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BIOEN - Bioenergy Program

Our team

The Sugarcane Transcriptome

We study signaling and regulatory networks in sugarcane and develop tools for a systems biology approach in this grass. As a starting point we intend to characterize three agronomical traits of interest: drought, brix and lignin content.

We are doing an integrated analysis of the sugarcane transcriptome and physiological changes associated to sucrose content, stress responses and fiber quality and content. We would like to be able to alter carbon partition in this crop to generate an energy grass. As a starting point sugarcane metabolic pathways are being mapped in conjunction with the transcriptome data.

We are focusing on the study of gene categories with a well known regulatory role (Transcription Factors, Protein Kinases and Phosphatases), producing transgenics and developing a database and computacional tools to integrate the several levels of information.

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Sugarcane Genome Sequencing

Sugarcane cultivars derive from a recent interspecific hybrid obtained by crossing Saccharum officinarum and Saccharum spontaneum and represent relevant feedstock used worldwide for biofuel production.

The challenge in a sugarcane sequencing project is the size (10 Gb) and complexity of its genome structure that is highly polyploid and aneuploid with a complete set of homo(eo)logous genes predicted to range from 8 to 10 copies (alleles). Although sugarcane's monoploid genome is about 1 Gb, its highly polymorphic nature represent another significant challenge for obtaining a genuine assembled monoploid genome.

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Transcription Factors and Regulatory Networks

We intend to implement the ChIP-Seq technology in sugarcane, to identify TF targets and gene promoters.

The results will have multiple direct consequences on breeding programs that frequently select for CREs and TF changes in search for genotypes better adapted to the environment and with increased agronomical performance.

We also participate in the development of the GRASSIUS database to establish sugarcane, rice, maize and sorghum regulatory networks.

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Sugarcane Protein Kinases

Protein Kinases activate signaling cascades in response to environmental stimuli and our studies point to a predominant role of PKs in the regulation of sucrose content and drought responses.

To identify new genes associated to brix, drought and lignin content we are characterizing the transcriptome of genotypes and cultivars that contrast for these traits using olinonucleotide arrays. Genes of interest will be functionally evaluated by generating transgenics altered for their expression. A catalogue of Sugarcane Signal Transduction components has been produced.

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Development of biotechnological tools for sugarcane

SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids

 Download PDF | Read in Nature.com

Many plant species of great economic value (e.g., potato, wheat, cotton, and sugarcane) are polyploids. Despite the essential roles of autopolyploid plants in human activities, our genetic understanding of these species is still poor. Recent progress in instrumentation and biochemical manipulation has led to the accumulation of an incredible amount of genomic data. In this study, we demonstrate for the first time a successful genetic analysis in a highly polyploid genome (sugarcane) by the quantitative analysis of single-nucleotide polymorphism (SNP) allelic dosage and the application of a new data analysis framework. This study provides a better understanding of autopolyploid genomic structure and is a sound basis for genetic studies. The proposed methods can be employed to analyse the genome of any autopolyploid and will permit the future development of high-quality genetic maps to assist in the assembly of reference genome sequences for polyploid species.

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Sucest-Fun Database

To integrate the immense amount of public data and those generated by our group a robust computational infrastructure and database has been developed. The SUCEST-FUN database integrates the SUCEST sequences, promoters, CREs, expression data, agronomical, physiological and biochemical characterization of sugarcane cultivars.

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BIOEN Fapesp Bioenergy Program

The BIOEN Program aims to integrate comprehensive research on sugarcane and other plants that can be used as biofuel sources, thus assuring Brazil’s position among the leaders in the area of Bioenergy.

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About


Dr. Glaucia Souza holds a degree from the Biosciences Institute of University of São Paulo  (1988), PhD in Biochemistry at the Institute of Chemistry  (1993), post-doctorate in molecular genetics at La Jolla Cancer Research Foundation  (1994) and post-doctorate in molecular genetics at Baylor College of Medicine  (1996).

Post-doctoral position for two years at University of São Paulo, Brazil

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