An EST survey of the sugarcane transcriptome.pdf

Theor Appl Genet (2004) 108:851–863 DOI 10.1007/s00122-003-1510-y O R I G I NA L PA P ER H.-M. Ma · S. Schulze · S. Lee · M. Yang · E. Mirkov · J. Irvine · P. Moore · A. Paterson An EST survey of the sugarcane transcriptome Received: 7 February 2003 / Accepted: 30 September 2003 / Published online: 29 November 2003
Springer-Verlag 2003 Abstract Its large genome and high polyploidy makes sugarcane (Saccharum spp.) a singularly challenging crop to study and improve using genetic approaches. To provide large numbers of functionally characterized candidate genes that might be tested for direct association (rather than distant linkage) with economically important traits, we sequenced the 50 ends of 9,216 clones from three cDNA libraries (apex, leaf and mature internode), representing 3,401 non-redundant sequences. About 57% of these sequences could be assigned a tentative function based on statistically significant similarity to previously characterized proteins or DNA sequences. Another 28% corresponded to previously identified, but uncharacter- ized, sequences. Some of the remaining unidentified sequences were predicted to be genes which could potentially be new to plants or unique 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 a detailed Arabidopsis protein database 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 studies to accelerate isolation of agronomically important genes from the cumbersome sugarcane genome. Introduction Sugarcane, the sucrose-storing member of the genus Saccharum, is a perennial grass with solid stems that have become adapted for high sucrose storage. More than 60% of sucrose, a leading commodity important in the human diet, is produced from sugarcane. Sugarcane also ranks number one worldwide in bi