Transcriptional Dynamics of Source-Sink Balance in Sugarcane, and the R570 Transcriptome to Support Sugarcane Genome Sequencing Initiative

Sugarcane research has identified and characterized a suite of proteins involved in biomass production. However, the molecular mechanisms responsible for the crosstalk between different regulatory and signaling pathways still need to be further elucidated to better understand plant growth patterns and biomass production. In this study we developed ways to apply analyses of gene regulatory network in molecular, physiological and genetic data of two contrasting sugarcane genotypes submitted to changes in the sink:source ratio. The lowest sucrose content genotype shows the highest levels of chlorophylls and a highest efficiency in the photosystem II. This genotype also shows high levels of sucrose in leaves but do not accumulate high levels of sucrose in the stems. The de novo transcriptome analyses results in a total of 191,871 transcripts. Alignment against Sorghum genome showed that ~13.3% of transcripts could be ncRNAs. With the comparison of gene networks against different plant species was possible to reduce measurement noise and to reinforce the common signal present in the networks. Using the differential expressed genes identified in the source-sink experiments we can detect more than 50% genes inside regulatory complex conserved across sugarcane and rice. We also detected several gene clusters, including many hubs, which incorporate different regulatory genes (ncRNAs, siRNAs, and miRNAs). In source-sink experiment was possible to detect that 1% of transcripts change its expression to response to the sink manipulation and 5% of transcripts show differential expression between the contrasting sugarcane genotypes. The sugarcane source-sink gene regulatory network shows a strong negative correlation between photosynthetically genes and genes involved in the cell wall metabolism. Finally, we also use R570 transcriptome to obtain a large-scale idea about the degree of polymorphism within the modern sugarcane genotypes expressed sequences. This data would be made available for BAC assembly, and is very useful to help the identification of alternative spicing and ncRNA. This study brings new knowledge on the diversification of the regulatory network that controls sucrose metabolism and source-sink balance in sugarcane. The results should contribute to improve our ability to manipulate the biomass production through classical breeding or biotechnological approaches.