Transcriptome Analysis and Functional Genomics of Sugarcane

Sugarcane is a genetically complex polyploid with increasing economic importance as a feedstock for biofuel production. The characterization of sugarcane genes and their association with biological traits such as sugar accumulation, biomass yield and stress tolerance has so far primarily relied on studies of the sugarcane transcriptome. Associations of gene expression with biological traits have been based on alterations in the timing and intensity of gene expression with various treatments and developmental stages, and in some instances, by genotypic correlations using segregating populations or genotypes contrasting for traits. The transcriptome of sugarcane is complex and includes transcripts of homo(eo)logues reflecting the highly polyploid genome of commercial sugarcane hybrids derived recently from two Saccharum species. The impact of this genomic complexity on transcription will be greatly informed by data emerging from the International Sugarcane Genome Sequencing Project. Increasingly, expressed gene sequences are exploited as genetic markers for traits in genome mapping and association studies. Reverse genetics approaches are possible in sugarcane but only very few sugarcane genes have had their specific functions examined in transgenic sugarcane plants. An integration of genome, transcriptome and metabolome data is emerging that will inform the molecular breeding of this important sugar and energy crop. © 2011 Springer Science+Business Media, LLC.