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United States Department of Agriculture

Agricultural Research Service

Title: The Maize Genome: Ready to Tile and to Target for Research

Authors
item Coe Jr, Edward
item Cone, Karen - UNIVERSITY OF MISSOURI
item Sanchez-Villeda, Hector - UNIVERSITY OF MISSOURI
item Schaeffer, Mary
item Gardiner, Jack - UNIVERSITY OF MISSOURI
item McMullen, Michael
item Davis, Georgia - UNIVERSITY OF MISSOURI
item Wing, Rod - UNIV OF ARIZONA-TUCSON
item Soderlund, Cari - UNIV OF ARIZONA-TUCSON
item Paterson, Andrew - UNIV OF GEORGIA-ATHENS

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: October 3, 2003
Publication Date: January 10, 2004
Citation: Coe Jr, E.H., Cone, K., Sanchez-Villeda, H., Polacco, M.L., Gardiner, J., Mcmullen, M.D., Davis, G., Wing, R., Soderlund, C., Paterson, A. 2004. The maize genome: ready to tile and to target for research [abstract]. Plant and Animal Genome. 12:76.

Technical Abstract: High-resolution genetic maps and deep physical maps of maize, anchored inter se, are ready for targeted research studies and for tiling and sequencing. This 2,300 Mb genome assembles readily, even though highly duplicated and rife with recently diverged, nested retrotransposons and other repetitive sequences. From HindIII, EcoRI, and MboI BAC libraries of inbred line B73, 290,000 agarose BAC fingerprints (15X) were assembled initially into contigs using FPC. Phase I manual editing for the June 2003 build drew together 3,500 contigs assembled at 10e-12. Manual editing advanced further with the aid of an end-joining utility and over 13,000 markers, including 9,300 unigenes addressed to the BACs with 40bp overgos. Further precise physical addressing of genetically mapped markers is by PCR on 48x48x48, 6-dimensional BAC pools. Targeted SNP mapping is on EST unigenes that are associated with unanchored contigs. These data and tools have largely anchored the contigs, some exceeding 8 Mb, to the genetic map. Contig order and orientation devolves from over 2000 markers mapped genetically at high resolution, which give virtually perfect correlation with physical order. A 'neighbors' map, derived by intercalation of loci from other informative populations, combines over 5,800 mapped loci in approximate order, and assists editing. Software tools to systematize, to validate, to link, to pipe, and to integrate large, diverse, high-throughput datasets are available. See <a href="http://www.maizemap.org/">maizemap</a> and <a href="http://genome.arizona.edu/fpc/maize/">FPC/maize</a> for views and downloads. Side-by-side dynamic views of the physical and genetic map from a database environment are in an <a href="http://www.maizemap.org/iMapDB/iMap.html">Integrated Map</a> (iMap) presentation. Supported by NSF #9872655.

Last Modified: 8/21/2014
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