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Genomics

Now, the details

International collaboration starts the full sequencing of sugarcane

eduardo cesarFrom one day to the next, researchers from the Chemistry Institute of the University of São Paulo (USP) revealed some 335 million pairs of bases of the DNA of sugarcane, 11 times the output of the two years of the Sucest Sugarcane Genome project, closed in 2001. The test was the kickoff for a new project, coordinated by molecular biologist Glaucia Souza. She plans to go beyond Sucest in terms of both the quantity of data and the questions about the workings of the genome of this plant that has become synonymous with renewable energy and fuel.

“We found that it is useless to know the genome without knowing how it works,” says Glaucia. Sucest sequenced sugarcane’s functional DNA, disregarding those genes whose function was unknown. In the last few years, however, the genome of other grasses – such as sorghum and rice – showed that to improve plant productivity one must understand how the activity of the genes is controlled, this being the function of the DNA segments known as promoters.

Glaucia is pursuing these promoters. More precisely, her plan is to sequence the DNA of plants of the SP 803280 sugarcane variety (the one most heavily represented in Sucest), grown with different levels of water availability and producing greater or smaller amounts of sugar. The results should be useful to obtain a more drought-resistant and more productive type of sugarcane.

In the tests carried out to date, biologist Carlos Hotta, who is conducting a postdoctoral project at Glaucia’s laboratory, analyzed sugarcane DNA broken down into small fragments. The next step is to select genes to be sequenced, using, for instance, a new technique to separate the active genes. A re-run of Sucest, but with better technology. Then, the new molecular biology tools will enable the team to find and to detail the genes’ promoters.

The efficiency results from a piece of equipment acquired this year, a large scale pyrosequencer. “The method is totally different from that of traditional sequencers,” explains Hotta. The secret lies in mixing the genetic material in a solution with oil and shaking it up in such a way as to form bubbles, each one with the precise size needed to accommodate one microsphere with a single DNA fragment adhered to it, which will then be multiplied millions of times there. Millions of these spheres on a glass slide are sequenced simultaneously.

The project has only just begun. Glaucia plans to have the complete genome in four to five years. She will achieve this not only with Hotta’s help, but also with the collaboration of other Brazilian groups from USP and from the State University of Campinas, as well as foreigners from South Africa, Australia, France and the United States. France is focusing on the Reunion Island cultivar and Australia on the variety of the Queensland program besides the one most studied in Brazil, while the United States are examining ancestral species of domestic sugarcane: Saccharum officinarum, which is sugar-rich, and S. spontaneum and S. robustum, which are disease-resistant. “The workshops that we have organized under Bioen (the FAPESP Bionergy Research Program) to bring researchers together were crucial to solidify such work relationships,” says Glaucia.

The project
Sugarcane signaling and regulatory networks (nº 08/52146-0); Type Projeto Temático – Bioen; Coordinator Glaucia Mendes Souza – USP; Investiment R$ 5.107.837,57

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