Genomics makes plants more resistant

Researchers from São Paulo and California share advances in genomic applications for improving sugarcane, peanuts and wheat

By Diego Freire, in Davis

Agência FAPESP – The identification of genes responsible for important processes in plant biology has helped in developing crops that are more resistant to pests and diseases, and better adapted to global demands for food and energy. Some of these advances made by Brazilian and U.S. researchers were presented during FAPESP Week California in Davis, November 20, 2014.

Paulo Mazzafera, professor of the Institute of Biology at the University of Campinas (IB-Unicamp) presented research studies on controlling lignin biosynthesis in sugarcane that can result in a genetically modified plant better suited to ethanol production using sugarcane bagasse.

Lignin, the macromolecule that gives terrestrial plants their stiffness, resistance and impermeability, protects the sugarcane, but also makes it hard to use bagasse to produce ethanol since it impedes the chemical reactions that release sugars from the cell wall for fermentation.

The research studies conducted by Mazzafera and his group seek to identify genes to produce a genetically modified sugarcane with either a low or high concentration of lignin, according to the production objectives.

“This would allow us to reduce the concentration of lignin or alter its characteristics to facilitate the fermentation process. Or else increase the concentration of lignin so it could be used as a “super-sugarcane” since the burning of biomass can be used to generate electricity,” explained Mazzafera, member of the FAPESP Area Panel Committee on Agricultural and Veterinary Sciences.

Five genes related to the lignin concentration in sugarcane were identified under the scope of the thematic project, Control of lignin biosynthesis in sugar cane: many gaps still to be filled.

“These genes are associated with the quantity and type of lignin component, which is the focus of our studies. Some of them act in directing the biosynthesis of one of the components that form the lignin – the syringyl for example – and others, the transcription factors, control other genes. The modification of these genes aims at altering the proportion of syringyl lignin and controlling the chemical reactions that give rise to the polymer,” Mazzafera explained.

Field tests were conducted in six different locations between the states of São Paulo and Goiás, and it was determined that two of these genes can be expressed by the researchers in the environment to alter the lignin composition.

“Thus, the lignin would become chemically easier to remove, consequently yielding more cellulose and making it easier to use in ethanol production,” Mazzafera said.

Experiments are currently being conducted to super-express these genes in rice, used as a test plant, and in sugarcane itself. The studies are being carried out by Paula Macedo Nobile and Michael dos Santos Brito, under the guidance of Silvana Creste at the Campinas Institute of Agronomy (IAC), with funding from FAPESP.

For Richard Michelmore of the Genome Center at the University of California, Davis (UCD), the studies carried out to improve sugarcane in Brazil are part of a global context of changes.

“We live at a time of important changes in the paradigms of biology with the use of genomic information for medical and agricultural benefits, and Brazil has made major contributions, especially in biomass and ethanol,” Michelmore told Agência FAPESP.

Michelmore presented the technologies used by the Genome Center and their applications in studies with various plants. Among the most recent projects, the researcher highlighted the Genome Center’s participation in the International Peanut Genome Initiative, a consortium that involved researchers from the United States, Brazil, China, India and Israel in sequencing the peanut genome, characterizing the genetic and phenotypic variation of farmed and wild peanuts to develop genomic tools for improving the plant.

In April of this year, all the data from the sequencing was made available to the international science community on the Internet at:

“The findings are being shared with researchers all over the world so that they can contribute, among other advances, to developing more productive plants and more resilient varieties of peanut,” Michelmore said.

The peanut currently being grown is tetraploid – it has four complete sets of chromosomes as a result of the crossing of two different wild species over 4,000 years ago. Thus, the species carries two separate genomes.

The consortium researchers sequenced the DNA of the two ancestors in Michelmore’s laboratory at UCD. “Now, with the maps of the genome generated, geneticists can look for genetic alterations involved in domestication of the species and perhaps introduce characteristics of wild peanut that can improve the crops, such as disease resistance and drought tolerance,” he said.

Michelmore also presented his findings on the use of state-of-the-art sequencing technology in accessing information on the genome of the Puccinia striiformis, the fungus that causes wheat stripe rust. The disease is characterized by the appearance of rust stripes on the leaves of the plants and can entail losses of up to 40% of production.

“The sequencing was done at our laboratories, in the DNA Technologies Service, and the use of Next Generation Sequencing (NGS) technology significantly increased the speed and efficiency of the process, representing a considerable reduction in costs compared to traditional sequencing technologies,” he explained.

The results of the sequencing are available in the GenBank, a collection of all publicly available DNA sequences, overseen by the National Institutes of Health of the United States.

FAPESP Week California was held on two campuses of the University of California: November 17-18, 2014 in Berkeley and November 20-21 in Davis. The event was supported by the Brazil Institute of the Woodrow Wilson Institute for Scholars in Washington, DC.