In silico analysis of transcriptome and genome sequences in sugarcane: SNPs identification, allele specific expression analysis and, development and characterization of microsatellite markers

Abstract

The sugarcane to be among the species most important economically in the world, have been a major source of sugar and alcohol production. The development of genetic markers, specific PCR, as the microsatellite (SSR) and SNPs, can generate information that will help the sugarcane breeding programs. This project proposes the continuation of work that began with the development of microsatellite markers from expressed sequence ESTs (EST-SSR) and genomics markers transcripts-associated. So far, 65 have been developed and characterized EST-SSR markers, which were published (Marconi et al., 2011) along with other markers previously characterized. Besides these, 326 were further developed SSR genomic, which were identified as being associated with a gene of sugarcane. For the continuity of this project, we propose the analysis of the transcriptome, using the RNA-Seq technology to transcripts mapping into six parents of three mapping populations in our laboratory. In order to identify differentially expressed transcripts, and subsequent identification of SNPs for these sequences. Furthermore, it is proposed that a study is designed to detect allele-specific expression. To implement this project, and all the support offered by the laboratory where the research will be carried out, it still is co-supervision with Dr. Renato Vicentini, which assists in the analysis of bioinformatics (AU)