UD leads $5.3-million research project on rice e...(leotides in the DNA or its associated pr...)

State-of-the-art sequencing by synthesis (SBS) technology developed by Solexa Inc., in Hayward, Calif., will provide the data essential to the project. This novel deep sequencing tool, which can decode tens of millions of sequences during a single run, has become available over the last year. The application of SBS to epigenetics research was demonstrated in the human genome only within the past few months. The UD-led effort will be one of the first large-scale projects to use this approach in crop plants.

If you think of a gene as part of a set of chromosomes, a gene is just a small fraction of a percent of a complete genome, Meyers said. If we learn about that gene by random sampling, by using 50 million total sequences, which is what SBS provides, we can characterize that gene at depth, he noted. Using this method, we can obtain statistically robust data for nearly all genomic regions in a single experiment.

The scientists will use the technology to look for chemical modifications in chromatin, the building-block material of chromosomes, consisting of DNA and the proteins that interact with it. The scientists want to know how the chromatin is configured and what role changes in the material play in plant development.

Formerly, we had a very narrow picture of a plant's genome; with these new sequencing technologies, we now have the opportunity to acquire a comprehensive picture at fine detail, Meyers said. It's like looking through a high-powered telescope--but now we have a wide-angle lens on that telescope to take in a view with both breadth and depth.

Besides studying the state of the genome using a variety of different strains of rice plants, the research team will develop
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