Navigation Links
2 pioneering plant genomics efforts given a funding boost by National Science Foundation
Date:9/6/2012

Cold Spring Harbor, NY 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."


'/>"/>
Contact: Peter Tarr
tarr@cshl.edu
516-367-8455
Cold Spring Harbor Laboratory
Source:Eurekalert

Related biology news :

1. Pioneering self-contained smart village offers world model for rural poverty relief
2. BGI, GE Healthcare team up on pioneering stem cell science projects
3. Good news for nanomedicine: Quantum dots appear safe in pioneering study on primates
4. Clemson plant pathologist working to raise cucurbit yields, lower production costs
5. Gardeners delight offers glimpse into the evolution of flowering plants
6. Danforth Plant Science Center hosts 14th Annual Fall Symposium
7. No more sneezing, allergen-free house plants
8. No more sneezing, allergen free house plants
9. Plants fungi allies may not help store climate changes extra carbon
10. Plants unpack winter coats when days get shorter
11. Behind closed doors: Researchers show how probiotics boost plant immunity
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:4/26/2016)... 2016 Research and Markets has ... Market 2016-2020"  report to their offering.  , ,     ... The analysts forecast the global multimodal biometrics market ... the period 2016-2020.  Multimodal biometrics is ... as the healthcare, BFSI, transportation, automotive, and government ...
(Date:4/13/2016)... physicians supporting Medicaid patients in Central Florida ... telehealth thanks to a new partnership with higi.   ... can routinely track key health measurements, such as blood ... they opt in, share them with IMPOWER clinicians through ... location at no cost. By leveraging this data, IMPOWER ...
(Date:3/22/2016)... India , March 22, 2016 /PRNewswire/ ... market research report "Electronic Sensors Market for Consumer ... Proximity, & Others), Application (Communication & IT, ... Geography - Global Forecast to 2022", published ... industry is expected to reach USD 26.76 ...
Breaking Biology News(10 mins):
(Date:6/24/2016)... discussions on a range of subjects including policies, debt and ... Poloz. Speaking at a lecture to the Canadian ... to the country,s inflation target, which is set by both ... "In certain areas there needs to be ... why not sit down and address strategy together?" ...
(Date:6/24/2016)... ... June 24, 2016 , ... Researchers at the Universita Politecnica ... in people with peritoneal or pleural mesothelioma. Their findings are the subject of a ... , Diagnostic biomarkers are signposts in the blood, lung fluid or tissue of ...
(Date:6/23/2016)... 2016   Boston Biomedical , an industry ... to target cancer stemness pathways, announced that its ... Drug Designation from the U.S. Food and Drug ... including gastroesophageal junction (GEJ) cancer. Napabucasin is an ... cancer stemness pathways by targeting STAT3, and is ...
(Date:6/23/2016)... Houston Methodist Willowbrook Hospital has signed ... to serve as their official health care provider. ... will provide sponsorship support, athletic training services, and ... volunteers, athletes and families. "We are ... and to bring Houston Methodist quality services and ...
Breaking Biology Technology: