April 2002

From North Carolina State University

Framework for rice genome sequencing

Rice is arguably the most important food staple in the world. Research shows that about one-third of the world's population depends on it for more than 50 percent of their caloric intake. More than 500 million tons of rice are produced across the world annually. Dr. Ralph Dean, professor and director of North Carolina State University's Center for Integrated Fungal Research, is one of the co-authors of a research paper that describes the sequencing of the rice genome, published in the April 5 issue of the journal Science. Dean's work provided the framework for the genome's sequencing and assembly. The sequencing of the rice genome - which successfully lifts the veil from about 93 percent of it - represents a major milestone in genomics research. Possible benefits include higher-yield, more disease-resistant rice crops.

Moreover, the project confirmed that rice has a syntenic, or collinear, relationship with other cereal grasses - such as corn, wheat and barley - thus adding to the available genetic data for these crops. Since rice has the smallest genome of the cereal crops, this knowledge will allow scientists to understand where important genes are located within other cereals, and let them literally separate the wheat from the chaff. Dean started on the project at Clemson University, where he was a member of the faculty before coming to NC State in 1999 and where his work centered on plant pathogens, specifically rice blast, an important rice disease. He and fellow researchers studied both rice blast and rice in order to understand how the pathogen infects the host.

Using research funds from Novartis, now Syngenta, the biotechnology firm that sequenced the rice genome, Dean and his colleagues broke up the rice genome into libraries of smaller fragments of DNA called BACs, or bacterial artificial chromosomes. They then identified sequence tag connectors, or small tags of DNA, that showed how the fragments fit together, as in a jigsaw puzzle. This "fingerprinting" technique gave researchers a snapshot of all the genes in the rice genome. "If you likened this project to erecting a building, we provided the scaffolding that shows where and how the bricks and mortar fit," Dean says. Now that the genetic relationship between the cereal grasses has been confirmed, scientists will have a much easier time sequencing larger cereal genomes, like those for wheat, barley and eventually corn. Corn's genome is larger than that of humans.

"If you know where one gene is in barley, for example, you can get the neighboring gene because the order is linear with one found in rice," Dean says. "You'll be able to identify important genes in the other cereal grasses. This has exponentially added to the available data that one can use for a particular cereal crop."

This article comes from Science Blog. Copyright 2004

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