The University of British Columbia (UBC) is using data analytics to analyze the genomes of sunflowers and find natural pathways to increase global food production. Developments have the potential to reduce world hunger and improve people’s well-being.
Estimates show global population could grow by 2.5 billion by 2050. To keep pace with this growth and the changing diets of developing nations, the United Nation’s Food and Agricultural Organization (FAO) says food production must increase by 60% over the same period. The DivSeek Initiative, with which UBC collaborates, believes that using natural variation to enhance breeding in food crops such as rice, wheat, corn, soybeans and sunflowers offers one solution.
When wild crops were originally domesticated, the focus was on breeding for highest yield and simultaneous ripening. “In the process many useful traits that allowed food plants to grow under harsh conditions were inadvertently lost,” says Loren Rieseberg, professor and researcher with UBC’s botany department. “However, wild species that continue to exist in gene banks and landscapes around the world host a reservoir of valuable genes that can be reintroduced to create environmentally stronger crops that need less water, fertilizer and pesticide.”
Why sunflowers? Sunflower is also the only oil seed on the Global Crop Diversity Trust’s priority list of 25 food security crops. It is the 13th most widely grown crop in the world and produces a healthy oil that is gaining in importance as global fat consumption increases. Much of the genetic resource for the crop has been developed in the lab at UBC, meaning data is readily accessible.
Sunflower has a large genome, comprising 3.6 billion base pairs. It can take months and a variety of tools to conduct analysis. “To speed up our research, we needed faster technology and more efficient means to manage, analyze and store the vast amounts of data being produced,” explains Rieseberg.
At the same time, big data experts with SAP were seeking a high-level academic partner in plant genomics research with which to test algorithms used in their work with the human genome. Using benchmarks from this research, SAP demonstrated the analytic speed of its HANA in-memory database to UBC. The result is a research collaboration.
“When we came together, the university was working on the reference genome for sunflower and needed to map sequences from 550 different individuals, including samples from 12 wild extremophile species and equating to more than 10 terabytes of data,” says Timo Kubach, SAP Germany’s vice-president of new business and portfolio. “Over the course of a year, we learned about UBC’s needs and developed an algorithmic system that is now processing all the data sets.” The collaboration also contributed to training of UBC personnel in data analytics.
“As a plant biologist I was exposed to cutting-edge technology that allows basic and applied questions to be addressed in essentially any organism at the highest resolution and depth,” says Sariel Hubner, UBC postdoctoral researcher. “Translating our scientific methodologies into a high-throughput analytical platform was challenging at the beginning but now appears to be extremely efficient and successful.”
The long-term goal of the project is to find combinations of genes to create new sunflower varieties with attributes that are wanted and needed, such as increased yield as well as salt , drought, flooding and low-nutrient tolerance, adds Kubach. “With faster data processing capability, and the ability to analyze new plants for preferred traits before they reach full maturity, we are increasing the efficiency of plant breeding through natural methods.”
SAP’s algorithms are faster and out-performing what is considered best practice in the public sector, notes Rieseberg. “On a global scale they could be applied to all crops to help increase the precision and efficiency of conventional breeding cycles and ultimately help increase food production in sub-Saharan and other challenging locations.”
While other food crops are being analyzed in a similar manner around the world, primarily in private institutions, much of the resulting information is not publicly available. However, UBC is sharing its findings and information.
One surprising fact is that despite significant differences in appearance the genomes of sunflower seeds are quite closely related to the human genome in both structure and size: The human genome has 3.2 billion base pairs and 23 chromosomes, compared with 3.6 billion base pairs and 17 chromosomes in the sunflower.
These similarities have helped SAP to apply some of the algorithms developed with UBC to the search for optimum cancer drug treatments based on the genome data of a patient. The software is currently being reviewed by cancer research centres around the world.
“The possibility of a global food crises has galvanized governments, non-governmental organizations and institutions to action. At the same time, revolutionary advances in technology have allowed us to tap into more diversity than ever before,” says Rieseberg. “Being able to manage these new levels of data effectively was a major hurdle that SAP has helped us cross.”
This story was produced by Postmedia’s advertising department on behalf of SAP Canada for commercial purposes. Postmedia’s editorial departments had no involvement in the creation of this content.
Source:: National Post
