Projects to expand knowledge about plants of economic importance

The National Science Foundation (NSF) has made 22 new awards as part of the seventh year of its Plant Genome Research Program (PGRP). From apples to Zea mays, the program's goal is to expand knowledge about the biology of the plant kingdom, especially plants that people around the world rely on for food, clothing and other needs.

The awards involve researchers from 56 institutions in 22 states, as well as collaborators from 14 countries around the globe. The two- to five-year awards, ranging from $700,000 to $6.6 million, will explore the inner workings of plants' genes as well as the role genetics plays in plant development, metal tolerance, susceptibility to diseases and other economically important characteristics.

NSF's PGRP is part of the National Plant Genome Initiative established in 1998 as a coordinated national plant genome research program by the Interagency Working Group on Plant Genomes of the National Science and Technology Council. The long-term goal of this program is to understand the structure, organization and function of genomes of plants of economic importance and plant processes of potential economic value.

The 2004 awards focus in three main areas: detailed analysis of the genomes of key plants and families of plants; functional genomics — the study of relationships between genes and the biological roles they play; and databases and tools to capture, share and analyze the massive amounts of genomics data being produced by the scientific community. In addition, all projects continue the commitment of the PGRP to train the next generation of scientists by exposing students to research at the cutting edge of biological sciences. As many as 150 students will participate in this year’s new projects.

"The research supported will allow a deeper understanding of the basic life processes in plants, development of improved crops, as well as train a future generation of scientists,” said Mary Clutter, head of NSF's Biological Sciences directorate. "The outcomes of this work will impact every facet of our lives."

For example, a research consortium led by Cornell University will participate in an international project to sequence the gene-rich portions of the 12 chromosomes of tomato by developing the detailed map of the tomato genome. The map that will result from this work will pave the way for development of improved varieties of tomato and help scientists understand related plants, including potatoes, peppers, tobacco and coffee.

A project led by Indiana University will study the genomes of the Compositeae, a group of plants that includes important crop species such as lettuce, sunflower and artichoke, as well as noxious weeds such as Russian thistle. This work should shed light on the processes that shaped the genomes of these plants during domestication and identify the traits that lead to weediness. And a project at Mississippi State University will work to develop genomic tools for loblolly pine, the primary source of pulpwood for the U.S. paper industry and a major crop in the southeastern states.

A number of functional genomics studies will look at how genes contribute to the internal workings of an organism. A project at Pennsylvania State University, for example, will study the molecular genetic interactions between the rootstocks and scions of apple trees that affect the disease resistance and growth of the plant. Cotton is the world's most important fiber crop, and researchers at Texas A&M University will investigate the genetic and physiological pathways that lead to the development of cotton fibers.

Among the six projects focusing on aspects of maize (Zea mays), researchers at the University of Missouri-Columbia will lead a project to understand how DNA packaging in the nucleus can control whether genes are turned on or off, a step toward providing tools for manipulating gene expression in maize and other crop plants. University of Georgia researchers will study the structure and function of maize centromeres, which play a central role in cell division and ensure that the newly divided cells each receive a set of chromosomes.

A growing challenge is how to handle the massive amounts of data coming out of ongoing genomics projects and to make it readily accessible to the broader community of students, researchers and breeders. This year's awards include database awards to the University of Arizona focused on proteins involved in repackaging DNA so particular genes can be expressed during plant growth and development (ChromDB), to Cold Spring Harbor Laboratory on the genomes of grains and grasses (Gramene) and to the University of Tennessee on the genomics of poplars and related trees (Populus Genome Portal).

Also among this year's projects are two new "virtual centers," flexible collaborations of investigators at various institutions, all focusing on a common goal. One center, led by New York University in collaboration with the New York Botanical Garden, the American Museum of Natural History and Cold Spring Harbor Laboratory, will target evolutionary genomics, the genetic mechanisms by which important traits have evolved in plants, such as the development of seeds. The second center, led by Yale University in collaboration with the University of California, Davis, will focus on using experimental approaches to define every gene — perhaps as many as 60,000 — in the recently completed rice genome.

For more information see:
Plant Genome Research Program: http://www.nsf.gov/bio/dbi/dbi_pgr.htm
FY2004 PGRP Awards: http://www.nsf.gov/bio/pubs/awards/genome04.htm