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