011 Clinton Global Initiative in New York, although much of the work takes place in Nairobi. There, ICRAF houses a plant breeding academy for scientists and plant breeders from across Africa, as well as sequencing equipment. All of the genome data will be public. Shapiro said BGI committed to doing the sequencing at almost no cost, and many of the other services or equipment required are being donated as well.

The effort is a unique one, and has brought together some surprising partners: agricultural research organizations, founding member Mars, genome sequencing companies—and data technology companies like Google and IBM.

ICRAF collects samples of the crops to be sequenced, and after BGI does the initial sequencing of each crop’s genome in Shenzen, China, ICRAF does the resequencing, meaning it sequences 100 different varieties of each crop. "When we sequence a genome for the first time, it's quite hard to do. But to do it again for other varieties, it's much easier to do because we have a roadmap," says Allen Van Deynze, director of research at the Seed Biotechnology Center at the University of California, Davis, who is also involved in the AOCC. "Making a roadmap is hard, but driving on the road is easier and cheaper."

All of this adds up to a lot of data—several petabytes, which is equal to a million gigabytes—and it all has to be moved, analyzed, and stored. "We're generating quite a bit of data," says Van Deynze. "One of the limiting steps is not so much analyzing it as it is moving it around from place to place." It’s not technically unheard of to handle all this data—this isn’t the Hubble telescope, says Van Deynze—but it’s an enormous amount of data that would be very costly, perhaps prohibitively so, for the project to have to pay for storing or moving.

He says that Google has committed to transferring all that data between China, Nairobi, and Arizona. IBM has also expressed interest in helping; the discussion with them is too new to say yet what its specific role will be, but it would also likely involve data transfer and compression assistance.

The need for these large volumes of data storage and transfer isn't permanent—it's for the initial stage of sequencing and analyzing the genomes, which is expected to take about three or four years. After that, another partner, the National Science Foundation-funded iPlant Collaborative (based in Arizona), will take on the task of making the data available, online and in an easily digestible form, to the end users: plant breeders across Africa.

And that is the real goal—to create the capacity to, and start the process of, continuously improving the most important crops in African diets.

"I'm always trying to improve every crop that I work on—so the work we're doing for the first cultivars is just the beginning," says Shapiro. "We're training people to train people to build the capacity in Africa."

Improving these crops also offers a promising, long-term path to the original goal, of reducing malnutrition. "The fundamental things you need to be healthy have to be eaten," says Shapiro. "Supplementation might solve it for a moment, but you have to eat it. And that's what this is all about. Let's eat nutrition."

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