NSF Wheat EST Genomics Project
Resources
The NSF Wheat EST Genomics Project (The structure and function of the
expressed portion of the wheat genomes, NSF DBI-9975989) finished its third
year of a planned four on August 31, 2002. The US-based Project has available
several genomics resources to which we would like to call to your attention.
The overall Project web site is http://wheat.pw.usda.gov/NSF/.
1. cDNA libraries. 50 libraries have been assembled, primarily from a single
hexaploid wheat genotype subjected to a range of growth and environmental
conditions, and serve as the source of ESTs for the Project (http://wheat.pw.usda.gov/NSF/progress_library.html).
The Project goal was 30 libraries.
2. EST generation. The Project has exceeded its goal of 80,000 ESTs produced
and submitted to GenBank (http://wheat.pw.usda.gov/NSF/progress_est.html).
3. A set of hexaploid wheat deletion lines have been characterized for
the Project. Their breakpoints define a suite of 'bins' along the chromosome,
with at least 2 bins for every chromosome arm. These lines are the
standards for the physical mapping of ESTs for this Project. The Project deletion
lines are a subset of a larger set available from the Kansas State University
Wheat Genetics Resource Center: http://www.ksu.edu/wgrc/.
4. EST mapping. Selected unique ESTs are mapped to wheat deletion lines
resulting in their assignment to physically determined bins along the chromosome
arms. Progress in this mapping process is at http://wheat.pw.usda.gov/NSF/progress_mapping.html.
The available tools allow the mapped ESTs to be searched and ordered by location
from the chromosome level, the arm level, and the bin level.
5. Bioinformatics and database development. Two main databases have been
developed that allow users to query and search all the data generated in
this project, including EST data, their BLAST hits, contig assembly results,
and deletion mapping results (http://wheat.pw.usda.gov/NSF/progress_database.html).
The Project has contributed partial support to co-PI Tim Close and his
colleague Steve Wanamaker towards the development of HarvEST, now at version
0.86 (July 23, 2002). HarvEST is Windows-based software that allows searching
for EST's that are differentially expressed among cDNA libraries and it comes
with EST databases from several projects, including this Wheat EST Project.
HarvEST is downloadable at http://harvest.ucr.edu.
The co-PIs of the Project, who have developed these resources, are James
Anderson, Olin Anderson, Timothy Close, Jorge Dubcovsky, Jan Dvorak, Bikram
Gill, Kulvinder Gill, Perry Gustafson, Shahryar Kianian, Nora Lapitan, Henry
Nguyen, Mark Sorrells, and Camille Steber. Their contact information is available
at http://wheat.pw.usda.gov/NSF/participants.html.
Cal Qualset, PI
Pat McGuire, Project Manager
