Modern sugarcane cultivars are hybrids that have two subgenomes originated from S. officinarum and S. spontaneum. Recent hybridization process occurred in sugarcane is a great opportunity to study changes in gene expression such as transgressive gene expression, genome dominance and alternative splicing. The advent and subsequent widespread of next generation sequencing technologies has led to the increase of the gene expression studies in several polyploid plants. RNA-Seq data is a powerful resource for gene expression analysis offering a wide range of expression levels, and more informative to detect allele specific expression and variants. Preliminary data generated by initial Postdoc project (2015/16399-5) using an SNP-based approach to investigate the balance between genomic dosage and allele expression has showed that probably occurs homoeolog expression bias in sugarcane genome. However, this event needs to be investigated carefully to understand how homoeolog genes interact and what is the contribution of each subgenome to the gene expression in sugarcane hybrids. For this reason, this project was proposed to be executed in a research group that has a recognized experience with gene expression studies in polyploid organisms. A total of 30 RNA-Seq libraries from sugarcane hybrid and ancestral species obtained of leaf, culm, meristem and root that generated more than 700 million of paired end reads will be analyzed, yet genomic data obtained by BAC sequencing. To analyze these data, it is important a collaboration with a research group that has bioinformatic expertise related to NGS data analysis applied for gene expression studies.
News published in Agência FAPESP Newsletter about the scholarship: