Tools of the Trade

Pankaj Jaiswal is a co-creator of the new Gramene database that helps plant breeders develop new crop varieties (Photo: Truen Pence)
Pankaj Jaiswal is a co-creator of the new Gramene database that helps plant breeders develop new crop varieties (Photo: Truen Pence)

To find the genes that enable a crop — ryegrass or wheat, for example — to resist disease or tolerate drought can mean endless searching, not through one haystack but through many. And success is only the beginning of time-consuming breeding trials. Now scientists, farmers and plant breeders who feed the world have a new scientific resource at their disposal to help them cut through the DNA clutter.

An online gold mine known as the Gramene database is really a library of datasets, says one of its creators, Pankaj Jaiswal, assistant professor in Oregon State University’s Department of Botany and Plant Pathology and a faculty member in the Center for Genome Research and Biocomputing. While a post-doctoral scientist at Cornell University, Jaiswal helped to create the database, research tools and educational information that are revolutionizing the application of genomics to crop development. He continues to be one of Gramene’s principal investigators with colleagues at Cornell and the Cold Spring Harbor Laboratory in New York.

Supported by grants from the U.S. Department of Agriculture (USDA) and the National Science Foundation (NSF), Gramene focuses on grasses (family name: Gramineae), including wheat, corn and rice, which collectively provide about half of the world’s calories.

“What’s unique about Gramene,” says Jaiswal, “is that it builds relationships between scientists who work from a purely genetics and breeding perspective and the people who work from the molecular and biochemical perspective. It tries to bridge the gap between these two.” To develop crops with desirable characteristics, crop breeders can identify genes that are associated with specific traits, such as cold hardiness, disease resistance or flowering time.

And by providing genetic information about multiple species, the database bridges genomes that have been fully sequenced and are relatively well described, such as corn and rice, and those that are less well known, such as wheat and ryegrass. Commonalities between different genomes can generate important clues for breeders of new plant varieties.

Scientists use Gramene for basic science — understanding evolutionary relationships among difference species, for example — as well as for studies that seek innovations in plants for biofuel production or disease resistance. In 2008, USDA and university scientists, including Reed Barker of the Agricultural Research Service in Corvallis, used Gramene to identify likely candidates for disease resistance genes in perennial ryegrass, a mainstay of Oregon’s grass seed industry. The close similarities with disease resistance genes in rice, which had been studied and described in detail, led them to suggest that the ryegrass genes might have the same function.

Judging by the traffic on its website, Gramene has been a global hit. In the last year alone, its data files have been downloaded or viewed in more than 140 countries by about 220,000 visitors. Scientists have cited it as a model for an emerging plant knowledge system, says OSU plant geneticist Todd Mockler. Mockler’s lab participated in the recently completed sequencing of a small grass plant, Brachypodium, whose genome is now stored on Gramene. Brachypodium is a promising model for grass genomics studies.

Jaiswal, an acknowledged leader in developing standardized vocabularies (what scientists call “ontologies”) for the rapidly expanding plant genome sciences, also trains breeders and farmers to use Gramene. “We try to avoid too many scientific terms,” he says with a nod to the technical language of his profession, “but we can’t do that all the time.”


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OSU news release, Dec. 26, 2010. Pankaj Jaiswal contributed to the compete genome sequence of the woodland strawberry, a relative of commercially bred strawberry varieties. The plant shares genes with other fruit crops, including peaches, apples, cherries and plums.