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Title: Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes

Author
item LOKKO, YVONNE - IITA, IBADAN, NIGERIA
item Anderson, James
item RUDD, STEPHEN - CENTRE FOR BIOTECHNOLOGY
item RAJI, ADEBOLA - IITA, IBADAN, NIGERIA
item Horvath, David
item MIKEL, MARK - UNIVERSITY OF ILLINOIS
item KIM, RYAN - UNIVERSITY OF ILLINOIS
item LIU, LEI - UNIVERSITY OF ILLINOIS
item HERNANDEZ, ALVARO - UNIVERSITY OF ILLINOIS
item DIXON, ALFRED - IITA, IBADAN, NIGERIA
item INGELBRECHT, IVAN - IITA, IBADAN, NIGERIA

Submitted to: Plant Cell Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/4/2007
Publication Date: 5/31/2007
Citation: Lokko, Y., Anderson, J.V., Rudd, S.A., Raji, A.A., Horvath, D.P., Mikel, M.A., Kim, R.W., Liu, L., Hernandez, A.G., Dixon, A.G., Ingelbrecht, I.L. 2007. Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes. Plant Cell Reports. 26:1605-1618. DOI:10.1007/s00299-007-0378-8.

Interpretive Summary: Cassava is a staple food for over 600 million people in the tropics and subtropics and is increasingly used as an industrial crop for starch production. Cassava has a high growth rate under optimal conditions but also performs well in drought-prone areas and on marginal soils. To gain a better understanding of drought tolerance in cassava, we generated expressed sequence tags (ESTs) from tissue of both dehydration-stressed and well-watered plants. From a total of 18,166 ESTs we identified 8,577 unique gene clusters. Known functions could be assigned to 63% of the unigenes, while another ~11% were similar to genes with hypothetical or unclear functions. The remaining ~26% were not similar to other sequences in public databases suggesting that some may be novel to cassava. A number of unigenes obtained from the dehydration-stressed plants have recognized roles in drought responses, including those that encode late-embryogenesis-abundant proteins, transcription factors, heat-shock proteins as well as proteins involved in signal transduction and oxidative stress. Further screening of the unigene clusters indicated that approximately 3.3% of the ESTs contained short tandem repeats which have potential to be further developed into genetic markers. The tools and information obtained from this study will be important for dissecting the molecular basis of drought tolerance in cassava.

Technical Abstract: Cassava (Manihot esculenta Crantz) is a staple food for over 600 million people in the tropics and subtropics and is increasingly used as an industrial crop for starch production. Cassava has a high growth rate under optimal conditions but also performs well in drought-prone areas and on marginal soils. To increase the tools for understanding and manipulating drought tolerance in cassava, we generated expressed sequence tags (ESTs) from normalized cDNA libraries prepared from dehydration-stressed and control well-watered tissues. Analysis of a total of 18,166 ESTs resulted in the identification of 8,577 unique gene clusters (5,383 singletons and 3,194 clusters). Functional categories could be assigned to 63% of the unigenes, while another ~11% were homologous to hypothetical genes with unclear functions. The remaining ~26% were not significantly homologous to sequences in public databases suggesting that some may be novel and putatively specific to cassava. The dehydration-stressed library uncovered numerous ESTs with recognized roles in drought responses, including those that encode late-embryogenesis-abundant proteins thought to confer osmoprotective functions during water stress, transcription factors, heat-shock proteins as well as proteins involved in signal transduction and oxidative stress. The unigene clusters were screened for short tandem repeats for further development as microsatellite markers. A total of 592 clusters contained 646 repeats, representing 3.3% of the ESTs queried. The ESTs presented here are the first dehydration stress transcriptome of cassava and can be utilized for the development of microarrays and gene-derived molecular markers to further dissect the molecular basis of drought tolerance in cassava.