Two pioneering plant genomics efforts given a funding boost by National Science Foundation

September 6th, 2012
With research in plant biology "at a tipping point," in the words of a leading investigator, two pathbreaking efforts by scientists interested in making comparisons across and within sequenced plant genomes have been given a significant funding boost and vote of confidence from the National Science Foundation (NSF).

The NSF has announced that it will make a new research award to fund a project called Gramene for a 5-year period. The previous two awards to Gramene by the NSF were in 4-year cycles. In conjunction with the new award NSF will make new funds available to the Gramene project for developing a Plant Reactome, which serves to increase Gramene's functionality. The Plant Reactome will be modeled based on the Human Reactome project framework developed for the human genome, and funded by the National Institutes of Health (NIH), which will join NSF in supporting this portion of the work.

Doreen Ware, Ph.D., of the U.S. Department of Agriculture's (USDA) Agricultural Research Service (ARS) and an Adjunct Associate Professor at Cold Spring Harbor Laboratory (CSHL), is the principal investigator of the Gramene project. She says the new funding is particularly timely given the acute need for biologists to integrate uniquely valuable but often scattered bits of genomic and related data.

The urgency to maximize knowledge derived from plant genome data is clear: crop breeders are faced with the challenge of boosting yields to keep pace with surging global population, as well as with environmental pressures and changing climate patterns.

"By honing resources like Gramene," Ware says, "we are bringing to bear the knowledge and hidden insights that leading-edge information technology makes visible in order to serve the needs that plant biologists have in generating ever more sophisticated analyses of experimental data."

This convergence of curated data and the forging of new knowledge about biological systems – in the case of Gramene, knowledge about plants such as rice, maize and other crops that billions of humans rely upon for daily sustenance – "is what makes Gramene, Reactome and related efforts important not just for scientists, but for people everywhere," Ware says.

Both Gramene and Reactome are public online resources. Gramene's purpose is to provide added value to mountains of collected data on plant genomes. It has led the way in developing tools that have enabled plant scientists around the world to compare information among plants. This is particularly important because of a finding made when the very first plant genomes were decoded over a decade ago: there are striking resemblances across species. In fact, there is broad conservation in the grasses (rice, maize, sorghum, barley, oats, wheat and rye) even in the order of genes across the chromosomes.

These correspondences, where they exist, provide valuable clues about gene function across species – something that gives a boost to plant scientists and breeders in their efforts, for instance, to boost crop yields or extend a plant's range. Gramene also hosts the genomes of broad-leaf crops such as soybean, tomato, poplar and grapevine, as well as Arabidopsis, a widely studied non-crop plant that serves as a laboratory model for crops. In recent years Gramene has also incorporated "lower" plant genomes such as moss and algae, which lend insight into early events in plant evolution and adaptation.

Developers of Gramene and Reactome, prominently including Lincoln Stein, Ph.D., a leader in bioinformatics at the Ontario Institute for Cancer Research and CSHL, have been at the task of data curation and integration since the sequencing of the first plant and animal genomes.

"Many of the information resources are still underutilized because of the fragmentation of datasets and perhaps even more because of the scarcity of tools to make meaningful connections among them," says Dr. Stein, a past Gramene principal investigator who remains a senior investigator on the project.

Reactome, developed by Dr. Stein and colleagues and supported by the NIH, Ontario Research Fund, and EBI Industry Programme, is a curated database of pathways and reactions, accessible through visualization and analysis tools. It enables scientists to perform pathways-based analyses on various species, including plant species. In the current iteration of the project, the aim is to generate a dedicated Plant Reactome site.

Dr. Pankaj Jaiswal of Oregon State University, a leader in plant bioinformatics and a co-principal investigator of Gramene, notes that the new round of funding will enable Gramene developers to expand by 20 the number of plant genomes incorporated into the portal, as well as add new capabilities for studying gene expression, pathways and networks.

"Among our goals is to effectively deliver integrated datasets into the hands of plant geneticists, molecular biologists and evolutionary biologists, as well as plant breeders and also students by providing compelling, intuitive user-interfaces," Dr. Jaiswal says. There are no intellectual property restrictions on any of the Gramene data. Dr. Jaiswal's group at Oregon State University will lead the development of Plant Reactome with collaboration with collaborations from the Ware and Stein labs.

Another Gramene-related tool is called the Gene Expression Atlas, a platform that displays expression profiles developed at EMBL-European Bioinformatics Institute (EMBL-EBI). These interfaces, along with others, will provide an integrated analysis system built on structured metadata and implemented through a high-capacity data warehouse and advanced search engine.

Other senior investigators who have entered into close, new collaborations in the Gramene project include Crispin Taylor of the American Society of Plant Biologists (ASPB); and Helen Parkinson and Paul Kersey of EMBL-EBI.

Taylor explains that ASPB's specific objective is to develop mechanisms to facilitate the seamless integration of data objects in Gramene with associated articles published in the ASPB journals The Plant Cell and Plant Physiology. "This is a novel approach," he says, "that, in addition to providing important new venues for the discoverability of information in journal articles and databases in the plant sciences, ought to serve as a compelling example for other disciplines."

Provided by Cold Spring Harbor Laboratory

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