Comparison of the root, leaf and internode transcriptomes in sugarcane (Saccharum spp. hybrids)

The major carbon source and sink organs (roots, leaves and internodes) of sugarcane (Saccharum spp. hybrids) have different roles and consequently different apportioning of carbon into the major components of these organs. This study performed RNA-seq on two leaves, three internodes (of differing maturity) and roots in two similar commercial sugarcane genotypes to determine the patterns of gene expression associated with differences in carbon partitioning. A total of 18 RNA-seq libraries (in triplicate) were generated per genotype, thus yielding ∼0.6 billion high quality reads, with an average length of 125 bp, covering 90% of the long-read SUGIT transcriptome. RNA-seq, differential gene expression analysis, annotation and pathway analysis were performed. Transcript expression in active source organs (1st and 5th visible dewlap leaves) displayed higher expression in photosynthetic transcripts and some protein and respiratory transcripts, and low expression of most transcripts associated with cell-wall synthesis. Additionally, the transcription of some sucrose synthetic transcripts (sucrose phosphate synthase and sucrose phosphate phosphatase) was significantly higher than that in all other organs. Storage sinks (middle and bottom internodes) displayed lower expression of transcripts associated with UDP-glucose synthesis from sucrose and UDP-glucose conversion into cell-wall components than did meristematic sinks (immature internodes and root). Both meristematic sinks displayed lower transcript expression related to photosynthesis, and far higher expression of protein, cell-wall and respiratory-related transcripts, particularly in relation to source organs. Interestingly, transcription was higher for transcripts associated with lignin and hemicellulose synthesis in the roots but not immature internodes. Transcription closely aligned with differences in the biomass makeup of insoluble and soluble components in sugarcane organs. Similar transcriptional profiles observed across internodes of differing maturity, i.e., between immature and mature internodes, suggested that transcriptional changes in select sets of genes influence changes in the direction of carbon partitioning during maturation. This finding contrasts with the large transcriptional differences observed among major organ types. This knowledge may support efforts to develop sugarcane with biomass composition better suited to various end uses.