Ethanol takes off

In 2011, researchers at the University of São Paulo (USP) and the State University of Campinas (Unicamp) determined 10.8 gigabases of sugarcane DNA sequence, 33 times the amount sequenced by the two-year Sugarcane Genome Project, which ended in 2001 and mapped the genes expressed in the plant.

By Fabrício Marques

Revista Pesquisa FAPESP – In 2011, researchers at the University of São Paulo (USP) and the State University of Campinas (Unicamp) determined 10.8 gigabases of sugarcane DNA sequence, 33 times the amount sequenced by the two-year Sugarcane Genome Project, which ended in 2001 and mapped the genes expressed in the plant.

The recent research effort is part of two thematic projects, coordinated by molecular biologist Glaucia Souza and geneticist Marie-Anne Van Sluys, professors at USP, that aim to map the genes of sugarcane and are expected to conclude in 2013.

Given the complexity of the genome, 300 regions have already been organized into larger sections of 100,000 bases, each containing 5 to 14 contiguous sugarcane genes.

The researchers hope to extend their work beyond the findings of the Sugarcane Genome Project, both with regard to the quantity of data and questions addressing the detailed function of the genome of a plant that has become synonymous with renewable energy. Studies on graminaceous plants, such as sorghum and rice, have shown that, to improve the productivity of plants, one must know how gene activity is controlled via the function of DNA regions known as promoters.

The research is an example of how, with FAPESP’s support, knowledge on sugarcane and ethanol has advanced in the past 15 years. From the Sugarcane Genome Project (1998-2001), which mapped the genes expressed by sugarcane, to the FAPESP’s Bioenergy Research Program begun in 2008, for which Souza is the coordinator, the Foundation has been funding a broad-scale effort in which researchers from several knowledge areas collaborate to focus on improving the productivity of Brazilian ethanol and advancing the basic science and technology related to biomass energy generation.

During the three years of its existence, BIOEN has made considerable progress on a variety of projects. The Chemical Engineering School (FEQ) at Universidade Estadual de Campinas (Unicamp) has developed an innovative process for biokerosene production based on different types of vegetable oils, research that could make the fuel used in airplanes less polluting and less expensive.

After extraction and refining, the oil is placed in a reactor with a specific quantity of ethanol and a catalyzer, which is responsible for accelerating chemical reactions. “The greatest contribution of the biokerosene process is the high purity index of the final product,” comments Ruben Maciel Filho, professor at FEQ and coordinator of the study.

Van Sluys’ genome experience is the reason she became the lead investigator of the Thematic Project that aims to sequence a portion of the genome of two sugarcane strains (R570 and SP80-3280) and subsidize the development of molecular tools that will aid in the understanding of this genome.

One of the targets is the study of transposable elements, regions of DNA that can move from one location in the genome to another, sometimes leaving a copy at the previous site. “Improvement programs can also benefit from access to molecular information, with the potential for the development of markers,” comments Van Sluys.

Another project, led by Ricardo Zorzetto Vêncio of USP Ribeirão Preto’s Medical School, developed a pilot version of software that attempts to characterize the functions of sugarcane genes. The approach is innovative because it is not limited to attributing the function of a gene sequence observed in one organism to that of a sequence in another organism.
The idea is to utilize algorithms that consider the uncertainty of an association. “Instead of simply saying that a gene has a specific function, we want to say what the probability of it having this function is and to take into account different evidence like the evolutionary relationship to other genes or whether there is an experiment that confirms this function,” explains Vêncio. 

Augusto Garcia, a professor at USP’s Luiz de Queiroz Agriculture School (Esalq), is developing software focused on using genetic markers to aid genetic improvement programs, exploring both the genetics and the physiology of sugarcane. “This is one of the major expectations for obtaining crops more rapidly,” explains Glaucia Souza. Every year, the Sugarcane Technology Center tests 1 million seedlings in the quest to uncover more-productive plants, yet it takes 12 years to identify two or three promising varieties.

Studies conducted by André Meloni Nassar, the general director of the Institute for International Trade Negotiations (ICONE), have advanced the use of economic models to evaluate changes in land use caused by large-scale biofuel production. In the search for ethanol made from cellulose, one of the highlights is a project that evaluates how it is possible to break down the cell walls of lignified vegetables, such as sugarcane, through enzymatic hydrolysis.

Lignin is a macromolecule found in plants that is associated with cellulose in the cell walls. Its function is to add rigidity and resistance, such that breaking it down to obtain cellulosic ethanol is a challenge. “To understand how lignin removal can reduce the recalcitrance of cell walls, commercial varieties and hybrid sugarcane varieties with contrasting lignin levels have been evaluated,” explains Adriane Milagres, a professor at USP’s Lorena Engineering School and one of the coordinators of the project. “When the materials are treated with selected methods, the removal of 50% of the original lignin raises the level of cellulosic conversion up to 85% to 90%.”