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United States Department of Agriculture

Agricultural Research Service

Title: Anchoring 9371 Maize Est Unigenes to the Bac Contig Map by Two-Dimensional Overgo Hybridization

Authors
item Gardiner, Jack - UNIV OF MISSOURI
item Schroeder, Steven - UNIV OF MISSOURI
item Schaeffer, Mary
item Sanchez-Villeda, Hector - UNIV OF MISSOURI
item Morgante, Michelle - DUPONT - DELAWARE
item Tingey, Scott - DUPONT - DELAWARE
item Chou, Hugh - INCYTE GENOMICS
item Brinner, Shannon - INCYTE GENOMICS
item Wing, Rod - UNIV OF ARIZONA
item Coe Jr, Edward

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 16, 2003
Publication Date: April 1, 2004
Citation: Gardiner, J., Schroeder, S., Polacco, M.L., Sanchez-Villeda, H., Morgante, M., Tingey, S., Chou, H., Brinner, S., Wing, R., Coe Jr, E.H. 2004. Anchoring 9371 maize est unigenes to the bac contig map by two-dimensional overgo hybridization. Plant Physiology. 134:1317-1326.

Interpretive Summary: Crop plant research is poised to make revolutionary strides including: cloning target genes based on their function and/or their position in the genome; documenting all genes and their interplay; defining and exploring all the existing genetic diversity in a species; and using functional information and syntenic relationships of genes in closely related species to extrapolate gene function in crop plants. The challenge, however, is to develop a set of comprehensive and systematic resources to facilitate these research endeavors. Genomic resources in maize will undergird sequencing of the maize genome, and will complement and contribute to research in the cereals, other grasses, and other crop plants. This paper reports on the process of preparation of comprehensive and systematic genome resources for maize. Information from this study will be important to cereal grains research workers in advancing their efforts to use knowledge from genomics in maize improvement and to understanding how to use knowledge from each of the cereals in improvement of each, by comprehensive identification of gene functions, and by comparative genetic and physical mapping.

Technical Abstract: To construct a robust physical map that can be comprehensively integrated with the genetic map, we have used a two-dimensional 24 x 24 overgo pooling strategy to anchor maize EST unigenes to BACs on high-density filters. A set of 70,716 maize ESTs has been used to derive 10,723 "cornsensus" EST unigene assemblies. From these unigenes, 10,642 overgo sequences of 40 bp were applied as hybridization probes to 165,888 BACs (10X). A total of 165,254 BAC addresses were obtained for 9371 overgo probes, representing a 88% success rate. Over 96% of the successful overgo probes identified two or more BACs, while 5% identified more than 50 BACs. Approximately 54% of the BACs used in this study hybridized to one or more overgos. The majority of BACs identified (79%) hybridized to one or two overgos. A small number of BACs (approximately 1%) hybridized to six or more overgos, suggesting that these BACs must be gene rich. Approximately 3300 and 2500 overgos identified BACs that were contained within one or two BAC contigs, respectively. Overgos are a powerful approach for generating gene-specific hybridization probes for physical map development. Combined with genetic mapping, overgos are contributing significantly to assembling an integrated genetic and physical map for maize.

Last Modified: 4/17/2014
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