Development of an Expressed Sequence Tag (EST) Resource for Wheat (Triticum aestivum L.): EST Generation, Unigene Analysis, Probe Selection and Bioinformatics for a 16,000-Locus Bin-Delineated Map

Authors

G. R. Lazo, United States Department of Agriculture-Agricultural Research Service
S. Chao, University of California, Davis
D. D. Hummel, University of California, Davis
H. Edwards, University of California, Davis
C. C. Crossman, United States Department of Agriculture-Agricultural Research Service
N. Lui, University of California, Davis
D. E. Matthews, United States Department of Agriculture-Agricultural Research Service
V. L. Carollo, United States Department of Agriculture-Agricultural Research Service
D. L. Hane, University of California, Davis
F. M. You, University of California, Davis
G. E. Butler, University of Arizona
R. E. Miller, University of California, Davis
T. J. Close, University of California, Riverside, California
J. H. Peng, Colorado State University, Fort Collins
N. L. V. Lapitan, Colorado State University, Fort Collins
J. P. Gustafson, USDA-ARS
L. L. Qi, Wheat Genetics Resource Center, Kansas State University, Manhattan, Kansas
B. Echalier, Wheat Genetics Resource Center, Kansas State University, Manhattan, Kansas
B. S. Gill, Wheat Genetics Resource Center, Kansas State University, Manhattan, Kansas
M. Dilbirligi, Washington State University
H. S. Randhawa, Washington State University
K. S. Gill, Washington State University
R. A. Greene, University of California, Davis
M. E. Sorrells, University of California, Davis
E. D. Akhunov, University of California, Davis
J. Dvorak, University of California, Davis
A. M. Linkiewicz, University of California, Davis
J. Dubcovsky, University of California, Davis
K. G. Hossain, North Dakota State University, Fargo, North Dakota
V. Kalavacharla, North Dakota State University, Fargo, North Dakota
S. F. Kianian, North Dakota State University, Fargo, North Dakota
A. A. Mahmoud, North Dakota State University, Fargo, North Dakota
Miftahudin, University of Missouri, Columbia, Missouri
X.-F. Ma, University of Missouri, Columbia, Missouri
E. J. Conley, North Dakota State University, Fargo, North Dakota
J. A. Anderson, North Dakota State University, Fargo, North Dakota
M. S. Pathan, University of Missouri, Columbia, Missouri
H. T. Nguyen, University of Missouri, Columbia, Missouri
P. E. McGuire, University of California, Davis
C. O. Qualset, University of California, Davis
O. D. Anderson, U.S. Department of Agriculture-Agricultural Research Service

Date of this Version

10-2004

Comments

Published in Genetics 168: 585–593 (October 2004).

Abstract

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n = 6x = 42) wheat genome (Triticum aestivum L.). Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags (ESTs) representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection (113,220 ESTs). Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of ESTs into contigs. These contigs plus singletons (unassembled ESTs) were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5’ and 3’ sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics.