Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/24/2003
Publication Date: 3/18/2004
Citation: Ma, H., Schulze, S., Lee, S., Mirkov, E., Irvine, J., Moore, P.H., Paterson, A. 2004. An est survey of the sugarcane transcriptome. Theoretical and Applied Genetics 108:851-863. 2004.
Interpretive Summary: Current large scale genome projects on a variety of plants, animals, and microbes are making available vast amounts of information in the form of genomic sequence and expressed sequence tags (ESTs) that have potential application for increasing crop yield potentials. Data from national and international efforts to develop and catalog ESTs for major food crops such as rice, maize, and soybean are placed in public databases, but because world producers of cane sugar are leery of potential competitive advantages to be gained from sugarcane genome data, it is inadequate in the public domain. A collaborative project involving the Universities of Georgia and Texas A&M, and the USDA/ARS report a survey of 9216 ESTs of the sugarcane genome that are being made available to US sugarcane scientists. This data will provide a foundation for many new molecular level studies to accelerate isolation of agronomically-important genes from the large and complex sugarcane genome.
Technical Abstract: Its extremely high polyploidy level makes sugarcane (Saccharum spp.) an especially challenging crop to study and improve. To learn more about the structure and function of the sugarcane genome, we sequenced the 5' ends of 9216 clones from three tissue-specific cDNA libraries (apex, leaf, and mature internode). Organized according to tissue types, initial sequence clustering found 3401 non-redundant tags. About 57% of these sequences could be tentatively assigned a putative function based on statistically significant similarity to previously- characterized proteins or DNA sequences. Another 28% corresponded to previously-identified, but uncharacterized sequences. Some of the remaining unidentified sequences were predicted to be genes, which potentially could be new genes to plants or unique genes to sugarcane. Comparisons of the sugarcane ESTs to a large sorghum EST database revealed similar compositions of expressed genes between some different tissues. Comparison to the entire protein database of the botanical model Arabidopsis showed some highly conserved sequences, which might be useful DNA markers for pan-angiosperm comparative mapping. These EST sequences provide a foundation for many new molecular level studies to accelerate isolation of agronomically-important genes from the cumbersome sugarcane genome.