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By Susan McGinley
Sep 29, 2003
Scientists at the University of Arizona in Tucson and several collaborating institutions are developing tools that will unlock the genetic codes of maize and rice and serve as models for biological, agricultural and environmental research worldwide.
Rod Wing and Vicki Chandler, in the plant sciences department at the UA College of Agriculture and Life Sciences, and Cari Soderlund of the UA Institute for Biomedical Science and Biotechnology (IBSB) and the plant sciences department, are principal investigators on separate projects funded through the National Science Foundation (NSF) as part of the National Plant Genome Initiative (see sidebar).
Wing, professor of plant sciences and director of the Arizona Genomics Institute, was awarded a $9.7 million grant to develop a complete gene map of Oryza, the genus for every species of wild and domesticated rice.
"Rice feeds half the world's population and that's the group that will double in population in the next 50 years," Wing says. "We need to know all we can about it. We want to decode the rice genome to understand the regulatory mechanisms for disease resistance and drought control. Once we understand how this works we can design more drought-tolerant, disease resistant crops and grow them in a more environmentally friendly way on less land with fewer pesticides and less water."
Wing and his colleagues from the UA, Purdue and New York’s Cold Spring Harbor Laboratory are developing a closed model system to unravel and understand the evolution, physiology and biochemistry of the entire rice genus.
Called the Oryza Map Alignment Project, or OMAP, Wing says this will be the first project in any system where a complete genus - every species - will be characterized at the genome level.
"This has never, ever been done in animals or plants," Wing says.
Over millions of years the 13 known species of rice have evolved and adapted to different environments all over the world: swamp, shade, salt water and other conditions. Including the wild species of rice and aligning them with the genomes of domesticated rice species on the OMAP will enable researchers to find new genes for improving cultivated rice.
This resource will be a platform for researchers around the world to explore the diversity and evolution of rice genes and will serve as a model to establish similar systems in both plants and animals.
Genomics Research
According to researchers, the ultimate goal of genomics is to understand the structure and function of every gene in an organism. Genomics research includes three components:
- Structural genomics studies the structure and organization of genomes
- Functional genomics relates genome structure and organization to plant function at the cellular, organismal or evolutionary level
- Applied genomics uses genomic information and knowledge to develop improved plants and plant-based products for human uses
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Vicki Chandler, a Regents' Professor and co-director of the IBSB, is developing low cost, public sector microarray resources for analyzing gene expression in maize, the most economically important crop in the United States.
Chandler has received a $3.7 million NSF grant to continue this work, along with UA plant scientist David Galbraith and researchers at the Institute for Genomic Research (TIGR) in Maryland, the University of Wisconsin and the University of Minnesota.
Microarrays, also known as gene chips, are thousands of DNA samples arrayed in rows of orderly dots bonded to a specially prepared glass microscope slide. The first generation array that the Chandler group is designing will contain 50,000 genes out of an estimated 60,000 in the entire corn genome.
"We are developing the microarray chips, supplying them to researchers and also making available a large amount of baseline data that can be used to generate hypotheses that others can use to design experiments," Chandler says. "The idea is to show what the technology can do and educate people in how to best use it."
The entire corn genome will eventually be available on two glass slides, enabling researchers to monitor genes by turning them on and off under different conditions and learn more about how they work. All of the data will be quickly available in a public database. Investigators at institutions lacking the resources to conduct these experiments themselves will have access to the data, according to Chandler.
Adding to the strength of the maize genome project is Soderlund's research on the technical aspects of gene sequencing. Approximately 80 percent of the 2,400 megabase maize genome is repetitive DNA that generally does not contain genes. There is an initiative by the NSF Plant Genome Project to sequence the gene-rich regions of maize. Soderlund's contribution is the generation of sequences that will link the fragments of gene sequences across the repetitive regions.
"We will develop a web-based genome browser in order to verify our results and elucidate the structure of maize," Soderlund says. "This will also allow scientists around the world to view their genes of interest."
National Plant Genome Initiative: The National Plant Genome Initiative (NPGI) involves a number of federal agencies, including the National Science Foundation, the National Institutes of Health and the US Department of Agriculture.
The NPGI was established in 1998 with the understanding that the major challenges facing mankind in the 21st century are the need for increased food and fiber production, a cleaner environment, and renewable chemical and energy resources. Plant-based technologies can play a major role in meeting each of these challenges.
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Funded by a $925,712 grant from the same NSF genome initiative, this study will expedite maize genome sequencing and gene discovery, leading to more gene targets for crop improvement.
The increased emphasis on the plant genome in these and other projects will change fundamental plant science research related to agriculture, forestry, energy and the environment, as well as to the production of pharmaceuticals and other plant-based industrial chemicals and materials.
National Plant Genome Initiative funding has helped make the UA department of plant sciences one of the strongest in the country. The department has consistently pulled in $5 to 15 million annually for the past five years.
"For these individuals to receive such large grants from this highly competitive program is a testament to the strength of their research accomplishments and to the quality of these proposals," says Robert Leonard, head of the UA plant sciences department.
"Selection for grant awards of this magnitude does not occur without very strong endorsement from the scientific peers who reviewed the proposals. We are very pleased by and appreciative of their continued success," Leonard says.
- Updated: September 29, 2003
