The National Science Foundation has awarded a University of Delaware (UD) researcher $4.2 million for genetic studies of rice, a plant that feeds more than half of the world’s population and serves as a model for cereal crops of great economic importance in the United States.

The research is being conducted by Blake C. Meyers (photo), an assistant professor of plant and soil sciences who is affiliated with both the UD College of Agriculture and Natural Resources and the Delaware Biotechnology Institute.

The project was developed in conjunction with co-principal investigator Guo-Liang Wang, assistant professor in the Department of Plant Pathology at the Ohio State University, who will generate the rice tissues and treatments used in the analysis and assist in the analysis of the data. Lynx Therapeutics Inc. of Hayward, Calif. will generate data using a proprietary technology.

Meyers, who joined the UD faculty after doing postdoctoral work at the University of California at Davis and with the DuPont Co. at the Delaware Technology Park in Newark, said the recent availability of the genomic sequence facilitates functional analysis and molecular studies of the rice genes.

However, he said, most of these genes are as yet defined only by computational and not experimental approaches. As a result, computational gene predictions may not identify all RNA transcripts within the chromosomal sequence.

Meyers said the project is using Lynx Therapeutics’ transcriptional profiling technology called Massively Parallel Signature Sequencing, or MPSS, to characterize the diversity and expression patterns of rice transcripts.

“Defining the patterns and levels of gene expression in the rice genome will advance our understanding of rice molecular biology and genetic factors controlling important agronomical traits,” Meyers said.

He said this analysis of rice has broad practical implications for the improvement of other economically important cereals, such as corn, wheat, sorghum and barley, because nearly all genes present in these species are likely to have homologs, or similarities, in rice.

The MPSS data will be used to identify genes missed by computational approaches and will provide data that validate many genes previously predicted but never confirmed experimentally.

Meyers said MPSS will be used to assess gene expression under the following conditions:

• In diverse untreated rice tissues and a subset of these tissues under cold, drought and salt stress;
• In fungal- or bacterial-infected rice tissues in both susceptible and resistant plants; and
• In an Indica rice background and in a hybrid of Indica x Japonica. This experiment will measure differences in gene expression between the two rice varieties for which the genomic sequence is available.

The novel transcripts identified by the MPSS technology will be validated at the Delaware Biotechnology Institute by microarray analysis and by sequencing more than 500 novel transcripts, Meyers said.

All of the data�MPSS, microarray and sequence validation of transcripts�will be made available through a project web page.

Meyers said the web site will include query and analysis tools to facilitate public use of the rice MPSS data and will display the abundance and chromosomal locations of rice MPSS signatures.

Meyers said the new NSF grant extends his earlier work on Arabidopsis, a plant that is easy to grow and for which the genome sequence had been determined. In fact, the rice web site will be similar to that which has been developed for the model plant Arabidopsis at [http://www.dbi.udel.edu/mpss].

Meyers earned a bachelor’s degree in biology from the University of Chicago in 1992 and his master’s and doctoral degrees in genetics from the University of California at Davis in 1995 and 1998, respectively.

His father, Terry L. Meyers, is on the faculty of the English department at the College of William & Mary.

Meyers said he came to an interest in the life sciences early in life, developing a fascination with plants that eventually led him to this line of research.

The NSF grant to Meyers is part of a $100 million plant genome research project that involves 48 different institutions.

NSF is an independent federal agency that supports fundamental research and education across all fields of science and engineering, with an annual budget that exceeds $5 billion. Its plant genome program examines the structure and function of plant genes, particularly those important to agriculture, environmental concerns, energy and health.

According to Mary Clutter, assistant director of NSF's Directorate for Biological Sciences, this year's awards take advantage of the fruits of earlier genome projects to extend existing areas of research and to break entirely new ground.

“In key ways, these projects will expand what we know about the biology of the plant kingdom, including plants that have a major impact upon the lives of people around the world,” Clutter said. “In a relatively short time, genomics has created massive amounts of data and innovative, adaptable tools for biological research. These now make it possible for scientists, wherever they are, to approach important, challenging questions in new ways.”

Article by Neil Thomas
Photo by Kathy Atkinson