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Genomics

Sugar cane juice

International symposium discusses the direction sugar cane research is going in Brazil

Eduardo CesarExtracting juice: genomic research reveals the riches of sugar caneEduardo Cesar

In terms of products derived from sugar cane the best is yet to come.  These are developments coming from the project known as the Sugar Cane Genome, which is partly funded by FAPESP and which has catalogued the active genes of sugar cane. To take the next steps with a degree of safety geneticist Marie-Anne Van Sluys, from the University of São Paulo (USP), organized a meeting with Brazilian and international researchers at the Sugar Cane Genomics Workshop, held at FAPESP on August 4 and 5. Some of the guests were researchers from the United States and France who have experience of genomic projects with other members of the grass family, which include sugar cane, sorghum and rice. “The mistakes they learned and the things that went right with their projects will help us advance more quickly”, explains Marie-Anne.

The history of sugar cane is long and has given rise to a complex genome.  In ancient times the Asians chewed the sweet stalks of Saccharum officinarum. But when the population increased and the agricultural age arrived on a large scale it was necessary to make production of the sweet juice more efficient.  The solution was to cross the original species with one that was more resistant to disease, pests and adverse climate conditions: Saccharum spontaneum. Then, over the centuries farmers selected more resistant plants that produced more sugar, giving rise to the plant that since the 16th century has been important for the Brazilian economy. The genome reflects this history of cross breeding and the selection of characteristics: there are some ten copies of each gene, instead of the pair that goes to make up most animals.

Among the various copies of genes are the transposition elements, DNA strands that are duplicated and change place in the genome. Marie-Anne’s group has been following these errant DNA fragments that were until recently considered to be poisonous to the organism. The team from USP recorded the sequence of all the transposition elements it found and noticed that some of them also exist in rice, which 50 million years ago pursued a course of evolution that was independent of sugar cane. “This means they are old in terms of the evolution of grasses and therefore should not be poisonous”, concludes the geneticist. Another indication that the transposition elements play a beneficial role in the biology of the plant is that in many cases they are as active as the other genes. The group is still looking to describe these functions.

Applied science
Finding out in detail about the sugar cane genome is not merely curiosity. Every year that passes the Sugar Cane Technology Center (CTC) tests 1 million cuttings in its search for plants that are more productive than those that already exist. It is a slow process: it takes 12 years for 2 or 3 promising varieties to appear from this immense sugar cane plantation.

Genomic research helps this search by supplying lists of active sugar cane genes – the functional map that can help reduce the number of clones analyzed by the CTC by half. A major advance in this area comes from the partnership between geneticists Anete Pereira de Souza, from the State University of Campinas (Unicamp), and Antonio Augusto Franco Garcia, from USP’s Luiz de Queiroz Superior School of Agriculture (Esalq), who last year published the first functional sugar cane map in Molecular Breeding journal. They described more than 400 functional genetic markers, in an article that is about to be published. These are the parts of DNA responsible for producing sucrose, disease resistance and other characteristics that are essential to the economic value of plants. “We’re supplying this information to the whole worldwide community that works with sugar cane”, says Anete. “Each group will have to make its own map for the variety that it’s studying.” To facilitate the work last year she and Garcia published a computer program for constructing genetic maps that has already been used for other plants, like passion fruit and oranges.

For Anete, meeting with other international researchers that have experience with other systems is an opportunity to outline strategies for continuing to sequence the sugar cane genome in addition to opening up the way to establishing collaboration with those who are using technology that is not  fully understood or available in Brazil. With his experience with the sorghum genome geneticist Andrew Paterson, from Cornell University in the United States says that his work may be useful for research into sugar cane. “The great advantage of sorghum is that it has not undergone genome duplication and hybridization like sugar cane and therefore it has a very much simpler genome”, he explains. This means that the sorghum genome still has an organization that is closer to that of its ancestors, while sugar cane has been all mixed up as a result of duplication and transposition elements.

There is no lack of projects among Brazilian researchers involved in sugar cane research, which relies on funding from the FAPESP Program for Bioenergy Research (Bioen) that was launched in July. But in order to take such a large task to its final conclusion the best strategy is to join both forces and minds.

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