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Open Access Highly Accessed Research article

Wheat EST resources for functional genomics of abiotic stress

Mario Houde1, Mahdi Belcaid2, François Ouellet1, Jean Danyluk1, Antonio F Monroy3, Ani Dryanova3, Patrick Gulick3, Anne Bergeron2, André Laroche4, Matthew G Links5, Luke MacCarthy6, William L Crosby5 and Fathey Sarhan1*

Author Affiliations

1 Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal QC, H3C 3P8, Canada

2 Département d'Informatique, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal QC, H3C 3P8, Canada

3 Biology Department, Concordia University, 7141 Sherbrooke Street West, Montreal QC, H4B 1R6, Canada

4 Agriculture et Agroalimentaire Canada, Centre de recherches de Lethbridge, 5403, 1st Avenue South, C.P. 3000, Lethbridge AB, T1J 4B1, Canada

5 Department of Biological Sciences, University of Windsor, 401 Sunset ave, Windsor ON, N9B 3P4, Canada

6 Department of Computer Science, University of Saskatchewan, 176 Thorvaldson Building, 110 Science Place, Saskatoon SK, S7N 5C9, Canada

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BMC Genomics 2006, 7:149  doi:10.1186/1471-2164-7-149

Published: 13 June 2006

Abstract

Background

Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project.

Results

We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology.

Conclusion

We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals.