Overall $50 million plan will build framework for integrative, quantitative thinking

Boyce Thompson Institute Associate Scientist Thomas Brutnell is helping lead a group of life scientists and computer researchers who are attempting to solve one of the "grand challenges" in the plant sciences. The challenge is to predict how plants will grow and develop based on their particular genetic makeup and the various environments where they are found or planted. Solving this problem requires new computer software and computational capabilities, including powerful tools to allow scientists around the globe to collaborate on plant research.

The principles of iPlant, a nearly $50 million project funded by the National Science Foundation, include development of a cyberinfrastructure collaborative effort and also to train the next generation of scientists in computational thinking and to reinvent itself as the needs of the scientific community and technologies change. The formal name of the five-year effort is the Plant Science Cyberinfrastructure Collaborative (PSCIC) program.

iPlant hosted workshops for researchers from the biological and computational sciences that yielded the "grand challenge" questions that iPlant would tackle, as well as the tools, strategies and approaches needed to find answers to the questions.

The particular iPlant team involving Brutnell is the Genotypes to Phenotypes in Complex Environments (iPG2P) committee, which will help researchers study the relationship between plant genotypes – the genetic makeup of particular plants – and how those genotypes interact and express themselves in various environments. Brutnell's specific role is to help design a computational pipeline to process ultra high- throughput sequence datasets

"One of the great challenges in biology now is dealing with extremely large datasets, be it billions of bases of DNA sequence or millions of phenotypic measurements," said Brutnell, "We are working to make the processing and interrogation of these datasets easier."

"In a world where the environment is undergoing rapid change, predicting altered plant responses is central to studies of plant adaptation, ecological genomics, crop improvement, plant development and more," Brutnell said. Crop improvement activities could involve impact areas from international agriculture to biofuels.

"In nature, individual plants, like people, will have their own particular set of genes (alleles)," Brutnell said. "One of the questions is, can we breed for new traits based on a deeper understanding of the genetics in major crops? For example, we know that water will become more limiting in future agricultural settings. Can we find genes and pathways that help plants cope with water deficit? If so, we can then help plant breeders in identifying the most favorable alleles for their favorite crop"

Other leaders on the iPG2P team include Steve Welch, professor of agronomy at Kansas State University ; Doreen Ware, computational biologist with the U.S. Department of Agriculture's Agricultural Research Service; Dan Kliebenstein, plant physiologist at University of California, Davis; Ruth Grene, plant physiologist at Virginia Tech; Chris Myers, computational biologist at Cornell University; Steve Goff, iPlant project director at the University of Arizona; Dan Stanzione, deputy director of the University of Texas Advanced Computing Center, Austin; and Matt Vaughn, specialist in computational genomics at Cold Spring Harbor Laboratory, New York.

"Plants are good systems to work in, but genotype to phenotype issues go across all biology. Our task is not to solve individual biological problems but to develop the computational tools to work on the problem," Brutnell said. "When finished, iPlant computer systems will be able to handle huge amounts of data and able to create computer displays in easy-to-understand forms."

In addition to the iPlant working groups, Brutnell said, the University of Arizona and University of Texas are building extensive software systems to support the effort.