By Seth Truscott, College of Agricultural, Human & Natural Resource Sciences
PULLMAN, Wash. – Scientists at Washington State University are harnessing the power of “big data” to help growers create the next generation of healthy, sustainable forests and tree crops.
Dorrie Main, professor in the WSU Department of Horticulture, is leading a $3 million effort to create cyber-infrastructure that helps researchers and breeders share and use tree data. The National Science Foundation funded the grant in July.
Network of community input
Scientists are generating a wealth of data on tree genomes, genetics and breeding. The problem, Main said, is making sense of it all – especially once you add environmental and geographic data.
“Due to advances in gene sequencing technology, even small labs are putting out mountains of data,” she said. “Cumulatively, we’re talking about billions of data points. The big challenge is analysis and interpretation.”
To help people generate and use big data, Main and her colleagues aim to unify access to information through a network of community-driven databases, data mining and analysis tools, and educational modules. Such a network would allow scientists, students and tree breeders to share, filter and use data in meaningful ways, from basic discoveries to new varieties.
“We want to give breeders more tools to make good decisions,” Main said.
Unified system of tree information
Over the past decade, her team created seven public, open-source databases for 25 crops, such as the rose family (including almond, apple, cherry, peach, pear, raspberry and strawberry), citrus, cotton, cacao, legumes and blueberries. Those online databases act as clearinghouses for information on genomics, genetics and breeding.
The National Science Foundation project is the next step.
“This new grant will build a unified system of tree databases, help people build their own databases and then connect them in a way that’s currently unavailable,” Main said. These resources could help breeders more quickly create new, more adaptable varieties.
Staying ahead of disease, climate change
Building the network is urgent, Main said. Scientists are in a race with evolving diseases and a changing climate. She is excited about how shared information can help breeders.
“These tools could help scientists create crops that use the genetic diversity that already exists in their wild relatives,” she said. “We can develop new cultivars that require fewer chemicals, grow on marginal land and are adapted for harsher climates while still producing quality yields.”
Main’s team includes Sook Jung, associate research professor; Stephen Ficklin, associate professor of horticulture; and colleagues at the universities of Connecticut, Tennessee and Kentucky. The project will use servers at Main’s lab as well as WSU’S new Kamiak supercomputer.
Contact:
Dorrie Main, WSU professor of bioinformatics, 509-335-2774, dorrie@wsu.edu
