Sugarcane Genomics and Transcriptomics

Sugarcane is an important commercial crop belonging to Poaceae family and is a major source of sucrose and ethanol production worldwide. Sugarcane's large genome size, aneuploidy of commercial cultivars, and polyploidy of interspecific hybrids have always imposed a challenge for generation of genomic and transcriptomics resources for crop improvement. Despite of these hurdles, linkage maps based on different segregating populations has been constructed. Efforts to map QTLs controlling various traits are being carried out and map-based cloning has also been tried. Available EST data can now be used for SNP mining, expression profiling, discovering new genes, etc. The comparative analysis of sugarcane and sorghum genome revealed high similarity between the two genomes. This information will further expedite sugarcane improvement initiatives. The advent of high-throughput sequencing technologies such as Roche/454 and Illumina/Solexa is being used to gain knowledge on transcriptome of the cell under different stress conditions. RNA-seq can provide the sequences of all RNA molecules, including mRNA, rRNA, tRNA, and noncoding RNAs, produced in one or a population of cells. The data generated can be used to measure transcript levels, to find novel genes, fusion transcript, and splice junctions. Knowledge of the sugarcane transcriptome can provide information about synthesis of various biomolecules and their interactions with other metabolic pathways in the complex sugarcane genome. Both genomic and transcriptome resources of sugarcane are immensely important for improving yield as well as quality of sugarcane; this will help sugarcane farming community to a great extent.