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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

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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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Sugarcane current production worldwide is in the range of 75 tons/ha. We have calculated its theoretical potential to be 380 tons/ha.

We believe that biotechnology can help increase yield in this grass but biotechnological tools adequate for sugarcane are unavailable. Our group, together with other groups in the BIOEN Program is sequencing the sugarcane genome, annotating the genome and producing gene catalogues, developing methods for sugarcane transformation and phenotyping and developing an integrated database with datamining tools for this crop that we believe may help the community that works on sugarcane improvement.


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Hotta, C. T., Lembke, C. G., Ochoa, E. A., Cruz, G. M. Q., Domingues, D. S., Hoshino, A. A., Santos, W. D., Souza, A. P., Crivellari, A., Marconi, T. G., Santos, M. O., Melotto-Passarin, D. M., Mollinari, M., Margarido, G. R. A., Carrer, H., Souza, A. P., Garcia, A. A. F., Buckeridge, M. S., Menossi, M., Van Sluys, M-A. and Souza, G. M. (2010). The biotechnology roadmap for sugarcane improvement. Tropical Plant Biology. 10.1007/s12042-010-9050-5

Costa, M. D-B. L, Hotta, C. T., Carneiro, M. S., Chapola, R. G., Hoffmann, H. P., Garcia, A. A. F., Souza, G. M.  (2011). Sugarcane Improvement: How far can we go? Current Opinion in Biotechnology 23:1–6.

Nishiyama Jr, M. Y., Ferreira S. S., Tang P-Z, Becker S., Pörtner-Taliana A., Souza G. M. (2014). Full-length enriched cDNA libraries and ORFeome analysis of Sugarcane Hybrid and Ancestor Genotypes. PLoS ONE 9(9): e107351.

Garcia, A. A., Mollinari, M., Marconi, T. G., Serang, O. R., Silva, R. R., Vieira, M. L., Vicentini, R., Costa, E. A., Mancini, M. C., Garcia, M. O., Pastina, M. M., Gazaffi, R., Martins, E. R., Dahmer, N., Sforça, D. A., Silva, C . B., Bundock, P., Henry, R. J., Souza, G. M., Van Sluys, M. A., Landell, M. G., Carneiro, M. S., Vincentz, M. A., Pinto, L. R., Vencovsky, R., Souza, A. P. (2013). SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids. Sci Rep. Dec 2;3:3399.


Dr. Glaucia Souza conducts research in biotechnology and sugarcane genomics and coordinates the State of São Paulo Research Foundation Bioenergy Program. BIOEN aims at articulating public and private R&D, in academic and industrial laboratories, to advance and apply knowledge in fields related to bioenergy. Research ranges from biomass production and processing to biofuel technologies, biorefineries and sustainability. Dr. Souza is the Chairperson of the SCOPE Bioenergy & Sustainability project, a global assessment of current status and latest developments on bioenergy production and use to produce policy recommendations for the sustainable expansion of bioenergy in the world. The project involves contributions from 137 experts from 24 countries.