Last week I tried to explain “the cloud” to my six year-old son. It’s quite a turn of events for me to teach him anything about computers.
Lately, he’s been drawing pictures of people with conversation bubbles, so we talked about the cloud as a huge conversation bubble to which we all contribute. Now his pictures have cloud bubbles filled with words. He draws our dog with a ball in the cloud; his sister with a paintbrush; himself with an orange racecar; me with a pile of books.
So, when I ended up discussing plant genomics and the humongous amounts of data in the cloud with Dr. Christopher Cullis, department chair and professor of biology at Case Western Reserve University, I couldn’t help but picture him with a cloud bubble over his head.
In an age of technological advances and cloud computing, data is everywhere. Some of it, whether computer code or genome sequences, is quite complex. It’s what we do with that data—our ability to find it in the cloud, understand it, and translate it into something useful—that gives it meaning.
Toward Resilient and Fruitful Orphan Crops
Raised in Zimbabwe, Cullis is a Fulbright scholar who researches and sequences plant genomes, with a particular interest in African orphan crops. Orphan crops are indigenous food sources with little commercial value.
Corporations have poured millions of dollars into sequencing crops like wheat, soybean, and rice in an effort to discover ways to increase yields. Sequencing plants allows breeders to select and produce plant varieties that will grow despite harsh conditions and yield the most food resources.
Source: World Agroforestry Centre (Flickr: CC)
Much less work has been done on orphan crops grown in backyard plots in rural Africa, such as millet, sorghum, and cassava. Once neglected in the research community, a handful of organizations have been working to sequence these native plant species to improve their resilience and yields in developing nations.
One such organization, the African Orphan Crops Consortium (AOCC), was launched in 2011. AAOC aims to improve the nutrition, productivity, and climatic adaptability of some of Africa's most important food crops, helping to decrease the malnutrition and stunting that plagues the continent’s rural children.
The Health Impact of Undernutrition
Food insecurity in Africa threatens the lives of millions of vulnerable people. Undernutrition is responsible for 3.5 million child deaths per year, according to the World Health Organization. Undernutrition exacerbates common infections, putting children at greater risk of dying by increasing the frequency and severity of infection, as well as delaying recovery.
Poor nutrition in the first 1,000 days of a child’s life can also lead to stunted growth, which is irreversible and associated with impaired cognitive ability and reduced school and work performance. Overall, the prevalence trends for stunted growth are positive: the number of children affected fell from 199 million in 2000 to 161 million in 2013. Despite this improvement, stunted growth remains a significant issue. Worldwide, one in four children under the age of five had stunted growth in 2013, according to UNICEF.
Advances in Biotechnology Have Made Sequencing Faster and More Affordable
Recent technological advances have significantly reduced the costs of genome sequencing. These new high-throughput technologies pose a challenge for data storage and informatics operations.
“Five years ago,” Cullis told nuviun, “the bottleneck was getting the data. Now the concern is the development of bioinformatics and applications. We simply do not have the capacity to deal with the amount of information being generated.”
Cloud computing might be one solution, but Cullis warns that the scope of sequencing projects like AOCC might be too wide. Sequencing 50 different species might be less useful in addressing hunger than sequencing a few crops and investing in the training and development of people to apply the data. Cullis sees this as a longer-term project that may not be getting the funding it deserves.
Illumina, a global biotechnology company, has an annual grant program called the Agricultural Greater Good Initiative. AOCC is the 2015 recipient of this grant, and plans to use the grant of Illumina reagents and consumables to further its work studying the genetic diversity of African crops—particularly those grown by subsistence farmers.
“The Agricultural Greater Good Initiative is a perfect complement to the AOCC,” said Allen Van Deynze, Director of Research at UC Davis and member of the Steering Committee for AOCC. “With the award, we will sequence the transcriptomes for 50 species of African orphan crops to define the genes expressed in these species. All the work will be carried out in Africa.”
Based at the World Agroforestry Centre in Nairobi, AOCC plans to train 250 plant breeders in genomics and marker-assisted selection for crop improvement over a five-year period. The work could drive the creation of improved planting materials that would then be offered to farmers throughout Africa.
nuviun asked Prof. Cullis how long it might take for the genome sequencing to have an impact on the levels of undernutrition and food insecurity in Africa. Cullis told nuviun,
“even with boots on the ground to take advantage of the sequencing data, this is a project that could take decades.”
Is It Time for a Shift in R&D Budgets?
With current technology, scientists are able to sequence the genomes of plant species. However, this is only the first piece of a complex puzzle. More research and development will be required for the next steps, which involve storing, retrieving, analyzing, and applying the data.
Still though, one hopes that plant breeders might find a way to use the sequenced genomes and breed hardier, more productive plants for farmers in the developing world. Sequencing technologies have only been affordable for a few years. Perhaps, with a shift in investment dollars toward further development in bioinformatics and breeding, the cloud will produce manna for the children of Africa.
Jenn Lonzer has a B.A. in English from Cleveland State University and an M.A. in Health Communication from Johns Hopkins University. Passionate about access to care and social justice issues, Jenn writes on global digital health developments, research, and trends. Follow Jenn on Twitter @jnnprater3.
The nuviun blog is intended to contribute to discussion and stimulate debate on important issues in global digital health. The views are solely those of the author.